Overcoming Technical Barriers to the Sustainable Development

of Competitive Marine Aquaculture 

in the United States 

Summary of a Workshop on 

Enhancing Competitiveness of Sustainable Marine Aquaculture in the United States: 

Addressing Measurement Barriers to Technological Innovation 

Orlando, Florida 

13-14 February 2008 

Sponsored by 

National Institute of 

Standards and Technology 

National Oceanic and 

Atmospheric Administration 
2
3

NOAA Technical Memorandum NMFS F/SPO-100 

Certain commercial entities, equipment, or materials may be identified in this document in order 

to describe an experimental procedure or concept adequately. Such identification is not intended 

to imply recommendation or endorsement by the National Institute of Standards and Technology 

or the National Oceanic and Atmospheric Administration, nor is it intended to imply that the 

entities, materials, or equipment are necessarily the best available for the purpose. The 

recommendations outlined in this report are a summary of the views expressed by the workshop 

participants and do not necessarily represent the official position of NIST or NOAA. 

This document may be cited as follows: 

Browdy, C.L. and J.A. Hargreaves (editors). 2009. Overcoming Technical Barriers to the 

Sustainable Development of Competitive Marine Aquaculture in the United States. U.S. 

Department of Commerce, Silver Spring, MD USA. NOAA Technical Memo NMFS F/SPO100. 114pp. 

Acknowledgments 

This workshop was supported by a financial award from NIST to NOAA’s Hollings Marine 

Laboratory (HML) (Paul Sandifer, Fred Holland, and Craig Browdy, Principal Investigators). 

This workshop could not have been completed without the hard work of the section leaders: Dan 

Cheney – Pacific Shellfish Institute, Richard Langan – University of New Hampshire, Yonathan 

Zohar – University of Maryland Center for Marine Biotechnology and the guidance of the 

steering committee. We gratefully acknowledge the outstanding work of Susan Lovelace 

(NOAA/HML), (Linda Beth Schilling (NIST), Susan White (NOAAS/HML) and Doug Jones 

(NIST) as workshop facilitators. Thanks also to Virginia Fay (NOAA/NMFS), Kate Naughten 

(NOAA Aquaculture), Michael Rubino (NOAA Aquaculture) and Paul Sandifer (NOAA/NOS) 

for editorial assistance. 
4

Edited By: Craig L. Browdy and John A. Hargreaves 

Section Chairs: 

Coastal Shellfish Production 

Dr. Daniel Cheney 

 

Cage Production of Marine Finfish 

Dr. Richard Langan 

Land-based Production of Marine Finfish 

Dr. Yonathan Zohar 

 

Production of Marine Shrimp in Biofloc Based Systems 

Dr. Craig L. Browdy 

Steering Committee 

Craig L. Browdy – Chairman, South Carolina Department of Natural Resources 

Mike Amos – National Institute of Standards and Technology 

Paul Becker - National Institute of Standards and Technology 

Dan Cheney – Pacific Shellfish Institute 

John Cooksey –World Aquaculture Society 

Doug Drennan – United States Aquaculture Suppliers Association 

John Hargreaves – Proceedings Editor 

Betsy Hart – National Aquaculture Association 

Fred Holland – National Oceanic and Atmospheric Administration 

Gary Jensen – Department of Agriculture 

Doug Jones – National Institute of Standards and Technology 

John Kuklick - National Institute of Standards and Technology 

Richard Langan – University of New Hampshire 

Andy Lazur – National Oceanic and Atmospheric Administration 

Susan Lovelace - National Oceanic and Atmospheric Administration 

Barbara Montwill – Food and Drug Administration 

Paul Sandifer – National Oceanic and Atmospheric Administration 

Linda Beth Schilling – National Institute of Standards and Technology 

Jeff Silverstein –Department of Agriculture 

Carolyn Sotka – National Oceanic and Atmospheric Administration 

Jose Villalon – World Wildlife Fund 

Yonathan Zohar – University of Maryland Center for Marine Biotechnology 
5

FORWARD 

Aquaculture is the fastest growing form of food production in the world. It is also a significant 

source of protein for people in many countries, including the United States. Globally, nearly half 

the fish consumed by humans is produced by fish farms. This worldwide trend toward 

aquaculture production is expected to continue. At the same time, demand for safe, healthy 

seafood is also expected to grow. It is clear that the United States needs a robust aquaculture 

industry to meet rising seafood demand and to enhance domestic commercial and recreational 

fish and shellfish stocks. 

Technology innovation is a major source of the nation’s economic well-being. Therefore it is 

critical to identify the technological roadblocks which impede innovation as well as identify the 

needs in measurements which are linked to technology innovation. The primary function of the 

Addressing Barriers to Technological Innovations in Aquaculture workshop was to generate 

information from private and public sectors to ensure that the nation’s innovation and 

measurement needs in aquaculture were identified. If financial and other resources are made 

available and there is sufficient stakeholder interest, a research and innovation action plan could 

be developed based on this assessment. 

The National Institute of Standards and Technology (NIST) and the National Oceanic and 

Atmospheric Administration (NOAA) jointly facilitated the Addressing Barriers to 

Technological Innovations in Aquaculture workshop. Other key agencies in aquaculture also 

participated as part of the workshop steering committee, including the U.S. Department of 

Agriculture (USDA) and the Food and Drug Administration (FDA). Founded in 1901, NIST is a 

non-regulatory federal agency within the U.S. Department of Commerce. The NIST mission is 

to promote U.S. innovation and industrial competitiveness by advancing measurement science, 

standards, and technology in ways that enhance economic security and improve our quality of 

life. As a federal agency, under the U.S. Department of Commerce, NOAA is at the forefront of 

a national initiative to help the United States become more self-sufficient in the production of 

seafood. This initiative is based on sustainable commercial marine fisheries complemented by 

robust domestic aquaculture production. 

In the fifteen previous industry workshops conducted as part of the U.S. Measurement System 

Assessment (usms.nist.gov) by NIST, 164 industry technology roadmaps were reviewed and 723 

measurement needs in 11 industry sectors and technology areas identified. One would imagine 

technology and measurement needs across the sectors would vary tremendously. One would also 

imagine aquaculture’s technological needs to be completely unique from other industries. 

However there are many notable similarities in the needs identified. Many needs identified from 

this workshop also touch upon previously identified needs that crosscut industry sectors: 

3⁄4 Requirements to improve process control transcend nearly all sectors and demand 

increased accuracy, precision, resolution, sensitivity, and repeatability. 

3⁄4 Opportunities to use sensors to detect, monitor, and control a wide variety of quantities, 

properties and processes—in real time—are abundant. 
6

3⁄4 Reliable metrics for quantifying overall system performance—such as interoperability 

and conformance to specifications—are critically needed, as products and services are 

integrated or networked into collections of hardware and software technologies, including 

complex systems. 

Representing a variety of interests, including public and private research and development 

interests, industry, academia, and government and non-government entities, over 125 workshop 

participants helped identify and prioritize a more specific innovation and measurement needs 

agenda that addresses the technical infrastructure in the varied disciplines of aquaculture. By 

self-selecting into four working groups, participants identified how best to transfer knowledge 

and share priorities across industry, government, funding agencies, regulatory agencies, 

educational and not-for-profit institutions in order to build strong collaborations and 

partnerships. By the end of the workshop a roadmap of the innovation and measurement needs 

was outlined in four major areas: Biofloc-based Production of Marine Shrimp, Land-based 

Production of Marine Finfish, Coastal Shellfish Production, and Cage Production of Marine 

Finfish. The steps required to address these technical needs, as well as the consequences of 

inaction, were generally developed within these four breakout discussion groups. 

If utilized effectively, this roadmap will make a difference for NOAA and NIST and the way we 

view aquaculture research needs and for the many other organizations public and private, who 

comprise the aquaculture infrastructure of the United States. It is our hope the varied 

technological barriers identified by this workshop will be a key component of the nation's 

innovative focus in aquaculture for the future. The industry comprises an incredibly diverse 

assortment of activities from commerce and trade to food safety, bio-security, animal health care 

and nutrition, environmental impacts, production technologies, as well as basic science oriented 

research and innovation. The results of this workshop provide a broad vision of the aquaculture 

industry in the U.S. and its innovation and measurement needs as we continue to move toward a 

more robust and sustainable domestic aquaculture industry that is both environmentally and 

economically sustainable. 

Dr. Michael Rubino 

Manager, Aquaculture Program 

National Oceanographic and Atmospheric Administration 

Dr. Willie E. May 

Director, Chemical Science and Technology Laboratory 

National Institute of Standards and Technology 
7

TABLE OF CONTENTS 

FORWARD..................................................................................................................................... 5 

TABLE OF CONTENTS................................................................................................................ 7 

OVERCOMING TECHNICAL BARRIERS TO THE SUSTAINABLE DEVELOPMENT OF 

COMPETITIVE MARINE AQUACULTURE IN THE UNITED STATES............................... 11 

WORKSHOP EXECUTIVE SUMMARY..........................................................................................................................11

THE FOLLOWING SECTIONS IN THIS SUMMARY PROVIDE MORE DETAIL THE SCOPE FOR AN EXPANDED MARINE 

AQUACULTURE SECTOR IN THE US, BACKGROUND ON WORKSHOP STRUCTURE AND ORGANIZATION, AS WELL AS 

PRIORITIZED OUTCOMES OF THE DISCUSSIONS OF THE WORKSHOP BREAKOUT GROUPS. RESEARCH NEEDS ARE 

SUMMARIZED AND PRIORITIZED. SPECIFIC MEASUREMENT GAPS ARE ALSO DESCRIBED. DURING THE WORKSHOP 

SOME VERY IMPORTANT NON-TECHNICAL BARRIERS TO SECTOR DEVELOPMENT WERE IDENTIFIED AND THESE HAVE 

ALSO BEEN SUMMARIZED IN A SECTION ENTITLED NON-TECHNICAL BARRIERS. THE FINAL SECTION IN THE 

WORKSHOP SUMMARY DISCUSSES ROADMAP IMPLEMENTATION FOCUSING ON NEXT STEPS TO PROMOTE THE 

ADVANCEMENT OF US MARINE AQUACULTURE. THE SCOPE FOR AN EXPANDED MARINE AQUACULTURE SECTOR.12

THE SCOPE FOR AN EXPANDED MARINE AQUACULTURE SECTOR............................................................................13

WORKSHOP STRUCTURE AND ORGANIZATION .........................................................................................................13

PRIORITY RESEARCH NEEDS ....................................................................................................................................15

Genetic Improvement...........................................................................................................................................15

Shellfish:............................................................................................................................................................................ 16

Marine Shrimp:.................................................................................................................................................................. 16

Nutrition, Feeds, and Feeding Practices .............................................................................................................16

Marine Finfish: .................................................................................................................................................................. 17

Marine Shrimp:.................................................................................................................................................................. 17

Health Management.............................................................................................................................................17

Shellfish............................................................................................................................................................................. 17

Marine Finfish. .................................................................................................................................................................. 18

Marine Shrimp................................................................................................................................................................... 18

Reproductive Control...........................................................................................................................................18

Shellfish............................................................................................................................................................................. 18

Marine Finfish. .................................................................................................................................................................. 18

Production of Larvae and Juveniles ....................................................................................................................18

Shellfish............................................................................................................................................................................. 19

Marine Finfish. .................................................................................................................................................................. 19

Marine Shrimp................................................................................................................................................................... 19

Food Safety and Product Quality ........................................................................................................................19

Shellfish............................................................................................................................................................................. 20

Marine Finfish. .................................................................................................................................................................. 20

Marine Shrimp................................................................................................................................................................... 20

Environmental Performance and Impact.............................................................................................................20

Shellfish............................................................................................................................................................................. 21

Cage Culture of Marine Finfish......................................................................................................................................... 21

Land-Based Culture of Marine Finfish or Marine Shrimp................................................................................................. 21

System Engineering and Life-Support Systems....................................................................................................21

Shellfish............................................................................................................................................................................. 22

Cage Culture of Marine Finfish......................................................................................................................................... 22

Land-Based Culture of Marine Finfish. ............................................................................................................................. 22

Biofloc-Based Culture of Marine Shrimp.......................................................................................................................... 22

Economics and Marketing ...................................................................................................................................22

Biofloc-Based Culture of Marine Shrimp.......................................................................................................................... 23

Biofouling Control...............................................................................................................................................23

Inventory Estimation............................................................................................................................................23

RANKED SPECIFIC PRIORITY AREAS.........................................................................................................................23
8

Coastal Shellfish Production ...............................................................................................................................24

Cage Production of Marine Finfish.....................................................................................................................24

Land-Based Production of Marine Finfish..........................................................................................................24

Biofloc-Based Production of Marine Shrimp ......................................................................................................25

MEASUREMENT NEEDS.............................................................................................................................................25

Sensors.................................................................................................................................................................25

Analytical Techniques..........................................................................................................................................25

Diagnostic Tests ..................................................................................................................................................26

Metrics or Standards ...........................................................................................................................................26

Models .................................................................................................................................................................27

NON-TECHNICAL BARRIERS.....................................................................................................................................27

Regulations and Policy........................................................................................................................................27

User Conflicts......................................................................................................................................................28

Financial..............................................................................................................................................................28

Research ..............................................................................................................................................................28

Skilled Workers....................................................................................................................................................29

Technology Transfer............................................................................................................................................29

ROADMAP IMPLEMENTATION ...................................................................................................................................29

Demonstrating Feasibility ...................................................................................................................................30

A ROADMAP FOR COMMERCIALIZATION OF ADVANCED TECHNOLOGIES FOR THE 

FARMING OF MARINE SHELLFISH ....................................................................................... 31 

TECHNICAL CHALLENGES AND MEASUREMENT BARRIERS ......................................................................................31

TECHNOLOGY AT ISSUE............................................................................................................................................31

TECHNOLOGICAL INNOVATION AT STAKE ................................................................................................................31

ECONOMIC SIGNIFICANCE OF INNOVATION ..............................................................................................................32

CROSSCUTTING NON-TECHNICAL BARRIERS TO INNOVATION .................................................................................32

Research Integration and Management...............................................................................................................32

Regulatory, Siting, and Public Policy Issues .......................................................................................................33

Economics, Training, Markets, and Pricing........................................................................................................33

Technology Transfer............................................................................................................................................33

TECHNICAL AND MEASUREMENT BARRIERS TO THE INNOVATION ...........................................................................33

Cross-Cutting Measurement Challenges .............................................................................................................34

Genetics, Breeding, Larvae and Seed Supply ......................................................................................................34

Genetics and Breeding....................................................................................................................................................... 34

Integration and Coordination: ....................................................................................................................................... 34

Controls on Reproduction: ............................................................................................................................................ 35

Germplasm Collection and Preservation:...................................................................................................................... 35

Heritability Estimates:................................................................................................................................................... 36

Inbreeding: .................................................................................................................................................................... 36

Molecular Markers, Mapping and Genomic Enablement:............................................................................................. 36

Genetics and Breeding Technology Gaps: .................................................................................................................... 36

Genetics and Breeding Measurement Issues: ................................................................................................................ 37

Broodstock Maturation Systems........................................................................................................................................ 37

Systems Engineering:.................................................................................................................................................... 37

Feeds and Feeding:........................................................................................................................................................ 37

Reproductive Performance:........................................................................................................................................... 37

Health and Prevention of Disease Transfer ................................................................................................................... 38

Broodstock Maturation Technology Gaps and Measurement Issues:............................................................................ 38

Larval Culture Systems ..................................................................................................................................................... 38

Systems Engineering:.................................................................................................................................................... 38

Husbandry:.................................................................................................................................................................... 39

Larval culture systems technology gaps:....................................................................................................................... 39

Larval culture systems measurement issues: ................................................................................................................. 39

Nursery Systems................................................................................................................................................................ 39

Nursery Systems Technology Gaps: ............................................................................................................................. 40

Nursery Systems Measurement Issues: ......................................................................................................................... 40

Grow-out Systems ................................................................................................................................................41
9

Grow-out Systems Technology Gaps and Measurement Issues......................................................................................... 41

Harvest Systems...................................................................................................................................................42

Harvest Systems Technology Gaps and Measurement Issues............................................................................................ 43

Processing, Packaging and Transport.................................................................................................................43

Processing, Packaging, and Transport Technology Gaps .................................................................................................. 44

Processing, Packaging, and Transport Measurement Issues .............................................................................................. 45

SHELLFISH CULTURE SUB-GROUP MEMBERS ...........................................................................................................47

A ROADMAP FOR COMMERCIALIZATION OF CAGE PRODUCTION OF MARINE 

FINFISH ....................................................................................................................................... 49 

TECHNICAL CHALLENGES AND MEASUREMENT BARRIERS ......................................................................................49

TECHNOLOGY AT ISSUE............................................................................................................................................49

TECHNOLOGICAL INNOVATION AT STAKE ................................................................................................................49

ECONOMIC SIGNIFICANCE OF INNOVATION ..............................................................................................................49

TECHNICAL BARRIERS TO THE INNOVATION ............................................................................................................50

Fingerling Transport and Stocking......................................................................................................................50

Growout...............................................................................................................................................................50

Engineered Systems........................................................................................................................................................... 50

General Husbandry ............................................................................................................................................................ 52

Feeding .............................................................................................................................................................................. 53

Grading.............................................................................................................................................................................. 53

Harvesting ...........................................................................................................................................................54

Feeds and Nutrition .............................................................................................................................................54

Environmental Performance................................................................................................................................54

Feeds and nutrition ............................................................................................................................................................ 54

Benthos and Water Column............................................................................................................................................... 54

Fish Health ........................................................................................................................................................................ 55

Containment ...................................................................................................................................................................... 55

APPLICATION OF MEASUREMENT SCIENCE TO OVERCOMING TECHNICAL BARRIERS...............................................56

Technology Development Approach:...................................................................................................................56

CAGE CULTURE SUB-GROUP MEMBERS...................................................................................................................61

A ROADMAP FOR COMMERCIALIZATION OF LAND-BASED PRODUCTION OF 

MARINE FINFISH....................................................................................................................... 63 

TECHNICAL CHALLENGES AND MEASUREMENT BARRIERS ......................................................................................63

TECHNOLOGY AT ISSUE............................................................................................................................................63

TECHNOLOGICAL INNOVATION AT STAKE ................................................................................................................63

ECONOMIC SIGNIFICANCE OF THE INNOVATION ........................................................................................................64

CROSS-CUTTING NON-TECHNICAL BARRIERS TO INNOVATION.................................................................................65

TECHNICAL BARRIERS TO INNOVATION ...................................................................................................................65

Seed Production...................................................................................................................................................66

Broodstock Management and Spawning............................................................................................................................ 66

Hatchery and Larval Rearing:............................................................................................................................................ 66

Nursery:............................................................................................................................................................................. 67

Growout Production ............................................................................................................................................67

Microbial Process and Communities...................................................................................................................68

System Engineering .............................................................................................................................................69

Feeds and Nutrition .............................................................................................................................................69

Health Management and Disease Prevention......................................................................................................70

Economics............................................................................................................................................................71

Quality Control, Product Branding and Public Relations...................................................................................72

Regulatory Issues.................................................................................................................................................72

Short-Term Goals ................................................................................................................................................73

APPLICATION OF MEASUREMENT SCIENCE IN OVERCOMING TECHNICAL BARRIERS ...............................................73

APPENDIX I: DETAILED LIST OF TECHNOLOGICAL AND MEASUREMENT GAPS.........................................................86

LAND-BASED FINFISH CULTURE SUB-GROUP MEMBERS .........................................................................................91
10

A ROADMAP FOR COMMERCIALIZATION OF BIOFLOC-BASED PRODUCTION 

SYSTEMS TECHNOLOGIES FOR MARINE SHRIMP LITOPENAEUS VANNAMEI............ 93 

TECHNICAL CHALLENGES AND MEASUREMENT BARRIERS ......................................................................................93

TECHNOLOGY AT ISSUE............................................................................................................................................93

TECHNOLOGICAL INNOVATION AT STAKE ................................................................................................................93

Shrimp Stocks ......................................................................................................................................................93

Feeds and Feeding...............................................................................................................................................94

Systems Engineering............................................................................................................................................94

Biofloc Microbial Communities...........................................................................................................................95

ECONOMIC SIGNIFICANCE OF THE INNOVATION .......................................................................................................95

CROSSCUTTING NON-TECHNICAL BARRIERS TO INNOVATION .................................................................................96

Integration of Research and Commercialization Efforts .....................................................................................96

Regulatory Issues.................................................................................................................................................97

Economics............................................................................................................................................................97

Marketing and Processing...................................................................................................................................97

TECHNICAL BARRIERS TO INNOVATION ...................................................................................................................98

Health Management.............................................................................................................................................98

Seed Supply..........................................................................................................................................................98

Genetics and Breeding....................................................................................................................................................... 98

Seed Production:................................................................................................................................................................ 99

Production Systems..............................................................................................................................................99

Systems engineering:......................................................................................................................................................... 99

Feed Program......................................................................................................................................................99

Husbandry .........................................................................................................................................................100

Stocking and Harvesting of Nursery Systems ....................................................................................................101

Harvesting of Growout Systems.........................................................................................................................101

Prioritized Technology Gaps.............................................................................................................................102

APPLICATION OF MEASUREMENT SCIENCE TO OVERCOMING TECHNICAL BARRIERS.............................................103

Measurement Science Gaps...............................................................................................................................105

ROADMAPPING EXERCISE.......................................................................................................................................105

SHRIMP CULTURE SUB-GROUP MEMBERS..............................................................................................................117

REGISTERED PARTICIPANTS............................................................................................... 118 

LIST OF ACRONYMS .............................................................................................................. 120 
11

Overcoming Technical Barriers to the Sustainable 

Development of Competitive Marine Aquaculture in the 

United States 

Summary of a Workshop on 

Enhancing Competitiveness of Sustainable Marine Aquaculture in the United States: 

Addressing Measurement Barriers to Technological Innovation 

Orlando, Florida 

13-14 February 2008 

Sponsored by: 

National Institute of Standards and Technology 

National Oceanic and Atmospheric Administration 

Workshop Executive Summary

Technological innovation drives economic growth and development and is a key source of 

ongoing competitive advantage in a global economy, but innovation can be impeded by 

unresolved measurement barriers. Measurement barriers include development of methods, 

standards, instruments, and capabilities to evaluate sector progress and technological 

advancement. This document summarizes the outcome of a NIST-NOAA workshop designed to 

identify the priority research needs, and where appropriate, the measurement barriers that impede 

U.S. marine aquaculture innovation. The workshop focused on the critical technology gaps that 

affect the sustainable development of a commercial marine aquaculture sector based on four 

types of production systems: 

• shellfish aquaculture, 

• cage culture of marine finfish, 

• land-based culture of marine finfish, and 

• biofloc-based culture of marine shrimp. 

At the workshop, the main subject areas with identifiable technology gaps included: 

• genetic improvement, 

• nutrition, 

• health management, 

• reproductive control, 

• production of larvae and juveniles, 

• food safety and product quality, 

• environmental performance and impact, 

• system engineering and life-support systems, and 

• economics and marketing. 
12

It was clear from the workshop discussions that technical barriers to innovation can be addressed 

by strategic investment in high priority areas, particularly those with potential benefits that 

extend across technology platforms, and those that integrate research among disciplines. Also, 

cost-effective investments in research to address priority information and technology needs, 

combined with a stable regulatory environment, a streamlined permitting process, and publicprivate partnerships in demonstration systems can accelerate private-sector investment in the 

development of a sustainable and competitive marine aquaculture sector in the U.S. economy. 

The following sections in this summary provide more detail the scope for an expanded marine 

aquaculture sector in the US, background on workshop structure and organization, as well as 

prioritized outcomes of the discussions of the workshop breakout groups. Research needs are 

summarized and prioritized. Specific measurement gaps are also described. During the 

workshop some very important non-technical barriers to sector development were identified and 

these have also been summarized in a section entitled Non-Technical Barriers. The final section 

in the workshop summary discusses roadmap implementation focusing on next steps to promote 

the advancement of US marine aquaculture.
13

The Scope for an Expanded Marine Aquaculture Sector 

In 2007, the trade deficit for seafood in the U.S. was over $9 billion, with over 80% of the 

seafood consumed in the U.S. imported and about half of those imports from aquaculture. 

Production from U.S. marine aquaculture accounts for only 1.5% of the domestic seafood 

supply. Thus, there is enormous growth potential for production of safe, high-quality seafood 

that is farmed under federal and state environmental and food safety standards. 

Marine aquaculture in the U.S. encompasses the production of a wide variety of finfish, shellfish, 

and algae, most of which are marketed as high-value seafood. Currently production is dominated 

by molluscan shellfish, although salmon and shrimp are also important, as well as smaller 

quantities of other marine species. The following table indicates the quantity and value of U.S. 

aquaculture production and imports of three of the main seafoods consumed in the U.S. (from the 

U.S. Department pf Agriculture (USDA) Census of Aquaculture, 2005 and National Marine 

Fisheries Service Annual Summary of Imports and Exports of Fishery Products, 2007). 

Marine species thousand pounds million US$ 

Oysters, clams, mussels U.S. production 268,164 170.4

 Imports 80,416 125.3

Salmon U.S. production 20,726 37.4

 Imports 521,293 1,600 

Shrimp U.S. production 8,037 18.7

 Imports 1,223,434 3,896 

Shellfish is currently the most important and robust sector of commercial marine aquaculture in 

the U.S. The potential for additional growth is high despite constraints associated with food 

safety, water quality, user conflicts, and site availability. In addition, seafood import statistics 

suggest that there is tremendous potential for the broader marine aquaculture sector based on the 

culture of marine finfish in cages and land-based recirculating systems, and on the culture of 

marine shrimp in intensive, biofloc-based systems. 

Workshop Structure and Organization 

A two-day workshop sponsored by the National Institute of Standards and Technology (NIST) 

and the National Oceanic and Atmospheric Administration (NOAA) was held in Orlando, 

Florida from 13-14 February, 2008. The workshop, which attracted over 125 participants, served 

to provide a forum and focus for a broad range of input from knowledgeable and experienced 

participants from among the community of aquaculture producers and those providing 

technology and services to producers, academics, and representatives of relevant government 

agencies and non-governmental organizations. The goals of the workshop were to identify and 

prioritize the critical technology gaps and, if appropriate, identify associated specific 
14

measurement barriers that constrain technological innovation in the development of sustainable 

marine aquaculture in the United States. 

Four types of marine aquaculture systems were examined: coastal production of shellfish, cage 

culture of marine finfish, land-based production of marine finfish, and biofloc-based production 

of marine shrimp. These systems were selected on the basis of their potential for large-scale 

sustainable development in the U.S., the potential competitiveness of their products in a global 

seafood market, and technological innovations in research and development that are currently led 

by the U.S. 

For each marine production system, a preliminary technology roadmap that charts the 

development of a competitive and sustainable marine aquaculture sector was prepared for review 

before the workshop. Marketing, economics, financial feasibility, and risk analysis provided 

focus on the technological barriers that are directly related to commercial competitiveness. Each 

roadmap addressed the following questions: 

• What is the technology at issue? 

• What are the short-, medium- and long-term opportunities for technological innovation 

that should be considered? 

• What are the technological barriers to the innovation? 

• What is the economic significance of the innovation that can improve U.S. marine 

aquaculture competitiveness? 

• How can improvements in performance be measured and to what extent are measurement 

problems part of the technological barrier? 

• What are the potential solutions to the measurement part of the technological barrier? 

Innovative technologies were identified and described with the goal of spanning and integrating 

among all aspects of aquaculture production, including: 

• species selection, broodstock development, and genetic improvement 

• hatchery, fingerling and adult husbandry 

• nutrition, feeds, growth, and product quality 

• disease diagnostics and health management 

• production system design and engineering 

• environmental standards and waste management, and 

• harvesting, processing and marketing 

In break-out sessions during the workshop the roadmaps were discussed, additional input 

collected, and participants encouraged through facilitated discussion to identify and prioritize 

impediments to commercialization. The output from the break-out session was a list of 

technology, knowledge, and implementation gaps that constrain innovation and competitiveness 

of each of the targeted sustainable production systems. Another break-out session focused on 

defining potential solutions to technology gaps and issues raised in the first break-out session. 

Participants were encouraged to identify and define the measurement needs that impede research 

and development of the technological innovations that foster competitiveness. Workshop 

participants prioritized output into short-, medium-, and long-term needs through a combination 

of individual indications of importance and consensus-building discussion to rank the most 

important areas. In the wrap-up session, break-out group leaders summarized findings in a 
15

plenary session and solicited additional input from participants. Participants were also given 

opportunities to provide additional input during several rounds of post-workshop review of 

roadmaps and this document. 

A sustainable and competitive marine aquaculture sector in the United States must overcome 

numerous technical, regulatory, and economic barriers to innovation and commercial 

development. Although the workshop focused on technology innovation and measurement 

needs, the importance of the enabling environment – including regulatory streamlining and 

stability, the availability of investment capital for aquaculture businesses, and the overall policy 

environment – were identified as no less critical to the success of marine aquaculture 

development. 

This document identifies priority areas for future research and development investments that 

target the most critical technology gaps and measurement needs, the solutions of which can lead 

to improved competitiveness and large-scale development of the marine aquaculture industry in 

the U.S. Accompanying this document are roadmaps that detail the research needs for four 

marine aquaculture production systems. 

Priority Research Needs 

Some of the research needs to overcome technical barriers are common to multiple technology 

platforms. For example, research on feeds to improve the environmental sustainability and 

culture performance of fish and shrimp aquaculture will be beneficial irrespective of specific 

technology platform. Other research needs are specific to particular culture systems. The costeffectiveness of investment in research can be maximized by investing in priority areas that are 

relevant to multiple technology platforms. 

Many of the technology areas that are described here apply broadly to aquaculture in general, but 

the specific needs of each area with respect to the four technology platforms are emphasized. 

Cross-cutting research areas include: genetic improvement, feeds and nutrition, health 

management, reproductive control, larval production, environmental monitoring and 

management, waste treatment, and system engineering. Research needs in economic 

performance and product quality and safety were also identified. The following were identified 

as high priority areas. Ordering of priorities varies somewhat with technology platform, but in 

general research needs are presented in order from higher to lower priority. A sustained, 

coordinated, and well-supported effort will be necessary to yield the benefits from discoveries 

and technology development. 

Genetic Improvement

The genetic basis for growth, feed conversion, disease resistance, processing yield, and other 

commercially important production traits is poorly understood and represents a barrier to 

improved production performance. Selective breeding programs should continue to emphasize 

traits of commercial importance, especially growth rate, feed conversion efficiency, and disease 

resistance. Long-term advancement of improved culture performance of shellfish, marine 

finfish, and shrimp requires genetic improvement programs based on the application of 
16

conventional selective breeding (selection, crossbreeding, hybridization) aided by molecular and 

other genetic tools. 

. 

Some relevant molecular tools are available, but are only moderately well developed and applied 

to genetic improvement of a limited number of commercially important species. Other tools 

have not been applied to the genetic improvement of species with commercial potential. Yet 

other much-needed tools with specific relevance to genetic improvement of existing and 

emerging species with commercial potential have not been developed. Examples of molecular 

tools include specific microsatellite and single-nucleotide polymorphism markers, DNA 

microarrays, quantitative trait loci maps, expressed sequence tag libraries, and whole genome 

sequences. 

Although genetic improvement of all cultured species can lead to substantial gains in 

productivity, it was not identified as a priority area for marine finfish at this time. Compared to 

freshwater finfish, the culture of non-salmonid marine finfish is relatively new and fish captured 

from wild populations are used as broodstock. For shellfish and marine shrimp, the specific 

goals of research programs in genetic improvement are: 

Shellfish: Establish selective breeding programs for commercially important and emerging 

shellfish species and continue to support current breeding and genetics research. Develop new 

molecular and other tools to elucidate the genetic basis for commercially important production 

traits (e.g., improved meat-to-shell ratio, resistance to disease, heat or salinity stress). 

Marine Shrimp: Continue to invest in robust selective breeding programs for penaeid shrimp. 

Develop new or use existing molecular tools to understand the genetic basis of shrimp 

production performance and disease resistance, and apply discoveries to improve the efficiency 

and genetic gains of selection programs. Develop methods for monosex female production. 

Nutrition, Feeds, and Feeding Practices

Feed typically represents the largest variable cost item in commercial aquaculture for systems 

where animals are fed. Feeds and nutrition are critical priority areas for marine finfish and 

marine shrimp technology platforms, and for shellfish hatcheries. Identification and evaluation 

of dietary protein and lipid sources suitable as alternative ingredients to fishmeal and fish oil in 

aquaculture feeds is a pressing research need, particularly in the context of rapidly rising 

commodity grain prices. Diet formulations must be improved to increase the efficiency of the 

fishmeal and fish oil resources used in feeds. There is also a critical need to develop highefficiency, low-polluting diets that are optimized for species, life-stage, and culture system. 

Research is needed to evaluate finishing diets that can be used to affect the nutrient composition, 

especially the fatty acid profile, of cultured seafood. Research on attractants and diet palatability 

is needed. Basic nutrition research on the nutrient requirements of different life-stages of most 

species of marine finfish with culture potential is required. Research and development efforts 

are needed to evaluate feed delivery systems, including information-intensive or “smart” 

systems, remotely operated feeding systems, and feeding regimes or protocols to realize the 

production potential of genetically improved finfish and shrimp. Finally, the overall 

environmental impact (i.e., ecological footprint) associated with feeding requires additional 

review, followed by periodic re-evaluation. 
17

Technology gaps related to nutrition and feeds of shellfish apply during the hatchery phase and 

are addressed in the section on larval production below. Following are the specific goals of 

research programs in the nutrition of marine finfish and shrimp. 

Marine Finfish: Improve the efficiency of feed formulations. Evaluate diets with fishmeal and 

fish oil from fish processing by-products. Develop high-performance, cost-effective diets with 

protein sources that are alternatives to fishmeal and fish oil. Identify nutrients in fishmeal not 

present in other ingredients. Understand the link between broodstock nutrition and gamete 

quality. Improve understanding of larval digestive physiology. Improve diets specifically 

manufactured for optimum performance in recirculating systems. Understand the effect of diet 

on recirculating system performance. Evaluate the broader impact of feed use in terms of 

ecological footprint (e.g., Life-Cycle Assessment). 

Marine Shrimp: Improve feed formulations that maximize the efficiency of fishmeal, minimize 

the ecological footprint of all ingredients, and promote water quality. Integrate formulations 

with contributions of natural productivity and maximize the benefits from suspended solids 

(biofloc) to shrimp growth. Improve inventory control and optimize feeding efficiencies. 

Health Management

High-density confinement and other environmental stressors, weak control over the type and 

density of pathogens, and limited options for practical disease control are factors that make 

health management and disease control a major concern in all forms of marine aquaculture. This 

area is a priority for all technology platforms. The role of common stressors or combinations of 

stressors in aquaculture production systems on the immunity and health of cultured animals is 

poorly understood. Further, understanding of the genetic basis for the relationship between 

immunity and health is lacking. Probiotics and immunostimulants represent alternatives to 

antibiotics, but realization of the full potential of these materials requires additional research to 

understand the underlying mechanisms that influence efficacy. Research is also necessary to 

establish protocols and standards for practical application of these materials. Development of 

new vaccines, particularly those targeting emerging diseases, requires an ongoing research effort. 

New tools and application of existing tools are needed to monitor pathogens and disease 

outbreaks in aquaculture production systems, including shellfish growing areas. The effects of 

hatchery methods, larval nutrition, and water quality on the health of cultured juveniles require 

additional research effort. Finally, evaluation and refinement of biosecurity protocols to prevent 

the exchange of pathogens between aquaculture facilities and the environment is needed 

The specific goals of research programs in health management for production systems used to 

culture shellfish, marine finfish, and shrimp are: 

Shellfish. Develop real-time diagnostic tests for important pathogens of shellfish. Develop field 

tests for stress indicators and other measures of shellfish condition. Develop cost-effective 

vaccines or disease treatments for shellfish. Explore water treatment measures to improve larval 

and juvenile survival and growth in hatcheries. 
18

Marine Finfish. Identify the genetic basis of fish health. Develop sensitive diagnostic tools to 

measure fish stress and health. Assess probiotic approaches to enhance fish growth and health 

and improve understanding of the underlying mechanisms related to efficacy. Improve vaccine 

development and delivery efficiency. Develop and evaluate rapid diagnostic tools for 

assessment of pathogens, particularly Vibrio species, especially during fingerling transfer to 

cages. Develop management techniques for control of sea lice and gill parasites. Develop 

techniques to manage the effects of harmful algal blooms. 

Marine Shrimp. Improve understanding of the factors affecting shrimp health and fitness. 

Develop diagnostic tools that permit rapid assessment of stress and disease. Develop standard 

biosecurity protocols, including pathogen monitoring and disease control systems. Establish 

protocols for management response to early warnings of stress or disease. 

Reproductive Control

Control over reproduction to achieve consistent, year-round spawning and the production of 

high-quality gametes and larvae are priority areas for shellfish, marine finfish, and shrimp. The 

identity and role of natural spawning cues and pheromones on fish reproduction requires further 

research. The role of the endocrine system on reproduction must be better understood to enable 

predictable volitional or induced spawning. Additional research is required to evaluate the role 

of broodstock husbandry and nutrition on the number and quality of gametes and offspring. For 

shellfish and marine finfish, mass production techniques that will reliably result in the 

reproductive isolation of cultured stocks from wild populations must be developed and 

evaluated. 

The specific goals of research programs in reproductive control for shellfish and marine finfish 

follow. Control over reproduction is not seen as a priority area that constrains the development 

of commercial marine shrimp aquaculture in the U.S. 

Shellfish. Develop improved methods for the reliable mass production of sterile animals to 

minimize or eliminate genetic interactions between wild and cultured populations of native 

shellfish. Create tools to assess maturation and potential reproductive performance in 

broodstock. 

Marine Finfish. Improve understanding of endocrine regulation of reproduction and spawning. 

Establish protocols and evaluate techniques for consistent, year-round production of juveniles. 

Optimize gamete quality and supply. Evaluate methods for assessing and controlling gamete 

quality. Understand the link between broodstock nutrition and gamete quality. Improve 

broodstock performance through species-specific selective breeding programs. Develop reliable 

and effective methods of sterilization as a means to mitigate potential effects of escape. 

Production of Larvae and Juveniles

Almost all culture systems require the production of juveniles in hatcheries, although shellfish 

aquaculture as currently practiced in some areas remains dependent to a varying degree on 

natural recruitment. In the future, aquaculture will require the consistent and controlled 

production of large quantities of healthy juveniles with high performance potential. Hatchery 

technologies must be engineered to reduce production variability and to allow for controlled 
19

production under diverse conditions. The quality and number of fingerlings required (i.e., large 

batches) are major constraints on the development of offshore cage culture of finfish. 

Broodstock, hatchery, and nursery operations must be established to meet the increasing demand 

for larvae and juveniles. Standardized stress tests are needed to gauge juvenile quality. 

Research is necessary to better understand larval digestive physiology and larval diets, including 

live foods and microdiets that replace live foods. Research is also needed to improve 

understanding of the species-specific physical requirements (e.g., water flow, light) for larval 

rearing. 

The specific goals of research programs in larval production of shellfish, marine finfish, and 

marine shrimp are: 

Shellfish. Establish the capacity for real-time monitoring of larval and juvenile condition, live 

food quality, and biosecurity in shellfish hatcheries. Assess water quality management and other 

techniques that minimize, eliminate, and control specific pathogens and contaminants in algae 

and shellfish larval production systems. 

Marine Finfish. Establish species-specific criteria for physical and biological requirements for 

hatchery production of juveniles. Establish standards for larval and juvenile quality. Improve 

tailored microdiets to replace live foods, along with supporting probiotic regimens. Increase the 

level of husbandry automation (e.g., in-tank counting and grading, tank cleaning, stage-specific 

harvesting). Establish standard techniques for counting stocked fingerlings. Identify the speciesand site-specific optimum size for transfer of fingerlings to production cages. 

Marine Shrimp. Develop replacements for live foods in larval culture. Establish standards for 

postlarval quality and fitness. Develop non-invasive methods to accurately count post-larvae and 

juveniles. 

Food Safety and Product Quality

Food safety is not only a critical priority area for marketing shellfish, but is an important issue in 

the marketing of all cultured seafood. Most shellfish are marketed as a fresh and live product so 

the real or perceived risk of consumption of shellfish that are contaminated with human 

pathogens is a serious impediment to further expansion of consumer markets. Other potential 

contaminants of concerns are marine biotoxins, Vibrio and other marine bacteria, viruses in 

growing area waters, and biotoxin and pathogen accumulation between harvest and consumption. 

Sensitive, standardized, and high-throughput methods are needed to allow expansion of testing 

for microbial contaminants, organic and inorganic pesticides and chemicals, antibiotic and other 

drug residues, and other contaminants. More rapid and cost-effective tools are needed to detect 

and quantify human pathogens in shellfish and natural waters, and harmful algal blooms and 

their toxins that are present above established food safety or toxicity thresholds. Research is 

necessary to develop diagnostic tests for human pathogens in shellfish, especially Vibrio species. 

Further, there is a need to define safety standards and action thresholds with respect to microbial 

pathogens and to develop the tools for risk analysis. In the absence of tests for specific 

pathogens, there is a need to establish indicators that can serve as proxies for food safety 

pathogens that are difficult to detect and measure directly. Collectively, these tests will provide 

the basis to assure consumers of the safety of cultured seafood and provide a competitive 
20

marketing advantage to U.S. growers who produce seafood under stringent regulatory oversight 

of food safety. In the realm of product quality, tests are needed for nutritional and flesh quality 

in shellfish, finfish, and shrimp. Tests to identify cultured seafood can aid in product 

traceability, market branding, certification programs, and differentiating cultured from wild 

populations. Methods for improving shellfish product quality (e.g., cleaning, sterilization) using 

ozone or pressure need further evaluation. Similarly, methods should be developed that avoid 

potential problems and remediate product quality of shrimp and shellfish with off-flavors that 

could be associated with recirculating systems. The relationship between feed composition and 

the nutrient composition (e.g., fatty acid profile) of aquaculture products needs evaluation and 

refinement. 

The specific goals of research programs in food safety and product quality for shellfish, marine 

finfish, and marine shrimp are: 

Shellfish. Develop and refine rapid test methods for detecting human pathogens, marine 

biotoxins, and environmental contaminants in water and shellfish. Establish uniform standards 

for infection, toxin, or contaminant thresholds. Evaluate indicators that can serve as proxies for 

pathogen measurement. Establish alternatives to fecal coliform bacteria as an indicator 

organism. Provide practical product quality measurement tools for processors and shippers of 

shellfish products. 

Marine Finfish. Develop diets and feeding practices to minimize contaminants and optimize the 

fatty acid profile of the final product. Develop alternative feeds to minimize the risk of 

concentration and accumulation of environmental contaminants in the final product. Develop 

systems to monitor flavor quality in fish cultured in land-based recirculating systems. 

Marine Shrimp. Develop products that can provide added value or some other premium quality 

over competitive products and can be distinguished in the market through branding or labeling. 

Examples include fatty-acid enrichment, organic certification and marketing live or fresh-neverfrozen shrimp. 

Environmental Performance and Impact

Monitoring and managing the beneficial and adverse environmental effects of aquaculture are 

high-priority areas. The application of cost-effective monitoring tools is needed to demonstrate 

compliance with discharge permits and performance standards. Research is necessary to further 

evaluate interactions between aquaculture and the environment. In particular, standard 

approaches are needed to assess environmental carrying capacity of local culture areas during 

preliminary site assessments. These techniques should also consider the cumulative effects of 

multiple facilities. 

With cage culture, carrying capacity refers to understanding the near-field solid waste 

assimilation capacity of sites and the far-field effects of dissolved nutrient waste release. With 

shellfish culture, carrying capacity refers to the relationship between primary production, 

hydrodynamics, and shellfish production. Research is also needed to assess and optimize the 

environmental effects of shellfish harvest methods and other farming practices. Some of the 

specific environmental impacts and risk sources that require further investigation include benthic 
21

impacts and site remediation, disease transfer between wild and cultured populations, and the 

effect of escaped fish and shellfish on wild populations. 

Land-based systems pose different types of environmental impacts that may need to be 

monitored and managed, such as footprint associated with the production of feedstuffs and feed 

manufacture, energy use, effluent reuse, and waste disposal. Environmental performance should 

be evaluated in terms of standardized sustainability metrics, which are currently lacking. 

The specific goals of research programs in environmental management for coastal shellfish 

aquaculture and cage culture of marine finfish and land based culture systems are: 

Shellfish. Characterize the effect of farming methods on the environment, indexed to reference 

sites. Develop and evaluate mechanized harvest methods to increase management efficiency, 

reduce labor costs, and minimize environmental impacts. Develop standard geo-referenced and 

relational databases that integrate environmental monitoring with shellfish production data to 

track shellfish from broodstock and larval culture through the production and supply chain. 

Cage Culture of Marine Finfish. Develop cost-effective ways to assess sites and evaluate 

environmental performance of cage aquaculture that can predict the potential for adverse impacts 

(e.g., benthic, disease transfer, escaped fish) and beneficial effects (e.g., habitat creation). 

Evaluate the suitability of easily measured indicators or indices of the environmental effects of 

aquaculture on the marine environment. Further develop and validate models of environmental 

performance and carrying capacity. 

Land-Based Culture of Marine Finfish or Marine Shrimp. Develop standardized 

sustainability metrics and explore methods to better characterize the ecological footprint of land 

based recirculation systems. Issues such as efficiencies and costs of manufacture and 

transportation associated with feeds formulated for these systems, efficiencies of energy 

utilization per unit production, effluent and waste generation per unit seafood production and 

sustainable disposal alternatives should be addressed.

System Engineering and Life-Support Systems

Some future marine aquaculture systems will be intensive, and therefore rely increasingly on 

engineering for critical life-support and waste treatment services, mechanization of management 

operations, and reduction of risk. Research is required to improve biofiltration and waste 

treatment technology for land-based marine finfish and shrimp production systems and water 

treatment processes for shellfish hatcheries. Further elucidation of design specifications for 

waste treatment and life-support systems according to species and life-stage is needed. 

Fundamental research on microbial processes and their relationships with water quality and 

target crop performance is also required. Establishment of metrics to assess changes in the 

efficiency of biophysical resource use can guide management improvements that enhance 

economic competitiveness. 

In general, engineering needs are specific to culture system, species, site, and facility. The 

specific goals of research programs in engineering are: 
22

Shellfish. Improve hatchery and nursery technology and culture techniques. Develop costeffective real-time water quality monitoring and control processes for water intake and holding 

systems in hatcheries. Improve mechanization or automation of harvesting, predator deterrence 

or exclusion, biofouling control, and other operations during grow-out. Explore alternate and 

non-destructive predator protection and exclusion methods. Develop processing, packaging, 

transport, and storage techniques to maintain product quality and food safety and minimize 

ecological footprint. 

Cage Culture of Marine Finfish. Evaluate improved materials, cage designs, and construction 

techniques to reduce the risk of fish escape from containment breaches caused by adverse 

weather, predators, and human error. Establish performance criteria and standards for 

containment technologies (e.g., structure, integrity). Develop highly mechanized, remotely 

operated systems (e.g., feeding, biofouling control). Develop generic automated monitoring and 

control systems for cage management operations – especially feeding, depth control, fish 

inventory assessment, and cage biofouling control – to maintain an optimal environment for fish 

production. Develop software systems that involve remote sensing, feedback systems, and 

neural networks for intelligent control of cage culture operations. Evaluate on-site energy 

generation from waves, ocean currents, or wind. Develop deepwater mooring and containment 

systems, including tension-leg and single-point moorings, and untethered cage systems. 

Land-Based Culture of Marine Finfish. Improve the energy efficiency, cost-effectiveness, and 

biosecurity of life-support, biofiltration, and waste treatment technology. Optimize microbial 

communities and processes to maximize waste removal and water reuse, and the efficiency of 

probiotic support. Improve system energy efficiency, particularly for maintaining water 

temperature. Establish standards and specifications for waste treatment and disposal, and lifesupport systems. Develop generic and standard production systems suitable for the culture of 

multiple marine finfish species. Increase the level of system automation, particularly for routine 

husbandry operations. Evaluate the co-production of energy (methane) from solid waste. 

Biofloc-Based Culture of Marine Shrimp. Improve the cost-effectiveness of life-support 

technology. Improve system energy efficiency, particularly for maintaining water temperature. 

Establish standards and specifications for system engineering design, with the goal of improving 

production efficiency as measured by shrimp growth and production potential. Demonstrate 

standard management techniques to establish, manage and maintain the structure, abundance, 

and activity of stable biofloc communities that maximize contributions to shrimp growth and 

water quality management. Improve methods to collect, dewater, digest, and dispose of waste 

solids. Improve methods for denitrifying, desalting, and treating water to reclaim minerals for 

reuse. 

Economics and Marketing

Better understanding of the economic performance of marine aquaculture production systems is 

needed to stimulate investment. Economic and financial analysis at the firm or facility level is 

needed, including estimation of capital requirements and production costs, return on investment, 

and internal rate of return. The models should also include sensitivity, cash flow, and a 

comprehensive risk analysis. Generic business plans and economic audits for each marine 

aquaculture system should be used to focus research priorities on areas that are significant to 
23

reducing risk and maximizing economic performance. A market analysis must be completed 

before any species is farmed or an aquaculture business developed. The marketing analysis 

should include estimation of supply and demand, analysis of supply chains, assessment of market 

depth, and evaluations of consumer attitudes and perceptions toward cultured seafood. It should 

also determine the potential for market strategies that can increase the demand for cultured 

seafood products such as grading, branding, labeling, certification, and adding value. 

Although there is a general need for economics and marketing research for all species and 

culture systems, the specific research needs identified for biofloc-based marine shrimp culture 

are: 

Biofloc-Based Culture of Marine Shrimp. Develop accurate, flexible, and user-friendly 

financial bio-economic models that include sensitivity and risk analyses. Apply studies to 

determine the potential size of the market for value-added products. 

Biofouling Control

The colonization of aquaculture netting, equipment, and structures with biofouling organisms 

can reduce the growth and survival of cultured animals and increase the risk of containment 

failure. Research is needed on technologies and management approaches to control biofouling in 

marine aquaculture, particularly for culture systems with direct exposure to the marine 

environment. Further improvement of non-toxic and fouling-resistant materials and coatings is a 

critical need. Alternatively, automated and remotely operated net cleaners are needed to control 

biofouling in cage culture. 

Inventory Estimation

Efficient feeding and other aspects of culture system management requires knowledge of the 

number and size of finfish, shellfish, or shrimp in a production unit. Direct population sampling 

is the most widespread current practice, but this is often impractical (especially in large culture 

units), can have a negative impact on growth or health, and may lead to biased estimations of 

inventory. Cost-effective and non-lethal technologies are needed to assess inventory, count 

juveniles at stocking, and estimate population size. Collection, processing, and integration of 

this information in real time allows control of feeding and water quality management operations. 

Ranked Specific Priority Areas 

The areas requiring research and development effort for each technology platform are prioritized 

on the basis of three criteria: 

• Feasibility. An evaluation of the scientific and technical potential for overcoming 

technological barriers. What is technically feasible? What can be accomplished through 

research? How difficult is it to overcome the barrier? 

• Importance/Relevance/Urgency. How pressing is the need? How critical to overall 

success is overcoming this particular gap? 

• Socio-economic Impact. Projections of expected benefits and consequences. Are results 

broadly applicable or narrowly focused? What is the relative return on investment made 

to overcome a gap? 
24

Priorities are described in terms of the most important goals for that area, with special emphasis 

on those areas with measurement needs. The priority areas are described with short phrases; 

more detailed descriptions of each area are provided above and in the roadmaps for each 

production system. Areas are listed in order from higher to lower priority. In most cases, the 

areas indicated are viewed as critical, high-priority needs that must be addressed in the short to 

medium term. 

Coastal Shellfish Production Coastal Shellfish Production

• food safety and product quality 

• reproductive control 

• genetic improvement 

• database management and tracking (traceability) 

• shellfish health and condition 

• farming methods 

• larval and live food production 

Cage Production of Marine Finfish

Issues related to species selection, genetic improvement, and hatchery production of larvae and 

juveniles were addressed by the land-based marine finfish group and are not discussed here. 

However, they were identified as high priority technology gaps that must be addressed for the 

development of a sustainable and competitive marine aquaculture sector based on the cage 

culture of marine finfish. The priority needs for cage culture of marine finfish are: 

• assessment of environmental performance 

• nutrition and feeds 

• cage integrity 

• fingerling transport and transfer 

• disease diagnosis 

• integrated, self-regulating, and autonomous operational control 

Land-Based Production of Marine Finfish

Given the diversity of marine finfish species considered as suitable candidates for aquaculture, 

criteria for selecting among candidate marine finfish species with commercial culture potential 

are needed. A decision matrix that applies these criteria can be used to evaluate and prioritize 

candidate species. The priority research needs for land-based marine finfish culture are: 

• life-support systems 

• induced spawning 

• larval rearing 

• nutrition and feeds 

• fish health and stress 
25

Biofloc-Based Production of Marine Shrimp Production of Marine Shrimp

• production system engineering and design 

• suspended solids (biofloc) management 

• waste management and treatment 

• genetic improvement 

• feeds and feeding 

• health and biosecurity 

• value-added products 

• bio-economic models 

Measurement Needs 

The measurement needs for marine aquaculture can be divided into two overlapping categories. 

In one category are measurement needs to advance aquaculture science. These measurement 

needs require the development or application of sophisticated and advanced scientific and 

engineering tools and techniques. Advances in genetic improvement, health diagnostics, stress 

and digestive physiology will require development and application of these new tools. In 

another category are the measurement needs for the operation and management of commercial 

facilities, particularly as part of monitoring and control systems. Measurement tools for 

commercial facilities must be robust and cost-effective. 

Sensors

Sensors have been widely used in aquaculture, particularly in monitoring water quality. Ideal 

sensors in aquaculture would be low-cost, robust, resistant to biofouling, self-calibrating, permit 

remote operation, and provide measurements in real time. Sensors for aquaculture can be 

mechanical, chemical, thermal, biological, optical, and acoustic and used for detection, 

monitoring, and control. Sensors can be used to measure the basic physical, biological, and 

chemical components of system function. The value of sensors increases with connection to 

control equipment that manages life-support systems or automates husbandry operations. 

Sensors are available to measure temperature, salinity, dissolved oxygen, and water currents, 

although wider use of some sensors is constrained by high cost and uncertain reliability. Sensors 

to measure or estimate phytoplankton and microbial biomass and activity need improvement. 

Sensors (e.g., video, sonar) and image analysis can be used for biomass estimation, inventory 

control, equipment inspection, environmental observation, and farm security. These sensors can 

be used as components of feeding systems in cage culture. In some cases, sensors exist, but cost 

reduction is needed for routine application. 

Analytical Techniques

Most research laboratories have well-developed analytical capability, but most commercial 

facilities have only the most basic analytical equipment. Technology-intensive marine 

aquaculture is also knowledge- and information-intensive, increasing the need for enhanced 

analytical capability using new tools and techniques. Some of the research addressing technical 

barriers will need new tools or application of tools that are used elsewhere. The value of many 
26

techniques can be improved by increasing accuracy and precision, reducing cost, improving 

simplicity, and increasing the timeliness of results. 

Standard analytical techniques are needed to measure: 

• biochemical and physiological indices of shellfish, finfish, and shrimp, including those of 

the endocrine and immune systems, and changes in response to stress 

• gamete quality, especially egg biochemical composition 

• microbial activity 

• nutrient bioavailability from feeds 

• fatty acid profiles of diets and cultured seafood products 

• organoleptic quality of cultured seafood 

Diagnostic Tests

Most diagnostic tests in aquaculture have been applied in research settings, not as simple field 

kits employed at commercial facilities. Diagnostic tests should be accurate, sufficiently 

sensitive, cost-effective, non-destructive, rapid, and preferably provide timely results to guide 

management decisions. Real-time polymerase chain reaction (PCR) is an example of such a test, 

although it is cost-prohibitive in a commercial setting and requires a skilled technician. 

Diagnostic tests are needed to: 

• confirm the presence of important human pathogens and biotoxins (e.g., paralytic 

shellfish poisoning toxin) in shellfish or water at culture sites 

• evaluate sources of microbial contaminants that impact shellfish growing areas 

• evaluate and quantify contaminants in cultured seafood 

• identify and quantify the most important pathogens of shellfish, finfish, and shrimp, 

particularly to demonstrate disease-free status (e.g., specific pathogen free (SPF) for 

certification of juveniles for transfer and stocking 

• evaluate general health status (i.e., immunocompetence) of cultured animals 

• evaluate flesh quality (freshness, organoleptic quality, fatty acid profile) 

• identify or mark fish, shellfish, or shrimp to be able to trace product through the supply 

chain or to evaluate the effect of escaped culture animals on wild populations 

Metrics or Standards

Establishing standards has been critical to the success of many industrial sectors of the economy. 

In aquaculture, few technology standards exist and many system designs are idiosyncratic. 

Metrics and standards are needed for many aspects of marine aquaculture production and 

marketing. 

Standards are needed for: 

• infection thresholds (i.e., action levels) of fish or human pathogens 

• contaminants, such as pesticides, metals, organic compounds, drug and anti-biotic 

residues 

• organoleptic quality (flavor, texture, “freshness,” shelf-life) 

Standard methods and metrics are needed to: 
27

• quantify culture system performance, particularly efficiency measures and environmental 

performance 

• assess broodstock readiness to spawn (e.g., with gene chips that measure the activity of 

genes for hormones that control egg maturation) and performance 

• quantify fingerling and shrimp post-larval quality (e.g., stress tests) and performance 

• prevent diseases, especially in hatcheries and recirculating systems (i.e., biosecurity) 

• evaluate feed ingredient digestibility 

Models

The value of information from primary research can be improved by integration into models. 

Models can be constructed in a variety of domains: 1) physical, such as hydrodynamic models 

of ocean currents or shallow intensive tanks; 2) ecological, such as models to estimate waste 

assimilation capacity, nutrient dynamics in recirculating systems, and shellfish and primary 

production; and 3) economic, such as models for culture system performance, business, and 

market demand. Some models may be constructed and apply across multiple domains. The most 

useful models will be 1) developed into operational tools to forecast conditions in each domain, 

2) integrated into monitoring, control, and decision-support system software, or 3) applied as a 

tool in environmental regulation. 

Non-Technical Barriers 

Although the focus of the workshop and this document is on the technical barriers to innovation 

in marine aquaculture, other factors play roles of varying importance to technology development 

and the establishment of commercial marine aquaculture. 

Regulations and Policy

The process of obtaining approvals and permits for coastal aquaculture projects is a major 

impediment to the development of marine aquaculture in the United States. Permits from a 

spectrum of federal, state, and local agencies are required for marine aquaculture, and the 

permitting process is often difficult, time-consuming, and costly. Permitting remains an 

uncertain, uncoordinated, unstable, and inconsistent process, indicating that clear guidelines are 

needed. Permits regulate the selection of sites, the species that may be cultured, and on-site 

operations. Constraints on siting limit the expansion of shellfish aquaculture, particularly for 

small-scale producers, and offshore cage culture projects. The proposed National Offshore 

Aquaculture Act seeks to streamline the permitting process for federal waters, but congressional 

approval remains pending. There is a need for comprehensive nearshore planning (through the 

Coastal Zone Management Act or other mechanisms) that includes zoning for aquaculture, 

including marine technology parks. There is also a need to transition from individual to general 

permits under the National Pollutant Discharge Elimination System and the U.S. Army Corps of 

Engineers Nationwide Permit 48 for shellfish aquaculture. Efforts to educate regulators and 

assist permit applicants with regulatory clearance are needed. 
28

User Conflicts

Some members of the public hold negative perceptions of the practices and products of 

aquaculture. Coastal areas are used for a variety of commercial and recreational activities that 

inevitably conflict with aquaculture projects. Increasing coastal population and the 

accompanying transition to an increasing proportion of users who are not dependent on the 

marine environment for their livelihood have given rise to objections to siting aquaculture 

facilities in productive nearshore areas. Objections are raised to the privatization of what is 

understood to be open-access resources. To foster good relations, the public should be provided 

with science-based information that describes the benefits of U.S. marine aquaculture, industry 

practices, and aquaculture-environment interactions. A better understanding of market and 

nonmarket benefits and costs associated with marine aquaculture is needed to address necessary 

tradeoffs among stakeholder groups. 

Financial

Some types of modern commercial aquaculture are capital intensive and so the availability of 

investment capital and interest rates on borrowed capital constrains economic development. A 

thorough risk analysis can guide investment and financing decisions. Business and marketing 

plans with a comprehensive economic and financial analysis, including consideration of market 

dynamics and uncertainties, are needed. Financial information provided by commercial 

producers is necessary to assess economic performance, develop business plans, and conduct 

market analysis. New and existing producers need training in business management skills. 

Strong public sector investment in research to develop state-of-the-art knowledge and evaluate 

best practices can serve as an incentive for potential investors. A favorable and incentive-driven 

investment climate for marine aquaculture remains a daunting task and is becoming more 

challenging in the current economic environment. 

Research

A major constraint to enhancement of the technical competitiveness of marine aquaculture in the 

U.S. is the lack of long-term vision and poor coordination of private, state, and federal research 

activities and infrastructure. This barrier can be addressed through strategic planning and 

coordination among relevant agencies, especially NOAA and USDA. Strategic planning can be 

used to leverage funds in targeted areas and improve the likelihood of realizing success with 

competitive funding opportunities. With few exceptions, there is no dedicated funding stream 

for long-term marine aquaculture research projects. Rather, research is largely supported by a 

fragmented array of short-term grant programs. Although increased long-term funding levels 

can improve the competitiveness of marine aquaculture, more efficient use of existing funding 

and limited portfolios to solve practical problems that are relevant to the needs of commercial 

aquaculture development are also needed. Funding for aquaculture research and development, 

including demonstration projects, requires consistency, continuity, integration, and evaluation of 

cost-effectiveness to ensure success and attract long-term commitment by the private sector. 

Appropriately funded government-industry-academic partnerships in targeted integrated 

multidisciplinary efforts should be encouraged. Short-term, extramural funding sources (e.g., 

earmarks and competitive grant programs, such as the NIST Technology Innovation Program) 

can complement coordinated longer-term, intramural funding sources from government agencies 

such as NOAA and the USDA Agricultural Research Service. Available Small Business 

Innovation Research (SBIR) programs should also be promoted to the commercial aquaculture 
29

sector to encourage proprietary research or activities more suitable for private patents. Research 

should be applied with a view towards understanding effects across the supply chain; for 

example, how research results implemented on-farm will affect product quality and market 

value. 

Skilled Workers

Modern, technically sophisticated marine aquaculture requires skilled workers to manage and 

operate marine aquaculture facilities and trained scientists to staff university and government 

research laboratories. Marine aquaculture will compete with agriculture and other sectors of the 

economy for the services of individuals with desirable skills and experience. Many prominent 

university-based aquaculture programs have contracted, although some programs, most notably 

those of 1890 Land Grant universities, are expanding. Non-degree technical programs 

emphasizing the practical skills desired for employment at aquaculture production facilities are 

lacking. Thus, a deficit of skilled and experienced workers can constrain marine aquaculture 

development. Support is needed for infrastructure and training programs at marine aquaculture 

research or production facilities operated by universities, government agencies, or aquaculture 

businesses. The availability of expertise within the United States to address priority marine 

aquaculture research needs and measurement barriers remains an open question. Marine 

aquaculture investigators in the U.S. have relationships with international colleagues that range 

from informal professional contacts to formal networks. 

Technology Transfer

A formal and vigorous technology transfer program will be necessary to extend technology 

innovations to new and existing producers. Sea Grant and Land Grant college extension 

programs will be the critical agents of technology transfer and producer training. Although the 

National Sea Grant Program has an extension function, it is not as nearly well-developed as the 

agricultural extension effort supported by Land Grant universities, particularly for aquaculture. 

The effectiveness of any transfer program will depend, in part, on demonstration of technologies 

at an appropriate commercial scale to encourage adoption. Commercial-scale yield verification 

programs that evaluate and demonstrate improved practices and technologies with cooperating 

producers can accelerate technology transfer. 

Roadmap Implementation 

A technological advanced marine aquaculture sector will be knowledge-intensive and thus 

require new information and technologies to supplement and extend the current understanding of 

aquaculture production systems. In some cases, technology gaps will be overcome with new 

knowledge or tools and in other cases they will be addressed by demonstrating success in 

application and integration of existing knowledge or tools. 

Overcoming technical barriers and increasing production efficiency requires solving problems 

holistically, recognizing the interrelationships among areas of investigation and across 

disciplines. Thus, these problems are best addressed systematically by teams of researchers, 

each with complementary expertise to address components of the technical barriers. This 

approach can increase the value of research investments. An economic audit of a production 

system can identify areas of greatest risk or greatest economic return and impact. Economic 
30

analysis is a critical component to guide research priorities and evaluate the cost-effectiveness of 

investments in research and development. 

In general, the capability to address technical barriers is present in the United States among the 

university- and government-based research and extension communities, assisted by commercial 

producers. However, critical needs may not be met because aquaculture competes with other 

sectors of the economy for individuals with desirable skill sets. Partnerships with international 

colleagues on issues of mutual interest can enhance the competitiveness of marine aquaculture in 

the U.S. 

Finally, overcoming technical barriers requires periodic assessment of progress. Clear 

definitions of success can be achieved by developing criteria and quantitative measures to 

evaluate outcomes, impacts, and progress in overcoming barriers. 

Demonstrating Feasibility

The focus of this workshop was on identifying specific technical barriers that constrain the 

development of a sustainable and competitive commercial marine aquaculture sector. 

Overcoming these barriers will require strategic and careful investment in research and 

development by public and private sectors, perhaps in partnership. The development of a 

competitive marine aquaculture sector in the United States can be stimulated by establishing 

commercial-scale pilot systems to demonstrate and refine the economic and environmental 

performance of each of the main technology platforms. In the case of shellfish aquaculture, one 

pilot system should be established at each of the three main coastal areas where shellfish are 

cultured in the United States (Pacific Northwest, Mid-Atlantic, Gulf of Mexico). At least three 

demonstration systems should be established to evaluate the cage culture of marine finfish, and 

at least one each for land-based marine finfish and biofloc-based shrimp systems. Project goals, 

evaluation criteria, and standards of success must be clearly defined. 

Obviously, establishing and operating a commercial-scale demonstration facility is costly, so 

creative funding mechanisms that equitably share risks must be explored. One option is a 

private-public partnership that is part of university-supported technology parks or business 

incubators, particularly for diagnostic services or high-value, specialty applications. Another 

variation would be to establish a private-public partnership where private-sector investors, 

perhaps supported by a venture capital fund, would provide funding for capital equipment 

(facilities and equipment). The investors would also support a general and technical 

management team. Public agencies would support the efforts of investigators who would 

provide conceptual engineering designs, generic business plans, and evaluate technology and 

management approaches in a commercial setting. In either case, clear agreements about 

intellectual property, patents, and licensing agreements must be in place. 
31

A Roadmap for Commercialization of Advanced 

Technologies for the Farming of Marine Shellfish 

Technical Challenges and Measurement Barriers 

Technology at Issue 

Advanced technologies for farming of marine shellfish.

Technological Innovation at Stake 

Marine shellfish aquaculture accounts for a large fraction of the total world production of 

aquacultured seafood, with an annual production in 2005 trailing only cyprinids (freshwater 

carps and similar species). It is also extremely diverse with a wide range of species cultured, 

culture methods, and technological development. In the United States, molluscan shellfish 

accounted for approximately 1/3rd of the total domestic aquaculture production of 526,280 metric 

tons in 2007 (FAO Global Aquaculture Production Statistics). It is a traditional and expanding 

industry on the West Coast, and an expanding industry in the eastern and southern U.S. 

Historically oysters accounted for the bulk of the production, but in recent years other shellfish 

have become increasingly important. These include mussels; hard, softshell, Manila, and 

geoduck clams; scallops; and abalone. While U.S. aquaculture production of these species is 

increasing, it does not meet the domestic demand for shellfish. Nor does it provide sufficient 

opportunities for export of shellfish products. 

The U.S. shellfish aquaculture sector, government agencies and tribal entities are faced with 

numerous near-term to long-term opportunities and challenges. Advances in shellfish hatchery, 

nursery and grow-out systems require new technologies to enhance production of currently 

cultured species, the culture of new species, and restoration of wild stocks. These technologies 

can be made possible by combined private and public sector research, education, and training 

efforts. Coupled with technological advancements are international and national policies and 

programs calling for the support and development of robust, economically effective and 

environmentally sound aquaculture practices. In order to meet increasing world demand for 

shellfish and other seafood products and to reduce rising seafood deficits, assistance is needed 

for technology development to enhance shellfish aquaculture production in shore-based, 

offshore, and land-based environments. 

This shellfish technology roadmap integrates previous efforts to establish research goals for 

shellfish aquaculture with the combined input of shellfish growers, researchers, and public 

agency specialists from the workshop. Beginning in 1999 with updates through 2008, a West 
32

Coast research cooperative, the Pacific Shellfish Institute (PSI), prepared a broad list of goals 

through 2015 and prioritized the research needed to achieve them. These goals and priorities 

were subsequently adapted by the East Coast Shellfish Research Institute to develop a 

coordinated research, education and training effort on the East Coast. Similar recommendations 

were made during an oyster research and restoration workshop sponsored by Maryland Sea 

Grant in 2003. These documents were circulated to research institutions, granting entities, and 

resource management agencies for comment. 

Expert input to this shellfish roadmap was facilitated by a working group with diverse interests, 

professional experiences, geographic representation, and institutional membership. Working 

group members were provided with an outline of key problem areas and were asked to comment 

on and enhance the outline, and to respond to ongoing updates in the shellfish roadmap. 

Economic Significance of Innovation

Technological innovation for shellfish aquaculture can take many forms. It has the potential to 

markedly increase U.S. shellfish production, expand export opportunities, and improve 

understanding of the complex interrelationship between the natural and human environment in 

these production systems. The recent development of geoduck clam (Panopea abrupta) 

aquaculture in the western U.S. offers an excellent case example of the economic effects of new 

technology. Geoduck are large (0.75 to 1 kg at harvest) and relatively fast-growing (4-5 year 

growout) clams with a high biomass density at harvest (90+ mt/ha [80,000+ lb/acre]) and strong 

market demand from Asia. The development of geoduck aquaculture is closely linked to 

hatchery, nursery, grow-out, harvest and transportation technologies which must be adapted 

specifically to create an optimized product for the producer and consumer. The geoduck 

aquaculture sector is expected to increase with improvements in those technologies. U.S. 

production is projected to be over 2,000 mt by 2010 with a farm-gate value of about $20 million 

(Jonathan King, Northern Economics, Anchorage, personal communication). New technology 

applications are beginning to drive economic development in other parts of the shellfish 

aquaculture sector. Examples include: 

• development of intensive hatchery and nursery systems 

• application of genetic tools to improve shellfish yields, survival and appearance/taste 

• experiments with methods to modify the production cycle and access non-traditional 

growing areas (such as offshore systems) 

• intensive production systems 

• precision harvesting methods to reduce harvest area disturbance and increase yields 

• processing methods to control product quality, food safety, and facilitate transport. 

Crosscutting Non-Technical Barriers to Innovation 

Research Integration and Management

A major constraint to enhancing the technical competitiveness of marine aquaculture in the U.S., 

including shellfish aquaculture on the West Coast, is the lack of long-term vision and a 

coordinated private, state and federal research infrastructure. The present fragmented approach 
33

is impeding the development of important shellfish research programs and uniform 

environmental management systems. For example, shellfish breeding programs must integrate 

genetic technologies with husbandry, nutrition, disease management, and production systems in a 

long-term strategy to improve the efficiency and yield of shellfish farming. While the West 

Coast has had the benefit of two long-term research projects on genetic improvement of Pacific 

oysters, both of which have produced new knowledge, limited progress has been made towards 

applying that knowledge to commercial breeding. The industry continues to grow wild animals, 

with only rudimentary knowledge of yields, production efficiencies, and environmental effects. 

This is not necessarily a result of specific technological gaps but is more likely caused by a lack 

of integration of existing research findings with commercial production methods. 

Regulatory, Siting, and Public Policy Issues

Progress in key regulatory and policy areas is critical to open opportunities for application of 

new technologies in aquaculture. For example, provisions of the Coastal Zone Management Act 

encourage states to do comprehensive nearshore aquaculture planning. NOAA is promoting 

aquaculture development in the Exclusive Economic Zone and indicating the need for further 

growth in nearshore waters. However, without a comprehensive state-level planning process, 

user conflicts and water quality issues will impede expansion of shellfish aquaculture. 

Economics, Training, Markets, and Pricing

These largely social issues are essential components in marine aquaculture development. 

Specific cross-cutting examples include a marketing strategy to increase demand and price for 

species currently under cultivation and identify market opportunities for new species; educating 

the general public, consumers, waterfront owners, resource managers, boaters, and others 

regarding the benefits of shellfish, shellfish culture, and the industry’s need for a clean healthy 

environment; and increased support for formal undergraduate and graduate training in marine 

aquaculture centers and laboratories at community colleges, universities, tribal and other 

research facilities. Other common areas of interest are country-of-origin labeling, product 

branding, organic labeling, advertising tools, specialty and value-added products and markets, 

business training for new entrants and existing farmers, investment capital at reasonable rates, 

and improved economic metrics for production volumes and values. 

Technology Transfer

There are many examples of currently available technologies in the scientific literature and in 

various locations around the world, which are not being employed by the U.S. marine shellfish 

aquaculture sector. There is a strong need to develop more effective methods of transferring the 

most efficient methodologies available in a manner to encourage adoption by the industry. This 

requires extension and outreach efforts including demonstration at an appropriate scale to 

convince producers or processors to adapt efficient technology. This effort requires new and 

traditional extension and outreach methods.

Technical and Measurement Barriers to the Innovation 

Despite the high potential for growth of shellfish aquaculture in the U.S., significant technical 

gaps and impediments remain. These are organized according to stages of the production cycle 
34

and by tasks or operations within each stage. Listed first are those which are cross-cutting with 

other marine aquaculture sectors. These are followed with examples of technologies and 

processes specific to the shellfish aquaculture sector. A summary of these key technologies is 

provided in Table 1. 

Cross-Cutting Measurement Challenges

Many of the technological aspects of aquaculture development have broad cross-cutting 

measurement requirements. Specific examples include: 

• multiculture / multitrophic systems – production and yield measurements 

• broodstock integrity and grow-out performance – identification and markers 

• health management, disease control / prevention, and biosecurity – disease and 

contaminant monitors and detectors 

• feed supplies – monitoring and production of balanced non-algal diets that are 

economically feasible 

• ecological carrying capacity and sustainability (environmental footprint) – productivity 

measurements 

• temperature, salinity, light, pH, chlorophyll a, ammonia, nitrite, nitrate and phosphorus 

concentrations, and other environmental parameters – water quality measurement devices 

that are designed for continuous operation, provide reliable and stable operation over 

time, are cost-effective, and robust 

• water management for hatchery and nursery systems – flow control, water quality 

maintenance 

• energy, product, and materials management – monitoring heat reclamation and energy 

use 

Genetics, Breeding, Larvae and Seed Supply

While most shellfish produced in the U.S. originate from wild sources of seed, hatcheries and 

controlled nursery systems are increasingly playing a greater role in commercial and restoration 

aquaculture. These facilities give producers greater control over sources of broodstock, allow 

selection for favorable characteristics, and help stabilize seed supplies. Nevertheless, shellfish 

hatcheries are at an early stage of development, with many elements needing technological 

improvement. 

Important methods currently at a very early stage of development are: 1) the use of DNA 

microarrays to study the effects of certain treatments, diseases, and developmental stages on 

gene expression in cultured shellfish, and to assist breeding programs in assessing genome 

content in selected animals; 2) sterilization methods, including triploidy, coupled with breeding 

procedures which effectively predict the in-field production characteristics of sterilized animals 

vs. non-sterilized individuals; and 3) suitable trace-back tools to provide improved growth and 

survival performance guidance for breeding programs, and to enhance the abilities of hatcheries 

to produce the highest quality larvae and seed. 

Genetics and Breeding 

Integration and Coordination: Improved tracking procedures or methods are needed 

throughout the production cycle. This system should be able to track shellfish production from 
35

spawning to consumption and would ideally include information on parental genetics, 

performance traits in the hatchery and the field, environmental conditions, and grow-out 

technique used. This kind of farm-level data is critical in a number of ways. It would provide, 

for example, de facto field trials of various stocks, strains, and families in a variety of production 

environments and tracking data to quickly identify and isolate both shellfish and human disease 

issues. It would also provide long-term data to evaluate the impacts of selective breeding and 

improvements in husbandry technology. 

In addition to production tracking systems, a publicly-financed research hatchery could produce 

large arrays of genetic families and impose various experimental conditions (e.g., temperature, 

food level) using highly automated systems. This would allow a major scale-up of breeding 

efforts, moving beyond the current limitation of about 50 families. Something on the order of a 

few hundred small, flow-through larval tanks would be appropriate. Such a facility would also 

require expanded nursery and grow-out systems. 

Controls on Reproduction: There are two major constraints to controlling reproduction in 

shellfish. First, a better understanding and application of triploidy in species other than oysters is 

needed, especially when native species are cultured in proximity to wild populations. This is 

critical because, unless there is a way to prevent cultured shellfish from interbreeding with wild 

stocks, a complex system of growing only non-improved locally-derived stocks may be 

necessary to prevent translocation. This would create a complete roadblock to genetic 

improvement through selective breeding if domestication selection produces genotypes that are 

inferior under natural conditions. The application of triploidy for isolating aquaculture stocks 

from wild congeners can amplify efforts to increase stock improvements in cultured species by 

eliminating or reducing genetic risk issues. The best way to assure that this does not occur is to 

prevent interbreeding altogether by using sterile animals for culture. Measures of success for 

different methods of producing sterile animals are needed, including the stability of sterility. 

Triploidy may not be the only approach, but has proven effective with oysters. Other methods to 

prevent reproduction in cultured shellfish that require further investigation include genetic 

manipulation to knock out key genes involved in sexual maturation, development of all-female 

lines in species with genetic sex determination, and selective breeding for delayed maturation 

and fast growth so animals can be harvested before reproducing. 

The second issue is how to conduct selective breeding for triploids or other non-reproductive end 

products. Because triploids are sterile, it is impossible to use the best-performing animals as 

broodstock. Also, it is unknown whether it is best to carry out selection on diploids and/or 

tetraploids in order to improve triploid performance. Therefore, large collections of genetic 

material in diploid and tetraploid forms must be available to find the best combinations. Other 

approaches to reproductive control may have other unknown implications with respect to 

selective breeding for genetic improvement. 

Germplasm Collection and Preservation: Critical to maintenance of selectively bred shellfish is 

the need to facilitate the transfer of genetic materials in ways that do not involve moving whole 

animals, is not subject to intensive disease testing and quarantine requirements, and does not 

require the maintenance of a large-scale broodstock repository. This could be facilitated by 
36

understanding how to freeze, store, and distribute cryopreserved sperm, eggs, and embryos that 

have been certified as disease free and thus are not restricted in terms of transport. For model 

organisms such as Drosophila and Arabidopsis, there are large collections of lines and crosses 

that researchers can obtain at nominal costs. Such collections are used for basic scientific 

research or as sources of novel genes for selective breeding. With shellfish, lines of oysters have 

been produced in France that are resistant and susceptible to summer mortality (a disease 

affecting oysters). At this point, the only way these animals can be imported into the U.S. is to 

go through a multi-year process of growing a generation in quarantine and conducting an 

expensive suite of disease tests. Frozen embryos certified as disease-free could be made 

available to U.S. producers within a much shorter time. 

Heritability Estimates: Heritability is often misunderstood because it is a characteristic of a 

specific population and not the whole species. Furthermore, genetic correlations among multiple 

traits may be more important than single-trait heritability because these can complicate multitrait selection or produce unexpected results if selection is based on single traits. An efficient 

way to estimate heritability and genetic correlations with reasonable precision is needed. 

Reasonable estimates of genetic correlations require a half-sib mating scheme involving at least 

50 half-sib families (i.e., 150 full-sib families). Current hatchery limitations make this extremely 

difficult. The other option is to mix families and sort them out using molecular markers, but this 

can be expensive. One way to minimize these expenses would be to develop some kind of 

standard set of multiplexed marker loci that allows inexpensive and rapid genotyping of enough 

markers to allow parentage determination at low cost. 

Inbreeding: Inbreeding is typically avoided, but depending on the approaches to genetic 

improvement, it can be desirable. Specifically, if cross-breeding to obtain heterosis (“hybrid 

vigor”) is indicated as the best alternative, then a large array of highly inbred lines is needed to 

construct and test hybrid combinations. This will require the creation of a very large set of 

inbred lines. 

Molecular Markers, Mapping and Genomic Enablement: A better DNA microarray is needed 

for Pacific oysters and other shellfish species. A microarray has been produced for Eastern 

oysters; however, it is not very useful for other species. The Eastern oyster array contains a 

limited number of Pacific oyster genes, and many of those are not fully described or annotated. 

A reasonably priced, high-quality, high-coverage microarray would go a very long way toward 

improving understanding of how oysters and other shellfish interact with pathogens, physical 

stress, and pollution. 

Genetics and Breeding Technology Gaps: Information on the performance of improved 

molluscan stocks is difficult to obtain and expensive to produce. Improved systems for 

evaluating the performance of lines or stocks of bivalves under field conditions are greatly 

needed. This will require better husbandry systems that control for density-dependent 

interactions between individuals and enable evenly distributed availability of suspended foods to 

test animals – both factors that contribute significantly to variability in performance. Reducing 

the time needed to obtain a production “signal” is greatly needed as a means to reduce costs and 

time between subsequent generations. Both selection and crossbreeding approaches to stock 

improvement would benefit from research on systems that enable faster and more accurate 
37

measurement of individuals or stocks at the larval or seed stage that serve as predictors of adult 

performance. The development of microarrays may be very useful in this regard. Markerassisted selection programs remain elusive but equally valuable as a means to evaluate stocks 

routinely and help predict production characteristics based on analysis of broodstock. Further 

development of the genetic tools needed to elucidate the genetic basis of economically important 

traits and enable genetic-level selection in a variety of cultured shellfish species is needed. 

The development of industry-supported programs that enable the shellfish sector to learn about 

and incorporate genetic improvement are in great need of support. Genetic improvement 

programs need coordinated baseline data for evaluation of strains, integration of environmental 

and production data, and tracking of geo-located data at all levels. Genetic improvement has 

largely focused on Eastern and Pacific oysters and needs to be extended to other mollusk species. 

Genetics and Breeding Measurement Issues: A key issue to monitor is how improved stocks are 

utilized by industry. Without industry participation, stock improvement programs should be a 

secondary objective for funding agencies. It is critical to demonstrate to industry that stock 

improvement can increase profitability, and outreach should be scaled up to enable growers to 

utilize improvements. Modeling of the Australian oyster industry would be a useful approach for 

U.S. growers. There is a need to better apply the Land Grant university agricultural experiment 

station model to shellfish aquaculture. 

Other measurement needs include 1) cost-effective genome sequencing tools for key commercial 

shellfish species; 2) adaptation and application of current geographic information system (GIS) 

technology for product tracking coupled with technical support at the industry level and 

centralized data collection; and 3) measures of the social acceptability of applied technologies. 

Broodstock Maturation Systems 

Broodstock can be held in controlled environments in hatcheries to stimulate the growth and 

development of reproductive products. The goal of broodstock maturation systems is to 

accelerate the spawning cycle and/or facilitate spawning independent of the normal seasonal 

periods. 

Systems Engineering: Broodstock systems are typically placed inside larval culture systems 

with modest control of water quality and management of water flows. Measurement 

requirements are the same as described below for larval culture systems. Automation of the 

control and operation of these systems will greatly reduce the required labor. 

Feeds and Feeding: The feed requirements for broodstock are different from larvae and 

juveniles (markedly so for abalone). Typically feeds are live microalgae, but prepared diets are 

also used. Availability of balanced, prepared diets for shellfish is a major impediment to 

development of large-scale holding systems. 

Reproductive Performance: Reproductive performance is linked to fecundity, fertilization rates, 

and hatching rates. Significant measurement issues include identifiers of gamete maturation, sex 

type, and spawning indicators. 
38

Health and Prevention of Disease Transfer: Disease in broodstock can be associated with the 

use of diseased wild shellfish or through the introduction of disease organisms in the culture 

system. Diseases may be transferred through the culture system and/or reduce reproductive 

performance of broodstock. Non-technical options include improved screening standards for 

Reportable Diseases and tools to measure broodstock health. 

Broodstock Maturation Technology Gaps and Measurement Issues: The development of 

hatchery-based systems to supply molluscan larvae and seed that are characterized by a “high 

health” certification, genetic improvement of larvae and seed (for a variety of production traits), 

and widespread availability remains an elusive set of goals for shellfish aquaculture worldwide. 

Few broodstocks used in the industry have an associated genetic-performance history. 

Information on all stocks used for seed production should be fully pedigreed with associated 

performance information for phases of grow-out that is comparable to the disease history 

information that is much more widely available today. Further, little is typically known about 

reproductive parameters associated with broodlines. Age at first reproduction, level of 

reproductive effort and output, gametogenic response to environmental cues and predicted sex 

ratio in both broodstocks and progeny are all likely under some genetic control but are not 

known for most broodstocks utilized. Most information for suspension feeding bivalves is 

available for commercially farmed oysters only. 

Nutrition of broodstock animals is not well understood with specific reference to the interplay 

between nutrition and maturation, environmental cues (e.g., temperature, light, salinity) and the 

onset of maturation processes (e.g., glycogen storage and/or gametogenesis). Information on 

endogenous factors (e.g., hormonal controls) influencing the onset of gametogenesis in bivalves 

of commercial importance is needed, as is better information on nutritional needs (e.g., sterols 

and other constituents of microalgae that are not well understood with respect to maturation 

processes in suspension-feeding bivalves). 

Other technology gaps and measurement issues include: 1) hatchery and nursery culture methods 

for broodstock maintenance, and larval and juvenile rearing; 2) rapid methods to assess and 

monitor algal nutritional quality and improve feed delivery; 3) real-time monitoring of bacterial 

flora in culture systems; 4) low-cost sterilization or treatment of culture water that does not affect 

water quality; 5) tools to determine or measure food composition and performance of algae and 

manufactured diets (also directed at biosecurity issues); 6) development of measurement 

parameters to determine environmental conditions that allow selection of specific organisms in 

algae production; 7) technology to selectively eliminate specific organisms in a mix of algae 

(such as acoustic tools, probiotics); and 8) non-invasive and cost-effective methods for rapid 

determination of reproductive condition. 

Larval Culture Systems 

Systems Engineering: Larval culture typically employs complex systems for water filtration, 

purification, and heating. Most aspects of these systems are similar to those employed for flowthrough finfish culture, with the exception of the use of water-borne feeds. Recent experiments 

to intensify culture systems have demonstrated the need for sensitive real-time tools to monitor 

feed quality, feeding rates, and other biological indicators. Methods of measuring and/or 

managing fouling in all shellfish culture systems are also needed. 
39

Husbandry: Management and monitoring of larval growth, metamorphosis, and survival are 

often the most labor-intensive aspects of hatchery operations. Most shellfish hatcheries use live 

microalgal feeds grown in batch or continuous incubators. Some prepared feeds, such as 

packaged microalgae concentrates, may be used. Similar to the health management and disease 

prevention requirements for broodstock, the susceptibility of shellfish larvae to a wide variety of 

viral, bacterial, and protozoan diseases places a significant burden on hatchery operators. Larval 

transport does not pose any significant measurement challenges other than a need to ensure that 

transport temperatures and durations do not exceed expected ranges. There are needs for 

automated methods to clean, feed, measure feed concentrations, count larvae, and other 

parameters in husbandry systems. 

Larval culture systems technology gaps: The availability of adequate supplies of larvae and seed 

when growers need them has been virtually impossible to achieve on a consistent basis. This 

calls for the need for better production systems that focus on bottlenecks, including better 

information on broodstock maturation cues, larval husbandry, and nursery system development. 

Often, live algal food supplies are limiting. This severely limits the ability to consistently rear 

larvae and early-phase seed to a size or age when survival improves. Replacement of algal feed 

with cost-effective, balanced diets of the correct particle size formulated from prepared 

ingredients would eliminate many of these problems. Primary research and rapid technology 

transfer of information on bivalve nutrition on a species-specific basis is greatly needed. Water 

quality and water treatment options have improved but there is no technology in place that 

enables consistent monitoring of water quality in real-time for the pathogenic bacteria, viruses or 

water pollutants that may have profound consequences for viability of embryos, larvae and small 

seed. Probiotic approaches are under study in a variety of locales for bivalve systems but they 

have not yet been applied commercially on a large scale. Commercially available probiotic 

water treatments are largely ineffective for bivalve systems. 

Larval culture systems measurement issues: Important measurement parameters are growth 

rates, larval quality, and larval quantification. There is a critical need for measurement 

parameters associated with key genetic information that is obtained in part by having pedigreed 

lines of broodstock. Key measurement tools should assist in feed management, health and 

pathogen monitoring, disease prevention, monitoring the utility of probiotic and antibiotic 

applications, and assessing larval settlement, induction and synchrony. 

Prepared feed must be the correct size for effective utilization by shellfish. Low cost and easily 

used instrumentation to measure feed particle size and feed concentration in water are needed. 

Methods to measure feed constitutions and determine if each feed particle contains the complete 

balance of nutrients are needed. Easy to use, cost-effective instruments and methods to 

determine algae species composition, particle size of algae, and algae concentration in water are 

needed. 

Nursery Systems 

Nursery systems associated with larval hatcheries usually consist of downwelling and/or 

upwelling technologies that are put in place when larvae reach the pediveliger stage, or larval 

phase when individuals are competent to settle and metamorphose. These may consist of 
40

systems with a small volume and flow-through capability (e.g., soft-drink bottles) where feed 

and water are supplied continuously or semi-continuously under temperature controlled 

conditions or larger systems that rely on setting tanks and screens and larger volumes of water 

and feed. Invariably, as seed grow, space becomes limiting and feed costs increase significantly. 

Outdoor nursery systems typically rely on upwelling tanks and/or raceway systems. Depending 

on the value of the species cultured, hatchery operators carefully monitor the volume of seed that 

can be produced with the algal production capability of the facility. Increased use of floating 

upwelling systems is usually warranted because costs for live or artificial supplemental feeds are 

high and increase dramatically with size of bivalve seed. 

Water quality for nursery systems containing newly settled individuals must be assiduously 

monitored. Water treatment is phased to accommodate the needs of the species cultured. 

Treatment options can include primary filtration, ultraviolet sterilization, carbon treatments, 

passage of seawater through biological media and foam fractionation to remove proteins, toxins 

and other metabolites that may be harmful to newly settled seed. This phase of culture is 

typically the point where high losses are seen in most if not all bivalve and gastropod hatchery 

facilities. Oyster nursery systems benefit from the use of spat-on-shell technologies because spat 

can often be placed into the natural environment with adequate predator protection quite soon 

after settlement. Clams, mussels, and other commercially valuable species (e.g., abalone) 

typically require a longer nursery phase. 

Nursery Systems Technology Gaps: Critically needed are alternatives to removing most 

particulate and biological constituents of seawater prior to addition of cultured algae and use for 

nursery phase animals. Systems that can grow large quantities of algae without bacterial 

contamination are needed. Reliance on commonly cultivated microalgal species for use in 

nursery culture systems should be replaced by using native algae that is produced on site in tanks 

or closed systems. Research is needed on the nutritional value of uncommonly cultivated 

microalgae for use with bivalve and gastropod nurseries. Control of bacteria and/or toxins in 

high-density nursery culture is needed. Probiotic approaches better knowledge of the interplay 

between water quality, seed health and viability are needed. 

Direct seeding of pediveligers onto suitable beach substrates, as has been examined for Pacific 

oysters and Manila clams, should be further examined to reduce costs. This approach may have 

significant utility for shellfish restoration efforts. 

Nursery Systems Measurement Issues: A database that monitors larval and seed output on an 

annual basis is needed to measure progress toward eliminating or reducing variability in larval 

and seed supplies from nursery systems. Seed production, availability, species diversity, survival 

and growth are all factors that can be measured that will help gauge improvement in these 

systems as a result of increased attention though research and development. 

Instruments noted under larval culture above for measuring feed composition, particle size, 

nutrient content, and concentration in the water are needed for all stages of growth for all 

cultured shellfish species. 
41

Grow-out Systems 

All shellfish, with the exception of abalone (grown in land-based tanks or raceways), are raised 

to market size using variations of on-bottom or suspended open-water culture systems. Bottom 

culture of shellfish is often seen as a traditional enterprise, and is (with geoducks being a recent 

exception) widely viewed as environmentally acceptable aquaculture. Bottom cultured animals 

often exhibit varying growth, shell shape and other characteristics. They can be markedly 

influenced by sediment composition, organic content, and other variables. For example, Manila 

clam shells are often darker or less well marked when grown in fine-grain sediments, or oysters 

may exhibit higher mortalities when the underlying sediments become increasingly anoxic. 

Therefore determination of sediment characteristics and sediment and water column chemistry is 

a valuable measurement tool for the shellfish farmer. 

Off-bottom culture is a preferred method in many areas of the world, and is common in the U.S. 

for mussel and oyster culture. For oysters, this method gives the grower greater control over 

shell shape, and sometime shell color. It also facilitates the production of a more uniform or 

consistent product size and can allow continuous product harvest. A primary advantage of 

controlled or containerized culture systems is that they improve the capability of growers to 

manipulate the production system and improve the quality of their product during grow-out. For 

example, in protective containment, geoduck clams can have better meat coloration and texture, 

faster growth, and a higher market price than wild harvested animals. 

Until recently there has been little effort to identify optimal configurations and construction 

features of shellfish grow-out systems. The systems are typically configured to the maximum 

extent (or maximum permitted) of available and accessible water surface or bottom areas. 

Recent efforts to model carrying capacity and ecological interactions in these systems have also 

provided insights on methods to optimize production and monitor associated environmental 

parameters. Land and resource use conflicts, and urban growth are increasingly influencing the 

type and intensity of environmental monitoring required of shellfish farmers. 

Grow-out Systems Technology Gaps and Measurement Issues 

• accurate real-time and low-cost instruments for measurement of a variety of water quality 

parameters (e.g., temperature, salinity, dissolved oxygen, pH, pCO2/TCO2, ammonia, 

chlorophyll a, and certain contaminants) in intertidal environments at the sediment-water 

interface 

• practical field-deployable tools to measure biological activity – photosynthesis, 

respiration, nitrification/denitirification, bacterial and algae productivity, sediment 

organic content, and animal abundance, diversity, and seasonality 

1. low-cost instruments that measure wave height, tidal surge and flow and other physical 

parameters that effect shellfish production over growing areas; little is known about how 

these physical factors interact to provide the desired food to shellfish growing on natural 

bottom or in the water column 

• simplified tools to assess and manage shellfish production and the associated biological 

community -- phytoplankton/macroalgae/seagrass/harmful algal blooms, bacteria 

(including Vibrios and pathogens), animal competitors and predators 
42

• procedures to examine the relationships between environmental variables and key 

production characteristics, and contribute to the development of predictive models 

• environmental/crop monitoring and modeling tools that integrate water quality reporting 

with husbandry and production 

• inventory and growth monitoring and modeling 

• direct measurement of production carrying capacity of suspended and bottom culture 

systems 

• application of underwater video or other observational methods to assess shellfish 

behavior, phytoplankton (flow cam), other flora and fauna (i.e., fish, shrimp) 

• improved methods to monitor animal physiological state (such as hormone production, 

respiration rate, excretion, stress indicators) under field conditions 

• veterinary health monitoring; measures of the condition and health of shellfish 

• shellfish condition and disease detection measures that are rapid, non-destructive, costeffective and automated 

• enhanced technology transfer from existing applications. 

Harvest Systems 

Harvest systems include materials/product handling systems and tools to enhance/ensure product 

quality and food safety, and to minimize environmental effects. Material/product handling is not 

so much a measurement issue as a material design problem. Efficient, robust, and cost-effective 

materials handling systems are needed to reduce labor costs. These may include improved 

product containment methods which reduce both the handling effort and damage to harvested 

shellfish. Some harvest practices are under great environmental scrutiny and consequently have 

significant measurement requirements to assess sediment alterations and harvest-induced 

turbidity. These practices would benefit from observations aimed at reducing or minimizing 

environmental effects. 

A key issue affecting bivalve grow-out systems revolves around food safety at harvest. Bivalve 

shellfish are usually grown in estuaries and are typically associated with streams and rivers 

draining large upland watersheds. These watersheds may be undeveloped, but more often, 

receive some form of human inputs that can increase pollutant loads to estuaries. Shellfish, 

being filter-feeding animals, can concentrate a wide variety of potentially harmful materials 

including pathogenic bacteria and viruses, protozoa, biotoxins, heavy metals and organic 

contaminants. Much effort in terms of shellfish health and safety is focused on management of 

potential human pathogens. Primary pathogens are monitored by indicator organisms to 

characterize the likelihood of pathogenic enteric bacteria and viruses – such as Salmonella and 

Norovirus (formerly “Norwalk-like virus”). Other methods are used to detect marine Vibrio

bacteria, protozoa, biotoxins, heavy metals and contaminants. In order to prevent disease 

outbreaks and protect human health, a complex suite of measures is in place to control harvest 

and processing practices, monitor and maintain growing waters, and manage international and 

interstate transport and movement of shellfish and shellfish products. In shellfish growing areas 

of the U.S., farmers and harvesters are currently responsible for adhering to monitoring 

guidelines to handle and track live and fresh shellfish products. Growers may be forced out of 

business or find their markets restricted if their farm area is closed to harvest by a public health 

agency due to bacteria or other form of contamination. 
43

Harvest Systems Technology Gaps and Measurement Issues 

There is a strong incentive for developing reliable and cost-effective methods to determine the 

presence of harmful bacteria, viruses, heavy metals, and marine biotoxins in shellfish and 

growing waters prior to harvest. For example, tools to differentiate economically and quickly 

between safe and pathogenic Vibrios are presently lacking. Because of the potential negative 

economic impacts of Vibrio outbreaks and the uncertainties involved in the detection of 

pathogenic strains, the development/improvement of rapid and field-deployable diagnostic 

abilities has ranked among the highest priorities for U.S. shellfish growers for several years. 

Similarly, diagnostic and measurement tools have been recommended for other important 

bacterial pathogens, heavy metals, and biotoxins. An ideal measurement system would provide 

field deployment capabilities with real-time results, have a non-technical user interface, use precalibrated unit-use packaging, be compatible with water and tissue analysis, and have multianalyte flexibility (e.g., HAB toxins; water contaminants, including bacteria, viruses, and 

pollutants). 

There is need for instrumentation to reliably and continuously monitor environmental variables. 

Desired sensors must be stable over time, reliably measure what the operator thinks they are 

sensing, be robust, require recalibration only after an extended time of use, be cost effective, and 

usable by farmers and their employees. Similar instruments are needed for monitoring the size 

and concentration of particles in the water, including algae, prepared feeds, organic debris, and 

other particle types. Instruments and methods to monitor growth rate, shellfish movement on the 

bottom or in growing containers, and to monitor stress in shellfish are needed. 

Other technology gaps and measurement issues include: 1) methods for the early detection of 

contamination allowing expansion of shellfish harvest areas and reducing shellfish harvest area 

monitoring costs; 2) rapid test procedure(s) to detect/monitor human pathogens in water and in 

the product; 3) ability to quickly differentiate pathogenic and non-pathogenic strains; 4) 

pathogen indicators other than fecal coliforms; 5) improvements in harvest efficiency through the 

use of crop mapping and incorporation of global positioning systems and geographic information 

systems technology; 6) environmentally friendly mechanization, material handling, predator 

deterrence and exclusion, 7) better assessment of allied technologies for possible technology 

transfer; 8) policy issues are important, especially the baseline socially acceptable farming 

practices; 9) better standards of human health infection thresholds; 10) the lack of approved realtime technology to measure specific pathogen or proxies to pathogens with sufficient relevant 

cost-effective precision and accuracy; and 11) effective measures of indexed ecosystem structure 

to characterize biological community structure, and net effects of farming methods. 

Processing, Packaging and Transport

Shellfish are highly perishable and there are a variety of methods to maintain or improve shelf 

life, and reduce or minimize the loss of flavor and texture during storage. Processing of shellfish 

has until recently been limited to packing of a fresh product, or production of canned, smoked, or 

dried products. A growing number of shellfish are now treated with a variety of processing 

methods, primarily to add value, and improve product quality and ease of use. All of these 

methods fall into the general category of post-harvest processing. Post-harvest processing (PHP) 

methods available to shellfish producers include: 
44

• fresh and raw processing -- Shellfish are consumed live and/or raw; temperature control 

and rapid transport from the shellfish growing areas to the market are necessary to 

maintain the highest quality. New processing technology and product handling systems 

for processing plants are good areas of focus. Cleaned and byssus-free fresh mussels are 

often sold in Europe in non-odor, non-drip plastic bags – either Modified Atmosphere 

Packaging or vacuum packs which greatly enhance product quality and shelf life. 

• Individually Quick Frozen (IQF) -- Freezing shellfish to extend shelf life was first 

applied in 1989; and, presently, there are many facilities using this technique for oysters 

and other shellfish. The largest of the IQF facilities frequently employ cryogenic 

freezing to accelerate the freezing cycle. 

• Heat – Cool Pasteurization (HCP) -- Initially developed in 1995 for oysters by a private 

firm in Louisiana, HCP involves submerging fresh unshucked oysters into warm water 

followed by immediate cold water immersion. This process reduces Vibrio and results in 

a raw product with a fresh taste, good shelf life, high yield, good appearance, and low 

processing cost. 

• Irradiation -- Effective in reducing to non-detectable levels the presence of pathogenic 

Vibrio in shellfish but high doses are required for the reduction of viral loading. Reports 

of irradiation affecting shellfish taste, appearance, and shelf life appear to be associated 

with high dose levels. Advantages of irradiation may be outweighed by the limited 

availability and high capital cost of large-scale processing facilities, reduced efficacy for 

viruses, and consumer reluctance to purchase irradiated food products. 

• High Hydrostatic Pressure (HHP) -- Pioneered in the prepared meat and juice industries, 

the application of HHP to bivalve shellfish was approved in 1999. HHP is now utilized 

commercially on the U.S. Gulf and West Coasts primarily to process oysters. At 

moderate pressures of up to 300 MPa or approximately 44,000 lb/in2

, it facilitates the 

oyster-shucking process and extends the shelf-life of raw shellfish due to the reduction of 

spoilage bacteria. Higher pressures are also effective inactivating the hepatitis A virus 

and possibly other pathogenic viruses. HHP has largely been used to process Eastern and 

Pacific oysters; however, it is equally effective for hard clams (to shuck and pasteurize 

the product) and non-bivalve shellfish (lobster and crab) destined for the raw market. 

Processing, Packaging, and Transport Technology Gaps 

Processing and packing methods can have a major effect on shellfish meat quality. For example, 

the typical U.S. oyster freshwater pack (Japan packs in saltwater) can result in a pH shift, 

product degradation, and browning of meats. Altering water packing or washing phases could 

have a positive effect on shelf life. Product shrinkage is also a serious problem for packers and 

retailers. Reducing shrinkage could provide a fresher and more uniform product. There is an 

immediate need to review meat-washing technologies and evaluate whether shelf life and/or 

quality could be extended by changes in processing and packing methods. 

Application of energy monitoring and conservation to the shellfish processing can lower costs 

and improve efficiencies. Electrical, propane, natural gas, gasoline, and diesel fuel are all used 

in processing and little effort has been applied to reduce these fuel inputs by conservation, more 

efficient process, and recycling energy streams (e.g., heat lost in steam). 
45

Shellfish growers have little control over commercial trucking regulations and temperature 

recording devices do not always tell the whole story in palletized shipping and may, in fact, give 

false readings. Improved packaging that holds loading temperature targets may be the most 

effective method for ensuring freshness and quality in the near term. 

Technology gaps for processing also include the need for: 1) continuous HHP processing, 2) 

low-cost non-radioactive irradiation and/or high pressure processing equipment accessible to 

small-scale producers, 3) sustainable and environmentally acceptable packaging (recyclable 

containers, recyclable insulation, returnable containers), 4) improved shellfish depuration (where 

legal), 5) time control to maintain harvest temperatures, 6) improved process efficiencies, 

especially to move away from batch processing, 7) a low-cost oyster shucking machine, 8) 

alternative methods to ensure pathogen elimination using, preferably, PHP that does not kill the 

animal, 9) improved en-route temperature monitoring systems, radio frequency identification 

(RFID) tags, barcode tags, and external temperature labeling. 

Processing, Packaging, and Transport Measurement Issues 

Measurement needs for processing, packaging, and transport include: 

• instruments that easily and rapidly determine freshness of processed shellfish (electronic 

quality “sniffers”) and are correlated with consumer preferences 

• measuring quality freshness by employing a pH shift recording device within the package 

as an alternative to the current standard sell-by-date 

• methods and instruments to monitor contaminants, including metals, bacteria, toxins etc., 

and evaluate nutrient concentrations in processed and/or packaged shellfish 

• cooling methods/kill curves for non-lethal reduction bacterial loads in shellfish 

• effective measures of growth rates/loading for different pathogen type and between 

processed shellfish species 

• alternative monitoring guidance to reduce pathogen loads during transport 

• non-contact instruments to determine and automatically sort shellfish in the shell or meats 

by size or quality factors. 
46

Table 1. List of technology actions and goals for marine shellfish culture 

Technology Goals

Genetics and breeding

Integration and coordination Adult performance Ability to predict from young animals

Triploidy, etc. Sterilization methods Offer increased yield with limited wild stock effects

Germplasm preservation Long-term germplasm storage Allow ready access to germplasm

Heritability estimates Genetic markers Low cost and standardized for multiple species

Inbreeding studies Mass rearing of multiple families Increase breeding capacity

Molecular markers, mapping DNA microarrays Improve performance in multiple species

Information systems Database development Enhanced tools to evaluate breeding performance

Broodstock maturation systems

Systems engineering Broodstock maintenance Automate holding and feeding

Reproductive performance Reproductive parameters Rapid non-destructive determination

Feeds and feeding Feed requirements and interactions Measure and predict feed performance

Health and disease prevention Health and condition during holding Real-time and accurate diagnostic procedures

Larval culture systems

Systems engineering Larval maintenance Automate rearing and feeding

Husbandry Culture density Methods to optimize density, growth, survival

Feeds and feeding Feed production and consumption Measure and predict feed performance

Health and disease prevention Health and condition during holding Real-time and accurate diagnostic procedures

Nursery systems

Systems engineering Juvenile maintenance Automate rearing and feeding

Husbandry Culture density Methods to optimize density, growth, survival

Health and disease prevention Health and condition during holding Real-time and accurate diagnostic procedures

Growout systems 

Systems engineering Culture systems Production automation and trace back tools

Information systems Database development Trace-back tools to evaluate performance

Husbandry Environmental monitoring Real-time, reliable and low cost measurement tools

Health and disease prevention Health and condition during growout Real-time and accurate diagnostic procedures

Harvest Systems 

Systems engineering Harvest methods Improved mechanization to reduce impacts

Harvest assessment Environmental monitoring Real-time, reliable and low cost measurement tools

Product quality and safety Status of product at harvest Rapid, real-time and accurate procedures

Human health standards Human pathogen/toxics Improved monitoring tools / different indicators

Processing, Packaging and Transport

Systems engineering Processing Further automate process systems

Systems engineering Processing and packaging Product "sniffers" and other detection methods

Systems engineering Packaging -- public health Rapid/tamper-resistent, real-time measurements

Systems engineering Transport Improved methods to monitor quality

Category
47

Shellfish Culture Sub-group Members

Sub-Group Chair: Dan Cheney, Pacific Shellfish Institute, WA – general shellfish 

aquaculture and ecology 

Sub Group Members

Peter Becker, Little Skookum Shellfish Growers, WA – farm systems, oceanography, economics 

Colin Brannen, World Wildlife Fund, DC – molluscan dialog 

Mark Camara, Oregon State University and USDA ARS, OR -- genetics, molecular biology 

Chris Davis, University of Maine, ME – farm systems, oceanography 

Jonathan (Joth) Davis, Taylor Shellfish Farms, WA – broodstock management and hatchery 

systems, genetics, farm systems, ecology 

Bill Dewey, Taylor Shellfish Farms, WA – public policy and regulations, farm systems 

Ralph Elston, AquaTechnics, WA – shellfish disease 

Dennis Hedgecock, University of Southern California, CA -- genetics 

Addison Lawrence, Texas A&M University, TX – urchin culture 

Carter Newell, Blue Hill Hydraulics, ME – farm system, production tools, modeling 

Dave Nisbet, Nisbet Oyster Company, WA – farm systems, processing, marketing 

Bob (Skid) Rheault, Moonstone Oyster Co., RI – farm systems, ecology and marketing 

Brent Vadopalas, University of Washington, WA – genetics 

Katharine (Trina) Wellman, Northern Economics, Inc., WA – shellfish economics 

Fred Wheaton, University of Maryland, MD – production systems, engineering 
48
49

A Roadmap for Commercialization of Cage Production of 

Marine Finfish 

Technical Challenges and Measurement Barriers 

Technology at Issue 

Technology for production and environmental management of sea cage farming of marine finfish 

Technological Innovation at Stake 

In order to meet increasing demand for seafood and reduce rising trade deficits, the U.S. needs to 

enhance aquaculture production in land-based, nearshore and offshore sectors. Technologies and 

production methods for nearshore sea cage culture of a few species of finfish (e.g., salmon, trout) 

are well developed, however, suitable sites in protected waters are limited, and further 

development has been impeded by environmental concerns, disease and parasites, containment 

breaches, and multiple use conflicts. Technologies to improve environmental performance, 

create more secure containment barriers, manage fish health (diseases and parasites), reduce 

production costs (feed, labor) and produce new species for culture may result in expansion of 

nearshore cage culture. There is tremendous opportunity for expansion of cage culture in open 

ocean waters, however, the technology suitable for high energy ocean environments is in an early 

stage of development, and farms operating in exposed waters are small, production costs are 

high, and economic risk is not well known. Development and integration of technologies to a 

high level of automation for conducting routine operations is needed for offshore farming to 

expand. In addition, additional data on environmental effects of ocean farming at a commercial 

scale (e.g., 2-5,000 MT annual production) are needed in order to overcome impediments due to 

environmental concerns, and to inform the policy and regulatory framework for domestic 

offshore farming. 

Economic Significance of Innovation 

Restoring U.S. nearshore cage production to its 2001 peak would add approximately 

$80,000,000 in farm gate value to the existing sector. Additional production beyond that amount 

may or may not be possible due to space constraints. If technology for large scale offshore 

production could be achieved, (e.g., 50 U.S. farms each producing 5,000 MT) the farm gate 

value would be in the $1.5-2 billion by 2025, and perhaps double or triple that mount by 2050. 

In addition, technologies for offshore farming developed in the U.S, would be highly sought after 

internationally. 
50

Technical Barriers to the Innovation 

This cage culture roadmap addresses technology gaps in the production cycle from the point 

when juveniles are transferred from land-based facilities to sea cages in nearshore or offshore 

locations. While prior production stages are critical to the supply of healthy seed stock, the 

assumption was that those stages would be covered by the land-based finfish culture sub-group, 

as for the most part, these production stages take place primarily in land-based systems. The 

technology gaps are organized according to stages in the production cycle and by 

tasks/operations within each stage. As some technology gaps apply to different stages of the 

cycle, or for more than one purpose, they may be listed more than once. In addition, those that 

are cross cutting with other aquaculture sectors are tagged with a “C” and measurement 

technologies with an “M”. A summary of technology areas, goals prioritized by the breakout 

group, and technology gaps for marine cage culture of finfish is provided in Table 2. 

It should be emphasized that addressing each of the individual technology gaps is important, 

however, integration of these technologies into “intelligent” fully automated farming systems 

must be achieved to realize production goals. 

It should also be noted that all the workshop participants agreed that government sanctioned, 

publicly supported programs and demonstration facilities to develop, demonstrate and evaluate 

offshore technologies and farming practices at commercial scale are needed to reduce private 

sector financial risk, and to generate economic and environmental data to stimulate private sector 

investment and inform a rational regulatory framework. 

Fingerling Transport and Stocking

Technology for transport of juvenile fish is well developed for nearshore culture, however, since 

transit time to offshore cages will likely be longer, additional care must be taken to insure the 

fish are not overly stressed. Therefore, it is important that fish are in optimal condition (health 

and nutritional status) prior to transport, and that the size at transport to offshore cages is 

appropriate for the species and the in-cage conditions (e.g., current velocities, mesh size). 

Transport procedures, nursery cage and growout systems that facilitate secure and efficient 

transfer and stocking, minimize stress and mortality of fingerlings are needed. Appropriate 

standards for fingerling quality need to be established to inform growers of the level of risk to 

the stock during and after transport. In addition, it is often difficult to count post-transfer 

mortalities of juveniles, therefore, technologies to count mortalities of very small fish are needed. 

Growout

Engineered Systems (labor reduction, safety, integrity of infrastructure) 

On-site energy generation (e.g. wind, wave, tidal) to power farms (e.g. lights, feeders, 

instruments) could help control costs, in addition to reducing the risks of fossil fuels spills which 

can affect the profitability and sustainability of sea cage farming. Technology that can capture 

natural energy available at coastal and ocean sites would reduce farming costs, improve safety 

and insure long-term sustainability. Technologies must be properly scaled and affordable. 
51

Self-cleaning or non-fouling containment barriers are needed. Biofouling increases weight and 

drag on cage and mooring systems and reduces the flow of oxygenated water through the 

containment volume. In addition, biofouling communities may harbor parasites and disease 

causing organisms that can affect fish health. Coatings commonly used to reduce biofouling 

contain toxic substances (e.g. copper) and it is unlikely that the use of these coatings will be 

allowed in the future. Current methods of biofouling removal require divers, which is both 

costly and dangerous. Changing nets during production cycles, another common practice, is also 

labor intensive, and creates increased risk of escapement. Biofouling control, either through the 

use of non-toxic antifouling materials or coatings, or automated (robotic) cleaning systems 

would improve both profitability and worker safety. 

Lower cost but sufficiently robust submersible cages for open ocean/high energy sites are needed 

as sea conditions at exposed oceanic sites prohibit the use of surface referenced cages. Currently 

available submersible cages are more costly per unit volume than surface cages. Reducing costs 

and increasing the volume of submersible cages without sacrificing structural integrity would 

improve profitability of farming at open ocean sites. Performance standards for assessing the 

structural integrity of cages are needed. 

Deep water moorings and/or cage systems are needed as offshore waters present challenges due 

to wind and wave conditions. There is also the challenge of mooring cages in deep water (e.g.> 

100 m) where the mooring line scope typically used for multi-anchor grid systems would require 

a very large seafloor footprint and incur a large up-front capital cost as well as high maintenance 

costs. Mooring options for deep water include tension leg, single point and untethered cages, 

however, none of these options have been demonstrated for large scale offshore farming. Single 

point mooring systems and untethered cages have the added benefit of dispersing organic wastes 

over a larger area, thereby reducing the potential for benthic impacts. 

At many deepwater and oceanic sites, a seasonal thermocline can develop, creating temperature 

differentials through the water column of as much as 10°C. Since temperature affects feeding, 

growth and metabolism of the fish, it is important to position cages at depths with optimal 

temperature for stock performance. In addition, the ability to raise and lower a cage at a 

controlled speed reduces stress on fish (temperature and pressure acclimation) and provides 

greater opportunity for live marketing of fish with pressure sensitive swim bladders. Therefore, 

precision depth controls for submersible cages would be an important advance. 

Technology is needed to remotely observe the behavior (swimming, response to feed delivery) 

and condition (parasites, health) of stock relative to real-time environmental conditions 

(temperature, oxygen, current velocity). 

More secure containment barriers materials are needed as currently used materials consist 

primarily of woven synthetic netting which is susceptible to wear and tear, can be breached by 

accidents (e.g. boat propellers and other equipment), predators and in some cases by the cultured 

fish (e.g. cod) and lead to escapement. Alternative materials must be developed to reduce the 

risk of escapement. 

Another gap is the lack of remote barrier integrity monitoring systems. Breaches in the 
52

containment barrier, particularly small holes or tears, can go unnoticed, allowing fish to escape. 

Remote methods of inspection (e.g. robotics) or alternatively breach alarms are needed to alert 

farm managers that action to correct the breach is required. 

Robotic devices to perform routine tasks would reduce labor costs and improve worker safety. 

Remote communication and control of these devices would also reduce the need for site visits to 

farms, further reducing operational costs. 

Wireless broadband data communication among surface nodes and to shore could significantly 

improve operations. Real-time remote observation of stock (video, acoustic data) requires greater 

bandwidth than can be delivered by today’s affordable wireless technologies. Low cost, reliable 

technologies are needed to transmit large amounts of data in real-time over distances up to 20 

miles. 

A system for alerting growers to mortality events and enumerating mortalities would be a critical 

improvement for fish health management, and could reduce the risk to containment system 

breaches from predators/scavengers attracted by dead fish. Technology that could enumerate 

mortalities in real or near real-time would alert managers to any health problems and allow for 

prompt removal without the need for costly inspection dives. 

Integrated, “intelligent” farming systems with automatic feedback /neural network programming 

would be am important advance for the sea cage systems of the future. Automated systems with 

artificial intelligence capability for decision making that can integrate observations (stock and 

environment) with operations (e.g. feeding, harvest, grading) would greatly reduce production 

costs and labor requirements. 

General Husbandry 

Diagnostics and treatments for diseases and parasites of new/emerging species are needed. 

Current knowledge of diseases and parasites to which many of the new species may be 

susceptible is minimal, therefore research into the diseases/parasites that affect these species in 

the wild, followed by rapid and reliable diagnostics and vaccines or other treatments for cultured 

fish are needed (C). 

Precision depth control of submersible cages and remote monitoring of stock and environmental 

conditions would be important advances to promote general husbandry and management (see 

more detailed description in growout engineering section above) (M). 

Breeding programs based on "native stock" that will enhance the culture performance of the 

selected species and the possibility to produce sterile fish or mono-sex stocks that will reduce or 

eliminate in-cage spawning are needed to address concerns over the effects of escapes (including 

those resulting from in-cage spawning) on native fish (C). 

In-cage biomass measurement linked to feeding programs could greatly increase feeding 

efficiency. The amount of feed delivered to a cage is based on a percentage of the total biomass 

in the cage, therefore accurate measurement of total biomass is needed so that fish are not 
53

overfed (wasted feed) or underfed (sub optimal growth). Technologies to estimate the biomass 

of individual fish exist, however, technologies that can provide accurate counts of fish in a cage 

do not. Therefore, accurate assessments of total biomass within a cage cannot be made. Clearly, 

as described above, a method for alerting the manager to mortality events and enumerating dead 

fish could also improve general husbandry and management (M). 

Feeding 

Development of mobile, remotely-controlled feeders would be an important advance. Extreme 

weather events can pose risks of damage to centralized feeding systems moored at the surface. 

In addition, transferring feed and fuel from vessels to moored feeders in rough sea conditions 

poses risks for spills and injury to personnel. Mobile feeders that could brought to safe harbor 

prior to the onset of heavy weather, as well as to re-fuel and replenish feed supply would help to 

avert those risks. 

On-site remotely operated feeding systems with even dispersion within the cage(s) and equipped 

with full automation and video monitoring would providing for “intelligent” feedback control 

and manual overrides could greatly improve feed programs reducing costs and waste. Uneven 

distribution of feed within a cage can lead to differential growth rates of stock. Remote control 

and observation of programmed feeding, would improve feeding efficiency and stock 

performance (M). 

The high cost and finite quantity of feed ingredients like fishmeal and fish oil represent 

challenges to profitability as well as expansion of marine finfish culture. Alternatives, including 

land based plants, marine plants and invertebrates, or other ingredients that are competitive (e.g. 

fish processing waste), from both performance (including species–specific nutrition, 

physiological considerations, and waste minimization) and cost standard for carnivorous marine 

species are needed. In addition, feed supplements that improve health and reduce stress should 

be developed, as should finishing diets to improve product quality (flavor, texture, shelf-life) 

prior to harvest and marketing (C). 

As the culture of new/emerging species is commercialized, improved feed formulations and 

feeding regimes must be developed that increase feed conversion and reduce waste. More 

research is needed on the nutritional requirements of new and emerging species and on feeding 

regimes (frequency, speed of delivery) will be necessary to improve performance and reduce 

costs and waste (feed and feces). Other considerations for feed formulations include buoyancy 

and low effluent formulations (C). 

As described in more detail above, information from in-cage biomass measurement and 

monitoring and enumeration of mortalities should be linked to feeding programs to increase feed 

efficiency (M). 

Grading 

Low stress in-cage grading systems that do not require divers are needed. Unequal growth rates, 

often exacerbated by feeding hierarchies established within a cohort can lead to poor 

performance by slower growers. In-cage grading in surface cages requires SCUBA diving, is 

difficult, labor intensive and stressful on the fish. It is all but impossible in submerged systems. 
54

Passive grading technologies for surface and submerged systems are needed to reduce costs and 

improve stock performance. 

Harvesting

Development of methods for improving harvesting efficiencies would be an important 

advancement. Non-diving technologies for rapid harvest at sea with options for live harvest or 

fresh killed fish are needed. Commonly used methods for both surface and submerged cages 

consist of “concentrate and pump” and submerged cages require divers to concentrate the fish. 

In addition to the labor costs and risk to divers in the cage, this method is stressful on the fish, 

which in turn affects flesh quality in fish destined for the fresh killed market, and survivability of 

fish harvested for the live market. More efficient, passive and size selective harvest methods are 

needed to reduce costs and optimize product quality. Technological advances to achieve this 

goal could include: 1) new harvest vessel design with greater live haul capacity, 2) towable 

harvest cages, 3) conditioning fish to respond to environmental cues (self harvest) and 4) low 

stress, size selective partial cage harvesting. 

Feeds and Nutrition

Feeds represent the most important component of variable costs associated with marine fish 

production. High inclusion rates of marine fish meals and oils have been identified as significant 

potential impediments to large scale expansion of marine fish culture. Improved feed ingredients 

including land based and marine plants, invertebrates, or other novel crude protein sources are 

needed. Significant obstacles to formulating reduced fishmeal diets include assuring growth 

performance while overcoming potential problems with anti-nutritional factors. Improved 

understanding of nutritional requirements could reduce over-formulation, while improving 

growth even as expensive marine proteins and oils inclusion rates are lowered. Additives aimed 

at improving digestibility and gut health as well as potential application of enzymes may also 

have potential to improve feed performance. All of these technologies would have to be 

competitive from both performance and cost standards for carnivorous marine species. 

Environmental Performance

Feeds and nutrition 

As described above, new feed formulations and feeding regimes based on requirements of 

existing or new/emerging species could increase feed conversion and reduce waste improving 

environmental performance (C).

Benthos and Water Column 

Reducing potential environmental impacts to benthos and water quality could be achieved 

through the integration of several technology improvements described above. These include 1) 

fully automated video enabled remotely operated feed systems with manual overrides, 2) remote 

biomass and abundance measurement linked to feeding programs to increase feed efficiency, 3) 

deep water mooring/cage systems, 4) self-cleaning or non-fouling containment barriers. 
55

Rapid, reliable, affordable and ecologically relevant indicators (e.g., chemical, visual imagery) of 

impact to benthic communities are needed to establish performance based-standards for 

environmental compliance. Current methods of assessing impact are either costly (benthic 

community analyses), too spatially variable to be reliable or representative of actual condition 

(sediment sulfide, redox), or costly and difficult to do in deep water (diver surveys). 

Physicochemical measurements or visual imagery that are highly correlated to the condition 

(biomass, diversity) of infaunal and epifaunal communities are needed. 

Capabilities for assimilative capacity modeling and verification including predictive modeling 

and assessment (monitoring) must be improved. Considerations include: 1) ability to determine 

both adverse and beneficial effects (M), 2) ability to measure and predict resuspension dynamics 

of waste feces and feed for key species or families of fishes (M), 3) understanding and predicting 

the rates and drivers for respiration/decomposition of organic carbon and other oxygen 

demanding discharges from cages (M), 4) methods to determine fish and shellfish fecal settling 

rates, which is a primary factor driving initial dispersion (M), 5) determination of benthic to 

water column coupling for flux of aquaculture wastes (M). 

Fish Health 

Fish health is an important environmental consideration. A few of the potential advancements 

described above have direct relevance to fish health. These include 1) development of vaccines 

and treatments for diseases and parasites of existing and new/emerging species (C), 2) precision 

depth control of submersible cages 3) remote monitoring of stock and environmental conditions 

(M). In addition, more information is needed on potential for transfer of disease causing 

organisms from farmed to wild fish. This has been cited as an important potential negative 

environmental impact from cage culture operations, however, actual empirical evidence that 

farmed fish are the source of the organisms affecting wild fish is lacking. Some improved means 

of measuring the transport of organisms from cage sites to wild fish is needed. 

Containment 

Improving containment of cultured fish would improve industry sustainability. Several potential 

technology advances that could achieve this goal were described above including 1) lower cost, 

yet sufficiently robust submersible cages, 2) more secure containment barriers (new materials) 3) 

remote barrier integrity monitoring and 4) sensing and control of robotic devices for monitoring 

and cleaning of cages. 

Breeding programs based on “native stocks” could allow for enhanced culture performance while 

eliminating potential adverse effects associated with culture of non-indigenous species. 

Similarly, possibilities of production of sterile fish or mono-sex stocks would reduce or eliminate 

in-cage spawning and/or if there are escapes, eliminate potential for mating with wild fish. 

Technologies for rapid, easily identifiable, low cost and low stress methods of marking farmed 

fish would allow for identification of the source of potential escapees. 
56

Application of Measurement Science to Overcoming Technical 

Barriers 

Approaches to applying measurement science for addressing bottlenecks should include clear 

articulation of the problem, a review of current state of the technology, identification of 

opportunities for technology transfer from other industries/uses, a science-based research and 

development process followed by demonstration and third party evaluation of technologies. An 

example of how a solution to a measurement technology might be developed is presented below. 

Measurement problem: The amount of feed delivered to a cage is based on a percentage of the 

total biomass in the cage, therefore accurate measurement of total biomass is needed so that fish 

are not overfed (wasted feed) or underfed (sub optimal growth). Technologies to estimate the 

biomass of individual fish exist, however, technologies that can provide accurate counts of fish 

in a cage do not. Therefore, accurate assessments of total biomass within a cage cannot be made. 

Measurement need: In-cage biomass measurement linked to feeding programs to increase 

feeding efficiency

Technology Development Approach:

1. Review current status of abundance and biomass measurement technologies. 

Technology to estimate the biomass of individual fish is commercially available (e.g., Vaki 

Biomass Counter) as are technologies to count fish (e.g.,Vaki Bioscanner Fish Counter) 

provided they are channeled through a pipeline or trough. While technology like the 

Bioscanner can provide accurate counts during transfers, it cannot provide accurate counts of 

fish within a cage without pumping from one containment volume to another (which is not 

practical, particularly for submerged cages). 

2. Identify technology gap 

In this case it is the inability to get accurate counts of fish in a cage, which when combined 

with data on average biomass of individual fish, total in-cage biomass can be estimated and 

feed can be metered out accordingly. 

3. Identify technologies from other sectors that may be applied to this problem 

Potential solutions include acoustic (e.g. multibeam sonar) and optical (e.g. video) 

technologies 

4. Conduct research on the state of the science/technology for each option and select the 

technology that appears to have the highest potential to solve the problem. Consideration 

needs to be given to costs, operational requirements (e.g. operator skill level), and 
57

practicality of the environment in which the application will be applied. 

5. Adapt existing technology or build a prototype for use in scientifically valid trials –must be 

done in conjunction with end users, who in this case are farm managers and operators 

6. Make changes adaptations based on results of trials 

7. Demonstrate effectiveness/utility and submit to third party evaluation/assessment of 

technology, preferably at a publicly supported facility 

8. Develop final commercial version of fish counting technology and 1) create programming to 

link to output from individual biomass estimator and 2) create user output interface of total 

in-cage biomass. 

9. Add value by developing programming that links biomass estimation, data from in-cage 

sensors and cameras to intelligent automated feeding systems. 
58

Table 2. Technology areas, goals prioritized by the breakout group, and technology gaps for marine cage 

culture of finfish. The number in parentheses following each goal is the # of votes cast during the 

prioritization exercise. 

Technology Area Goals (# votes ) Technology Gaps 

Transfer of juveniles and 

nursery culture 

 

Fingerling quality Measures of “fitness” of juveniles prior to 

transfer to sea cages (9) 

Inability to measure condition 

Transport and submerged 

cage transfer 

Pre-transport conditioning (nutrition) and safe 

efficient, low stress transport methods that are 

species and life stage-specific (3) 

Transport difficult and stressful 

for offshore cages 

Nursery cages Technologies for efficient deployment and 

demobilization (1) 

Difficult to install/remove in 

submerged cages 

Growout: engineered 

systems 

 

Integrated “intelligent” 

farming systems 

Capabilities for autonomous (remote 

observation and control) operations that 

achieve optimal production results, maintain 

optimal environment for stock, inform 

operators of system failure (15) 

Complete, autonomous farming 

systems for offshore waters not 

available 

Mobile, remotely controlled 

open ocean feeders 

Offshore feed systems that can move to safe 

harbor in storms and can go to port to re-stock 

and refuel (11) 

Technology has not been 

developed 

In-cage biomass 

measurement 

Technology to determine stock numbers and 

size (10) 

Technology not available 

Untethered cages Reduce footprint, cost, and potential for 

benthic impacts (10) 

None have been developed to 

date 

Biofouling 

control/management 

Reduce labor/diving, reduce seafloor 

deposition from cleaning (8) 

Non-toxic fouling resistant 

materials/coatings, automated 

remotely controlled net cleaners 

not currently available 

Deep ocean mooring 

technologies 

Affordable deep water mooring technologies 

(7) 

Technology exists (e.g. oil and 

gas) but is too costly 

Remote monitoring of stock 

and environmental 

conditions 

Observe and manage feeding (5) Technology not available for 

submerged cages 

On-site energy generation 

(wind, wave, etc) 

Reduce costs and emissions, prevent fuel spills 

(4) 

Properly scaled, affordable and 

accessible technologies not 

available 

Sensing and control of 

robotic devices 

Technologies to reduce labor/diving (3) Technologies not developed 

Single point moorings 

(SPMs) 

Reduce cost and complexity of moorings (3) No SPMs have been developed 

or demonstrated for large scale 

farming 

More secure containment 

barriers 

Reduce/prevent escapement (3) Need proven and affordable 

materials 
59

Table 2 (continued). Technology areas, goals prioritized by the breakout group, and technology gaps for 

marine cage culture of finfish. The number in parentheses following each goal is the # of votes cast during 

the prioritization exercise. 

Technology Area Goals (# votes ) Technology Gaps 

Growout: engineered 

systems (continued) 

 

Precision depth control of 

submersible cages 

Optimize conditions for stock, improve safety 

and efficiency of routine operations, options for 

efficient live harvest (2) 

Technology not developed 

Low cost and robust cages 

(surface and submersible) 

Reduce infrastructure costs (1) Proven submersible cages too 

expensive; stronger surface 

cages are needed 

Site security Alert operators to natural and unnatural events 

(1) 

No off the shelf technology 

available 

Growout: feeds and feeding 

Feed formulation High conversion, low effluent feeds, optimize 

buoyancy/sinking rates (14) 

Needs further development 

Fishmeal and fish oil 

replacements 

Nutritious and digestible alternatives to reduce 

costs and improve long-term sustainability (12) 

Fishmeal and fish oil 

replacements for carnivorous 

marine species in development 

Use of fish processing waste Efficient and safe use of processing waste for 

feeds (5) 

Processing, formulation and 

transport systems need to be 

developed 

Finishing diets Diets to improve flavor and texture prior to 

harvest 

Needs development (4) 

Feed delivery Even distribution of feed in submerged cages 

(4) 

Current methods exacerbate 

feeding hierarchies 

Feed supplements Improve health, increase growth (4) Not currently available for most 

species 

Growout: General 

Husbandry 

 

Vaccines Improve fish health, reduce use of antibiotics 

(5) 

Not available for most pathogens 

Predator control Reduce predation on stock (5) Materials, site selection to 

avoid/reduce predator 

interactions, removal of 

mortalities (4) 

Selective 

breeding/sterilization 

Improve growth rates, disease resistance/reduce 

potential for impacts from escapees (3) 

Breeding programs/ broodstock 

lines and techniques for 

producing sterile offspring not 

developed for most species 

Diagnostics and treatment Improved fish health (3) Diseases/parasites for many 

marine fish are not known, 

therefore, no diagnostics or 

treatments exist 
60

Table 2 (continued). Technology areas, goals prioritized by the breakout group, and technology gaps for 

marine cage culture of finfish. The number in parentheses following each goal is the # of votes cast during 

the prioritization exercise. 

Technology Area Goals (# votes ) Technology Gaps 

Harvesting 

Low-stress, partial cage 

harvesting 

Improve efficiency and reduce stress on fish (4) Methods not developed 

Offshore harvest/service 

vessels 

Ocean going vessels that can harvest/service 

cages in rough sea conditions (3) 

Technology has not been 

developed 

Self harvesting fish Develop environmental cues (e.g. acoustic, 

visual) to direct fish into harvest tunnels/cages 

(1) 

Methods not developed 

Environmental 

Performance 

 

Environmental monitoring 

performance metrics 

Rapid and reliable monitoring methods and 

performance-based standards (14) 

No uniformity in standards, 

measured parameters or methods 

Assimilative capacity 

modeling and verification 

Match production volume to assimilative 

capacity (11) 

Assimilative capacity and 

adverse or beneficial effects not 

well known 

Disease transfer Determine extent/severity of disease transfer 

from farmed to wild fish (6) 

Extent/severity of the problem 

not well documented 

Feeding Real-time ability to control feeding in offshore 

cages (prevent over and under feeding) (3) 

Off the shelf technology does 

not exist 

Escapes More robust containment barriers (2) Materials in current use 

vulnerable to damage 

Offshore site assessments Standard methods for characterizing sites in the 

EEZ (1) 

Methods do not exist 
61

Cage Culture Sub-Group Members 

Sub-Group Chair: Richard Langan, Director, Atlantic Marine Aquaculture Center, 

University of New Hampshire 

Sub Group Members

Neil Sims- President and Co-Founder of Kona Blue Water Farms, Kona, HI (offshore fish 

farmer) 

Jack Rensel- Rensel Associates Aquatic Sciences Consultants, Arlington, Washington 

(environmental consultant) 

John Forster- Forster Consulting Inc, Port Angeles, Washington (aquaculture consultant) 

Randy Cates- president and founder of Cates International, Inc. Kailua, Oahu, HI (offshore fish 

farmer) 

Steve Page- Ocean Farm Technologies, Inc. (cage developer/vendor) 

Langley Gace- Ocean Spar, LLC (cage and supporting technology developer/vendor) 

Joe Hendrix- AquaLine AS (cage developer/vendor) and SesFish Mariculture (offshore fish 

farming) and representative on the Gulf of Mexico Fisheries management Council 

Sebastian Belle- Executive Director of the Maine Aquaculture Association 

Michael Chambers- University of NH- Senior Project Manager for the Open Ocean Aquaculture 

Program 

Brian O’Hanlon- President and Founder of Snapperfarm, Inc, Culebra, Puerto Rico (offshore fish 

farming) 

Chris Heinig- MER Assessment Corporation, Brunswick, ME (environmental consultant) 

Daniel Benetti- - Associate Professor, Division of Marine Affairs & Policy; Director, 

Aquaculture Program, University of Miami 

Mark Drawbridge- Senior Research Biologist Aquaculture for Stock Enhancement and Food 

Production, Fisheries Ecology- - Hubbs Sea World Research Institute, San Diego, CA. 

John Sowles- Director, Division of Ecology, Maine Department of Marine Resources, West 

Boothbay Harbor, ME 

Donald B. Kent, Senior Research Biologist, Aquaculture for Stock Enhancement and Food 

Production, Fisheries Ecology, Hubbs Sea World Research Institute, San Diego, CA 

Paula Sylvia, Research Biologist, Aquaculture for Stock Enhancement and Food Production, 

Hubbs Sea World Research Institute, San Diego, CA 

William Hawkins, Executive Director, Gulf Coast Research Laboratory and Professor, 

Department of Coastal Sciences, University of Southern Mississippi, Ocean Springs, MS 

George Nardi, Co-founder and Chief Technical Officer, Great Bay Aquaculture (finfish hatchery 

and growout), Portsmouth, NH 

Chris Duffy, Co-founder and Operations Manager, Great Bay Aquaculture (finfish hatchery and 

growout), Portsmouth, NH 

Barbaros Celikkol, Professor of Ocean Engineering, University of New Hampshire 

Davis Tze, Managing Director, Aquacopia Venture Partners, LLC (aquaculture venture capitol), 

New York, NY 

David Berlinsky, Associate Professor of Fisheries and Aquaculture, University of New 

Hampshire 

Bruce Anderson, President, Oceanic Institute, Waimanalo, HI 
62

Michael Tlusty, Aquaculture Specialist, New England Aquarium, Boston, MA 

Cliff Goudey, Director, Center for Fisheries Engineering Research, MIT, Cambridge, MA 

Peter Smith, Sr. Vice President, Waldemar S. Nelson and Company, Inc. (ocean engineering) 

New Orleans, LA 

Nick Brown, Center for Cooperative Aquaculture Research, University of Maine, Franklin, ME 

Charles Helsley, Professor Emeritus, University of Hawaii at Manoa 

George Leonard, Ocean Conservancy 
63

A Roadmap for Commercialization of Land-Based 

Production of Marine Finfish 

Technical Challenges and Measurement Barriers 

Technology at Issue 

Land-based closed system production of marine finfish in recirculation systems. 

Technological Innovation at Stake 

Anthropogenic activities such as intensive fishing, environmental pollution and marine and coastal 

habitat degradation, together with emerging environmental changes associated with global climate 

issues, have been adversely linked to dramatic declines in marine biodiversity. Human-driven 

erosion of marine biodiversity has recently been projected to lead to the collapse of all currently 

fished taxa by 2048. Reversing this trend, restoring marine biodiversity, and meeting the everincreasing global demand for seafood consumption will require the integration of fisheries 

management, pollution reduction, habitat restoration and, to a large extent, development of 

environmentally sustainable marine aquaculture. 

Responding to the continuous decline in fishery harvests and in an effort to meet seafood 

consumption, aquaculture has become the world’s fastest growing sector of food production, 

increasing nearly 60-fold during the last five decades. Currently, however, farmed marine species 

account for only 36% (3.2% for finfish) of the global shellfish and finfish aquaculture production 

and provide only 11.5% (1.1% for finfish) of all seafood products, inclusive of fisheries and 

aquaculture. It is clear that in order to ease fishing pressures on marine stocks, the production of 

marine species (especially finfish) through aquaculture must be accelerated. 

Two primary obstacles impede the ecologically sustainable growth of marine aquaculture: its 

interaction with the environment, and the use of fish proteins and oils as aquafeed components. The 

future expansion of marine fish production through aquaculture will largely depend on our ability to 

reduce its potential risk and impact on the environment and the development of alternative animal 

protein sources. In the US, as well as globally, there are two emerging avenues to address the 

environmental concerns and to increase the competitiveness and environmental compatibility of 

marine aquaculture: off-shore open ocean cage culture, and land-based, recirculating mariculture. 

This document addresses the latter approach. 

There are several benefits to land-based mariculture systems. They have minimal or no interaction 

with the environment and can be engineered to generate near-zero waste discharge to the 

environment. They can be fully bio-secure and pose little or no risk of farmed fish escaping to the 

wild. They can thus be used to grow native or non-native species, and potentially high performance 
64

genetically modified fish. Moreover, when land-based operations use artificial seawater, they can 

produce disease- and contaminant-free finfish. The environmental conditions in the systems can be 

fully tailored to meet the physiological requirements of the species of interest and lead to optimal 

performances and fastest growth to market size. They are thus generic and can accommodate any 

species of fish, as dictated by its economic value. They can be located anywhere, in rural or urban 

locations or in the immediate proximity of the market, thereby reducing the carbon footprint of the 

operation. 

With its ample aquaculture, biotechnological and engineering expertise and resources, the US is well 

positioned to become a global leader in developing economically feasible and environmentally 

responsible land-based, recirculating finfish mariculture. Such technology can not only stand alone, 

but is also a necessary component to supply seed for cage culture’s growing production, thereby 

making the mariculture industry highly competitive and an engine of economic development in this 

country. 

Economic significance of the innovation 

As noted above, aquaculture has been steadily growing and has, in fact, been the fastest 

growing sector in the US and world agricultural industries. During the last 10 years, global 

aquaculture (food fish and aquatic plants) production has expanded with extraordinary growth, 

reaching a total production in 2004 of 59.4 million tonnes and a value of $70.3 billion (FAOSOFIA, 2007). Despite the industry’s overall growth, the culture of freshwater species still 

comprises about three-fifths of global aquaculture production. The farming of marine species 

must be accelerated to meet the challenge of providing seafood to the growing world population, 

especially in the face of dwindling marine landings. The development of land-based recirculating 

aquaculture systems that are capable of high density production and economically viable annual 

output will significantly increase market supply and geographic distribution of marine finfish 

products. 

The benefit of marine fish production through recirculating systems is that it provides year-round 

production in high density growout tanks with minimum environmental impact, water losses, and 

maximum use of land and space. Additionally, all environmental parameters are fully tailored to 

meet the requirements of the species of interest to guarantee optimal performance. 

Not surprisingly, production costs are always the determining factor for the economic viability of 

an aquaculture operation. A significant expenditure is shipping cost to final destination markets, 

which are largely metropolitan areas. Land-based RAS systems provide unique site selection 

flexibility, compared to cage/offshore operations, and can offer potential advantages for 

distribution, market access and value-added products (e.g., freshness factor, live products, etc). 

The RAS alternative, though a technically and financially challenging endeavor, has great 

potential for secure and sustainable fish production. Moreover, RAS has been already 

demonstrated with several marine fish, including cod, halibut, flounder, seabream, and 

barramundi among others. 

The adoption of land-based recirculating aquaculture systems (RAS) as a primary fish production 

method on a global scale is going to require demonstration of a return on investment (ROI) at a 
65

level similar to other investments with similar risk profiles. The two major sources of risk for 

RAS investment are production risk related to the uncertainty about system performance at full 

scale operation and market risk related to uncertainty about the price performance of the target 

species at increasing market quantities. Most aquaculture products have seen major price 

declines accompanying significant expansion of production (e.g., U.S. catfish industry, tilapia, 

Atlantic salmon and shrimp). The ability to produce a variety of species in RAS should provide 

some reduction of market risk. Production risk can be decreased by ensuring the system is 

performing at its economic optimum. Technical advances and commercial-scale pilot projects 

will allow potential investors to examine production costs under a range of production 

performance parameters and to determine the optimum operating procedures for production. It 

will also allow technology developers/licensors to convey the expected risk in return on 

investment. 

Cross-cutting Non-technical Barriers to Innovation 

The development of technical advantages or solutions to current limitations of marine RAS will 

require the combined effort of the research community (universities, state and federal research 

labs, etc) and the private sector (see the summary of workshop technical recommendations in 

Tables 3-9). It will also require concerted efforts and advancements in areas related to the 

economics, marketing and regulation of RAS operations. Areas of concern/focus have been 

identified and loosely prioritized (see Table 10 - Economics & Marketing and Table 11 – 

Regulations at the end of document). 

Technical Barriers to Innovation 

The development of more economically feasible recirculating, land-based marine finfish production 

systems will require addressing and overcoming many gaps in technology and performance 

quantification for all components of the system. Increasing the degree of containment and, as a 

result, environmental compatibility and bio-security, brings about bigger engineering and biological 

challenges and barriers. 

The roadmap first addresses gaps specific to production systems (e.g., broodstock, hatchery), 

followed by barriers that are relevant to all components of land-based operations (e.g. microbial 

processes, system engineering, health management). Finally, non-system gaps are addressed, such as 

system economy, regulatory aspects, and others. A specific example is also given of how developing 

measurement technologies can help advance land-based marine aquaculture. Summary tables of 

ranked priorities listing the workshop technical findings/consensus and goals of future efforts and 

potential deliverables are provided at the end of this document. The order of tables reflects the 

importance of topics as prioritized by the workshop breakout group. However, for the sake of 

subtopic continuity, the discussion areas within the text have been rearranged. Also included is a 

detailed list of measurement and technological gaps in the different categories that was developed by 

all members of the subgroup (attached as Appendix I). 
66

Seed Production

Juveniles for either cage or recirculating mariculture operations must be produced on-land. With 

the expansion of marine aquaculture in the US and the promotion of offshore aquaculture, seed 

production has become a major bottleneck to the growth of the industry, second only to 

regulatory constraints. Increasing the production volume, as well as diversifying into additional 

species, requires a concerted research effort. Species to be farmed in the US must be clearly 

identified and prioritized. Affordable, unlimited numbers of juveniles for stocking into growout 

systems must be available on demand and year-round for priority species. They must be top 

quality and disease-free. Size-specific temperature tolerances must be well understood for 

stocking fish into ocean systems out-of-season. Genetic selection programs, aided by advanced 

molecular tools, will provide the best performing fish to be used as broodstock. Transgenic 

technologies should be researched towards developing optimally “tailored” fish for multiple 

traits, to be farmed in fully bio-secure, land-based operations. New approaches to producing 

sterile fish should be explored to reduce the risk of farmed fish breeding with wild stocks, as well 

as to enhance performance. 

Although much progress has been made during the last decade in developing seed production 

technologies, several technological and measurement gaps still exist, which will be addressed 

separately for the three components of juvenile production: broodstock, larval rearing and 

nursery. 

Broodstock Management and Spawning: Broodstock fish must be managed to promote 

spawning on demand all year round. While this has been achieved for a number of fish species, 

several recent candidates for marine aquaculture in the US either do not spawn at all in captivity, 

reproduce very sporadically, or only spawn seasonally. In others, sperm production is impaired. 

Land-based broodstock operations must be contained and maintain full control over all 

environmental parameters, to provide optimal conditions for gametogenesis and spawning and to 

enable phase-shifted, year-round spawning. Ovulation and spawning must be induced at will 

either using environmental conditions or hormone therapies. FDA-approved spawning agents 

and auxillary programs (such as seed banks and selective breeding programs) must be 

established for industry-wide use. Hormonal and molecular indicators of reproductive and 

gonadal development in male and female broodstock must be developed and studied. Endocrine 

and genomic-based technologies need to be used to measure and assess reproductive success, 

maturational competence and the need for - or response to - hormonal spawning induction. Biotic 

and abiotic parameters contributing to gamete and egg quality must be understood and measured, 

and indicators and standards established, to provide best quality embryos and juveniles. Other 

long-term obstacles, such as poor control of maturation, lack of gamete cryopreservation 

technology, unreliable sex control, and unpredictable sterilization methods must also be solved. 

See Table 4 for additional details. 

Hatchery and Larval Rearing: Mass-producing early life stages of marine finfish is a complex 

undertaking, as the larvae in most marine species are small in size and require live feed and a 

food chain for the first few weeks of their life. Moreover, several finfish (e.g., flat fish) undergo 

distinct metamorphosis during larval development, which requires special care. Consequently, 

mortality during larval rearing in marine fish is relatively high. Increasing survival rates is the 

main challenge in larval rearing that requires overcoming technological and measurement gaps. 
67

In addition to survival, rates of deformity can be high in some species, which may negatively 

affect fish performance and marketability downstream. Standardized species-specific quality 

standards, as well as measurement technologies must be established for current and emerging 

aquaculture species. The production of live feed, including microalgae, rotifers, copepods and 

Artemia, should be optimized and standardized based on a better understanding of their biology. 

Detailed knowledge of early developmental processes, at the molecular, cellular and 

physiological levels should lead to better larval rearing protocols and increased survival rates. 

Biotechnological approaches should be evaluated for increased efficiency and decreased cost of 

producing live feeds (such as heterotrophic fermentation of microalgae), using live feed to 

deliver beneficial compounds (such as nutrients, enhancers of immune response and growth, 

therapeutics, etc.). Artificial diets to replace live feeds, based on an enhanced and speciesspecific understanding of digestion physiology, should also be investigated. The role of 

microbial communities and probiotic processes in larval growth and survival should be better 

understood. Measurement technologies (molecular, physiological, chemical and physical) are 

needed to assess live feed production efficiency, larval health, quality and developmental 

success, as well as to optimize feeding protocols and environmental conditions. 

Automation of husbandry protocols (in-tank counting and grading methods, larval tank cleaning, 

stress-free harvesting, etc) should be advanced. Optimal culture environments should also be 

identified by species (e.g., species-specific light requirements, larval stressors, probiotic and 

microbial support, etc) for mariculture operations. See Table 3 for additional details. 

Nursery: Post-larvae are grown in intermediate tank systems to a size at which they can be 

safely moved to growout tanks or cages. Many of the technological and measurement gaps in the 

nursery phase are similar to those addressed in the Growout Production section below. 

Technological issues specific to the nursery stage include better understanding of optimal 

rearing conditions for maximal growth, weaning of fish from live feed to artificial diets and the 

occurrence of cannibalism. An enhanced species-specific understanding of developmental 

physiology and maternal immunity transfer would also be beneficial. Increasing weaning 

success and reducing cannibalism in intensive systems must be based on a species-specific 

understanding of the digestive system and of feeding and aggression behaviors. Growth, overall 

performance and handling/husbandry issues are addressed in the following sections. See Table 3 

for additional details. 

Growout Production

Because of the ability to fully control all environmental parameters in the tanks (salinity, 

temperature, photoperiod), fully contained, recirculating systems have the potential to produce 

fish at optimal performance. Understanding the physiology and molecular basis of metabolism 

and growth, and the effect of environmental culture parameters on those processes, is essential to 

producing healthy fish with the fastest growth rate to market size. This understanding is also 

required to develop genomic, proteomic and metabolomic tools to measure, assess and predict 

the physiological robustness of processes underlying performance, with the goal of optimizing 

them. Biotechnological approaches should be evaluated for improving fish growth and overall 

performance, including growth enhancers and transgenic approaches. Measuring stress indicators 

is required to assess and optimize the well-being of the fish under different culture conditions, as 

well as to develop methods for stress-reduction when handling the fish. Efficient and harmless 
68

husbandry strategies for grading, moving and harvesting the fish should be researched and 

established. Reliable and cost-effective systems that incorporate automation for critical culture 

steps are needed. Automatic, real-time and on-line technologies should become available for 

constantly monitoring water chemistry and quality parameters. Automation of operations, 

thereby minimizing handling from larval to growout stages, is imperative. In addition, automated 

methods for removal and disposal of mortalities are needed. See Table 6 for additional details. 

Microbial Process and Communities

The most essential component of recirculating, land-based marine systems is the microbial activity 

occurring in the system. The microbial communities/processes are responsible for removing 

dissolved and solid waste and enable water re-use and full containment. In short, the health of the 

microbial consortia is as intimately tied to production success as it is the health of the fish. 

Numerous technological and measurement gaps remain to be addressed in this area, which to date 

has been understudied and poorly applied in marine systems. Designing the specifications and limits 

of biofilters and solids separation equipment is not currently done based on strong science. 

Biofiltration in marine recirculating systems is a “black box” that needs to be fully characterized, 

understood and improved. Microbial communities/processes occurring in marine systems are unique 

and significantly different than those found in freshwater systems. Aerobic, anaerobic, autotrophic 

and heterotrophic bacteria responsible for nitrogen, phosphorous, sulfite, carbon dioxide CO2 and 

sludge removal should be characterized, measured and optimized. In addition, bacteriophages that 

can aid in controlling water quality and disease should be identified and studied in more detail. Tools 

of functional and meta-genomics, proteomics and metabolomics must be utilized to characterize and 

measure microbial species, consortia and processes. Automatic, real-time, one-line methods must be 

developed to measure microbial species abundance and activity, as well as water quality parameters. 

The interaction between microbiota of the cultured fish, the water, and the biofilters has to be 

measured and understood, with a view toward attaining stable microbial systems and optimal 

bacterial-fish performances. The inclusion of prebiotic and probiotic approaches, both to enhance 

fish health and growth as well as to feed bacteria, should be used more frequently. However, 

identification of probiotic species and species-specific mechanisms of effects must be more 

intensively studied. In addition to biotic parameters, the effect of abiotic parameters (such as 

temperature and water salinity, as well as the type of feed and the source of water) on the 

microbiology of the system, must be analyzed and assessed. This will enable the optimization of 

cold and warm water systems, as well as a range of salinities. Microbially-mediated conversion (on a 

large scale) of waste products to energy is a critical component that will hasten the establishment of 

more environmentally and economically competitive systems. However, thus far, these conversion 

processes are poorly understood or unquantified. 

The development of ‘green technology’ in recirculating mariculture also extends beyond seafood 

production. Improved economics and reduced cost of waste disposal and/or treatment can be gained 

through optimized water retrieval from microalgae systems, the use of algal cultures for methane and 

biodiesel production, and the identification of species and co-products for integrated marine systems. 

These areas warrant further study and technology development in the near future. See Table 5 for 

additional details. 
69

System Engineering

Another very important gap to be addressed is the efficient and cost effective engineering of the 

recirculating systems. Seed production operations will require technologies to maintain high quality 

water even under closed or semi-closed conditions. However, seed production operations are 

relatively small compared to the volume and flow requirements that must be met during food-fish 

growout (which, to be economically feasible, must accommodate densities of over 100 kg/m3

). The 

technical and financial success of the land-based approach is impacted by multiple issues. 

Engineering will be required to overcome issues of scale for the culture tanks, the life support 

systems, and system hydrodynamics. In addition, due to the corrosive nature of saltwater, the type 

of materials and building designs are all barriers that will impact the success and the economy of the 

land-based approach. Mechanical and biological filtration systems have to be space and cost 

effective, and long-lived, while striving for full waste removal and zero discharge to the 

environment. One of the biggest impediments to the commercial development of land-based systems 

is their energy efficiency (or lack of). Systems must not only be engineered to use as little energy as 

possible, but must also possess improved denitrification and the value-added ability to collect their 

waste products to generate bio-energy to off-set a portion of the energy cost. Systems must be also 

engineered to provide full bio-security, including the prevention of farmed fish escaping to the wild, 

and the transmission of diseases between cultured and wild fish and vice versa. 

Measurement technologies must be developed to analyze and assess the durability, efficiency, cost 

effectiveness and environmental compatibility of the systems. Automatic, on-line measurement 

methods and instrumentation must be engineered for water chemistry and quality, as well as for 

indicators of system and fish performance. Standard methods and language for describing and 

evaluating system performances and life phase-specific production systems, optimized for either 

broodstock, hatchery or growout, must be developed and implemented. To this end, defining and 

measuring ‘full recirculation’ for marine systems and the implementation of novel waste 

removal/utilization technologies will be important. See Table 7 for additional details. 

Feeds and Nutrition

Feeds often represent over 50% of the variable costs of production and it is vital to minimize 

these costs to make production economically viable. Sustainability, nutrient retention/discharge 

and fecal integrity are also all critical considerations in the development of efficient land-based 

aquaculture systems. Fish meal has been the primary protein ingredient in aquaculture feeds for 

decades. Not only can the use of fish meal introduce contaminants, but the practice is no longer 

considered to be sustainable, and the supply is severely limited with no more expansion possible. 

Alternate protein sources need to be developed from plants, algae, seafood processing wastes or 

co-products from industrial uses such as bio-diesel or ethanol production. Any source that 

economically provides available nutrients with a minimum of anti-nutritional factors (ANFs) 

should be considered. Moreover, ANFs and anti-metabolites in current sources should be 

identified and removed. These materials, which act against the digestion process, are prominent 

in plant proteins and other feed component sources. Likewise, currently unidentified positive 

nutrients in fish meal that are not found in alternate ingredients should be identified, preferably 

species-specific. Recent research with salmonids has demonstrated that total replacement of fish 

meal is feasible, yet specific requirements of marine carnivores need to be addressed (e.g., 

taurine). 
70

Aquaculture feeds are sometimes over-formulated, resulting in excessive nutrient discharge that 

requires over-sized biofilters. In order to reduce initial and operational costs, diets need to be 

formulated to have minimal nutrient discharge or maximal nutrient retention. Identifying feed 

attractants and improving palatability will undoubtedly aid in this effort, as will improved feed 

and pellet characteristics, better measurement protocols and ‘smart’ delivery systems. In 

addition, in order for recirculation systems to efficiently remove fecal wastes, the fecal pellet 

should ideally be dense and durable. Some formulations result in loose feces that degrade water 

quality and reduce the efficiency of particulate removal equipment. 

Fish oil has been used as an energy source in aquaculture feeds, and like fish meal, supplies are 

limited and can be a direct source of environmental contaminants (i.e., polychlorinated biphenyls, 

heavy metals, phosphates). To this end, fish meal and oil production via aquaculture may become 

safer and more sustainable source. Fish oil does contribute significantly to the heart-healthy 

characteristics of farmed fish. As dietary fish oil is replaced, the final product quality must be 

maintained through the development of finishing diets essential to restore the heart-healthy 

characteristics of the fillets. Finishing diets are just part of a life stage, or phase-feeding approach, 

which is essential to efficient production. Diets for broodstock maturation, larval production 

(weaning from live feeds in some cases), juvenile and growout production will all be important. 

Each phase of production will have different goals with regard to formulations. Feed cost is the 

most important consideration for growout diets, whereas survival is more important for larval and 

weaning diets. Scientific and technological advancements will lead to the development of tailored, 

environmentally friendly and cost effective diets, as well as better life stage and species-specific 

diets. The identification of immunostimulants and the formulation of science-based ‘prophylactic 

diets’ that help prevent diseases will also enable higher productivity and enhanced costeffectiveness. The identification and characterization of genes regulating metabolic processes will 

greatly aid our understanding of fish food conversion efficiency, as well as the ultimate fate of feed. 

Measurement technologies, to include biochemical, physiological and molecular assays (e.g., gene 

chips for evaluating product quality and diet performance), are needed to assess and monitor the diet 

efficiency, performance and compatibility with the recirculating system. See Table 8 for additional 

details. 

Health Management and Disease Prevention

One of the major risks in fully contained, land-based operations is the introduction of pathogens 

leading to the rapid spread of disease. Technological gaps range from the need to establish rigorous 

protocols to avoid pathogen introduction and overcome outbreaks, to the development of antibiotic 

alternatives (drug-free production), better diagnostics, and prophylactic tools. Better-designed 

facilities and health management protocols (BMPs) are also key components to reducing aquaculture 

mortalities. Measurement gaps include the efficient detection and quantification of pathogens and 

the characterization/assessment of fish stress and disease parameters. Molecular technologies and 

gene chips should be developed and tested for rapid and sensitive early diagnostics and for 

measuring viral, bacterial or eukaryotic disease agents. Effective vaccines/multi-vaccines and more 

efficient delivery methods must be developed for major pathogens, based on live or attenuated 

microbes or on DNA/RNA approaches. New antibiotics that will specifically eliminate the 

pathogens but not affect the beneficial microbes responsible for waste removal need to be evaluated. 

Immunological, biochemical and molecular tools will be used to assess the efficiency of the vaccines 

and/or antibiotics, and the health status of the cultured fish. Additional and improved anesthetics 
71

would also be useful to the field. A more complete understanding of environmental impacts on the 

fish immune system is essential. Species-specific genes related to fish health must be identified and 

utilized for screening protocols (e.g., broodstock health screening) and health management regimes. 

The use of probiotic, immunostimulant and immunomodulant approaches in recirculating 

mariculture systems are all promising to some degree, but optimized and predictable responses and 

clear mechanisms of action must be established. Further investigations into technological and 

measurement approaches will certainly enhance health performance, real-time evaluation and 

assessment of fish welfare in marine production systems. See Table 9 for additional details. 

Economics

In order for land-based growout systems to become a competitive and robust contributor to 

future US marine aquaculture, they must be economically feasible, produce fish at a cost that can 

compete in an increasingly global seafood market, and allow for reasonable profits. The increase 

in control of the production system and reduction of environmental impacts resulting from 

recirculating aquaculture come at a cost compared with alternative production systems. These 

increased costs are attendant in both the initial capital investment and recurring operating costs. 

To make recircultating aquaculture competitive with other production technologies, it is 

imperative that the systems be optimized from an economic perspective, to keep production costs 

at a minimum. To this end, modeling and business planning for large-scale recirculating marine 

aquaculture ventures must become more widely available. The lack of demonstration projects at 

a meaningful scale has hampered the collection of commercial-scale operations data, including 

economies of scale and cost functions, as well as the assessment of economic feasibility and the 

identification of bottlenecks (see Table 10). Appropriately-scaled RAS demonstration projects 

would also allow for meaningful comparisons to cage production, projections of market demand, 

and development of market plans (including market dynamics, consumer perception analyses, 

value-added brand effectiveness, pricing structure, specialty markets, new species R&D, etc). 

See also the Quality Control, Product Branding and Public Relations section and the Short Term 

Deliverables section of this text, as well as Tables 10 and 12, for additional details on RAS 

economics, marketing, demonstration projects and related topics. 

The relative differential in costs between recirculating aquaculture and other production 

technologies may differ when comparing direct costs of production versus the “full” costs as 

measured by Life Cycle Assessment research. This is because commercial fishing and various 

aquaculture technologies can have very different external costs that should be included in the 

cost calculations. It is essential that the full costs of seafood production (i.e., the direct and 

indirect or external costs) be used in comparing these technologies. The quantification of the 

societal costs of seafood production can lead to improved government policies concerning 

aquaculture. 

There are some areas in which recirculating aquaculture has a distinct comparative advantage over 

other production technologies. For example, they have the added value of potentially improved 

biosecurity for producing non-native or genetically modified fish. A comprehensive evaluation of 

species for use in recirculating aquaculture will enable the industry to capitalize on this advantage. 

Another advantage may relate to the health and safety of seafood raised in recirculating systems. A 

better understanding of the demand for seafood, particularly related to consumer perceptions, will 

contribute to the expansion of the industry. As noted above, the need to analyze market demand and 
72

perception, conduct product testing and measure value-added product benefits could potentially be 

addressed via multi-stakeholder demonstration projects. External costs of production and the real 

cost of reducing environmental impacts could also be better quantified. See Tables 10 and 12 and the 

Short Term Deliverables section of this text for additional details. 

Quality Control, Product Branding and Public Relations

Seafood and aquaculture products are praised by health care professionals, and thought of by the 

consumer as products that support a healthy lifestyle. It is essential for farmed products to 

support that concept by being free of contaminants and high in the nutrients that provide the 

healthful benefits (and value-added differentiation for marketing; see also Table 10). The 

primary source of contaminants is from poor quality feed ingredients, which in the past has been 

fish oil and fish meal. Development of alternative feeds (see also Feed and Nutrition section of 

text, as well as Table 8) will decrease the possibility of bio-concentration and accumulation of 

these pollutants in the final product. However, it will be vital to develop a monitoring system to 

prevent the sale of product that may be considered “contaminated”. While fish oil often carries 

the pollutants, it is also the source of the healthy omega-3 fatty acids that give seafood a good 

reputation for supporting heart health. Development of diets and feeding practices to minimize 

contaminants and optimize the fatty acid profile of the final product is essential. 

The flavor and texture of the final product is affected by diet, feeding practices and water quality. 

Bacteria and algae have been known to affect flavor of aquaculture products. Even if the product 

has the correct fatty acid content and contains no pollutants, an unacceptable flavor and texture 

will render the product to have very little value. Systems need to be developed to optimize these 

characteristics and to monitor them during production. See Table 10 for additional details. 

Regulatory Issues

Regulatory issues have increasingly become a major challenge and roadblock to developing 

aquaculture operations. A brief synopsis of issues (not ranked or prioritized) has been included in 

Table 11 and in the detailed list of technological and measurement gaps included at the end of this 

text (Appendix I). 

Aquaculture practices that interact with the environment, such as flow-through ponds or floating 

cages require multiple permits, at both the federal and state government levels. There is a 

pressing need for policymakers to provide clear guidelines regarding the regulations that must be 

met by industry, as well as to facilitate the regulatory process and enable a “one-stop-shop” for 

aquaculture permits. In the case of land-based operations, it is important to carefully analyze and 

assess threats to the environment and evaluate regulatory solutions. Near-zero discharge landbased systems should be able to quickly meet regulatory requirements related to environmental 

pollution, although they may still require nominal sewage discharge permits. In recent years, 

land-based marine operations (such as marine fish hatcheries) have increasingly begun to operate 

with a higher percentage of water recirculation – i.e., becoming more contained. The reasons for 

this can be summarized as follows: 

• Coastal seawater sources are often contaminated from other natural and human inputs. 

Operators using less makeup water can cost-effectively filter and sterilize it and thereby 

make it more suitable for culturing fish, especially early life stages of marine organisms, 

which are highly sensitive to pollutants and pathogens. 
73

• Discharge regulations are becoming more and more stringent – especially in regard to 

nutrient inputs. As a point source discharge, mariculture outfalls are easy “targets” 

compared to more generalized watershed runoff in coastal areas. Less water coming in 

means less water going out, which facilitates treatment of discharge. 

• Coastal properties, as well as the associated aesthetics are very highly valued. Near-zero 

discharge land-based facilities could be operated in more remote, inexpensive areas. 

• The farming of non-native or transgenic species will require that facilities are fully biosecure, which will necessitate a high level of “control” over facility operation and the 

discharge characteristics to prevent escapement. 

Short-Term Goals

Since recirculating and contained marine aquaculture operations are still largely experimental and 

not widely implemented in the industry, addressing technological and measurement gaps should lead 

to a few deliverables within the next five years. First, candidate species for land-based systems 

should be identified, including cold and warm water species. Candidate species should be prioritized 

based on their economic value, their market, the availability of seed production technologies and 

their amenability to tank systems (Table 12). For several representative species, demonstration landbased operations should be established, capable of producing up to 20 MT of fish annually. Several 

of these demonstration farms should be strategically located regionally and paired with offshore 

demonstration farms to provide a source of seedstock. The land-based demonstration should consist 

of all production components, to include broodstock, hatchery, nursery and growout systems. Based 

on those demonstration systems, a business plan can be improved and ground-truthed for larger-scale 

production of the relevant species. Demonstration projects will need to be conducted under the 

partnership of multiple stakeholders, including federal, state, academic, private, and environmental 

entities. Funding sources for large-scale demonstration projects will need to be identified and 

secured. The business plan should include conceptual engineering designs of the operation under 

consideration. See Table 12 for additional details. 

Application of Measurement Science in Overcoming Technical 

Barriers 

Land-based marine aquaculture must rely on re-using the seawater, either obtained from the natural 

environment (if the operation is located in proximity to the coast) or artificial saltwater. The degree 

of water re-use will determine the level of containment of the systems, and as such its environmental 

compatibility and bio-security. Recycling the seawater relies on microbial communities and 

processes that consume fish waste and in doing so remove it from the system and allow for the water 

to be re-used. As the percent of recycled water increases, the system accumulates more toxic 

compounds and must include an increased complexity of microbial species to efficiently eliminate 

them. Inoculating and maintaining the microbial consortia that will enable efficient waste removal 

through “biofiltration” of the culture water is a major technological challenge in marine land-based 

operations. A variety of biofiltration systems have been described in the literature and used in the 

industry. Measurement sciences and technologies are badly needed to open the biofiltration “black 

box” and to fully characterize, understand and improve the bacteria and processes involved in waste 

removal. Microbial communities/processes occurring in marine systems are unique and include 
74

aerobic, anaerobic, autotrophic and heterotrophic bacteria responsible for nitrogen, phosphorous, 

sulfate, sulfite, CO2 and sludge removal. 

Correlations between different biofiltration techniques (trickling filter, fluidized-bed, moving-bed 

and more) their microbial community structure, and their efficiency in aerobic/anaerobic microbial 

nitrogen removal processes, must be made and measured in real time. Such information will allow us 

to best fit the biofiltration technology to system requirements. Moreover, definitions of “good” or 

“bad” microbial communities in aquaculture biofilters have to be put into a coherent evaluation 

index that represents their competence to support adequate water quality. For example the ratio 

between autotrophic and heterotrophic bacteria in aerobic nitrifying biofilters can be correlated to 

ammonia oxidation rate and put into an “efficiency index” for each of the different biofiltration 

techniques. Anaerobic nitrogen removal processes such as anammox and denitrification need to be 

measured, evaluated and put into process numbers and values that can be used for systems 

engineering and initial design. Moreover, best biofiltration configurations for applying these 

processes must be determined and evaluated in pilot and up-scale recirculating Aquaculture Systems 

(RAS). 

Assessing the microbial communities and activities of marine RAS will require multiple traditional 

and molecular methods. Community analysis, identification of the bacterial species and measuring 

abundance can be carried out by traditional culturing methods and by 16S rDNA gene analysis using 

a denaturing gradient gel electrophoresis (DGGE) method. Phylogenetic assignments of the 

microbial community can be also performed by a terminal restriction fragment length polymorphism 

(T-RFLP) method that is based on terminal restriction fragment lengths obtained from the digestion 

of communal microbial DNA with a series of restriction enzymes. Correlating the microbial 

community to activity will require the use of functional and meta-genomics tools, as well as 

proteomics and metabolomics methods that must be developed to measure microbial activities and 

relevant processes in real time. Gene chip and micro-array technology must be specifically designed 

to evaluate expression of functional genes that are relevant to waste removal processes (i.e., 

ammonia-oxidizing genes, nitrate and nitrite reduction genes, etc). Moreover, such gene chips can be 

loaded with genes that are relevant for the detection of pathogenic bacteria, thus improving 

possibilities for early detection and disease prevention. Understanding and measuring the microbial 

species and activities involved in marine waste removal, and their correlation to biotic and abiotic 

parameters (e.g., fish species, feed type, salinity, source of water, temperature) will enable us to 

engineer and tailor optimal biofltration systems and, thus, allow for efficient and cost effective 

water-reuse to enable land-based operations. 

Establishing and understanding the mutual relations between water quality parameters, fish growth 

and the biofilter microbial community/activity will require on-line measurement of many water 

quality parameters. Some measurement techniques need to be developed and adapted to marine 

systems. For example, on-line monitoring system for nitrate, nitrite and ammonia, as well as water 

alkalinity and turbidity, are not readily available. These parameters have to be monitored in real time 

and correlated to the microbial community/activity of the different biofiltration configurations. 

Finally, in order to increase the environmental sustainability and economic feasibility of land-based 

marine aquaculture systems, an efficient microbially-mediated technology must be developed to 

eliminate marine sludge, preferably producing fuel-grade bio-gas in the process. Again, using the 
75

microbiological and molecular techniques listed above, marine bacterial and archeal organisms that 

are known to convert sludge to methane must be studied, characterized, inoculated and augmented in 

the sludge removal component of the marine recirculating systems. This will lead to the engineering 

of an optimal bio-reactor that efficiently digests and eliminates the solid waste produced by the fish, 

while off-setting the cost associated with the system’s energy needs. 
76

Table 3. Ranked priorities for larval rearing and nursery technologies 

Priority Technology Area Goals Techno

#1 Measurements of performance and 

quality 

Standardized species-specific quality standards • Understanding species-sp

#2 Tailored and inert feed formulations Artificial microdiets to replace live feeds • Understanding digestion p

• Methods to prevent nutrie

for consumption and dige

• Better floatation/buoyanc• Maximize chemoattractan• Weaning protocols

#3 Food chain production High density, optimal quality production of 

algae, rotifer, Artemia, copepods, etc. 

• Reliable stable automated 

organisms 

#4 Automation of husbandry • In-tank counting and grad

• Larval tank cleaning • Stress-free harvesting of l

-- ID of optimal environments for larval 

culture 

ID by species; Stress tests 

• Too few • Larval tank cleaning • Understanding species- sp

-- Counting and grading methods Automated counting and grading systems • In-tank passive grading a-- Probiotic support Optimize microbial communities and ecology -- Understanding developmental physiology -- Transfer of maternal immunity 
77

Table 4. Ranked priorities for broodstock and spawning technologies 

Priority Technology Area Goals Techno

#1 Year-round, consistent and induced 

spawning 

Develop protocols for and techniques for ondemand seed production • Understanding broodstoc

• Understanding natural cu

• FDA approval of spawnin

• Seed bank (embryos) • Broodstock security

#2 Assessing and controlling gamete quality Optimal quality and supply of gametes; 

Maternal delivery of therapeutants 

• Standards and indicators • Lack of quality gametes 

#3 Selective breeding Improved broodstock program by species #4 Endocrine and molecular measurements 

of performance 

Evaluation of water quality on breeding 

-- Gender identification, sex control Produce optimally performing seeds; 

Maximize efficiency of broodstock operations 

• Sex change control in her• Induced sterilization 

-- Gamete cryopreservation • Inability to cryopreserve -- Control of maturation • ID cues 

• Better understanding and 
78

Table 5. Ranked priorities for microbial processes and water quality technologies 

Priority Technology Area Goals Techno

#1 Dissolved and solid waste (nutrients) 

treatment 

Cost-effective large scale solids removal and dewatering; Full utilization of all waste assets 

• Designing the specs and l

separation equipment 

• Understanding polycultur• Accurate simple water ch

nitrate, etc) 

#2 Bio-energy production Convert sludge to fuel, offset cost • Algae ponds for biodiesel

• Water retrieval from micr

#3 Microbial consortia and processes Establish and maintain stable microbial 

consortia and processes enabling optimal fish and bacterial performance 

• ID and improvement of n• ID and measure microbia• Innoculum; innoculation • Monitoring/probes • Economy of scale models 

#3 

(tie) 

Probiotic activities Use probiotic approaches to enhance fish health 

and growth; Probiotics and microbiota to feed the bacteria 

• ID probiotic spp. and spe

effects 

-- Environmental, biotic and abiotic effects Optimize microbes and biofilters for different 

environments (cold, warm, salinity) 

• Measure and optimize the 

-- Integrated marine aquaculture model 

systems 

Improved economics and reduced cost of wastes • ID species and co-produc
79

Table 6. Ranked priorities for growout production technologies 

Priority Technology Area Goals Techno

#1 Measuring and optimizing performance Achieving fastest time to market size at maximal 

density and survival; Feed efficiency; Stress tolerance; Streamlined costs; Maintain product quality (texture, oxidation rate, shelf life, flavor, fillet yield, etc); Reducing cannibalism; Preventing precocious puberty 

• Understanding dynamics 

managing of off-flavors 

• Understanding the physi• Digestibility by species • Control of sex differenti• Real-time measurement • Tailored feeding schedu

#2 Enabling species diversification Flexible and generic systems • ID new species (single s

suitable for land-based s

• ID environmental condit

performance 

#3 Genetic and molecular approaches Improved quality and performance (faster 

growth, improved fatty acid ratios, etc) 

• Understanding genetic m• Constructs and gene inse

#4 Automation of operations Minimal handling from larval to growout stages; 

Efficient and cost-effective grading, counting, harvesting, biomass estimation, feeding systems, mortality removal 

• Reliable and cost-effecti• Loss/damage of product • Limited market 

-- Water recirculation and reuse Optimize water quality; 

Maximizing water reuse 

• Unknown water quality 

-- Rearing post-nursery environment Cost-effective rearing environment (reduced 

capital and energy costs) 

• ID environmental condit

effective performance 
80

Table 7. Ranked priorities for system engineering technologies 

Priority Technology Area Goals Technol

#1 Biofilters and life support systems Most efficiently maintaining optimal water 

quality; Long-lived filters; Energy efficiency 

• Denitrification • Establish species specific b• Non-corrosive materials • Energy efficiency 

#2 Energy balance/efficiency Reduce energy costs • Cost-efficient heat and coo

• Alternative energy sources 

#3 Defining, measuring recirculation 100% seawater recycle (in some cases) • Novel waste removal/utiliza#4 Buildings/greenhouses/tanks/ 

Materials 

Cost-effective, energy efficient and manageable operations tailored to the fish of interest 

• Cost-effective non-corrosiv• Tank insulation choice 

-- Life-phase specific production systems Systems optimized for broodstock, hatchery, 

growout etc 

• CFD modeling for mixing a• Tank color 

-- Bio-security No interaction with the environment -- Material handling, processing and 

distribution 

Cost-effective marking systems for fish Cost effective, efficient distribution and storage of fish, feed, etc Harvesting Chemical additions Extensive automation 

-- Automated, real time monitoring Online water quality monitoring -- Ergonomics/Safety Optimized production and safety 
81

Table 8. Ranked priorities for feeds and nutrition technologies 

Priority Technology Area Goals Technol

#1 Fish meal and oil replacement Maximize fish conversion efficiency ; 

Produce from aquaculture fish meal and oil for feed; ID and remove anti-nutrients 

• ID by species unidentifie

not found in alternate ing

• ID genes useful in unders

#2 High efficiency/ non-polluting diets Optimized for recirculation systems; 

Identify attractants and improved palatability 

#3 Species and life phase specific 

nutritional requirements and diets 

Diets that help prevent diseases; Develop diets for different species and production systems; 100% survival 

• Develop diets for all life • ID immunostimulants • New gene chips for evalu

performance 

#4 Non-contaminated feeds Develop diets deprived of heavy metals, PCBs, 

etc 

• Reduced phosphates 

-- Feed and pellet characteristics Standardized suite of measurement protocols -- Feed delivery systems Smart delivery systems -- Ultimate fate of feed -- Feed economy 
82

Table 9. Ranked priorities for health management technologies 

Priority Technology Area Goals Tech

#1 Measuring fish health and stress Develop sensitive diagnostic tools • ID and understand

• ID species-specifi• Nondestructive br

protocols 

#2 Probiotics, immunostimulants and 

immunomodulants 

Uniform optimized predictable response • ID and understand

#3 Vaccine development and efficient delivery Develop efficient multi-vaccines and 

simple delivery methods 

• Stable and effectiv

immersion, mecha

#4 Health management protocols Reduce transport-related deformities; 

Optimizing hygiene barriers 

• Understanding the 

immune system 

• Assessing efficacy 

-- New, compatible antibiotics Alternatives to antibiotics • Limited available 

• Understand mecha

-- Improved anesthetics • Too few anesthetic-- Design for health management Drug-free production environment • Good fish health m-- Measuring fish welfare • Standardized defin
83

Table 10. Ranked priorities for economics and marketing 

Priority Focus Area Goals Implemen

#1 

Modeling and business planning (near-term) 

Effective sensitivity and risk analyses to guide investment decisions, research and business operations; A comprehensive plan that includes marketing dynamics and other aspects (see below) 

• Commercial data c• Cost functions (ho

compare) 

• Lack of demonstra

scale (!) 

#1 (tie) 

Economic feasibility and bottlenecks (near-term) 

Profit maximization and cost reduction; Relative cost comparisons (by species, region and market); Economy of scale 

• Commercial data c• Cost functions (ho

compare) 

• New species R&D • Lack of demonstra

scale 

• No measurement o

market segments 

#1 (tie) 

Compare to cage production (near-term) 

Quantify the full costs of aquaculture production, including the external costs, environmental costs, etc (not just the costs to the grower) 

• Estimates of exter• Real costs of redu• Lack of demonstra

scale 

#2 Market demand and perception analysis; flesh 

quality 

Establish that consumers care about the value added approach/brand 

• Marketing plans (t

surveys, consumer 

• Product testing 

#3 Measuring added-value (eg, organically grown, 

cleaner, non-native, etc) 

Higher value by differentiation from other products 

• Demand models • Quantify food/tran

user 

#3 (tie) 

Product branding and specialty markets Industrial consumers of juvenile fish 

-- Industrial consumers of juvenile fish Meeting cost expectations of industrial 

consumers 

-- What is the marketing chain? Is there a market? Define the market dynamics • Market dynam
84

Table 11. Breakout group report on regulatory issues* 

Focus Area Goals Impl

Assess environmental risk (Detailed goals were not provided by breakout group) (Implementatio

the breakout gr

Assess regulatory roadblocks and solutions Facilitate regulatory clearance (State, Federal); One stop permitting Provide clear guidelines to prospective aquaculturists 

* Regulatory issues were not been prioritized or discussed in detail by the breakout group. 
85

Table 12. Breakout group report on short term goals 

Technology Area Goals Tec

Identify a list of top candidate species by category (eg warm water, cold water, etc) (Note: Developing a matrix-based system for grading each 

spp and the identification of bottlenecks was suggested) 

Develop the criteria and weigh the criteria for candidate spp.; Use the overall categories (eg., Broodstock and Spawning, Larval Rearing, etc) as an initial selection and sorting criteria for candidate species identification and demonstration 

Understanding the flow charts of all necessary components for culture of species above 

Lack of data (see listings under Economics and Marketing) 

Develop business plans for species identified above Provide conceptual engineering designs (xx tons) By species, establish business plans for above 

species; Capitalize on existing infra-structure, methodologies, expertise, etc 

• Lack of systems • An inventory of 

exist 

Establish demonstration systems Clearly define the goals of the pilot/demonstration 

systems; Establish criteria for demo projects; Established partnerships between multiple stakeholders (federal, private, environmental, etc) 

• Lack of establis

projects 

• Lack of funds fo

(may need a comfunds; establishe
86

Appendix I: Detailed List of Technological and Measurement Gaps 

Seed Production

Broodstock management and spawning 

• establishment of full control over environmental parameters 

• development of reliable gender identification protocols 

• measurement of physiological, endocrine, molecular and genomics-based parameters 

associated with broodstock performance, fecundity and year-round spawning 

• development of measurement technology to include biochemical and genomic-based 

assessments for gamete quality 

• measurement of environmental stresses (biotic and abiotic) using physiological and genebased technologies 

• examination of genetic considerations, selective breeding 

• management of broodstock for consistent and year-round performance 

• assessment and measurement of the need for hormonal spawning induction 

• development of gene and hormonal “chips” to evaluate acquisition of maturational 

competence (small and large species) 

• establish methods for production of sterile fish 

• control sex reversal in sequential hermaphrodites 

Hatchery and Larval Rearing 

• optimized environmental conditions 

• phase-specific rearing protocols (density and feeding) 

• larval phase 

• post-larvae/early juvenile phase(s) 

• microalgae, rotifer, copepod and Artemia rearing capabilities 

• multiple measurement technologies at the different trophic levels and water quality to 

standardize and optimize production efficiency 

• probiotic support during larval rearing 

• develop a better understanding the nutritional needs during the ontogeny of larval fishes 

in order to reduce or eliminate the incidence of malformation and malpigmentation 

• establishment of weaning processes and prepared microdiets that will replace some or all 

of the live food requirement 

• development of inert feeds which can completely replace the need for live prey 

Nursery Production 

• growth of post-larvae to around 40 gr. 

• measurements of growth, metabolism and performance parameters, to include 

physiological, molecular and genomic-based parameters and technologies 

• assessment of biotechnological approaches to optimize performance and growth 

• control sex differentiation and production of monosex populations 
87

• optimized tank dynamics (e.g. current velocities and water depth) as a means of 

improving water quality and fish performance, and reducing cannibalism, etc 

• automation of size-grading and enumeration (via camera systems, etc) 

• reduce labor – current methods are not supportable 

• minimize cannibalism 

Growout Production 

• improvement of current capabilities to achieve consistent high holding densities (up to 75 

kg/m3) 

• optimization of current state-of-the-art toward fully recirculating systems (zero water or 

sludge discharge) 

• conversion of sludge to methane 

• establishment of flexible conditions to allow for species diversification 

• development of multiple measurement technologies to monitor fish growth, metabolism 

and overall performance, physiological, molecular and genomic-based parameters 

• development of gene chip, proteomic and metabolomic approaches to measure overall 

performance (for this and other life cycle stages) 

• assessment and optimization of growout conditions (temperature, salinity, etc); tailor 

environmental conditions for species of interest (for this and other life stages) 

• evaluation of biotechnological approaches to promote growth and performance 

• establishment of methods for stress reduction (grading, fish move, etc) 

• improvement of harvest and inventory management - automatic systems (fish pumps, 

etc.) and passing grading devices 

• measurement of water chemistry and quality parameters, including oxygen, pH, 

ammonia, nitrite, nitrate, phosphate, sulfide, COD, BOD, salinity, redox potential and 

methane production 

• development of automation and real-time technology for all measurements 

Microbial Processes and Communities

• full characterization of the microbial consortia responsible for waste removal (dissolved, 

solid) under different environmental conditions (temperature, salinity, water source) 

• study of microbial processes taking place in the system (aerobic, anaerobic, nitrification, 

denitrification, sulfur reduction, annamox, methanogenesis, etc.), including bacteriophage 

activities 

• development of automated, real-time and online measurements for water/system 

chemistry 

• development of specific molecular tools to monitor biofilters (gene chip, proteomics, 

metabolomics), especially in regard to anaerobic microbes 

• development of detailed molecular, microbial, physiological and analytical measurement 

technologies related to microbial processes and water chemistry 

• study of intestinal micro-biota as affected by both feed and the environment 

• assessment of microbial communities in the culture water, to include potential pathogens 

and probiotics 

• spectrum of water sources may require different water treatments (artificial; coastal; 

groundwater) 
88

System Engineering

• assessment and development of all engineering aspects of the system, to include tanks, 

life support systems, mechanical and biological filtration units, gas transfer devices, and 

chemical balance (such as CO2 and pH control) 

• assessment of the performance of marine biofilters 

• different types of filters including MB, FSB, RBC, etc 

• cold water versus warm water biofilters in marine conditions 

• seaweed incorporation 

• overcome scale-up issues in culture tank design 

• rapid removal of solids 

• create optimum swimming speeds 

• overcome scale-up issues in foam fractionation 

• influence of salinity, ozone, and surfactants 

• side-stream requirements to meet water quality objectives 

• assessment of continuous water disinfection (e.g., ozone & UV) technology 

• characterize dose requirements for different obligate marine pathogens 

• develop practices to avoid production of toxic bromine or bromate 

• determine safe water quality limits for new marine species, e.g., carbon dioxide, oxygen, 

total gas pressure, ammonia, nitrite, nitrate, calcium, magnesium, swimming speed, etc. 

• evaluate the consequences of reducing the amount of make-up water used in the system 

(i.e., closing the system) 

• product quality, especially off-flavor and potential toxicity 

• water quality 

• fish performance, especially health and growth rate 

• evaluate building designs and costs for marine recirculation systems: corrosion 

resistance; insulation factors; energy efficiencies; HVAC designs; vapor barriers 

• suitability of different building types according to region and species 

• materials choice for marine recirculation systems (i.e., engineering and architectural 

choices): corrosion resistance; cost; durability; toxicity to fish 

• establish standard methods and language for describing and evaluating recirculation 

systems, for example: 

• water reuse fraction based on system volume or flow replacement, cumulative 

feed burden per makeup flow (kg/m3) 

• what, how and where (in the system) to measure water quality parameters 

• standardize techniques for marine CO2 measurements that are appropriate and 

practical for aquaculture use 

• establish standard practices for emergency and backup procedures and equipment 

• develop sensors and monitoring and control equipment that is technically and 

economically appropriate for aquaculture applications 

Energy Considerations 

• develop ‘low head’ systems that are more energy efficient per unit production 

• analyze and measure energy usage (input and output) and carbon footprint 

• investigate use of alternative energy technologies for powering land-based systems – 

explore possible synergies between energy production & aquaculture, for example: 
89

• building designs 

• heat pumps – heating & chilling 

• methane production from system’s sludge 

• solar – heating/chilling 

• wind – direct pumping versus turbine 

Bio-security 

• assessment of the full containment capabilities of the system for use with non-native 

species and potentially transgenic species 

• assessment of the need to develop biological controls for escapes (polyploids, steriles, 

etc) 

• assessment of techniques for the prevention of disease transmission between cultured and 

wild fish and vice versa (e.g., influent and effluent sterilization to eliminate the access or 

potential discharge of living pathogens) 

• develop methods to evaluate the health status of the cultured animals and adjust cultural 

practices to prevent potential problems 

Feeds and Nutrition

• development and assessment of alternate protein ingredients to fish meal 

• development and assessment of specific diets for the different life phases: broodstock, 

larvae, weaning, juveniles, growout 

• development and assessment of high efficiency, less polluting diets, tailored for 

recirculating systems and relevant to the microbial consortia 

• development of finishing diets for specific products (i.e., high omega-3) 

• development of molecular assays for assessing physiological nutritional quality of diet 

Health management and disease prevention

• measurement of fish and system health using genomic-based technology and gene chips; 

automation of data-collecting systems 

• development of standards for disease-free systems 

• establishment of health-management protocols to avoid and overcome pathogens and 

diseases 

• development of precise and rapid molecular pathogen diagnostics 

• vaccine development: live, attenuated, genetic 

• evaluation of new antibiotics and probiotic approaches 

• establishment of advanced molecular techniques (gene chips, etc) as industry standards 

System Economy

• analysis of the economic measures and feasibility of the system for several marine finfish 

systems 

• comparison of the economics of land-based versus net-pen (inshore and offshore) 

• analysis of seafood markets and demand including product perception 

• review of economic bottlenecks and optimization of systems from an economic 

standpoint 
90

• assessment of the economic feasibility and competitiveness of land-based operations 

• promotion of added value: bio-security and non-native species 

• critical examination of funding and financing 

Quality Control and Product Branding

• measurement of potential chemical pollutants in the system and the fish 

• Evaluation of the retention of undesired heavy metals, chemical pollutants, pathogens, 

etc, in closed systems 

• determination of fish “wholesomeness ” and effect of feed formulation 

• measurement of fish flavor and texture and effect of feed formulation 

• development of standards to brand fish products as “environmentally sustainable” or 

“healthy” products 

• promotion of the environmental sustainability of recirculating mariculture 

Regulatory issues

• provide guidelines for fish health and genetic monitoring plans 

• provide risk analysis for environmental impacts based on species, geography, and 

production systems 

Federal and state regulations 

• clear current regulatory roadblocks for marine aquaculture 

• evaluate individual threats and regulatory solutions 

• non-natives; GMOs 

• interactions with environment (minimal and maximal) 

• issues with federal & state EPA – NPDES permits 

• National Aquatic Animal Health Plan – USF&W, FDA, USDA, EPA 

• provide clear guidelines of regulations that must be met by prospective aquaculturists 

• consider the creation of "aquaculture parks" or areas covered by general permits to 

facilitate the growth of the industry while ensuring protection of the environment 

Short-term goals

• identify candidate species 

• candidate cold water species 

• candidate warm water species 

• native and non-native 

• establishment of a number of demonstration systems (<20 MT production) to include all 

components (broodstock, hatchery, nursery, growout) for several key species: cobia; 

halibut; cod; salmon; redfish 

• development of conceptual engineering design for a commercial on-land operation (1000 

ton production?) 

• development of relevant business plan(s) 
91

Land-Based Finfish Culture Sub-Group Members 

Sub-group Chair: Yoni Zohar, Center of Marine Biotechnology, University of Maryland 

Biotechnology Institute 

Sub Group Members

Rick Barrows, ARS/USDA 

David Berlinsky, University of New Hampshire 

Reg Blaylock, The University of Southern Mississippi, Gulf Coast Research Laboratory 

Barbara Block, Stanford University 

Nick Brown, University of Maine 

Jim Carlberg, Kent SeaTech 

Walt Dickhoff, NOAA 

Mark Drawbridge Hubbs-Seaworld Research Institute 

Joan Holt, University of Texas Marine Science Institute 

Scott LaPatra, Clear Springs Foods 

Doug Lipton, University of Maryland 

Christopher Mann, Pew Charitable Trusts 

Kevan Main, Mote Marine Laboratory 

George Nardi, Great Bay Aquaculture 

Raul Piedrahita, University of California 

Michael Schwarz, Virginia Tech and VSAREC 

Steve Summerfelt, Fresh Water Institute, WV 

Yossi Tal, Center of Marine Biotechnology, University of Maryland Biotechnology Institute 
92
93

A Roadmap for Commercialization of Biofloc-Based 

Production Systems Technologies for Marine Shrimp 

Litopenaeus vannamei

Technical Challenges and Measurement Barriers 

Technology at Issue 

Land-based closed system super-intensive shrimp culture utilizing microbial bioflocs to enhance 

growth, sustain production, cycle wastes and reduce production costs. 

Technological Innovation at Stake 

Production of marine shrimp in super-intensive systems close to large population centers in the 

continental U.S. offers unique opportunities for developing new markets for consistent high 

quality fresh local shrimp products. Consistent production of shrimp on a continuous basis in 

proximity to large markets can offer opportunities for product differentiation and brand 

development. At present there are no reliable domestic sources for fresh, never frozen shrimp, 

available on a consistent basis. However, achieving consistent year-round production, while 

maintaining control over production costs, remains a significant technological challenge. High 

costs of land, labor and energy require increasingly complex engineering systems to achieve high 

production intensities. Similarly, maintaining high growth rates and consistent survivability 

requires improved seed stocks and cost-effective specially designed feeds. Finally, 

environmental sustainability requires innovative approaches to water reuse and waste 

management. Key components of the present super-intensive production system include: 1) 

availability of improved SPF shrimp stocks, facility biosecurity and maintenance of the health of 

the target crop; 2) high quality feeds and efficient feeding practices; 3) advanced systems 

engineering for heating, oxygenation, particle filtration, water quality monitoring, alarm systems, 

automated backup systems and waste management; and 4) development and management of 

biofloc communities to support system water quality and boost shrimp performance. 

Shrimp Stocks

Increased availability of high quality, genetically improved, disease resistant post larvae (PL) 

have resulted in greater consistency in shrimp growth, size at harvest and survival of stocked 

animals. Economic and biosecurity concerns have forced shrimp producers to consider 

protection of cultured animals through more stringent production methods – both to avoid 

diseases and to prevent spread of diseases. Since the early 1990s research by the U.S. Marine 

Shrimp Farming Program has demonstrated the advantages of stocking SPF shrimp as the basis 

for intensive culture systems. Over the past decade, production has shifted to SPF stocks of 

Litopenaeus vannamei worldwide. As shrimp prices have declined, producers have been forced 

to improve efficiency and reliance on high quality sources of brood stocks as an important 
94

strategy for some of the most successful producers. Genetic selection has played an important 

role in improving the growth and survivability of these SPF lines. Increasingly sophisticated 

breeding programs have contributed to continuing improvements in growth and resistance to 

Taura Syndrome Virus. 

At the same time, aquaculture producers have increasingly applied principles of biosecurity, 

which form the cornerstone of modern agricultural production systems. The present superintensive production systems technologies rely upon the best fast growing SPF stocks available 

on the market produced in enclosed systems managed under stringent biosecurity protocols. 

Production efficiencies of the system have been improved by including a nursery phase. This 

provides several advantages including assurance of stock quality and animal health prior to 

stocking, better control over shrimp stocking numbers, survivability and system biomass 

estimates during the growout cycle, more efficient use of production area by stocking shrimp at 

higher densities during the nursery phase and shortening the growout cycle by stocking animals 

well into the linear growth portion of the shrimp life cycle. 

Feeds and Feeding

It is well recognized that feed inputs are the major driver of the dynamics of intensive zero 

exchange shrimp culture systems. Control of feeding rates is one of the most important factors 

in assuring optimal shrimp growth while minimizing waste production and controlling variable 

production costs. Feed formulation is also a critical consideration in terms of feed costs, and 

shrimp growth rates. In general, financial analyses show that small increases in direct costs such 

as feed can be more than offset by incremental increases in growth. However, inefficient feeding 

practices or increases in costs without consistent increases in growth have a strong negative 

effect on financial viability. Recent studies have indicated that controlled application of nutrientdense high protein feeds can improve growth performance when compared to lower protein diets 

offered on an iso-nitrogenous basis. As discussed below, the formulation of feeds can have an 

important indirect effect on the system microbial community. Inputs of carbon and nitrogen 

must be considered as part of overall management of the biofloc communities upon which 

system stability depends. Thus, some researchers suggest a lower protein feed formulation 

strategy to encourage heterotrophic biofloc production. Others rely more on nitrifiers in the 

biofloc recommending feeding strategies which rely upon careful control of application rates and 

use of nutrient-dense high protein feeds with highly digestible ingredients. 

Systems Engineering

The present production system technologies are based on well mixed raceways to assure 

resuspension of particulate matter. Flow and mixing are accomplished by aeration and/or 

injection of recirculated water in growout raceways and by use of aeration in nursery raceways. 

The high carrying capacities projected for the systems require external particle filtration 

fractionation or settling to reduce total suspended solid loads. High feeding rates in these 

systems require significant supplemental aeration in nursery tanks and addition of supplemental 

oxygen to meet demand of the target crop and of the water column microbial community. High 

rates of oxygen demand necessitate monitoring, alarm and backup systems to assure oxygen 

supply in the event of power failure. One of the most important engineering components is the 

design of the enclosures and supplemental heating which will be critical for maintenance of 

optimal growing temperatures year round in the U.S. Sustainability and operation of the systems 
95

away from the coast necessitates waste collection, treatment and return of treated water. 

Treatment systems should be designed to dewater and digest volatile solids; to promote 

denitrification reducing nitrate levels and restoring alkalinity; and to recover salts. By returning 

treated wastewater and supplementing for lost salts and trace minerals, system water quality can 

be maintained while minimizing the need for fresh seawater inputs and solid waste disposal. 

Biofloc Microbial Communities

When shrimp are reared at high densities without water exchange, a biofloc develops in the 

ponds that has several advantages for shrimp culture. These include increased recycling of waste 

and mineralization of nutrients within the system and improved water quality stability. The 

diverse microbial community in the biofloc-dominated systems is thought to increase 

competition with potentially pathogenic microbes including vibrios, reducing problems with 

non-excludable pathogens. In addition, the natural productivity associated with these bioflocs has 

been shown to provide growth enhancing factors which improve shrimp production. 

Additional research has been conducted on the dynamics of the microbial communities in these 

systems, methods for measuring microbial activity and some techniques for manipulation of the 

makeup of these communities. Research has demonstrated that typically, ponds undergo an algal 

bloom and crash. Typically bioflocs include an active heterotrophic community and varying 

levels of photoautotrophic activity. The relative mix of bacteria and algae with very high feed 

inputs into the system is dependant upon intensity of cropping of biofloc particles, resulting light 

levels, and nutrient balances within the system. Chemoautotrophic nitrifiers make up a third 

important component of the community in biofloc systems. Nitrification is a significant 

component of overall microbial activity serving to control ammonia and nitrite levels in the 

system once the community becomes established. High levels of nitrification necessitate 

supplementation or regeneration of system alkalinity. The relative balance between these 

community components may vary depending upon management inputs and philosophies. 

This roadmap focuses on a detailed review of super-intensive biofloc based shrimp production 

technologies to document key technology gaps and the most significant areas where innovation 

can lead to improved competitiveness. Although current configurations could compete in limited 

specialty markets, successful competition with commodity products will require significant 

reductions in production costs coupled with improvements in growth and production rates for an 

overall doubling in production efficiencies. Maintaining this level of improvement and 

translating it into industry growth in the short term will require integrated approaches which 

partner academic, government, and industry groups with appropriate resources. Translating 

these investments into economic gains will require not only the identification of areas where 

improvements would be most beneficial but also the directing of scientific resources towards 

outcomes which can be measured to document and assure progress. 

Economic Significance of the Innovation 

In 2006, penaeid shrimps represented the 6th largest aquaculture commodity produced in the 

world by volume, ranking second overall in terms of value (FAO The State of World Fisheries 

and Aquaculture 2006). According to the FAO Aquaculture Production Database, in 2005 
96

penaeid shrimp aquaculture was valued at over 10.6 billion dollars (FAO Fishstat Plus). Shrimp 

imports into the U.S. in 2006 were valued at 4.1 billion dollars accounting for 31 percent of total 

edible imports into the country (NOAA Fisheries of the United States 2007). Per capita 

consumption of shrimp in the U.S. has increased over 27% from 3.2 lbs in 2000 to a record 4.4 

lbs per person per year in 2006. The growing demand for shrimp in this country has been fueled 

by increasing world aquaculture production and declining shrimp prices. 

Although the U.S. has been a global leader in the development of technologies for shrimp 

production, U.S. shrimp aquaculture production has been declining. Historically, domestic 

aquaculture shrimp production has made a very limited contribution to total shrimp supply in the 

U.S. As a result, domestic aquaculture producers have taken whatever is the prevailing 

commodity shrimp market price. As prices have dropped, U.S. producers applying traditional 

production technologies have been unable to compete on commodity markets. The cost of 

producing shrimp in the U.S. is high due to land, labor, energy and effluent compliance costs. 

Growing seasons are limited constraining consistency in product availability. Regulatory 

burdens have also contributed to reduced competitiveness of the U.S. shrimp aquaculture 

industry. 

The present technologies overcome many of these constraints. Production levels of almost 

50,000 lbs per acre per crop are almost 5 times higher than typical intensive pond production 

rates and are 2.5 times higher than the most successful current intensive pond production levels. 

This increase in production density reduces the overall cost per unit area or volume and allows 

for intensification of management inputs. It also allows for enclosure of production systems 

which is crucial for biosecure year round production. It is this continuous production which can 

further multiply annual production levels by a factor of four to almost 200,000 lbs per acre per 

year. Most importantly, consistent year round production allows for staggering of crops and 

consistency in supply of fresh product that can be differentiated from commodity imports. In the 

long tern, research efforts should be directed at significantly reducing production costs to 

approach those of foreign producers. As innovations lead to improved productivity, production 

costs can be reduced allowing for industry expansion as system outputs become competitive with 

low cost foreign producers. 

The immense size of the U.S. shrimp market and growing consumer demand suggest a large 

initial market for fresh local products even with a significant mark-up over imported commodity 

shrimp. Each percentage point of market penetration in 2006 would have translated into 13.1 

million pounds of production. However, long term success and growth of the sector will require 

significant continued innovation to further reduce cost of production and improve 

competitiveness with commodity products. 

Crosscutting Non-Technical Barriers to Innovation 

Integration of Research and Commercialization Efforts

Some of the most important factors in reducing production costs are economies of scale. On the 

other hand, scale up of current technologies will involve significant opportunities for 

modifications in current experimental or pilot scale applications. The development of large-scale 

commercially viable demonstration projects supported by experts in current state of the art 
97

research scale systems has often been a missing link in public and private investments in 

technology development. This has, at times, resulted in lack of focus in experimental efforts 

aimed at promoting commercial scale technology development and in “reinventing the wheel” in 

some commercial scale operations. A new paradigm is needed targeting scientific research 

coupled with commercial scale applications applying a robust and diverse funding base. This 

could lead to solving short term problems associated with scale up while improving systems 

applications for improved competitiveness in the medium and long term. 

A blending of economic costs and biological decisions needs to be made. Modeling efforts 

which integrate economics and biological responses should be supported. Researchers need to 

identify critical areas to reduce costs and concurrently determine key factors limiting biological 

responses while improving understanding of interactions between the two. 

Regulatory Issues

Regulatory issues may also impede commercialization of these technologies in some 

jurisdictions. The species most amenable to production of food shrimp in biofloc systems is L. 

vannamei. These shrimp are amenable to high stocking rates, are able to take advantage of 

microbial productivity in biofloc systems, and most importantly, stocks are available which are 

free of a long list of excludable pathogens and have been selected for growth performance over 

many generations. As the species is not indigenous to the U.S., current regulations in some 

jurisdictions may limit or prohibit commercial aquaculture production. Similarly, issues related 

to siting of large scale projects relative to land costs, cost of seawater or sea salts, sociological 

factors, protection of ground waters, disposal of waste, biosecurity, etc. all require some 

regulatory input. It is the bewildering array of local, state, and federal regulatory agencies that 

can constrain industry development. A coherent best management practices-based one-stop 

regulatory authority could improve the outlook for commercialization of sustainable U.S. 

aquaculture industries. 

Economics

Economic modeling and planning is a key component of developing strategies to improve 

competitiveness. Accurate prediction of fixed and variable costs combined with effective 

sensitivity analyses will allow prioritization of efforts aimed at reducing production costs. 

Models can help define potential economies of scale and can provide a basis for examining cost 

effectiveness of efforts to improve energy efficiencies. 

Marketing and Processing

As described above, the price of commodity shrimp has been on a downward trend for several 

years. This can be attributed to increasing supplies of white shrimp and decreasing production 

costs as Asian pond production efficiencies improve and as production areas expand. While 

these trends have led to growing global markets and per capita consumption rates, dropping 

commodity prices decrease competitiveness of high cost technology intensive production 

systems. Thus, in the near term, some premium must be achieved over imported commodity 

shrimp to assure financial viability. Emphasis must be placed on the processing and marketing 

of better quality live/fresh/frozen shrimp products. Efforts to determine the magnitude of 

specialty fresh product and or branding premiums along with estimates of the depth of these 
98

markets would help in determining initial feasibility and potential scope of financially viable 

commercialization efforts which rely upon specialty marketing. This will require attention to 

post harvest processing techniques to market product forms most advantageous for 

differentiation from imported commodity shrimp. These efforts can be facilitated by 

measurement and certification of quality in terms of sustainability of production systems, flesh 

quality, food safety, and human health benefits. Credible eco-labeling efforts, organic 

certification and effective product branding offer additional opportunities for marketing 

premiums which can improve competitiveness. 

Technical Barriers to Innovation 

Health Management

The maintenance of the health of the shrimp under culture is a critical prerequisite to 

profitability. Health assurance begins with use of SPF stocks and control of facility biosecurity. 

Tools for the evaluation of health status on an ongoing basis to see subacute indications of 

declines in fitness are needed. Existing tools for rapid diagnosis and longer term confirmation of 

acute pathologies should be refined. Emerging non-listed pathogens and disease caused by nonexcludable pathogens will continue to be a problem. Pathogens need to be studied to develop 

diagnostics and improve basic knowledge. Methods to avert disease, immunostimulation and 

approved chemotheraputants for prophylaxsis or to treat disease outbreaks from non-excludable 

pathogens (including vibriosis) will be needed. This will necessitate better understating and 

control of microbial communities as addressed below. Improved appropriate applications for 

probiotics and better understanding of how to encourage growth of non-pathogenic microbes in 

the systems is necessary. Fundamental to these efforts are tools to measure immune status, 

fitness and health of the target crop on an ongoing basis. 

Seed Supply

Genetics and Breeding: A stable year round supply of healthy genetically improved fast 

growing robust postlarvae is a critical prerequisite to industry competitiveness. Basing 

production of food shrimp on L. vannamei provides an important advantage in that much effort 

has gone into the closing of its life cycle and genetic selection for this species. Today there are 

commercial companies in the U.S. devoted to development of SPF, disease-resistant breeding 

stocks of L. vannamei selected for fast growth. These efforts are currently devoted to producing 

stocks for shrimp production in open pond systems. A focused breeding effort targeting 

performance in these biosecure closed systems would speed improvement. This would also 

avoid potential selection for traits which may be of significance in open pond systems in Asia but 

which could be negatively correlated with growth and other critical performance characteristics 

in the more biosecure systems. Efforts related to selection for new traits relative to survivability 

or production related characteristics such as dress out percentage could also improve 

competitiveness if new strains are protected and used only in domestic production systems. In 

the long term, improvement of genomic enablement for the species will allow for discovery 

science that could lead to important breakthroughs enhancing production and fitness related 

traits. Measurement technologies in the area of genetics and breeding will include objective 

assessments of heritability, genetic gains, pedigree tracking, and inbreeding coefficients. 

Development of molecular tools should include markers for traits of interest and for stock 

identification, genome maps, and functional genomic tools such as microarrays. 
99

Seed Production: Maturation and hatchery technologies are well developed for L. vannamei

although further attention to scalability issues and development of closed system hatcheries have 

implications for vertical integration especially during early phases of industry development. 

Improvement of maturation systems technologies to enhance efficiency of systems engineering, 

to eliminate reliance on fresh feeds and to otherwise maximize reproductive performance would 

be beneficial if nauplii quality and systems efficiencies are increased. Larval culture systems 

improvements in areas of systems engineering should focus on physical characteristics such as 

mixing, microbiology, and water reuse technologies. Systems still rely on live feeds and 

continuing incremental improvements in developing artificial diets should improve production 

efficiency and consistency. Developments in additives like pre- and probiotics, disinfectants and 

nutrients to enhance microbial activity should be beneficial. Husbandry improvements in 

assessing larvae and postlarvae, harvest and counting methods and transport techniques could be 

envisioned. Measurement technologies in the area of maturation and larval rearing should focus 

on determination of water quality conditions and organic loading, fitness of the broodstock, 

nauplii, larvae and postlarvae, fecundity in terms of oocyte and sperm development, mating, 

spawning, egg production, fertilization, hatch and metamorphosis rates. Determination of 

mixing and settling rates, microbial community composition and activity, feed nutritional quality 

and water quality effects, effectiveness of probiotics and disinfectants, as well as accuracy and 

efficiency of PL quantification should improve competitiveness of hatchery operations. 

Production Systems

Systems engineering: Systems engineering for commercial scale applications of super-intensive 

closed system shrimp production technologies is one of the most important technical gaps to 

commercial competitiveness. It involves a highly complex set of issues which all interrelate, 

many of which are highly sensitive to changes in scale. First, the size, and type of enclosure for 

the systems is of paramount importance in terms of capital costs, energy efficiencies, and 

secondary effects on systems operations. Use of barn type structures, greenhouses or 

combinations of the two is a fundamental issue which relates back to importance of light, energy 

efficiencies and initial investment costs. Interrelationships between economic factors which vary 

by geographic location and biological factors which vary with operational methodologies 

complicate optimization. Second, optimal tank designs, dimensions, and materials may also vary 

according to specifics of the production system, relative cost and availability of materials in 

different parts of the U.S., and management philosophies. Alternative operational systems 

(automated where appropriate) for aeration and circulation, water heating, systems monitoring 

and control, filtration, waste treatment, water conditioning and reconditioning, and waste 

disposal offer many different potential options and solutions all of which have important 

implications for production efficiencies. Areas for which measurements could be applied to 

drive innovation aimed at simplifying operations and reducing costs include: efficiencies of 

water use; mixing and oxygen transfer efficiencies; heat transfers and energy efficiencies; 

accuracy of monitoring and control systems; effectiveness and cost of filtration alternatives; and 

waste treatment efficiencies. 

Feed Program

Feed is one of the most important components of variable costs. The feed is the driver of the 

system both in terms of nutrient inputs and shrimp performance. Feed effects on shrimp growth 
100

and production, both direct and indirect, are a major component of system financial returns. 

Feed nutrient quality, nutrient density and physical properties should be optimized to promote 

cost effectiveness, growth and condition. Management of feed inputs is critical to maximize 

growth while eliminating water quality deterioration from overfeeding, and optimize nitrogen 

conversion efficiencies from feed to shrimp. This would include the amount of feed offered, 

frequency, timing, opportunities for automation, etc. Feed additives including 

immunostimulants, gut microflora stimulants (prebiotics), probiotics, etc. can offer opportunities 

to improve shrimp growth, condition and feed conversion efficiency. Feeds and feeding must 

also be considered in the framework of overall system sustainability. The ratio of live weight 

unit of forage (reduction) fisheries used to produce one live weight unit of product is an 

important measure of long term sustainability of global fishery resources. Development of 

fishmeal and fish oil replacements are important in this regard and may become a prerequisite to 

organic certification. Finally, consideration of the flavor, appearance and human health 

characteristics of the final product depend upon feed inputs and may offer opportunities for 

development of specialty finishing diets. Application of measurement science to optimization of 

a feeds program in terms of costs, financial returns, and sustainability of the technology involves 

both traditional and new approaches. Methods for determination of digestibility, leaching, 

attractability, nutrient densities, nutrient toxicities, feed conversion efficiencies, shrimp 

performance and feed conversion efficiencies are well documented. Further efforts are necessary 

to better measure feed performance in these systems to better formulate feeds for this 

application. Some things can be measured in small scale systems allowing for quantification of 

contributions from system productivity and thereby optimizing formulations to supplement and 

not duplicate. More problematic is measurement of long term impacts of feeds in systems 

reusing water between crops. Buildups of excess nutrients and potentially toxic trace metals and 

anti-nutritional factors must be measured. New measures of conversion efficiency of marine 

proteins can enhance sustainability. Finally, measures of product palatability, appearance and 

quality in terms of human heath effects offer opportunities for optimizing diets and development 

of finishing diets with an eye towards improving competitiveness through product 

differentiation. 

Husbandry

In the general area of husbandry are some of the most significant challenges to stability and 

efficiency of production in biofloc-based systems. Maintenance of optimal water quality is a 

challenge in that system designs and cost prohibitions for inland systems preclude any significant 

use of seawater exchange to maintain growing conditions. At inland locations, protection of 

aquifers and waste disposal can be significant issues. Management of water quality must be 

accomplished through the exchange of water within the system and through the proactive 

maintenance of optimal biofloc communities in the systems over individual growing cycles and 

between multiple cycles over time. It is this management of biofloc communities which present 

one of the greatest opportunities for improvement in competitiveness and one of the greatest 

risks to consistency over time. Optimizing microbial communities will require improved 

understanding of relative advantages and disadvantages of the heterotrophic bacterial growth, the 

blooms and crashes of different species of algae, the relative activity of chemoautotrophs 

responsible for processes of nitrification and denitrification, as well as the effects of ciliate 

grazers and other zooplankton. Once strategies targeting specific community compositions and 

levels of microbial activity are designed, development of management protocols to achieve these 
101

ratios will be necessary. Techniques must be optimized for direct application of probiotics and 

algal inoculations, and indirect management through control of nutrients, filtration, light, etc. 

Management of long term water quality profiles must take into consideration build up of waste 

materials and nutrients from feed inputs and supplementation of micronutrients which may be 

depleted over time. Clearly, optimization of husbandry and system management will depend 

upon accurate measurement and analysis of traditional water quality parameters in real time. 

Development of targeted monitoring systems will be crucial to enable managers to react to 

changes in water quality. Innovation to optimize biofloc and water management for system 

productivity, profitability and sustainability will require new strategies for measuring community 

composition and activity. Better metrics for description or quantification of floc densities and 

improved understanding of the significance of measures like total suspended solids (TSS), 

volatile suspended solids (VSS), turbidity, light absorbance, etc. are needed. Community 

composition can be measured through direct microscopic observation and application of more 

indirect methods such as quantification of algal pigments, or analysis of bacterial strains using 

DGGE techniques. Measurement of activity will require accurate determination of oxygen 

fluxes due to respiration and photosynthesis or indirect measurements of changes in nitrogen 

species. Once accurate estimates are made, models can be developed to better understand carbon 

and nitrogen fluxes within the system. Similarly, correlations can be made with shrimp growth 

and fitness to optimize productivity if techniques can be developed to accurately determine 

shrimp survival, condition and growth in real time. 

Stocking and Harvesting of Nursery Systems

Nursery systems can contribute to increased profitability in a number of ways. They can provide 

for a buffer to accept PL from hatcheries as they become available. Better facility utilization, 

short-cutting growout cycles allows for higher production rates per unit area per year. A nursery 

can allow for quarantine and elimination of poorly performing batches of postlarvae in a timely 

manner particularly if a pre-stocking acclimation station is included in facility designs. This is 

particularly important when postlarvae are procured from outside sources. Survivability of 

juveniles can be more predictable than that of direct stocked postlarvae improving management 

during the production cycle. Benefits of nursery systems are maximized by efficient and rapid 

transfer of juveniles from nursery to growout. Optimizing design and operation of nursery 

systems depends upon appropriate sizing of production units coupled with efficient scheduling of 

stocking and harvest to allow for efficient cycling of on-growing systems. Development of more 

accurate methods to estimate survivability and performance of juveniles during this phase would 

improve management efficiency. Improved techniques for rapid accurate measurement of 

harvest biomass and condition of juveniles integrated with more automated and efficient transfer 

technologies could improve control during subsequent growout. 

Harvesting of Growout Systems

Improving overall competitiveness requires appropriate design and husbandry of growout 

systems as described above along with successful harvest strategies. Harvesting systems should 

be automated and should facilitate water recovery while assuring product quality. Effective postharvest handling techniques for live or fresh shrimp could improve quality delivered to the 

customer. Growers will need to design harvest timing strategies based on market demands and 

to develop alternative partial harvest techniques. These efforts will require good models of 

system economics, of risks associated with delayed harvest and of key market segments. Better 
102

control of molt synchrony would improve the percentage of high quality product. Measurement 

of compensatory growth and density effects on system productivity help optimize harvest 

strategies in general and partial harvest strategies in particular. Accurate assessment of product 

quality is a prerequisite to improvement of harvest and post harvest product handling. 

Clearly, there is an urgent need to build and operate pilot shrimp production systems in different 

locations to demonstrate to the aquaculture industry that the current technologies work and to 

compare comparative advantages of the production systems in various locations. 

Prioritized Technology Gaps

During the workshop, participants discussed and prioritized technical gaps to technology 

innovation for industry competitiveness. A tabular summary of technological areas, goals and 

technology constraints was complied during the first breakout session. Summaries were made 

for systems engineering, husbandry, feeds programs, health, seed supply, as well as economics 

and marketing as summarized in Tables 13-18 respectively. In each table, results of 

prioritization exercises are shown by numbers in parentheses. Participants prioritized all of the 

technology areas in the first exercise and then prioritized all of the technology gaps in a second 

round. 

After the workshop a final summary was complied and distributed to participants for comment. 

The priorities were ranked based on the following: 

• Feasibility. An evaluation of the scientific and technical potential for overcoming 

technological barriers. What is technically feasible? What can be accomplished through 

research? How difficult is it to overcome the barrier? 

• Importance/Relevance/Urgency. How pressing is the need? How critical to overall 

success is overcoming this particular gap? 

• Socio-economic Impact. Projections of expected benefits and consequences. Are results 

broadly applicable or narrowly focused? What is the relative return on investment made 

to overcome a gap? 

The following are final prioritized summaries of areas needing research and development effort 

for biofloc-based production systems technologies for the marine shrimp Litopenaeus vannamei 

with special emphasis on those areas with measurement needs. 

1. System Engineering and Life-Support Systems. Improve the cost-effectiveness of lifesupport technology. Improve system energy efficiency, particularly for maintaining 

water temperature. Establish standards and specifications for system engineering design, 

with the goal of improving production efficiency as measured by shrimp growth and 

production potential. Establish standard management techniques to establish, manage, 

and maintain the structure, abundance, and activity of stable biofloc communities that 

maximize contributions to shrimp growth and water quality management. Improve 

methods to collect, dewater, digest, and dispose of waste solids. Improve methods for 

denitrifying, desalting, and treating water to reclaim minerals for reuse. 
103

2. Genetic improvement. Continue to invest in robust selective breeding programs for 

penaeid shrimp. Develop new and use existing molecular tools to understand the genetic 

basis of shrimp production performance and disease resistance and apply discoveries to 

improve selection. Develop methods for monosex female production. 

3. Feeds and feeding. Develop feeds that maximize the efficiency of fishmeal use, 

minimize the ecological footprint of all ingredients, improve water quality, and maximize 

the contribution from biofloc to shrimp growth. Improve techniques for monitoring 

shrimp density and survival throughout growout in order to optimize feeding rates. 

4. Health and biosecurity. Improve understanding of the factors affecting shrimp health 

and fitness. Develop diagnostic tools that permit rapid assessment of stress and disease. 

Develop standard biosecurity protocols, including pathogen monitoring and disease 

control systems. Establish protocols for management response to early warnings of stress 

or disease. 

 

5. Value-added products. Develop products that can provide added value or some other 

premium quality over competitive products and can be distinguished in the market 

through branding or labeling. Examples include fatty acid enrichment, organic 

certification, and marketing live or fresh-never-frozen shrimp. 

6. Bio-economic models. Develop accurate, flexible, and user-friendly financial models 

that include sensitivity and risk analysis. Apply marketing studies to determine market 

depth for value added products. 

7. Larval culture. Develop replacements for live foods in larval culture. Establish standards 

for postlarval quality and fitness. Develop non-invasive methods to accurately count 

post-larvae and juveniles. 

 

Application of Measurement Science to Overcoming Technical 

Barriers 

For biofloc-based super-intensive shrimp systems, an example of a key technology gap and 

illustration related measurement science constraints is as follows. A key technical gap 

constraining competitiveness may be the management of the complex structure and activity of 

system microbial assemblages to promote shrimp performance, water quality and system 

assimilation efficiencies. The highly complex microbial communities in these systems include 

algal assemblages, complex bacterial communities, as well as grazers and larger zooplankton 

components. The activity of these microbes includes primary production, heterotrophic 

metabolism, as well as important chemoautotrophic processes of nitrification and denitrification. 

Development and application of management interventions depend upon effective measurement 

of impacts produced by the microbial community structure and function on shrimp performance. 

Examples of measurement technologies to document community structure include direct 

epifluorescent microscopic examination to facilitate enumeration of algae (450-750 nm 
104

chlorophyll cube), bacteria (DAPI (4',6-diamidino-2-phenylindole) staining with 320-520 nm 

DAPI cube), or cyanobacteria (525-725 nm rhodamine cube). Recent work with fatty acid 

profiling of the biofloc communities shows promising results for monitoring bacteria dynamics. 

Techniques such as DGGE, high-performance liquid chromatography (HPLC) analysis of algal 

pigments, pyrosequencing of DNA, biolog systems and others also can be used to better 

characterize these complex communities. In-situ continuous recording Chl a, phycocyanin, and 

phycoerythrin electrodes (YSI 6600 series Sondes) are being used to monitor changes in the algal 

community and to warn of cyanobacteria blooms. Continuous measurement of 

photosynthetically active radiation (PAR) available throughout the biofloc water column is being 

applied to better understand the drivers of microbial community structure. Other measures of 

physical structure such as suspended and volatile solids or biofloc particle size may be associated 

with or promoting of important taxa. Microbial biofloc communities exhibiting varying 

structures are being studied for potential supplemental nutritional value to shrimp through 

analyses for proximate analyses and detailed lipid analyses of fatty acid contributions. Promoting 

desired assemblages from both water quality and supplemental nutritional perspectives depends 

upon development of effective and efficient techniques for enumerating and/or qualitatively 

describing and characterizing relative and absolute abundance of the major functional microbial 

taxa. 

In addition to accurately describing biofloc community structure, reliably characterizing and 

measuring community metabolic activity is crucial for optimizing system processes and for 

achieving predictability in understanding system demands for oxygen, alkalinity, nutrients, 

minerals and other key inputs. Techniques applied to date have measured total system (including 

shrimp) primary production and respiration by short term removal of aeration and continuous 

recording of dissolved oxygen changes using YSI 6600 Sondes. Such measurements can be 

coupled with enhanced light-dark bottle measures of the microbial biofloc community using a 

rotating ambient water incubator to keep the biofloc in suspension and an automated titrator to 

ensure precise oxygen measurements. These approaches enable accurate prediction of oxygen 

demand in the system for both the microbial community and growing shrimp. Incorporation of 

specific metabolic inhibitors permit further description of the relative metabolic activity of 

prokaryotes, photoautotrophs, and chemoautotrophic nitrifiers. Additional direct short term 

measurements of changes in several chemical species in spiked samples permit quantification of 

nitrification and denitrification rates. Dynamic system models constructed from the 

measurements of biofloc community structure and function are being developed to better 

understand the drivers and control mechanisms of these systems with the goal of enhanced 

predictability and improved management strategies. 

Both the structural and functional community characterizations must be correlated with target 

crop performance and overall efficiencies. While most of the technologies described are 

research tools for improved understanding of these systems, it is essential that the most relevant 

measurement technologies for optimizing target crop productivity be identified, prioritized, and 

incorporated into routine management protocols. For example, research suggests that shrimp 

growth may be enhanced by a diatom-dominated algal community and inhibited by 

cyanobacteria attached to biofloc particles. The aquaculturist might then manage for a 

community that falls within certain limits of PAR light penetration by cropping solids while 

retaining sufficient particulate levels to maintain a functioning nitrification community sufficient 
105

to handle the loading rates of the system. Incorporation of a few other easily measured 

community-critical parameters such as silicate levels as well as the standard shrimp-critical 

parameters like dissolved oxygen will permit optimization of management protocols. Measuring 

the effect of the microbial community on shrimp performance is a complex undertaking which 

requires development of replicated systems which can be managed to reliably reproduce an 

optimal community structure and function. This type of holistic approach and systems outlook is 

constrained by the large numbers of variables which can have significant primary and secondary 

effects on performance. Much effort to accurately and dependably measure biofloc communities 

will be required to identify the key system drivers necessary for an efficient, economically 

competitive, technologically-based shrimp aquaculture industry in the United States. 

Measurement Science Gaps

During the workshop, participants selected priority technology gaps identified during the first 

breakout session for further discussion during breakout session 2. The second session addressed 

measurement parts of the technological gaps identifying measurement standards and needs which 

can foster this innovation and lead to new technical breakthroughs. The results of this second 

breakout session are shown in Table 19. Although preliminary, these lists suggest important 

areas where targeted science focused on standards and measurement techniques can lead to 

innovation and to development of means to track progress over time. 

Roadmapping Exercise 

On the final morning of the workshop participants worked on building a first draft of a 

technology roadmap for biofloc-based production systems technologies for the marine shrimp 

Litopenaeus vannamei. In the exercise, participants explored an extended look at the future of 

the technology and, where possible, to apply metrics to drive innovation and improvement in key 

areas. The result is a preliminary list of technology needs organized according to short, medium 

and long term goals. The results provide an initial diagram that lays out a vision for future 

development, give examples of specific measurable objectives, and suggest a plan for moving 

the technology forward over time. The exercise was limited in time and scope and the 

preliminary draft results are presented in Figure 1. However, this type of planning exercise can 

drive the development of a mix of focused research activities with measurable goals aimed at 

driving technology innovation forward. 
106

Table 13. Breakout group report on shrimp biofloc production systems engineering. Numbers in 

parentheses indicate number of votes assigned to each item during the prioritization exercise for technology 

areas and technology gaps 

Technology Area Goals Technology Gaps 

Buildings/greenhouses (8) Enclose systems cost effectively for 

energy efficiency and for conditions 

which support biofloc and shrimp 

performance. 

• Designs that can be thermally adaptive 

and efficient (4) 

• Systems that provide natural light; 

compare systems that use sunlight 

(natural) and sunlit systems (quality of 

light) (2) 

• Structural integrity, corrosion (1) 

• Ventilation requirements and moisture 

control (0) 

• Span – cost/benefit (0) 

Production units (15) Design cost effective production units 

for simplicity, and maximum 

performance and operability. 

• Dimensions/size/design (including size of 

property and greenhouse; shape) (7) 

• Depth (2) 

• Artificial substrates (3) 

• Materials (0) 

Aeration, circulation and 

oxygenation (8) 

Assure adequate dissolved oxygen 

levels and efficient mixing. 

• Tank hydraulics (methodology) (0) 

• Water movement technologies (1) 

• Air or oxygen delivery systems (2) 

• Gas balance; CO2 (0) 

Water heating (6) Maintain temperatures at set levels 

within acceptable limits (+/- 1) 

• Heat delivery (0) 

• Efficiency/Insulation of system (1) 

• Exchange (0) 

• Heating-cooling (0) 

• Solar/alternate heat sources (0) 

• Biofloc = biofuel (0) 

• Heat recovery (1) 

Monitoring and control 

systems (8) 

Apply cost effective monitoring and 

control to facilitate management and 

protect crops 

• Photosynthesis (1) 

• Dissolved oxygen monitoring (2) 

• Microbial structure and activity (1) 

• Population size/total biomass (animal) 

(10) 

• Equipment monitoring and feedback 

(remote) (0) 

Filtration systems (8) Provide cost effective options for 

cropping of biofloc to manage 

microbial community structure 

abundance and activity 

• Floc cropping methods (7) 

• Hybrid systems – external/internal 

biofiltration (3) 

Waste management and 

treatment (26) 

Develop effective methods for 

collecting, dewatering, digesting, 

denitrifying, and desalting waste and 

for treating water and minerals for 

reuse. 

• Separate biofloc management (9) 

• Ozone use (1) 

• Phosphates (0) 

• Digestion of solids. Minimize feed waste. 

Methane production (2) 
107

Table 14. Breakout group report on shrimp husbandry in biofloc systems. Numbers in parentheses indicate 

number of votes assigned to each item during the prioritization exercise for technology areas and technology 

gaps 

Technology Area Goals Technology Gaps 

Water quality (15) Assure optimal water quality at all times while 

minimizing water use within and between 

crops 

• Define optimal parameters (3) 

• Frequency of measurement (0) 

• Initial treatment of incoming water (0) 

• Salt/salinity (ion concentration) (5) 

• Micronutrients (0) 

• Nutrient model, pathways (0) 

• Alkalinity (3) 

• Trace mineral depletion over time (0) 

• Denitrification (6) 

Biofloc 

development and 

management (25) 

Manage systems to establish and maintain 

biofloc communities which maximize 

contributions to shrimp growth and water 

quality management 

• Microbial community structure and 

activity, is light needed, bacteria versus 

algae (7) 

• Control, stability, C:N ratios (5) 

• Inoculation/Start up (1) 

• Preparation /optimum density (4) 

• Pre-/pro-biotics (1) 

Nursery systems 

harvest and 

transfer (2) 

Establish harvest and transfer protocols which 

minimize stress and promote management of 

growout phase 

• Stocking number estimations (5) 

• Optimal size and density (0) 

• Multiple staging/direct stocking (0) 

• Handling and transfer stress (0) 

• Transfer protocols (0) 

• Juvenile fitness (0) 

Growout (Final) 

harvest logistics 

(3) 

Apply harvest techniques which are efficient 

and contribute to product quality 

• Stress management (0) 

• Multiple staging (0) 

• Live harvest techniques/equipment (2) 

• Partial harvesting (5) 

• Chill-chain (0) 

• Grading (0) 

• Hazard Analysis Critical Control Point 

(HACCP) procedures (0) 

Water quality (15) Assure optimal water quality at all times while 

minimizing water use within and between 

crops 

• Define optimal parameters (3) 

• Frequency of measurement (0) 

• Initial treatment of incoming water (0) 

• Salt/salinity (ion concentration) (5) 

• Micronutrients (0) 

• Nutrient modeling, pathways (0) 

• Alkalinity (3) 

• Trace mineral depletion over time (0) 

• Denitrification (6) 

Biofloc 

development and 

management (25) 

Manage systems to establish and maintain 

biofloc communities which maximize 

contributions to shrimp growth and water 

quality management 

• Microbial community structure and 

activity, is light needed, bacteria versus 

algae (7) 

• Control, stability, C:N ratios (5) 

• Inoculation/Start up (1) 

• Preparation /optimum density (4) 

• Pre-/pro-biotics (1) 
108

Table 14 (continued). Breakout group report on shrimp husbandry in biofloc systems. Numbers in 

parentheses indicate number of votes assigned to each item during the prioritization exercise for technology 

areas and technology gaps

Technology Area Goals Technology Gaps

Nursery systems 

harvest and 

transfer (2) 

Establish harvest and transfer protocols which 

minimize stress and promote management of 

growout phase 

• Stocking number estimations (5) 

• Optimal size and density (0) 

• Multiple staging/direct stocking (0) 

• Handling and transfer stress (0) 

• Transfer protocols (0) 

• Juvenile fitness (0) 
109

Table 15. Breakout group report on shrimp feed programs for biofloc systems. Numbers in parentheses 

indicate number of votes assigned to each item during the prioritization exercise for technology areas and 

technology gaps (NR not ranked, added after the exercise) 

Technology Area Goals Technology Gaps 

Physical 

characteristics (3) 

Enable feeds which attract shrimp 

and maintain optimal physical 

characteristics until consumed 

• Water stability/leaching, Extrusion/pellet (1) 

• Density (1) 

• Particle size (0) 

• Buoyancy (0) 

• Hardness/fines/durability (1) 

Nutrient quality, 

density, toxicity (4) 

Optimize feed formulations to meet 

nutritional demands to maximize 

growth and production while 

maintaining water quality 

• Digestibility/nutrient availability (2) 

• Attractants (0) 

• Palatability (0) 

• Nutritional requirements (NR) 

• Storage time (shelf life) (0) 

• Effect on human health/nutrition (0) 

• Ingredient costs efficiency (2) 

• Toxic factors (0) 

Relationship with 

contributions from 

bioflocs (9) 

Maximize contributions of natural 

productivity by designing 

complementary feeds 

• Requirements (1) 

• Specially-designed diets (NR) 

• Relationship between feed and biofloc 

management (NR) 

• Feed – biofloc (NR) 

• Biofloc- shrimp (growth factor)(NR) 

Pre- and pro-biotics 

(0) 

Maximize contributions of gut 

microflora to shrimp performance 

• Efficacy (0) 

• Strains(0) 

Feeding timing, 

frequency, amounts 

(9) 

Optimize feeding protocols for 

maximum economic return 

• Automation/feed delivery/frequency (2) 

• Relationship with oxygen demand (0) 

• Demand/feed trays(2) 

Sustainability - 

fishmeal fish oil 

replacement (12) 

Maximize shrimp edible flesh 

production per pound of edible fish 

input 

• Approach zero inclusion (2) 

• Alternative proteins (10) 

• Alternative oils/human health (2) 

Sustainability of 

other ingredients (0) 

Minimize the ecological footprint of 

all feed ingredients 

• Toxicity factors (0) 

• Algal supplements (0) 
110

Table 16. Breakout group report on shrimp health in biofloc systems. Numbers in parentheses indicate 

number of votes assigned to each item during the prioritization exercise for technology areas and technology 

gaps (NR not ranked, added after the exercise) 

Technology Area Goals Technology Gaps 

Fitness (6) Maintain optimal shrimp health and 

fitness 

• Shrimp condition (growth/survival) (11) 

• Activity – morbidity (0) 

• Shell quality (0) 

• Immune system response (0) 

• Stress test (0) 

• Baseline (0) 

Disease (9) Accurately diagnose disease and have a 

working understanding of significant 

pathogens and pathologies. 

• Disease ID/diagnostics (1) 

• Real time Pathogen monitoring (NR) 

• Emerging pathogen (2) 

• Pathogen control (6) 

• Beneficial versus bad bacteria (0) 

Biosecurity (6) Exclude pathogens through effective 

biosecurity protocols, escapement, 

toxicity, and predation 

• Pathogen control (disinfection) (2) 

• Detection/toxicity monitoring (0) 

• Vector/predator monitoring/management (2) 

• Escapement monitoring (0) 

• Exclusion (0) 

• Inputs (feed/water) (0) 

Chemotheraputants 

(0) 

Control infectious disease with safe and 

effective treatments. 

• Approved drugs by life stage (1) 
111

Table 17. Breakout group report on shrimp seed supply for biofloc systems. Numbers in parentheses 

indicate number of votes assigned to each item during the prioritization exercise for technology areas and 

technology gaps (NR not ranked, added after the exercise) 

Technology Area Goals Technology Gaps

Genetic selection and 

breeding and Molecular 

biology (25) 

Assure access to genetically 

improved stocks; Enable molecular 

tools for improving the understanding 

of the genetic basis for shrimp health 

and production performance 

• Genotyping, molecular identification 

(1) 

• Diversity preservation (4) 

• Multi-species breeding program (NR) 

• Selection programs (14) 

• Heritability (0) 

• Marker assisted selection (0) 

• Genome mapping (0) 

• Genetic protection, Monosex (4) 

Maturation systems (1) Consistently produce desired 

quantities of high quality healthy 

nauplii cost effectively 

• Broodstock feeds / pelleted (3) 

• Recirc systems (0) 

• Intensive broodstock production (0) 

• Spawning water reconditioning (1) 

Larval culture systems (0) Consistently produce desired 

quantities of high quality PL cost 

effectively. 

• Recirc systems (2) 

• Pre- and pro-biotics (0) 

• Year round supply availability (0) 

• Live feed replacements (0) 
112

Table 18. Breakout group report on shrimp economics and marketing for biofloc systems. Numbers in 

parentheses indicate number of votes assigned to each item during the prioritization exercise for technology 

areas and technology gaps (NR not ranked, added after the exercise) 

Technology Area Goals Technology Gaps

Modeling and business 

planning (14) 

Develop and refine accurate financial 

models which are flexible and user friendly 

• Accessibility to all, User friendly (0) 

• Bioeconomic models (tied to 

biological performance) (7) 

• Inclusion of environmental 

sustainability (5) 

• Regulatory compliance costs (0) 

• Sensitivity analyses, risk assessment 

and uncertainty (2) 

• Geographic sensitivity (1) 

Flesh Quality (5) Demonstrate shrimp flesh quality which 

outperforms competition 

• Contaminants (NR) 

• Taste, flavor (biofloc effects (3) 

• Organoleptic analysis (NR) 

• Firmness (2) 

• Shelf life, Melanization, 

hepatopancreas condition (1) 

Processing (14) Assure post harvest methods which 

differentiate and bring out qualities to 

provide a competitive advantage in the 

marketplace 

• Irradiation (1) 

• Byproduct use (chitin) (5) 

• Automation (7) 

• On farm HACCP procedures – food 

safety (0) 

• Melanization control (0) 
113

Table 19. Breakout group report on measurement standards and needs for biofloc-based shrimp production 

systems 

Technology Gap What are the measurement or standards needs? 

Shrimp fitness • Activity 

• Feed consumption 

• Systematic health screening checks 

• Lesions 

• Gut fullness/content analysis 

• Biochemical indices 

• Physiological indices (hematocrit) 

• Color 

• Stress response 

• Mouth and gill exams 

• Muscle opacity 

• Condition factor (weight and carapace length) 

• Uniformity of size 

• Diseases 

• Deficiencies 

Crop biomass inventory • Video 

• Activity 

• Sonar 

• Waste collection 

• Mortalities 

• Feed consumption 

• Stocking 

• Stocking mortality 

• Sampling (sub selections and tag and release etc.) 

• Oxygen consumption 
114

Table 19 (continued). Breakout group report on measurement standards and needs for biofloc 

based shrimp production systems

Technology Gap What are the measurement or standards needs? 

Waste management and treatment. Technologies 

to manage nitrogen within the system, to 

maximize N and P conversion efficiencies, to 

reclaim salt and to digest sludge. 

• Filtration efficiencies 

• Settling efficiencies 

• Percent recovery of solids (solids/kg shrimp) 

• Percent recovery of salt (salt use/kg shrimp) 

• Chloride content of waste 

• Nitrogen utilization efficiency 

• Carbon, nitrogen and phosphorous modeling and budgeting 

• Water use efficiency 

• Measurement of phosphorous and other micronutrient 

discharge 

• Relationship of feeds formulation, digestibility, nutrient 

requirements 

• Micronutrient and macronutrient depletion and 

accumulation 

• Alkalinity consumed (bicarbonate used/kg shrimp) 

• Measuring the reduction of organic material 

Genetic improvement • Breeding value and heritability 

• Genetic markers 

• Persistence of a trait 

• Genetic component of growth and survival 

• Disease resistance 

• Real life commercial trials 

• Comparison with baseline wild stock 

• Genomics 

• PL quality (physiological) 

Production unit design • Standardize production metrics 

• Measurement of hydrodynamics 

• Heating efficiencies 

• Oxygenation efficiencies 

• Variable cost efficiencies (energy) 

• Lighting 

• Density 

• Unit cost (per cubic meter of capacity or kg shrimp) 

• Space utilization efficiencies (2 and 3-dimension) 

• Ergonomic designs 

• Personnel usage efficiency 

• Safety 
115

Table 19 (continued). Breakout group report on measurement standards and needs for biofloc-based shrimp 

production systems 

Technology Gap What are the measurement or standards needs? 

Biofloc management • Density, Turbidity, TSS, VSS, etc. 

• Autotroph vs. heterotroph (structure and activity) 

• Composition 

• Light and epifluorescent microscopy, image analysis 

• Fluorometrics 

• Molecular techniques (DGGE, PCR etc.) 

• Isotope studies (nutritional uptake, conversion) 

• DAPI 

• fluorescence in situ hybridization (FISH) 

• Stability, consistency 

• Reproducibility 

• Beneficial: pathogenic ratio 

• Harmful algal species (presence, abundance) 

• Cyanobacterial abundance and control 

• Nutrient composition analysis 

• Floc consumption rates, vitamin and amino acid availability 

• Automated measurements 

• Harvest on pre-set level 

• Hydraulic residence time (HRT)/Floc age 

• Photosynthetically active radiation availability 

• Fatty acid composition 

• Oxygen production and consumption 

• Floc particle size 

• Floc growth inhibitor (pathogens, toxins) 

• Floc effect on shrimp 

• Number of protozoans 

• Trophic composition 

• Algal inoculation success 

• Carbon:nitrogen ratio of floc 

• Standardize measurements to understand or effect 

management input 
FIGURE 1. Initial roadmap diagram for future development of biofloc-based production systems for marine shrimp Litop

Examples are given of specific measurable objectives suggesting a plan for moving the technology forward 

Near Term

High quality consistent reliable year round seed supplies. Genetic pedigree tracking. Track estimated breeding values. Apply seed quality metrics.Shrimp fitness and growth rates. Production (4-8 kg/m3). Performance consistency. Survival and inventory control.Production system engineering and design. Process models. Efficiency metrics <500 1/kg. <7 kwh/kg salt use/kg.Biofloc control. Waste Management. Bicarbonate use/kg solid waste produced/kg.Feed quality and management. Environmental sustainability. Efficiency metrics: FCR, fish biom a ss/kg Nitrogen transformation efficiency (N=30%). Carbon footprints.Specialty MarketsEconomic Models. $/kgConsumer education

Genetic Improvement. EBV increase of 0.04 g/wk/gen. Improve survival and new production traits. Apply molecular markers, functional genomic tools.Diagnostic tools. Focus on non-excludable pathogens. Molecular treatments and new theraputants. Emerging pathogens.Performance improvements. Production (8-16 kg/m3) . Improving efficiency: cost/kg. Advanced systems engineering. Increased energy efficiency <250 1/kg <5 kwh/kg.Optimization and standardization of Floc. Waste byproduct use. Feed/System interactions. Feeding efficiencies: FCR, FCE (Nitrogen conversion = 50%).

Genetically improvestablish new EBV assisted selection. Transgenic stocksReceptor knockouand improved perfPerformance impro(16-32 kg/m3)Improving efficiencFully automated pkwh/kg <100 1/kgEnergy production waste.New ingredientsIncorporation of byconversion = 75%)

Medium Term Lon

New product development. Organic and other value added. Increased shelf life. Branding.

Consumer prefereOutcompete comm
117

Shrimp Culture Sub-Group Members 

Sub-Group Chair: Craig L. Browdy, Assistant Director, Marine Resources Research 

Institute, South Carolina Department of Natural Resources 

Sub Group Members

Tony Ostrowski, Vice President, Oceanic Institute - Director US Marine Shrimp Farming 

Program 

Clete Otoshi, Oceanic Intitute – Shrimp production systems 

Jeff Lotz, University of Southern Mississippi – Shrimp health and shrimp production systems 

Don Lightner, University of Arizona – Shrimp health 

Tzachi Samocha, Texas Agrilife Research, Texas A&M University Shrimp hatchery and 

production systems 

Addison Lawrence, Texas A&M University – Shrimp nutrition 

Terry Hanson, Mississippi State University – Economist 

Allen Davis, Auburn University – Shrimp nutrition and production 

Lorenzo Juarez, Shrimp Improvement Systems – Shrimp breeding and hatchery 

Tomas Losordo, NC State University – Engineering 

Benedict Posadas, Mississippi State University – Shrimp economics marketing and processing 

Peter Van Wyk , Scientific Associates LLC – Shrimp production systems 

Jose Villalon, World Wildlife Fund – Shrimp sustainability and certification 

David Brune, Clemson University – Engineering and shrimp production systems 

Doug Ernst, Natural Shrimp Co. – Shrimp production systems 

Jim Anderson, Magnolia Shrimp Farm – Shrimp systems commercialization 

Bart Reid, Organic Aquaculture Institute – Shrimp production 

Fritz Jahncke, Harlingen Shrimp Farms – Shrimp hatchery and production 

Mike Timmons, Cornell University – Engineering 

Doug Jones, National Institute of Standards and Technology – Project manager
118

Registered Participants 

1. Bruce Anderson, Oceanic Institute 

2. Paul Anderson, University of Florida 

3. Frederic Barrows, USDA-ARS 

4. Dan Bearden , NIST 

5. Peter Becker, Little Skookum Shellfish 

Growers LLC 

6. Diane Bellis, United Soybean Board 

7. Daniel Benetti, RSMAS University of 

Miami 

8. David Bengtson, University of Rhode 

Island 

9. David Berlinsky, University of New 

Hampshire 

10. Reginald Blaylock, University of Southern 

Mississippi 

11. Peter Blyth, AQ1 Systems 

12. Brian Boudreau, Magnolia Shrimp LLC. 

13. Colin Brannen, World Wildlife Fund 

14. Nathan Brennan, Mote Marine Laboratory 

15. Craig Browdy, SCDNR Waddell 

Mariculture Center 

16. Nick Brown, Center Cooperative 

Aquaculture Research 

17. Mark Camara, USDA - Agricultural 

Research Service 

18. Jim Carlberg, Kent Seatech 

19. Michael Chambers, University of New 

Hampshire 

20. Jesse Chappell, Fisheries Dept. Auburn 

University 

21. Daniel Cheney, Pacific Shellfish Institute 

22. Steven Craig, Virginia Tech 

23. Christopher Davis, Maine Aquaculture 

Innovation Center 

24. D. Allen Davis, Fisheries Dept. of Auburn 

University 

25. Megan Davis, Harbor Branch 

Oceanographic Institution 

26. Bill Dewey, Taylor Shellfish Company 

27. Walton Dickhoff,, NOAA Fisheries 

28. Helen Dixon, Mariculture, Inc 

29. Mark Drawbridge, Hubbs-SeaWorld 

Research Institute 

30. Douglas Drennan, Aquaculture Systems 

Technologies, LLC 

31. Patricia L. Duncan, Fort Valley State 

University 

32. James M. Ebeling, Aquaculture Systems 

Technologies, LLC 

33. Doug Ernst, NaturalShrimp Corp. 

34. George Flick, Virginia Tech 

35. Vance Flosenzier, Pisces Innovations LLC 

36. John Forster, Forster Consulting, Inc. 

37. Don Freeman, USDA, ARS, SNARC 

38. Mike Gafford, Hubbs-SeaWorld Research 

Institute 

39. Ryan Gandy, Bay Shellfish Co. 

40. Brian Gelder, AquaVentures LLC 

41. Andrew Giesen, Novus International Inc. 

42. Chris Good, The Freshwater Institute 

43. Clifford Goudey, Massachusetts Institute 

of Technology 

44. Gil Griffis, United Soybean Board 

45. Terry Hanson, Mississippi State University 

46. Steven Hart, Indiana Soybean Alliance 

47. William Hawkins , Gulf Coast Res Lab, 

Univ Southern Miss 

48. Chuck Helsley, Univ. of Hawaii at Manoa 

- SOEST 

49. Curtis Hemmel, Bay Shellfish Co. 

50. Yosuke Hirono, Aquatic Eco-Systems, Inc. 

51. G. Joan Holt, UT Marine Science Institute 

52. Armen Hovnanian, NA 

53. Paul Hundley, HDR-FishPro 

54. Fritz Jaenike, Harlingen Shrimp Farms, 

Ltd. 

55. Tomas Jamir, NOAA/NMFS-Southeast 

Science Center 

56. Gary Jensen, USDA-CSREES 

57. Tom Johnson, HDR FishPro 

58. Doug Jones, NIST 

59. Lorenzo Juarez, Shrimp Improvement 

Systems 

60. John Kucklick, NIST 

61. Richard Langan, University of New 

Hampshire 

62. Addison Lawrence, Texas A&M 

University 

63. Andy Lazur, University of Maryland/Sea 

Grant 

64. Kenneth Leber, Mote Marine Laboratory 

65. George Leonard, Ocean Conservancy 

66. Morey Levovitz, GreatBay Aquaculture 

67. Scott Lindell, Marine Biological 

Laboratory 

68. Doug Lipton, University of Maryland 
119

69. Jeff Lotz, Gulf Coast Research Lab 

70. Susan Lovelace, Hollings Marine 

Laboratory/NOAA 

71. Kevan Main, Mote Marine Laboratory, 

Inc. 

72. Lori Marsh, Virginia Tech 

73. Steve Massar, Scientific Associates 

74. Ignacio Masson, Gulf Coast Research 

Laboratory 

75. Desmond Maynard, NOAA Fisheries 

Service 

76. Ewen McLean, Virginia Tech 

77. Gary E. Miller, Advanced Aquacultural 

Technologies, Inc. 

78. Barbara Montwill, Food and Drug 

Administration 

79. George Nardi, Great Bay Aquaculture 

80. Kate Naughten, NOAA Aquaculture 

Program 

81. Ana Nobre, Faculdade de Ciências e 

Tecnologia 

82. David O'Brien, NOAA Aquaculture 

Program 

83. Paul Olin, California Sea Grant 

84. Clete Otoshi, Oceanic Institute 

85. Steve Page, Ocean Farm Technologies Inc. 

86. Tim Pfeiffer, USDA, ARS, SNARC 

87. Paul Picard, Pond Pros LLC 

88. Mikki Powers, Nutra Fish 

89. Andrew Ray, S.C. Department of Natural 

Resources 

90. Bart Reid, Organic Aquaculture Institute 

91. Robert Rheault, ECSGA / Moonstone 

Oysters 

92. Marty Riche, USDA, ARS 

93. Mills Rooks, Ocean's Bounty Seafarms, 

LLC 

94. Michael Rubino, NOAA Aquaculture 

Program 

95. Dave Russell, Virginia Cobia Farms 

96. Michael Rust, NOAA/Northwest Fisheries 

Science Center 

97. Tzachi Samocha, TAES-Shrimp 

Mariculture Research Lab. 

98. Paul Sandifer, Hollings Marine Lab 

99. Linda Beth Schilling, NIST 

100. Michael Schwarz, Virginia Tech 

101. Jeffrey Silverstein, USDA, ARS 

102. Neil Anthony Sims, Kona Blue Water 

Farms 

103. Brian Small, USDA, ARS, Catfish 

Genetics Unit 

104. Peter Smith, W.S. Nelson and Co., Inc. 

105. Al Stokes, SCDNR Waddell Mariculture 

Center 

106. Fred Story, Oceans Bounty Partners 

107. John Stubblefield, Center of Marine 

Biotechnology, UMBI 

108. Steven Summerfelt, Conservation Fund 

Freshwater Institute 

109. Paula Sylvia, Hubbs-SeaWorld Research 

Institute 

110. Yossi Tal, Center of Marine 

Biotechnology, UMBI 

111. Jesse Trushenski, Southern Illinois 

University 

112. Wayne Van Toever, Alchem Industries 

113. Peter Van Wyk, Scientific Associates 

114. Jesus Venero, SCDNR Waddell 

Mariculture Center 

115. Jose Villalón, World Wildlife Fund 

116. Humberto Villarreal, CIBNOR, S.C. 

117. Wade Watanabe, University of North 

Carolina Wilmington 

118. David Weinstein, Dawson James 

Securities 

119. Chuck Weirich, USDA, ARS, SNARC 

120. Katherine Wellman, Northern Economics, 

Inc. 

121. Fred Wheaton, University of Maryland 

122. Susan White, Hollings Marine Laboratory 

123. Terhea Williams, University of Maine 

124. Paul Wills, Harbor Branch Oceanographic 

Institution 

125. Paul Zajicek, Florida Dept. of 

Agriculture/Div. of Aquaculture 

126. Gintautas Zavadzkas, AcuaGenesis Int. 

LLC 

127. Thomas R. Zeigler, Zeigler Bros., Inc. 

128. Yonathan Zohar, Center of Marine 

Biotechnology, UMBI
120

 LIST OF ACRONYMS

C Celsius 

C carbon 

Chl a chlorophyll a 

CO2 carbon dioxide 

CZMA Coastal Zone Management Act 

DAPI 4',6-diamidino-2-phenylindole 

DGGE denaturing gradient gel electrophoresis 

DNA deoxyribonucleic acid 

EPA Environmental Protection Agency 

FAO Food and Agriculture Organization (of the United Nations) 

FDA Food and Drug Administration 

GIS geographic information system 

HAB harmful algal bloom 

HACCP Hazard Analysis Critical Control Point 

HCP heat-cool pasteurization 

HHP high hydrostatic pressure 

HRT hydraulic residence time 

IQF individually quick frozen 

kg kilogram 

L. Litopenaeus 

lbs pounds 

m meter 

MT metric ton 

N nitrogen 

NIST National Institute of Standards and Technology 

nm nanometer 

NOAA National Oceanic and Atmospheric Administration 

NPDES National Pollution Discharge Elimination System 

P phosphorus 

PAR photosynthetically active radiation 

PCR polymerase chain reaction 

pH the measurement of the concentration of hydrogen ions in a solution 

PHP post harvesting processing 

PL post larvae 

PSI Pacific Shellfish Institute 

RAS recirculating aquaculture system 

SPF specific pathogen free 

TSS total suspended solids 

U.S. United States 

USDA U.S. Department of Agriculture 

UV ultraviolet 

VSS volatile suspended solids