National Algal Biofuels 

Technology Roadmap

MAY 2010

BIOMASS PROGRAM

U.S. DOE 2010. National Algal Biofuels Technology Roadmap. U.S. Department of Energy, Office of Energy Efficiency and 

Renewable Energy, Biomass Program. 

Visit http://biomass.energy.gov for more information

National Algal Biofuels 

Technology Roadmap

A technology roadmap resulting from the National Algal Biofuels Workshop

December 9-10, 2008

College Park, Maryland

Workshop and Roadmap sponsored by the U.S. Department of Energy 

Office of Energy Efficiency and Renewable Energy 

Office of the Biomass Program

Publication Date: May 2010

John Ferrell

Office of Energy Efficiency 

and Renewable Energy

Office of the Biomass Program

(202)586-5340

john.ferrell@ee.doe.gov

Valerie Sarisky-Reed

Office of Energy Efficiency 

and Renewable Energy

Office of the Biomass Program

(202)586-5340

valerie.sarisky-reed@ee.doe.gov

Roadmap Editors:

Daniel Fishman,1 Rajita Majumdar,1 Joanne Morello,2 Ron Pate,3 and Joyce Yang2

Workshop Organizers:

Al Darzins,4 Grant Heffelfinger,3 Ron Pate,3 Leslie Pezzullo,2 Phil Pienkos,4 Kathy Roach,5 Valerie Sarisky-Reed,2 and the 

Oak Ridge Institute for Science and Education (ORISE)

A complete list of workshop participants and roadmap contributors is available in the appendix.

Suggested Citation for This Roadmap:

1

BCS, Incorporated 2Office of the Biomass Program 3Sandia National Laboratories 

4

National Renewable Energy Laboratory 5MurphyTate LLC
This report is being disseminated by the Department of Energy. As such, the document 

was prepared in compliance with Section 515 of the Treasury and General Government 

Appropriations Act for Fiscal Year 2001 (Public Law No. 106-554) and information 

quality guidelines issued by the Department of energy. Further, this report could be 

“influential scientific information” as that term is defined in the Office of Management 

and Budget’s Information Quality Bulletin for Peer Review (Bulletin). This report has 

been peer reviewed pursuant to section II.2 of the Bulletin.
Preface i

Preface

Welcome to the U.S. Department of Energy (DOE) Biomass Program’s National Algal Biofuels Technology 

Roadmap. Prepared with the input of more than 200 scientists, engineers, industry representatives, research 

managers, and other stakeholders, this document represents the synthesis of the Biomass Program’s National Algal 

Biofuels Technology Roadmap Workshop, comments gathered during a public comment period, and supporting 

scientific literature. This Roadmap is intended to summarize the state of technology for algae-based fuels and 

document the research and development challenges associated with producing them at a commercial scale. 

Renewable energy lies at the intersection of some of our nation’s most pressing issues: our energy security, our 

economic wellbeing, and the stability of our global climate. These national challenges require near-term solutions 

as well as investments in nascent technologies that show promise for the future. Therefore, while DOE works to 

deploy renewable energy and energy-efficient projects across the country today, it remains committed to fostering 

technologies that could yield substantial benefits over time. Achieving cost-competitive, sustainable algal biofuels 

will entail years of research and careful planning, but their significant potential to serve as renewable transportation 

fuels warrants our thorough consideration of what efforts are necessary to make them a commercial-scale reality. 

DOE has recently revived its investment in algal biofuels in response to the increased urgency of lowering 

greenhouse gas emissions and producing affordable, reliable energy, as well as the recognition that we will not 

likely achieve these goals via one technology pathway. Through appropriated dollars and the American Recovery 

and Reinvestment Act of 2009, DOE is investing in a variety of research, development, and demonstration (RD&D) 

projects that seek to tackle key technical hurdles associated with commercializing algal biofuels. Meanwhile, other 

federal agencies, private companies, and the academic community are also increasing their efforts to optimize and 

commercialize this renewable energy source. 

This Roadmap lays the groundwork for identifying challenges that will likely need to be surmounted for algae and 

cyanobacteria to be used in the production of economically viable, environmentally sound biofuels. It is intended to 

serve as a resource for researchers, engineers, and decision-makers by providing a summary of progress to date and 

a direction for future algae RD&D activities, and we hope it fosters and informs participation from existing and new 

stakeholders as the next steps are taken to advance algal biofuels. DOE looks forward to continuing its work with 

diverse partners in evaluating renewable energy options and facilitating development of those that carry the greatest 

benefits today and in the years to come.

Valerie Sarisky-Reed

Acting Manager, Biomass Program

U.S. Department of Energy
 ii Executive Summary

“

”

Developing the next generation of biofuels is key to our 

effort to end our dependence on foreign oil and address the 

climate crisis – while creating millions of new jobs that can’t 

be outsourced

 — Secretary of Energy Steven Chu at the White House

ceremony on May 5, 2009, announcing $800 

million in new biofuel research activities 

I

n recent years, biomass-derived fuels have received 

increasing attention as one solution to our nation’s 

continued and growing dependence on imported 

oil, which exposes the country to the risk of critical 

disruptions in fuel supply, creates economic and social 

uncertainties for businesses and individuals, and impacts 

our national security. The Energy Independence and 

Security Act of 2007 (EISA) established a mandatory 

Renewable Fuel Standard (RFS) requiring transportation 

fuel sold in the U.S. to contain a minimum of 36 billion 

gallons of renewable fuels, including advanced and 

cellulosic biofuels and biomass-based diesel, by 2022. 

While cellulosic ethanol is expected to play a large role 

in meeting the EISA goals, a number of next generation 

biofuels show significant promise in helping to achieve 

the goal. Of these candidates, biofuels derived from algae 

have the potential to help the U.S. meet the new RFS 

while at the same time moving the nation ever closer to 

energy independence. To accelerate the deployment of 

advanced biofuels, President Obama and Secretary of 

Energy Steven Chu announced the investment of $800M 

in new research on biofuels in the American Recovery 

and Renewal Act. This announcement included funds 

for the Department of Energy (DOE) Office of Energy 

Efficiency and Renewable Energy’s (EERE) Biomass 

Program to invest in the research, development, and 

deployment of commercial algae-to-biofuel processes. 

Additional funding is being directed to algae-to-biofuel 

research both in EERE and other government agencies 

and programs.

The term algae can refer to microalgae, cyanobacteria 

(the so called “blue-green algae”), and macroalgae (or 

seaweed). Under certain conditions, some microalgae 

have the potential to accumulate significant amounts 

of lipids (more than 50% of their ash-free cell dry 

weight). These characteristics give great potential for 

an immediate pathway to high energy density, fungible 

fuels. These fuels can also be produced using other algae 

feedstocks and intermediates, including starches and 

sugars from cyanobacteria and macroalgae. In addition 

to fungible biofuels, a variety of different biofuels and 

products can be generated using algae precursors. 

There are several aspects of algal biofuel production that 

have combined to capture the interest of researchers and 

entrepreneurs around the world. These include: 

1) high per-acre productivity, 2) non-food based 

feedstock resources, 3) use of otherwise non-productive, 

non-arable land, 4) utilization of a wide variety of water 

sources (fresh, brackish, saline, marine, produced, and 

wastewater), 5) production of both biofuels and valuable 

co-products, and 6) potential recycling of CO2 and other 

nutrient waste streams. 

The DOE-supported Aquatic Species Program, an effort 

undertaken from 1978 to 1996, illustrated the potential 

of algae as a biofuel feedstock. Much has changed since 

the end of the program. Rising petroleum prices and a 

national mandate to reduce U.S. dependence on foreign 

oil, provide environmental benefits, and create economic 

opportunities across the nation have renewed interest in 

developing algal feedstocks for biofuels production.

While the basic concept of using algae as an alternative 

and renewable source of biomass feedstock for biofuels 

has been explored previously, a scalable, sustainable 

and commercially viable system has yet to emerge. 

The National Algal Biofuels Technology Roadmap 

Workshop, held December 9-10, 2008, was convened 

by DOE-EERE’s Biomass Program. The two-day event 

brought together more than 200 scientists, engineers, 

Executive Summary

A culture of the microalgae Botryococcus. Photo courtesy of the 

Provasoli-Guillard National Center for Culture of Marine Phytoplankton 

(CCMP).
Executive Summary iii

algal biomass production systems at commercial 

scale. By documenting the challenges across the algal 

biomass supply chain and highlighting research and 

coordination needs and gaps, this document will serve to 

guide researchers and engineers, policymakers, federal 

agencies, and the private sector in implementing national 

research, development, and deployment efforts. 

In summary, the Roadmap Workshop effort suggests 

that many years of both basic and applied science and 

engineering will likely be needed to achieve affordable, 

scalable, and sustainable algal-based fuels. The ability 

to quickly test and implement new and innovative 

technologies in an integrated process will be a key 

component to accelerating progress. 

research managers, industry representatives, lawyers, 

financiers, and regulators from across the country to 

discuss and identify the critical challenges currently 

hindering the economical production of algal biofuels at 

commercial scale. 

This document represents the output from the Workshop, 

supporting scientific literature, and comments received 

during a public comment period. The Roadmap 

document is intended to provide a comprehensive state 

of technology summary for fuels and co-products from 

algal feedstocks and to document the feasibility and 

techno-economic challenges associated with scaling 

up of processes. This document also seeks to explore 

the economic and environmental impacts of deploying 
 iv Executive Summary

FROM ALGAE TO BIOFUELS

An Integrated Systems Approach to Renewable E nergy 

 Systems and Techno-Economic Analysis: Guiding the Research and 

MICROALGAE CYANOBACTERIA MACROALGAE

ALGAE FEEDSTOCKS CULTIVATION

Algae as feedstocks for bioenergy refers to a diverse group of 

organisms that include microalgae, macroalgae (seaweed), 

and cyanobacteria (formerly called “blue-green algae”). 

Algae occur in a variety of natural aqueous and terrestial 

habitats ranging from freshwater, brackish waters, marine, 

and hyper-saline environments to soil and in symbiotic 

associations with other organisms. 

Understanding, managing, and taking advantage of the 

biology of algal strains selected for use in production 

systems is the foundation for processing feedstocks into 

fuels and products. Isolating new strains directly from unique 

environments will ensure versatile and robust strains for mass 

culture needed in biofuels applications.

Microalgae and cyanobacteria can be cultivated via 

photoautotrophic methods (where algae require light to 

grow and create new biomass) in open or closed ponds or via 

heterotrophic methods (where algae are grown without light 

and are fed a carbon source, such as sugars, to generate new 

biomass). Macroalgae (or seaweed) has different cultivation 

needs that typically require open off-shore or coastal facilities. 

Designing an optimum cultivation system involves leveraging 

the biology of the algal strain used and inegrating it with the 

best suited downstream processing options. Choices made for 

the cultivation system are key to the affordability, scalability, 

and sustainability of algae to biofuel systems.

Example Cultivation Systems

POLICY SITING AND RESOURCES

Fermentation Tanks

Closed Photobioreactors

Open Ponds

FROM ALGAE TO BIOFUELS

An Integrated Systems Approach to Renewable Energy that is 

Development Path Toward a
Executive Summary v

CONVERSION

Conversion to fuels and products is predicated on a basic 

process decision point:

1) Conversion of whole algal biomass;

2) Extraction of algal metabolites; or

3) Processing of direct algal secretions.

Conversion technology options include chemical, 

biochemical, and thermochemical processes, or a 

combination of these approaches. 

The end products vary depending on the conversion 

technology utilized. Focusing on biofuels as the end-product 

poses challenges due to the high volumes and relative low 

values associated with bulk commodities like gasoline and 

diesel fuels.

End Uses:

EXTRACTION

Abundant, Affordable, and Sustainable

2-O-C

CH2-O-C

O

R1

CH-O-C

O

R2

CH2-O-C

O

R3

Three major components can be extracted from algal 

biomass: lipids (including triglycerides and fatty acids), 

carbohydrates, and proteins. While lipids and carbohydrates 

are fuel precursors (e.g., gasoline, biodiesel and jet fuel), 

proteins can be used for co-products (e.g., animal/fish 

feeds). 

Most challenges in extraction are associated with the 

industrial scale up of integrated extraction systems. 

While many analytical techniques exist, optimizing 

extraction systems that consume less energy than 

contained in the algal products is a challenge due to the 

high energy needs associated with both handling and 

drying algal biomass as well as separating out desirable 

products. Some algal biomass production processes are 

investigating options to bypass extraction, though these are 

also subject to a number of unique scale-up challenges. 

Algal Lipid: Precursor to Biofuels

Bio-Crude

• Biogas

• Co-products 

(e.g., animal feed, fertilizers,

industrial enzymes, 

bioplastics, and surfactants)

• Biodiesel

• Renewable Hydrocarbons

• Alcohols

 HARVESTING / DEWATERING 

Some processes for the conversion of algae to liquid 

transportation fuels require pre-processing steps such as 

harvesting and dewatering. Algal cultures are mainly grown 

in water and can require process steps to concentrate 

harvested algal biomass prior to extraction and conversion. 

These steps can be energy-intensive and can entail siting 

issues.

Commercially Viable Algal Biofuel Industry

REGULATIONS AND STANDARDS
 vi Executive Summary
Contents vii

1. Overview....................................................................................................................................1

About the Roadmap...............................................................................................................................................1

1.1 America’s Energy Challenges .............................................................................................................................1

Advantages of Algal Feedstocks ......................................................................................................................3

1.2 A History of Domestic Algal Biofuels Development ...............................................................................3

Early Work to 1996 .................................................................................................................................................3

Research from 1996 to Present.........................................................................................................................5

1.3 Algae-to-Biofuels: Opportunity and Challenges Today..........................................................................5

Technology and Analysis Challenges..............................................................................................................5

Regulations and Standards.................................................................................................................................7

Public-Private Partnerships ................................................................................................................................7

References.................................................................................................................................................................7

2. Algal Biology ...........................................................................................................................8

2.1 Strain Isolation, Screening and Selection ....................................................................................................8

Isolation and Characterization of Naturally Occurring Algae ...............................................................8

Role of Culture Collections as National Algae Data Resource Centers .............................................9

Selecting Algal Model Systems for Study ...................................................................................................10

2.2 Algal Physiology and Biochemistry ............................................................................................................. 11

Photosynthesis and Light Utilization ..............................................................................................................11

Carbon Partitioning and Metabolism..............................................................................................................11

Algal Carbohydrates ............................................................................................................................................ 12

Lipid Synthesis and Regulation....................................................................................................................... 12

Biohydrogen .......................................................................................................................................................... 15

2.3 Algal Biotechnology..........................................................................................................................................16

The Genetic Toolbox ............................................................................................................................................ 16

Enabling Technologies: “Omics” Approaches and Bioinformatics .................................................... 19

Applications of Biotechnology to Algal Bioenergy ................................................................................20

Considerations of Genetic Modifications.................................................................................................... 22

References.............................................................................................................................................................. 23

3. Algal Cultivation....................................................................................................................29

3.1 Cultivation Pathways.......................................................................................................................................... 29

Microalgae and Cyanobacteria....................................................................................................................... 29

Macroalgae.............................................................................................................................................................30

3.2 Scale-Up Challenges ......................................................................................................................................... 31

Stability of Large-Scale Cultures .................................................................................................................. 31

Contents
 viii Contents

System Productivity............................................................................................................................................ 32

Nutrient Sources, Sustainability, and Management ............................................................................... 32

Water Management, Conservation, and Recycling ................................................................................ 33

References.............................................................................................................................................................. 35

4. Downstream Processing: Harvesting and Dewatering........................................................37

4.1 Approaches for Microalgae.............................................................................................................................37

Harvesting................................................................................................................................................................37

Drying....................................................................................................................................................................... 38

4.2 Approaches for Macroalgae ........................................................................................................................ 38

Harvesting............................................................................................................................................................... 38

Preprocessing........................................................................................................................................................ 39

4.3 Systems Engineering ...................................................................................................................................... 39

References..............................................................................................................................................................40

Preliminary Look at Energy Balance ...........................................................................................................40

5. Extraction of Products from Algae ......................................................................................42

5.1 Current Practices for Lipid Extraction........................................................................................................42

Mechanical Disruption (i.e., Cell Rupture).................................................................................................. 42

Organic Co-solvent Mixtures...........................................................................................................................43

Accelerated Solvent Extraction......................................................................................................................44

Selective Extraction ............................................................................................................................................44

Subcritical Water Extraction............................................................................................................................45

Supercritical Fluid Extraction..........................................................................................................................45

Heterotrophic Production.................................................................................................................................45

5.2 Challenges............................................................................................................................................................46

References..............................................................................................................................................................46

6. Algal Biofuel Conversion Technologies ..............................................................................48

6.1 Direct Production of Biofuels from Algae ................................................................................................48

Alcohols ...................................................................................................................................................................49

Alkanes.....................................................................................................................................................................49

Hydrogen ................................................................................................................................................................50

6.2 Processing of Whole Algae...........................................................................................................................50

Pyrolysis...................................................................................................................................................................50

Gasification.............................................................................................................................................................. 51

Liquefaction ........................................................................................................................................................... 52

Supercritical Processing.................................................................................................................................... 53

Anaerobic Digestion of Whole Algae........................................................................................................... 53

6.3 Conversion of Algal Extracts ........................................................................................................................ 53

Chemical Transesterification............................................................................................................................54
Contents ix

Biochemical (Enzymatic) Conversion.......................................................................................................... 55

Catalytic Cracking................................................................................................................................................ 55

Conversion to Renewable Diesel, Gasoline, and Jet Fuel .................................................................... 56

6.4 Processing of Algal Remnants after Extraction.....................................................................................57

References.............................................................................................................................................................. 58

7. Co-products .......................................................................................................................... 61

7.1 Commercial Products from Microalgae and Cyanobacteria............................................................... 61

7.2 Commercial Products from Macroalgae...................................................................................................64

7.3 Potential Options for the Recovery of Co-products............................................................................64

References.............................................................................................................................................................. 67

8. Distribution and Utilization..................................................................................................69

8.1 Distribution ...........................................................................................................................................................69

8.2 Utilization..............................................................................................................................................................70

Algal Blendstocks to Replace Middle-Distillate Petroleum Products..............................................70

Algal Blendstocks for Alcohol and Gasoline-Range Petroleum Products.......................................71

References...............................................................................................................................................................72

9. Resources and Siting ..........................................................................................................73

9.1 Resource Requirements for Different Cultivation Approaches ....................................................... 73

Photoautotrophic Microalgae Approach.....................................................................................................73

Heterotrophic Microalgae Approach ............................................................................................................74

Photoautotrophic Macroalgae Approach....................................................................................................74

9.2 Resources Overview..........................................................................................................................................75

Climate .....................................................................................................................................................................75

Water.........................................................................................................................................................................77

Carbon Dioxide.....................................................................................................................................................80

Land............................................................................................................................................................................ 81

9.4 Integration with Water Treatment Facilities .......................................................................................... 83

Wastewater Treatment and Recycling Applications.............................................................................. 83

Algae Production Techniques for Wastewater Treatment Plants .....................................................84

Main Research Needs for Algae Production with Wastewater .........................................................86

9.5 Co-location of Algal Cultivation Facilities with CO2-Emitting Industries....................................86

The Opportunity in Co-Locating with CO2-Emitting Sources............................................................. 87

Barriers to Co-Location of Algae Production with Stationary Industrial CO2 Sources ............88

Directions for Research and Development................................................................................................88

References..............................................................................................................................................................90
 x Contents

10. Systems and Techno-Economic Analysis ...........................................................................93

10.1 Objectives of Techno-Economic Analysis .............................................................................................. 93

10.2 TEA Scope and Methods ..............................................................................................................................94

10.3 Suggestions for TEA and LCA Approach (Workshop Results and Discussion)..................... 97

10.4 Systems Analysis .............................................................................................................................................99

Overview .................................................................................................................................................................99

Engineering Analyses and GIS Assessments ..........................................................................................100

Impact of Geographic Variability of Inputs on Algal Biofuel Production Costs .........................102

Life Cycle Analysis ............................................................................................................................................. 104

10.5 Algae Production Costs and Uncertainties .........................................................................................104

10.6 Preliminary System Dynamics Modeling ............................................................................................104

10.7 Potential Directions for R&D Effort ....................................................................................................... 105

11. Public-Private Partnerships ..............................................................................................109

11.1 The Benefits of Algal Biofuels Public-Private Partnerships ........................................................... 109

11.2 Components of Successful Public-Private Partnerships ...................................................................110

11.3 Forums for Public-Private Partnerships...................................................................................................110

11.4 Partnership Challenges in the Algal Biofuels Industry........................................................................111

11.5 Modeling Partnerships for Technology Development.........................................................................111

References..............................................................................................................................................................114

Appendices ............................................................................................................................115

Appendix 1 : Workshop Participants..................................................................................................................115

Appendix 2: Contributors......................................................................................................................................122

Appendix 3: Respondents to Request for Information on the Draft Roadmap ..............................124
1. Overview 1

The Biomass Program (Program) of the U.S. Department 

of Energy (DOE) Office of Energy Efficiency and 

Renewable Energy is committed to advancing the vision 

of a viable, sustainable domestic biomass industry that 

produces renewable biofuels, bioproducts and biopower, 

enhances U.S. energy security, reduces our dependence 

on oil, provides environmental benefits, and creates 

economic opportunities across the nation. The Program’s 

goals are driven by various federal policies and laws, 

including the Energy Independence and Security Act 

of 2007. To accomplish its goals, the Program has 

undertaken a diverse portfolio of research, development, 

and deployment (RD&D) activities, in partnership 

with national laboratories, academia, and industry. 

Algal biofuels offer great promise in contributing to 

the Program’s vision, as well as helping to meet the 

Renewable Fuels Standard (RFS) mandate established 

within EISA. The RFS mandates blending of 36 billion 

gallons of renewable fuels by 2022, of which only 15 

billion gallons can be produced from corn-based ethanol. 

Biofuels derived from algae can meet these l onger-term 

needs of the RFS and represent a significant opportunity 

to impact the U.S. energy supply for transportation 

fuels. Despite their potential, the state of technology 

for producing algal biofuels is regarded by many in 

the field to be in its infancy and there is a considerable 

amount of RD&D is needed to achieve affordable, 

scalable, and sustainable algal-based biofuels.

About the Roadmap

The framework for National Algal Biofuels Technology 

Roadmap was constructed at the Algal Biofuels 

Technology Roadmap Workshop, held December 9-10, 

2008, at the University of Maryland-College Park. The 

Workshop was organized by the Biomass Program to 

discuss and identify the critical challenges currently 

hindering the development of a domestic, commercialscale algal biofuels industry. A major objective of the 

Workshop was to gather the necessary information 

to produce an algal biofuels technology roadmap 

that both assesses the current state of technology and 

provides direction to the Program’s RD&D efforts. 

More than 200 stakeholders were convened at the 

Workshop, representing a diverse range of expertise from 

industry, academia, the national laboratories, government 

agencies, and non-governmental organizations. The 

Workshop provided a stimulating environment to explore 

topics affecting the development of algal biofuels industry. 

1. Overview

The Workshop was able to capture the participants’ 

experience and expertise during a series of technical 

break-out sessions that spanned critical aspects of the 

algal biomass supply chain and cross-cutting issues. 

The outcomes from the Workshop provided key inputs 

to the development of this Algal Biofuels Technology 

Roadmap. The full proceedings of the Workshop can 

be found at http://www.orau.gov/algae2008pro/. 

Following the release of the initial draft of the Roadmap, 

a 60-day public comment period was held to allow 

Workshop participants to evaluate the Roadmap for 

fidelity and incorporate new information, viewpoints, 

and criticisms not captured during the Workshop. All 

comments are noted in the Appendix of this document. 

Every attempt was made to ensure that the Roadmap 

development process was transparent and inclusive.

 

This Roadmap presents information from a scientific, 

economic, and policy perspectives that can support 

and guide RD&D investment in algal biofuels. While 

addressing the potential economic and environmental 

benefits of using algal biomass for the production of 

liquid transportation fuels, the Roadmap describes 

the current status of algae RD&D. In doing so, it lays 

the groundwork for identifying challenges that likely 

need to be overcome for algal biomass to be used in 

the production of economically viable biofuels. 

1.1 America’s Energy Challenges

As global petroleum supplies diminish, the United 

States is becoming increasingly dependent upon foreign 

sources of crude oil. The United States currently imports 

approximately two-thirds of its petroleum, 60% of 

which is used for producing transportation fuels. The 

rising energy demand in many rapidly developing 

countries around the world is beginning to create 

intense competition for the world’s dwindling petroleum 

reserves. Furthermore, the combustion of petroleumbased fuels has created serious concerns about climate 

change from the greenhouse gas (GHG) emissions.

In 2007, the Energy Independence and Security Act 

(EISA) was enacted, which set new standards for 

vehicle fuel economy, as well as made provisions that 

promote the use of renewable fuels, energy efficiency, 

and new energy technology research and development. 

The legislation establishes production requirements for 

domestic alternative fuels under the Renewable Fuels 

Standard (RFS) that increase over time (Exhibit 1.1). 
2 1. Overview 

microalgae have demonstrated potential oil yields that 

are significantly higher than the yields of oilseed crops 

(Exhibit 1.2). Potential oil yields from certain algae 

strains are projected to be at least 60 times higher than 

from soybeans, approximately 15 times more productive 

than jatropha, and approximately 5 times that of oil palm 

per acre of land on an annual basis (Rodolfi et al., 2009). 

Advanced biofuels face significant challenges in meeting 

the ambitious targets set by EISA. As required by EISA, 

advanced biofuels must demonstrate GHG emissions 

across their life cycle that are at least 50% less than GHG 

emissions produced by petroleum-based transportation 

fuels. Significant acreage and productivity will be required 

for biomass production to generate sufficient feedstock 

to meet the RFS mandates. Cellulosic feedstocks were 

identified by the Billion Ton Study as a significant source 

of biomass (Perlack et al., 2005). However, the study 

did not explore the potential of algae, while algae may 

offer comparable biomass productivity as lignocellulosic 

feedstocks – the key biomass resource factored in the study.

 

Many pathways are currently under consideration for 

production of biofuels and bioproducts from components 

of biomass. The most promising among these are routes 

to advanced biofuels such as high energy density fungible 

fuels for aviation and ground transport. Algal biomass may 

offer significant advantages that complement traditional 

feedstocks towards these fuels. For example, oleaginous 

UNIQUE ADVANTAGES OF ALGAL FEEDSTOCK FOR 

ADVANCED BIOFUELS

• High area productivity

• Minimizes competition with conventional agriculture

• Utilizes a wide variety of water sources

• Recycles stationary emissions of carbon dioxide

• Compatible with integrated production of fuels and 

co-products within biorefineries

Exhibit 1.1 Renewable Fuel Standard volume requirements (billion gallons) 

Cellulosic biofuels and biomass-based diesel are included in the advanced biofuel requirement.

CELLULOSIC

BIOFUEL

REQUIREMENT

BIOMASS-BASED

DIESEL

REQUIREMENT

ADVANCED BIOFUEL

REQUIREMENT

TOTAL RENEWABLE

FUEL REQUIREMENT

2009 N/A 0.5 0.6 11.1

2010 0.1 0.65 0.95 12.95

2011 0.25 0.80 1.35 13.95

2012 0.5 1.0 2.0 15.2

2013 1.0 a 2.75 16.55

2014 1.75 a 3.75 18.15

2015 3.0 a 5.5 20.5

2016 4.25 a 7.25 22.25

2017 5.5 a 9.0 24.0

2018 7.0 a 11.0 26.0

2019 8.5 a 13.0 28.0

2020 10.5 a 15.0 30.0

2021 13.5 a 18.0 33.0

2022 16.0 a 21.0 36.0

2023 b b b b

a

 To be determined by EPA through a future rulemaking, but no less than 1.0 billion gallons.

b

 To be determined by EPA through a future rulemaking.
1. Overview 3

Early Work to 1996

Proposals to use algae as a means of producing energy 

started in the late 1950s when Meier (1955) and Oswald 

and Golueke (1960) suggested the utilization of the 

carbohydrate fraction of algal cells for the production of 

methane gas via anaerobic digestion. A detailed engineering 

analysis by Benemann et al. (1978) indicated that algal 

systems could produce methane gas at prices competitive 

with projected costs for fossil fuels. The discovery that 

many species of microalgae can produce large amounts of 

lipid as cellular oil droplets under certain growth conditions 

dates back to the 1940s. Various reports during the 1950s 

and 1960s indicated that starvation for key nutrients, such 

as nitrogen or silicon, could lead to this phenomenon. 

The concept of utilizing the lipid stores as a source of 

energy, however, gained serious attention only during 

the oil embargo of the early 1970s and the energy price 

surges through the decade; this idea ultimately became 

a major push of DOE’s Aquatic Species Program.

The Aquatic Species Program represents one of the most 

comprehensive research efforts to date on fuels from 

microalgae. The program lasted from 1978 until 1996 

and supported research primarily at DOE’s National 

Renewable Energy Laboratory (NREL, formerly the 

Solar Energy Research Institute). The Aquatic Species 

Program also funded research at many academic 

institutions through subcontracts. Approximately $25 

million (Sheehan, 1998) was invested during the 18-year 

program. During the early years, the emphasis was on 

using algae to produce hydrogen, but the focus changed to 

liquid fuels (biodiesel) in the early 1980s. Advances were 

made through algal strain isolation and characterization, 

studies of algal physiology and biochemistry, genetic 

engineering, process development, and demonstrationscale algal mass culture. Techno-economic analyses 

and resource assessments were also important aspects 

of the program. In 1998, a comprehensive overview 

of the project was completed (Sheehan et al., 1998). 

Some of the highlights are described briefly below.

The Aquatic Species Program researchers collected 

more than 3,000 strains of microalgae over a seven-year 

period from various sites in the western, northwestern, 

and southeastern U.S. representing a diversity of aquatic 

environments and water types. Many of the strains were 

isolated from shallow, inland saline habitats that typically 

undergo substantial swings in temperature and salinity. 

The isolates were screened for their tolerance to variations 

in salinity, pH, and temperature, and also for their ability 

to produce neutral lipids. The collection was narrowed 

to the 300 most promising strains, primarily green algae 

(Chlorophyceae) and diatoms (Bacillariophyceae).

Advantages of Algal Feedstocks

Algae can be preferred feedstock for high energy density, 

fungible liquid transportation fuels. There are several 

aspects of algal biofuel production that have combined to 

capture the interest of researchers and entrepreneurs around 

the world: 

• Algal productivity can offer high biomass yields per

acre of cultivation.

• Algae cultivation strategies can minimize or avoid

competition with arable land and nutrients used for

conventional agriculture.

• Algae can utilize waste water, produced water, and 

saline water, thereby reducing competition for limited 

freshwater supplies.

• Algae can recycle carbon from CO2-rich flue emissions 

from stationary sources, including power plants and 

other industrial emitters.

• Algal biomass is compatible with the integrated 

biorefinery vision of producing a variety of fuels and 

valuable co-products.

1.2 A History of Domestic 

Algal Biofuels Development

The advantages of algae as a feedstock for bioenergy 

have been apparent since the mid-twentieth century. 

Although, a scalable, commercially viable system has 

not yet emerged, earlier studies have laid foundational 

approaches to the technologies being explored today. 

CROP OIL YIELD 

(GALLONS/ACRE/YR)

Soybean 48

Camelina 62

Sunflower 102

Jatropha 202

Oil palm 635

Algae 1,000-6,500b

Exhibit 1.2 Comparison of oil yields from biomass feedstocksa

a

 Adapted from Chisti (2007)

b

 Estimated yields, this report
4 1. Overview 

After promising microalgae were identified, further 

studies examined the ability of many strains to induce 

lipid accumulation under conditions of nutrient stress. 

Although nutrient deficiency actually reduces the 

overall rate of oil production in a culture (because of the 

concomitant decrease in the cell growth rate), studying 

this response led to valuable insights into the mechanisms 

of lipid biosynthesis. Under inducing conditions, some 

species in the collection were shown to accumulate as 

much as 60% of their dry weight in the form of lipid, 

primarily triacylglycerides (TAGs) (Chisti, 2007). 

Cyclotella cryptica, an oleaginous diatom, was the focus 

of many of the biochemical studies. In this species, growth 

under conditions of insufficient silicon (a component of 

the cell wall) is a trigger for increased oil production. A 

key enzyme is acetyl-CoA carboxylase (ACCase), which 

catalyzes the first step in the biosynthesis of fatty acids used 

for TAG synthesis. ACCase activity was found to increase 

under the nutrient stress conditions (Roessler, 1988), 

suggesting that it may play a role as a “spigot” controlling 

lipid synthesis, and thus the enzyme was extensively 

characterized (Roessler, 1990). With the advent of the first 

successful transformation of microalgae (Dunahay et al., 

1995), it became possible to manipulate the expression of 

ACCase in an attempt to increase oil yields. These initial 

attempts at metabolic engineering identified a pathway to 

modify the gene encoding in the ACCase enzyme, however, 

no effect was seen on lipid production in these preliminary 

experiments (Jarvis et al., 1999; Sheehan et al., 1998).

Additional studies focused on storage carbohydrate 

production, as biosynthesis of these compounds competes 

for fixed carbon units that might otherwise be used for 

lipid formation. For example, enzymes involved in the 

biosynthesis of the storage carbohydrate, chrysolaminarin 

in C. cryptica were characterized (Roessler, 1987 and 

1988) with the hope of eventually turning down the 

flow of carbon through these pathways. The termination 

of the Aquatic Species Program in 1996 halted further 

development of these potentially promising paths to 

commercially viable strains for oil production.

During the course of the Aquatic Species Program 

research, it became clear that novel solutions would be 

needed for biological productivity and various problematic 

process steps. Cost-effective methods of harvesting 

and dewatering algal biomass and lipid extraction, 

purification, and conversion to fuel are critical to successful 

commercialization of the technology. Harvesting is a 

process step that is highly energy- and capital-intensive. 

Among various techniques, harvesting via flocculation 

was deemed particularly encouraging (Sheehan et al., 

1998). Extraction of oil droplets from the cells and 

purification of the oil are also cost-intensive steps. The 

Aquatic Species Program focused on solvent systems, but 

failed to fully address the scale, cost, and environmental 

issues associated with such methods. Conversion of 

algal oils to ethyl- or methyl-esters (biodiesel) was 

successfully demonstrated in the Aquatic Species 

Program and shown to be one of the less challenging 

aspects of the technology. In addition, other biofuel 

process options (e.g., conversion of lipids to gasoline) 

were evaluated (Milne et al., 1990), but no further fuel 

characterization, scale-up, or engine testing was carried out.

Under Aquatic Species Program subcontracts, 

demonstration-scale outdoor microalgal cultivation 

was conducted in California, Hawaii, and New Mexico 

(Sheehan et al., 1998). Of particular note was the Outdoor 

Test Facility in Roswell, New Mexico, operated by 

Microbial Products, Inc. (Weissman et al., 1989). This 

facility utilized two 1,000 m2 outdoor, shallow (10-20 cm 

deep), paddlewheel-mixed raceway ponds, plus several 

smaller ponds for inocula production. The raceway design 

was based on the “high rate pond” system developed at 

University of California-Berkeley. The systems were 

successful in that long-term, stable production of algal 

biomass was demonstrated, and the efficiency of CO2

utilization (bubbled through the algae culture) was shown 

to be more than 90% with careful pH control. Low 

nighttime and winter temperatures limited productivity in 

the Roswell area, but overall biomass productivity averaged 

around 10 g/m2/day with occasional periods approaching 

50 g/m2/day. One serious problem encountered was that 

the desired starting strain was often outgrown by faster 

reproducing, but lower oil producing, strains from the wild.

Several resource assessments were conducted under the 

Aquatic Species Program. Studies focused on suitable land, 

saline water, and CO2 resources (power plants), primarily 

in desert regions of the Southwest (Maxwell et al., 1985). 

Sufficient resources were identified for the production 

of many billions of gallons of fuel, suggesting that the 

technology could have the potential to have a significant 

impact on U.S. petroleum consumption. However, the 

costs of these resources can vary widely depending 

upon such factors as land leveling requirements, depth 

of aquifers, distance from CO2 point sources, and other 

issues. Detailed techno-economic analyses underlined 

the necessity for very low-cost culture systems, such 

as unlined open ponds (Benemann and Oswald, 1996). 

In addition, biological productivity was shown to have 

the single largest influence on fuel cost. Different cost 

analyses led to differing conclusions on fuel cost, but 

even with optimistic assumptions about CO2 credits and 

productivity improvements, estimated costs for unextracted 

algal oil were determined to range from $59 - $186 per 
1. Overview 5

barrel (Sheehan et al., 1998). It was concluded that algal 

biofuels would not be cost-competitive with petroleum, 

which was trading at less than $20/barrel in 1995. 

Overall, the Aquatic Species Program was successful 

in demonstrating the feasibility of algal culture as a 

source of oil and resulted in important advances in the 

technology. However, it also became clear that significant 

barriers would need to be overcome in order to achieve 

an economically feasible process. In particular, the work 

highlighted the need to understand and optimize the 

biological mechanisms of algal lipid accumulation and to 

find creative, cost-effective solutions for the culture and 

process engineering challenges. Detailed results from the 

Aquatic Species Program research investment are available 

to the public in more than 100 electronic documents on 

the NREL Web site at www.nrel.gov/publications.

Also from 1968-1990, DOE sponsored the Marine Biomass 

Program, a research initiative to determine the technical 

and economic feasibility of macroalgae cultivation and 

conversion to fuels, particularly to substitute natural gas 

(SNG) via anaerobic digestion (Bird and Benson, 1987). 

Primary efforts were focused on open ocean culture of 

California kelp. Similar to the findings of the Aquatic

Species Program, researchers concluded that algal-derived 

SNG would not be cost-competitive with fossil fuel gas.

Research from 1996 to Present

Since the end of DOE’s Aquatic Species Program in 

1996, federal funding for algal research has come 

from DOE, the Department of Defense, the National 

Science Foundation, and the Department of Agriculture. 

Recent initiatives, such as a major Defense Advanced 

Research Projects Agency solicitation, the Air Force 

Office of Scientific Research (AFOSR) algal bio-jet 

program, and several DOE Small Business Innovative 

Research (SBIR) request for proposals, suggest that 

funding levels are beginning to increase. Additionally, 

DOE’s Advanced Research Projects Agency-Energy 

(ARPA-E), Office of Science, Office of Fossil Energy, 

and Biomass Program are all funding research activities 

that include investigating microalgae, cyanobacteria, and 

macroalgae for biofuels and beneficial re-use of CO2. 

Additionally, a number of U.S. national labs are 

increasingly focusing on algal biofuels research. State 

funding programs and research support from private 

industry also make up a significant proportion of 

research funding. Private investment in algal biofuels 

has been increasing at a dramatic rate over the last few 

years, significantly outpacing government funding. 

1.3 Algae-to-Biofuels: 

Opportunity and Challenges 

Today

Abundant, affordable, and sustainable feedstocks are the 

lifeblood of the burgeoning biofuels industry today. 

Algae must be considered as part and parcel of the 

feedstock mix for producing advanced biofuels. In 

contrast to the development of cellulosic biofuels 

which benefit from a direct agricultural and process 

engineering lineage, there is no parallel agricultural 

enterprise equivalent for cultivating algae at a similar 

scale. A sizable and strategically structured investment 

to tackle the challenges of algal biofuels is thus 

needed to support commercialization activities.

Based on the information provided at the Workshop, it was 

determined that a great deal of RD&D is still necessary 

to reduce the level of risk and uncertainty associated with 

the algae-to-biofuels process so it can be commercialized. 

Further, these activities must be accompanied with 

conducive developments on the non-technical fronts – 

regulations and standards, and public-private partnerships. 

By reviewing the technology gaps and cross-cutting needs, 

the Roadmap aims to guide researchers and engineers, 

policymakers, federal agencies, and the private sector 

in implementing a nationally coordinated effort toward 

developing a viable and sustainable algal biofuel industry.

Technology and Analysis Challenges

This Roadmap seeks to lay down the first comprehensive 

state of technology summary for fuels and co-products

 from algal feedstocks and to document the feasibility and 

techno-economic challenges associated with commercial 

scaling up of processes. 

Cyclotella cells, Courtesey of CCMP.
6 1. Overview FEEDSTOCK CONVERSION INFRASTRUCTURE

OVERCOMING BARRIERS TO ALGAL BIOFUELS: TECHNOLOGY GOALS

PROCESS 

STEP R&D CHALLENGES

Algal Biology

• Sample strains from a wide variety of environments for maximum diversity

• Develop small-scale, high-throughput screening technologies

• Develop open-access database and collections of existing strains with detailed characterization

• Investigate genetics and biochemical pathways for production of fuel precursors

• Improve on strains for desired criteria by gene manipulation techniques or breeding

Algal 

Cultivation

• Investigate multiple approaches (i.e., open, closed, hybrid, and coastal/off-shore systems; phototrophic, heterotrophic, 

and mixotrophic growth)

• Achieve robust and stable cultures at a commercial scale

• Optimize system for algal productivity of fuel precursors (e.g., lipids)

• Sustainably and cost-effectively manage the use of land, water, and nutrients

• Identify and address environmental risks and impacts

Harvesting and 

Dewatering

• Investigate multiple harvesting approaches (e.g., sedimentation, flocculation, dissolved air floatation, filtration, 

centrifugation, and mechanized seaweed harvesting)

• Minimize process energy intensity

• Lower capital and operating costs

• Assess each technology option in terms of overall system compatibility and sustainability

Extraction and 

Fractionation

• Investigate multiple approaches (e.g., sonication, microwave, solvent systems, supercritical fluid, subcritical 

water, selective extraction, and secretion)

• Achieve high yield of desired intermediates; preserve co-products

• Minimize process energy intensity

• Investigate recycling mechanisms to minimize waste

• Address scaling challenges, such as operational temperature, pressure, carrying capacity, side reactions, and separations

Fuel 

Conversion

• Investigate multiple approaches to liquid transportation fuels (e.g., direct fuel production, thermochemical/catalytic 

conversion, biochemical conversion, and anaerobic digestion)

• Improve catalyst specificity, activity, and durability

• Reduce contaminants and reaction inhibitors

• Minimize process energy intensity and emissions over the life cycle 

• Achieve high conversion rates under scale-up conditions

Co-products

• Identify and evaluate the co-production of value-added chemicals, energy, and materials from algal remnants 

(e.g., biogas, animal/fish feeds, fertilizers, industrial enzymes, bioplastics, and surfactants)

• Optimize co-product extraction and recovery

• Conduct market analyses, including quality and safety trials to meet applicable standards

Distribution 

and Utilization

• Characterize algal biomass, intermediates, biofuel, and bioproducts under different storage and transport scenarios for 

contamination, weather impacts, stability, and end-product variability 

• Optimize distribution for energy and costs in the context of facility siting

• Comply with all regulatory and customer requirements for utilization (e.g., engine performance and material compatibility)

Resources 

and Siting

• Assess and characterize land, climate, water, energy, and nutrient resource requirements for siting of microalgae 

(heterotrophic & photoautotrophic) and macroalgae production systems

• Integrate with wastewater treatment and/or CO2 emitter industries (in the case of heterotrophic approach)

• Address salt balance, energy balance, water & nutrient reuse, and thermal management 

PURSUING STRATEGIC R&D: TECHNO-ECONOMIC MODELING AND ANALYSIS

Given the multiple technology and system options and their interdependency, an integrated techno-economic modeling and analysis spanning the entire 

algae to biofuels supply chain is crucial in guiding research efforts along select pathways that offer the most opportunity to practically enable a viable 

and sustainable algae-based biofuels and co-products industry. FEEDSTOCK CONVERSION INFRASTRUCTURE
1. Overview 7

Regulations and Standards

While the Roadmap’s primary objective is to highlight 

the technical challenges and opportunities associated 

with algal biofuels commercialization, it is recognized 

that RD&D activities need to be carried out under a 

framework of standards, regulation, and policy. Algal 

biofuel developers need to foresee and understand the 

potentially applicable legal requirements early on in the 

research and development process to help ensure algae 

are legally and safely developed and the end-products 

(i.e., biofuels and co-products) comply with applicable 

consumption standards. Being a nascent industry, there 

are no existing standards for various aspects of algal 

biofuels production. However, RD&D activities can inform 

further development of applicable laws and standards.

Public-Private Partnerships

A collaborative framework of public-private partnerships 

offers an opportunity to jointly address the technological, 

economic, and policy and regulatory challenges as 

resolution of these issues will likely require participation 

from multiple entities. However, structuring publicprivate partnerships for successful ventures is a challenge 

in itself given the myriad issues and interests, such as 

intellectual property rights. Also, supporting education 

will be critical to create intellectual talent and the 

workforce needed to allow this industry to grow.

References

Benemann, J.R., Pursoff, P. & Oswald, W.J., 1978. Engineering Design and Cost Analysis of a Large-Scale Microalgae Biomass System. 

Final Report to the US Energy Department, NTIS# H CP/ T, 1605(UC-61), 91.

Chisti, Y., 2007. Biodiesel from microalgae. Biotechnology Advances, 25(3), 294–306.

Dunahay, T.G., Jarvis, E.E. & Roessler, P.G., 1995. Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophila. 

Journal of Phycology, 31(6), 1004–1011.

Jarvis, E. & Roessler, P., 1999. Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase 

activities from Cyclotella cryptica - US Patent 5928932 Abstract. Available at: [Accessed November 3, 2009].

Meier, R.L., 1955. Biological cycles in the transformation of solar energy into useful fuels. Solar Energy Research, 179–183.

Milne, T.A., Evans, R.J. & Nagle, N., 1990. Catalytic conversion of microalgae and vegetable oils to premium gasoline, with 

shape-selective zeolites. Biomass, 21(3), 219-232.

Oswald, W.J. & Golueke, C.G., 1960. Biological transformation of solar energy. Adv. Appl. Microbiol, 11, 223–242.

Perlack, R.D. et al., 2005. Biomass as feedstock for a bioenergy and bioproducts industry: the technical feasibility of a billion-ton

 annual supply, ORNL/TM-2006/66, Oak Ridge National Laboratory, Oak Ridge, TN..

Rodolfi, L. et al., 2008. Microalgae for oil: strain selection, induction of lipid synthesis and outdoor mass cultivation in a low-cost 

photobioreactor. Biotechnol Bioeng, 102(1), 100–112.

Roessler, P.G., 1988. Effects of silicon deficiency on lipid composition and metabolism in the diatom Cyclotella cryptica. 

J. Phycol, 24, 394–400.

Roessler, P.G. & Ohlrogge, J.B., 1993. Cloning and characterization of the gene that encodes acetyl-coenzyme A carboxylase in the alga

Cyclotella cryptica. Journal of Biological Chemistry. 
8 2. Algal Biology 

Additionally, within an aqueous habitat, algae are 

typically found in planktonic (free floating) and benthic 

(attached) environments. Planktonic algae may be used 

in suspended mass cultures, whereas benthic algae may 

find application in biofilm-based production facilities. 

Isolation Techniques

For isolation of new strains from natural habitats, 

traditional cultivation techniques may be used such as 

enrichment cultures (Andersen and Kawachi, 2005). 

However, some algal strains take weeks to months to 

be isolated by traditional methods (for a comprehensive 

review of algal culturing techniques, see Anderson, 

2005). For large-scale sampling and isolation efforts, 

high-throughput automated isolation techniques involving 

fluorescence-activated cell sorting (FACS) have proven 

to be extremely useful (Sieracki et al., 2004). Because of 

morphological similarities when comparing many algal 

species, actual strain identification should be based on 

molecular methods such as rRNA sequence comparison, or 

in the case of closely related strains, other gene markers.

Screening Criteria and Methods

An ideal screen would cover three major areas: growth 

physiology, metabolite production, and strain robustness. 

The term growth physiology encompasses a number 

of parameters such as maximum specific growth rate, 

maximum cell density, tolerance to environmental variables 

(temperature, pH, salinity, oxygen levels, CO2 levels), and 

nutrient requirements. Because all of these parameters 

require significant experimental effort, the development 

of automated systems that provide information regarding 

all parameters simultaneously would be helpful. 

Screening for metabolite production may involve 

determining the cellular composition of proteins, lipids, 

and carbohydrates, and measuring the productivity of 

the organism regarding metabolites useful for biofuels 

generation. The exact screens employed would depend 

on the cultivation approaches and fuel precursor desired. 

For example, a helpful screen for oil production would 

allow for distinction between neutral and polar lipids, 

and would provide fatty acid profiles. Furthermore, 

many strains also secrete metabolites into the growth 

medium. Some of these could prove to be valuable coproducts, and new approaches are needed to develop 

screening methods for extracellular materials.

2. Algal Biology

The term “algae” commonly refers to a diverse mix of 

organisms from different kingdoms of life. Traditionally, 

algae have been unified based on their ability to carry out 

photosynthesis and live in aquatic habitats. Algae can be 

single or multi-cellular and pro- or eukaryotic, and though 

they typically live in aquatic environments and are capable 

of photosynthesis, this is not always the case. Algae include 

microalgae (unicellular eukaryotic organisms), macroalgae 

(seaweeds), and cyanobacteria (historically known as 

blue-green algae). Due to their diverse characteristics, the 

type and strain of algae being cultivated will ultimately 

affect every step of the algae to biofuels supply chain. 

2.1 Strain Isolation, 

Screening and Selection 

Isolation and Characterization of 

Naturally Occurring Algae 

The goals of algae isolation and screening efforts are to 

identify and maintain promising algal specimens for 

cultivation and strain development. Because it is not yet

 known how algae will be cultivated on a mass scale, 

new strains should be isolated from a wide variety of 

environments to provide the largest range in metabolic 

versatility possible. 

Natural Habitats

Algae can be isolated from a variety of natural aqueous 

habitats ranging from freshwater to brackish water, marine 

and hyper-saline environments, and soil (Round, 1984). 

Furthermore, large-scale sampling efforts should be 

coordinated to ensure broadest coverage of environments 

and to avoid duplication of efforts. The selection of 

specific locations can be determined by sophisticated site 

selection criteria through the combined use of dynamic 

maps, Geographic Information Systems (GIS) data and 

analysis tools. Ecosystems to be sampled could include 

aquatic (i.e., oceans, lakes, rivers, streams, ponds, and 

geothermal springs, which includes fresh, brackish, 

hypersaline, acidic and alkaline environments) and 

terrestrial environments in a variety of geographical 

locations to maximize genetic diversity. Collection sites 

can include public lands as well as various sites within 

our national and state park systems. In all cases, questions 

of ownership of isolated strains should be considered.

Sampling strategies should not only account for spatial 

distribution but also for the temporal succession brought 

about by seasonal variations of algae in their habitats. 
2. Algal Biology 9

industry has further exacerbated the flow of relevant strain 

data. Some minimal growth information is available from 

existing culture collections, but it is very difficult to obtain 

more detailed information on growth, metabolites, and 

robustness of particular existing strains. The establishment 

of a central strain, open access repository could accelerate 

R&D of algae-based biofuels production systems. 

A number of algal strains are currently available from 

culture collections such as UTEX (The Culture Collection 

of Algae at the University of Texas at Austin, Texas), with 

about 3,000 strains, and CCMP (The Provasoli-Guillard 

National Center for Culture of Marine Phytoplankton at the 

Bigelow Laboratory for Ocean Sciences in West Boothbay 

Harbor, Maine), with more than 2,500 strains. However, 

because many of the strains in these collections have been 

cultivated for several decades, some may have lost original 

properties, such as mating capability or versatility regarding 

nutrient requirements. To obtain versatile and robust strains 

that can be used for mass culture in biofuels applications, 

it would be prudent to consider the isolation of new, native 

strains directly from unique environments. For both direct 

breeding and metabolic engineering approaches to improve 

biofuels production, it will be important to isolate a wide 

variety of algae for assembly into a culture collection that 

will serve as a bioresource for further biofuels research.

As the major culture collections already collect and 

document data on strains, they could potentially 

serve as nuclei for the development of national algae 

resource centers. Culture collection organizations 

could be responsible for the gathering and 

dissemination of detailed information about potentially 

valuable strains. Information could include:

1. Strain name (species, subspecies name, taxonomy,

 reference)

2. Strain administration (number in collection,

preservation)

3. Environment and strain history (specific habitat,

 collector)

4. Strain properties: Cytological, biochemical, molecular,

 & screening results

5. Mutants

6. Plasmids and Phages

7. Growth conditions (media, temperature, pH) & 

germination conditions

8. Biological interaction (symbiosis, pathogenicity, 

toxicity)

9. Practical applications (general and industrial)

10. Omics data (Genomics, Transcriptomics, Proteomics, 

 or Metabolomics)

For mass culture of a given algal strain, it is also 

important to consider the strain’s robustness, which 

includes parameters such as culture consistency, 

resilience, community stability, and susceptibility to 

predators present in a given environment. Previous 

studies revealed that algae strains tested in the laboratory 

do not always perform similarly in outdoor mass 

cultures (Sheehan et al., 1998). Therefore, to determine 

a strain’s robustness, small-scale simulations of mass 

culture conditions will need to be performed. The 

development of small-scale but high-throughput screening 

technologies is an important step in enabling the testing 

of hundreds to thousands of different algal isolates.

At this time, the bottleneck in screening large numbers of 

algae stems from a lack of high-throughput methodologies 

that would allow simultaneous screening of multiple 

phenotypes, such as growth rate and metabolite 

productivity. Solvent extraction, for example, is the most 

common method for determination of lipid content in algae, 

but it requires a significant quantity of biomass (Ahlgren et 

al., 1991; ) (Bligh and Dyer, 1959). Fluorescent methods 

using lipid-soluble dyes have also been described, and 

though these methods require much less biomass (as little 

as a single cell), it has not yet been established if these 

methods are valid across a wide range of algal strains (Elsey 

et al., 2007; de la Jara et al., 2003). Further improvements 

in analytical methodology could be made through the 

development of solid-state screening methods. Not only 

are rapid screening procedures necessary for the biofuels 

field, but could prove extremely useful for the identification 

of species (particularly in mixed field samples) necessary 

for the future of algal ecology. It could also reduce 

the number of redundant screens of algal species.

Role of Culture Collections as National 

Algae Data Resource Centers

Culture collections are necessary to preserve the diversity 

of natural habitats, protect genetic material, and provide 

basic research resources. At present, only a few major 

algal collection centers exist in the United States and 

other countries. They currently maintain thousands 

of different algal strains and support the research and 

industrial community with their expertise in algae 

biology. The function of a culture collection often 

transcends simple depository functions. They may also 

support research on determining strain characteristics, 

cryopreservation, and phylogeny either by themselves 

or in connection with outside collaborators. 

Currently, no central database exists that provides global 

information on the characteristics of currently available 

algal strains. Protection of intellectual property in private 
10 2. Algal Biology 

that naturally make abundant amounts of the desired 

product. In such a strain, cellular metabolism is already 

geared toward production, which simplifies characterization 

and possible strain development for production.

Secretion of Products or Intermediates 

The ability of an algal species to secrete fuel precursors 

may be attractive because it could reduce or skip the cell 

harvesting step. However, there may be practical problems 

to consider, such as, if the desired product is volatile, 

then collection of the atmosphere above the culture will 

be necessary to isolate it, which will necessitate the use 

of closed bioreactors. Also to be considered is whether 

secretion actually makes the product more readily 

available. For example, although there are algae known 

to secrete long-chain hydrocarbons (e.g., Botryococcus 

braunii), they are still associated with the cells in a lipid 

biofilm matrix, and thus are not free to form an organic 

hydrocarbon phase in solution (Banerjee et al., 2002). Even 

if sustainable secretion could be achieved, it is not clear 

what the effect of a lipid emulsion in an algal culture would 

be. For example, an abundance of exported lipids could 

unfavorably alter fluidics properties or provide a carbon 

source favoring growth of contaminants. Finally, secretion 

of either intermediates or products into the growth medium 

could make these compounds vulnerable to contaminating 

microbes for catabolism. Pilot-scale experimentation 

and further metabolic engineering is required to evaluate 

possible advantages and disadvantages of secretion.

Capability for Heterotrophic or 

Mixotrophic Growth

Heterotrophic or mixotrophic growth capabilities may 

be attractive attributes of algal strains. In some species, 

addition of supplemental carbon results in increased lipid 

accumulation (Xu et al. 2006), even under mixotrophic 

conditions where the substrate is not known to be 

transported into the cell (Ceron Garcia et al., 2006). If 

the carbon source is utilized by the cell, growth in both 

light and dark periods is possible, and high cell densities 

can be achieved. A potential disadvantage of the addition 

of external carbon sources is the possibility of increased 

contamination by undesired microbes living off the carbon 

source. However, this is not generally a problem with wellestablished fully-heterotrophic fermentation technologies 

that are currently deployed worldwide at massive scale to 

manufacture everything from cancer drugs to high- volume/

low- cost commodities such as lysine and ethanol.

Selecting Algal Model Systems 

for Study

Given the diversity of algae, a large number of model 

systems could be studied. However, in a practical sense, 

the number of algal systems that can be studied in depth 

has to be limited because a critical mass of researchers 

is required to make progress on a given species. 

In relation to biofuels, there are two types of algal model 

systems to consider studying: species or strains amenable 

to providing information on basic cellular processes 

regarding the synthesis of fuel precursors, and species 

or strains with characteristics useful for large-scale 

growth. Species with sequenced genomes and transgenic 

capabilities are the most amenable to investigating cellular 

processes since the basic tools are in place. However, it 

was shown in the Aquatic Species Program that not all 

strains that grow well in the laboratory are suitable for 

large-scale culturing (Sheehan, 1998), so it is possible 

that other strains will be chosen for production. Adapting 

the lessons learned from laboratory model strains to 

strains known to be capable of large-scale growth may be 

feasible, but we cannot be certain that laboratory strains 

and production strains will be sufficiently related to allow 

for lessons from the former to be applied to the latter. 

Useful Algal Characteristics 

Culture stability over long periods will be a key to low cost 

production of biofuels. Rapid growth is important both 

for overall productivity and the ability to compete with 

contaminating strains. Other traits like the ability to grow to 

high cell density in continuous culture may allow a strain to 

be maintained while at the same time reducing the amount 

of water to be processed daily. Resistance to predators and 

viruses could also be a useful phenotype. Also the ability 

to flocculate without addition of chemical flocculating 

agents could reduce the costs of harvest as long as it could 

be controlled to avoid settling in the cultivation system.

Targeting Desired Fuel Product or Intermediate

One consideration in choosing model systems is the 

type of fuel, intermediate, or co-product to be produced. 

Possible fuel types of interest could include H2, lipids, 

isoprenoids, carbohydrates, alcohols (either directly or 

through biomass conversion), or methane (via anaerobic 

digestion). Co-products could include pharmaceuticals 

(therapeutic proteins and secondary metabolites), food 

supplements, or materials for nanotechnology (in the 

case of the silica cell wall of diatoms). A reasonable first 

approach to identify model species that are optimal for 

the production of a desired fuel is through a survey of the 

literature, or a screen of environmental isolates for species 
2. Algal Biology 11

strategies to prevent the over-absorption of light energy, 

which can lead to oxidative damage. A large majority of 

absorbed incident light is dissipated as heat and could be 

considered “wasted.” Even with this photoprotection, under 

certain light regimes, photoinhibition or the reduction 

of photosynthesis due to light damage can still occur 

(Long et al., 1994; Foyer et al., 1994; and Niyogi, 1999). 

In an effort to overcome this barrier, it was shown that 

reducing the size of the chlorophyll antenna can increase 

the efficiency of light utilization (Polle et al., 2002). 

There is still much to learn about the dynamics and 

regulation of the photosynthetic apparatus (Eberhard et al., 

2008). More emphasis should be placed on understanding 

these processes if we are to better engineer the capture 

and utilization of light energy for biomass production. 

Carbon Partitioning and Metabolism

Knowing how and when carbon is partitioned in a cell into 

lipids and/or carbohydrates could be very useful for biofuels 

strain development and designing cultivation strategies. 

Understanding carbon partitioning will require extensive 

knowledge of metabolic pathways. Metabolic networks 

have been reconstructed in various microbes from genomic 

and transcriptomic data, pathway analysis, and predictive 

modeling (Vemuri and Aristidou, 2005). Research has also 

been done in plant systems to understand carbon flux in 

biosynthetic and degradative pathways (Lytovchenko et al., 

2007; Schwender et al., 2004; Allen et al., 2009; Sweetlove 

and Fernie, 2005; Libourel and Shachar-Hill, 2008). 

However, carbon partitioning in algae is less understood 

and research on how algal cells control the flux and 

partitioning of photosynthetically fixed carbon into various 

groups of major macromolecules (i.e., carbohydrates, 

proteins, and lipids) is critically needed (Boyle and Morgan, 

2009; Yang et al., 2002). A fundamental understanding of 

‘global’ regulatory networks that control the partitioning 

of carbon between alternative storage products will 

be important for metabolic engineering of algae. 

Further, a link between starch and lipid metabolism has 

been established. Starch is a common carbon and energy 

storage compound in plants and algae, and shares the 

same precursors with the storage lipid TAG (Exhibit 

2.1). It is, therefore, possible that TAG and starch could 

be inter-convertible, a potentially important implication 

for biofuel production. In young Arabidopsis seeds 

and Brassica embryos, starch transiently accumulated 

and starch metabolism was most active before the lipid 

accumulation phase (Kang and Rawsthorne, 1994; Ruuska 

et al., 2002), indicating that starch is an important storage 

compound and its synthesis precedes oil accumulation. 

More recently, studies in higher plants showed that when 

2.2 Algal Physiology 

and Biochemistry

Many algae are photosynthetic organisms capable of 

harvesting solar energy and converting CO2 and water to 

O2 and organic macromolecules such as carbohydrates 

and lipids. Under stress conditions such as high light or 

nutrient starvation, some microalgae accumulate lipids 

such as triacylglycerols (TAG) as their main carbon storage 

compounds. Certain microalgal species also naturally 

accumulate large amounts of TAG (30-60% of dry weight), 

and exhibit photosynthetic efficiency and lipid production 

at least an order of magnitude greater than terrestrial crop 

plants (Hu et al., 2008). Cyanobacteria and macroalgae, as 

a general rule, accumulate mostly carbohydrates, with lipid 

accumulation in macroalgae typically being less than 5% of 

total dry weight (Mcdermid and Stuercke, 2003), although 

concentrations approaching 20% lipid have been reported 

in some species (Chu et al., 2003; Mcdermid and Stuercke, 

2003). Lipids and carbohydrates, along with biologically 

produced hydrogen and alcohols, are all potential biofuels

 or biofuel precursors. It is, therefore, important to 

understand the metabolic pathways and processes that 

generate them in order to advance biofuels production.

Photosynthesis and Light Utilization

When algae are cultivated photosynthetically, the 

efficiency of photosynthesis is a crucial determinate 

in their productivity, affecting growth rate, biomass 

production, and potentially, the percent of biomass 

that is the desired fuel precursor. Though theoretical 

biomass productivity values in the range of 100-200 g/

m2/day have been presented (Chisti, 2007), there is no 

current consensus on the true maximum productivity of 

algae. Theoretical productivity is an important concept, 

however, because it can be used to set achievable goals for 

both cultivation process design and strain improvement 

projects. It may be useful to carry out photosynthetic 

efficiency studies in algae similar to those that have 

been carried out for plants (Zhu et al., 2007 and 2008)

There are many good reviews available that cover basic 

algal photosynthetic processes (Nelson et al., 1994; 

Eberhard et al., 2008; Nelson and Yocum, 2006; Krause and 

Weis, 1991). Regardless of the cultivation practices used 

to maximize light exposure (see Chapter 3), there remains 

limitations of algal photosystems regarding light utilization. 

The majority of light that falls on a photosynthetic algal 

culture at greater than laboratory scale is not utilized. In 

high cell density cultures, cells nearer to the light source 

tend to absorb all the incoming light, preventing it from 

reaching more distant cells (Christi, 2007). Even when 

exposed to high light, algal photosystems have built-in 
12 2. Algal Biology 

or absence of other structural polysaccharides varies 

greatly. There are also many algae that completely lack 

cellulose and have other polymers that provide structure 

to the cell (Raven et al., 1992), while some algae lack 

cell walls entirely. Diatoms are also unique among algae 

for the presence of silica in their cell walls. Some red 

algae also have a thick extracellular matrix composed 

of important products such as agar or carrageenan. 

Most cyanobacteria have a peptidoglycan layer and cell 

envelope similar to those of gram-negative bacteria, and 

are encased in a polysaccharide sheath (Hoiczyk and 

Hansel, 2000). An important lesson is the recognition of the 

diversity of algal polysaccharides and cell walls, and the 

technical challenges these structures may present in strain 

manipulation, feedstock potential, and extraction processes.

Lipid Synthesis and Regulation

Primary Pathway for TAG Synthesis

Some algae, naturally or under stress conditions, 

accumulate significant quantities of neutral storage lipids 

such as triacyglycerols (TAG), which are important 

potential fuel precursors. The major pathway for the 

formation of TAG in plants first involves 

de novo fatty acid synthesis in the stroma of plastids. 

The synthesis of cellular and organelle membranes, as 

well as of neutral storage lipids such as TAG, use 16 or 

18 carbon fatty acids as precursors. TAG is formed by 

incorporation of the fatty acid into a glycerol backbone 

via three sequential acyl transfers (from acyl CoA) 

in the endoplasmic reticulum (ER) (Exhibit 2.1). 

TAG biosynthesis in algae has been proposed to occur 

via the above Kennedy pathway described in plants. 

Fatty acids produced in the chloroplast are sequentially 

transferred from CoA to positions 1 and 2 of glycerol3-phosphate, resulting in the formation of the central 

metabolite phosphatidic acid (PA) (Ohlrogge and Browse, 

1995). Dephosphorylation of PA catalyzed by a specific 

phosphatase releases diacylglycerol (DAG). Since 

diglycerides are usually present in high amounts in rapidly 

growing cultures, it may be of interest to research these 

TAG intermediates. In the final step of TAG synthesis, 

a third fatty acid is transferred to the vacant position 3 

of DAG by diacylglycerol acyltransferase, an enzyme 

that is unique to TAG biosynthesis (Lung and Weselake, 

2006; Athenstaedt and Daum, 2006). The acyltransferases 

involved in TAG synthesis may exhibit preferences 

for specific acyl CoA molecules, and thus may play an 

important role in determining the final acyl composition 

of TAG (Hu et al., 2008). Alternative pathways to convert 

membrane lipids and/or carbohydrates to TAG have 

recently been demonstrated in bacteria, plants and yeast 

in an acyl CoA-independent way (Arabolaza et al., 2008; 

starch synthesis was impaired or inhibited, plant embryos 

or seeds accumulated 40% less oil (Periappuram et al., 

2000; Vigeolas et al., 2004). While these results provide 

an indication that starch synthesis is linked to lipid 

synthesis, the nature of the interaction is unknown.

In microalgae, such an interaction has been also 

indicated by studies on the diatom Cyclotella cryptica 

(Roessler, 1988). It could, therefore, be fruitful to 

further research de novo starch synthesis, degradation, 

and interaction with lipid metabolism in algae. 

Algal Carbohydrates

Algae are incredibly diverse in the kind of simple 

and complex carbohydrates that they use for 

carbon storage and cell structure. If carbohydrates 

are to be used as fuel precursors, for example for 

fermentation to produce alcohols, it is important to 

determine the predominate types that are present.

Many green microalgae are plant-like, featuring rigid 

cellulose-based cell walls and accumulating starch as 

their main carbohydrate storage compound. Several 

algae commonly use starch for energy storage, including 

some red algae and dinoflagellates. Other algae, for 

example many brown algae and diatoms, accumulate 

carbohydrates such as laminaran, mannitol, or fucoidin as 

food reserves. Cyanobacteria often store large quantities 

of glycogen (Chao and Bowen, 1971; Yoo et al., 2002). 

These major storage polysaccharides represent potential 

biochemical feedstocks for conversion to liquid fuels. 

Microorganisms capable of fermenting laminarin and 

mannitol from Laminaria hyperborea to ethanol have 

been identified and partially characterized (Horn et al., 

2000a and 2000b). Other abundant polysaccharides, 

for example alginate found in many brown algae, are 

considered less suitable for ethanol fermentation because 

the redox balance favors formation of pyruvate as the 

end product (Bird and Benson, 1987). However, these 

polysaccharides may still prove useful as intermediates 

to other types of conversion processes and final fuels. 

Another important consideration in algal strains is the 

composition and structure of the polysaccharide cell 

wall. These structures can be an important source of 

carbohydrates, but like those from plants, must typically 

be broken down into simpler sugars before conversion 

into biofuels. Cell walls can also be a technical barrier, 

for example, when trying to access DNA for genetic 

manipulations, or efficiently extracting biofuel precursors 

from cells in mass culture. As mentioned above, many 

algal cell walls from different groupings are cellulosebased, though their physical structure and the presence 
2. Algal Biology 13

Dahlqvist et al., 2000; Stahl et al., 2004). Such pathways 

have not yet been studied in algae. Moreover, PA and 

DAG can also be used directly as substrates for synthesis 

of polar lipids, such as phosphatidylcholine (PC) and 

galactolipids. These pathways are worth investigating 

when developing strains for improved lipid production.

The regulation of the synthesis of fatty acids and 

TAG in algae is relatively poorly understood. This 

lack of understanding may contribute to why the lipid 

yields obtained from algal mass culture efforts fall 

short of the high values (50 to 60%) observed in the 

laboratory (Hu et al., 2008; Sheehan et al., 1998). 

Understanding lipid regulation can help to maximize 

scenarios for lipid production and strain improvement.

Because fatty acids are common precursors for the 

synthesis of both membrane lipids and TAG, how the 

algal cell coordinates the distribution of the precursors to 

distinct destinations or how the inter-conversion between 

the two types of lipids occurs needs to be elucidated. If the 

ability to control the fate of fatty acids varies among algal 

taxonomic groups or even between isolates or strains, the 

basal lipid and TAG content may represent an intrinsic 

property of individual species or strains. If this proves to 

be true, it could be a challenge to extrapolate information 

learned about lipid biosynthesis and regulation in laboratory 

strains to production strains. Similarly, it will be difficult 

to use information regarding lipid biosynthesis in plants 

to develop hypotheses for strain improvement in algae. 

As an example, the annotation of genes involved in lipid 

metabolism in the green alga Chlamydomonas reinhardtii 

has revealed that algal lipid metabolism may be different 

from that in plants, as indicated by the presence and/or 

absence of certain pathways and by the size of the gene 

families that relate to various activities (Riekhof et al., 

2005). Thus, de novo fatty acid and lipid synthesis should 

be studied in order to identify key genes, enzymes and new 

pathways, if any, involved in lipid metabolism in algae. 

Alternative Pathways to Storage Lipids

Algae may possess multiple pathways for TAG synthesis, 

and the relative contribution of these individual pathways 

to overall TAG formation may depend on environmental 

or culture conditions. Analyzing different algae could help 

to elucidate the possible pathways of TAG synthesis: the 

de-novo Kennedy Pathway, the potential pathway for lipid 

formation from starch reserves mentioned earlier, and other 

Starch

Amylases

Acetyl-CoA

ACCase

KAS I

KAS II

SAD

C16 - C18 CoA

Phosphatidic acid

Triacylglycerol

PDAT?

Phospholipids

GDAT?

Galactolipase?

PDH CO2

CO2

Mitochondria

3-PGA

Diacylglycerol (DAG)

AcetylER

AGPPase

Oxaloacetate

TCA cycle

Pyruvate

3-PGA

Acetyl-CoA

Central

Metabolic

DAGT

Pyruvate

Starch Glc6P

Glc6P

Lipid Body

Chloroplast

Glycolipids

Figure 2.1 Major pathways for fatty acid 

and TAG synthesis in plants and algae

3-PGA: 3-phosphoglycerate; Accase: acetyl 

CoA carboxylase; ACP: acyl carrier protein; 

AGPPase: ADP glucose pyrophosphorylase; 

ER: Endoplasmic reticulum; GDAT: putative 

glycolipids: DAG acyltransferase; Glc6P: 

glucose-6-phosphate; KAS: 3-ketoacyl-ACP; 

PDAT: Phospholipids: DAG acyltransferase; 

PDH: pyruvate dehydrogenase (putative 

pathways were proposed in dashed lines).
14 2. Algal Biology 

The TAG synthesis pathway is also often coordinated 

with secondary carotenoid synthesis in algae (Rabbani 

et al., 1998; Zhekisheva et al., 2002). The molecules 

(e.g., β-carotene, lutein, or astaxanthin) produced in 

the carotenoid pathway are sequestered into cytosolic 

lipid bodies. Carotenoid-rich lipid bodies serve as a 

‘sunscreen’ to prevent or reduce excess light from striking 

the chloroplast under stress. TAG synthesis may also 

utilize phosphatidylcholine, phatidylethanolamine or 

toxic fatty acids excluded from the membrane system 

as acyl donors, thereby serving as a mechanism to 

“detoxify” these compounds and deposit them in the 

form of TAG. Because of the potential importance of 

stress conditions on lipid production in algae, the exact 

relationship between oxidative stress, cell division, 

and storage lipid formation warrants further study. 

Lipid Body Formation and Relationship 

to Other Organelles

Despite the economic importance of algae as a source of 

a wide range of lipophilic products, including vitamins, 

hydrocarbons and very long-chain ω-3 and ω -6 fatty 

acids, there have been relatively few studies on lipid 

bodies in algae compared with plants and fungi. The study 

of lipid-body biogenesis in plants has focused largely on 

the role of oleosins (Murphy, 1993; Huang, 1992). This 

is understandable in view of their exclusive localization 

on lipid-body surfaces, their apparently widespread 

distribution and their great abundance in many lipidstoring seeds. Nevertheless, there are now doubts about 

the role of oleosins in the biogenesis of plant lipid bodies. 

It has been suggested that oleosins may be primarily 

associated with the stabilization of storage lipid bodies 

during the severe hydrodynamic stresses of dehydration 

and rehydration that occurs in many seeds (Murphy, 2001).

Lipid bodies may dock with different regions of the ER 

and plasma membrane, or with other organelles such as 

mitochondria and glyoxysomes/peroxisomes, in order 

to load or discharge their lipid cargo (Zehmer et al., 

2009). In oil-producing microorganisms, as rapid lipid 

body accumulation occurs, a close relationship is often 

found between neutral lipids like TAG and the membrane 

phospho- and glyco- lipids (Alvarez and Steinbuchel, 

2002). This relationship may be both metabolic, with acyl 

and glycerol moieties exchanged between the different 

lipid classes, and spatial, with growing evidence of 

direct physical continuities between lipid bodies and 

bilayer membranes. In order to better understand lipid 

metabolism in algae, the structure and function of lipid 

bodies, and their interactions with other organelles 

related to storage lipid formation requires further study.

potential pathways to convert membrane phospholipids and 

glycolipids into TAG. The thylakoids of chloroplasts are 

the main intracellular membranes of eukaryotic algae, and 

their lipid composition dominates extracts obtained from 

cells under favorable growth conditions. Algal chloroplasts 

contain monogalactosyldiacylglycerol as their main lipid 

(~50%), with smaller amounts of digalactosyldiacylglycerol 

( ~20%), sulfoquinovosyldiacylglycerol (~15%) and 

phosphatidlyglycerol ( ~15%) (Harwood, 1998). Under 

stress conditions as degradation of chloroplasts occurs, 

the fate of these abundant lipids remains unclear. It has 

been proposed that these alternative pathways that convert 

starch, excess membrane lipids, and other components into 

TAG play an important role for cell survival under stress. 

Organelle Interactions

Chloroplast membranes control the exchange of metabolites 

between the plastid and the cytoplasm. As mentioned 

earlier, the chloroplast stroma is the primary location 

for fatty acid biosynthesis in plants. Fatty acids can then 

be either assembled into glycerolipids at chloroplast 

membranes or they can be exported to the ER and 

assembled into lipids for cellular membranes. Some 

glycerolipids assembled at the ER are then returned to 

the plastid where they are assimilated. Lipid trafficking 

is, therefore, an important aspect of membrane formation 

and lipid fate (Benning, 2008). Current work in plants 

is focused on deciphering lipid transport across plastid 

envelopes. Such work is also important in algae to 

better understand the interaction among organelles as 

it relates to lipid formation and lipid trafficking.

Oxidative Stress and Storage Lipids

Under environmental stress conditions (such as nutrient 

starvation), some algal cells stop division and accumulate 

TAG as the main carbon storage compound. Synthesis of 

TAG and deposition of TAG into cytosolic lipid bodies 

may be, with exceptions, the default pathway in some 

algae under stress conditions (Hu et al., 2008). In addition 

to the obvious physiological role of TAG as a carbon and 

energy storage compound, the TAG synthesis pathway 

may also play a more active and diverse role in the stress 

response. The de novo TAG synthesis pathway can serve 

as an electron sink under photo-oxidative stress (discussed 

earlier). Under high light stress, excess electrons that 

accumulate in the photosynthetic electron transport chain 

induce over-production of reactive oxygen species, which 

may in turn cause inhibition of photosynthesis and damage 

to membrane lipids, proteins, and other macromolecules. 

However, the formation of fatty acids could help consume 

excess electrons, and thus relax the over-reduced electron 

transport chain under high light or other stress conditions. 
2. Algal Biology 15

2007). There are two major types of hydrogenases, those 

containing iron (which are generally H2-evolving), or 

both nickel and iron (which are generally H2-uptake 

enzymes). One of the most important characteristics 

of hydrogenases is that they are O2 sensitive. 

Four biological challenges limiting biohydrogen production 

in algae have been identified: (a) the O2 sensitivity of 

hydrogenases, (b) competition for photosynthetic reductant 

at the level of ferredoxin, (c) regulatory issues associated 

with the over production of ATP, and (d) inefficiencies in 

the utilization of solar light energy (Seibert et al., 2008). 

These challenges could be addressed by (a) engineering 

hydrogenases with improved tolerance to O2 (Cohen 

et al., 2005), (b) identifying metabolic pathways that 

compete with hydrogenases for photosynthetic reductant, 

and engineering their down-regulation during H2

production (Mathews and Wang, 2009), (c) engineering 

the photosynthetic membrane for decreased efficiency of 

photosynthetic-electron-transport-coupled ATP production 

(ATP is not required for H2 production), and (d) engineering 

the photosynthetic antenna pigment content for increased 

efficiency of solar light utilization (Polle et al., 2003). 

Besides biochemical analysis to study algal lipids 

and carbohydrates, studies involving Expressed 

Sequence Tag (EST) analysis, cDNA microarray 

analysis, and proteomic studies, for example, would 

also help provide information about photosynthetic 

carbon partitioning and lipid/carbohydrate synthesis 

in algae. Based on such information, metabolic 

engineering through genetic manipulation represents 

yet another strategy for the production of algal oils. 

Biohydrogen 

Some microalgae and cyanobacteria can produce H2, a 

potential fuel product, in the following reactions: 2H2O 

+ light energy → O2 + 4H+ + 4e- → O2 + 2H2. Three 

pathways have been described in green algae: two lightdriven H2

-photoproduction pathways, and a third, lightindependent, fermentative H2

 pathway coupled to starch 

degradation (see Exhibit 2.2) (Melis et al., 2000; Gfeller 

and Gibbs, 1984). As a substrate, the light-driven pathways 

can either employ water (through photosystems II and 

I) or NADH from the glycolytic breakdown of stored 

carbohydrate (through photosystem I). In all pathways, 

ferredoxin (FD) is the primary electron donor to the 

hydrogenase enzyme. Hydrogenases are the enzymes 

responsible for releasing molecular H2 (Ghirardi et al., 

Glycolysis

Photosynthesis

fixation

CO2

FD(ox)

Acetyl-CoA + CO pyruvate 2

FD (red)

FD

ADP ATP

NAD++H+

NAD++H+

2H2O

O2

+2H+

NADH

Photosystem I

Photosystem II

Chl

P680

Chl

P700

P700*

P680*

NPQR

starch

H2ase

PFOR

H2

2H+

A0

A1

Fx

FA/FB

Pheo

QA

QB

PQ

PC

Cyt b

 Cyt f

-1.2

-0.8

-0.4

0.0

0.4

0.8

1.2

Energy (Volts)

Figure 2.2 Three different pathways for H2 production

Two are driven by light and the third occurs in the dark. Either 

water or starch can be the electron donor. Carbon is fixed under 

normal photosynthesis with water as the donor, but the electron 

acceptor is switched at the level of ferredoxin (FD) from CO2 to 

protons under conditions that lead to H2 production. (Drawing 

courtesy of Prof. M. Posewitz, Colorado School of Mines )
16 2. Algal Biology 

Recently there has been a focus on using cyanobacteria to 

produce H2 (Tamagnini et al., 2002; Prince and Kheshgi, 

2005). While many of the challenges described above 

exist in these organisms, they are typically more easily 

engineered than eukaryotic algae and have more O2-

tolerant hydrogenases (Ghirardi et al., 2009). A possibility 

to improve the efficiency of biological H2 production 

includes developing biohybrid (those with biological 

and synthetic components) and synthetic photosynthetic 

systems that mimic the fuel-producing processes of 

photosynthetic organisms. In all cases, more knowledge 

of photosynthesis, hydrogen evolution pathways, and 

hydrogenase structure and function is required.

To circumvent the inhibition of hydrogenase by O2, 

another option for H2 production is to take advantage 

of the fermentation pathways that exist in some algae 

for H2 production at night, using the carbon reserves 

produced during the day. In cyanobacteria, fermentation is 

constitutive, accounting for their ability to adapt quickly 

to changing environmental conditions (Stal and Krumbein, 

1987). All cyanobacteria examined thus far employ the 

Embden-Meyerhof-Parnas (EMP) pathway for degradation 

of glucose to pyruvate. From here, several cyanobacteria 

were found to use pyruvate-ferredoxin oxidoreductase, 

which reduces ferredoxin for subsequent H2 production 

via nitrogenase or hydrogenase (Stal and Moezelaar, 

1997). This temporal separation of H2 production from 

photosynthesis has been demonstrated in the unicellular 

cyanobacteria Cyanothece sp. ATCC 51142 (Toepel et 

al., 2008) and Oscillatoria (Stal and Krumbein, 1987), 

using nitrogenase as the catalyst. Using hydrogenase as 

the catalyst, the unicellular non-N2-fixing cyanobacterium 

Gloeocapsa alpicola can evolve H2 from the fermentation 

of stored glycogen (Serebryakova et al., 1998). Similarly 

under non-N2 fixing condition, the hydrogenase from 

Cyanothece PCC 7822 produces H2 in the dark and 

also excretes typical fermentation byproducts including 

acetate, formate, and CO2 (van der Oost et al., 1989).

It is well established that dark fermentation suffers from 

low H2 molar yield (less than 4 moles of H2 per mol 

hexose) (Turner et al. 2008). This is due to the production 

of organic waste by-products described above along 

with ethanol. In order to fully realize the potential of H2

production via indirect biophotolysis, several challenges 

must be addressed: (a) improve photosynthetic efficiency 

to increase the yield of carbohydrate accumulation; 

(b) remove or down-regulate competing fermentative 

pathways thus directing more of the cellular flux toward H2

production; and (c) learn to express multiple hydrogenases 

so that electrons from both ferredoxin (Fd) and NAD(P)

H can serve as electron donors to support H2 production. 

2.3 Algal Biotechnology

The biotechnology industry grew from more than 100 

years of basic biology and genetics R&D. Collectively, 

biological process engineering breakthroughs directly 

enabled new multi-billion dollar commercial enterprises 

for agriculture, human health, and the production of 

chemicals. Thus, the importance of being able to harness 

biotechnology approaches to generate algae with desirable 

properties for the production of biofuels and bioproducts 

cannot be overlooked. However, methods to manipulate 

algae genetically remain far behind those developed 

for commonly used bacteria, fungi and higher plants. 

Efforts should be undertaken to understand the fundamental 

genetic and cellular processes involved in the synthesis 

and regulation of potential fuel precursors from diverse 

species of algae. While a better understanding of the basic 

biology of algal growth and metabolite accumulation 

using modern analytical approaches will provide a wealth 

of hypotheses for strain improvements, the limited algal 

genetic toolbox that can be used to modify processrelevant strains remains a significant technical hurdle. 

Thus, this subsection seeks to 1) address the genetic 

tools available to modify algal strains, 2) describes 

enabling technologies and analyses that can be applied 

for biofuels and bioproducts, and 3) highlights a few 

examples of how algal biotechnology has been applied 

to date. Methods to cultivate and process algae in 

commercial settings are no less important to biotechnology, 

and these are the subjects of Chapters 3 and 4.

The Genetic Toolbox

Because biological productivity is a key driver for 

economic viability, the ability to improve on native strains 

is a potentially important element in the research effort 

toward algal biofuels. Genetic approaches are commonly 

used to introduce genes, to delete or disrupt genes, and to 

modify genes or gene expression in a particular organism. 

Some of these methods can also be used to study the 

localization of gene products (mRNAs and proteins) 

within cells. For algae that undergo sexual reproduction, 

the toolbox allows traits to be recombined into a single 

individual by mating parental strains. For all of these 

approaches, the stability of the desirable trait through many 

generations and the possibility of unintended horizontal 

gene transfer to other organisms are important research 

questions to consider in the context of mass production. 

Mutagenesis

The generation and characterization of mutants is a 

powerful approach to understand gene function and 

potentially generate strains with desirable characteristics. 
2. Algal Biology 17

As long as an appropriate screening process is 

developed, spontaneous mutants arising from errors 

in DNA replication can be identified. However, this 

approach is limited by the low frequency of naturally 

occurring mutations, which necessitates a large amount 

of screening. Mutants are more readily generated by 

standard chemical or UV-based mutagenesis approaches. 

Drawbacks of this approach include the introduction 

of multiple mutations in a genome and the difficulty 

in mapping the locus responsible for the phenotype.

Targeted or tagged mutagenesis offers the advantage of 

simplified identification of the mutated gene. Targeted 

approaches rely on homologous recombination (if the 

native gene is to be entirely replaced), or introduction of 

a modified copy of the gene that inserts elsewhere into 

the genome. Certain strategies can also enable changes 

in gene expression. Tagging can be accomplished 

by introducing a selectable marker randomly into 

the genome (Adams et al., 2005), or through the 

use of transposons (Miller and Kirk, 1999).

Any mutagenesis approach requires an appropriate 

screening technique to enrich for and isolate mutants. This 

can include either a requirement for mutants to grow under 

certain conditions (e.g., in the presence of an antibiotic), or 

to exhibit a characteristic phenotypic change that is easily 

assayed. For the latter, changes in fluorescence properties, 

e.g., reduced chlorophyll fluorescence (Polle et al., 2002), 

or increased neutral lipid accumulation via Nile Red 

staining (Cooksey et al., 1987) can be screening criteria.

Given a well-developed screening approach, iterative 

selection could be used to generate useful algal strains 

without the need to generate genetically engineered 

(GE) algae—something that could be desirable for 

large-scale algal production. 

Selectable Markers

A powerful way to manipulate genomes is the ability to 

introduce DNA into the cell, and to select for cells in which 

the DNA is present. Typically, this is accomplished by 

introducing an antibiotic resistance gene as a selectable 

marker (Hasnain et al., 1985; Dunahay et al., 1995), 

along with the DNA of interest on an extra-chromosomal 

element called a plasmid. Marker systems that take 

advantage of the ability to genetically complement 

auxotrophic and metabolism mutants have also been 

achieved (Kindle et al., 1989; Debuchy et al., 1989). An 

important consideration is that the use of antibiotics in 

large-scale production has two major drawbacks. The 

first concern is the cost of the antibiotic. The second 

concern is the environmental implications of widespread 

antibiotic use, which could exacerbate current problems 

with increased antibiotic-resistant microbes. Antibiotic 

resistance is a powerful tool for research; however, other 

methods may need to be considered for production scale. 

For research purposes, the decision as to which antibiotic 

selection marker to use includes whether the antibiotic 

compound is sensitive to light and whether its potency is 

modulated by the salinity of the growth medium. Several 

antibiotic markers have been developed for microalgae, 

including resistance to neomycin, kanamycin (Hasnain 

et al., 1985; Dunahay et al., 1995), zeocin (Apt et al., 

1996; Hallmann and Rappel, 1999), and nourseothricin 

(Poulsen et al., 2006). The mechanism of antibiotic 

resistance can also be an important factor. For example, 

zeocin resistance requires stoichiometric binding of the 

antibiotic by the resistance protein, whereas nourseothricin 

is inactivated enzymatically. A direct comparison of the 

two has shown that the nourseothricin system generates 

larger numbers of transformants (Poulsen et al., 2006), 

presumably because requirements for expression levels 

of the gene are lower and less taxing to the cells.

Sophisticated metabolic engineering could require the 

introduction of multiple selectable or complementary 

markers. Most of the current selectable markers are derived 

from bacterial genes, but markers based on resistance 

generated by conserved ribosomal protein mutations have 

also been successful (Del Pozo et al., 1993; Nelson et 

al., 1994). Caveats are that the mutated gene may need 

to be expressed at a higher level than the native gene 

(Nelson et al., 1994), or that the native gene may need to 

be replaced in order to generate the phenotypic effect. For 

complementation approaches, appropriate mutations must 

be generated in the species of interest, ideally in wellcharacterized genes that can be easily complemented.

Once an appropriate antibiotic resistance or 

complementing gene is identified, constructs must be 

made to place the gene under control of an expression 

element that functions in the species of interest. This 

typically involves using control elements from a 

highly expressed gene in that species. However, there 

are examples of control elements that work across 

evolutionarily diverse species (Dunahay et al., 1995). 

Transformation Methods

Gene transfer systems have been established in many 

algal strains, including cyanobacteria (Synechococcus, 

Synechocystis, Anabaena, Nostoc, Arthrospira), 

green algae (Chlamydomonas, Dunaliella, Chlorella, 

Volvox), diatoms (Cyclotella, Navicula, Phaeodactylum, 

Thalassiosira), dinoflagellates (Amphidinium, 
18 2. Algal Biology 

Gene Expression Control Elements

Gene expression control elements (also known as 

transcriptional regulators) can modulate the levels 

of mRNA, which can then subsequently affect algae 

traits. Frequently, transgenes are overexpressed by 

using strong control elements, but considering the 

need for balance in cellular metabolism, intermediate, 

slightly elevated, or reduced levels of expression may 

be desirable. Control element strength can be evaluated 

by monitoring mRNA levels by quantitative PCR or 

high throughput transcriptomics (i.e., microarrays). 

In addition, inducible and repressible promoters that 

can be actuated by simple manipulations are desirable, 

allowing for precise control over the timing of gene 

expression. The nitrate reductase promoter has proven 

useful in this regard in microalgae, because it is induced 

with nitrate in the growth medium, and repressed with 

ammonium (Poulsen and Kroger, 2005). Identification of 

other inducible or repressible control elements would be 

useful for both research and commercial applications.

RNA Interference (RNAi)

RNAi can be a useful tool to down-regulate gene 

expression, especially in the study of polyploid organisms 

or when dealing with redundant genes where traditional 

genetic manipulations are difficult. RNAi operates 

through double-stranded RNAs that are cut down to 

small sizes and used to target suppression of specific 

genes by base pairing. RNAi can inhibit transcription 

(Storz et al., 2005) and control translation by either 

cleaving specific mRNAs or sequestering them away 

from the ribosome (Valencia-Sanchez et al., 2006). 

Two general types of RNAi vectors can be constructed 

– one containing an inverted repeat sequence from the 

gene to be silenced, and another in which bidirectional 

transcription generates the double stranded RNA. 

RNAi approaches have been investigated primarily 

in the model green alga, Chlamydomonas reinhardtii, 

although there is a recent report of the method being 

used in a red alga (Ohnuma et al., 2009). In a practical 

sense, selecting for functional RNAi can be problematic 

(Fuhrmann et al., 2001). Even on vectors containing both 

a selectable marker and an RNAi construct, only a small 

percentage of selected transformants will have functional 

RNAi. One solution to this problem was developed in 

C. reinhardtii. The selection process was based on a 

high-throughput phenotypic screen for functional RNAi 

by co-targeting an amino acid synthesis pathway along 

with the desired gene of interest (Rohr et al., 2004). 

Symbiodinium), red algae (Cyanidioschyzon, 

Porphyridium, Gracilaria, Porphyra), brown algae 

(Laminaria, Undaria) and euglenoids (Euglena). 

Hallmann (2007) provides a comprehensive review of 

algal transgenics and implications for biotechnology.

A common method for introducing DNA into algal cells 

is the biolistic (“gene gun”) approach (Armaleo et al. 

1990), which is useful for both nuclear and chloroplast 

transformation (Boynton et al., 1988; Dunahay, 1993). 

Other successful methods include electroporation 

(Shimogawara et al., 1998), vortexing with glass beads 

(Kindle et al., 1991) or silicon carbide whiskers (Dunahay, 

1993). For most of these approaches, a fundamental 

challenge to introducing DNA into a cell is the nature of 

the cell wall. If methods exist to remove or perforate the 

cell wall, then chemically based methods of transformation 

could be applied. Many transformation methods also exist 

for cyanobacteria, including conjugation, electroporation, 

and biolistic approaches (Matsunaga and Takeyama, 1995).

Sexual Crossing

Breeding of desired characteristics from a number of 

phenotypic variants can allow for strain development 

without creating GE algae. Algal strains often contain 

multiple copies of their genome, and so recessive genotypes 

may not manifest unless that genotype is allowed to 

“breed true” though a series of sexual crosses. Many 

macroalgae species are capable of sexual reproduction, 

and traditional mutagenesis and breeding has been used 

to improve commercial varieties of seaweed since the 

1950s (Bird and Benson, 1987). With the exception of 

Chlamydomonas, classical genetic approaches using 

sexual crossing are not well developed in microalgae, 

but this methodology could prove to be extremely 

important. Some diatoms can be propagated vegetatively 

only for a limited number of generations and must be 

crossed periodically to maintain culture viability. 

Homologous Recombination

Homologous recombination-based gene integration 

approaches are common in many strains of cyanobacteria, 

but less so in microalgae. DNA introduced into the nucleus 

of microalgal cells generally integrates randomly into 

the genome (Dunahay et al., 1995). Gene replacement 

via homologous recombination is more desirable than 

random integration because it can overcome phenotypic 

dominance issues when more than one copy of the 

gene is present, and can be used to knockout genes. 

Successful recombination approaches have included the 

addition of long flanking regions to the gene of interest 

(Deng and Capecchi, 1992), use of single stranded DNA 

(Zorin et al., 2005), or co-introduction of recombinase 

genes with the transforming DNA (Reiss et al., 1996). 
2. Algal Biology 19

reduced and more coverage is obtained in a shorter 

period of time, obtaining a genome sequence should 

be strongly considered for any strains being developed 

for biofuels research or production. It must be noted 

though, that the genomic data are only as useful as 

the annotation (the assignment of gene functions or 

families), so it will be important to provide sufficient 

resources to allow for detailed analysis of the data. 

Genome size in algae can vary substantially, even in 

closely related species (Connolly et al., 2008). One 

reason for this variation is likely to be the accumulation 

of repeated sequences in the larger genomes (Hawkins 

et al., 2006). Even though new sequencing technologies 

readily enable accumulation of data for large genomes, 

assembly of such data (especially with short read lengths) 

can be more challenging in repeat-laden genomes.

Eukaryotic algae constitute members from at least eight 

major phyla, all featuring a complex series of primary 

and secondary endosymbioses (Falkowski et al., 2004). 

It is likely that the different symbioses have affected the 

distribution of DNA between the plastid and nucleus 

(Wilhelm et al., 2006), which could impact the regulation 

and processes of fuel precursor production. A genomic 

survey of representatives from all major algal classes is 

desirable, with a special focus on classes or individual 

species within classes that make abundant fuel precursors.

Except for cyanobacteria, for which over 20 completed 

genome sequences are available, the nuclear genomes 

of only a handful of microalgal species have been fully 

or partially sequenced to date.1 These species include 

unicellular green algae (C. reinhardtii, Volvox carteri), a 

red alga (Cyanidioschizon merolae), several picoeukaryotes 

(Osteococcus lucimarinus, Osteococcus tauris, Micromonas 

pussilla, Bathycoccus sp.), a pelagophyte (Aureococcus 

annophageferrens), a coccolithophore (Emiliania huxleyi), 

and several diatoms (Phaeodactylum tricornutum, 

Thalassiosira pseudonana, Fragilariopsis cylindrus). 

Genome sequencing projects are also underway for the 

macroalga Porphyra purpurea at the Joint Genome Institute 

(U.S. Department of Energy) and for Ectocarpus siliculosus 

at Genoscope - Centre National de Séquençage (France). 

Bioinformatics analysis of sequenced genomes, especially 

at the basic level of gene annotation, will be essential 

to make sequence data usable. If not properly done, 

bioinformatics can represent the largest stumbling block 

to achieving that goal. Quality standards and appropriate 

training should be established at the onset of activities 

to ensure consistent and useful annotation. This could 

Directed Evolution of Enzymes/Proteins

Regarding core cellular metabolic processes, a 

substantial amount of regulation occurs at the protein 

level, including allosteric activation and metabolic 

feedback. Indeed, this level of regulation integrates 

the proteome with the metabolome. Although time 

consuming, approaches to modify proteins by genetic 

engineering so that they function more efficiently or 

have other favorable characteristics could be valuable 

for the development of algal biofuels technology.

Protein Tagging Technologies

Tagging proteins with fluorescent markers is useful in 

determining their intracellular location and can provide 

at least semi-quantitative evaluation of their abundance 

in a simple measurement. This information could be 

useful in monitoring intracellular metabolic processes 

associated with biofuel precursor production. Green 

fluorescent protein and its derivatives are the most 

widely used and versatile protein tags, but others have 

demonstrated utility and some possible advantages 

(Regoes and Hehl, 2005; Gaietta et al., 2002).

Enabling Technologies: “Omics” 

Approaches and Bioinformatics

High throughput approaches, such as genomics, 

transcriptomics, and proteomics, have enabled in-depth 

analyses to be performed in a whole cell context. Together, 

these methods have revolutionized the study of organisms 

both in culture and in natural habitats. These biological 

advancements have been complemented by developments in 

computer sciences, creating the new field of bioinformatics 

where powerful new databases and search algorithms are 

helping biologists share and build upon experimental results 

in ways and timescales that were never before possible. 

Algal species are being analyzed using these analytical 

approaches to better understand the underlying 

cellular processes and regulation involved in 

defining the attributes of the strain. Undoubtedly, the 

characterization of these cellular processes will prove 

useful for applications, forming the foundation for 

applied research and technology development.

Sequencing and Annotating Algal Genomes

Sequenced genomes are an essential basis of information 

for the interpretation of transcriptomic and proteomic 

data. With the development of more powerful sequencing 

methods, in which costs have been substantially 

 1 For a listing, visit http://genome.jgi-psf.org/euk_cur1.html
20 2. Algal Biology 

Metabolomics and Lipidomics

The metabolome is the collection of small molecular 

weight compounds in a cell that are involved in growth, 

maintenance, and function. Because the chemical 

nature of metabolites varies more than for mRNA 

and proteins, different metabolomic analysis tools 

are applied, including liquid chromatography mass 

spectrometry, gas chromatography mass spectrometry, 

and nuclear magnetic resonance (Dunn et al., 2005). 

There is a distinction between metabolomics, which 

involves the identification and analysis of metabolites, 

and metabonomics, which is the quantitative 

measurement of the dynamic multi-parametric metabolic 

response of living systems to pathophysiological 

stimuli or genetic modification (Nicholson et al., 

1999). Both metabolomics and metabonomics may 

be important in terms of algal biofuels research. 

Lipids are a subset of the molecular repertoire of the 

algae cell. Lipid analysis is done using mass spectrometry 

approaches (Han and Gross, 2005; Dettmer et al., 2007). 

Quantitative comparison of lipid type and abundance are 

critical components of lipid-based biofuels approaches as 

lipid characteristics can determine the suitability of the 

final fuel produced. Monitoring lipid characteristics under a 

variety of different cultivation regimes can also help inform 

process engineering and improve yields (Yu et al., 2009).

Applications of Biotechnology 

to Algal Bioenergy

Cyanobacteria

Genetic manipulation of cyanobacteria is generally 

more advanced than that of eukaryotic algae because 

many of the tools developed for bacterial genetics are 

applicable in cyanobacteria. For example, spontaneous 

transformation, double-homologous recombination, 

and protein tagging are routine in some cyanobacterial 

systems, and at least half a dozen selectable markers 

are available for Synechocystis (Vermaas, 1998). 

Cyanobacteria generally do not accumulate storage 

lipids, but they are prolific carbohydrate and secondary 

metabolite producers. Some strains can double 

quickly (less than 10 hours), and some strains can fix 

atmospheric nitrogen and produce hydrogen. Moreover, 

many can be genetically manipulated, making them 

attractive organisms for biofuels production.

Synechocystis has been used extensively for the study of 

carbon metabolism toward production of hydrocarbon 

fuels and intermediates. The genome of this strain 

was sequenced over a decade ago, the first among 

photosynthetic organisms (Kaneko et al., 1996). Many 

include the standardization of using a particular sequencing 

approach that provides sufficient coverage of ESTs to 

ensure accurate gene modeling. Comparative genomics 

approaches between related organisms and organisms 

that carry out similar functions can also help assign gene 

function and identify metabolic pathways of interest.

Currently, at least10 other algal genomes, as well as 

another dozen or so EST projects, are underway. It is 

notable that while these projects represent a very useful 

survey, the rationale for sequencing these organisms was 

not related to lipid production or other biofuels efforts. 

Therefore, there are still a large number of useful algal 

species to sequence that are related to biofuels production, 

such as Dunaliella sp., Nannochloropsis sp., Scenedesmus 

sp., Chlorococcum sp., and Pseudochlorococcum sp. 

Transcriptomics

While genome sequencing will be an important component 

of any algal biofuels technology development effort, 

quantitative transcriptome profiling using new, high 

throughput sequencing technologies will also become 

increasingly important because it will not only help 

with genome annotation (for example, identifying 

coding regions of DNA), but it is also emerging as a 

robust approach for genome-wide expression analysis 

in response to particular environmental conditions.

New, high-throughput sequencing technologies enable 

comprehensive coverage of transcripts and quantification of 

their relative abundance. Most transcriptomics approaches 

evaluate mRNA levels, however, small RNAs also play 

major regulatory roles in algae (Bartel, 2004; Cerutti 

and Casas-Mollano, 2006). Small RNAs have been 

identified in microalgae (Zhao et al., 2007) and should be 

considered in investigations of gene expression regulation, 

especially with regard to translational regulation. 

Proteomics

The cellular complement of proteins reflects its metabolic 

potential, and ultimately determines how a cell functions 

in response to the environment. Mass-spectrometry 

approaches allow for robust evaluation of soluble and 

membrane-associated proteins in the form of protein 

peptides. These approaches not only enable protein 

identification, but also allow for protein quantification and 

detection of post-translational modifications (Domon and 

Aebersold, 2006; Tanner et al., 2007; Castellana et al., 

2008). In the absence of genomic information, proteomic 

approaches can also help assess the metabolic potential of 

organisms that may be difficult to isolate, or can determine 

functional diversity of a community of organisms. 
2. Algal Biology 21

diversity of algae is important to identify species that 

are adept at making fuel precursors and with high 

productivity under various environmental conditions.

Chlamydomonas reinhardtii is the most studied eukaryotic 

algae. In addition to having a sequenced nuclear genome 

(Merchant et al., 2007) and well developed transgenic 

capabilities, it can be sexually crossed. It is not an abundant 

lipid producer, but nevertheless, C. reinhardtii can serve 

as a model system for understanding the fundamentals of 

lipid synthesis and regulation. Lipid production, like the 

production of other carbohydrate-based storage compounds, 

is also often dependent on environmental conditions, 

some of which await elucidation and development. 

A possible drawback of C. reinhardtii is the fact that 

nuclear expression of foreign genes is still problematic 

due to codon bias (Heitzer et al., 2007), RNA silencing 

(Cerutti et al., 1997), and positional effects (Ferrante et 

al., 2008). However, strategies to address these issues are 

being developed, and stable and successful expression 

of foreign genes in C. reinhardtii has been recently been 

reported (Neupert et al., 2009; Ferrante et al., 2008). 

Chloroplast transformants are also stable, and chloroplast 

protein expression systems are well developed.

Chlorella is another well-studied genus of green algae, 

and some species are abundant lipid producers. In 

C. protothecoides, the addition of an external carbon source 

induces heterotrophic growth, which increases both growth 

rate and lipid production, resulting in greater than 50% 

dry weight lipid (Xu et al., 2006). The genome sequence 

of Chlorella NC64A was recently completed.2 Several 

examples of Chlorella transformation have been reported, 

although the stability of the expression of the foreign 

genes is still questionable (Leon and Fernandez, 2007 ).

Dunaliella salina has several useful characteristics for 

large-scale biofuels production. It produces abundant 

lipids (Weldy and Huesemann, 2007), and because 

it has outstanding salt tolerance (from 0.1 M to near 

saturation), it can be grown under extreme conditions 

that could reduce the growth of possible contaminating 

organisms. The genome sequence of D. salina is 

currently being determined (estimated size 130 Mb), and 

transgenic strains have been reported (Li et al., 2007).

Diatoms were a major focus in the Aquatic Species Program 

given their ability to accumulate high amounts of lipids 

(Sheehan et al., 1998). Diatoms are responsible for 20% 

of the total global carbon fixation (Armbrust et al., 2004), 

suggesting favorable growth rates for biomass production. 

A distinguishing feature of diatoms is their silica cell walls, 

photosynthesis and carbon metabolism mutants have been 

generated, and high-throughput analytical techniques 

have been applied to the study of its transcriptome, 

proteome, and metabolome (Singh et al., 2008; Fulda et 

al., 2006; Koksharova et al., 2006; Eisenhut et al., 2008).

Transgenic approaches have enabled the production and 

secretion of cellulose, sucrose (Nobles and Brown, 2008), 

ethanol (Deng and Coleman, 1999), and isobutanol (Atsumi 

et al., 2009) in Synechococcus. Relatedly, Synechococcus

and Anabaena strains have been studied for their hydrogen 

production potential (Tamagnini et al., 2002). The latter is a 

filamentous strain that can form heterocysts, which are cells 

with specialized structure and metabolism that function 

anaerobically (important for the production of hydrogen).

Despite all of the progress, a comprehensive understanding 

of carbon metabolism and regulation is not yet available 

in all cyanobacteria. In order to redirect carbon to a fuel 

production pathway, it will be necessary to further 

characterize the dominant carbon storage compounds 

(sinks) in cyanobacteria, including glycogen, 

glucosylglycerol, sucrose, and polyhydroxybutyrate 

(PHB), and the conditions that trigger carbohydrate 

accumulation. For example, it is known that glycogen 

accumulates under normal growth conditions in 

Synechocystis, whereas glucosylglycerol and sucrose 

can accumulate under salt stress (Yoo et al., 2007; 

Xiaoling Miao et al., 2003). It has also been shown that 

PHB accumulates under nitrogen depleting conditions 

(Miyake et al., 2000). It has not been shown how these 

pathways can be manipulated for the benefit of biofuels 

production. These studies can not only serve to advance 

the understanding of how the production of different 

carbon storage molecules are controlled in response to 

physiological conditions, but may also serve to guide the 

development of other types of algae for biofuels production.

Microalgae

Unicellular eukaryotic microalgae are the product of 

over 3 billion years of evolution, and are highly diverse 

(Falkowski et al., 2004). Multiple endosymbiotic events 

occurred during the evolution of microalgae. These 

events likely had significant effects on the metabolic 

pathways and regulation of fuel precursor synthesis. 

For example, fatty acid synthesis, which occurs in the 

chloroplast, is at least partly regulated by nuclear-encoded 

gene products, and there are fundamental differences in 

the interaction between the nucleus and chloroplast in 

algae with different extents of endosymbiosis (Wilhelm 

et al., 2006). Continued exploration of the evolutionary 

 2 http://genome.jgi-psf.org/ChlNC64A_1/ChlNC64A_1.home.html
22 2. Algal Biology 

Advances in seaweed cell and molecular biology are 

currently being applied toward a better understanding 

of seaweed genetics and cell function. For example, 

restriction fragment length polymorphisms (RFLPs) and 

random amplified polymorphic DNA (RAPD) analysis 

are used in seaweed population genetics (Alberto et al., 

1999; Bouza et al., 2006; Dutcher and Kapraun, 1994; Ho 

et al., 1995; Niwa et al., 2005), and strain selection and 

characterization (Jin et al., 1997; Meneses and Santelices, 

1999; Niwa et al., 2005). Use of gene-specific probes 

(Jacobsen et al., 2003; Moulin et al., 1999; Roeder et al., 

2005), and expression profiling (Collen et al., 2006) are 

being applied to understand cell function in representatives 

of red, brown, and green seaweeds. Recombination of 

existing genes through selection and procedures such 

as protoplast fusion will be the basis for new strain 

creation where outplanting of individuals for growth 

in natural environments is a goal. Genome sequencing 

projects will facilitate efforts such as global genomic 

and proteomic profiling, constructing detailed pathways 

for secondary metabolite production, and metabolic 

engineering of seaweed genes to create valuable products.

Considerations of Genetic 

Modifications

Despite the great promise of GE algae, there is nevertheless 

a great deal of uncertainty regarding the need for or 

the appropriateness of deploying these strains. For the 

purpose of this report, GE algae are defined as strains 

carrying coding sequences obtained from a foreign 

species. Since the beginning of the deployment of GE 

organisms, there have usually been built in safeguards to 

prevent the release of GE organisms to avoid potential 

disruption of ecosystems. However, even with these 

safeguards, there have been several unintended releases 

of GE organisms over the past 15+ years (GAO report, 

2008). Understanding the basic biology that will inform 

such aspects as lateral gene transfer, potential for toxin 

production, potential for large-scale blooms and subsequent 

anoxic zone formation, and choice of cultivation methods 

in terms of organism containment, are very important. 

Despite the uncertainty regarding the development of 

GE algae as production strains, development of genetic 

tools is still imperative from a research standpoint.

and their requirement for silicon as a nutrient for growth. 

Silicon limitation is one trigger for lipid accumulation 

in diatoms. This is advantageous for studying the lipid 

induction response, because silicon metabolism is not 

believed to be tightly coupled with the metabolism of other 

nutrients. Two diatom genome sequences are complete 

(Armbrust et al., 2004; Bowler et al., 2008), and four more 

are underway.3 None of the sequencing projects has thus far 

been focused explicitly on biofuels. Transgenic techniques 

are well established for several diatom species (Dunahay et 

al., 1995; Apt et al., 1996; Fischer et al., 1999; Zaslavskaia 

et al., 2000), and regulatory gene expression control 

elements have been identified (Poulsen and Kroger, 2005). 

With the development of robust gene silencing approaches 

and possibly with homologous recombination, the gene 

manipulation toolkit for diatoms will be fairly complete.

Macroalgae

Macroalgae, or seaweeds, represent a broad group of 

eukaryotic photosynthetic marine organisms. They are 

evolutionarily diverse and abundant in the world’s oceans 

and coastal waters. They have low lipid content as a 

general rule but are high in carbohydrates that can be 

converted to various fuels. Unlike microalgae, they are 

multicellular and possess plant-like structural features. 

They are typically comprised of a blade or lamina, the 

stipe, and holdfast for anchoring the entire structure to 

hard substrates in marine environments. The life cycles 

of macroalgae are complex and diverse, with different 

species displaying variations of annual and perennial 

life histories, combinations of sexual and asexual 

reproductive strategies, and alternation of generations.

Macroalgae are historically classified as Phaeophyta 

(brown algae), Chlorophyta (green algae), and Rhodophyta 

(red algae) on the basis of their predominant pigments. 

Currently, taxonomic affinities are under re-examination 

with the use of molecular tools and phylogenetic 

markers. As such, the status of macroalgal systematics 

is in a state of flux (Ali et al., 2001; Baldauf, 2003). 

In general, each of the major macroalgal groups has 

affinity with corresponding microalgal forms. For 

example, the brown macroalgae such as the kelps are 

classified as Heterokonta within the Chromalveolata, 

which includes diatoms. Green macroalga such as Ulva 

(also known as sea lettuce) are classified together with 

common green microalgae such as Chlamydomonas

and Chlorella as Chlorophyta. Red macroalgae such 

as Porphyra spp. also have microalgal counterparts, 

such as the unicellular alga Porphyridium cruentum.

 3 http://www.jgi.doe.gov
2. Algal Biology 23

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3. Algal Cultivation 29

3.1 Cultivation Pathways

Microalgae and Cyanobacteria

Given the multiple pathways to cultivating microalgae 

and cyanobacteria, it is premature to predict whether 

algal cultivation in closed (e.g., photobioreactors), open 

(e.g., open ponds) or hybrid systems will prevail in the 

industry. It is, therefore, important that cultivation R&D 

projects are closely associated with techno-economic 

(TE) analysis that can evaluate the cultivation system 

in the context of upstream and downstream processing 

to identify the best-suited cultivation system. 

Broadly speaking, algae can be cultivated via 

photoautotrophic or heterotrophic methods, both varying in 

their challenges and advantages (Exhibit 3.1 compares the 

various features of both approaches). 

Photoautotrophic Cultivation

For photoautotrophic cultivation strategies where algae 

require light to grow and create new biomass, capital costs 

for closed photobioreactor construction are currently higher 

3. Algal Cultivation

than for open ponds raceways. However, it is important to 

acknowledge the advantages and disadvantages of both 

photoautotrophic cultivation approaches.

Traditionally, photobioreactors have suffered from 

problems of scalability, especially in terms of mixing and 

gas exchange (both CO2 and O2). Though photobioreactors 

lose much less water than open ponds due to evaporation, 

they do not receive the benefit of evaporative cooling 

and so temperature must be carefully maintained. 

Open ponds, however, are subject to daily and seasonal 

changes in temperature and humidity. Photobioreactors 

are unlikely to be sterilizable and may require periodic 

cleaning due to biofilm formation, but long-term culture 

maintenance is likely to be superior to that in open ponds 

where contamination and “foreign” algae are more 

readily introduced. Photobioreactors can also provide a 

higher surface to volume ratio and so can support higher 

volumetric cell densities, reducing the amount of water that 

must be processed and thus the cost of harvest (Christi, 

2007). Both types of cultivation systems must contend with 

maximizing light exposure. Many of these issues are being 

addressed through improved material usage and enhanced 

ADVANTAGES CHALLENGES

Photoautotrophic

 Cultivation

Closed 

Photobioreactors

• Less loss of water than open ponds

• Superior long-term culture 

maintenance

• Higher surface to volume ratio can 

support higher volumetric cell 

densities

• Scalability problems

• Require temperature maintenance as they 

do not have evaporative cooling

• May require periodic cleaning due to 

biofilm formation

• Need maximum light exposure

Open Ponds

• Evaporative cooling maintains 

temperature

• Lower capital costs

• Subject to daily and seasonal changes in 

temperature and humidity

• Inherently difficult to maintain 

monocultures

• Need maximum light exposure

Heterotrophic

 Cultivation

• Easier to maintain optimal conditions 

for production and contamination 

prevention 

• Opportunity to utilize inexpensive 

lignocellulosic sugars for growth

• Achieves high biomass 

concentrations

• Cost and availability of suitable 

feedstocks such as lignocellulosic sugars

• Competes for feedstocks with other 

biofuel technologies

Exhibit 3.1 Comparative features of microalgal cultivation approaches
30 3. Algal Cultivation 

Tokuda, 1993) and the phycocolloid-producing seaweeds 

Gracilaria, Hypnea, Sargassum, Turbinaria, and 

Gelidiella (Collantes et al., 2004; Kumar et al., 2004; 

Kumar et al., 2007). Growth of plantlets regenerated from 

protoplasts is possible in both the laboratory (Dipakkore 

et al.et al., 2005, Reddy et al.et al., 2006) and field 

(Dai et al., 2004; Dai et al., 1993). Recent studies have 

shown that Porphyra, in particular, appears especially 

promising for growing plants from protoplasts (Dai et 

al., 2004; Dai et al., 1993; Dipakkore et al., 2005).

Macroalgae can be cultivated in off-shore, near-shore, or 

in open pond facilities. The operation of large offshore 

seaweed farms was initially tested by the Marine 

Biomass Program through several deployments of kelp 

on growth structures in deep waters off the coast of 

Southern California; using artificially upwelled water 

as a nutrient source. While it was determined that such 

structures would support growth of kelp, difficulties were 

encountered with the stability of either the structures 

themselves or the stability of the attachment of kelp to 

the structures. However, modern prototypes for offshore 

growth of the kelp, Laminaria hyperborean, have been 

successfully tested in the North Sea (Buck and Buchholz, 

2004; Buck, 2005), thus providing optimism for future 

efforts. Near-shore coastal environments are already 

being exploited by countries like China, Japan, and Chile, 

which have viable seaweed aquaculture industries. In 

the United States and Europe, environmental regulations 

and popular resistance against use of coastal regions for 

aquaculture represent challenges that will need to be 

overcome due to the conflicting uses of coastal zones. 

Land-based pond systems have also been considered 

for macroalgal cultivation (Friedlander, 2008; Hanisak, 

1987), both as free-standing algal farms and in an 

integrated aquaculture scenario in co-culture with finfish 

and mollusks. In the latter, wastes from the other species 

represent a nutrient supply for the macroalgae. Porphyra

spp., Saccharina latissima and Nereocystis luetkeana have 

been successfully co-cultured with salmonid fish species 

(Bruton et al., 2009). Advantages of the land-based systems 

over those in water have been listed as 1) ease of plant 

management; 2) use of plants with or without holdfast 

structures; 3) ease of nutrient application without dilution; 

4) avoidance of open sea problems such as bad weather, 

disease, and predation; and 5) possibility of farm operations 

located in close proximity to conversion operations 

(Chynoweth, 2002). For contribution to a biofuels 

marketplace, considerable scale-up from current activities, 

improvement in strain selection, and major technological 

improvements in efficiency of water movements and 

pond construction costs are needed (Friedlander, 2008). 

engineering designs. Though TE analyses for both open 

pond and photobioreactor systems have been published or 

presented (see Chapter 10), much of the information used 

for these analyses is based on assumptions or proprietary 

data. As a result, it remains to be seen which system 

will be preferred at scale over long periods of operation. 

Additionally, in hybrid systems, photobioreactors could 

play a critical role as breeder/feeder systems linked to 

open raceways, providing high cell density algal inocula 

for production ponds (Ben-Amotz, 1995) or a series of 

linked turbidostats or chemostats (Benson et al., 2007).

Heterotrophic Cultivation

In heterotrophic cultivation, algae are grown without light 

and are fed a carbon source, such as sugars, to generate 

new biomass. This approach takes advantage of mature 

industrial fermentation technology, already widely used to 

produce a variety of products at large scale. Heterotrophic 

cultivation presents a different set of advantages and 

challenges compared with photoautotrophic methods. 

Optimal conditions for production and contamination 

prevention are often easier to maintain, and there is the 

potential to utilize inexpensive lignocellulosic sugars for 

algal growth. Heterotrophic cultivation also achieves high 

biomass concentrations that reduces the extent and cost of 

the infrastructure required to grow the algae (Xu, 2006). 

The primary challenges with this approach are the cost and 

availability of suitable feedstocks such as lignocellulosic 

sugars. Because these systems rely on primary productivity 

from other sources, they could compete for feedstocks 

with other biofuel technologies. A related approach 

is mixotrophic cultivation, which harnesses both the 

photoautotrophic and heterotrophic ability of algae.

Macroalgae

Macroalgae require unique cultivation strategies. Modern 

macroalgal cultivation technology that is based on the use 

of artificially produced seed as a source of propagules has 

been in practice since the 1950s. Typically, seeds grown 

in greenhouses are attached to substrates (usually rope 

structures), then reared to plantlet size and transplanted 

to coastal farms for grow-out to harvestable size. 

Modern tools developed in the larger plant breeding 

community are now available to seaweed biologists 

and culturalists to advance the vegetative propagation 

of seaweeds through cell and tissue culture techniques. 

Although the field is still at an early stage of development, 

the micropropagation of plants is a concept that has 

been adopted by seaweed biologists (Garcia-Reina et al., 

1991). Demonstrations of successful callus formation and 

plantlet regeneration have been reported in commercially 

important seaweeds such as Undaria (Kawashima and 
3. Algal Cultivation 31

Stability of Large-Scale Cultures 

Systems for large-scale production of biofuels from algae 

must be developed on scales that are orders of magnitude 

larger than all current worldwide algal culturing facilities 

combined. In certain cultivation systems, it will be 

challenging to maintain algal monocultures on this scale; 

it may become necessary to understand and manage the 

communities that will be present. Some members of the 

community will be of positive value, such as those that 

can scavenge and recycle nutrients or synthesize essential 

vitamins. Others will compete for shared resources, and 

still others will cause culture disruption. One of the more 

worrisome components of large-scale algae cultivation 

is the fact that algal predators and pathogens are both 

pervasive and little understood (Becker, 1994; Honda et 

al., 1999; Cheng et al., 2004; Brussaard, 2004). Fungal 

and viral pathogens are common, although current 

understanding of their diversity and host range is very 

limited. Wilson et al., (2009) point out that though there 

may be between 40,000 and several million phytoplankton 

species, there have only been 150 formal descriptions of 

phycoviruses. Chytrid fungi have also been known to cause 

the collapse of industrial algal cultivation ponds (Hoffman 

et al., 2008), but very little is known about host specificity 

and even less is known about host resistance mechanisms. 

Important questions concerning this threat 

to large-scale algal cultures include: 

• Are agricultural or municipal waste streams—a 

potentially significant source of nutrients for algal 

cultivation—actually a liability because of significant 

reservoirs of algal pathogens and predators?

• To what extent will local “weedy” algae invade 

and take over bioreactors and open ponds?

• What prevention or treatment measures 

might limit such takeovers?

Methods for rapid, automated or semi-automated biological 

and chemical monitoring in production settings will 

be essential for assessing the health and compositional 

dynamics of algal cultures. The methods must be sensitive, 

selective, and inexpensive, as well as potentially provide 

for real-time monitoring. “Environmental” DNA sequence 

analysis can contribute to the development of PCR-based 

(Zhu et al., 2005; Boutte et al., 2006; Viprey et al., 2008) 

or flow-cytometry-based taxonomic assays, e.g., TSAFISH (Marie et al., 2005). Continuous monitoring will 

be necessary in open systems since seasonal variation in 

competitors, predators, and pathogens is expected (Hoffman 

et al., 2008; Rittmann et al., 2008; Wilson et al., 2009). 

Other options for algal cultivation are being investigated 

including the harvesting of naturally occurring marine algal 

blooms, and the use of algal mat or biofilm cultivation 

schemes. It should be noted that, especially in open 

systems, monocultures are inherently difficult to maintain 

and require significant investment in methods for detection 

and management of competitors, predators, and pathogens. 

One possible approach to contend with this is to cultivate 

a mixed or natural assemblage of organisms in an attempt 

to maximize total harvested biomass. This model would 

require a downstream biorefinery capable of processing 

simple and complex carbohydrates, proteins, and lipids 

into a variety of useful products. Nutrients, including 

CO2, must also be managed in a way that balances 

productivity and pathogen sensitivity with the plasticity of 

algal physiological adaptation. The cost-benefit analysis 

of supplemental CO2 in large-scale algal cultivation 

has yet to consider the intricacies of biological carbon 

concentration mechanisms (Wang and Spalding, 2006 ).

3.2 Scale-Up Challenges

The inherent difficulties of scaling up from laboratory 

to commercial operations present both technical 

and economic barriers to success. Because of the 

pervasiveness of issues related to scale, an investment 

in “open source” test bed facilities for public sector 

RD&D may foster more cultivation research. 

Nutrient sources and water treatment/recycling are 

technically trivial and inexpensive at small scales and 

yet represent major technical and economic problems at 

commercial scales. Tapping into existing agricultural or 

municipal waste streams will lower nutrient costs but could 

introduce unacceptable pathogens, chemical compounds, or 

heavy metals into the biomass stream (Hoffman et al., 2008; 

Wilson et al., 2009). Additionally, little is known about 

artificial pond ecology or pathology, and investigation into 

these areas will be important for the development of largescale cultivation risk mitigation and remediation strategies. 

Four broad cultivation challenges have emerged 

that are important to address for economically 

viable, commercial-scale algal cultivation: 

• Culture stability;

• Standardized metrics for system-level 

productivity analysis;

• Nutrient source scaling, sustainability and 

management; and

• Water conservation, management, and recycling. 
32 3. Algal Cultivation 

transportation and the volatile market for carbon credits will 

be a major challenge for TE feasibility studies; diverging 

business models are already apparent on these issues. 

Better methods to detect the amount of desired fuel 

precursor produced will be required to assess the 

productivity of potential strains. Fluorescent and Nuclear 

Magnetic Resonance-based methods for rapid lipid content 

screening in algae have been developed and applied to 

many different types of phytoplankton with mixed results 

(Cooksey et al., 1987; Reed et al., 1999; Eltgroth et al., 

2005; Gao et al., 2008). These tools, as well as others such 

as Near Infra Red spectroscopy, need to be more rigorously 

studied, automated, and adapted for rapid, inexpensive 

high-throughput monitoring. The synthesis of new nontoxic, permeable, fluorescent indicators other than Nile Red 

are also important. For example, derivatives of the Bodipy 

molecule with higher lipophilicity or lower quantum yields 

in aqueous solvent may prove to be more reliable indicators 

of algal lipid contents (Gocze and Freeman, 1994). 

There is an immediate need to standardize productivity 

models and establish protocols for measurement of yields, 

rates, densities, metabolites, and normalization. Along 

with standards, coordinated research amongst analytical 

chemists, physiologists, biochemists, and genetic, 

chemical, civil and mechanical engineers is needed for 

rapid progress. National and international efforts toward 

generating quality assurance policy standards early on 

in the development of an algal biofuel industry could 

facilitate the deployment of algal based-biofuels by 

ensuring consistent, fit-for-purpose fuels, and products. 

Nutrient Sources, 

Sustainability, and Management

Nutrient supplies for algal cultivation have a sizeable 

impact on cost, sustainability, and production siting. 

The primary focus is the major nutrients – nitrogen, 

phosphorous, iron, and silicon (in the case of diatoms). 

Nitrogen, phosphorous, and iron additions represent a 

significant operating cost, accounting for 6-8 cents per 

gallon of algal fuel in 1987 U.S. dollars (Benemann and 

Oswald, 1996). This calculation takes into account a 50% 

rate of nutrient recycle. Phosphorous appears to be an 

especially important issue as there have been calculations 

that the world’s supply of phosphate is in danger of running 

out (Abelson, 1999). Requirements for additional nutrients, 

such as sulfur, trace metals, vitamins, etc. must also be 

considered, but vary depending upon the specific strain and 

water source chosen. The use and availability of carbonbased nutrients for heterotrophic growth will also affect 

the economics and sustainability of such systems. Strain 

selection should take nutrient requirements into account. 

Furthermore, developing an understanding of pond 

speciation, predator-prey relationships, and ecology 

dynamics will be important. Early detection schemes for 

invasive species, predators, and pathogens will be a key 

to the success of remedial actions and for determining 

when decontamination and subsequent restart procedures 

represent the only alternative. This information will 

also inform efforts at developing robust, competitive 

production strains. The frequency of contamination 

events that require decontamination/restarts will be an 

important parameter in the cost of production because of 

productivity lost during down time, and because of the 

potential need to either discard or treat the contaminated 

culture prior to water recycle. The development of 

chemical treatments or physiological adaptations and 

genetic modifications of production strains may become 

necessary. Dynamic pond monitoring will be important 

for both wild-type and genetically modified algae, 

whose competitiveness in the field cannot be accurately 

predicted. Thus, a significant investment toward basic 

research in multi-trophic, molecular-level algal ecology 

will be an important component of the investment 

portfolio required for developing the potential of algae. 

System Productivity

Research at the interface between basic algal biology and 

cultivation science and engineering will yield significant 

improvements in productivity while at the same time 

lower the cost of production. Utilization of existing and 

new knowledge related to the physiological regulation of 

lipid or carbohydrate accumulation coupled with scalable 

cultivation schemes should lead to enhancements in 

productivity. For example, nitrogen nutrition has long 

been known to affect lipid accumulation in phytoplankton 

(Ketchum and Redfield, 1938; Shifrin and Chisholm 

1981; Benemann and Oswald, 1996; Sheehan et al., 

1998). More recent data suggest that high salt and high 

light stress in some marine phytoplankton may also 

result in increases in lipid content (Azachi et al., 2002). 

From a productivity standpoint, supplemental CO2 has 

long been known to increase algal growth rate, and 

this area is receiving new attention from the search for 

renewable, sustainable fuels. New approaches are split 

between using algae to scrub CO2 from emission gasses 

(Rosenberg et al., 2008; Douskova et al., 2009) and a focus 

on better understanding the mechanisms of biological 

CO2 concentration from ambient air (Lapointe et al., 

2008; Spalding 2008). There is justification to carry out 

R&D in both areas, as siting requirements for efficient 

algal cultivation may rarely coincide with high-volume 

point sources of CO2 (see Chapter 9). The cost of CO2
3. Algal Cultivation 33

Another approach to reduce nutrient costs is to pursue 

a diligent recycle. The final fuel product from algal oil 

contains no nitrogen, phosphorous, or iron; these nutrients 

end up primarily in the spent algal biomass. From a 

sustainability perspective, nutrient recycle may prove 

to be more valuable than using the spent biomass for 

products such as animal feed. If the biomass residues are, 

for example, treated by anaerobic digestion to produce 

biogas, then most of the nutrients will remain in the 

digestor sludge and can be returned to the growth system 

(Benemann and Oswald, 1996). The processes through 

which these nutrients are re-mobilized and made available 

for algal growth are not well understood. This may be 

particularly problematic for recycling of silicon, which is 

a component of the diatom cell walls. In the future, it may 

also become necessary to expand the limits of analysis 

to include recycling of nutrients from animal waste. 

Nutrient sourcing and the control of nutrient 

levels are vitally important factors for cultivation 

economics, productivity, and sustainability issues. 

Important research areas therefore include:

• TE and life cycle analysis to understand the cost, 

energy, and sustainability implications of various 

nutrient sources and recycling scenarios 

• Studies to explore the mechanisms of nutrient 

recycling, e.g., from anaerobic digestion sludges

• Geographic Information System (GIS) analyses of 

wastewater resources to understand availability, 

compatibility with cultivation sites, and potential 

impact of such sources on algal biofuels production

Water Management, 

Conservation, and Recycling

One of the main advantages of using algae for 

biofuels production is their ability to thrive in water 

unsuitable for land crops, such as saline water from 

aquifers and seawater. At the same time, however, 

water management poses some of the largest issues 

for algal biofuels. If not addressed adequately, water 

can easily become a “show-stopper,” either because of 

real economic or sustainability problems or because of 

loss of public support due to perceived problems. 

With large cultivation systems, water demands will be 

enormous. For example, a hypothetical 1 hectare (ha), 20 

cm deep open pond will require 530,000 gallons to fill. 

In desert areas, evaporative losses can exceed 0.5 cm per 

day (Weissman and Tillet, 1989), which is a loss of 13,000 

gallons per day from the 1 ha pond. Though the water used 

to initially fill the pond can be saline, brackish, produced 

Nitrogen is typically supplied in one of three forms: 

ammonia, nitrate, or urea. The ideal form of nitrogen 

is a function of relative costs and the specific strain’s 

biology. Because synthetic nitrogen fixation processes 

utilize fossil fuels (particularly natural gas), costs are tied 

to fossil fuel prices, and the very large required energy 

inputs should be accounted for in life cycle analyses. 

It is possible to consider the use of nitrogen-fixing 

cyanobacteria as a way to provide nitrogen biologically, 

perhaps in co-culture with eukaryotic algae. However, 

such a scheme will certainly have some impact on overall 

productivity levels as photosynthetic energy could 

be diverted from carbon fixation to nitrogen fixation, 

which may or may not be compensated for by the “free” 

nitrogen. Note also that flue gas fed to algal cultures may 

provide some of the nitrogen and sulfur needed from 

NOx and SOx (Doucha, 2005; Douskova et al., 2009).

Careful control of nutrient levels is also critical. Limitation 

of a key nutrient will have serious impacts on biomass 

productivity, but it may also be desirable to use nutrient 

limitation (e.g., nitrogen, phosphorous, or silicon) as a 

means to induce oil accumulation in the cells (Sheehan 

et al., 1998). On the other hand, too much of a particular 

nutrient may prove toxic. Also, unused nutrients in 

the culture medium pose a problem for waste water 

discharge. Although economics dictate that the bulk of 

water derived from the harvesting step must be returned 

to the cultivation system (where remaining nutrients 

can feed subsequent algal growth), a certain amount 

of “blowdown” water must be removed to prevent salt 

buildup. If this blowdown water contains substantial 

nitrogen and phosphorous, disposal will become a problem 

due to concerns of eutrophication of surface waters.

Finding inexpensive sources of nutrients will be important. 

Reagent grade sources of nutrients could make the price 

of a gallon of algal fuel cost-prohibitive. Agriculturalor commodity-grade nutrients are more applicable, but 

their costs are still significant. Therefore, utilizing the 

nutrient content of municipal, agricultural, or industrial 

waste streams is a very attractive alternative. Currently, 

algae are used in some wastewater treatment facilities 

because of their ability to provide oxygen for the bacterial 

breakdown of organic materials and to sequester nitrogen 

and phosphorous into biomass for water clean-up. 

Utilizing agricultural run-off also poses economic benefits 

by preventing eutrophication. A potential problem with 

this approach however is the impact on facility siting. 

Wastewater treatment facilities, for example, tend to be near 

metropolitan areas with high land prices and limited land 

availability, and it is not practical to transport wastewater 

over long distances. Further research into the availability 

and compatibility of wastewater resources is warranted. 
34 3. Algal Cultivation 

water from oil wells, municipal wastewater, or other lowquality water stream, the water being lost to evaporation 

is fresh water, and continually making up the volume with 

low-quality water will concentrate salts, toxins, and other 

materials in the culture. This can be prevented by adding 

fresh water—a costly and often unsustainable option—or 

by disposing of a portion of the pond volume each day 

as “blowdown.” The amount of blowdown required for 

salinity control is dependent upon the acceptable salt level 

in the culture and the salinity of the replacement water. 

Conservation of water can be addressed to some extent 

through facility design and siting. An advantage of 

closed photobioreactors over open ponds is a reduced 

rate of evaporation. The added cost of such systems must 

be balanced against the cost savings and sustainability 

analysis for water usage for a given location. Note however 

that evaporation plays a critical role in temperature 

maintenance under hot conditions through evaporative 

cooling. Closed systems that spray water on the surfaces 

or employ cooling towers to keep cultures cool will lose 

some if not possibly all of the water savings of such 

systems under these conditions (Flickinger,1999). A critical 

part of the analysis that goes into siting an algal facility 

will be to analyze the “pan evaporation” rates at specific 

sites in conjunction with water cost and availability.

Water recycling is essential, but the amount that can 

be recycled depends on the algal strain, water, process, 

and location. Some actively growing algal cultures can 

double their biomass on a daily basis, meaning that half 

the culture volume must be processed daily. This is an 

enormous amount of water (260,000 gallons per day in the 

1 ha example above). To contain costs, it is desirable to 

recycle most of that water back to the culture. However, 

accumulated salts, chemical flocculants used in harvesting, 

or biological inhibitors produced by the strains themselves 

could impair growth if recycled to the culture. Furthermore, 

moving around such large volumes of water is very 

energy-intensive and can impose a significant cost.

Treatment may be essential for water entering and exiting 

the process. Incoming water (surface water, groundwater, 

wastewater, or seawater) may be suitable as is, or may 

require decontamination, disinfection, or other remediation 

before use. The blowdown water exiting the process will 

also most likely require treatment. Disposal of the spent 

water, which could contain salts, residual nitrogen and 

phosphorous fertilizer, accumulated toxics, heavy metals 

(e.g., from flue gas), flocculants, and residual live algal 

cells, could pose a serious problem, and treatment (e.g., 

desalination, activated charcoal filtration, etc.) of the 

recycled stream could be cost-prohibitive. Surface disposal 

and reinjection into wells may be an option as regulated 

by the Environmental Protection Agency and already 

practiced by the oil industry, but live cells could adversely 

affect biodiversity of neighboring ecosystems or result 

in the dissemination of genetically modified organisms. 

Sterilization of blowdown water, however, would be a 

very costly and energy-intensive proposition.

Because of the importance of issues surrounding the use 

of water, research in the following areas is warranted:

• GIS analysis of water resources, including saline 

aquifers, and their proximity to utilizable cultivation 

sites that may have lower pan evaporation rates

• Understanding the long-term effects of drawing 

down saline aquifers, including the geology of these 

aquifers and associations with freshwater systems

• Analysis and definition of the regulatory landscape 

surrounding discharge of water containing various

levels of salt, flocculants, toxins (including heavy 

metals), and live cells

• Developing cultivation systems with minimal 

water consumption. This could include reducing 

evaporative cooling loads through such strategies 

as selecting thermotolerant strains of algae

• Studying water recycle and methods to maximize 

recycle (and minimize blowdown), while effectively 

managing the accumulation of salt and other inhibitors

• Investigating ways to reduce the cost of water 

treatment, makeup water/recycle, and water 

movement (pumping costs)
3. Algal Cultivation 35

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4. Downstream Processing: Harvesting and Dewatering 37

Conversion of algae in ponds, bioreactors, and off-shore 

systems to liquid transportation fuels requires processing 

steps such as harvesting (Dodd and Anderson, 1977; 

Butterfi and Jones, 1969; McGarry and Tongkasa, 1971), 

dewatering, and extraction of fuel precursors (e.g., lipids 

and carbohydrates). These energy-intensive processes are 

only now being recognized as critically important. Cultures 

with as low as 0.02 - 0.07% algae (~ 1 gm algae/5000 

gm water) must be concentrated to slurries containing 

at least 1% algae given the known processing strategies 

(Borowitzka, 1988). The final slurry concentration will 

depend on the extraction methods employed and will 

impact the required energy input. As the desired percentage 

of dry biomass increases, energy costs climb steeply. Final 

slurry concentration also impacts plant location because 

of transportation, water quality, and recycling issues. A 

feasible algae-to-fuel strategy must, therefore, consider the 

energy costs and siting issues associated with harvesting 

and dewatering. Addressing these issues requires careful 

analysis of engineering designs, combined with RD&D to 

develop specific processing technologies to support those 

designs and a fundamental understanding of how algal 

biology can impact harvesting and dewatering strategies.

Processing technologies depend on the algal feedstocks 

being considered. Processes that pertain to unicellular algae

 are quite different from the approaches applicable 

to macroalgae.

4.1 Approaches for Microalgae

Harvesting

Flocculation and Sedimentation

Microalgae and cyanobacteria remain in suspension in 

well-managed high growth rate cultures due to their 

small size (~1 to 30 μm). This facilitates the transport of 

cells to the photoactive zone through pond or bioreactor 

circulation. Their small sizes, however, make harvesting 

more difficult. Flocculation leading to sedimentation occurs 

naturally in many older cultures. In managed cultures, some 

form of forced flocculation usually involving chemical 

additives, is required to promote sedimentation at harvest.

A number of different forms of forced flocculation have 

been employed. Chemical additives that bind algae or 

otherwise affect the physiochemical interaction between 

algae are known to promote flocculation (Lee et al., 

1998; Knuckey et al., 2006; Pan et al., 2001). Alum, lime, 

cellulose, salts, polyacrylamide polymers, surfactants, 

chitosan, and other man-made fibers are some chemical 

additives that have been studied. Manipulating suspension 

4. Downstream Processing: Harvesting and Dewatering

pH with and without additives is also effective, and 

autoflocculation in the form of photosynthetically driven 

CO2 depletion for pH control has been studied (Sukenik 

and Shelaf, 1984). Bioflocculation where algae are cocultured with another organism that promotes sedimentation 

has also been considered (Lavoie and Delanoue, 1987). 

Finally, electroflocculation and electrocoagulation offer 

the advantages of no added chemicals (Chen, 2004; 

Mollah et al., 2004; Poleman and Pauw, 1997). 

Optimizing flocculation methods, type, mixtures, 

concentrations, and chemistry to maximize algae recovery 

will very likely depend on strain selection, the mechanism 

of algae-flocculant interactions, and on empirical 

determinations in particular processes. It is possible to 

imagine selecting/designing strains to aggregate on cue 

or designed with a particular flocculant interaction in 

mind. Culture manipulation techniques, therefore, may 

be useful for promoting flocculation. Future research in 

flocculation chemistry must take into account the following:

• Chemical flocculant recovery techniques are required 

to minimize cost and control water effluent purity.

• The effect of residual flocculant or pH manipulation 

in recycled water on culture health and stability 

and lipid production must be understood and 

controlled. Likewise, the presence of flocculant in 

further downstream extraction and fuel conversion 

processes must be understood and controlled.

• The environmental impact of flocculant or pH 

manipulation in released water effluent, and fuel 

conversion and use must be considered.

• Bioflocculation, electroflocculation, and 

electrocoagulation must be scaled-up with cost and 

energy analysis.

• Optimized sedimentation tank designs with integration 

into further downstream dewatering techniques, water 

recycling and flocculate recovery are required.

Flocculation and Dissolved Air Flotation

Flocculation and Dissolved Air Flotation (DAF) was 

established for sewage treatment and later studied in 

algae harvesting (Sim et al., 1988; Botes and Vanvuuren, 

1991; Edzwald, 1993; Phochinda and White, 2003; 

Kwak et al., 2005; Bare et al., 1975; Koopman and 

Lincoln, 1983). Flocculation is used to increase the 

size of the algae aggregates, and then air is bubbled 
38 4. Downstream Processing: Harvesting and Dewatering 

Centrifugation

Centrifugation is widely used in industrial suspension 

separations and has been investigated in algal harvesting 

(Molina et al., 2003). The efficiency is dependent on 

the selected species (as related to size). Centrifugation 

technologies must consider large initial capital equipment 

investments, operating costs, and high throughput 

processing of large quantities of water and algae. The 

current level of centrifugation technology makes this 

approach cost-prohibitive for most of the envisioned 

large-scale algae biorefineries. Significant cost and 

energy savings must be realized before any widespread 

implementation of this approach can be carried out.

Other Harvesting Techniques

A number of other techniques at various stages of 

R&D have been proposed to harvest and dewater 

microalgae. These include, but are not limited to, the 

use of organisms growing on immobilized substrates 

where the amount of initial water is controlled and 

the growth substrate can be easily removed; acoustic 

focusing to concentrate algae at nodes; manipulation of 

electric fields; and bioharvesting, where fuel precursors 

are harvested from higher organisms (e.g., shrimp and 

tilapia) grown with algae (Johnson and Wen, 2009).

Drying

Drying is required to achieve high biomass concentrations. 

Because drying generally requires heat, methane drum 

dryers and other oven-type dryers have been used. 

However, the costs climb steeply with incremental 

temperature and/or time increases. Air-drying is possible 

in low-humidity climates, but will require extra space and 

considerable time. Solutions involving either solar or wind 

energy are also possible.

4.2 Approaches for Macroalgae 

Harvesting

Currently, of the roughly 1.6 million dry metric tons 

of total seaweed harvested worldwide, about 90% is 

derived from cultivated sources (Roesijadi et al., 2008). 

Manual harvesting is common for both cultivated and 

natural systems, and mechanized harvesting methods, 

which can involve mowing with rotating blades, suction, 

or dredging with cutters, have also been developed. 

Invariably, such mechanized harvesters require boats 

or ships for operation. Modern seaweed harvesting 

vessels can be equipped with pumps to direct harvested 

seaweeds directly into nets or other containment structures 

(Ugarte and Sharp, 2001). Application of mechanical 

through the suspension causing the algal clusters 

to float to the surface. The algae-rich top layer is 

scraped off to a slurry tank for further processing. 

All of the issues arising from the use of flocculants 

for sedimentation (e.g., floc optimization, water and 

algae purity, and flocculant reclamation) are also 

encountered in flocculation and DAF. In addition to 

flocculant efficiency, recovery is largely dependent on 

bubble size and distribution through the suspension. 

DAF facilities require optimized integration with any 

engineered design for further downstream processing.

Filtration

Solid/liquid filtration technologies are well studied, 

and filtration without prior flocculation can be used 

to harvest and dewater algae (Ferguson et al., 1995; 

Downing et al., 2002; Saidam and Butler, 1996). 

Microalgae and cyanobacteria present unique filtration 

challenges because most strains considered for energy 

feedstocks have cell diameters less than 10 μm. 

Filtration is conceptually simple but potentially 

very expensive, and can be optimized through 

further understanding of several issues:

• The filter pore size is critically important as it is 

defined by the size of the algae species and algae 

aggregation rate. Small algae pass through larger 

pores decreasing filter efficiency. Decreasing pore 

size, however, leads to blinding, the blocking of filter 

pores, and reduction of filtering rates. Culture purity 

becomes important as a distribution of microorganism 

size will affect filtration efficiency and blinding rates.

• Filter material also influences filtration and recovery 

efficiency. Materials can be used that optimize filtration 

and have the ability to remove the algae later. For 

instance, filter materials with controlled hydrophobicity 

and/or algae affinity can be developed. Durability and 

blinding are also issues.

• Filtration design is an important variable with both 

static and dynamic filtering operations. Moving filters 

have been used in drum and cylinder press designs 

(Oswald, 1991). Power costs will certainly influence 

design.

• An important step is recovering the algal biomass from 

the filter. Washing the filter is one practice, but doing 

so leads to re-dilution of the product. Filtration designs 

should consider minimal or no washing requirements.
4. Downstream Processing: Harvesting and Dewatering 39

Milling is used to reduce seaweeds to particle sizes that are 

\more efficiently processed. Smaller particles, with higher 

surface area to volume ratios, will have higher reaction 

efficiency during anaerobic digestion for biogas, 

fermentation for alcohols, and hydrothermal liquefaction 

for bio-oils.

Macroalgae have less of a demand for dewatering as 

part of the pretreatment process. Anaerobic digestion, 

fermentation, and hydrothermal liquefaction have either 

a high tolerance or requirement for water. Dewatering 

may be more important as a method to increase shelf-life 

and reduce weight and associated transportation costs if 

algae are to be transported from sites of harvest to distant 

processing plants (Bruton et al., 2009). Dewatering to 

about 20 - 30% water content is noted to have a stabilizing 

influence, which is beneficial for transportation and other 

processes requiring further drying (Bruton et al., 2009). In 

anaerobic digestion and fermentation, shredded or milled 

macroalgal biomass can go directly into either reactions 

or extractions. Hydrothermal conversions are suited for 

wet biomass and become efficient at 15 - 20% solids or 

80 - 85% water content (Peterson et al., 2008). Although 

some dewatering of seaweeds whose water content 

approaches 90% may be necessary, the exact ratio of water 

to solids for marine biomass remains to be determined. 

4.3 Systems Engineering 

While specific process technologies have been studied, 

breakthroughs are still needed in each, given the 

importance as well as current cost and achievable 

scale of harvesting and dewatering. Further, new 

strategies should be developed to combine and integrate 

these processes in order to take an algae culture and 

convert it into slurry of a specific concentration. 

This has yet to be demonstrated on a commercially 

relevant scale and remains a significant challenge. 

A critical gap is the energy requirements of these processes 

are not only largely unknown but unbounded. This has 

important implications for plant design to answer simple 

questions like “What percentage of the total plant energy 

requirements or what percentage of that made available by 

algae must be directed toward harvesting and dewatering?”. 

Ultimately, a unit operations analysis of energy input 

for a range of dry weight content based on extraction 

needs is required with consideration of capital equipment 

investments, operations, maintenance, and depreciation.

The cost of harvesting and dewatering will depend on the 

final algae concentration needed for the chosen extraction 

method. This will likely be a significant fraction of the 

total energy cost of any algae-to-fuel process and a 

significant fraction of the total amount of energy available 

harvesters in European seaweed operations have been 

described in a recent feasibility analysis for seaweeds as 

a biofuels feedstock in Ireland (Bruton et al., 2009).

The concept of large off-shore macroalgae farms and 

associated biorefineries has from the outset included 

mechanized harvesting techniques. The exact nature of 

such mechanization will obviously depend on the form 

of cultivation and type of algae being cultured. For 

example, attached forms that tend to stand upright, such 

as Macrocystis, may be amenable to mowing. Floating 

seaweeds such as Sargassum spp. could be cultivated in 

floating pens, and low growing attached forms such as 

Gracilaria will require different approaches compatible with 

their growth characteristics. In forms such as Laminaria 

grown on off-shore rings (Buck and Buchholz, 2004), 

harvesting may require retrieval and transport to shore. 

Similarly, cultivation in land-based pond systems will 

require technology appropriate for that mode of culture. 

As a result of growing concern about the potential 

environmental consequences of harvesting natural 

populations of seaweed near-shore, strict regulations 

have been put in place in some countries (Pringle and 

Tseng, 1989). To manage seaweed harvests, laws have 

stipulated the percentages of harvestable stock allowed to 

be harvested and the intervals between harvests to allow 

growth and recovery of biomass (Ugarte and Sharp, 2001). 

The establishment of large offshore seaweeds may alleviate 

pressure from near-shore environments and create market 

opportunities for products apart from fuels, although 

issues related to sustainability and potential environmental 

consequences will need to be carefully evaluated.

Preprocessing

The general preprocessing requirements for macroalgal 

biomass prior to extraction or direct conversion have 

been categorized as follows (Bruton et al., 2009):

• Removal of foreign objects and debris, e.g., by washing 

• Milling

• Dewatering

Seaweeds immediately following harvest can have 

stones, sand, litter, adhering epifauna and other forms of 

debris that should be removed before further processing. 

Screening for debris is considered mandatory, with 

the degree of screening dependent on the mode of 

culture and end-use. Algae that are grown in suspension 

culture, as opposed to attached to the bottom culture, 

will likely have less debris, and the amount of debris 

will likely have less impact in procedures that can 

utilize whole seaweeds (Bruton et al., 2009).
40 4. Downstream Processing: Harvesting and Dewatering 

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Botes, V., L.R.J. Vanvuuren. (1991). Dissolved air flotation for the removal of algae and inorganic turbidity on a large-scale. Water 

Supply: IWSA/IAWPRC Joint Specialized Conference on Coagulation Flocculation, Filtration, Sedimentation and Flotation. 9(1), 133. 

Bruton, T., H. Lyons, Y. Lerat, M. Stanley, and M. B. Rasmussen. (2009). A review of the potential of marine 

algae as a source of biofuel in Ireland. Sustainable Energy Ireland, Dublin, Ireland

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to hydrodynamic forcing in the north sea. Aquaculture. 250, 674-691.

Butterfi, B.A., J. Jones. (1969). Harvesting of algae grown in agricultural wastewaters. 

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Ferguson, C., G.S. Logsdon, D. Curley, C. Ferguson. (1995). Comparison of dissolved air flotation and direct filtration.

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Johnson, M., & Wen, Z. (2010). Development of an attached microalgal growth system for 

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of vaporization of water at 0.54 watt-hours/gram, energy 

balance can become an issue in systems that propose 

to take algal biomass and concentrate / dry it to enable 

downstream processing and extraction because of the 

high volumes of water that must be evaporated away. 

In spite of gaps in data precluding more detailed 

analyses, algal biofuel production schemes at scale will 

likely need to implement innovative technologies and 

integrated systems in order to overcome this challenge. 

Possible approaches may include developing strains of 

algae with much higher energy content than available 

today, along with innovative solutions to lower the 

energy intensity of harvesting and drying algae.

from algae. A quick and preliminary energy balance 

example shown below provides some food for thought 

regarding harvesting and dewatering technologies.

Preliminary Look at Energy Balance 

The energy content of most algae cells is of the order 

of 5 watt-hours/gram if the energy content of lipids, 

carbohydrates, and proteins and the typical percentage 

of each in algae are considered (Illman et al., 2000). It 

is possible to estimate the energy requirements in watthours/gram of algae for harvesting, de-watering, and 

drying as a function of the volume percentage of algae 

in harvested biomass. The energy requirements for 

flocculation and sedimentation and the belt filter press are 

expected to be minimal. However, based on the latent heat 
4. Downstream Processing: Harvesting and Dewatering 41

Lee, S.J., S.B. Kim, G.S. Kwon, B.D. Yoon, H.M. Oh. (1998). Effects of harvesting method and growth stage on the flocculation of the 

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hydrothermal media: A review of sub- and supercritical water technologies. Energy & Environmental Science. 1, 32-65.

Phoochinda, W., D.A. White. (2003). Removal of algae using froth flotation. Environmental Technology. 24(1), 87.

Poelman, E., N. Pauw. (1997). Potential of electrolytic flocculation for recovery of microalgae. Resources, Conservation, and Recycling. (19), 1.

Pringle, J. D., C. K. Tseng. (1989). Overview of a workshop on production and utilization of commercial 

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Roesijadi, G., A. E. Copping, M. H. Huesemann, J. Forster, and J. R. Benemann. (2008). Techno-economic feasibility analysis of offshore 

seaweed farming for bioenergy and biobased products. Battelle Pacific Northwest Division Report Number PNWD-3931. 

Saidam, M.Y., D. Butler. (1996). Algae removal by horizontal flow rock filters. Advances in Slow Sand and 

Alternative Biological Filtration. 327.

Sim, T.S., A. Goh, E.W. Becker. (1988). Comparison of centrifugation, dissolved air flotation and drum 

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The case of ascophyllum nodosum. Cah. Biol. Mar 42, 63-70.
42 5. Extraction of Products from Algae 

are attempting to bypass this step—the dynamics of 

extraction in aqueous phase systems serves as a starting 

place for industrial-scale extraction operations. 

Lipid extraction includes the following approaches: 

solvent-based extraction relying on microwaves and or 

sonication for cell disruption; using solvents to “milk” algal 

cells without disrupting cellular functions; and extraction 

bypass schemes that attempt to engineer algal systems 

that secrete products directly into the growth medium. 

Mechanical Disruption (i.e., Cell Rupture)

Algal biofuel schemes that rely on the accumulation of 

intra-cellular lipids are the focus of this discussion. To 

be successful, any extracting solvent must be able to (1) 

penetrate through the matrix enclosing the lipid material, 

(2) physically contact the lipid material, and (3) solvate the 

lipid. As such the development of any extraction process 

must also account for the fact that the tissue structure 

and cell walls may present formidable barriers to solvent 

access. This generally requires that the native structure 

of the biomass must be disrupted prior to extraction. 

Effective mechanical disruption can help offset the need 

to use elevated temperature and pressure processes that 

force the solvent into contact with desired biopolymers. 

Different methods can be used to disrupt the cell membrane 

prior to the application of the extraction solvents. 

Mechanical disruption can include cell homogenizers, 

bead mills (or bead-beating), ultrasounds, and autoclaving 

(Mata et al., 2010). Non-mechanical methods include 

process such as freezing, application of organic solvents, 

osmotic shock, and acid, base, and enzyme reactions (Mata 

et al., 2010). The use of microwaves to disrupt cells and 

increase efficiencies of vegetable lipid and oil extraction 

is a promising development (Cravotto et al., 2008; Virot 

et al., 2008), though applications outside of analytical 

labs are unclear. For waste treatment, pretreatment of 

sewage sludge with “focused pulse” sonication has been 

shown to improve methane gas production and biosolids 

reduction in sludge digestion (Rittman et al., 2008). 

Recent work on extraction of lipids from three different 

types of oleaginous microalgae compared bead beating, 

sonication, autoclaving, osmotic shock, and microwaves 

and suggested that microwave disruption prior to solvent 

extraction is the most efficient method (Lee et al., 2010). 

5. Extraction of Products from Algae 

While relatively limited volumes of bioproducts are 

currently produced from algal feedstocks, algal biomass 

suffers from a lack of well-defined and demonstrated 

industrial-scale methods for extracting and separating of 

oils and lipids required for enabling biofuel production. 

Existing extraction techniques are mainly suitable for 

analytical- and laboratory-scale procedures, or for the 

recovery/removal of high-value products. To produce 

algal biofuels as competitive bulk commodity, extraction 

techniques employed must be efficient and effective. 

Extraction depends on identifying the particular biological 

component for extraction, which is dependant on the 

algal species and growth status. Additionally, different 

harvest process operations (discussed in the Chapter 4) 

operations could affect extraction processes, as well as the 

fuel conversion process. While many terrestrial feedstocks 

can be removed from their environment at total solids 

>40%, microalgae and cyanobacteria may be cultivated 

as single cells suspended in water at concentrations below 

1% solids. While macroalgae are more like traditional 

feedstocks, different logistical challenges arise from 

their offshore production and harvesting. Many effective 

extraction techniques require concentrated substrates, thus 

a high degree of concentration may be necessary before 

some types of extraction can begin. For this reason, 

some algae-to-biofuels processes attempt to bypass the 

extraction step by either converting whole algal biomass or 

by inducing the secretion of the desired product directly. 

A shortfall of relevant information on efficient extraction 

of lipids and oils at larger-scale is limiting the algal-based 

biofuel development. Laboratory-scale comparisons of 

extraction of lipids from microalgae (Lee et al., 2010) and 

macroalgae (Aresta, Dibenedetto, and Barberio, 2005) 

have been carried out, but these techniques often rely 

on freeze dried, pulverized biomass. While considerable 

knowledge exists for the separation of plant biomass 

lipid extracts and preparation for conversion to biodiesel 

(Zhang et al., 2003), little is known about the scaleup separation challenges for extracted algal lipids. 

5.1 Current Practices for 

Lipid Extraction

The basis for lipid extraction from algal biomass is 

largely in the realm of laboratory-scale processes that 

serve analytical rather than biofuel production goals. 

Assuming a system that requires extraction of oils and 

lipids from harvested biomass—as noted, some systems 
5. Extraction of Products from Algae 43

Application of Organic Two-Solvent Systems for 

Lipid Extraction from Microalgae:

Iverson et al. (2001) found that the Bligh and Dyer method 

grossly underestimated the lipid content in samples of 

marine tissue that contained more than 2% lipids but 

worked well for samples that contained less than 2% 

lipids. The sequence of solvent addition can also affect 

extraction (Lewis et al., 2000). Starting from freeze dried 

biomass, it has been demonstrated that the extraction of 

lipids was significantly more efficient when solvents were 

added in order of increasing polarity (i.e. chloroform, 

methanol, and then water) (Lewis, 2000). They explained 

their results in terms of initial contact of the biomass with 

nonpolar solvents weakening the association between the 

lipids and cell structure, prior to their dissolution in the 

monophasic system of water, chloroform, and methanol. 

These important results have a key impact on liquid phase 

extraction systems applied to “wet” biomass because they 

suggest that the water will form a solvent shell around the 

lipids, making it more difficult for less polar solvents such 

as chloroform to contact, solubilize, and extract the lipids. 

It is also noteworthy that the extraction efficiency was not 

improved (when water was added first), despite the added 

agitation in the form of sonication or additional methanol. 

Direct Transesterification of Lipids into 

Fatty Acid Methyl Esters (FAMES)

To increase analytical efficiency, Lepage and Roy (1984) 

proposed the direct transesterification of human milk and 

adipose tissue without prior extraction or purification for 

improved recovery of fatty acids. In general, this approach 

suggested that a one-step reaction that added the alcohol 

(e.g., methanol) and acid catalyst (e.g., acetyl chloride) 

directly to the biomass sample and followed with heating 

at 100 ̊C for an hour under sealed cap would increase 

fatty acid concentrations measured (as compared to 

Bligh and Dyer co-solvent system), give relatively high 

recoveries of volatile medium chain triglycerides, and 

eliminate the need to use antioxidants to protect unsaturated 

lipids. This method was applied to dried microalgal 

biomass in a modified approach to include hexane in 

the reaction phase in order to avoid a final purification 

step (Rodriguez-Ruiz et al., 1998). It was found that the 

entire reaction could be shortened to 10 minutes if the 

mixture was incubated at 100 ̊C under a sealed cap. 

Continuing efforts along this path, it was found that when 

applying direct transesterification using an acid catalyst 

(i.e., acetyl chloride), the efficiency of the reaction 

increased when a second “less polar” solvent such as 

diethyl ether or toluene was mixed with the methanol to 

modify the polarity of the reaction medium (Carvalho and 

Malcata, 2005). In general, these findings suggest that 

Organic Co-solvent Mixtures

The concept of like dissolves like is the basis behind the 

earliest and well-known co-solvent extraction procedure 

(Bligh and Dyer, 1959). After the extraction reaction is 

complete, water (which is not miscible with chloroform) is 

added to the co-solvent mixture until a two-phase system 

develops in which water and chloroform separate into 

two immiscible layers. The lipids mainly separate to the 

chloroform layer and can then be recovered for analysis. 

Chloroform will extract more than just the saphonifiable 

lipids (i.e., the unsaponifiable lipids such as pigments, 

lipoproteins, and other lipid and non-lipid contaminants) 

(Fajardo et al., 2007). Consequently, other combinations 

of co-solvents have been proposed for the extraction of 

lipids: hexane/isopropanol for tissue (Hara & Radin, 

1978); dimethyl sulfoxide/petroleum ether for yeast 

(Park et al., 2007); hexane/ethanol for microalgae 

(Cartens et al., 1996); and hexane/isopropanol for 

microalgae (Nagle & Lemke, 1990). The hexane system 

has been promoted because hexane and alcohol will 

readily separate into two separate phases when water is 

added, thereby improving downstream separations. 

Similarly, less volatile and toxic alcohols (e.g., ethanol and 

isopropanol) have been suggested in place of methanol. 

One example is the hexane/ethanol extraction co-solvent 

system (Grima et al., 1994). In other cases, single alcohol 

(e.g., 1-butanol and ethanol) solvents have been tried 

(Nagle & Lemke, 1990). In these applications, the alcohol 

is first added as the extracting solvent. Separation is then 

achieved by adding both hexane and water in proportions 

that create a two phase system (hexane and an aqueous 

hydroalcoholic) that partition the extracted lipids into 

the nonpolar hexane (Fajardo et al., 2007). In general, 

applications using pure alcohol (ethanol and 1-butanol) 

performed similarly, if not slightly better than alcohol/

hexane mixtures, but never more than 90% of the Bligh and 

Dyer co-solvent method. More, pure alcohol solutions of 

greater carbon length (such as butanol) have not compared 

well against the hexane/ethanol co-solvent system. 

These results suggest that the two most important criteria 

when selecting a co-solvent system to extract lipids are: 

(1) the ability of a more polar co-solvent to disrupt the cell 

membrane and thus make it sufficiently porous and

(2) the ability of a second less polar co-solvent to better 

match the polarity of the lipids being extracted.

To avoid the use of elevated temperature and pressure to

push the solvent into contact with the analyte (at the cost 

of a very high input of energy), disruption of the cell

membrane may be necessary. 
44 5. Extraction of Products from Algae 

ASE is more efficient if extracting solvent, sample-solvent 

ratio, extraction temperature, and time have been optimized 

(Denery et al., 2004). Denery and coworkers optimized

 the extraction of carotenoids from Dunaliella salina

and showed that higher or equal extraction efficiencies 

(compared to traditional solvent technology) could be 

achieved with the use of less solvent and shorter extraction 

times. The performance of ASE extraction was compared 

to that of traditional Folch method for microalgae grown 

on dairy manure effluent (Mulbry et al., 2009). The 

ASE , depending on the solvent, extracted 85 - 95% 

of the fatty acid content in the harvested microalgae 

compared to 44 - 55% of the fatty acids extracted by 

the Folch method in the first solvent extraction cycle. 

What remains unclear is the effectiveness of such 

an approach at large scale in terms of how to handle 

large amounts of biomass, separate out desirable 

lipids, and optimize the energy cost. The latter is also 

noteworthy in the context that ASE by definition uses 

non-aqueous solvents and therefore, must use dried 

biomass, a step that also requires energy input.

Selective Extraction

Hejazi et al. (2002) proposed the two-phase system of 

aqueous and organic phases for the selective extraction of 

carotenoids from the microalgae Dunaliella salina. Their 

observations were that solvents with lower hydrophobicity 

reach critical concentrations more easily and in the 

process, break down the cell membrane. By using solvents 

of higher hydrophobicity, the effect of the solvent on 

the membrane decreased and the extraction efficiency 

for both chlorophyll and β-carotene decreased as well. 

By applying a measurement of solvent hydrophobicity 

based on the partition coefficient of the solvent in a twophase system of octanol and water, screening viability 

and activity tests of Dunaliella salina in the presence of 

different organic phases indicated that cells remained 

viable and active in the presence of organic solvents with 

a log P (octanol ) > 6 and that β-carotene can be extracted 

more easily than chlorophyll by biocompatible solvents. 

This work has served as the basis for the development of 

a technology that proposes to use solvents such as decane 

and dodecane in the presence of live microalgal cells, 

concentrated for the extraction of triglycerides without 

loss of cell viability and extraction of membrane-bound 

free fatty acids. Conceptually, the cells can be returned 

to their original bioreactor for continued growth and 

production of triglycerides for biofuels production. For 

example, some have proposed a modified technique to 

“milk” oils or neutral lipids from algae using biocompatible 

solvents and applied sonication. If this process can be 

the effectiveness of the second co-solvent (i.e., reaction 

medium) depends upon its ability to solubilize the target 

lipids coupled with its miscibility with methanol. 

All the preceding co-solvent systems, however, 

remain largely bench-scale methods that are difficult 

to scale up to industrial processes due to the actual 

solvent toxicity and the low carrying capacity of the 

solvents (i.e., it is only efficient on biomass samples 

containing less than 2% w/w lipids). Accordingly, 

single solvent systems at elevated temperature and 

pressure have gained favor for two principle reasons: 

• the elevated temperature and pressure increase the 

rate of mass transfer and degree of solvent access 

to all pores within the biomass matrix and;

• the elevated pressures can reduce the dielectric 

constant of an otherwise immiscible solvent (and 

by analogy, the polarity) to values that match the 

polarity of the lipids (Herrero et al., 2006). 

Consequently, the issue of solvent access to the material 

being extracted is as important as the miscibility of the 

analyte in the solvent. This observation is a key driving 

force behind the consideration of solvent extraction 

systems at elevated temperature and pressure. 

Accelerated Solvent Extraction

Accelerated solvent extraction (ASE) was first proposed 

in the mid 1990s (Richter et al., 1996), using the 

technique on 1 - 30 g samples of dried biomass. ASE 

uses organic solvents at high pressure and temperatures 

above their boiling point. In general, a solid sample 

is enclosed in a sample cartridge that is filled with an 

extraction fluid and used to statically extract the sample 

under elevated temperature (50 - 200 ̊C) and pressure 

(500 - 3000 psi) conditions for short time periods 

(5 - 10 min). Compressed gas is used to purge the 

sample extract from the cell into a collection vessel. 

ASE is applicable to solid and semi-solid samples that 

can be retained in the cell during the extraction phase 

(using a solvent front pumped through the sample at the 

appropriate temperature and pressure). It has been proposed 

for the extraction of liquid extracts (Richter et al., 1996; 

Denery et al., 2004) and lipids from microalgae (Schäfer, 

1998). In addition to improving yields and reducing 

extraction time, ASE can also be applied to remove coextractable material from various processes, to selectively 

extract polar compounds from lipid-rich samples, and 

to fractionate lipids from biological samples (ref). 
5. Extraction of Products from Algae 45

extraction techniques have been used in the commercial 

extraction of substances from solid substrates, e.g. 

caffeine from coffee beans, for more than two decades 

(Brunner, 2005). The majority of applications have used 

CO2 because of its preferred critical properties (i.e., 

moderate critical temperature of 31.1 ̊C and pressure of 

73.9 bar), low toxicity, and chemical inertness (Luque de 

Castro et al., 1999), but other fluids used have included 

ethane, water, methanol, ethane, nitrous oxide, sulfur 

hexafluoride, as well as n-butane and pentane (Herrero et 

al., 2006). The temperature and pressure above the critical 

point can be adjusted as can the time of the extraction. 

Supercritical extraction is often employed in batch mode, 

but the process can also be operated continuously (Brunner, 

2005). One of the more attractive points to supercritical 

fluid extraction is that after the extraction reaction has 

been completed and the extracted material dissolved into 

the supercritical fluid, the solvent and product can be 

easily separated downstream once the temperature and 

pressure are lowered to atmospheric conditions. In this 

case, the fluid returns to its original gaseous state while 

the extracted product remains as a liquid or solid. 

Supercritical fluid extraction has been applied for the 

extraction of essential oils from plants (Reverchon et 

al., 2006), as well as functional ingredients and lipids 

from microalgae (Mendes et al., 1994; Metzger and 

Largeau, 2005). Lipids have been selectively extracted 

from macroalgae at temperatures of 40 - 50 ̊C and 

pressures of 241 - 379 bar (Chueng, 1999). However, 

economical production of biofuels from oleaginous 

microalgae via supercritical processing is challenged 

by the same issues of energy-intensive processing and 

scaling up the process that is developed mainly for 

analytical usage. Use of methanol as the solvating fluid 

has the effect of converting lipids, via transesterification, 

to biodiesel (see Chapter 6 for more detail). 

Heterotrophic Production

Other methods for extraction and fractionation include 

the production of oils using heterotrophic algae. In this 

scenario, non-photosynthetic algae are grown using 

sugars as energy source and using standard industrial 

fermentation equipment (Barclay et al., 1994). Some 

private companies have engineered algae that secrete oil 

into the fermentation media that can be recovered and 

later refined into a biofuel; this approach significantly 

reduces the capital and operating cost for an extraction 

process. The potential benefits of this approach are the 

use of standard fermentation systems, higher productivity 

compared to photosynthetic systems, ease of scale-up, 

avoidance of expensive extraction scheme(s), the ability to 

applied to microalgae slurries with suspended solid 

concentrations as low as 1 wt%, this method may provide 

a unique avenue for the selective extraction of lipids 

suitable for biofuels (e.g., triglycerides) that excludes 

the extraction of lipids that cannot be transesterified, 

as well as pigments (such as chlorophyll), which can 

be difficult to separate from the desired lipids. 

Subcritical Water Extraction

Subcritical water extraction (also known as hydrothermal 

liquefaction) is based on the use of water, at temperatures 

just below the critical temperature, and pressure high 

enough to keep the liquid state (Soto and Luque de Castro, 

2001) . The technique, originally termed “pressurized hot 

water extraction,” was initially applied to whole biomass 

hemicellulose as a pretreatment prior to its use as a 

fermentation substrate (Mok et. al., 1992). More recently, 

however, it has been applied for the selective extraction 

of essential oils from plant matter (Eikani et al., 2007), 

functional ingredients from microalgae (Herrero et al., 

2006), and saponins from oil-seeds (Güçlü-Üstündağ et 

al., 2007). The basic premise to subcritical water extraction 

is that water, under these conditions, becomes less polar 

and organic compounds are more soluble than at room 

temperature. There is also the added benefit of solvent 

access into the biomass matrix that occurs at the higher 

temperatures as discussed above. In addition, as the water is 

cooled back down to room temperature, products miscible 

at the high temperature and pressure become immiscible 

at lower temperatures and can be easily separated. Some 

of the more important advantages described for subcritical 

water extraction include shorter extract times, higher 

quality of extracts, lower costs of the extracting agent, 

and environmental compatibility (Herrero et al., 2006). 

With respect to microalgae, however, whether grown 

phototrophically or heterotrophically, one of the more 

attractive aspects is the use of water as the solvent, 

thereby eliminating the need for the dewatering step. A 

major constraint, however, as with accelerated solvent 

extraction, is the difficulty with designing a system at 

large scale and the high-energy load required to heat the 

system up to subcritical temperatures. Large-scale design 

will also require a significant cooling system to cool 

the product down to room temperature to avoid product 

degradation, creating additional energy use challenges.

Supercritical Fluid Extraction

Supercritical fluid extraction utilizes the enhanced solvating 

power of fluids above their critical point (Luque de 

Castro et al., 1999). It can be processed using solid and 

liquid feeds (Reverchon et al., 2006). Supercritical fluid 
46 5. Extraction of Products from Algae 

contact between the solvent and the solute. Increased 

pressure facilitates enhancing the transport of the solvent 

to the analytes that have been trapped in pores. The 

pressure also helps to force the solvent into matrices 

that would normally not be contacted by solvents under 

atmospheric conditions. Mechanical disruption can 

reduce the pressure and temperature requirements.

Separation of Desired Extracts from Solvent Stream 

Extraction processes can yield undesirable components, 

such as chlorophyll and non- transesterifiable lipids. 

Very little information is available on this critical 

step that is necessary before converting the algal 

biocrude into finished fuels and products.

Energy Consumption and Water Recycle

For sustainable biofuels production, the following 

benchmark can be considered: the extraction process 

per day should consume no more than 10% of the total 

energy load, as Btu, produced per day. As discussed in 

Section 4.3, a preliminary look at the energy balance 

does not suggest that this is an insurmountable barrier, 

but it does serve to highlight the need for innovation 

to achieve sustainable commercial-scale systems. 

maintain the integrity of the fermentation catalyst and use 

of sugar-based feedstocks. However, significant downsides 

to this approach include many of the same feedstock 

logistics challenges faced by the nascent lignocellulosic 

industry. Chief amongst is the logistical challenge of 

securing a sustainable biomass feedstock to supply to feed 

large-scale heterotrophic “algal-refinery” operations. 

5.2 Challenges

Presence of Water Associated with the Biomass 

The extraction process is affected by the choice of 

upstream and downstream unit operations and vice 

versa. The presence of water can cause problems at 

both ends at larger scales. When present in the bulk 

solution, water can either promote the formation of 

emulsions in the presence of ruptured cells or participate 

in side reactions. At the cellular level, intracellular 

water can prove to be a barrier between the solvent 

and the solute. In this context, the issue of solvent 

access to the material being extracted is as important 

as the miscibility of the analyte in the solvent. This is a 

principal motivation behind the application of extraction 

techniques at elevated temperatures and pressures.

Increasing the temperature helps to disrupt the solutematrix interactions and to reduce the viscosity and 

surface tension of the water, thereby improving the 

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48 6. Algal Biofuel Conversion Technologies 

products, and this conservation law must also hold 

true for the algae biorefineries of the future if they 

are to achieve significant market penetration.

A large number of potential pathways exist for the 

conversion from algal biomass to fuels. These pathways can 

be classified into the following three general categories: 

1) Those that focus on the direct algal production 

of recoverable fuel molecules (e.g., ethanol, 

hydrogen, methane, and alkanes) from 

algae without the need for extraction;

2) Those that process whole algal biomass 

to yield fuel molecules; and

3) Those that process algal extracts (e.g., lipids, 

carbohydrates) to yield fuel molecules. 

These technologies are primarily based on similar 

methods developed for the conversion of terrestrial 

plant-based oils and products into biofuels, although the 

compositional complexities of the output streams from 

algae must be dealt with before these can be applied 

effectively. Pros and cons of these pathways within each 

of these categories are discussed below, and a summary 

of each fuel-conversion technology is given. Inputs, 

complexity, cost, and yields are provided (where known), 

and key barriers and RD&D opportunities are listed. 

6.1 Direct Production of 

Biofuels from Algae

The direct production of biofuel through heterotrophic 

fermentation and growth from algal biomass has certain 

advantages in terms of process cost because it can 

eliminate several process steps (e.g., oil extraction) 

and their associated costs in the overall fuel production 

process. Heterotrophic growth also allows for maintaining 

highly controlled conditions, which first could be oriented 

toward biomass production and then oil production. Such 

a system can generate extremely high biomass (hundreds 

of grams per liter) and a high percentage of that biomass 

as lipid (well over 50%). The system is readily scaled up 

and there is an enormous potential to use various fixed 

carbon feedstocks (which would bring down the cost of 

production). These approaches are quite different from 

the usual algal biofuel processes that use algae to produce 

biological oils which is subsequently extracted and used as 

a feedstock for liquid fuel production, typically biodiesel. 

There are several biofuels that can be produced directly 

from algae, including alcohols, alkanes, and hydrogen. 

6. Algal Biofuel Conversion Technologies 

Potentially viable fuels that can be produced from algae 

range from gaseous compounds like hydrogen and methane, 

to alcohols and conventional liquid hydrocarbons, to 

pyrolysis oil and coke. Attractive targets for this effort, 

however, are the liquid transportation fuels of gasoline, 

diesel, and jet fuel. These fuel classes were selected as the 

best-value targets because 1) they are the primary products 

that are currently created from imported crude oil for the 

bulk of the transportation sector, 2) they have the potential 

to be more compatible than other biomass-based fuels with 

the existing fuel-distribution infrastructure in the U.S., and 

3) adequate specifications for these fuels already exist.

The primary objective of this chapter is to summarize a 

number of potentially viable strategies for converting algal 

biomass into replacements for petroleum gasoline, diesel, 

and jet fuel. When a fuel meets all customer requirements, 

it is referred to as “fit for purpose.” While a successful 

fuel-conversion strategy will address the full range of 

desired fit-for-purpose properties (e.g., distillation range, 

ignition characteristics, energy density, etc.), these desired 

fuel characteristics are driven primarily by customer 

requirements and are discussed later in Chapter 8. This 

chapter focuses on fuel conversion strategies from a variety 

of perspectives to establish the current state-of-the-art, 

as well as identify critical challenges and roadblocks.

Several emerged the Algal Roadmap Workshop in 

relation to conversion of algal feedstocks to fuels. These 

are noted here to help establish a reasonable framework 

for the most promising concepts for algal biofuels. 

• First, the feedstock, conversion process, and 

final fuel specifications are highly interdependent 

and must be considered together if an optimal 

process is to be identified. As a result, accurate 

and detailed feedstock characterization (including 

both composition and variability) is essential, 

since this is an upstream boundary condition for 

the entire downstream fuel-conversion process. 

• Second, life cycle analysis of energy and carbon will 

be a key tool in selecting the preferred fuel conversion 

technologies from those discussed in this chapter. 

• Third, the greatest challenge in algal fuel conversion is 

not likely to be how to convert lipids or carbohydrates 

to fuels most efficiently, but rather how best to use 

the algal remnants after the lipids or other desirable 

fuel precursors have been extracted. All of the 

petroleum feedstock that enters a conventional 

petroleum refinery must leave as marketable 
6. Algal Biofuel Conversion Technologies 49

In addition to ethanol, it is possible to use algae to produce 

other alcohols, such as methanol and butanol, using a 

similar process technology, although the recovery of 

heavier alcohols may prove problematic and will need 

further R&D. The larger alcohols have energy densities 

closer to that of gasoline but are not typically produced 

at the yields that are necessary for commercial viability. 

Alkanes

In addition to alcohols, alkanes may be produced directly 

by heterotrophic metabolic pathways using algae. Rather 

than growing algae in ponds or enclosed in plastic 

tubes that utilize sunlight and photosynthesis, algae can 

be grown inside closed reactors without sunlight. The 

algae are fed sugars, the cheap availability of which 

is a key consideration for cost-effective production of 

biofuels; these sugars are themselves available from 

renewable feedstocks such as lignocellulosic biomass, 

in a pressure and heat-controlled environment. This 

process can use different strains of algae to produce 

different types of alkanes; some algae produce a mix of 

hydrocarbons similar to light crude petroleum. These 

alkanes can theoretically be secreted and recovered 

directly without the need for dewatering and extraction, 

but more often are associated with the algae and thus must 

be recovered through dewatering and extraction. With 

further processing, a wide variety of fuels can be made. 

The process of growing the algae heterotrophically may 

present some advantages over typical photoautotrophicbased technologies. First, keeping the algae “in the dark” 

causes them to produce more alkanes than they do in the 

presence of sunlight. While their photosynthetic processes 

are suppressed, other metabolic processes that convert 

sugar into alkanes can become active. Second, some have 

shown the growth rate of the algae to be much higher 

than traditional methods (Xu et al., 2006). This is possible 

because instead of getting energy for growth from sunlight, 

the algae get concentrated energy from the sugars fed into 

the process. These higher cell concentrations reduce the 

amount of infrastructure needed to grow the algae, and 

enable more efficient dewatering if is actually required. 

Using algae to convert cellulosic materials, such as 

switchgrass or wood chips, to oil may have an advantage 

over many other microorganisms under development 

for advanced biofuel production. When lignocellulosic 

biomass is pretreated to allow for enzymatic hydrolysis 

for production of sugars, many toxic byproducts are 

released including acetate, furans, and lignin monomers. 

In most other processes, these toxic compounds can 

add process costs by requiring additional conditioning 

Alcohols

Algae, such as Chlorella vulgaris and Chlamydomonas 

perigranulata, are capable of producing ethanol and other 

alcohols through heterotrophic fermentation of starch 

(Hon-Nami, 2006; Hirayama et al., 1998). This can be 

accomplished through the production and storage of 

starch via photosynthesis within the algae, or by feeding 

sugar to the algae directly, and subsequent anaerobic 

fermentation of these carbon sources to produce ethanol 

under dark conditions. If these alcohols can be extracted 

directly from the algal culture media, the process 

may be drastically less capital- and energy-intensive 

than competitive algal biofuel processes. The process 

would essentially eliminate the need to separate the 

biomass from water and extract and process the oils.

This process typically consists of closed photobioreactors 

utilizing sea-water with metabolically enhanced 

cyanobacteria that produce ethanol or other alcohols while 

being resistant to high temperature, high salinity, and 

high ethanol levels—previous barriers to commercialscale volumes (Hirano et al., 1997). There have been 

reports of preliminary engineered systems, consisting of 

tubular photobioreactors (Hirano et al., 1997). One key 

aspect of the system is that a source of cheap carbon, such 

as a power plant, is typically used to supply CO2 to the 

bioreactors to accelerate the algae growth. An example 

of this process technology links sugar production to 

algal photosynthesis. There are claims that this process 

may consume more than 90% of the system’s CO2

through photosynthesis, wherein a portion of the carbon 

in these sugars is converted into ethanol. The ethanol 

is secreted into the culture media and is collected in 

the headspace of the reactor, purified, and stored. 

This technology is estimated to yield 4,000 - 6,000 gallons 

per acre per year, with potential increases up to 10,000 

gallons per acre per year within the next 3 to 4 years 

with significant R&D. It is theoretically estimated that 

one ton of CO2 is converted into approximately 60 - 70 

gallons of ethanol with this technology. With such yields, 

the price of captured CO2 becomes significant, and may 

require a price less than or equal to $10 per ton to remain 

cost-competitive. Further breakthroughs that enable more 

efficient production systems and the development of new 

process technologies may be critical in terms of long-term 

commercial viability. Scaling of these systems to largescale commercial biorefineries will also require significant 

advances in process engineering and systems engineering. 

Metabolic pathway engineering within these algae, enabled 

by metabolic flux analysis and modern genomics tools, may 

further help in producing a commercially viable organism. 
50 6. Algal Biofuel Conversion Technologies 

There are four major categories of conversion 

technologies that are capable of processing whole 

algae: pyrolysis, gasification, anaerobic digestion, 

and supercritical processing (Exhibit 6.1). 

Pyrolysis

Pyrolysis is the chemical decomposition of a condensed 

substance by heating. It does not involve reactions with 

oxygen or any other reagents but can frequently take 

place in their presence. The thermochemical treatment of 

the algae, or other biomass, can result in a wide range of 

products, depending on the reaction parameters. Liquid 

product yield tends to favor short residence times, fast 

heating rates, and moderate temperatures (Huber et al., 

2006). Pyrolysis has one major advantage over other 

conversion methods, in that it is extremely fast, with 

reaction times of the order of seconds to minutes.

Pyrolysis is being investigated for producing fuel from 

biomass sources other than algae. Although synthetic diesel 

fuel cannot yet be produced directly by pyrolysis of algae, a 

degradable alternative liquid called bio-oil can be produced. 

The bio-oil has an advantage that it can enter directly 

into the refinery stream and, with some hydrotreating and 

hydrocracking, produce a suitable feedstock for generating 

standard diesel fuel. Also, higher efficiency can be achieved 

by the so-called “flash pyrolysis” technology, where finely 

ground feedstock is quickly heated to 350 - 500 ̊C for 

less than 2 seconds. For flash pyrolysis, typical biomass 

feedstocks must be ground into fine particles. This is 

one area where algae have a major advantage over other 

biomass sources because it exists fundamentally in small 

units and has no fiber tissue to deal with. Several pilot 

plants for fast pyrolysis of biomass have been built in the 

past years in Germany, Brazil, and the United States, but 

bio-oil from pyrolysis is not a commercial product at the 

current time (Bridgwater, 2004). Even with the increased 

interest in converting biomass into liquid transportation 

fuels, it appears fast pyrolysis to create bio-oil, especially 

from algae, is a relatively new process (Bridgwater, 2007). 

There are several reports on the pyrolysis of algae in the 

scientific literature (Demirbas, 2006; Miao and Wu, 2004). 

A significant roadblock in using pyrolysis for algae 

conversion is moisture content, and significant dehydration 

must be performed upstream for the process to work 

efficiently. It is unclear exactly how much more difficult 

it would be to convert algae into a bio-oil compared 

to other biomass sources due to uncertainties in the 

ability to dehydrate the feedstock; no comprehensive 

and detailed side-by-side comparison was found in 

the scientific literature. It appears that pyrolysis will 

not be cost-competitive over the short-term unless an 

steps or the concentration of biomass hydrolysate 

in the conversion step. Algae may prove to be more 

resistant to these compounds and sugar conversion. 

Hydrogen

The production of hydrogen derived from algae has 

received significant attention over several decades. 

Biological production of hydrogen (i.e., biohydrogen) 

technologies provide a wide range of approaches to 

generate hydrogen, including direct biophotolysis, 

indirect biophotolysis, photo-fermentation,

and dark-fermentation (see Chapter 2). 

There are several challenges that remain before 

biological hydrogen production can be considered a viable 

technology. These include the restriction of photosynthetic

 hydrogen production by accumulation of a proton 

gradient, competitive inhibition of photosynthetic

hydrogen production by CO2, requirement for 

bicarbonate binding at photosystem II (PSII) for efficient 

photosynthetic activity, and competitive drainage of 

electrons by oxygen in algal hydrogen production.

The future of biological hydrogen production depends 

not only on research advances, i.e., improvement in 

efficiency through genetically engineered algae and/or the 

development of advanced photobioreactors, but also 

on economic considerations, social acceptance, and the 

development of a robust hydrogen infrastructure 

throughout the country. 

6.2 Processing of Whole Algae

In addition to the direct production of biofuels from 

algae, the whole algae can be processed into fuels 

instead of first extracting oils and post-processing. These 

methods benefit from reduced costs associated with 

the extraction process, and the added benefit of being 

amenable to processing a diverse range of algae, though 

at least some level of dewatering is still required. 

Macroalgae has specifically received some attention as a 

gasification feedstock and initial work shows that while 

some key differences exist as compared to terrestrial 

crops, certain species are suitable for gasification (Ross et 

al., 2008). Polysaccharides, such as mannitol, laminarin, 

and fucoidin, represent the main macroalgae biochemical 

feedstocks for conversion to liquid fuels (McHugh, 2003). 

Lipid content of a variety of macroalgal species is typically 

less than 5% of total dry weight (McDermid & Stuercke, 

2003), too low for conversion to biodiesel, although 

concentrations approaching 20% are reported in some 

species (Chu et al., 2003; McDermid & Stuercke, 2003).
6. Algal Biofuel Conversion Technologies 51

Gasification

Gasification of the algal biomass may provide an extremely 

flexible way to produce different liquid fuels, primarily 

through Fischer-Tropsch Synthesis (FTS) or mixed 

alcohol synthesis of the resulting syngas. The synthesis 

of mixed alcohols using gasification of lignocellulose is 

relatively mature (Phillips, 2007; Yung et al., 2009), and it 

is reasonable to expect that once water content is adjusted 

for, the gasification of algae to these biofuels would be 

comparatively straightforward. FTS is also a relatively 

mature technology where the syngas components (CO, CO2, 

H2O, H2, and impurities) are cleaned and upgraded to usable 

liquid fuels through a water-gas shift and CO hydrogenation 

(Okabe et al., 2009; Srinivas et al., 2007; Balat, 2006). 

Conversion of bio-syngas has several advantages over other 

methods. First and foremost, it is possible to create a wide 

variety of fuels with acceptable and known properties. 

Additionally, bio-syngas is a versatile feedstock and it 

can be used to produce a number of products, making 

the process more flexible. Another advantage is the 

possibility to integrate an algal feedstock into an existing 

thermochemical infrastructure. It may be possible to feed 

algae into a coal gasification plant to reduce the capital 

investment required, address the issue of availability 

inexpensive dewatering or extraction process is also 

developed. Additionally, since pyrolysis is already a 

relatively mature process technology, it is expected 

that only incremental improvements will occur and a 

breakthrough in conversion efficiency appears unlikely.

While algal bio-oil may be similar to bio-oil from 

other biomass sources, it may have a different range 

of compounds and compositions depending on the 

type of algae and upstream processing conditions 

(Zhang et al., 1994). Another research paper 

demonstrated that the bio-oil produced by pyrolysis 

of algae can be tailored by carefully controlling the 

algal growth conditions (Miao and Wu, 2004). 

Unfortunately, there are also significant gaps in the 

information available about the specifications for 

converting algal bio-oil and the resulting products. The 

optimal residence time and temperature to produce different 

algal bio-oils from different feedstocks need to be carefully 

studied. Work also needs to be performed to understand the 

detailed molecular composition of the resulting bio-oils. 

Additionally, research is needed on the catalytic conversion 

of the resulting algal bio-oils. Another area of interest is the 

development of stabilizers for the viscosity of the bio-oil 

and acid neutralizing agents, so the bio-oil may be more 

easily transported throughout the upgrading process. 

Algae

Pyrolysis Gasification Supercritical

Fluids

Anaerobic

Digestion

SynGas

Liquid or

Vapor Fuel

Catalytic

Upgrading

Catalytic

Upgrading

Biogas

Fischer

Tropsch

Higher Alcohol

Synthesis

MeOH

EtOH, etc. Hydrogen Liquid

Hydrogen Fuels

Transportation

Fuels - Liquid or

Gas

Exhibit 6.1 Schematic of the potential conversion 

routes for whole algae into biofuels
52 6. Algal Biofuel Conversion Technologies 

for indirect gasification of algae. It would be desirable to 

determine the feasibility of using the oxygen generated 

by algae for use in the gasifier to reduce or eliminate the 

need for a tar reformer. Also, it would be useful to leverage 

ongoing syngas-to-ethanol research using cellulosic.

Liquefaction

Direct hydrothermal liquefaction in subcritical water 

(defined as water held in a liquid state above 100oC by 

applying pressure) is a technology that can be employed to 

convert wet algal biomass to a range of liquid fuels (Patil et 

al., 2008). This technology is a representation of the natural 

geological processes known to be involved in the formation 

of petroleum-based fossil fuels realized over greatly 

shortened time scales. These technologies harness the high 

activity of water in subcritical environments that is capable 

of decomposing the algal biomass into smaller molecules 

of higher energy density or more valuable chemicals. The 

main product of this liquefaction process is a “bio-crude” 

that typically accounts for 45% wt. of the feedstock on a 

dry ash free basis and has energy content that is comparable 

to diesel and can be upgraded further. There are reports 

(Goudriaan et al., 2000) that claim the thermal efficiency, 

defined as the ratio of heating values of bio-crude products 

and feedstock plus external heat input, as high as 75%. 

Prior work in direct liquefaction of biomass was very 

active, and there are a few reports that used algal biomass 

as a feedstock. Liquefaction of Dunaliella tertiolecta

with a moisture content of 78.4 wt% produced an oil 

yield of about 37% (organic basis) at 300 ̊C and 10 MPa 

(Minowa et al., 1995). The oil obtained at a reaction 

temperature of 340 ̊C and holding time of 60 min had 

a viscosity of 150 - 330 mPas and a calorific value of 

36 kJ g−1, comparable to those of fuel oil. In the same 

report it was concluded that liquefaction technique was 

a net energy producer from the overall process energy 

balance. A maximum oil yield of 64% using Botryococcus 

braunii as a feedstock has also been reported. The 

algal biomass was processed by liquefaction at 300 ̊C, 

catalyzed by sodium carbonate (Sawayama et al., 1995). 

There have also been comparative studies that report the 

liquefaction technique was more effective for extraction 

of microalgal biodiesel than using the supercritical carbon 

dioxide (Aresta et al., 2005). Liquefaction of algae is 

considered a promising technological approach but due 

to limited information in hydrothermal liquefaction 

of algae to date, more research in this area is needed 

before it can become a commercially viable option.

for dedicated biomass plants, and improve the process 

efficiency through economy of scale. Additionally, since 

FTS is an exothermic process, it should be possible to use 

some of the heat for drying the algae during a harvesting/

dewatering process with a regenerative heat exchanger.

The key roadblocks to using FTS for algae are thought 

to be similar to those for coal (Yang et al., 2005), with 

the exception of any upstream process steps that may be 

a source of contaminants which will need to be removed 

prior to reaching the FT catalyst. FTS tends to require 

production at a very large scale to make the process 

efficient overall. However, the most significant problem 

with FTS is the cost of clean-up and tar reforming. Tars 

have high molecular weight and can develop during 

the gasification process. The tars cause coking of the 

synthesis catalyst and any other catalysts used in the 

syngas cleanup process and must be removed. The four 

basic mechanisms to deal with tar-related problems are:

• Fluidized-bed gasification and catalytic reforming

• Fluidized-bed gasification and solvent tar removal

• Fluidized-bed gasification and 

subsequent thermal tar cracker

• Entrained-flow gasification at high temperature

A demonstration plant for gasification of wood chips 

with catalytic cracking of the tar is currently being 

built in Finland in a joint venture of the Technical 

Research Centre of Finland (VTT), Neste Oil, and 

Stora Enso. A solvent tar removal demonstration was 

installed in a plant in Moissannes, France in 2006.

Tar formation can be minimized or avoided via entrainedflow gasification at high temperatures (Hallgren et al., 

1993). While this technology requires sub-millimeter 

sized particles, algae may have a unique advantage 

in this process. Typically, it is difficult to reach such 

a small size with other biomass sources and doing so 

usually requires pretreatment, but certain species of 

algae may not require pretreatment due to their inherent 

small size. Another approach for tar-free syngas was 

demonstrated in a pilot plant in Freiberg, Germany, 

built by Choren Industries GmbH. The pilot plant used 

two successive reactors. The first reactor was a lowtemperature gasifier that broke down the biomass into 

volatiles and solid char. The tar-rich gas was then passed 

through an entrained-flow gasifier where it was reacted 

with oxygen at high temperature. (Raffelt et al., 2006). 

Even though FTS is a mature technology, there are still 

several areas that should be investigated and require R&D. 

First, it is necessary to determine the optimum conditions 
6. Algal Biofuel Conversion Technologies 53

Supercritical Processing

Supercritical processing is a recent addition to the portfolio 

of techniques capable of simultaneously extracting 

and converting oils into biofuels (Demirbas, 2006). 

Supercritical fluid extraction of algal oil is far more efficient 

than traditional solvent separation methods, and this 

technique has been demonstrated to be extremely powerful 

in the extraction of other components within algae (Mendes, 

2007). This supercritical transesterification approach can 

also be applied for algal oil extracts. Supercritical fluids 

are selective, thus providing high purity and product 

concentrations. Additionally, there are no organic solvent 

residues in the extract or spent biomass (Demirbas, 2009). 

Extraction is efficient at modest operating temperatures, 

for example, at less than 50 ̊C, ensuring maximum 

product stability and quality. Additionally, supercritical 

fluids can be used on whole algae without dewatering, 

thereby increasing the efficiency of the process. 

The supercritical extraction process can be coupled with 

a transesterification reaction scheme to enable a “one 

pot” approach to biofuel production (Anitescu et al., 

2008). Although it has been only demonstrated for the 

simultaneous extraction and transesterification of vegetable 

oils, it is envisioned as being applicable for the processing 

of algae. In this process variant, supercritical methanol 

or ethanol is employed as both the oil extraction medium 

and the catalyst for transesterification (Warabi et al., 

2004). In the case of catalyst-free supercritical ethanol 

transesterification, it has been demonstrated that this 

process is capable of tolerating water, with a conversion 

yield similar to that of the anhydrous process in the 

conversion of vegetable oils. While the occurrence of 

water in the reaction medium appears as a factor in process 

efficiency, the decomposition of fatty acids is the main 

factor that limited the attainable ester content (Vieitez et 

al., 2008; Vieitez et al. 2009). Similar results have been 

observed for supercritical methanol processing of vegetable 

oils (Hawash et al., 2009). Because decomposition was 

a consequence of temperature and pressure conditions 

used in this study, further work should be focused on the 

effect of milder process conditions, in particular, lower 

reaction temperatures. In the case of combined extraction 

and transesterification of algae, further study will also 

be needed to avoid saponification. It also remains to 

be seen whether the processing of whole algae in this 

fashion is superior, in terms of yield, cost, and efficiency, 

to the transesterification of the algal oil extracts.

The economics of supercritical transesterification process, 

at least in the case of vegetable oil processing, have been 

shown to be very favorable for large-scale deployment. 

One economic analysis has been conducted based on a 

supercritical process to produce biodiesel from vegetable 

oils in one step using alcohols (Anitescu et al., 2008). 

It was found that the processing cost of the proposed 

supercritical technology could be near half of that of the 

actual conventional transesterification methods (i.e., $0.26/

gal vs. $0.51/gal). It is, therefore, theoretically possible 

that if the other upstream algal processing costs could 

be mitigated through the addition of a transesterification 

conversion process, the overall algal biorefinery 

could become cost-competitive with fossil fuels. 

The clear immediate priority, however, is to demonstrate 

that these supercritical process technologies can be 

applied in the processing of algae, either whole or its 

oil extract, with similar yields and efficiencies at a 

level that can be scaled to commercial production. In 

particular, it must be demonstrated that this process can 

tolerate the complex compositions that are found with 

raw, unprocessed algae and that there is no negative 

impact due to the presence of other small metabolites.

Anaerobic Digestion of Whole Algae

The production of biogas from the anaerobic digestion 

of macroalgae, such as Laminaria hyperbore and 

Laminaria saccharina, is an interesting mode of gaseous 

biofuel production, and one that receives scant attention 

in the United States (Hanssen et al., 1987). The use of 

this conversion technology eliminates several of the 

key obstacles that are responsible for the current high 

costs associated with algal biofuels, including drying, 

extraction, and fuel conversion, and as such may be a 

cost-effective methodology. Several studies have been 

carried out that demonstrate the potential of this approach. 

A recent study indicated that biogas production levels 

of 180.4 ml/g-d of biogas can be realized using a twostage anaerobic digestion process with different strains 

of algae, with a methane concentration of 65% (VergaraFernández et al., 2008). If this approach can be modified 

for the use of microalgae, it may be very effective 

for situations like integrated wastewater treatment, 

where algae are grown under uncontrolled conditions 

using strains not optimized for lipid production. 

6.3 Conversion of Algal Extracts

The conversion of extracts derived from algal sources is 

the typical mode of biofuel production from algae. There is 

an obvious and critical link between the type of extraction 

process used and the product composition, and as such, a 

fundamental and exhaustive understanding of the different 

types of inputs to the conversion technologies must be 

in place. The most common type of algal extracts under 

consideration are lipid-based, e.g., triacylglycerides, which 
54 6. Algal Biofuel Conversion Technologies 

water and free acids, and therefore, mitigate saponification 

and emulsification, enhancing the product recovery 

(Ataya et al., 2007). Though acid catalysts have these 

advantages, they are not currently preferred due to their 

lower activity than the conventional transesterification 

alkaline catalysts. Higher temperatures and longer reaction 

times are, therefore, generally required as a result. In 

order to compensate for this, heteropolyacids (HPA), 

such as H3PW12O40/Nb2O5, have been shown to lower the 

required temperatures and decrease the reaction times 

(Alsalme et al., 2008; Cao et al., 2008). Recently, it was 

shown that HPA-catalyzed transesterification of vegetable 

oil achieves higher reaction rates than conventional 

mineral acids due to their higher acid strength (L. Xu 

et al., 2008). The apparent higher activity of certain 

HPAs with respect to polyoxometallates of higher 

strength resulted in lower pretreatment temperatures. 

One recommended research focus would be to further 

develop these homogeneous catalysts to tolerate the 

contaminants expected to be present in algal extracts.

In addition to alternative catalysts, there are other 

processing variants that appear promising. An alternative 

heating system that can be used to enhance the kinetics of 

transesterification involves the use of microwaves (Refaat 

& El Sheltawy, 2008). When the transesterification reaction 

is carried out in the presence of microwaves, the reaction 

is accelerated and requires shorter reaction times. As a 

result, a drastic reduction in the quantity of co-products 

and a short separation time are obtained (Lertsathapornsuk 

can be converted into biodiesel. This section discusses 

chemical, biochemical, and catalytic processes that can 

be employed to convert algal extracts. (Exhibit 6.2).

Chemical Transesterification

The transesterification reaction is employed to convert 

triacylglycerols extracted from algae to FAMEs (fatty 

acid methyl esters), which is simply a process of 

displacement of an alcohol group from an ester by 

another alcohol (Demirbas, 2009). Transesterification 

can be performed via catalytic or non-catalytic reaction 

systems using different heating systems that are required 

to initiate the reaction. This technology is relatively 

mature and has been demonstrated to be the “gold 

standard” in the conversion of vegetable oils into biodiesel 

(Hossain et al., 2008). In addition to the classic basecatalyzed methanol approach, it has been shown that 

transesterification of algal oil can be achieved with ethanol 

and sodium ethanolate serving as the catalyst (Zhou & 

Boocock, 2006). The products of these reactions are 

typically separated by adding ether and salt water to the 

solution and mixing well. Biodiesel is then separated 

from the ether by a vaporizer under a high vacuum. 

Another route is found in acid-catalyzed transesterification 

reactions (Wahlen et al., 2008). The replacement of 

soluble bases by liquid acid catalysts such as H2SO4, HCl 

or H3PO4 is also considered an attractive alternative as 

the acidic catalysts are less sensitive to the presence of 

Algal Oil Extracts

Catalytic

Cracking

Enzymatic

Conversion

Chemical

Transesterfication

Biodiesel

(ME)

Catalytic

Upgrading

Gasoline,

Kerosene,

Diesel, Olefin

Aromatics Diesel

Liquid or

Vapor Fuel

Catalytic

Upgrading

Diesel

Exhibit 6.2 Schematic of the various conversion 

strategies of algal extracts into biofuels
6. Algal Biofuel Conversion Technologies 55

that a co-solvent mixture may be critical in defining 

the optimal reaction medium for the lipases. This work 

indicates that the use of this co-solvent mixture in the 

enzymatic biodiesel production has several advantages: 

(a) both the negative effects caused by excessive methanol 

and co-product glycerol can be eliminated completely; 

(b) high reaction rates and conversion can be obtained; 

(c) no catalyst regeneration steps are needed for lipase 

reuse; and (d) the operational stability of the catalyst is 

high. Again, as with other approaches, one of the most 

significant roadblocks to demonstrating the validity of 

this approach lies in the conversion of algal oil extracts 

at a commercial scale and at competitive prices. 

To that end, much R&D is needed in the discovery, 

engineering, and optimization of enzymes that are 

capable of producing these reactions in a variety of 

environments and on different types of oil feedstocks 

(Lopez-Hernandez et al., 2005). Bioprospecting for 

the enzymes in extreme environments may produce 

novel enzymes with desired characteristics that are 

more suitable for industrial applications (Guncheva 

et al., 2008). Enzyme immobilization may also play 

a key role in developing an economic method of 

biocatalytic transesterification (Yamane et al., 1998). 

Other important issues that need further exploration 

are developing enzymes that can lyse the algal 

cell walls; optimizing specific enzyme activity to 

function using heterogeneous feedstocks; defining 

necessary enzyme reactions (cell wall deconstruction 

and autolysin); converting carbohydrates into 

sugars; catalyzing nucleic acid hydrolysis; and 

converting lipids into a suitable diesel surrogate. 

Catalytic Cracking

The transesterification catalysts presented above are 

very strong and relatively mature in the field of biofuel 

production. Although very effective and relatively 

economical, these catalysts still require purification 

and removal from the product stream, which increases 

the overall costs. One potential solution to this is the 

development of immobilized heterogeneous and/

or homogeneous catalysts that are very efficient and 

inexpensive (McNeff et al., 2008). Acid and basic catalysts 

could be classified as Brönsted or Lewis catalysts. 

However, in many cases, both types of sites could be 

present and it is not easy to evaluate the relative importance 

of the two types of sites in the overall reaction in terms 

of efficiency and cost. Lewis acid catalysts, such as 

AlCl3 or ZnCl2, have been proven as a viable means of 

converting triacylglycerols into fatty acid methyl esters. 

et al., 2008). These preliminary results indicate that 

microwave processing may be cost-competitive with the 

more mature conversion processes currently available. 

In addition, catalysts may be used to enhance the 

impact of microwave irradiation (Yuan et al., 2008).

In the ultrasonic reactor method, ultrasonic waves cause 

the reaction mixture to produce and collapse bubbles 

constantly. This cavitation provides simultaneously 

the mixing and heating required to carry out the 

transesterification process (Armenta et al., 2007). Thus 

using an ultrasonic reactor for biodiesel production 

drastically reduces the reaction time, reaction temperatures, 

and energy input (Kalva et al., 2008). Hence the process 

of transesterification can run inline rather than using the 

time-consuming batch process used in traditional basecatalyzed transesterification (Stavarache et al., 2007). It is 

estimated that industrial-scale ultrasonic devices can allow 

for the processing of several thousand barrels per day, but 

will require further innovation to reach production levels 

sufficient for massive and scalable biofuel production.

Biochemical (Enzymatic) Conversion

Chemical processes give high conversion of triacylglycerols 

to their corresponding esters but have drawbacks such as 

being energy-intensive, difficulty in removing the glycerol, 

and require removal of alkaline catalyst from the product 

and treatment of alkaline wastewater. Use of biocatalysts 

(lipases) in transesterification of triacylglycerols for 

biodiesel production addresses these problems and 

offers an environmentally more attractive option to the 

conventional processes (Svensson and Adlercreutz, 

2008). Although enzymatic approaches have become 

increasingly attractive, they have not been demonstrated 

at large scale mainly due to the relatively high price of 

lipase and its short operational life caused by the negative 

effects of excessive methanol and co-product glycerol. 

These factors must be addressed before a commercially 

viable biochemical conversion process can be realized.

One critical area that needs to be addressed is the solvent 

and temperature tolerance of the enzymes in order to 

enable efficient biocatalytic processing. The presence of 

solvents is sometimes necessary to enhance the solubility 

of the triacylglycerols during the extraction process, 

and the enzymes used in the downstream conversion 

process must be able to function in the presence of these 

solvents to varying degrees to enable cost-effective 

biofuel production (Fang et al., 2006). There have been 

some recent reports of using a solvent engineering 

method to enhance the lipase-catalyzed methanolysis of 

triacylglycerols for biodiesel production (Su and Wei, 

2008; Liao et al., 2003). In particular, it has been noted 
56 6. Algal Biofuel Conversion Technologies 

The presence of a co-solvent, such as tehtrahydrofuran, 

can play a vital role in achieving high conversion 

efficiencies of up to 98% (Soriano et al., 2009). 

In another example, catalysts derived from the titanium 

compound possessing the general formula ATixMO, in 

which A represents a hydrogen atom or an alkaline metal 

atom, M a niobium atom or a tantalum atom, and x is an 

integer not greater than 7, were employed in vegetable oil 

transesterification. The catalysts obtained are stable and 

give high glycerol yield with high activities. A typical 

FAME yield of 91% and glycerol yield of 91% were 

obtained in a fixed-bed reactor at 200 ̊C and 35 bar, using 

HTiNbO3 as the catalyst. Vanadate metal compounds 

are stable, active catalysts during transesterification, 

with TiVO4 being the most active (Cozzolino et al., 

2006). This catalyst is also more active than HTiNbO3, 

producing the same yields with lower residence times. 

Double-metal cyanide Fe-Zn proved to be promising 

catalysts resulting in active transesterification of oil. 

These catalysts are Lewis acids, hydrophobic (at reaction 

temperatures of about 170 ̊C), and insoluble. Moreover, 

they can be used even with oils containing significant 

amounts of free fatty acids and water, probably due to the 

hydrophobicity of their surface. The catalysts are active 

in the esterification reaction, reducing the concentration 

of free fatty acids in non-refined oil or in used oil. Other 

catalyst examples include MgO, CaO, and Al2O3.

One of the most difficult challenges is finding an ideal 

heterogeneous catalyst that has comparable activity 

in comparison to the homogenous catalyst at lower 

temperatures than the ones currently used (~220 - 240°C). 

At these temperatures, the process pressure is high 

(40 - 60 bar), which translates to very costly plant design 

and construction requirements. Many of the catalysts 

presented above seem to be good candidates for industrial 

process development but must resist poisoning and the 

leaching of active components. There remain significant 

fundamental studies and unanswered questions that must 

be completed before these catalysts are fully understood. 

One particular concern is the stability and longevity of 

the catalysts in a representative reaction environment. 

Conversion to Renewable Diesel, 

Gasoline, and Jet Fuel 

All of the processes that take place in a modern petroleum 

refinery can be divided into two categories, separation 

and modification of the components in crude oil to yield 

an assortment of end products. The fuel products are a 

mixture of components that vary based on input stream 

and process steps, and they are better defined by their 

performance specifications than by the sum of specific 

molecules. As noted in chapter 8, gasoline, jet fuel, and 

diesel must meet a multitude of performance specifications 

that include volatility, initial and final boiling point, 

autoignition characteristics (as measured by octane number 

or cetane number), flash point, and cloud point. Although 

the predominant feedstock for the industry is crude oil, the 

oil industry has begun to cast a wider net and has spent 

a great deal of resources developing additional inputs 

such as oil shale and tar sands. It is worth noting that the 

petroleum industry began by developing a replacement 

for whale oil, and now it is apparent that it is beginning to 

return to biological feedstocks to keep the pipelines full. 

Gasoline, jet fuel, and diesel are generally described as 

“renewable” or “green” if it is derived from a biological 

feedstock, such as biomass or plant oil, but have essentially 

the same performance specifications as the petroleumbased analog. A major characteristic of petroleum-derived 

fuels is high energy content which is a function of a 

near-zero oxygen content. Typical biological molecules 

have very high oxygen contents as compared to crude oil. 

Conversion of biological feedstocks to renewable fuels, 

therefore, is largely a process of eliminating oxygen and 

maximizing the final energy content. From a refinery’s 

perspective, the ideal conversion process would make use 

of those operations already in place: thermal or catalytic 

cracking, catalytic hydrocracking and hydrotreating, 

and catalytic structural isomerization. In this way, the 

feedstock is considered fungible with petroleum and 

can be used for the production of typical fuels without 

disruptive changes in processes or infrastructure. 

Various refiners and catalyst developers have already 

begun to explore the conversion of vegetable oils and 

waste animal fats into renewable fuels. Fatty acids are 

well suited to conversion to diesel and jet fuel with few 

processing steps. This process has already provided the 

renewable jet fuel blends (derived from oils obtained 

from jatropha and algae) used in recent commercial jet 

test flights. On the other hand, straight chain alkanes 

are poor starting materials for gasoline because they 

provide low octane numbers, demanding additional 

isomerization steps or high octane blendstocks. 
6. Algal Biofuel Conversion Technologies 57

6.4 Processing of Algal 

Remnants after Extraction

One other critical aspect in developing a conversion 

technology that derives benefit from every potential 

input is the conversion of algal remnants after 

conversion of algal feedstock into fuel. This 

includes the anaerobic digestion of algal remnants 

to produce biogas, as well as the fermentation of 

any recoverable polysaccharides into biofuels. 

Anaerobic digestion can be effectively used as a means 

of producing biogas from algae and algal remnants after 

extraction (Ashare and Wilson, 1979). In particular, the 

organic fractions of the algae remaining after oil extraction 

are amenable to anaerobic digestion. In addition, once 

the algae has been harvested, little if any pretreatment 

is required. The biogas product typically contains 60% 

methane and 40% CO2 by volume. The liquid effluent 

contains soluble nitrogen from the original algal proteins; 

the nitrogen can be recovered in the form of ammonia 

for recycle to the culture. There will also likely be a high 

amount of polysaccharides and other oligosaccharides 

present in the algal remnants that are well suited for 

traditional fermentation into ethanol and other biofuels.

Algal lipids can be processed by hydrothermal treatment 

(basically, a chemical reductive process). Referred to as 

hydrotreating, this process will convert the carboxylic 

acid moiety to a mixture of water, carbon dioxide, or 

carbon monoxide, and reduce double bonds to yield 

hydrocarbons. Glycerin can be converted to propane 

which can be used for liquefied petroleum gas. 

The primary barrier to utilizing algae oils to make 

renewable fuels is catalyst development. Catalysts in 

current use have been optimized for existing petroleum 

feedstocks and have the appropriate specificity and activity 

to carry out the expected reactions in a cost-effective 

manner. It will be desirable to tune catalysts such that the 

attack on the oxygen-bearing carbon atoms will minimize 

the amount of CO and CO2 lost, as well as the amount of 

H2 used. Refinery catalysts have also been developed to 

function within a certain range of chemical components 

found within the petroleum stream (e.g., metals, and sulfur 

and nitrogen heteroatoms) without becoming poisoned. 

Crude algal oil may contain high levels of phosphorous 

from phospholipids, nitrogen from extracted proteins, and 

metals (especially magnesium) from chlorophyll. It will 

be necessary to optimize both the level of purification of 

algal lipid as well as the tolerance of the catalyst for the 

contaminants to arrive at the most cost-effective process.
58 6. Algal Biofuel Conversion Technologies 

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7. Co-products 61

conversion of algal biomass to other biofuels has already 

been discussed (see Chapter 6); this chapter will focus on 

the non-fuel co-products.

Under the biorefinery concept (Exhibit 7.1), the production 

of industrial, high-value and high-volume chemicals from 

amino acids, glycerol, and nitrogen-containing components 

of algal biomass becomes feasible (Mooibroek et al., 2007) 

and must be considered in determining the economics of 

the process.

The use of terms such as “high volume” or “high value” 

can be extremely subjective, as a “high value” product 

to a fine chemical producer might be well over several 

dollars/lb, but considerably under a dollar for a commodity 

producer. For the purposes of the Roadmap, a reasonably 

valued chemical is defined as one that will cost roughly 

$0.30 - $1.00/lb, and can be produced at a volume of 

roughly 100 - 500 x106 lbs/yr.

7.1 Commercial Products from 

Microalgae and Cyanobacteria

A large number of different commercial products have been 

derived from microalgae and cyanobacteria. As summarized 

in Exhibit 7.2, these include products for human and animal 

nutrition, poly-unsaturated fatty acids, anti-oxidants, 

coloring substances, fertilizers and soil conditioners, and 

a variety of specialty products such as bioflocculants, 

biodegradable polymers, cosmetics, pharmaceuticals, 

polysaccharides, and stable isotopes for research purposes.

7. Co-products 

The “guiding truth” is that if biofuel production is 

considered to be the primary goal, the generation of other 

co-products must be correspondingly low since their 

generation will inevitably compete for carbon, reductant, 

and energy from photosynthesis. Indeed, the concept of 

a biorefinery for utilization of every component of the 

biomass raw material must be considered as a means to 

enhance the economics of the process. This chapter will 

address these options and discuss how some of them 

are better opportunities as they will not readily saturate 

corresponding markets in the long term. 

This chapter will also address within the context of the 

biorefinery the possibility of coupling biomass cultivation 

with CO2 mitigation (for carbon credits) and wastewater 

treatment (for nutrient removal) to provide additional 

benefits to the technology, without invoking competing coproducts.

Using appropriate technologies, all primary components 

of algal biomass – carbohydrates, fats (oils), proteins and 

a variety of inorganic and complex organic molecules – 

can be converted into different products, either through 

chemical, enzymatic or microbial conversion (see Chapter 

6). The nature of the end products and of the technologies 

to be employed will be determined, primarily by the 

economics of the system, and they may vary from region to 

region according to the cost of the raw material (Willke and 

Vorlop, 2004). Moreover, novel technologies with increased 

efficiencies and reduced environmental impacts may have 

to be developed to handle the large amount of waste that 

is predicted to be generated by the process. The topic of 

Biorefinery

Aquaculture Primary Refinery Industry

Raw biomass,

wastewater, CO2

Conversion

Complex

Substances

Inorganics

Energy

Carbohydrates

Fats

Proteins

Products and

residues from

conversion

processes Special substances:

pigments, dyes, flavors,

aromatic essences,

enzymes, hormones, etc.

Heat, electricity

Modified from Kamm and Kamm, 2007

Exhibit 7.1 An overview of 

the biorefinery concept
62 7. Co-products 

Spirulina, Tetraselmis, and Thalassiosira. Both the 

protein content and the level of unsaturated fatty 

acids determine the nutritional value of microalgal 

aquaculture feeds. The market size, currently at ~700 

million US$, is expected to expand significantly.

• Animal Feed Additive: Microalgal biomass has also 

been used with good results (i.e., better immune 

response, fertility, appearance, weight gain, etc.) as 

a feed additive for cows, horses, pigs, poultry, and 

even dogs and cats. In poultry rations, microalgal 

biomass up to a level of 5 - 10% (wt.) can be safely 

used as a partial replacement for conventional proteins 

(Spoalore et al., 2006). The main species used in 

animal feed are Spirulina, Chlorella and Scenesdesmus. 

The market for microalgal animal feeds, estimated 

to be about 300 million US$, is quickly growing. 

However, it is important to note that since the flue 

gas from coal-fired power plants that will be used 

to supply carbon dioxide to the cultures will contain 

significant amounts of lead, arsenic, cadmium and 

other toxic elements, the resulting non-oil algal 

biomass is very likely to be unsuitable for use as an 

animal feed, particularly given the fact that algae 

are known to be effective at metal absorption.

Polyunsaturated Fatty Acids (PUFAs)

Microalgae can also be cultured for their high content 

in PUFAs, which may be added to human food and 

animal feed for their health promoting properties 

(Benemann, 1990; Radmer, 1994 and 1996). The most 

commonly considered PUFAs are arachidonic acid (AA), 

docohexaenoic acid (DHA), γ-linolenic acid (GLA), and 

eicosapentaenoic acid (EPA). AA has been shown to be 

synthesized by Porphyridium, DHA by Crypthecodinium

and Schizochytrium, GLA by Arthrospira, and EPA by 

Nannochloropsis, Phaeodactylum and Nitzschia (Spolaore 

et al., 2006). However, only DHA has been produced thus 

far on a commercial scale by microalgae. All other PUFAs 

are more cost-effectively produced from non-algal sources 

(e.g., GLA from evening primrose oil). Although small, 

the DHA oil market is quickly growing, having presently a 

retail value of 1.5 billion US$.

Anti-Oxidants

A number of anti-oxidants, sold for the health food market, 

have also been produced by microalgae (Borowtizka, 1986; 

Benemann, 1990; Radmer, 1996). The most prominent 

is β–carotene from Dunaliella salina, which is sold either 

as an extract or as a whole cell powder ranging in price 

from 300 to 3,000 US$ per kg (Spolaore et al., 2006). The 

market size for β–carotene is estimated to be greater than 

280 million US$.

By definition, these existing markets (and associated 

production plants and distribution channels) are for highvalue products or co-products from algae, not commodity 

products. Yet the existing fossil fuels market is and the 

future algal-based biofuels market (designed in part to 

supplant the fossil fuels market) must be commodities 

based to meet required volumes at price points acceptable 

to the consumer. With the possible exception of the existing 

market for microalgal biomass for animal nutrition and 

soil fertilizer, the biofuels markets will involve volumes 

(of biomass, product, etc.) and scales (sizes and numbers 

of commercial plants) that are significantly less than those 

associated with the existing high-value algae-derived 

products.

Therein lies a major conundrum associated with the 

nascent algal-derived biofuels market: in the long term, 

massive lipid production dominates; yet in the short term, 

co-products of higher value in the marketplace must be 

pursued in order to offset the costs of production of algalderived biofuels. Although it is clear that co-products may 

improve the economic viability of some algae processes 

in the short-term, the goal of the industry is to produce 

transportation fuels below their market price, thereby 

increasing fuel supplies without drastically increasing price. 

This situation, is anticipated to continue until 1) a sufficient 

number of the challenges outlined earlier in the Roadmap 

for biofuel production have been overcome and associated 

life cycle costs are reduced to realize sustainable biofuel 

production at volumes and pricepoints that meet consumer 

demands or 2) new co-products that are low cost and have 

very large potential markets are developed.

Food and Feed

• Human Health Food Supplement: The consumption of 

microalgal biomass as a human health food supplement 

is currently restricted to only a few species, e.g., 

Spirulina (Arthospira), Chlorella, Dunalliella, and 

to a lesser extent, Nostoc and Aphanizomenon 

(Radmer, 1996; Pulz and Gross, 2004; Spolaore et 

al., 2006). 

The production includes ca. 3,000 t/yr Spirulina; ca. 

2,000 t/yr Chlorella; ca. 1,200 t/yr Dunaliella; ca. 

600 t/yr Nostoc; and ca. 500 t/yr Aphanizomenon. 

The market, currently at about 2.5 billion 

US$, is expected to grow in the future.

• Aquaculture: Microalgae are also used as feed in the 

aquaculture of mollusks, crustaceans (shrimp), and 

fish (Benemann, 1990; Malcolm et al., 1999). Most 

frequently used species are Chaetoceros, Chlorella, 

Dunaliella, Isochrysis, Nannochloropsis, Nitzschia, 

Pavlova, Phaeodactylum, Scenedesmus, Skeletonema, 
7. Co-products 63

the related carotenoids lutein and zeaxantin, have also 

been used in the feed of carp and even chicken (Puls and 

Gross, 2004; Spolaore et al., 2006). Phycobiliproteins, 

i.e., phycoerythrin and phycocyanin, produced by 

the cyanobacterium Arthrospira and the rhodophyte 

Porphyridium, are used as food dyes, pigments in 

cosmetics, and as fluorescent reagents in clinical or research 

laboratories (Spolaore et al., 2006).

Coloring Agents

Microalgae-produced coloring agents are used as natural 

dyes for food, cosmetics, and research, or as pigments 

in animal feed (Borowitzka, 1986; Benemann, 1990). 

Astaxanthin, a carotenoid produced by Hematococcus 

pluvialis, has been successfully used as a salmon feed to 

give the fish meat a pink color preferred by the consumers 

(Olaizola, 2003; Spolarore et al., 2006). Astaxanthin, and 

COMMERCIAL PRODUCT MARKET SIZE

(TONS/YR)

SALES VOLUME

(MILLION $US/YR) REFERENCE

BIOMASS

Health Food 7,000 2,500 Pulz&Gross (2004)

Aquaculture 1,000 700 Pulz&Gross (2004)

Spolaore et al., (2006)

Animal Feed Additive No available information 300 Pulz&Gross (2004)

POLY-UNSATURATED 

FATTY ACIDS (PUFAs)

ARA No available information 20 Pulz&Gross (2004)

DHA <300 1,500 Pulz&Gross (2004)

Spolaore et al., (2006)

PUFA Extracts No available information 10 Pulz&Gross (2004)

GLA Potential product, no current commercial market Spolaore et al., (2006)

EPA Potential product, no current commercial market Spolaore et al., (2006)

ANTI-OXIDANTS

Beta-Carotene 1,200 >280 Pulz&Gross (2004)

Spolaore et al., (2006)

Tocopherol CO2 Extract No available information 100-150 Pulz&Gross (2004)

COLORING SUBSTANCES

Astaxanthin < 300 (biomass) < 150 Pulz&Gross (2004)

Spolaore et al., (2006)

Phycocyanin No available information >10 Pulz&Gross (2004)

Phycoerythrin No available information >2 Pulz&Gross (2004)

FERTILIZERS/SOIL CONDITIONERS

Fertilizers, growth promoters, 

soil conditioners No available information 5,000 Pulz&Gross (2004)Metting&Pyne (1986)

Exhibit 7.2 Summary of microalgae commercial products market
64 7. Co-products 

Fertilizers

Currently, macroalgae (i.e., seaweeds) are used as a plant 

fertilizer and to improve the water-binding capacity and 

mineral composition of depleted soils (Metting et al., 1990). 

Microalgal biomass could in principle serve the same 

purpose. Furthermore, plant growth regulators could be 

derived from microalgae (Metting and Pyne, 1986).

Other Specialty Products

There are a number of specialty products and chemicals 

that can be obtained from microalgae. These include 

bioflocculants (Borowitzka, 1986), biopolymers and 

biodegradable plastics (Philip et al., 2007; Wu et al., 2001),

cosmetics (Spolaore et al., 2006), pharmaceuticals and 

bioactive compounds (Burja et al., 2001; Metting and Pyne, 

1986; Olaizola, 2003; Singh et al., 2005; Pulz and Gross, 

2004), polysaccharides (Benemann, 1990; Borowitzka, 

1986; Pulz and Gross, 2004), and stable isotopes for 

research (Benemann, 1990, Radmer, 1994; Pulz and Gross, 

2004). The market for these specialty products is likely to 

be very small due to their specialized applications.

7.2 Commercial Products 

from Macroalgae

Macroalgae possess high levels of structural 

polysaccharides that are extracted for their commercial 

value (Exhibit 7.3). They include alginate from brown 

algae and agar and carrageenen from red algae. Alginate, 

which occurs in high concentrations in brown seaweeds, 

is considered recalcitrant to ethanol fermentation since 

the redox balance favors formation of pyruvate as the end 

product (Forro, 1987). 

7.3 Potential Options for the 

Recovery of Co-products

Co-products from algal refineries should address one 

of these three criteria to be commercially viable and 

acceptable:

1. Identical to an existing chemical, fuel, or other product. 

In this instance, the only issue is price. The production 

cost of the new product must be equivalent to the 

material it replaces and to be competitive typically, it 

must be produced at a cost 30% lower than the existing 

material (shutdown economics). This sets a high bar 

but has been achieved for some chemicals and proteins/

nutritional products.

2. Identical in functional performance to an existing 

chemical, fuel or other product. Here price is a major 

factor, but the source of the material can often provide 

some advantage. This occurs with natural oils which 

manufacturers in many cases would prefer if the costs 

were comparable, or with replacements such as algal 

proteins for distillers dried grains from corn dry grind 

ethanol processing. Price becomes less of an issue if 

the product can be labeled “organic” and thus saleable 

at a premium.

PRODUCT VALUE

Human Food (Nori, aonori, kombu, wakame, etc.) $5 billion

Algal hydrocolloids

Agar (Food ingredient, pharmaceutical, biological/microbiological) $132 million 

Alginate (Textile printing, food additive, pharmaceutical, medical) $213 million 

Carrageenen (Food additive, pet food, toothpaste) $240 million 

Other uses of seaweeds

Fertilizers and conditioners $5 million

Animal Feed $5 million

Macroalgal Biofuels Negligible

TOTAL $5.5-6 BILLION

Exhibit 7.3 Global value of seaweed products per annum (McHugh, 2003)
7. Co-products 65

production systems, it may be difficult to identify large 

enough markets for potential co-products. Therefore, one 

option would be to convert as much of the lipid-extracted 

biomass into energy, which could then be either sold on 

the open market or used on-site in the various biorefinery 

operations.

The most promising energy recovery technology, both 

from a practical and economic perspective, is the anaerobic 

digestion of lipid-extracted biomass. Anaerobic digestion of 

whole (i.e., non-extracted) micro and macroalgal biomass 

has been successfully demonstrated, with reported methane 

yields of about 0.3 l per gram volatile solids (Huesemann 

and Benemann, 2009). The economic value of the produced 

methane is equivalent to about $100 per ton of digested 

biomass, which is significant in terms of reducing the 

overall cost of liquid biofuels production. The residuals 

remaining after anaerobic digestion could either be recycled 

as nutrients for algal cultivation or could be sold as soil 

fertilizers and conditioners, as is currently already done for 

certain waste water treatment sludges (see http://www.unh.

edu/p2/biodiesel/pdf/algae_salton_sea.pdf).

In addition to anaerobic digestion, thermochemical 

conversion technologies, such as pyrolysis, gasification, 

and combustion, could also be potentially considered for 

the recovery of energy from the lipid-extracted biomass 

(see Chapter 6). These technologies are able to convert 

a much larger fraction of biomass into fuels. However, 

these technologies are still in the testing and development 

stage, and because of their large energy inputs (temperature 

and pressure), could have poor or even negative energy 

balances (Huesemann and Benemann, 2009). Nevertheless, 

3. New material with unique and useful functional 

performance characteristics. In this case, the issues 

are less related to costs and more to the functional 

performance and potentially enhanced performance of 

the new product.

There are at least five different options for recovering 

economic value from the lipid-extracted microalgal biomass 

(Exhibit 7.4). These are: 

• Option 1 – Maximum energy recovery from 

the lipid extracted biomass, with potential 

use of residuals as soil amendments

• Option 2 – Recovery of protein from the lipidextracted biomass for use in food and feed

• Option 3 – Recovery and utilization of non-fuel lipids

• Option 4 – Recovery and utilization of carbohydrates 

from lipid-extracted biomass, and the glycerol 

from the transesterification of lipids to biodiesel

• Option 5 – Recovery/extraction of fuel 

lipids only, with use of the residual biomass 

as soil fertilizer and conditioner

Each option and its associated technologies and future 

research needs are discussed below.

Option 1. Maximum Energy Recovery from the 

Lipid-Extracted Biomass, with Potential Use of 

Residuals as Soil Amendments

Given the large amounts of lipid-extracted biomass residues 

that will likely be generated in future microalgal biofuels 

Algal Biomass

Extract Lipids

for Fuel

Proteins as

Co-Products

Non-Fuel

Lipids

Carbohydrates

Surfactants/ Bioplastics

Ethanol/ Butanol/ Glycerol

Food/ Feed Supplement

Soil Fertilizer/ Conditioners

Ash/ Soil Amendments

Energy

Option 3

Chemical/ Biological Conversion

Option 2

Processing

Option 1

Burn Residue

Option 5

Dry Residue Processing

Recycle Nitrogen Gases

Option 4

Chemical/ Biological Conversion

Exhibit 7.4 Overview of the five 

potential options for the recovery 

and use of co-products
66 7. Co-products 

the thermochemical conversion of lipid-extracted biomass 

has the potential advantage that the resulting nitrogencontaining gases (e.g., ammonia and nitrous oxides) could 

be recycled into the microalgal culture ponds, thereby 

reducing the expense for nitrogen fertilizers. Furthermore, 

the mineral-rich ash generated by these thermochemical 

processes could possibly be used for nutrient recycle or as a 

soil amendment.

Option 2. Recovery of Protein from the Lipid-Extracted 

Biomass for Use in Food and Feed

Following the extraction of lipids from the microalgal 

biomass for liquid biofuel production, the protein fraction 

from the residual biomass could be extracted and used as 

a food and feed supplement. As was pointed out above, 

the market for animal feed (cattle, pigs, poultry, fish, and 

pets) is already very large and growing (estimated to rise 

to approximately 60 million tons per year for distillers dry 

grains plus soluble (DDGS)) (Berger and Good, 2007). 

The current price for DDGS ranges from $110 - 150 per ton 

(http://www.ams.usda.gov/mnreports/sj_gr225.txt). Since 

protein is generally the key and often limiting ingredient 

in animal feed, supplementation with microalgal proteins 

could be advantageous. Furthermore, human nutrition may 

also benefit from supplementation with microalgal proteins. 

The byproduct material, which contains proteins, might 

make a useful animal feed. However, feeding studies 

indicate that algae cannot be used as a high percentage 

of feed, due to issues such as taste of the meat or eggs, 

and interactions with animal digestion. Furthermore, the 

overall size of the animal feed market is small, relative 

to the amount of byproduct that would be produced, and 

the individual local markets for animal feed are often not 

located adjacent to areas where algae may be produced. As 

a result, byproduct markets are likely to be overwhelmed, 

and byproduct prices will be greatly depressed versus 

current levels.

In addition, it may be possible to recover important 

enzymes such as cellulases or other industrial enzymes 

from the lipid-extracted biomass. However, this option 

would require the use of specially selected or engineered 

microalgal strains capable of producing these enzymes. The 

market for industrial enzymes, specifically cellulases for 

pretreating lignocellulosic feedstocks prior to fermentation 

to fuel ethanol, is potentially very large. Assuming that (a) 

microalgal cellulases could be provided at a cost of less 

than $0.20 per gallon ethanol; (b) approximately 100 grams 

of cellulase are needed per gallon of ethanol; and (c) at 

least 10.5 billion gallons of lignocellulosic ethanol will be 

produced by 2020, the projected market for cellulases is 

potentially very large, i.e., 1 billion kg.

Option 3. Recovery and Utilization of Non-fuel Lipids

It is well known that microalgae can synthesize a variety 

of fatty acids with carbon numbers ranging from C10 to C24, 

depending on the algal species and culturing conditions 

(Hu et al., 2008). Since the generation of gasoline, jet fuel, 

and diesel substitutes will require specific ranges of carbon 

chain length, it will be necessary to either separate the 

product into the appropriate range or rearrange the carbon 

chains through catalytic cracking and catalytic reforming. 

It may be worthwhile, however, to separate specific 

lipids present in the algal oil that have utility as chemical 

feedstocks for the manufacture of surfactants, bioplastics, 

and specialty products such as urethanes, epoxies, 

lubricants, etc. 

Option 4. Recovery and Utilization of Carbohydrates 

from Lipid-Extracted Biomass, and the Glycerol from the 

Transesterification of Lipids to Biodiesel

After the extraction of lipids, the residual microalgal 

biomass may contain sufficient levels of carbohydrates that 

could be converted through anaerobic dark fermentations 

to hydrogen, solvents (acetone, ethanol, and butanol), and 

organic acids (formic, acetic, propionic, butyric, succinic, 

and lactic) (Huesemann and Benemann, 2009; Kamm and 

Kamm, 2007; Kawaguchi et al., 2001). Hydrogen and 

ethanol could be used as biofuel, while butanol and organic 

acids could serve as renewable feedstocks for the chemicals 

industry. For example, butanol is a valuable C4 compound 

for chemical synthesis of a variety of products, including 

polymers that are currently produced from fossil oilderived ethylene and propylene, thus butanol could serve 

as a renewable substitute (Zerlov et al., 2006). Similarly, 

succinate is an intermediate in the production of a variety 

of industrial surfactants, detergents, green solvents and 

biodegradable plastics (Kamm and Kamm, 2007). Lactic 

acid, which can be converted into polypropylene oxide, 

is the starting material for the production of polyester, 

polycarbonates and polyurethanes; it is also used in the 

industrial production of green solvents, and its applications 

include the pharmaceutical and agrochemical industries 

(Datta et al., 1995).

Glycerol, a byproduct of the transesterification of 

microalgal lipids to biodiesel, could also be anaerobically 

fermented to the above mentioned and other end products 

(Yazdani and Gonzalez, 2007). Furthermore, glycerol 

could be converted by certain bacteria to 1,3-propanediol, 

which is used in the formulation of a variety of industrial 

products such as polymers, adhesives, aliphatic polyesters, 

solvents, antifreeze, and paint (Yazdani and Gonzalez, 

2007; Choi, 2008). Finally, glycerol could be used to 

generate electricity directly in biofuel cells (Yildiz and 
7. Co-products 67

microalgal metabolites, including sugars and complex 

carbohydrates; and the development of genetic engineering 

tools to improve yields of desired products, including 

carbohydrates, if desired.

Option 5. Recovery (Extraction) of Fuel Lipids Only, with 

Use of the Residual Biomass as Soil Fertilizer 

and Conditioner

In case none of the above mentioned four options are 

economical, i.e., the recovery and use of energy, proteins, 

non-fuel lipids, and carbohydrates is not cost-effective, it 

is possible to revert to the most simple option (Option 5), 

which involves the extraction of only fuel lipids and the 

subsequent use of the biomass residues rich in nitrogen and 

organic matter as soil fertilizer and conditioners. As was 

mentioned above, the market for organic fertilizer is large 

and potentially growing.

Kadirgan, 1994). Once again, the issue of scale enters in. 

Production of 1 billion gallons of biodiesel will result in 

the formation of more than 400,000 tons of glycerol (http://

www.biodieselmagazine.com/article.jsp?article_id=377). 

As the current production levels for biodiesel (700 million 

gallons in 2008) already has the market for glycerol 

saturated, additional capacity from algal lipids may find it 

exceedingly difficult to find uses.

It may also be possible to extract microalgal 

polysaccharides for use as emulsifiers in food and industrial 

applications (Mooibroek et al., 2007). Finally, microalgal 

carbohydrates could be recycled into pulp and paper 

streams, substituting for lignocellulosic materials derived 

from forestry resources.

As was the case with Option 3, this option will also require 

R&D efforts as discussed under Chapter 2, Algal Biology; 

specifically, these are the development of high throughput 

technologies for the quantitative characterization of 

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Microbiology. Suppl. No. 5. (31), 247-256. 

Berger, L.L., D. L. Good. (2007). Distillers dried grains plus solubles utilization by livestock and poultry in corn-based ethanol in Illinois 

and the U.S. A Report from the Department of Agricultural and Consumer Economics, University of Illinois, Champaign-Urbana.

Borowitzka, M.A. (1986). Microalgae as sources of fine chemicals. Microbiological Sciences. 3(12), 372-375. 

Burja, A.M., B. Banaigs, E. Abou-Mansour, J.G. Burgess, and P.C. Wright. (2001). Marine cyanobacteria – A prolific source of natural 

products. Tetrahedon. (57), 9347-9377. 

Choi, W.J. (2008). Glycerol-based biorefinery for fuels and chemicals. Recent Patents on Biotechnology. (2), 173-180.

Datta, R., S.P. Tsai, P. Bonsignore, S.H. Moon, J.R. Frank. (2006). Technological and economic potential of poly(lactic acid) and lactic acid 

derivatives. FEMS Microbiological Review. (16), 221-231.

Forro, J. (1987). Microbial degradation of marine biomass. Developments in Aquaculture and Fisheries Science (Netherlands). 

Hu, Q., M. Sommerfeld, E. Jarvis, M. Ghirardi, M. Posewitz, M. Seibert, A. Darzins. (2008). Microalgal triacylglycerols as feedstocks for 

biofuel production: Perspectives and advances. The Plant Journal. (54), 621-63. 

Huesemann, M.H., J.R. Benemann. (2009). Biofuels from microalgae: Review of products, processes, and potential, with special 

focus on Dunaliella sp. The alga dunaliella: biodiversity, physiology, genomics, and biotechnology. Science Publishers, 

New Hampshire. 

Kamm, B. M. Kamm. (2007). Biorefineries – multi product processes. Advances in Biochemical Engineering/Biotechnology. 

(105),175-204.

Kawaguchi H, K. Hashimoto, K. Hirata, K. Miyamoto. (2001). H2 production from algal biomass by a mixed culture of rhodobium marinum 

A-501 and lactobacillus amylovorus. Journal of Biosciences Bioengineering. (91), 277-282.

McHugh, D. J. (2003). A guide to the seaweed industry. Food and Agriculture Organization. 

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Phycology. SPB Academic Publishing, The Hague, Netherlands. 589-627. 
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Mooibroek, H., N. Oosterhuis, M. Giuseppin, M. Toonen, H. Franssen, E. Scott, J. Sanders, A. Steinbüchel. (2007). Assessment 

of technological options and economical feasibility for cyanophycin biopolymer and high-value amino acid production. Applied 

Microbiology Biotechnology. (77), 257-267.

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Philip, S., T. Keshavarz, I. Roy. (2007). Polyhydroxyalkanoates: Biodegradable polymers with a range of applications. Journal of Chemical 

Technology and Biotechnology. (82), 233-247. 

Pulz, O., W. Gross. (2004).Valuable products from biotechnology of microalgae. Applied Microbiology and Biotechnology. (65), 635-648. 

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Bioengineering. 101(2), 87-96. 

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Wu, G.F., Q.Y. Wu, Z.Y. Shen. (2001). Accumulation of poly-b-hydroxybutyrate in cyanobacterium synechocystis sp. PCC6803. 

Bioresource Technology. (76), 85-90. 

Yazdani, S.S., R. Gonzalez. (2007). Anaerobic fermentation of glycerol: A path to economic liability for the biofuels industry. 

Current Opinion Biotechnology. (18), 213-219.

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Zerlov, V.V., O. Berezina, G.A. Velikodvorskaya, W.H. Schwarz. (2006). Bacterial acetone and butanol production by industrial 

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(71), 587-597. 
8. Distribution and Utilization 69

It is also anticipated that gasoline and diesel range fuels 

from algae will not require significant distribution system 

modifications during or after processing in the refinery.

While the demonstration flights mitigate some 

infrastructure concerns, other distribution aspects 

concerning algal biomass, fuel intermediates, and final fuels 

remain poorly studied:

• First, the stability of the algal biomass under different 

production, storage, and transport scenarios is 

poorly characterized, with some evidence suggesting 

that natural bacterial communities increase the 

rate of algae decomposition (Rieper-Kirchner, 

1990). In the context of a variety of culturing and 

harvesting conditions differing in salinity, pH and 

dewatering levels, it is difficult to predict how 

these factors will influence biomass storage and 

transport, and the quality of the final fuel product. 

• Second, an issue that impacts oleaginous microalgae 

feedstocks is that the transport and storage mechanisms 

of algal lipid intermediates have not yet been 

established. It is conceivable that these “bio-crudes” 

will be compatible with current pipeline and tanker 

systems. However, it is known that the presence 

of unsaturated fatty acids causes auto-oxidation of 

oils (Miyashita and Takagi, 1986), which carries 

implications for the producers of algae and selection 

for ideal lipid compositions. It is also known that 

temperature and storage material have important 

implications for biodiesel stability (Bondioli et al., 

1995). Thus, materials and temperature considerations 

similar to plant lipids may be possibly taken into 

account for the storage of algae lipids (Hu et al., 2008). 

• Third, depending on whether it will be dewatered/

densified biomass and/or fuel intermediates that are to 

be transported to the refinery, conforming to existing 

standards (e.g., container dimensions, hazardous 

materials and associated human health impacts, and 

corrosivity) for trucks, rails, and barges is critical 

to minimizing infrastructure impacts. The optimal 

transport method(s) should be analyzed and optimized 

for energy-inputs and costs, within the context of 

where the algae production and biorefinery facilities 

are to be sited. These have been challenging issues 

for lignocellulosic feedstocks (Hess et al., 2009) and 

can be expected to influence the economics of algal 

biofuels as well.

8. Distribution and Utilization

Distribution and utilization are challenges associated with 

virtually all biofuels. Although the biofuel product(s) 

from algal biomass would ideally be energy-dense 

and completely compatible with the existing liquid 

transportation fuel infrastructure, few studies exist that 

address outstanding issues of storing, transporting, 

pipelining, blending, combusting, and dispensing algal 

biomass, fuels intermediates, biofuels, and bioproducts. 

Being intermediate steps in the supply chain, distribution 

and utilization need to be discussed in the context of earlier 

decision points, such as cultivation and harvesting. In turn, 

these logistics through end-use issues influence siting, 

scalability, and the ultimate economics and operations of 

an integrated algal biofuels refinery. As a variety of fuel 

products – ethanol, biodiesel, higher alcohols, pyrolysis oil, 

syngas, and hydroreformed biofuels – are being considered 

from algal biomass resources, the specific distribution and 

utilization challenges associated with each of these possible 

opportunities is discussed.

8.1 Distribution

Lowering costs associated with the delivery of raw 

biomass, fuel intermediates, and final fuels from the 

feedstock production center to the ultimate consumer 

are common goals for all biofuels. In all cases, biofuels 

infrastructure costs can be lowered in four ways:

• Minimizing transport distance between process units;

• Maximizing the substrate energy-density and stability;

• Maximizing compatibility with existing infrastructure 

(e.g. storage tanks, high capacity; delivery vehicles, 

pipelines, dispensing equipment, and end-use vehicles); 

and

• Optimizing the scale of operations to the parameters 

stated above.

Distribution is complicated by the fact that several 

different fuels from algae are being considered, as 

discussed in detail in Chapter 6 (Algal Biofuel Conversion 

Technologies). Ethanol, biodiesel, biogas, renewable 

gasoline, diesel, and jet fuels are all possible products 

from algal biomass. Each of these different fuels has 

different implications for distributions. Some of these fuels 

appear to be more compatible with the existing petroleum 

infrastructure. Specifically, jet-fuel blends from a variety 

of oil-rich feedstocks, including algae, have been shown 

to be compatible for use in select demonstration flights 

(Buckman and Backs, 2009; Efstathiou and Credeur, 2009). 
70 8. Distribution and Utilization 

Typically, compliance with specifications promulgated by 

organizations such as ASTM International ensures that a 

fuel is fit for purpose (ASTM International, 2009a, 2009b, 

2009c, 2009d, and 2009e). Failure of a fuel to comply with 

even one of the many allowable property ranges within 

the prevailing specifications can lead to severe problems 

in the field. Some notable examples included: elastomercompatibility issues that led to fuel-system leaks when 

blending of ethanol with gasoline was initiated; coldweather performance problems that crippled fleets when 

blending biodiesel with diesel was initiated in Minnesota 

in the winter; and prohibiting or limiting the use of the 

oxygenated gasoline additive MTBE in 25 states because 

it has contaminated drinking-water supplies (McCarthy 

and Tiemann, 2000). In addition to meeting fuel standard 

specifications, algal biofuels, as with all transportation 

fuels, must meet Environmental Protection Agency 

regulations on combustion engine emissions.

As is true of any new fuel, it is unlikely that new 

specifications will be developed for algal fuels in the near 

term (i.e., at least not until significant market penetration 

has occurred); hence, producers of algal fuels should 

strive to meet prevailing petroleum-fuel specifications. 

Nevertheless, research and technology advancements 

may one day yield optimized conversion processes which 

can deliver algae-derived compounds with improved 

performance, handling, and environmental characteristics 

relative to their petroleum-derived hydrocarbon 

counterparts. If significant benefits can be demonstrated, 

new specifications can be developed (e.g., ASTM D6751 

and D7467).

The discussion below is divided into separate sections that 

deal with algal blendstocks to replace gasoline-boilingrange and middle-distillate-range petroleum products, 

respectively. These classifications were selected because 

the compounds comprising them are largely distinct and 

non-overlapping. Within each of these classifications, 

hydrocarbon compounds and oxygenated compounds are 

treated separately, since their production processes and inuse characteristics are generally different.

Algal Blendstocks to Replace 

Middle-Distillate Petroleum Products

Petroleum “middle distillates” are typically used to create 

diesel and jet fuels. The primary algae-derived blendstocks 

that are suitable for use in this product range are biodiesel 

(oxygenated molecules) and renewable diesel (hydrocarbon 

molecules). The known and anticipated end-use problem 

areas for each are briefly surveyed below.

Ethanol is another likely fuel from algae. With over 

10 billion gallons per year produced and consumed 

domestically, distribution-related issues for ethanol has 

been studied for some time, and algal ethanol can benefit 

from these analyses. While not as energy dense as purely 

petroleum-derived fuels, ethanol is an important fuel 

oxygenate that can be used in regular passenger vehicles 

and special flex-fuel vehicles at up to 10% and 85% gasohol 

blends, respectively. However, considerable infrastructure 

investments need to be made for higher ethanol blends 

to become even more attractive and widespread. One 

issue is that ethanol is not considered a fungible fuel; it 

can pick up excessive water associated with petroleum 

products in the pipeline and during storage, which causes 

a phase separation when blended with gasoline (Wakeley 

et al., 2008). One possible way to address this is to build 

dedicated ethanol pipelines; however, at an estimated 

cost of $1 million/mile of pipeline, this approach is not 

generally considered to be economically viable (Reyold, 

2000). Another possibility is to distribute ethanol blends by 

rail, barge, and/or trucks. Trucking is currently the primary 

mode to transport ethanol blends at an estimated rate of 

$0.15/ton/kilometer (Morrow et al., 2006). This amount is 

a static number for low levels of ethanol in the blends (5% 

to 15%); as the ethanol content in the blend increases, the 

transport costs will also increase due to the lower energy 

density of the fuel.

8.2 Utilization

The last remaining hurdle to creating a marketable new 

fuel after it has been successfully delivered to the refueling 

location is that the fuel must meet regulatory and customer 

requirements. As mentioned in Chapter 6, such a fuel is 

said to be “fit for purpose.” Many physical and chemical 

properties are important in determining whether a fuel is fit 

for purpose; some of these are energy density, oxidative and 

biological stability, lubricity, cold-weather performance, 

elastomer compatibility, corrosivity, emissions (regulated 

and unregulated), viscosity, distillation curve, ignition 

quality, flash point, low-temperature heat release, metal 

content, odor/taste thresholds, water tolerance, specific 

heat, latent heat, toxicity, environmental fate, and sulfur 

and phosphorus content. Petroleum refiners have shown 

remarkable flexibility in producing fit-for-purpose fuels 

from feedstocks ranging from light crude to heavy crude, 

oil shales, tar sands, gasified coal, and chicken fat, and are 

thus key stakeholders in reducing the uncertainty about the 

suitability of algal lipids and carbohydrates as a feedstock 

for fuel production.
8. Distribution and Utilization 71

Oxygenates: Biodiesel

Biodiesel is defined as “mono-alkyl esters of long 

chain fatty acids derived from vegetable oils or animal 

fats” (ASTM International, 2009b). Biodiesel has been 

demonstrated to be a viable fuel for compression-ignition 

engines, both when used as a blend with petroleum-derived 

diesel and when used in its neat form (i.e., 100% esters) 

(Graboski and McCormick, 1998). The primary end-use 

issues for plant-derived biodiesel are: lower oxidative 

stability than petroleum diesel, higher emissions of nitrogen 

oxides (NOx), and cold-weather performance problems 

(Knothe, 2007). The oxidative-stability and cold-weather 

performance issues of biodiesel preclude it from use as a 

jet fuel. The anticipated issues with algae-derived biodiesel 

are similar, with added potential difficulties including: 

1) contamination of the esters with chlorophyll, metals, 

toxins, or catalyst poisons (e.g., sulfur and phosphorus) 

from the algal biomass and/or growth medium; 2) undesired 

performance effects due to different chemical compositions; 

and 3) end-product variability.

Hydrocarbons: Renewable Diesel and 

Synthetic Paraffinic Kerosene

The hydrocarbon analog to biodiesel is renewable diesel, 

which is a non-oxygenated, paraffinic fuel produced 

by hydrotreating bio-derived fats or oils in a refinery 

(Aatola et al., 2009). Algal lipids can be used to produce 

renewable diesel or synthetic paraffinic kerosene (SPK), 

a blendstock for jet fuel. These blendstocks do not have 

oxidative-stability problems as severe as those of biodiesel, 

and renewable diesel actually tends to decrease engineout NOx emissions. Nevertheless, unless they are heavily 

isomerized (i.e., transformed from straight- to branchedchain paraffins), renewable diesel and SPK will have 

cold-weather performance problems comparable to those 

experienced with biodiesel. Also, as was the case with algal 

biodiesel, contaminants and end-product variability are 

concerns.

Algal Blendstocks for Alcohol and 

Gasoline-Range Petroleum Products

While much of the attention paid to algae is focused on 

producing lipids and the subsequent conversion of the lipids 

to diesel-range blending components (discussed above), 

algae are already capable of producing alcohol (ethanol) 

directly, and there are several other potential gasoline-range 

products that could be produced by algae-based technology/

biorefineries. Petroleum products in the alcohols and 

gasoline range provide the major volume of fuels used by 

transportation vehicles and small combustion engines in 

the United States. Ethanol or butanol are the most common 

biofuels currently being considered for use in gasoline, 

and these alcohols can be produced from fermentation of 

starches and other carbohydrates contained in algae.

Additionally, the hydro-treating of bio-derived fats or 

oils in a refinery will typically yield a modest amount of 

gasoline-boiling-range hydrocarbon molecules. Refiners 

refer to this material as “hydro-cracked naphtha.” This 

naphtha tends to have a very low blending octane and 

would normally be “reformed” in a catalytic reformer 

within the refinery to increase its blending octane value 

prior to use in a gasoline blend.
72 8. Distribution and Utilization 

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9. Resources and Siting 73

9.1 Resource Requirements for 

Different Cultivation Approaches

Photoautotrophic Microalgae Approach

Assessments of resource requirements and availability 

for large-scale, land-based photoautotrophic microalgal 

cultivation were conducted during the Aquatic Species 

Program (Sheehan et al., 1998), focusing primarily on 

the Southwest and southern tier of the United States 

(e.g., Maxwell et al., 1985; Lansford et al., 1990; 

Feinberg et al., 1990). Sufficient land, water, and 

CO2 resources were identified at the time to suggest 

that the production of billions of gallons of algal 

biofuel could be supported if sufficiently high algae 

productivities could be achieved affordably at scale. 

Many of the findings of these earlier assessments still 

apply today and the potential remains for biofuels 

and other co-products derived from photoautotrophic 

microalgae to significantly contribute to meeting U.S. 

transportation fuel needs and displacing petroleum use. 

Exhibit 9.2 provides a simple high-level overview of 

the major resource and environmental parameters that 

pertain to the algae biofuels production inputs of climate, 

water, CO2, energy, nutrients, and land. These parameters 

are of greatest importance to siting, facilities design, 

production efficiency, and costs. For each parameter, a 

variety of conditions may be more or less cost-effective 

for the siting and operation of algal biomass production. 

Additional resources include materials, capital, labor, 

and other inputs associated with facilities infrastructure 

and conducting operations and maintenance.

In addition to coastal and inland photoautotrophic 

microalgae production, off-shore marine environment 

concepts are also being proposed. This scenario 

9. Resources and Siting 

The development and scale-up of algal biofuels 

production, as with any biomass-based technology and 

industry, needs to be analyzed from a site location, as 

well as from a resource availability and use perspective. 

Critical requirements—such as suitable land and climate, 

sustainable water resources, supplemental CO2 supply, 

and other nutrients—must be appropriately aligned in 

terms of their geo-location, characteristics, availability, 

and affordability. To achieve success regarding both 

technical and economic performance without adverse 

environmental impacts, the siting and resource factors 

must also be appropriately matched to the required growth 

conditions of the particular algae species being cultivated 

and the engineered growth systems being developed and 

deployed. The sustainability and environmental impacts 

of national algae production capacity build-up and 

operation over time will be important complementary 

aspects of the siting and resources issues that will also 

need careful consideration and analysis using tools 

and methodologies discussed later in chapter 10. 

This chapter provides an overview of the issues associated 

with site location and key resources for various microalgae 

and macroalgae production approaches (Exhibit 9.1). 

Further, an in-depth discussion is included on the potential 

to couple land-based microalgae biomass production 

with wastewater treatment and industrial sources of 

concentrated CO2, both of which influence siting decisions 

for algal biofuel production. Integration with wastewater 

treatment can play an additional important role in the 

sourcing of nutrients from both the input wastewater 

and from possible nutrient recycling from residual 

algal biomass. The status of algae-based wastewater 

treatment and necessary technical improvements for 

co-producing algal biofuels are described. Similarly, 

the challenges associated with coupling industrial 

CO2 sources with algae production are outlined.

ALGAE PRODUCTION APPROACH KEY RESOURCE REQUIREMENTS

Photoautotrophic microalgae production Climate, water, CO2

, other nutrients, required 

energy inputs, and land

Heterotrophic microalgae production

Sourcing of suitable organic carbon feedstock, water, energy, 

and other inputs required for siting and operating industrial 

bioreactor-based algae production and post-processing to fuels 

and other co-products

Photoautotrophic macroalgae production Availability of suitable coastal and off-shore marine site locations

Exhibit 9.1 Key resource issues for different algae systems
74 9. Resources and Siting 

organic carbon-rich waste streams, and lignocellulosic 

biomass, thereby sharing many of the same feedstock 

supply issues with first- and second-generation biofuels. 

Use of sugars from cane, beets, other sugar crops, and 

from the hydrolysis of starch grain crops can, after 

sufficient scale-up of production and demand, lead to the 

problem of linking biofuel production with competing 

food and feed markets. The preferred source of sugars 

and other appropriate organic carbon feedstocks for 

greatest sustainable scale-up potential and avoidance of 

adverse food/feed market impacts would be based on 

the use of carbon-rich waste streams and the successful 

deconstruction of lignocellulosic materials. The latter 

has the greatest feedstock scale-up potential and is being 

pursued and reported elsewhere through bioenergy 

programs under DOE and Department of Agriculture 

(USDA; e.g., Perlack et al., 2005; DOE, 2006a). This 

includes siting and resource issues that are closely 

coupled with the production, availability, supply logistics, 

and pretreatment of lignocellulosic biomass feedstock 

that is expected to be capable of national scale-up to 

over one billion tons annually (Perlack et al., 2005). 

Photoautotrophic Macroalgae Approach

Options for siting macroalgae (also known as seaweed 

or kelp) biomass production include offshore farms, 

near-shore coastal farms, and land-based ponds. The 

merits of each should be carefully evaluated, taking into 

consideration factors such as the scale of farms required 

to meet production needs, cost and availability of space 

can be represented by extension of Exhibit 9.2 to 

conceptually include the equivalence of land and 

culture facilities with off-shore areas and structures. A 

similar conceptual extension holds for the application 

of Exhibit 9.2 to off-shore macroalgae production.

 

Heterotrophic Microalgae Approach

Heterotrophic microalgae biomass and metabolite 

production is based on the use of organic carbon feedstock 

in the form of sugars or other relatively simple organic 

compounds instead of photosynthesis. The algae are 

cultivated in the dark in closed industrial bioreactors 

that could potentially be established in many locations 

throughout the country. Achieving affordable scale-up and 

successful commercial expansion using the heterotrophic 

approach relies on the cost-effective availability of organic 

carbon feedstock—a resource that ultimately links back to 

a photosynthetic origin (Exhibit 9.3). Heterotrophic and 

photoautotrophic approaches to microalgae production 

have different siting and resource input implications 

and thus present synergistic integration opportunities. 

Heterotrophic production can be characterized as more of 

an industrial operation with a significant upstream logistics 

trail associated with the sourcing of the needed biomassderived input feedstocks, whereas photoautotrophic 

production, in terms of cultivation and harvesting, is more 

akin to agriculture and serves as the point of origin for the 

biomass feedstock supply for the downstream value chain. 

Resource issues for the heterotrophic approach are more 

largely associated with the upstream supply of organic 

carbon feedstock derived from commodity crops, selected 

Algal

Production Harvesting

Processing 

and

Conversion

Climate

CO2

 Nutrients

Nutrient

Recycle

Water Land

Liquid and 

Gasous Fuels

Secondary

Products

Resources and 

Enviromental 

Parameters

Climate

Insolation

Temperature

Evaporation

Severe Storms

Water

Location

Supply/ Demand

Salinity

Allocation

Land

Topograghy

Use/ Cover

Ownership

Soils

Geology

Exhibit 9.2 Key siting and resource 

elements for algae biofuel production

(Adapted from Maxwell et al., 1985)
9. Resources and Siting 75

production, particularly in the case of land-based 

microalgae production. As illustrated in Exhibit 9.4, key 

factors include solar radiation, temperature, precipitation, 

evaporation, and severe weather. Closed photobioreactors 

are less sensitive to climate variability than open ponds 

due to the more controlled environment that closed 

systems can provide. Temperature and availability of 

sunlight, both seasonally and annually, will most directly 

affect productivity, whereas precipitation, evaporation, 

and severe weather will affect water supply and water 

quality in open systems. Heterotrophic algae production 

in closed industrial bioreactor systems utilize mature 

bioreactor technology that can provide relatively clean 

and protected environmental control needed to optimize 

growth conditions for higher biomass density cultures. 

Heterotrophic algal cultures can be one to two orders of 

magnitude higher in biomass density than possible with 

open photoautotrophic systems that typically achieve no 

more than about 1 gram per liter culture density. From a 

resource use perspective, the heterotrophic approach can 

reduce both water and energy-use intensity in the algae 

production operation. Closed heterotrophic bioreactor 

systems are decoupled from the variable ambient 

outdoor climate, weather conditions, and day/night light 

and temperature cycles. This is done at the expense of 

and nutrients, environmental impacts, and competition 

with other uses. The co-siting of macroalgal farms with 

other structures such as windfarms (Buck et al., 2004) 

has also been proposed as a way of leveraging other 

technologies to facilitate the cultivation of macroalgae. 

Based on the scale of macroalgae cultivation practices 

currently being used to meet non-fuel product demand 

(annual global production of about 1.4 million dry 

metric tonnes for food products), the level of production 

would need to be greatly expanded for biofuels. 

A major challenge lies in finding and developing new 

environments and cultivation approaches that will support 

production of macroalgae at the larger scales and lower 

costs needed to supply the biofuels market. Additional 

research, technology development, and favorable regulatory 

framework for coastal and offshore environment use could 

help enable cultivation at scales to meet production goals.

9.2 Resources Overview

Climate 

Sunlight and Temperature Needs

Various climate elements affect photoautotrophic algae 

Ligno-Cellulosic

Plant Material

Ligno-Cellulosic

Deconstruction

& Seperation

Lignin

Autotrophic

algae production

- open ponds

- closed PBRs

- hybrid mix 

Low-Density Algal

Biomass Harvesting

High-Density Algal

Biomass FHarvesting

CHP

Dewatering

Extraction &

Seperation

Sugars and Other

Organic Carbon

Feedstock

Heterotropic algae

production in 

closed bioreactors Co-Products

Biomass

Residue

Oil Feedstock

Fuels

CO2

 Sourceess

- power plants

- other industrial

Nutrient-Rich

Water Treatment

- muni WWT

- ag CAFO

- lake, rivers

or Other 

Non-Fresh Waters

CO2

Water,

N, P, K,

other

Synergistic Project

Intergration Opportunities

Exhibit 9.3 High-level 

illustration of heterotrophic 

and photoautotrophic 

approaches to microalgal 

biomass and biofuels 

production
76 9. Resources and Siting 

geographical regions were: annual average cumulative 

sun hours ≥ 2800, annual average daily temperature 

≥ 55°F, and annual average freeze-free days ≥ 200. 

It was recognized from the outset that the correlation 

of these annual average climate criteria with what 

might actually be achieved with annual average algae 

productivity in large-scale deployed systems could 

only be taken as a gross indicator. Within that context, 

however, the results are suggestive and consistent with 

the more recent assessment by Pacific Northwest National 

Laboratory (PNNL) using higher GIS resolution and 

more information-rich climate and meteorological data. 

Projections of annual average algae biomass production 

from the PNNL study show clear patterns relating climate 

to total biomass growth, with the higher growth regions 

having gross qualitative similarity to Exhibit 9.4 and the 

southern tier states showing greatest productivity potential 

based on the modeling assumptions used. In Exhibit 9.4 

(a), the lack of attractiveness of the Gulf Coast region 

from southeast Texas to northwest Florida is attributed 

to the lower annual average solar insolation available, 

whereas PNNL study suggests projected productivities in 

this region could be relatively high. This is likely due to 

more moderate annual average temperatures despite lower 

solar insolation. These results should be considered simply 

indicative at this point rather than predictive, but suggest 

preference for lower latitude, i.e., lower elevation sites.

 

Additional factors could conceivably overcome what 

might otherwise appear to be uneconomical site and 

resource conditions for algae production. This could 

include situations where co-location of inland microalgae 

production at higher latitudes might be possible with 

high-cost systems, controls, and enclosures requiring 

energy input for environmental control. For the case of 

offshore marine macroalgae production, the ocean or sea 

environment provides a buffer that moderates temperature 

variation, with the major climate element affecting algal 

growth being the availability of sunlight. Storm and ocean 

dynamics affecting waves, currents, and marine nutrient 

transport cause additional impacts on productivity.

Equally important for photoautotrophic microalgae growth 

with both open and closed cultivation systems is the 

availability of abundant sunlight. A significant portion 

of the United States is suitable for algae production 

from the standpoint of having adequate solar radiation 

(with parts of Hawaii, California, Arizona, New Mexico, 

Texas, and Florida being most promising). The more 

northern latitude states, including Minnesota, Wisconsin, 

Michigan, and the New England states, would have 

very low productivity in the winter months. Growth of 

algae is technically feasible in many parts of the United 

States, but the availability of adequate sunlight and the 

suitability of climate and temperature are key siting and 

resource factors that will determine economic feasibility. 

Preferred Geographic Regions for Algae Production

Exhibit 9.4 presents some simple GIS-based scoping 

conducted by Sandia National Laboratories. The goal 

was to provide a preliminary high-level assessment 

identifying preferred regions of the United States for 

photoautotrophic microalgae production based on 

the application of selected filter criteria on annual 

average climate conditions, the availability of nonfresh water, and the availability of concentrated sources 

of CO2. The climate criteria used to narrow down the 

Exhibit 9.4 Rough scoping assessment of preferred site locations for outdoor algae production

a) Regions with annual average climate conditions meeting 

selected criteria: ≥ 2800 hour annual sunshine, annual 

average temperature ≥ 55 ̊ F, and ≥ 200 freeze-free days

 b) Fossil-fired power plant sources of CO2 within 20 miles of 

municipal wastewater facilities in the preferred climate 

region
9. Resources and Siting 77

locations. It is encouraging that researchers today 

are not only concerned with finding algae with high 

biomass productivity and oil content yield, but also with 

algae that grow well under severe climate conditions, 

particularly extremes in temperature, both high and low. 

Water Requirements 

Precipitation affects water availability (both surface 

and groundwater) at a given location within a given 

watershed region. Areas with higher annual average 

precipitation (more than 40 inches), represented by specific 

regions of Hawaii, the Northwest, and the Southeast, 

are desirable for algae production from the standpoint 

of long-term availability and sustainability of water 

supply. Evaporation, discussed later in this section, is 

closely coupled with climate and will increase water 

requirements for an open algae growth system. Evaporative 

loss can be a critical factor to consider when choosing 

locations for open pond production. Evaporation is a 

less important concern for selecting locations of closed 

photobioreactors, although evaporative cooling is often 

considered as a means to reduce culture temperature. 

The southwestern states (California, Arizona, and New 

Mexico) and Hawaii have the highest evaporation rates 

in the United States, with more than 60 inches annually. 

A thorough evaluation of evaporative water loss is 

needed to assess water requirements, implications for 

sustainable production scale-up, and overall economics. 

Evaporative water loss is discussed in a later subsection. 

Severe Weather Events and Elements

Severe weather events, such as heavy rain and flooding, 

hail storms, dust storms, tornadoes, and hurricanes pose 

serious concerns in the inland regions of the central states, 

Southwest, Southeast, and coastal areas. These weather 

events can contaminate an open system environment or 

cause physical damage to both open and closed systems, 

and need to be taken into account when looking at 

prospects for algae production in both inland and coastal 

regions of the United States. Offshore marine algae 

production will be subject to severe weather impacts 

in the form of wind, waves, and currents that can cause 

disruption or damage to physical structures and operations. 

The marine environment can also be highly corrosive 

to materials and usually demands both the use of higher 

quality and more costly materials and greater maintenance.

Water

General Water Balance and Management Needs

One of the major benefits of growing algae is that, unlike 

most terrestrial agriculture, algal culture can potentially 

utilize non-fresh water sources having few competing 

industrial operations capable of providing excess heat and 

power for cost-effective environmental control of the algae 

cultivation. This would, however, require a more refined 

analysis for systems that would likely be closed and highly 

integrated with co-located industries providing synergistic 

opportunities for utilizing waste heat and energy. Such 

analyses should include assessment of the monthly or 

seasonal solar radiation and ambient temperature ranges; 

it should also establish minimum economically feasible 

operational requirement values for heating in the winter 

and, for closed reactors, cooling in the summer. 

Seasonal Considerations 

Various species of microalgae have potential for biofuel 

feedstock production and are capable of growing under 

a wide range of temperatures. High annual production 

for a given species grown photoautotrophically outdoors, 

however, will require that suitable climatic conditions 

exist for a major part of the year (Maxwell et al., 1985). 

Therefore, a critical climate issue for both open and closed 

photobioreactor systems is the length of economically 

viable growing season(s) for the particular strains of algae 

available for productive cultivation. For outdoor ponds, 

the conventional crop analogy for this is the length of time 

between the last killing frost in the spring and the first 

killing frost in the fall. For closed photobioreactors, the 

conventional crop analog is the greenhouse and the limiting 

energy and cost needed to maintain internal temperature 

throughout the seasons. Availability and rotation of 

different algal species capable of good productivity in 

cold season and hot season conditions, respectively, would 

provide greater flexibility and could extend otherwise 

limited periods of commercially viable algae production. 

The primary geographical location factors for determining 

length of growing season are latitude and elevation, 

which have major influence on the hours and intensity 

of available sunlight per day and the daily and seasonal 

temperature variations. Areas with relatively long growing 

seasons (for example, 240 days or more of adequate solar 

insolation and average daily temperatures above the lower 

threshold needed for economically viable growth) are 

the lower elevation regions of the lower latitude states 

of Hawaii, Florida, and parts of Louisiana, Georgia, 

Texas, New Mexico, Arizona, and California. Other local 

climate and weather conditions will also have influence. 

Thorough analysis (preferably on a state-by-state basis) 

with detailed data is needed to assess areas most suitable 

for algae production based on this climate factor. Discovery 

and development of algae species capable of increased 

productivity under wider ranges of light and temperature 

conditions can also potentially lead to increased annual 

average productivities in more geographically diverse 
78 9. Resources and Siting 

uses, such as saline and brackish ground water, or “coproduced water” from oil, natural gas, and coal-bed 

methane wells (Reynolds, 2003; USGS, 2002). However, 

for open pond systems in more arid environments with 

high rates of evaporation, salinity and water chemistry 

will change with evaporative water loss, thereby changing 

the culture conditions. This will require periodic blowdown of ponds after salinity build-up, periodic addition 

of non-saline make-up water to dilute the salinity buildup, the application of desalination treatment to control 

salinity build-up, or highly adaptive algae that can thrive 

under widely varying conditions. Open algal ponds may 

have to periodically be drained and re-filled, or staged as a 

cascading sequence of increasingly saline ponds each with 

different dominant algae species and growth conditions. 

Implementing water desalination would impose additional 

capital, energy, and operational costs. Disposal of high 

salt content effluent or solid byproducts, from pond 

drainage and replacement, or from desalination operations, 

can also become an environmental problem for inland 

locations. Some salt byproducts may have commercial 

value, depending on the chemistry. Water balance and 

management, along with associated salt build-up and 

management issues, from both a resource perspective 

and an algal cultivation perspective, are important areas 

for future research, modeling, and field assessment. 

Analysis of U.S. Water Supply and Management

Total combined fresh and saline water withdrawals in the 

United States as of the year 2005 were estimated at 410,000 

million gallons per day (Mgal/d), or 460,000 acre-feet 

per year (Kenny et al., 2009). Saline water (seawater and 

brackish coastal water) withdrawals were about 15% of 

the total. Almost all saline water, about 95%, is used by 

the thermoelectric-power industry in the coastal states 

to cool electricity-generating equipment. In 2005, nearly 

one-half of the total U.S. withdrawals (201,000 Mgal/d) 

were for thermoelectric-power generation, representing 

41% of all freshwater, 61% of all surface water, and 95% 

of all saline-water withdrawals in 2005. Withdrawals 

for irrigation of crops and other lands totaled 128,000 

Mgal/d and were the second-largest category of water 

use. Irrigation withdrawals represented 31% of all water 

withdrawals, and 37% of all freshwater withdrawals 

(Kenny et al., 2009). At the national scale, total combined 

fresh and saline water withdrawals more than doubled 

from about 180 billion gallons per day in 1950 to over 400 

billion gallons per day in 1980. Total withdrawals since 

the mid-1980s have remained relatively flat at slightly 

over 400 billion gallons per day, with the majority (85%) 

being fresh (Hutson et al., 2004; Kenny et al., 2009). 

The relatively flat national water withdrawal trend over 

the past 25 years, following the more than doubling of 

water demand over the 30 years prior to that, reflects 

the fact that fresh water sources in the Untied States are 

approaching full allocation. Growing demand for limited 

fresh water supplies in support of development and 

population increase has thus far been offset by increased 

conservation and by the increased re-use of wastewater. 

Many of the nations’ fresh ground water aquifers are under 

increasing stress, and the future expansion of fresh water 

supplies for non-agricultural use must increasingly come 

from the desalination of saline or brackish water sources 

and from the treatment and reuse of wastewater, all of 

which have increasing energy demand implications (DOE, 

2006b; Hightower et al., 2008; Kenny et al., 2009). 

The stress on fresh water supplies in the United States is 

not restricted to the more arid western half of the country, 

but is also becoming a local and regional concern at 

various locations throughout the eastern half of the country, 

where a growing number of counties are experiencing 

net fresh water withdrawals that exceed the sustainable 

supply from precipitation (DOE, 2006b; Hightower et al., 

2008; ). Climate change is also recognized as a factor that 

could have major effect on all sectors of water resources 

supply and management in the future (USGS, 2009). 

Scoping Out Water Requirements for Algae Production

Water use and consumption for algae-based biofuels will 

depend on the cultivation approach (photoautotrophic/

heterotrophic), with water use in upstream organic 

carbon feedstock production needing to be part of the 

heterotrophic assessment. Water use will also depend on 

the type of growth systems used for photoautotrophic 

microalgae (open vs. closed vs. hybrid combination), 

whether evaporative cooling is used for closed systems, 

and the site-specific details of climate, solar insolation, 

and weather conditions (cloud cover, wind, humidity, 

etc.). Also a complicating factor for evaporative water 

loss in open systems will be the degree of salinity of the 

water used for cultivation and the local latitude, elevation, 

ambient temperature variations, solar insolation, humidity, 

and wind conditions (Al-Shammiri, 2002; Hutchison et 

al., 1978; Kokya et al., 2008; Mao, 1999; Oroud, 1995). 

A significant source of water demand with inland algae 

production operations could be for the replacement of water 

continuously lost to evaporation from open cultivation 

systems. Whether or not this is a problem for sustainable 

algal industry scale-up will depend on the geographic 

location, climate conditions, and locally available water 

resources. This will be of greatest impact and concern in 

water-sparse locations, which also tend to be in the more 

arid and higher solar resource regions like the Southwest. 

A rough upper bound estimate of evaporative water loss 
9. Resources and Siting 79

co-produced water. Additional analysis, experimental 

investigation, and field trials at larger scales of operation are 

needed to understand how best to leverage these resources.

Developing and Mapping Water Resources for 

Algae Production

When considering the water resources needed for the 

future development and expansion of algal biofuel 

production, the use of non-fresh water sources will need 

to be emphasized in the face of the growing competition 

and demands on limited sustainable fresh water supplies 

(DOE, 2006b; NAS, 2007; Hightower et al., 2008). 

From a resource use standpoint, integrating algae 

production with wastewater treatment, discussed 

later in this chapter, has the potential benefits of 

productively using non-fresh wastewater resources 

for renewable fuels, putting less additional demand on 

limited fresh water supplies, reducing eutrophication 

of natural water bodies, and recycling nutrients.

The unique ability of many species of algae to grow in 

non-fresh water over a range of salinities means that, in 

addition to coastal and possible off-shore areas, other inland 

parts of the country can be targeted for algae production 

where brackish or saline groundwater supplies may be 

both ample and unused or underutilized. Unfortunately, 

quantitative information remains limited on U.S. brackish 

and saline groundwater resources in terms of their extent, 

water quality and chemistry, and sustainable withdrawal 

capacity. An improved knowledge base is needed to better 

define the spatial distribution, depth, quantity, physical and 

chemical characteristics, and sustainable withdrawal rates 

for these non-fresh ground water resources, and to predict 

the effects of their extraction on the environment (Alley, 

2003; Dennehy, 2004). Saline groundwater resources, 

particularly deeper aquifers that are largely unregulated 

by state engineers and water authorities, are also of 

increasing interest and potential competition for access as 

a source of water for treatment and use to meet commercial 

and residential development needs in high growth rate 

water-sparse regions like the Southwest (Clark, 2009). 

Depth to groundwater is pertinent to the economics of 

resource development. Along with geological data, depth 

information determines the cost of drilling and operating 

(including energy input requirements for pumping) a 

well in a given location (Maxwell et al., 1985). Suitable 

aquifers located closer to the surface and nearer to the 

cultivation site would provide a more cost-effective source 

of water for algae production than deeper sources located 

longer distances from the cultivation site. The location, 

depth, and chemical characterization of saline aquifers 

in the United States are areas of investigation in need 

of greater investment. The maps of saline groundwater 

with open systems was done as part of a hypothetical 

scale-up scenario study in preparation for the National 

Algae Roadmap Workshop, held in December 2008. 

The notional scale-up scenarios and assumptions made 

are discussed later in this chapter (see Exhibit 9.7). 

The evaporative loss estimates from the notional scenarios 

provide an indication of the potential magnitude of the 

issue, and were based on simply applying fresh water 

open horizontal pan evaporation data (Farnsworth et 

al., 1982a and 1982b; Shuttleworth, 1993; Woolhiser 

et al., 1984) to large area scale-up of algae cultivation 

with open systems. Extrapolations based on fresh water 

pan evaporation data will be worst-case and will likely 

be an over-estimate of what can be expected under 

actual operating conditions in the field. Open bodies of 

brackish and saline water will usually experience less 

evaporative loss than fresh water, as noted earlier.

The evaporation estimates suggest that water loss on the 

order of several tens of gallons of water per kilogram 

of dry weight biomass produced, or several hundreds of 

gallons of water per gallon of algal biofuel produced, 

could be a consequence of open system operation 

in the more arid and sunny regions of the country. 

The most optimistic production scenario was for the 

southwestern United States, which assumed annual 

average algal biomass and oil productivities of nearly 

31 g/m2 per day with 50% dry weight oil content. If less 

optimistic productivities are assumed, the estimated 

evaporative water loss intensities will be greater. 

Evaporative water loss associated with algae cultivation 

can be significantly reduced if closed systems are used. 

Evaluation of water use for the overall value chain from 

algal cultivation through harvesting and post-processing 

into fuels and other products will also be important. 

Along the way, additional water will be used and 

consumed, and may well also be saved, reclaimed, and 

recycled, depending on systems and process specifics. 

Water must be considered a key element of life cycle 

analysis for algal biofuels, as with other forms of 

bioenergy (NAS, 2007; Gerbens-Leenes et al., 2009).

In summary, water utilization for algal biomass and 

downstream production of biofuels, both in terms of 

overall input supply needs and consumption, warrants 

closer attention and assessment to better understand and 

refine water resource requirements. Water requirements 

information will not be well characterized until larger scale 

systems are implemented, monitored, and evaluated under a 

range of site locations and conditions. There is considerable 

untapped potential for utilizing brackish, saline, and 
80 9. Resources and Siting 

EIA, 2008 and 2009). Power generation alone (mainly 

using coal) represents over 40% of the total, or more than 

2 billion metric tons per year (EIA, 2008 and 2009). 

Barriers to Viable CO2 Capture and Utilization

The degree to which stationary CO2 emissions can 

be captured and used affordably for algae production 

will be limited by the operational logistics and 

efficiencies, and the availability of land and water 

for algae cultivation scale-up within reasonable 

geographic proximity of stationary sources.

As an example, a recent analysis suggests that for algae 

production to fully utilize the CO2 in the flue gas emitted 

from a 50-MWe semi-base load natural-gas-fired power 

plant would require about 2,200 acres of algae cultivation 

area (Brune et al., 2009). The CO2 generated by the power 

plant can only be effectively used by the algae during 

the photosynthetically active sunlight hours. As a result, 

the greenhouse gas emissions offset will be limited to an 

estimated 20% to 30% of the total power plant emissions 

due to CO2 off-gassing during non-sunlight hours and the 

unavoidable parasitic losses of algae production (Brune 

et al., 2009). Larger coal-fired base-load generators that 

typically output a steady 1,000 to 2500 MWe of power 

would each require many tens of thousands of acres of 

algae production and large volumes of water to provide a 

similar effective offset of 20% to 30% of the CO2 emitted.

The distance for pumping flue gas to algae cultivation 

systems will become a limiting factor that requires 

capture and concentration of CO2 from the flue gas for 

longer distance transport and distribution. Applications 

separating CO2 in large industrial plants, including natural 

gas treatment plants and ammonia production facilities, 

are already in operation today and under consideration for 

possible broader use for carbon capture and storage (CCS) 

in response to climate change (Rubin, 2005; Campbell 

et al., 2008). Photoautotrophic algae will only utilize 

CO2 during daylight hours when photosynthesis is active. 

The rate of effective CO2 uptake will also vary with 

the algae species, biomass growth rate, and details of 

growth system and incident light conditions. Therefore, 

the requirements for CO2 supply to enhance algae 

production, and the matching of CO2 source availability 

with algal cultivation facilities, is not a simple issue. In 

addition, it will be necessary to provide a CO2 source that 

is suitably free of materials potentially toxic to algae. 

An inventory of stationary industrial CO2 sources in 

the more promising regions of the country, including 

characterization of the CO2 emissions stream (e.g., 

rates and quantities of CO2 produced, content, and 

description of substances toxic to algal growth) and the 

local availability and distance to suitable land for algae 

resources are based on incomplete data that was largely 

developed by the USGS prior to the mid-1960s (Feth, 

1965; Dennehy, 2004). More detailed and up-to-date 

information is needed to improve our understanding 

of this resource in support of algae production siting 

analyses (Dennehy, 2004; NATCARB, 2008b). Produced 

water from petroleum, natural gas, and coal bed methane 

wells is another closely related and underutilized water 

resource that can range in quality from nearly fresh 

to hyper-saline (Reynolds 2003; USGS, 2002). 

The geographical location, spatial extent, depth, potential 

yield, recharge rate, sustainability of supply, and quality 

(chemical components and characteristics) are important 

information for assessing non-fresh groundwater aquifer 

resource availability and suitability for economic uses 

(Shannon, 2006), including algae production. A limited 

amount of this information is available for major 

aquifers. However, if these aquifers are spread over 

large geographic areas, detailed analysis is difficult 

and often lacking. Data on small, local aquifers may be 

available through state agencies and private engineering 

companies, but a significant effort will still be needed to 

locate, identify, collect, and analyze this information. 

Carbon Dioxide

The Carbon Capture Opportunity in Algae Production

Efficient algae production requires enriched sources of CO2 

since the rate of supply from the atmosphere is limited by 

diffusion rates through the surface resistance of the water 

in the cultivation system. Flue gas, such as from fossilfuel-fired power plants, would be a good source of CO2

. 

Algae production could provide excellent opportunities for 

the utilization of fossil carbon emissions and complement 

subsurface sequestration. However, algae production does 

not actually sequester fossil carbon, but rather provides 

carbon capture and reuse in the form of fuels and other 

products derived from the algae biomass. Any greenhouse 

gas abatement credits would come from the substitution 

of renewable fuels and other co-products that displace or 

reduce fossil fuel consumption. In addition, at some large 

scale of algae production, parasitic losses from flue gas 

treatment, transport, and distribution could require more 

energy input than the output energy displacement value 

represented by the algae biofuels and other co-products. 

Likely Stationary CO2 Emission Sources

Major stationary CO2 emission sources that could 

potentially be used for algae production are shown in 

Exhibit 9.5. The sources shown (NATCARB, 2008) 

represent over half of the more than 6 billion metric tons 

of CO2 emitted annually in the United States (EPA, 2009; 
9. Resources and Siting 81

production, is needed for making refined assessments for 

algae production siting and CO2 sourcing. One outcome 

of a hypothetical algae production scale-up scenario is 

the limited quantity of CO2 that would likely be available 

from stationary industrial point sources (e.g., Exhibit 

9.5) within practical transport distances of suitable algae 

production sites in a given geographical region. This 

can be expected to constrain the extent to which algal 

biofuels production can be affordably scaled up within 

any given region unless other factors drive the investment 

in expanding the nation’s CO2 pipeline infrastructure. 

Land

Factors for Evaluating Land for Algal Production

Land availability will be important for algae production 

because either open or closed systems will require 

relatively large areas for implementation, as is expected 

with any photosynthesis-based biomass feedstock. Even 

at levels of photoautotrophic microalgae biomass and oil 

productivity that would stretch the limits of an aggressive 

R&D program (e.g., target annual average biomass 

production of 30 to 60 g/m2 per day with 30% to 50% 

neutral lipid content on a dry weight basis), such systems 

would require in the range of roughly 800 to 2600 acres of 

algae culture surface area to produce 10 million gallons of 

oil feedstock, as will be discussed further in chapter 10. 

Land availability is influenced by various physical, social, 

economic, legal, and political factors, as illustrated in 

Exhibit 9.6. Hundreds of millions of acres of relatively lowproductivity, lower-value land exists in the United States 

(USDA, 2006 and 2009), including pasture, grassland, 

and relatively barren desert land. For a realistic appraisal 

of land for algae production (i.e., land that would be both 

suitable and potentially available for siting algae production 

facilities), several characteristics need to be considered. 

Physical characteristics, such as topography and soil, could 

limit the land available for open pond algae farming. Soils, 

and particularly their porosity and permeability 

characteristics, affect the construction costs and design 

of open systems by virtue of the need for pond lining or 

sealing. Topography would be a limiting factor for these 

systems because the installation of large shallow ponds 

requires relatively flat terrain. Areas with more than 5%

 slope could well be eliminated from consideration due to 

the high cost that would be required for site 

preparation and leveling. 

Land ownership information provides valuable insights 

on which policies and stakeholders could affect project 

development. Publicly and privately owned lands are 

subject to variable use, lease, and purchase requirements. 

For example, much of the land in the West is government 

owned, which means that environmental assessments and/

CATEGORY CO2

 EMISSIONS

(Million Metric Ton/Year) NUMBER OF SOURCES

Ag Processing 6.3 140

Cement Plants 86.3 112

Electricity Generation 2,702.5 3,002

Ethanol Plants 41.3 163

Fertilizer 7.0 13

Industrial 141.9 665

Other 3.6 53

Petroleum and Natural

Gas Processing 90.2 475

Refineries/Chemical 196.9 173

Total 3,276.1 4,796

Exhibit 9.5 Major stationary CO2 sources in the United States (NATCARB, 2008a)
82 9. Resources and Siting 

or environmental impact statements could be required 

as part of the approval process. Indian reservations also 

comprise a significant portion of this land. Land ownership 

can represent and impose political and regulatory 

constraints on land availability (Maxwell et al., 1985). 

Further, as with any form of biomass, algae productivity 

will be constrained by the available energy density 

in sunlight and the relatively low efficiencies of 

photosynthetic processes coupled with other systems losses. 

The result will be theoretical and practical upper limits on 

the amount of biomass growth that can be achieved per unit 

of illuminated surface (Weyer et al., 2009). Contributing to 

productivity limits per unit of illuminated surface area is the 

fact that algal cells nearest the illuminated surface absorb 

the light and shade their neighbors farther from the light 

source. Optimizing light utilization in algae production 

systems includes the challenge of managing dissipative 

energy losses that occur when incident photons that cannot 

otherwise be effectively captured and used by the algae 

in photosynthesis are instead converted to thermal (heat) 

energy in the culture media and surrounding cultivation 

system structures. Depending on the algae strain and 

culture system approach used, the dissipative heat loading 

can be a benefit in moderating culture temperatures and 

improving productivity under colder ambient conditions, 

or can lead to overheating and loss of productivity 

during hotter ambient conditions. Loss mechanisms that 

restrict the fraction of incident photon flux that can be 

effectively used to drive photosynthesis ultimately places 

practical upper limits on the biomass productivity.

Despite the practical upper limits that will naturally exist 

for algae productivity, the potential remains for high 

algae biomass production relative to more conventional 

crops, (chapter 10). It must be stressed that “potential” 

algal biomass and bio-oil production projections at 

commercial scale currently remain hypothetical rather 

than real, given that large-scale algae biomass production 

intended for bioenergy feedstock does not yet exist. 

Relatively large-scale commercial algae production 

with open ponds for high-value products can serve as a 

baseline reference, but currently reflect lower biomass 

productivities in the range of 10 - 20 g/m2 per day. This 

is significantly lower than the more optimistic target 

projections for biofuel feedstock of 30 - 60 g/m2 per day. 

However, such systems have not been optimized for 

higher-volume, lower-value production with algal strains 

developed and improved over time to be more suitable and 

productive for biofuel feedstock rather than those used 

for today’s high-value algae biomass product markets. 

Land Availability Constraints

Land use and land value affect land affordability. By 

reviewing the more recent economic analyses for algae 

biomass and projected oil production, the cost of land is 

often not considered or is relatively small compared to other 

capital cost. Land that is highly desirable for development 

and other set-asides for publically beneficial reasons may 

All

Land

Parcels

Physically

Suitable

Land

Politically

Available

Land

Affordable

Land

Available

Land

Typography

Land 

Ownership Current 

Land Value Systems

Engineering

Enviromental

Restrictions Current

Land Use Legislation

Water and and Regualtions

Climate

Resources Exhibit 9.6 Factors and process steps for evaluating and constraining 

the available and appropriately suitable land for algae production 

(Adapted from Maxwell et al., 1985 )
9. Resources and Siting 83

Wastewater Treatment and 

Recycling Applications

Municipal wastewater treatment facilities and agricultural 

dairy and feedlot operations located throughout the 

United States, particularly in the eastern half of the 

country, represent potential co-location sites for algae 

operations where nutrient-rich wastewater could be 

used for algae production, and the algae production can 

help provide nutrient removal service in the wastewater 

treatment. Two main types of algae production facility are 

envisioned: dedicated facilities, with the main purpose of 

biomass production, and wastewater treatment facilities, 

which produce algal biomass as a consequence of the 

wastewater treatment. Dedicated biomass production 

facilities will also require wastewater treatment and 

nutrient recycling. A subset of wastewater treatment 

facilities consist of evaporation facilities, which are 

used to dispose of wastewater or brines. The roles of 

these facility types in the development of an algae 

biofuels industry are discussed in this subsection.

Algae can be useful in the treatment of waters polluted with 

organic matter, excess nutrients (e.g., nitrogen, phosphorus, 

and potassium), metals, synthetic organic compounds, 

not be seen as suitable for algae production. The same 

applies to land highly suited for higher-value agricultural 

use. Beyond economics, this also avoids the perception 

and potential conflict of food and feed production versus 

fuel. Sensitive environmental or cultural land constraints 

will also reduce the overall land availability (Maxwell 

et al., 1985). Examples of this type of constraint include 

parks, monuments, wildlife areas, archaeological sites, 

and other historical sites. On the other hand, some land 

cover characteristics could present excellent opportunities 

for algae farming. Land cover categories such as barren 

and scrubland cover a large portion of the West and may 

provide an area free from other food-based agriculture 

where algae growth systems could be sited (Maxwell et al., 

1985). The availability and sustainability of water supplies 

in the West will also be a key consideration, as noted earlier.

9.4 Integration with Water 

Treatment Facilities 

Inevitably, wastewater treatment and recycling 

must be incorporated with algae biofuel production. 

The main connections of algae production and 

wastewater treatment are the following:

• Treatment technology is needed to recycle 

nutrients and water from algae biofuel processing 

residuals for use in algae production. 

• Imported wastewater provides nutrients and water to 

make-up inevitable losses. The imported wastewater 

would be treated as part of the algae production.

• Algae-based wastewater treatment provides a needed

service.

• Algae-based wastewater treatment can be 

deployed in the near-term and provides workforce 

training and experience in large-scale algae 

cultivation that would translate to future dedicated 

algae feedstock production facilities. 

For large-scale algae biofuel production, nutrients from 

wastewater (municipal and agricultural) would be captured 

by algae and then recycled from the oil extraction residuals 

for additional rounds of algae production. Nutrient 

recycling would be needed since wastewater flows in 

the United States are insufficient to support large-scale 

algae production on the basis of a single use of nutrients. 

Inevitable nutrients losses during algae production 

and processing could be made up with wastewater 

nutrients, which can also help supplement and off-set 

the cost of commercial fertilizers for algae production. 

Supply and cost of nutrients (nitrogen, phosphorus, and 

potassium) be a key issue for achieving affordable and 

sustainable scale-up of algae biofuels production.

POTENTIAL BENEFITS OF ALGAE PRODUCTION 

WITH WASTEWATER TREATMENT

Although algae-based wastewater treatment requires 

many times more land area than mechanical treatment 

technologies, in suitable climates, algae-based 

treatment has the following advantages: 

• Early opportunity to develop large-scale 

algae production infrastructure

• Development of skilled algae production workforce

• Potential for nutrient recycling at algae 

biomass production facilities

• Wastewater treatment revenue that 

offsets algae production costs

• Lower capital and O&M costs than 

conventional wastewater treatment

• Lower energy intensity than conventional 

wastewater treatment (a greenhouse gas benefit)

• Potential to be integrated with power plant 

or other CO2-emitting industry operations

• Potential to treat agricultural drainage 

and eutrophic water bodies
84 9. Resources and Siting 

As with other algae production systems, harvesting is a 

crucial step in wastewater treatment systems. The standard 

method is chemical addition to achieve coagulation and 

flocculation, followed by algae separation in dissolved 

air flotation units or sedimentation clarifiers. The cost 

of chemical addition ($0.10 - $0.17 per m3 treated) 

(Maglion, 2008) is high for biofuel production. Nonchemical flocculation processes (bioflocculation and 

autoflocculation) are far less costly, but research is 

needed to improve the reliability of these processes (as 

discussed in chapter 4). As noted above, the major types 

of wastewaters available for combined algae production 

and water treatment are those contaminated with organic 

matter and nutrients (e.g., municipal and industrial sources) 

and wastewaters mainly contaminated with inorganic 

nutrients (e.g., agricultural drainage, rivers, and lakes).

Treatment of Organic Wastewaters for Algae Production

Organic-rich wastewaters usually also contain nutrients, 

requiring two types of treatment. Algae are similar to 

plants in that they both produce oxygen and assimilate 

nutrients. These reactions are also the best-known 

mechanisms of wastewater treatment by algae. The 

dissolved oxygen algae release is used by treatment bacteria 

to oxidize waste organic matter (Exhibit 9.7). The ability 

of algae to assimilate dissolved nutrients down to trace 

concentrations is useful in wastewater treatment, if the 

nutrient-rich algae are then also removed from the water.

Less well-known are the ability of algal systems to provide 

natural disinfection and remove trace contaminants.

Disinfection is promoted via the production of oxygen 

radicals in the presence of sunlight, dissolved oxygen, 

and naturally occurring organic catalysts (Sinton et al., 

2002, Kohn et al., 2007). Heavy metals may be removed 

by adsorption to algal cells, which will be a benefit as 

long as the resulting metals concentrations in the algae 

biomass are not excessive or inhibitive for later use in 

the processing of fuel and other co-products. Finally, the 

interaction of algae and bacteria in wastewater cultures 

leads to degradation of a wide variety of synthetic 

organic compounds such as phenol and acetonitrile 

(Borde et al., 2003, Muñoz et al., 2005). The 

removal of trace contaminants (e.g., endocrine disrupting 

compounds such as human hormones and antibiotics 

from animal facilities) is an area in need of study. 

Mechanical treatment technologies typically hold 

the wastewater for less than 12 hours, whereas pond 

technologies hold the wastewater for at least several days 

and in an environment similar to many natural receiving 

waters. The bioaccumulation of trace contaminants in 

algae that would occur in the receiving waters, eventually 

harming higher organisms, might be prevented to a 

and potentially endocrine disrupting compounds (Oswald, 

1988; Woertz et al., 2009; Aksu, 1998; Borde et al., 

2002). High rates of algae production lead to high rates 

of nutrient removal and wastewater treatment. Thus, the 

objectives of biofuel feedstock production and wastewater 

treatment are aligned, at least in terms of maximizing 

biomass production. Maintenance of lipid-rich strains, 

or manipulation of culture conditions to promote lipid 

production, have yet to be demonstrated consistently 

for ponds, including wastewater treatment ponds. 

Algae-based treatment facilities are typically less expensive 

to build and to operate than conventional mechanical 

treatment facilities. For example, high-productivity algae 

ponds have a total cost that is about 70% less than activated 

sludge, which is the leading water treatment technology 

used in the United States (Downing et al., 2002). This 

cost savings, coupled with the tremendous need for 

expanded and improved wastewater treatment in the United 

States (EPA, 2008) and throughout the world, provides a 

practical opportunity to install algae production facilities 

in conjunction with wastewater treatment. The major 

classes of wastewaters to be treated are municipal, organic 

industrial (e.g., food processing), organic agricultural 

(e.g., confined animal facilities), and eutrophic waters 

with low organic content but high nutrient content (e.g., 

agricultural drainage, lakes, and rivers). Despite a seeming 

abundance of wastewater and waste nutrients, recycling of 

nutrients and carbon at algae production facilities will be 

needed if algae are to make a substantial contribution to 

national biofuel production. Even with internal recycling, 

importation of wastes and/or wastewater will still be 

needed in dedicated algae biomass production facilities 

to make up for nutrient losses (Brune et al., 2009). 

Algae Production Techniques for 

Wastewater Treatment Plants

Integration of algae production with wastewater treatment 

is illustrated schematically in Exhibit 9.7. Existing 

algae-based treatment facilities use relatively deep 

ponds (1-6 m). The great depths contribute to low algae 

productivity, but high productivity is not crucial to the 

treatment goals of these facilities (removal of organic 

matter and pathogens only). Ponds for more advanced 

treatment, including nutrient removal, need high algae 

productivities (as does biofuels feedstock production). 

These highly productive systems use shallow reactors, 

either high rate ponds (~30 cm) or algal turf scrubbers 

(~1 cm). Closed photobioreactors are not emphasized 

in this wastewater treatment discussion since they are 

likely to be economical only when also producing 

high-value products (>$100/kg biomass), which is 

unlikely when wastewater contaminants are present.
9. Resources and Siting 85

Clarifier Clarifier

Digestor Generator

High Rate 

Pond

Food 

Production

Option

Raw Sewage

Sludge CO2

kWh

Algae Biomass

Inputs

Liquid Biofuel

To Fertilizer

Treated 

Effluent

Products

Reclaimed Water

Fuels Fertilizer

b) Simplified conceptual system block diagram 

Algae

Bacteria

CO2

CO2

N

P CO2

N

P

O2

Waste

Water

Reclaimed

Water

Biomass

Organics

Sun

Exhibit 9.7 Integration of algae production with wastewater treatment for nutrient removal and biomass production:

a) Basic principles of operation;
86 9. Resources and Siting 

• Determine growth model parameters

• Develop algae grazer control strategies 

• Develop reliable low-cost algae harvesting 

techniques, such as bioflocculation, 

autoflocculation, micro-screening, etc.

• Demonstrate recycling of biofuel processing 

wastes for algae production 

• Determine the cost savings and greenhouse gas 

(GHG) emissions avoidance benefits compared to 

conventional wastewater treatment technologies.

9.5 Co-location of Algal 

Cultivation Facilities with 

CO2-Emitting Industries

This section includes findings from discussions held at the 

National Algal Roadmap Workshop break-out sessions, 

and additional input sought from managers at major 

electric utilities through later meetings and conference 

calls. These follow-on efforts were coordinated with the 

Electric Power Research Institute (EPRI), and included 

several large municipal electric utilities. The topics 

of discussion included the value proposition, desired 

outcomes, integration opportunities and challenges, market 

drivers, technical and market challenges, constraints 

on large-scale development, co-products, and potential 

opportunities for the federal government. Findings from 

these interviews and conference calls were integrated 

with the Workshop inputs in developing this section.

It is important to point out that amongst the numerous 

barriers to co-location of algal cultivation facilities with 

industrial CO2 sources identified at the Workshop and 

subsequent discussions with electric utilities, an overriding 

theme was that electric utilities primarily view algae 

cultivation as a means of CO2 capture as opposed to a 

method for producing biofuels and co-products. Thus, 

electric utilities may need to partner with algae cultivation/

technology companies and fuel refiners/distributers with 

very different business models and goals for algae 

production in order for this type of co-location to be 

widely commercialized. Furthermore, research efforts 

and policy evaluations would likely need to focus on 

both carbon capture and the production of biofuels and 

co-products to overcome barriers (technical, regulatory 

and economic) for algae facilities that are co-located 

with electric utilities and other industrial CO2 sources. 

great extend by pond treatment followed by algae 

harvesting. The processing of the algal biomass for fuel 

and other co-products would presumably destroy and 

neutralize the contaminants, but further investigation is

needed to confirm this. However, any heavy metals 

contaminating the algal biomass likely would remain in 

the waste from biofuel processing, potentially increasing 

the cost of waste disposal or recycling. For all biofuel 

feedstocks, routes of such contamination should be 

studied and preventative measures developed.

Treatment of Inorganic Wastewaters for Algae Production

In addition to the ability of algae systems to treat 

organic-rich wastewaters, their ability to treat highnutrient, low-organic content wastewaters will expand 

the opportunities for algae production systems. 

Agricultural drainage and eutrophic water bodies 

(e.g., Salton Sea, Calif.) are examples of such waters 

(Benemann et al., 2002). Treatment of nutrient-rich 

waters is likely to occur in more rural settings than 

treatment of municipal wastewaters, potentially leading 

to greater land availability and savings in land costs.

For algae-based treatment of low-organic content 

wastewaters, CO2 addition or slow atmospheric 

absorption is essential since inorganic carbon generation 

from decomposition of organic matter would not be 

significant. Treatment of agricultural drainage with 

algal turf scrubbers without CO2-addition and high 

rate ponds with CO2 addition has been demonstrated in 

California’s Central Valley and elsewhere (Craggs et 

al., 1996; Mulbry et al., 2008; Lundquist et al., 2004). 

High rate ponds might be used as components of 

evaporation systems needed to dispose of blow-down 

or other wastewater. The high rate ponds could create 

an algal product while performing the service of water 

evaporation. Evaporation ponds are currently used to 

dispose of agricultural drainage, oil field produced 

water, mine drainage, etc. As with any evaporation pond 

system, hazards to wildlife from toxic compounds (e.g., 

selenium, chromium) must be carefully evaluated.

Main Research Needs for Algae 

Production with Wastewater 

Successful use of high rate ponds specifically for 

nutrient removal/recycling requires resolution 

of several issues, as follows: 

• Large-scale (3-5 acre) demonstration of CO2-

enhanced high rate ponds for nutrient removal 

• Determine CO2 biofixation efficiency
9. Resources and Siting 87

Coal-fired power plants may be a convenient source of 

CO2 for algae production, but from an emissions control 

perspective, construction of algae systems at natural 

gas-fired power plants may be a better investment. The 

reason is that coal-fired power plants have higher CO2

emissions per unit energy produced than natural gas-fired 

power plants. Thus, using algae to capture the maximum 

amount of CO2 emissions from coal-fired plants would 

require proportionally larger algae production systems 

per unit energy produced and higher costs per unit energy 

produced. However, coal-fired plant flue gas typically 

has about a factor of two greater CO2 concentration 

(10 - 15%) than natural gas plants (5 - 6%), which can 

bring some advantage in terms of efficiency of capture, 

transport, and delivery of CO2 from the power plant to 

the algae cultivation site. Also, gas-fired power plants 

that operate as peaking plants rather than base-load 

generators will have intermittent operation that would 

introduce intermittency in the supply of CO2 for algae 

growth. The impact on algae production would depend 

on the phasing of the intermittency with respect to the 

daylight hours when photosynthesis is active. Gas-fired 

baseload generators would not be intermittent, but, as 

with baseload coal-fired plants, would also emit CO2

during periods of darkness when it cannot be utilized by 

the algae through photosynthesis. During those times, 

the CO2 would be emitted to the atmosphere if not 

captured and sequestered by other means (Rubin, 2005). 

The Opportunity in Co-Locating 

with CO2-Emitting Sources

Since photoautotropic algae growth requires CO2, and 

productivity can be enhanced by supplementing the 

limited CO2 available from the atmosphere, concentrated 

sources flue gas from fossil-fuel burning power plants 

and other CO2-emitting industrial sources can be 

beneficially used in algae production. Resulting costs for 

CO2 will be site-specific and dependent on methods of 

capture, conditioning, and distance of transport to algae 

cultivation sites. Costs are expected to be lower than for 

pure commercially supplied CO2, but economic viability 

must be determined case by case. Offset of fossil fuel 

consumption by algae biofuel and other co-products must 

be done with approaches that provide a net GHG emissions 

reduction. Co-location of algal cultivation with industrial 

CO2 sources is a promising area for further research.

While the information in this section focuses on fossilfired power plants, it is also relevant to other CO2

-intensive 

industries (e.g., cement manufacturing, fossil fuel 

extraction/refining, fermentation-based industries, some 

geothermal power production, etc.). The emissions from 

many of these facilities have higher CO2 concentrations 

compared to power plant flue gas, which typically ranges 

from about 5% to about 15%, depending on the type of 

plant and fuel used. This higher concentration would affect 

the sizing and operations of algae production facilities—

an aspect that could be incorporated into engineering 

models described in more detail in the Systems and 

Techno-Economic Assessment section of this report.

An important policy question to consider is the value 

of CO2 absorption by algae in any carbon-credit or 

cap and trade framework, in that the carbon will be 

re-released to the atmosphere when algal-derived 

fuels are combusted. While algae biofuels can be 

expected to result in a net reduction of overall GHG 

emissions, the process of capturing flue-gas CO2 to make 

transportation fuels may not rigorously be considered 

carbon sequestration. The regulatory implications 

of this will need to be addressed before utilities 

and fuel companies are likely to widely adopt algal 

cultivation co-located with industrial CO2 sources.

A variety of stationary industrial sources of CO2

are distributed throughout the United States. The 

quantitative breakdown, introduced earlier in Exhibit 

9.5, shows that fossil-fired power plants represent 

the majority of CO2 emissions from stationary 

sources. A number of large coal-burning power plants 

distributed across the southern tier states provide 

ample sources for algal growth on a large scale. 

ADVANTAGES OF CO-LOCATION OF 

ALGAE PRODUCTION WITH STATIONARY 

INDUSTRIAL CO2 SOURCES

• Abundant quantities of concentrated CO2 available 

from stationary industrial sources can supplement 

low concentration CO2 from the atmosphere. 

• Excess heat or power may be available to provide

heating or cooling for improved thermal 

management of algae cultivation systems – this 

will allow developing algal cultivation facilities 

under a broader range of geographic and climate 

conditions on or near a year-round basis.

• Excess wastewater or cooling water may be 

available, found often in proximity of power 

plants – overcoming a primary resource challenge 

for algae cultivation at scale, while providing 

beneficial re-use of cooling water and wastewater.

• Potential carbon credit for utilities. This will 

require establishing a U.S. policy on carbon 

absorption and re-use as transportation 

fuel in lieu of permanent sequestration.
88 9. Resources and Siting 

• Maintaining cultivation facilities during utility outages 

and through seasonal changes in algal growth rates: 

Detailed models will be needed to develop and evaluate 

approaches for managing the variable nature of both 

CO2 emissions and algal growth rates/CO2 uptake.

• Resistance from electric utilities: Electric utilities are 

not in the fuels business and regulated public utility 

commissions will be constrained in entering the fuel 

production arena. Their fundamental objective will be 

to capture CO2 as opposed to producing biofuels and 

co-products. Thus, mechanisms to encourage partnering 

between utilities and algae/fuel companies will be 

required, and new business models will be needed to 

commercialize this approach.

Directions for Research and Development

Several areas for research, as well as policy-development 

efforts, will be required for commercialization of 

algal cultivation facilities co-located with industrial 

CO2 sources and/or wastewater treatment facilities. 

The following directions have been identified:

• Develop computer models of algae production 

facilities that will aid the following:

▪ Rapid and consistent engineering design

▪ Techno-economic analyses

▪ Life Cycle Analysis and GHG abatement analysis

▪ National inventory of potential production sites

▪ Evaluation of economies of scale vs. advantages 

of decentralized production considering 

parasitic losses of CO2 transport, etc.

▪ Evaluation of temperature control (power 

plant cooling and algae pond heating)

▪ Development of efficient test-bed facilities

• Establish national algae biomass production test-beds

to conduct research at the pilot scale (3 - 10 acres). 

The test-beds would ideally be located at power plants, 

wastewater treatment facilities, ethanol plants or other

CO2 emitting industry facilities, and agricultural 

drainage/water body restoration sites that also represent

 a range geographical locations, solar resource, and

 climate conditions. This effort could involve a 

consortium of R&D organizations, universities, algal 

cultivation companies, algal technology companies,

refiners, distributors, and other participants coordinated

at the national level. Specific test-bed R&D 

topics relevant to power and wastewater utilities 

include:

▪ Technology evaluation at larger scales

▪ Determination of algae production facility model 

parameters

Barriers to Co-Location of Algae 

Production with Stationary Industrial 

CO2 Sources 

• Need for nutrient sources: While stationary industrial 

sources of concentrated CO2 can potentially provide 

ample carbon for photosynthesis-driven algal growth, 

in most cases there will not be a complementary 

nutrient (N, P, K) supply. Therefore nutrients must be 

brought in from other sources, or in some cases algal 

cultivation could be co-located with both stationary 

CO2 sources and nutrient sources such as wastewater 

treatment facilities and agricultural waste streams. 

• Unclear regulatory framework for carbon-capture 

credits: Until there are regulations in place that 

quantify carbon credits from algal growth facilities, 

the uncertainty may pose a barrier for wide commercial 

adoption of the technology.

• Land availability: Suitable and affordable vacant land 

may not be available adjacent to or near major 

power plants 

• Emissions from ponds are at ground level: Regulatory 

requirements from power plants and other stationary 

sources are governed by the Clean Air Act, and 

are based upon point-source emissions from high 

elevations. The use of flue gas to cultivate algae will 

involve non-point source emissions at ground level. 

• Capital costs and operational costs: There exists a 

need to evaluate capital costs and parasitic operational 

losses (and costs) for infrastructure and power required 

to capture and deliver industrial CO2 to ponds and 

grow/harvest algae. These costs and losses must be 

minimized and compared to other approaches for the 

capture and sequestration or reuse of carbon. Current 

estimates are that approximately 20% - 30% of a 

power plant’s greenhouse gas emissions can be offset 

by algae biofuel and protein production (Brune et al., 

2009). Although often referred to as a “free” resource, 

the capture and delivery of concentrated CO2 from 

stationary industrial sources as a supplement to enhance 

and optimize algae production will not be “free”.

• Too much CO2 near plants for realistic absorption: 

Large power plants release too much CO2 to 

be absorbed by algal ponds at a realistic scale 

likely to be possible near the power plant 

facility. The same generally holds true for other 

stationary industrial sources of CO2 (cement 

plants, ethanol plants, etc.). Also, CO2 is only 

absorbed during periods when sunlight is available 

and photosynthesis is active in the algae.
9. Resources and Siting 89

▪ Flue gas or other industrial source CO2 supply 

logistics, costs, and absorption/biofixation efficiency 

and algal biomass productivity given seasonal and

diel variations in photosynthesis and various 

water chemistries

▪ Control of algal biomass quality (ratios of lipids:

proteins: carbohydrates and C:N:P)

▪ Methods of nutrient and water recycling within 

production facilities; salinity and blowdown

 management.

▪ Algal biomass handling, storage, and processing 

prior to fuel extraction; flocculation harvesting; 

pathogen safety

▪ Beneficial management of residuals for soil carbon 

development, crop fertilization, etc. 

▪ Development of algal strains and their cultivation

techniques

▪ Investigate the safety of ground-level flue gas 

emissions from ponds including plume modeling 

and regulatory analysis

▪ Effects of various flue gases on algae production 

and co-product quality

▪ Scrubbing of flue gas for NOx, SOx, etc.

▪ Power plant cooling with treated wastewater in 

conjunction with algae production 

• Evaluate policies that would encourage partnering 

between public utilities/other industrial CO2 sources 

and algal cultivation/technology companies 

and refiners/distributors.

• Develop and train the future algae production/algae 

biomass processing workforce at the national test-bed 

and other sites. Develop university training programs. 
90 9. Resources and Siting 

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 10. Systems and Techno-Economic Analysis 93

challenges along each of these pathways, as discussed 

throughout the Roadmap. Systems modeling and analyses 

applied across this space and done at different levels of 

precision and granularity, ranging from individual unit 

operations to an integrated enterprise, to an overall regional 

or national resource and supply chain assessment, can 

provide informed guidance for targeting investments in 

select technologies, processes, systems, and deployment 

approaches. It can also help track performance and 

progress (technical, economic, and environmental) critical 

to meeting performance objectives and reaching goals for 

successful commercialization, as illustrated in Exhibit 10.2. 

In short, techno-economic modeling and analysis can 

serve a range of purposes and goals that include: 

• Assess technical performance and cost/benefit 

tradeoffs among different technologies, systems, 

and processes, e.g., comparative yield and 

energy balance for different pathways

• Assess economic impact of R&D strategies and 

investments, e.g., comparative cost per 

gallon of biofuel for different pathways

10. Systems and Techno-Economic Analysis

Successful development of an algae-based biofuels and 

co-products industry requires the optimum combination of 

technical innovations in systems and processes, coupled 

with economic feasibility in the practical implementation 

and integrated scale-up for commercial production 

and marketing. Enabling successful advancement and 

commercialization of the still relatively immature 

field of algal biofuels also requires the confidence and 

engagement of key public and private stakeholders so 

they can make necessary investments over time to reduce 

technical risks and overcome challenges to developing 

an algal biofuels industry. Toward this end, objective 

and quantitative modeling and analyses of systems and 

processes are needed that span different enterprise levels 

across the overall algae-to-biofuels supply chain. Such 

analyses can provide improved understanding and insight 

to help guide successful industry development within the 

real-world context of technical, environmental, political, 

infrastructural, and market conditions and constraints. 

10.1 Objectives of 

Techno-Economic Analysis 

Given the numerous potential approaches and pathways 

available for algae biofuels and co-products (as illustrated 

in Exhibit 10.1), significant investment is expected to be 

required to overcome the various technical and economic 

ALGAE

Cyanobacteria Unicellular 

Microalgae

Multicellular 

Macroalgae

Open Terrestrial

Systems

Closed Terrestrial

Systems

Open Offshore

Systems

Anaerobic

Digestion

Biodiesel Alcohols Biogas Co-Products Renewable

Hydrocarbons

Direct 

Synthesis

Thermochemical

Conversion

Biochemical

Conversion

Consolidated

Biomass Lipids Carbohydrates Proteins Hydrocarbons

& Alcohols*

Phototrophic Mixotrophic Phototrophic Heterotrophic Phototrophic

Hybrid 

Systems

Species

Selection &

Biology

Intermediate

Constituents

Conversion

Processes

End Use Fuels

& Products

Cultivation

System:

- Harvesting

- Dewatering

- Fractionation

- Separation

* Biologically produced in-situ by the organism

Exhibit 10.1 High level illustration of various approaches and pathways to developing algae-derived biofuelsand co-products
94 10. Systems and Techno-Economic Analysis 

10.2 TEA Scope and Methods

Exhibit 10.3 illustrates at a high level the essential 

elements of techno-economic modeling and analysis. 

These intersecting elements present a broad systems 

perspective that integrates the interdependent science 

and engineering aspects specific to developing algae 

biofuels, keeping environmental, economic, and 

policy aspects in view to provide critical insight 

and information needed for decision-support. 

Techno-economic assessment for algae biofuels is 

highly interdisciplinary and will range from GIS-based 

resource and siting assessment, to engineering modeling 

of systems and processes at the unit operations level, to 

interdependency analyses of the entire supply chain. Exhibit 

10.4 illustrates a broad systems perspective of issues and 

approaches for the overall algae biofuels supply chain from 

siting and resources to product end-use. The categories 

shown follow the process steps in the algal biofuel supply 

chain sequence. Such summarization of key areas to be 

addressed to enable algal biofuel production provides 

guidance for the scope of content that should be integrated 

into systems techno-economic modeling and analysis. 

• Assess environmental impact of R&D strategies 

and investments, e.g., comparative net greenhouse 

gas (GHG) emissions per gallon of biofuel for 

different pathways

• Assess consequences and constraints of alternative 

pathways for algal feedstock, biofuels, and coproducts industry build-up, e.g., land, water, CO2

, 

other nutrients, energy, and infrastructure.

• Inform R&D and business development investment 

decisions

• Inform policy decisions and explore “what if”

scenarios

• Provide insight and actionable information needed 

to successfully guide technical advancement, 

integrated system scale-up, and commercialization

DOE’s Biomass Program employs a wide range of 

analytical tools, data, and methodologies to support 

decision-making, guide research, and demonstrate 

progress toward goals. In conjunction with the Algae 

Roadmap, Biomass Program’s strategic and portfolio 

analysis efforts are expanding to include algae with 

techno-economic modeling and analysis (TEA), life cycle 

assessment (LCA), and geographic information system 

(GIS) based resource assessments. 

Stage-II Advances

Commercialization Threshold

Stage-I Advances

Cost & Risk

Reductions

Perfomance 

Improvements

Cost & Risk

Reductions

Perfomance 

Improvements

T0 T1 T2 (current status) (e.g., 5-15 years)

Cost, Performance, and Risk Metrics

Roadmap Timeframe Multi-Stage R&D,

Demonstration, Commercializtion, Deployment

Biofuel Conversion

Extraction & Fractionation

Harvesting & Dewatering

Algae Science & Biomass Production

Systems Infrastructure & Integration

Uncertainty Range

S&T, Systems & Processes Areas

Exhibit 10.2 Systems and Techno-Economic Modeling and Analysis as a decision-support tool

It can track and assess performance, and evaluate investment cost/benefit/risk tradeoffs to inform both technical and programmatic decisions
 10. Systems and Techno-Economic Analysis 95

The scope of TEA will ideally include the capability to 

apply and integrate detailed process engineering and 

physics-based modeling at the unit operations level 

with multi-scale and multi-path systems modeling and 

comparative tradeoff assessment. This can include 

geospatial (GIS-based) data collection, analysis and 

visualization, systems and processes optimization, 

and dynamic interdependency analyses of the overall 

supply chain at a local, regional, national, or global 

scale. A major environmental impact element will 

be life cycle analysis (LCA) to assess GHG impacts 

and other resource use footprint (e.g., water).

The overall goal is to capitalize on the power and insight 

available through application of well developed computer 

modeling and analysis tools combined with disparate 

database information that exists or can be developed. 

For example, a process-based algae growth model that 

accurately reflects and integrates the dynamic behavior of 

the key biological processes with the engineered growth 

system and its time-dependent physical and chemical 

conditions (including local time-varying climate and 

weather) can not only provide more detailed input to 

the techno-economical performance analysis of algae 

cultivation, but can also reveal opportunities for improved 

system and process design and operation. Since the 

characteristics of the biological system at the microscopic 

algae cell level affect the performance of the engineered 

cultivation system and processes at a higher integrated 

level, which in turn must function within climate and 

weather conditions that vary with geographical location, 

the approach needs to be both multi-level and multi-scale. 

An algae biofuels and co-products supply chain will be a 

complex interdependent system with numerous alternative 

pathways and functional elements and feedbacks at various 

spatial and temporal scales and resolutions, as suggested 

in Exhibit 10.5. System and process simulation and 

optimization under a system engineering framework can 

prove very beneficial for system design and operation. For 

example, optimizing conditions that produce the highest 

neutral lipid content of the algal biomass under a range 

of design conditions, when bio-oil feedstock production 

is the primary pathway and objective, may not lead to the 

highest overall biomass or lipid productivity. Similarly, 

achieving the most affordable and sustainable production 

of algal feedstock, in terms of resource use intensity 

and cost per unit of end-use biofuel produced under a 

specific set of scenario conditions, may not result from the 

pursuit of the algal oil production pathway altogether. 

Sensitivity analyses and global system optimization 

and comparative tradeoff assessments across a range of 

approaches and conditions are among the critical modeling 

and analysis needs. Meeting such needs requires a flexible 

modeling and analysis framework and suite of tools that 

can specifically address the broad scope and multiple 

pathways spanned by an algae biofuels supply chain 

system. Geospatial GIS-based data integration and analysis 

Algal Biomass & Biofuel

Production Systems,

Process Engineering

& Other Sciences

Energy & Fuel Economics;

Energy-Water-Environment

Interdepencies;

Carbon Emissions & 

Capture

Policy Analysis

Exhibit 10.3 Techno-Economic Modeling and 

Analysis addresses interdependent issues
96 10. Systems and Techno-Economic Analysis 

is also key to siting and resource assessment and the design, 

analysis and optimization of facilities location and supply 

chain logistics (from algae cultivation through end-use 

fuels and products biorefining, transport, and distribution). 

Algal biofuels remain an emerging field at a relatively 

immature stage of development. As a result, data for 

detailed unit operations and process analyses for different 

technical approaches for algae cultivation, harvesting, and 

post-processing into fuels and other co-products is currently 

sparse and uncertain. Selected modeling and analysis 

approaches can be used to effectively accommodate such 

uncertainty in data while still capturing the underlying 

dymanics of the overall system. Although quantitative 

uncertainty will remain, the results can provide qualitative 

system behavior and trends still useful in helping 

guide technical, economic, and policy decisions. More 

thorough analysis and modeling refinement, informed 

by field data expected to become available as largerscale pilot and demonstration projects are established 

and operated, will more clearly reveal the most critical 

challenges and guide investments and technical advances 

needed to enable successful commercialization of 

economical, scalable, and sustainable algal biofuels. 

SYSTEMS INTEGRATION & INTERDEPENDENCIES

Sitting & Inputs Algal Biology

S&T

Cultivation 

Systems

Harvesting & 

Dewatering

Extraction &

Fractionation

Conversion 

Processes Biofuels 

Co-Products,

& Services

Policy &

Regulation

Geolocation/

elevation 

Land characteristics

Climate/Weather

Solar Insolation

Water Souces/

Issuses

- brackish

- wastewater

- produced

- desalination 

 concentration

-marine

- fresh

- losses, re-use

- salt build-up

CO2 Sources

- power plants

- cement plants

- fermentation/ 

 other

Chemical/Materials

Energy/Power

Infrastructure

Species Selection 

& Matching to 

Growth Conditions

Characterization

Performance

Strain Improvement

Biomass Growth

& Oil Conditions

Photoautotrophic 

organism operation

Heterotrophic 

organism operation

Algae Pathogens, 

Predators, and 

Mitigations

Open Ponds

- lined

- unlined

- raceway

- wastewater

 treatment

Closed PBRs

- horizontal tube

- vertical tube

- vertical planar

- other

Hybrid System 

Combinations

- covered ponds

- pond/PBR mix

Heterotrophic

- Industrial

 Bioreactors

- Wastewater

 Facilities

Operations, 

Monitoring & 

Maintenance

Filtering

Flocculation/ 

Settling

Airlift Flocculation

Centriuge

Drying

Biological Assist

- brine shrimp

- fish

Other

Extract Processes

- Solvent

- Acoustic

- Electromagnetic

- Other

Seperation/

Fractionation

- Membrane

- Distillation

- Centrifuge

- Other

Intermediate 

Products

- TAG Oil

- Other Lipids

▪ Polar

▪ Neutral

- Carbohydrates

- Proteins

- Other

Compounds

- Water

Direct secretion 

of EtOH or 

hydrocarbon fuel 

precursors into 

growth medium, 

avoiding Harvest & 

Dewatering steps

Conversion Processes 

- Biochemical 

- Thermochemical 

- Digestion 

- Hydrotreat/

 Refine

Fuels

- Biodiesel

- Green diesel

- Aviation

- Gasoline-like

- EtOH

- Biogas/methane

- Other

Co-Products

- Feed

- Fertilizer

- Chemicals

Services

- Carbon capture

- Water treatment

Taxes

Incentives

Permitting

Enviromental 

Impact

Health & Safety

Algae Control 

& Regulation 

Other

Exhibit 10.4 Scoping the content for Systems Techno-Economic Modeling and Analysis: Key topic areas and issues for the overall algal 

biofuels supply chain 
 10. Systems and Techno-Economic Analysis 97

supply chain. Details of systems’ and processes’ technical 

and economic performance achieved by industry and 

other technology developers are also usually considered 

proprietary, and therefore, unavailable for broader use and 

objective assessment and validation. It was noted that there 

is a need and role for both integrated systems modeling as 

well as detailed engineering design and process modeling, 

and that the two should be coupled. Workshop participants 

generally agreed that modeling and analysis should be a 

critical part of a national algae biofuels research program 

and industry development effort, similar to the modeling 

and analysis efforts underway by DOE in support of the 

other bioenergy and biofuels programs. It is also expected 

that the needs for coupled models of differing fidelity and 

scales will be defined in the early stages of the systems 

modeling R&D effort and will evolve as time goes on.

Included in the Workshop discussions was the question of 

how best to approach the multiple and disparate paths 

and configurations of rapidly evolving systems and 

processes, as exemplified by Exhibit 10.7, that should 

be considered in algae biofuels modeling and analysis 

efforts. One approach with photoautotrophic microalgae 

is modeling major cultivation system categories 

10.3 Suggestions for TEA and 

LCA Approach (Workshop 

Results and Discussion)

Preparation for the Algae Roadmap Workshop and the 

discussion among participants during and after the event 

identified the need to clearly define the scope and determine 

the role that systems TEA and LCA can and should play 

in support of algal biofuels development. Also identified 

was the need to adapt, develop, and utilize a range of 

approaches, scales, and levels of detail best suited to 

perform the necessary modeling and analyses based on 

available and emerging information and data. Exhibit 

10.6 illustrates various complementary modeling and 

analysis approaches and techniques that come into play at 

different levels within the broad systems scope presented. 

Due to their more limited and immediate business 

objectives, individualized modeling and analysis efforts 

by industry and technology development organizations 

tend to focus on a technology or process, unit operation, 

production plant, or enterprise level rather than broader 

integrated systems modeling and analysis across the 

Policy & Regulation; Incentives & Barriers

Electric Power and Process Heat Generation

Siting

- Land (cost, location,

 tilt, geology, soil)

- Solar Insolation

- Temperatures

- Climate/Weather

Conditioning

or Treatment

Water Capture

& Re-Use

Harvesting

Carbohydrates

Dewatering

&/or Drying

Extraction

& Seperation

Conversion

Biofuels

Conversion

Coproducts

Proteins &

Other

Oil / Lipids

Algae

- Species

- Characteristics

- Requirements

- Performance

- GMOs

Resources

- CO2 / Flue Gas

- Water

- Nutrients (NPK)

- Labor

- Capital

- Materials

- Equipment

- Primary Energy

Cultivation

- Autotrophic

- Heterotrophic

- Open systems

- Closed systems

- Hybrid systems

Co-Gen

Energy 

Feedbacks

Nutrient 

Feedbacks

Nutrient 

Feedbacks

Biology

Feedbacks

Design

Feedbacks

Broader 

Environment

& Economy

Capital Construction, Operations, Monitoring, Maintenance, Replacement

Market Externalities: Cost of Energy, Cost of Petroleum & Conventional Fuels,

 Demand & Price for Co-Products vs. their alternatives, etc.

Exhibit 10.5 The dynamic coupling and interdependencies across the algal biofuels and co-products supply chain 
98 10. Systems and Techno-Economic Analysis 

of open pond, closed photobioreactors, or a hybrid 

combination, and activating only those portions of the 

hybrid configuration model desired. Beyond this, how 

to best conceptualize a model that spans the overall 

“beginning-to-end value chain” for algal biofuels 

production with adequate resolution and detail is very 

challenging and still emerging. The size of the “matrix” 

of possibilities could quickly become unmanageable. 

 

Developing numerous detailed models that are each 

uniquely customized to a specific combination of systems 

and processes and performance parameters is another 

approach, and essentially represents what exists today with 

various groups doing ad-hoc modeling and assessment 

specifically focused on their chosen approach and 

technologies (e.g., platform). The disadvantage of such a 

distributed and narrowly focused approach is that it is often 

done in isolation with limited or no consideration of other 

competing options and the broader scope of interdependent 

issues and tradeoffs that need to be addressed together to 

better inform technical, economic, and policy decisions 

at the state, regional, and national level. Narrowly 

focused and detailed technical and economic modeling 

and analysis is valuable and necessary for those doing 

engineering design, development, and optimization of 

specific technologies, processes and integrated systems 

for commercialization. Flexibility and usefulness 

could be increased to the extent that such modeling 

and analysis can be done using common standards, 

definitions, and interface approaches, across an emerging 

“community of practice” for the algae biofuels industry.

Standardized interface requirements and definitions could 

be established for system and process functional blocks that 

would enable the development of an open-source modeling 

and assessment platform with “plug & play” flexibility. 

Higher-Level Dynamic Meta-Systems Modeling (Integrated Analysis Framework)

• Broad value-chain scope... from resources & sitting through production to end use

• Algae biofuel and co-products industry scale-up potential, resource use, constraints & impacts

- Integration with existing infrastructure

- Required build-up of new infrastructure.. with time delays... with learning curves & 

improvement projections 

- Technical, economic, enviromental, and policy issues

• Feedbacks and Multiple Sector Interdependencies... can link to other models & analyses 

Static CAPEX & OPEX Calculations

• System and process equipment cost estimates

- Vendor/ Supplier cost estimates

• Engineering and construction cost estimates

- Engineering & construction estimates from 

industry

- ICARUS cost estimate software (or equivalent)

• Operations & Maintenance cost estimates

• Cost (& offsets) of co-product feedstock

 production

• Cost of biofuel production

• Cost (& offsets) of co-products production

• Carbon footprint cost accounting

Process Flow Enginering Modeling

• Mass & energy balance calculations 

(ASPEN+)

• Process GHG footprint (LCA) assessment

Geographic Information System 

(GIS) Analysis and Visualization

• Land resources (characteristics,

availability, etc.)

• Water resources (fresh wastewater,

other)

• Climate/ Weather/ Temperature

Conditions

• CO2

 resources ( point source emitters,

pipelines)

• Fuel processing, transport, storage

infrastructure

• Other infrastructure and enviromental 

features

Other LCA Modeling

• GREET (Argonne National Lab)

• LEM (UC/ Davis)... Etc.

Exhibit 10.6 Multiple levels and complementary approaches available for Algal Biofuels Systems and Processes Techno-Economic Modeling,

 GIS Analysis, and Life Cycle Analysis
 10. Systems and Techno-Economic Analysis 99

Work currently underway on the Knowledge Discovery 

Framework (KDF) by DOE’s Biomass Program is 

moving in this direction (Getman, 2009), and represents 

an example of a GIS-based information gathering 

and analysis platform that can be productively used 

and leveraged for algae biofuels development. 

10.4 Systems Analysis

Overview

System analysis is foundational to designing a strategy 

for algal biofuel deployment. A system is an aggregation 

of subsystems interacting such that the system is able to 

deliver an over-arching functionality. Exhibit 10.5 provides 

a high-level illustration of the interdependent character 

of the overall algae biofuels value chain that involves a 

broad range of systems, processes, and other technical 

and non-technical issues. To facilitate system-level 

thinking during the Workshop, a process flow diagram was 

developed and presented at every breakout track discussion 

to illustrate the intricate interdependencies of algal 

biofuel production. Exhibit 10.7 is a revised adaptation 

of the flow diagram that shows a representative number 

Much more detailed or custom models of individual 

subsystem or process blocks could then be developed by 

various others in industry, universities, and national labs, 

utilizing different techniques such as high performance 

physics-based modeling (e.g., computational fluid dynamics 

modeling of open raceway ponds or closed photobioreactor 

cultivation systems) or process engineering models using 

widely accepted and applied commercial process modeling

tools like AspenPlusTM or customized spreadsheets. 

Flexibility in being able to link custom subsystem 

or process models into an overall meta-system 

modeling and analysis framework would provide a 

capability that could be of significant value and benefit 

to different stakeholder communities such as: 

• DOE & national labs doing R&D, assessment, and 

tracking of program investments

• Other federal and state agencies (Department of 

Defense, USDA, EPA, etc.)

• Universities doing a wide range of technical/

economic/policy R&D and assessment

• Industry developing and commercializing technologies, 

systems, processes

• Private investment / funding sources

Exhibit 10.7 High-level multi-pathway algae biofuel process flow diagram for the algal biofuels and co-products supply chain 

5.1 Physical

(Thermo/Mechanical)

5.2 Electromagnetic

5.3 Chemical

5.4 BY PASS

C. Lipids

D. Carbohydrates

E. Proteins

F. Other

Metabolites

G. Fatty Acids

H. Triglycerides

6.1.1 Chemical

1.1.1 Microalgae

1.1.2 Cyanobacteria

1.1.3 Macroalgae

1.1 Algae species

2.1 Closed system 3.0 Harvesting

2.2 Open system

2.3 Hybrid systems

3.2 Filtering

3.4 BY PASS

4.1 Solar

8. Dried Algal

biomass

4.0 Drying

4.2 Fuel - Field

2.4 Off-shore systems

2.5 Biological assist

2.0 

1.2 Land Cultivation

1.3 CO2

1.3 Water

6.1.2 Thermochemical

6.1.3 Biochemical

6.2 Co-products

Conservation

6.1 Fuel

Conservation

I. Feed

J. Fertilizer

K. Chemicals

L. Materials

M. Biodiesel

N. Green diesel

O. Aviation

P. Gasoline-like

Q. Biogas / Methane

R. Ethanol

R. Hydrogen

Infrastructure

& Markets

- Transport

- Storage

- Distribution

- End Use

A. Wet algal or 

biological assist 

derivative biomass

3.5 Biological Assist 

Harvesting (shrimp,

fish excrement, etc.)

3.3 Centrifuging

3.1 Flocculation

& settling

1.5 Light or 

Alt. Energy Source

1.0

Inputs

5.0 Extraction 

& Separation
100 10. Systems and Techno-Economic Analysis 

technical information and data about the systems and 

processes involved to appropriately formulate and conduct 

accurate analyses. This may also require coupling 

with appropriate external data and driving functions 

such as time-dependent solar insolation, temperature, 

and other local environmental conditions. Simpler and 

more approximate preliminary spreadsheet analyses 

are more appropriate as a first step, especially where 

detailed process engineering data may be lacking. 

An example of this type of analysis is presented in 

Exhibit 10.8. Exhibit 10.8 represents a mass and energy 

balance systems level view of an algal biomass and algal 

lipid cultivation and extraction system. Inputs to each 

system component are shown, and each numbered node 

represents a mass or energy balance calculation. The 

value of this kind of systems mass and energy balance 

assessment is that it can help assess the overall viability 

of a given algal biomass production system and show 

what steps in the process are most energy intensive, thus 

highlighting areas for research and development. The 

development of mass and energy based systems models 

can help evaluate different proposed processes for 

overall viability and examine the sensitivity of different 

assumptions in individual processes to the overall system.

Geographic Information System (GIS) Visualization 

and Analysis tools (referenced also in chapter 9) 

are indispensible for algae production and supply 

chain systems analysis due to their ability to perform 

mapping and resource analysis spanning local, regional, 

and national scales. Critical climatic and natural 

resource data can be readily accessed, such as:

• Land and water resources 

(characteristics, availability, etc.)

• Climatic characteristics (temperature, 

precipitation, solar insolation, etc.)

• Water evaporation loss (function of climate, etc.)

• CO2 resources (point source emitters, pipelines) 

• Fuel processing, transport, storage infrastructure

• Other infrastructure and environmental features

Several critical resource factors will impact large-scale, 

sustainable production of microalgae biomass. These 

include climate and the adequate availability of water, 

efficiency of water use, availability of suitable land, 

and availability of supplemental CO2 and other nutrient 

(N, P, K) supplies. The impact that availability and cost 

of these resource can have on algae biofuel production 

scale-up was touched on earlier in chapter 9. The cost 

and benefit tradeoffs of CO2 capture through biofixation 

using photoautotrophic microalgae cultivation enhanced 

of multiple path process options available for every step 

in the algal biofuel production chain, from algae growth 

to fuel and co-product processing and end-use. Sub-level 

processes that made up different thematic topic discussion 

sessions in the Workshop are all inter-related. Collecting 

and understanding key information from each node in the 

process becomes the primary task of the systems analysis. 

Both Exhibit 10.5 and Exhibit 10.8 represent a large 

number of permutations of potential pathways to algal 

biofuel production, most of which are still immature and 

emerging. Many of the process steps will differ depending 

on the product or co-product chosen, and others beyond 

those selected for inclusion in the figures also exist or 

will likely emerge. Though it may seem daunting to 

attempt to develop a comparative analysis based on so 

many process permutations, there is precedence for this 

sort of undertaking in DOE’s Hydrogen Analysis (H2A) 

Project within the overall Hydrogen Program (DOE, 

2009). Established in 2003 in response to the Hydrogen 

Fuel Initiative, H2A was designed to consider various 

pathways toward a hydrogen economy, evaluate costs, 

energy and environmental tradeoffs and set research 

priorities and inform policy by sound analysis. The 

options for hydrogen production include goal gasification, 

nuclear energy, wind electrolysis, and organic molecule 

reforming. This program could serve as a guide for moving 

forward with analysis of algal biofuel production.

Other chapters of this Roadmap point out the lack 

of availability of detailed information about the 

characteristics of algae themselves and the characteristics 

(energy requirements and costs) of the systems and 

processes that are shown in the process flow diagram 

of Exhibit 10.8. A substantial number of barriers are 

enumerated and designated as goals to be achieved. 

Systems analysis can help manage the complexity of 

producing algal biofuels and co-products by quantifying 

uncertainties, identifying and appropriately modeling 

interdependencies and feedbacks, and comparing tradeoffs from various scenarios with regard to cost, risk, 

technical performance, and environmental impacts.

Engineering Analyses and 

GIS Assessments

Engineering analyses (technical and economic) at the 

unit operations level require the systematic calculation 

and tracking of mass and energy balances that include 

evaluation of the thermodynamic, hydrodynamic, 

biological, and chemical kinetics of the systems and 

processes used. Example engineering analysis tools 

include AspenPlusTM and FLUENTTM, among others, 

which require sufficient understanding and detailed 
 10. Systems and Techno-Economic Analysis 101

on the size and the optimum site locations of biorefinery 

facilities relative to upstream algae biomass production 

and downstream fuel and co-product markets. 

The combination of GIS resource assessment, including 

geographic location attributes and time dependent climate 

and weather data, with physics-based modeling of 

cultivation systems and algae growth, can provide powerful 

capabilities for estimating performance and for improving 

the technical design of systems and their operations for 

different site conditions. Exhibit 10.9 is an example of the 

application of high-performance computational modeling 

tools and capabilities to an open raceway pond system that 

includes an algae growth model driven by environmental 

(e.g., solar insolation, ambient temperature, nutrient 

concentrations, etc.) forcing functions and boundary 

conditions (James and Varun, in press). The possibility 

of combining these types of spatial and physical data to 

project possible algal production scenarios as a function of 

geography and climate is an interesting avenue of inquiry. 

Currently, the data available to implement this type of 

analysis are thought to be preliminary and refinement 

based on model improvement and validation with data 

from the operation and monitoring of larger scale algae 

production systems under a range of site and climate 

conditions with multiple species of algae could be useful. 

Economic analysis tools for static capital expense 

(CAPEX ) and operational expense (OPEX) calculations

are also integral to system analysis as they reveal financial 

investment or market incentives needed for algae biofuel 

deployment. Some examples are:

• POLYSYS

• ICARUS cost estimate software (or equivalent) 

• Equipment, Operation & Maintenance cost estimates

• Discounted cash flow analysis

• Cost (& offsets) of co-product feedstock production

• Cost of biofuel production

• Carbon footprint cost accounting

by the addition of CO2 from industrial sources will affect 

the economics of algal biofuel production. Potential 

CO2 capture and utilization in algae biomass production 

is discussed in more detail through a few selected 

example calculations presented later in this chapter. 

The economics of algae-based biofuels and co-products 

will depend in large measure on the degree to which algae 

feedstock production and downstream processing can be 

integrated with existing infrastructure and markets. At the 

front end of the supply chain, this will include the logistics 

and costs of supplying inputs needed for algae production 

(suitable siting, sourcing, and transport of water, nutrients, 

supplemental CO2, and energy). Midstream will be the 

logistics of transport, storage, and biorefining into fuels and 

other co-products, followed downstream by the necessary 

transport, storage, and distribution into the various end-use 

fuel and co-product markets at the end of the suppy chain. 

To the extent that operations can be effectively co-located 

or established within reasonable distances across the 

supply chain, the economics can be expected to improve. 

Producing biofuels that are highly compatible, or totally 

fungible, with the existing hydrocarbon fuel handling, 

distribution, and end-use infrastructure would result in 

easier and more widespread market acceptance. The 

same would apply to co-products and their potential 

markets. These and related issues should be an integral 

part of techno-economic modeling, analysis and LCA 

for algae, with the appropriate models, tools, and data 

sets developed and leveraged to provide the necessary 

assessment capabilities to guide research, business 

development, resource management, and policy decisions. 

At the downstream end, the relative location and 

logistical costs associated with fuel processing, 

transport, storage, and distribution infrastructure 

could benefit from GIS analysis. This information, for 

example, can help determine the practical upper limit 

Energy

Energy &

Other Inputs Energy

Solvent

H2

O Recycle

Energy

H2

O

& O2

Sunlight

& Water

Microalgae

Air & CO2

Nutrients

(N, P, K, etc.)

Facilities, Structures, and

Systems Infrastructure, Land,

Materials, Equipment, Utilities,

Site Preparation

Water

Capture &

re-use Potrential

Co-products

Residues:

Protein

Polar Lipid

Carbohydrate

TAGs & Other

Neutral Lipid

Biofuel Feedstock

Solvent

e.g., Hexane

Recovery

Neutral Lipid

Extraction

e.g., Hexane

Solvent

Secondary

Dewatering

e.g., Biomass

Drying

Primary 

Dewatering

e.g.,

microfiltration

& Centrifuge

Secondary

Harvesting

e.g.,

Dissolved Air

Flotation 

Primary 

Harvesting

e.g., 

Chemical

Flocculation

PhotoBioreactor

&/ or Pond

System

Exhibit 10.8 Notional baseline algae feedstock production system
102 10. Systems and Techno-Economic Analysis 

Computational Fluid Dynamics Model of Algal Raceway Pond Using Modified EPA 

and US Army Corps of Engineers Codes

• The Environmental Fluid Dynamics Code (EFDC) solves 3D Navier-Stokes 

equations of open channel flow to model speed, temperature,

 and nutrient gradients

• Solar insolation and other environmental, climate, and meteorological 

forcing functions

• Includes algal biomass growth model

• CE-QUAL couples nutrient kinetics and 22 independent variables

 (N, P, Si, O2...) to model growth rates.

Exhibit 10.9. Open raceway pond example of physics-based algae cultivation system modeling and anlaysis. Such analysis can enable both 

performance prediction and pond system design optimization after appropriate refinement and validation with monitored field system data 

(Adapted from James and Varun, in press)

area of cultivation systems needed to achieve a set 

amount of product; it will affect the amount of CO2

that can be captured; and it will affect the amount 

of culture that will need to be processed on a daily 

basis. The daily, seasonal, and annual variation in 

solar insolation, as well as other climate-related 

factors such as temperature and weather (cloud 

cover, precipitation, wind, etc.) will also affect both 

the productivity and reliability of production.

• Availability, cost, and sustainability of suitable water 

supplies for algae production will be a key input factor 

for inland cultivation, and will be heavily dependent 

on geographical location and local conditions. Areas 

of the country with the highest solar resource best 

suited for algae growth also tend to be more arid and 

subject to more limited water supplies. Under large 

commercial algae industry build-up scenarios, the 

amount of water required nationally could begin to 

approach the same order of magnitude as large scale 

agriculture, particularly with open systems subject to 

evaporative loss. Capture and re-use of non-fresh water, 

in particular, can potentially help fill this need, but will 

be dependent on the geographical location, availability, 

and affordable accessibility of such water sources.

• The supply, availability, and cost of organic carbon 

feedstock needed as input for heterotrophic microalgae 

production will play a major role in the commercial 

viability and extent to which national production 

capacity can expand using the heterotrophic approach. 

Sugar from commodity crops and other organic 

carbon materials from industrial or municipal waste 

streams can provide bridge feedstock in the nearRecent analysis suggests an upper theoretical limit on 

the order of ~38,000 gal/ac-yr and perhaps a practical 

limit on the order of ~4,350 - 5,700 gal/ac-yr, based 

on the expected losses, photosynthetic efficiency, and 

other assumptions made in the analysis (which include 

the availability of high solar insolation consistent with 

lower latitudes and/or high percentage of clear weather 

conditions, 50% oil content, etc.) (Weyer et al., 2009). 

Impact of Geographic Variability of 

Inputs on Algal Biofuel Production Costs

The various inputs necessary for algal biofuel production 

have been described earlier in this chaper and in other 

chapters of the Roadmap. Certain elements, like cost of 

power, water, and fertilizer, vary over the U.S. but these 

variations, though important for overall TE analysis, are 

not unique to the development of algal biofuel technology. 

There are, on the other hand, aspects of large scale 

macroalgae and microalgae cultivation (autotrophic, 

heterotrophic, and mixotrophic) for which geographical 

variation of resource availability will have major impacts 

on cost of production and scale for commercial viability. 

These aspects were discussed in some detail in 

Chapter 9, but it is appropriate here to briefly note

the following: 

• The average annual insolation is generally the 

dominant and rate-limiting factor for autotrophic algal 

productivity, and this factor varies widely across the 

country among inland, coastal, and offshore sites. 

This variation will determine the spatial surface 
 10. Systems and Techno-Economic Analysis 103

term, but major sustainable scale-up of national 

production capacity will demand the use of sugars 

and other suitable organic carbon source materials 

derived originally from lignocellulosic biomass. 

As with cellulosic ethanol, the logistics and costs 

associated with producing, transporting, and 

appropriately processing lignocellulosic biomass 

materials in the form of woody and herbaceous 

energy crops, waste materials from agriculture 

and forest industries, and municipal waste streams 

will be location-dependent. The affordability of 

generating organic carbon feedstock from such 

materials will also depend on technical advances 

and processing improvements needed to reduce the 

cost of lignocellulosic material deconstruction into 

simple sugars and other organic carbon compounds 

suitable for feeding heterotrophic microalgae.

• The supply, availability, and cost of other nutrients 

(i.e., N, P, K) required as inputs for algae growth will 

also play a role in commercial viability and extent of 

industrial build-up. Commercial fertilizer costs are 

tied closely to the cost of energy supplies (natural gas 

and petroleum), and can be an appreciable factor in 

operational costs for algae (Massingale et al., 2008) 

to the same extent as for large scale commercial 

agriculture (Huang, 2009; Malcolm et al., 2009). In 

the absence of nitrogen fixation, algae can require as 

much, if not more, nitrogen than conventional biomass 

crops on a mass balance basis (Alexander et al., 2008). 

Under large commercial algae industry build-up 

scenarios, the amount of nutrients required nationally 

could begin to approach the same order of magnitude 

as large scale agriculture, where recent cost and supply 

issues have had negative impacts on the industry 

(Huang, 2009). The capture and reuse of nutrients 

from various agricultural and municipal waste streams 

(Woertz et al., 2009) can potentially help supply 

nutrients for algae production scale-up, but this will be 

dependent on the geographical location, availability, 

and affordable accessibility of such nutrient sources. 

• CO2 availability and cost of delivery will play a major 

role in autotrophic microalgae cultivation scalability 

and operating expense. As noted here and in chapter 

9, it will be advantageous to co-locate cultivation 

facilities with stationary industrial CO2 sources, but this 

will not be feasible in all instances and thus, it may be 

necessary to transport CO2 over some distance. Even in 

the case of co-location, the size of an autotrophic algae 

facility will require extensive pipeline infrastructure for 

CO2 distribution, adding to the cost. The quality of the 

CO2 source will also play a role for algal growth, and 

some sources are likely to require more cleanup than 

others (especially if there are plans for animal feed as 

a co-product and/or if the CO2 source stream includes 

contaminants that inhibit algae growth). Algae can be 

effective at capturing and concentrating heavy metal 

contaminants (Aksu, 1998; Mehta and Gaur, 2005), 

such as are present in some forms of flue gas. This 

could impact the suitability of residual biomass for 

co-products like animal feed, and is a consideration that 

requires further investigation. Finally, carbon credits 

must also enter into this analysis, though it is not yet 

clear how best to factor this into the calculation. 

• Land prices and availability can also impact the cost 

of biofuel production at inland and coastal sites. 

For offshore sites, the right of access and use, and 

the associated logistics, risks, and costs of offshore 

marine operations will have a major impact on 

costs of production. Cost of site preparation and 

infrastructure facilities for offshore, coastal, and inland 

sites will all be location-dependent. It is reasonably 

straightforward to calculate the impact of the cost 

of land, and perhaps also for offshore sites, on the 

overall cost of total algal biomass and intermediate 

feedstock fraction (e.g., lipids, carbohydrates, 

proteins, other) production, but for each approach 

it will likely be an optimum minimum and range 

of size for a commercial production facility. If it is 

necessary to distribute the facility over a number of 

smaller parcels of land or offshore sites, it may not 

be possible to get the most benefit of economies of 

scale. The key tradeoffs will be between the cost 

of overall production (capital and operating costs) 

versus the matching of affordable production scale to 

the sustainable and affordable supply of the required 

input resources with the required output product 

processing and distribution infrastructure and markets. 

• As in traditional agriculture, the temperature during 

the growing season will restrict the ability to cultivate 

specific strains for extended durations. For open 

systems operating at inland sites in the summer, 

water evaporation rates will provide some level of 

temperature control, but evaporation will also add to 

operating cost (for water replacement and/or for salt 

management with brackish or saline water. Conversely, 

closed systems operating inland can overheat, 

requiring active cooling that can add prohibitively to 

the cost of operations. Waste heat and energy from 

co-located industries or the CO2 source may allow 

active thermal management for growth during periods 

of suboptimal (high or low) temperature, but applying 

this heat or energy to extensive algal cultivation 

systems will provide the same engineering problems 

and costs as transporting and distributing CO2. 
104 10. Systems and Techno-Economic Analysis 

In summary, the calculations for the cost of algal biofuel 

production will benefit from detailed inputs that take into 

consideration the variations in cost and availability of the 

essential elements for cultivation. While these variations 

may be minor relative to the technical uncertainties, it is 

likely that a technology that will require the production 

of immense volumes of biofuel at affordable cost so it 

can play a significant role in the national energy economy 

would be subject to narrow operating margins.

Life Cycle Analysis

Life Cycle Analysis (LCA) is a “cradle-to-grave” 

analysis approach for assessing the resource use and 

environmental impacts and tradeoffs of industrial systems 

and processes. LCA is important for assessing relative 

GHG emissions and other resource utilization (e.g., 

water, energy) impacts among different approaches to 

algal biofuels production, and in comparison with fuels 

based on other renewable and non-renewable feedstocks. 

LCA is considered to be a key element of the scope of TE 

modeling and analysis within the context of this roadmap. 

The systems modeling and analysis framework for algae 

biofuels must include the integration of appropriate 

LCA methodology and metrics (Curran, 1996; EPA, 

1993; ISO, 1997; EPA, 2006; EPA, 2009; UNEP, 

2005), and specifically leverage past and current LCA 

work specific to biofuels (ANL 2009; Delucchi, 2004) 

and including algae (Kadam, 1997, 2001 and 2002). 

The term “life cycle” refers to the major activities in the 

course of the product’s life-span, from manufacture, use, 

and maintenance, to final disposal, including the raw 

material acquisition required to manufacture the product 

(EPA, 1993). Exhibit 10.11 illustrates the typical life 

cycle stages considered in an LCA and the typical inputs/

outputs measured. LCA is a systematic technique to assess 

the environmental aspects and potential impacts associated 

with a product, process, or service. The process employs a 

phased approach that consists of four major components: 

goal definition and scoping, life cycle inventory analysis 

(LCI), life cycle impact assessment (LCIA), and 

interpretation as illustrated in Exhibit 10.12 (ISO, 1997). 

LCA methodologies, modeling, data base resources, and 

tools have been developed that include Argonne National 

Laboratory’s GREET “well-to-wheels” model (ANL, 

2009), the UC/Davis Lifecycle Emission Model (Delucci, 

2002 and 2004), and numerous others (EPA, 2009). In 

addition to net GHG emissions, LCA for biofuels can also 

assess impacts and tradeoffs associated with utilization 

intensity for water, energy, nutrients, and other resources. 

10.5 Algae Production 

Costs and Uncertainties

Data gathering and validation of technical and economic 

system performance for an industry that has yet to be 

commercially realized is one of the biggest challenges for 

techno-economic analysis. To facilitate the Workshop’s 

objectives of identifying needs, eliciting discussion, 

and compiling suggested directions for research and 

development from the participants, algal oil feedstock 

production cost analyses were reviewed based on a 

range of sources to gauge the status of algal biofuel 

technology. These included technical reports prepared 

for the U.S. Department of Energy (e.g., Benemann and 

Oswald, 1996), peer-reviewed literature (e.g., Tapie and 

Bernard, 1987), white papers / industry analyses, and 

personal communications with field experts. While most 

citable sources are quite dated, they also present a wide 

variability in approach to final costs (from per gallon 

of algal oil to per kg of “raw” biomass) and illustrate 

a general lack of demonstrated operating parameters 

and widely varying basic assumptions on a number of 

parameters from algal productivity to capital depreciation 

costs, operating costs, and co-product credits. These 

shortcomings of the existing literature and modeling 

knowledge base present a challenge in designing scaled 

up systems. There are indications, however, that a 

combination of improved biological productivity and 

fully integrated production systems can bring the cost 

down to a point where algal biofuels can be competitive 

with petroleum at approximately $100 per barrel. 

10.6 Preliminary System 

Dynamics Modeling 

Systems dynamics modeling is a powerful and flexible 

modeling approach that can foster collaborative analysis 

and scenario studies. A dynamics simulation model also 

provides an integrated analysis framework that can include:

• Broad value-chain scope: from resources and 

siting through production to end use

• Algae biofuel and co-products industry scale-up 

potential, resource use, constraints and impacts 

• Input resources, output flows, waste stream 

resource capture and reuse, co-generation

• Integration with existing infrastructure

• Required build-up of new infrastructure with time 

delays, learning curves and improvement projections

• Technical, economic, environmental, and policy issues

• Feedbacks and Multiple Sector Interdependencies 

with links to other models and analyses
 10. Systems and Techno-Economic Analysis 105

The development of a system dynamics model for 

conducting scenario analysis of algal biofuels production 

scale-up and operations was initiated as part of the roadmap 

effort and is currently a work in progress. The preliminary 

modeling uses algae production and resource availability 

data and assumptions from the same information 

sources discussed earlier in this chapter and in chapter 

9. Interactive graphical user interfaces,can facilitate the 

use of the model to conduct rapid ‘what if’ analyses and 

tradeoff studies using different yield scenarios, technical 

and economic performance for various pathways, and 

resource constraints. The model will eventually include 

more detailed systems and processes modules for multiple 

pathways being pursued for algae biofuels and co-products, 

along with the ability to do Monte Carlo simulation, 

varying parameters values within pre-set ranges in order 

to describe the uncertainty or robustness of model output.

10.7 Potential Directions 

for R&D Effort 

The model described above was initially prepared in 

outline form for the algae roadmap workshop, and has 

been developed further since the workshop. The model 

currently includes only a limited amount of available data. 

To adequately inform research and investment decisions 

for algal biofuel deployment, continued progress 

\in techno-economic analysis and the capture of data 

from fielded systems as they emerge over time can 

provided needed additional information. Workshop 

participants specifically suggested that the following 

areas be addressed in the modeling and analysis.

• Determine the current state of technology

• Identify critical path elements that offer opportunities 

for cost reduction

• Identify research areas most in need of support

• Identify external factors that will impact cost

• Provide plan for entry of algal biofuel into a renewable

 fuel portfolio

• Inform and perhaps guide formation and/or 

modifications to public policy

• Incorporate appropriate insights and benefit from 

alliances with industry associations

The Techno-Economic Analysis can accomplish this by:

• Stressing dynamics over detail initially, expanding 

detail later as available and needed

• Employing modular modeling, e.g. ISBL and OSBL

 approaches1

• Establishing interface requirements between 

sub-systems

Raw Materials Acquisition

Manufacturing

Use / Reuse / Maintenance

Recycle / Waste Management

System Boundary

Raw Materials

Energy

Atmospheric

Emissions

Waterborne

Wastes

Solid

Wastes

Other

Releases

Coproducts

INPUTS OUTPUTS

Exhibit 10.11 Scope of Life Cycle Analysis 

(Adapted from EPA 1993)
106 10. Systems and Techno-Economic Analysis 

Interpretatation

Goal Defination

and Scope

Inventory

Analysis

Impact

Assessment

Exhibit 10.12 Phases of a Life Cycle Analysis 

(Adapted from ISO, 1997)

• Leveraging university and industry resources

• Maintaining industry standard notation, units, etc.

Throughout the roadmap workshop and report development 

process, significant algae-to-biofuels production system and 

process performance uncertainties (technical and economic) 

have been identified along various steps in the value chain. 

These have been noted in this and earlier chapters of the 

Roadmap. Addressing the uncertainties in a systematic 

and integrated modeling and analysis framework will help 

guide needed investments and speed the deployment of an 

algal biofuels industry. A critical complementary need is 

the development, operation, monitoring, and evaluation of 

larger-scale algae biofuel production systems and processes 

that can provide data to validate and improve the modeling. 

When done in a closely coordinated spiral development 

fashion, the complementary bi-lateral feedback of 

information and insight between the modeling and analysis, 

and the experimental and operational investigations 

with larger-scale systems in the field, can facilitate 

more rapid technological advancement leading toward 

commercialization. 
 10. Systems and Techno-Economic Analysis 107

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Argonne National Laboratory (2009). The greenhouse gas, regulated emissions, and energy use in transportation 

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Benneman, J. and Oswald, W. (1996). Systems and economic analysis of microalgae ponds for conversion 

of CO2 to biomass. Report prepared for the Pittsburg Energy Technology Center. (Grant No. DE-FG22-

93PC93204). http://www.osti.gov/bridge/product.biblio.jsp?query_id=1&page=0&osti_id=493389 

Curran (1996). M.A. Curran (ed), Environmental Life Cycle Assessment. ISBN 0-07-015063-X, McGraw-Hill.

Delucchi, Mark (2004). “Conceptual and Methodological Issues in Lifecycle Analyses of Transportation Fuels“, UCD-ITS-RR-04-45, 2004.

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 http://www.hydrogen.energy.gov/h2a_analysis.html

Environmental Protection Agency (EPA). (1993). Life Cycle Assessment: Inventory Guidelines and 

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of Civil Engineers, v135, n11, pp. 1115-1122.
11. Public-Private Partnerships 109

The algal biofuels industry is evolving with numerous 

players, many focusing on one to a few elements in 

the algal biofuels value chain. Partnerships based 

on sharing of knowledge and capabilities for mutual 

benefit could pull together the current expertise and 

facilities, thereby facilitating growth and development 

of a sustainable, algal biofuels industry. The type of 

partnership most relevant to the advancement of the algal 

biofuels industry is perhaps the research partnership 

envisioned by the Council on Competitiveness (1996):

Partnerships are defined as cooperative 

arrangements engaging companies, universities, 

and government agencies and laboratories in 

various combinations to pool resources in pursuit 

of a shared R&D objective.

Exhibit 11.1 shows the potential benefits of 

collaboration between private entities (e.g., industry) 

and public entities (e.g., national laboratories and 

universities) for development of algal biofuels.A

While benefiting both private and public entities from 

shared investment toward mutual objectives, publicprivate partnerships have the potential to accelerate 

commercialization of algal biofuel technology, leading 

to rapid industry growth and a stable market.

Industry benefits from public-private partnerships from the 

exposure to fundamental science and engineering R&D, 

which can support a quickening pace of innovation. This 

could, in turn, increase the capital efficiency of commercial 

firms, many of which may be investor-backed and 

pre-revenue, as well as reduces the risk of private 

investment. By focsuing these partnerships on precompetitive research or critical problems shared by all 

11. Public-Private Partnerships 

The Workshop participants emphasized the need 

for DOE and other federal agencies to partner with 

national laboratories, academia, and industry. The 

participants, however, also noted the unique partnership 

environment in algal biofuels development, given 

the fact that the algal biofuels industry is still in its 

infancy. More specifically, given the current state of 

this industry, the business strategies of many existing 

companies are focused on one or more aspects of 

algae, but not necessarily producing transportation 

biofuels from cultivated algal biomass at scale. 

This chapter discusses potential models for public-private 

partnerships in general and specifically as related to algal 

biofuels. Various models for such partnerships employed 

in past efforts are discussed in the context of applicability 

to the algal biofuels challenge, including characteristics 

for membership and intellectual property models. 

11.1 The Benefits of Algal Biofuels 

Public-Private Partnerships

Since the 1980s, the U.S. has increasingly invoked 

public-private partnerships not only for large-scale 

infrastructure projects, but also for research and technology 

developments of national interest (Stiglitz and Wallsten, 

1999). Indeed, analyses of various federal agencies 

and government programs aimed at public-private 

partnerships are documented (Audretsch et al., 2002; Link 

et al., 2002), including specific studies on the impacts 

of DOE programs on the clean energy sector (Brown, 

2001; Brown et al., 2001; Gallagher et al., 2006).

Technolgy Commercialization

Industry Growth & Market Stability

Shared Investment 

Domestic Energy Supply

Sustainable Industry 

Development

Shared Benefits

Energy Security

Long-term Clean Fuel

Solution

Climate Change Migration

Jobs Creation

Clean Energy &

Science Leadership

Innovation Quickens

Shared Risk &

Capital Efficiency

Competitive Edge

Breakdown Legal &

Regulatory Hurdles

Growth Stimulates

Labor Pool

Public Benefits Private Benefits

Exhibit 11.1 Benefits of algal biofuels public-private partnerships

A In this situation, academia can be either public or 

private, realizing benefits in both categories.
110 11. Public-Private Partnerships 

Government solicitations are also an option to promote 

collaborative research to tackle complex problems 

through public-private partnerships. Often these types 

of solicitations are system-oriented, where no single 

entity can address the complex research challenge. 

This may result in the formation of teams of proposers 

in a project-level partnership. Such solicitations have 

the potential to accelerate technology development, 

particularly in instances in which the team would not 

have necessarily come together without a governmentfunded solicitation. However, these partnerships can 

only be expected to last for the life of the project, as 

they are often formed to serve no other purpose.

Consortia and trade organizations are membership 

organizations that may provide an opportunity for 

lasting partnerships. Partnerships are facilitated in 

these environments through collaborations among 

the membership. By maintaining an active directory, 

consortia and trade organizations can also be an effective 

vehicle for researchers looking for a new approach or 

new partnership, as well as a platform to share research. 

Through their structure, these organizations provide for 

opportunity to facilitate deeper collaborations. However, 

organizations that promote a closed circle of partners who 

have worked together for many years may not generate 

the new thinking and fresh approaches that could be 

gained through openness toward new partnerships.

In recent years, prizes have been offered by various 

organizations to support solving critical, national, or 

global problems, including the development of biofuels.B,C

Prize forums can pull together developed technology 

into a working system to solve a problem, and demand 

that the winning team meet or exceed certain success 

criteria. Prize forums can also leverage reward money 

from a variety of different funding sources (state and 

federal government, non-profit foundations, and private 

investors) into a single competition, and provide publicity 

and marketing toolsets for competitors to attract future 

investors. However, because some awards are based on 

having solved the problem, such forums may favor mature 

technology in the final stages of development where the 

focus can be on assembly into a working system. Basic 

research and early stage technology with limited funding 

may compete poorly in this type of award, with the ultimate 

solution only as good as existing technology will allow.

11.4 Partnership Challenges in 

the Algal Biofuels Industry

players (e.g., technology scale-up and demonstration, 

regulatory issues, labor), industry would retain its 

competitive edge, while increasing the opportunity to 

develop and license technology with new partners.

11.2 Components of Successful 

Public-Private Partnerships

At the highest level, successful partnerships have 

been identified to include the following attributes:

• The partners collaborate on the basis of

 common interest.

• The benefits of partnership outweigh the cost 

of collaboration.

• The partners can achieve more through collaboration

 than they can individually.

• The benefits received from the partnership should 

be proportional to the value of the contribution. 

• The partnership should not openly conflict with the 

interest of other groups (Micheau, 2008).

Partnerships can bring together parties that have not 

worked together before, which could both be a benefit 

(new complementary capability) and a challenge (the 

understanding of how to work together). Implicit in the 

concept of collaborating on a common basis is the sharing 

of pre-competitive research results, which could allow 

for the advancement of technology and know-how to 

levels beyond the capability of any individual entity.

11.3 Forums for PublicPrivate Partnerships

There are several forums for creating public-private

partnerships:

• Networking events such as seminars and conferences

• Team-oriented government solicitations

• Consortia and trade organizations

• Team-oriented prizes

Networking events such as workshops, conferences, and 

seminars can be important tools for creating a collaborative 

environment. Through these events, scientists and engineers 

can learn of new research, and potential partners can 

explore areas of mutual interest. These events are often 

the point at which new researchers can enter and where 

new thought or methodology is shared with the peers. 
11. Public-Private Partnerships 111

Public-private partnerships—whether they 

are formed or sustained through networking 

events, government solicitations, consortia, prize 

competitions, or trade organizations—can be an 

effective way to address technological, economic, 

and public-policy and regulatory challenges.

As discussed in greater detail in this document, several 

key technological challenges must be addressed for 

the algal biofuels to become viable. These include:

• An open environment to share ideas and technology 

across the entire algal biofuels value chain;

• Technology development in algal biology, 

algal growth and harvesting, algal oil 

extraction, and fuel conversion;

• Pre-commercial-scale user facilities that are 

accessible to researchers and developers 

to road-test their technologies;

• The generation of basic methods and standards; and

• Labor force and intellectual talent to draw upon.

Technology partnerships could be used for following 

objectives:

• Share knowledge of existing algal strains through 

an open access repository and collaborate on the 

development of new natural or GMO algal strains

• Share knowledge of algal cultivation and 

collaborate on the development of dynamic 

monitoring of growth operations

• Collaborate on the development of technologies 

for biomass harvesting and extraction of 

algal components from the biomass

• Share knowledge of fuel requirements 

and utilization to advance fuel conversion 

technologies toward marketable products

In the biofuels industry, technologies developed in the 

laboratory have traditionally not translated well to the 

field (Willems, 2009). Algal biofuels will likely face 

similar issues since natural environmental constraints 

could have a significant impact on algal productivity. A 

public-private partnership for pre-commercial-scale user 

facilities could allow for new technologies to be roadtested and scaled before full-scale deployment in the 

field. This type of partnership would greatly accelerate 

technology development, overcoming the lab-field 

scaling barrier and the lack of private capital to conduct 

such applied research. By reducing scaling risks, this 

type of partnership can help incentivize commercial 

investment of similar full-scale algal operations.

As this industry expands, it will need labor to run its 

operations, develop new algae-based fuels and co-products, 

and innovate new cost-cutting measures. Academia will 

be the workhorse that generates labor for this new industry. 

Collaborative partnerships, particularly between industry 

and academia, are needed to ensure that academia develops 

students capable of addressing the challenges industry faces 

in algal biofuels. Also, in order to fully realize the potential 

of the algal biofuels industry, public-private partnerships 

are needed to engage field experts (e.g., real estate 

developers, construction personnel, lawyers, marketing 

and public relations specialists, distributors) across the 

value chain to address technical and non-technical needs. 

11.5 Modeling Partnerships for 

Technology Development

Of the different forums for public-private partnerships, 

collaborative consortia for technology development are 

the most difficult to implement. These consortia require 

all of the key attributes for successful partnerships 

noted earlier. Therefore, it is useful to conceptualize 

the various models for public-private consortia in terms 

of the five attributes of successful partnerships within 

the context of particular scenarios (e.g., particular algal 

strain, dewatering pathway, conversion process, etc.) or 

end goals (specific intended use, performance aspects of 

the fuel, etc.). Doing so may help define the boundary 

problem(s) for focus by a public-private consortium 

and bring clarity to the composition, requirements, 

and expected contributions of the membership.

Considering the following four external characteristics 

can help evaluate consortia models:

• Openness. How inclusive is the membership 

to its industry (or segment thereof)?

• Technology Commercialization. Is it structured to 

develop and commercialize new technology?

• Industry Growth. Does it seek to grow the industry?

• Shared Investment. Does it share investment equitably?

Different consortia models exist and it is possible to 

compare some of these existing public-private consortia 

models against these four external characteristics, 

as illustrated in Exhibit 11.2. The exhibit compares 

PPP models from five different industry sectors – 

semiconductors, biofuels, nanotechnology, aviation, 

and information technology. These PPP models are 

mentioned only to serve as examples of the four external 

characteristics. Because the ecosystem in the algal 

biofuels industry is unique and differs greatly from 

the established industry sectors represented by most 

B http://www.xprize.org/future-x-prizes/energy-and-environment

C http://www.mitcep.org/
112 11. Public-Private Partnerships 

INDUSTRY FOCUS ENTITY TYPE OPENNESS OF PPP TECHNOLOGY

COMMERCIALIZATION INDUSTRY GROWTH SHARED INVESTMENT

Semiconductors

Non-Profit 

Corporation

(501c6) with 

physical 

facilities

• Open membership

• Represent 

industry interests

• Forums inspiring 

cross collaboration 

amongst members

• Public conferences 

• Collaborate on 

pre-competitive R&D 

selected by membership

• Transfer of technology by 

publication or memberwebsite data transfer

• Technology further 

developed to manufacturing 

solutions with external 

partners; then adopted

• PPP owns created IP and 

provides non-exclusive, 

royalty-free license to 

members

• PPP can also license IP to 

third parties

• Designed 

to increase 

competitiveness of 

existing US firms in 

marketplace

• Provides 

commercialization 

network that 

drives economic 

development

• Develops 

coordinated 

industry roadmap to 

focus R&D and spur 

on economic growth

• Cost-shared 

by government 

and industry at 

start-up

• Now funded 

solely by industry

Biofuels

Government 

Agency 

Research 

Centers

(not a 

separate legal 

entity with 

employees)

• Partners with 

industry and 

universities

• Public conferences 

and workshops

• Opportunities for 

collaboration

• R&D conducted at Research 

Centers or partner facilities

• Industry partners to 

commercialize developed IP

• IP licensed to interested 

parties with an evaluation 

of commercialization 

potential

• Transfer of technology by 

publication 

• Address gamechanging, high-risk 

barriers through 

targeted R&D 

• Industry growth 

supported through 

education

• Limited industry 

involvement to 

address issues on 

industry growth

• Government 

funding

• State funding

• Financial and 

other resources 

from national 

labs

Exhibit 11.2 Comparison of Some Public-Private-Partnership (PPP) Models

models presented, this industry may find that no specific model will meet all of its needs. However, for an algal biofuels 

public-private consortium to meet its specific mission successfully, it could be helpful to consider these attributes 

and models, discuss and debate the merits of each, and determine how to best adapt / implement these attributes.
11. Public-Private Partnerships 113

INDUSTRY FOCUS ENTITY TYPE OPENNESS OF PPP TECHNOLOGY

COMMERCIALIZATION INDUSTRY GROWTH SHARED INVESTMENT

Nanotechnology

Non-Profit 

Corporation

(501c6) with 

physical 

facilities

• Open membership

• Consortium of 

industry, academic 

and national lab 

partners;

• Technical 

workshops; 

technical, 

business, and 

social issues 

inspire cross 

collaboration 

amongst members 

• Pre-competitive research 

selected by all members

• Research conducted by 

national labs and member 

universities

• PPP provides non-exclusive, 

paid-up license to industry 

members

• Industry growth 

through education

• Technology 

only licensed to 

members

• Government 

funding for over 5 

years

• Founding 

member financial 

commitment for 

over 3 years

Aviation

Industry 

consortium 

with NASA 

& FAA (not a 

separate legal 

entity with 

employees

• Open membership,

• Consortium of 

industry, academic 

and government 

partners

• Collaborative research 

amongst consortium 

members designed 

to reduce technical, 

operational, and regulatory 

bottlenecks

• IP licensed exclusively or 

non-exclusively

• Commercialization afforded 

as members agree to cross 

license background and 

newly developed IP nonexclusively to each other 

royalty-free 

• Transfer of technology by 

publication, and transfer 

of knowledge through 

member-only database

• Technology 

development and 

standardization 

designed to reduce 

operational costs 

and increase 

general aviation 

market, including 

large established 

firms and small 

businesses

• Significant industry 

involvement 

provides market 

focus and 

commercialization 

network

• Government 

funding for over 8 

years

• Industry match 

for same number 

of years 

Information 

Technology Research

University 

of California 

Institute 

(not a separate 

legal entity 

with employees

• Donor-driven 

model

• Industry and 

university partners

• Numerous forums 

inspiring cross 

collaboration 

amongst 

researchers from 

universities and 

companies

• Research conducted by 

university 

• Software is open source 

licensed

• Other IP is either licensed 

non-exclusively, royaltyfree basis or exclusively, 

royalty basis as needed to 

achieve the widest possible 

dissemination.

• Industry growth 

supported through 

education

• Limited industry 

involvement 

through Advisory 

committee to 

address issues on 

industry growth

• State funding 

over 4 years

• University funds

• Industry gifts

• No federal 

funding
114 11. Public-Private Partnerships 

References

Audretsch, D.B., Link, A.N., and Scott, J.T. (2002). Public/private technology partnerships: evaluating SBIR-supported research. 

Research Policy. 31(1), 145-158.

Brown, M.A. (2001). Market failures and barriers as a basis for clean energy policies. Energy Policy. 29(14), 1197-1207.

Brown, M.A., Levine, M.D., Short, W., and Koomey J.G. (2001). Scenarios for a clean energy future. 

Energy Policy. 29(14), 1179-1196.

Council on Competitiveness. (1996). Endless frontiers, limited resources. Washington: U.S. R&D Policy for Competitiveness.

Gallagher, K.S., Holdren, J.P., and Sagar, A.D. (2006). Energy-technology innovation. Annual Review of Environment and Resources. 

31, 193-237.

Link, A.N., Paton, D., and Siegel, D.S. (2002). An analysis of public initiatives to promote strategic research partnerships. 

Research Policy. 31, 1459-1466.

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115 Appendices 

Appendices 

Walter Adey Smithsonian Institution

John Aikens Lybradyn

Mark Allen A2be Carbon Capture

Gennady Ananyev Princeton

Alex Aravanis Sapphire Energy

Ed Archuleta El Paso Water Utilities

Paul Argyropoulos Environmental Protection Agency

Ricardo Arjona Abengoa Bioenergy

Virginia Armbrust University of Washington

Bob Avant Texas A&M

Tom Avedisian U.S. Department of Energy

David Bayless Ohio University

Jacques Beaudry-Losique U.S. Department of Energy Biomass Program

Leslie Bebout NASA Ames Research Center

Lucie Bednarova General Motors

Amha Belay Earthrise Nutritionals

John Benemann Benemann Associates

Linda Benjamin Food and Drug Administration

Christoph Benning Michigan State

Isaac Berzin Interdisciplinary Center Herzliya, Lauder School of Government, Diplomacy 

And Strategy

Catalino Blanche U.S. Department of Agriculture 

Doug Borger Lockheed Martin

John Bouterse Envo Smart

Sara Boyd BCS, Inc.

Andrew Braff Wilson Sonsini Goodrich & Rosati

Jim Brainard National Renewable Energy Laboratory

Jerry Brand University of Texas at Austin

Tom Brennan Arch Ventures

Michael Briggs University of New Hampshire

Jim Bristow Joint Genome Institute

Kevin Brown -

Malcolm Brown University of Texas at Austin

Nathan Brown Federal Aviation Administration (Office of Environment And Energy)

Kent Bryan City of Celina

Appendix 1 : Workshop Participants
Appendices 116

William Buchan NASA Ames Research Center

Jay Burns Bionavitas

Arthur Butcher CPS Energy

Thomas Byrne Byrne & Co

Martin Carrera BP

Matt Caspari Aurora Biofuels

Chris Cassidy U.S. Department of Agriculture

Heriberto Cerutti University of Nebraska - Lincoln

Alice Chen Environmental Protection Agency

Parag Chitnis National Science Foundation

Daniel Cicero National Energy Technology Laboratory

Mike Cleary National Renewable Energy Laboratory

John Coleman Algenol

Jim Cook Univenture

Doris Cooksey CPS Energy

Keith Cooksey Montana State University

Michael Cooney University of Hawaii – Manoa

David Daggett Boeing

Al Darzins National Renewable Energy Laboratory

K.C. Das University of Georgia

John Datko Air Force Office of Scientific Research

Chris Davies Independence Bioproducts

Brian Davison Oak Ridge National Laboratory

Mark Decot U.S. Department of Energy Biomass Program

Michel Delafontaine Hawaii Biocrude

Gregg Deluga General Electric Global Research

Harrison Dillon Solazyme

Dan Drell Office of Science Biological and Environmental Research

Donn Dresselhuys Old Dominion University

Bruce Eldridge University of Texas at Austin

Tj Evens U.S. Department of Agriculture

Paul Falkowski Rutgers University

John Ferrell U.S. Department of Energy, Biomass Program

Daniel Fishman BCS, Inc.

Todd French Mississippi State

Christian Fritsen Desert Research Institute

Matthew Frome Solozyme

Maria Ghirardi National Renewable Energy Laboratory
117 Appendices 

Warren Gillette Federal Aviation Administration (Office of Environment And Energy)

Jim Gillingham Valero

Dan Ginosar Lawrence Livermore National Laboratory 

Robert Glass Lawrence Livermore National Laboratory

Steven Gluck Dow Chemical

Steve Gorin National Renewable Energy Laboratory

Alison Goss Eng U.S. Department of Energy, Biomass Program

Suzanne Goss Jacksonville Electric Authority

Paul Grabowski U.S. Department of Energy, Biomass Program

Michael Graves University of Massachusetts

Bailey Green Lawrence Berkeley National Laboratory

Eli Greenbaum Oak Ridge National Laboratory

Nathanael Greene Natural Resources Defense Council

Michael Gregoire U.S. Department of Agriculture

Tom Gross If, LLC

Arthur Grossman Stanford

Guritno “Guri” Roesijadi Pacific Northwest National Laboratory

Molly Hames U.S. Department of Energy, Golden Field Office

Anders Handlos Grauslund Novozymes

Zia Haq U.S. Department of Energy Biomass Program

Laurel Harmon UOP

Deanna Hatch Organofuels Incorporated

Pat Hatcher Old Dominion University

David Hazlebeck General Atomics

Bob Hebner University of Texas at Austin

Grant Heffelfinger Sandia National Laboratories

Erik Helm Environmental Protection Agency

William Henley Oklahoma State

Doug Henston Solix Biofuels

Jurg Heuberger County of Imperial

Kevin Hicks U.S. Department of Agriculture

Mark Hildebrand Scripps Institute

Masahito Hiratake Mitsubishi International

Kent Hoekman Desert Research Institute

Neil Hoffman U.S. Department of Agriculture

Ed Hogan Natural Resources Canada

John Hogan NASA Ames Research Center

John Holladay Pacific Northwest National Laboratory
Appendices 118

Andy Horne Natural Resources Development

Jeff Houff Hydrogeologic, Inc

Qiang Hu Arizona State University

Neil Huber Army

Michael Huesemann Pacific Northwest National Laboratory

Peter Hug Recombinant Innovation, LLC

J.C. Hunter-Cevera University of Maryland Biotechnology Institute

Mark Huntley University of Hawaii

Stephen J. Miller Chevron Chevron

Gil Jackson United States Agency for International Development 

Jacob Jacobson Idaho National Laboratory

Robert Jagusch Minnesota Muncipal Utilitees Association

Eric Jarvis National Renewable Energy Laboratory

Jeff Jeter Honda

Libby Jewett National Oceanic and Atmospheric Administration 

James “Jim” Sears A2be Carbon Capture

Michael Johnson Massachusetts Institute of Technology 

Glen Kertz Valcent

Alex Kinnier Khosla Ventures

Douglas Kirkpatrick Defense Advanced Research Projects Agency 

Melissa Klembara U.S. Department of Energy Biomass Program

Geetha Kothandaraman ConocoPhillips

Walt Kozumbo Air Force Office of Scientific Research

Heidi Kuehnle Kuehnle Agrosystems

Peter Lammers New Mexico State University

Cynthia Lane American Water Works Association

Todd Lane Sandia National Laboratories

Mario Larach Kai Bioenergy Corp.

Rachel Lattimore Arent Fox LLP

Edward Laws University of Hawaii at Monoa

Gordon Leblanc Petrosun

Joo-Youp Lee University of Cincinnati

Paul Lefebvre University of Minnesota

James Lester Stratus Consulting

Jack Lewnard Gas Technology Institute

Casey Lippmeier Martek

Kent Lohman Midwest Research Institute

Tryg Lundquist California Polytechnic State University
119 Appendices 

John Magnuson Pacific Northwest National Laboratory

Len Malczynski Sandia National Laboratories

Mike Manella ADM

Russell Martin Blue Source

Anthony Martino Sandia National Laboratories

Margaret McCormick Targeted Growth

Patrick McGinn National Research Council

John McGowen Biodesign Institute at Arizona State University

Diane McKnight University of Colorado-Boulder

Steve Meller Procter & Gamble

Omar Mendoza United States Air Force

Walter Messier Evolutionary Genomics

Blaine Metting Pacific Northwest National Laboratory

Anelia Milbrandt National Renewable Energy Laboratory

Greg Mitchell Scripps Institution of Oceanography

John Mizroch U.S. Department of Energy

Lissa Morgenthaler-Jones Livefuels

Jerry Morris Innovation/Biodomain - Shell Global Solutions Inc.

Kenneth Moss Environmental Protection Agency

Chuck Mueller Sandia National Laboratories

Jeff Muhs Utah State University

Walter Mulbry U.S. Department of Agriculture

Alyson Myers Kegotank Biofuels

Nick Nagle National Renewable Energy Laboratory

David Nobles University of Texas at Austin

Charley O’kelly Blue Marble Energy

Lou Ogaard CEHMM

Kelly Ogilvie Blue Marble Energy

John Ohlrogge Michigan State University

Jose Olivares Los Alamos National Laboratory

Phil Ovitt Senator Brownback Office

George Oyler Johns Hopkins University

Stephen P. Mayfield Scripps Research Institute

Mike Pacheco National Renewable Energy Laboratory

Paul Panesgrau National Renewable Energy Laboratory

Frank Parker Organofuels Incorporated

Helen Parker Algaelink, N.V.

Roberta Parry Environmental Protection Agency
Appendices 120

Ron Pate Sandia National Laboratories

Leslie Pezzullo U.S. Department of Energy, Biomass Program

Schild Philippe European Commission

Philip Pienkos National Renewable Energy Laboratory

Maria Piera Abengoa Bioenergy

John Pierce Wilson Sonsini Goodrich & Rosati

Daniel Pike AF Research Lab

Jennifer Pinkerton LA Department of Water & Power

Bradley Plantz University of Nebraska-Lincoln

John Plaza John Plaza

Robert Polak Phycal

Juergen Polle Brooklyn College

Matt Posewitz Colorado School of Mines

Steve Potts EPA Office of Water

Peter Pryfogle Idaho National Laboratory

Steve Przesmitski National Renewable Energy Laboratory

Theras Pugh American Public Power Association

Ron Putt Auburn University

Nigel Quinn Lawrence Berkeley National Laboratory

Kenneth Reardon Colorado State University

Hal Reed American Water

Valerie Reed U.S. Department of Energy, Biomass Program

Ron Reinsfelder Shell Global Solutions

Bruce Resnick Cargill

Curt Rich Van Ness Feldman

Mark Riedy Andrews Kurth

Kathy Roach MurphyTate, LLC

John Robbins Exxonmobil

Paul Roessler Synthetic Genomics

Roger Ruan University of Minnesota

Jim Ryan MOR Supercritical, LLC

Gerson Santos-Leon Abengoa Bioenergy

Richard Sayre Donald Danforth Plant Science Center

Philippe Schild European Commission

Gerald Seeley Old Dominion University/Company

Mark Segal Environmental Protection Agency

Mike Seibert National Renewable Energy Laboratory

Joel Serface Kleiner Perkins
121 Appendices 

Pamela Serino Defense Energy Support Center

Chris Shaddix Sandia National Laboratories

Alex Shearer SRI International

John Sheehan Sheehanboyce, LLC

Tanja Shonkwiler Jamestown Ny (Outside Counsel)

Blake Simmons Sandia National Laboratories

Knut Simonsen DTE Energy Resources, Inc.

Evan Smith The Verno Group

Seth Snyder Argonne National Laboratory

Milton Sommerfeld Arizona State University

Glenn Sonntag U.S. Department of Energy, Biomass Program

John Spear Colorado School of Mines

Karl Stahlkopf Hawaiian Electric Company, Inc.

Cai Steger Natural Resources Defense Council

Dan Stepan Energy & Environmental Research Center

Jake Stewart Organic Fuels

Mark Stone Desert Research Institute

Belinda Sturm Kansas University Transportation Research Institute

Sidhu Sukh University of Dayton

Xiaolei Sun Arizona Public Service

Sam Tagore U.S. Department of Energy, Biomass Program

Evonne Tang National Academy of Sciences

Jeff Tester Massachusetts Institute of Technology 

Robert Thomas South Australia R&D Institute

Jonathan Trent NASA Ames Research Center

Pat Unkefer Los Alamos

James Van Etten University of Nebraska

Peter Van Den Dorpel Algaelink, N.V.

Jean Vandergheynst UC Davis

Tom Verry National Biodiesel Board

Sanjay Wagle Vantagepoint Venture

Kevin Wanttaja Salt River Project

Michael Webber The University of Texas at Austin

Alan Weber Marc-IV Consulting

Donald Weeks University of Nebraska - Lincoln

Alan Weimer University of Colorado at Boulder

Zhiyou Wen Virginia Tech

Norman Whitton Sunrise Ridge Algae
Appendices 122

Appendix 2: Contributors

Jim Brainard National Renewable Energy Laboratory

Tom Brennan Arch Ventures

Bill Buchan NASA Ames Research Center

Mike Cleary National Renewable Energy Laboratory

Michael Cooney University of Hawaii – Manoa

Al Darzins National Renewable Energy Laboratory

Daniel Fishman BCS, Inc.

Maria Ghirardi National Renewable Energy Laboratory

Stephen Gorin National Renewable Energy Laboratory

Tom Gross IF, LLC.

Molly Hames U.S. Department of Energy Golden Field Office

Grant Heffelfinger Sandia National Laboratories

Mark Hildebrand Scripps Institution of Oceanography

John Hogan NASA Ames Research Center

Qiang Hu Arizona State University

Michael Huesemann Pacific Northwest National Laboratory

Eric Jarvis National Renewable Energy Laboratory

Geoff Klise Sandia National Laboratories

Alina Kulikowski-Tan Carbon Capture Corp

Pete Lammers New Mexico State University

Jared Largen BCS, Inc.

Elizabeth Willet Mars Symbioscience

Bryan Willson Colorado State University

Byard Wood Utah State University

Christopher Wood Platt River Power Authority

David Woodbury Biofuel Producers of America (Bpa

Paul Woods Algenol

Ben Wu Livefuels

Don Wyma National Intelligence Officer For Science And Technology

Joyce Yang U.S. Department of Energy Biomass Program

Chris Yeager Savannah River National Laboratory

Ross Youngs Univenture

Tim Zenk Sapphire Energy

Zhenqi Zhu Stevens Institute of Technology

Yonathan Zohar University of Maryland Biotechnology Institute
123 Appendices 

Yantao Li Arizona State University

Tryg Lundquist California Polytechnic State University

Rajita Majumdar BCS, Inc.

Len Malcynski Sandia National Laboratories

Tony Martino National Renewable Energy Laboratory

Steve Mayfield Scripps Institution of Oceanography

Anelia Milbrandt National Renewable Energy Laboratory

Joanne Morello U.S. Department of Energy, Biomass Program

Chuck Mueller Sandia National Laboratories

Nick Nagle National Renewable Energy Laboratory

Michael Pacheco National Renewable Energy Laboratory

Ron Pate Sandia National Laboratory

Leslie Pezzullo U.S. Department of Energy, Biomass Program

Philip Pienkos National Renewable Energy Laboratory

Juergen Polle Brooklyn College

Matthew Posewitz Colorado School of Mines

Ron Putt Auburn University

Kathy Roach MurphyTate, LLC.

Guri Roesijadi Pacific Northwest National Laboratory

Mike Seibert National Renewable Energy Laboratory

Joel Serface Kleiner Perkins

Chris Shaddix Sandia National Laboratories

Blake Simmons Sandia National Laboratories

Amy Sun Sandia National Laboratories

Joyce Yang U.S. Department of Energy, Biomass Program
Appendices 124

Appendix 3: Respondents to Request for Information 

on the Draft Roadmap

Daniel Angell TPA Inc.

Bob Avant et al Texas AM

Halil Berberoglu University of Texas

Shulin Chen et al Washington University

Barry Cohen National Algae Association

Anju Dahiya 1) The University of Vermont ; 2) General Systems Research LLC

Matthew Frome Solazyme

Michael R. Gale PetroAlgae, LLC

Arthur Grossman Carnegie Institution for Science (Staff member), Stanford University 

(Adjunct Professor), Solazyme (Chief of Genetics)

Douglas Haughey not listed

Joel E. Kostka Florida State University

David Lewis The University of Adelaide

Margaret McCormick Targeted Growth

Lissa Morgenthaler-Jones LiveFuels, Inc

Matt Peak Prize Capital

María Piera Alberola Abengoa

Matthew Posewitz Colorado School of Mines

Bruce Resnick Cargill

Bruce E. Rittmann Center for Environmental Biotechnology, Biodesign Institute, 

Arizona State University

G. Roesijadi Pacific Northwest National Laboratory

Mary Rosenthal Algal Biomass Organization

Richard Sayre and Ursula Goodenough Donald Danforth Plant Science Center and Washington University

Gerard Seeley Jr. Algal Farms Inc.

Mark Segal Environmental Protection Agency Office of Pollution Prevention and Toxics

Alexander D. Shenderov BioLogical Technologies, Inc.

Dr. Valentin Soloiu Georgia Southern University

Lance Stokes ECI Environmental Compliance

Jefferson Tester Cornell University

Willem Vermaas Arizona State University, School of Life Sciences

Marc von Keitz and Steve Heilmann University of Minnesota, Biotechnology Institute

David L. Wenbert The Eden Tube Project

Norman M. Whitton, Dr. Robert S Weber Sunrise Ridge Algae, Inc.

Paul Woods Algenol

Xiaohan Yang Oak Ridge National Laboratory

Tim Zenk Sapphire Energy

www.eere.energy.gov

DOE/EE-0332