Abstract:
A system and a method for producing biomass from a mixed community of algal species. The method comprises the steps of culturing the mixed community of at least two algal species as biofilms on transparent surfaces having structural features and an optical filter, providing a continuous supply of a culture medium comprising at least 0.5 mol/L aqueous (bi)carbonate and having a pH greater than 9. The method disclosed herein facilitates online monitoring of mixed community productivity by the quantification of oxygen production.

Description:
TECHNICAL FIELD 
       [0001]    This disclosure relates to phototrophic production of biomass. More specifically, this disclosure pertains to use of biofilms of phototrophic microbial communities to produce biomass for downstream processing into fuels. 
       BACKGROUND 
       [0002]    Fossil fuels are a non-renewable fuel source and their combustion results in the emission of the greenhouse gas carbon dioxide, with potential detrimental effects on Earth&#39;s ecosystems. Biofuels could offer a sustainable alternative for fossil fuels, yet the growth of terrestrial energy crops has severe environmental and socio-economic consequences. Using aquatic oxygenic microalgae, such as unicellular algae and cyanobacteria, as feedstock for biofuel production eliminates the drawbacks associated with growing terrestrial energy crops. The cultivation of unicellular algae and cyanobacteria does not compete with food or feed crops for arable land and water, since it does not require fertile soil and fresh water. Furthermore, the biomass yield of aquatic oxygenic phototrophs can be about one order of magnitude higher than that of terrestrial crops. 
         [0003]    Currently, several aspects of algal production limit a widespread use. For example, the required input of fossil fuels for the construction and operation of algae growth systems often surpasses the energy content of the produced biofuel, resulting in a negative energy balance. The monetary costs of growing algae for biofuel production are also too high to make algal biofuel economically competitive with fossil fuel. Because of its high cost, the current practice of growing algae mainly aims at high value products such as pharmaceuticals and food additives, instead of biofuels. 
         [0004]    Large-scale cultivation of photosynthetic microorganisms is usually performed in open ponds, raceway ponds, or tubular photobioreactors. A major drawback of open and raceway ponds is that only low concentrations of cells are achieved. This is caused by limitations in light penetration: only the cells at the very top layer in the pond are exposed to light, while the cells at the lower layers are shaded. This low cell concentration translates in very low volumetric productivities. 
         [0005]    Light limitation in tubular photobioreactors is partially alleviated by actively circulating the cells by mixing. Incorporation of mixing leads to increased cell density and reduced light saturation in the cells, but does so at the expense of increased energy input into the cultivation system. Furthermore, oxygen accumulation in the tubular photobioreactors commonly results in the inhibition of photosynthesis. 
         [0006]    The poor technological and economic performance of contemporary algal biofuel production systems has been attributed to a number of factors. Operational costs and energy consumption are high because the gas containing the CO 2  needs to be bubbled through bioreactors filled with diluted algae and the operation of the compressors for the gas bubbling consumes electricity. For example, the forced supply of CO 2  can make up ca. 50% of the cost of biomass production in a raceway pond system with a production rate of 3.0-3.6 kg m −2 d −1  (Slade et al., 2013,  Micro - algae cultivation for biofuels: Cost, energy balance, environmental impacts and future prospects.  Biomass and Bioenergy: 29-38). Others have estimated the cost of CO 2  inputs to be 36.5% of the total raw materials and utilities cost for the production of dry biomass of  Scenedesmus almeriensis  at a scale of 200 ton yr −1  (Acién et al., 2012,  Production cost of a real microalgae production plant and strategies to reduce it. Biotechnology Advances,  30: 1344-1353). 
         [0007]    Downstream processing of suspended algal cells into energy carriers requires an energy- consuming concentration step. Consequently, some processes use algal biomass for anaerobic digestion because less-concentrated algal feedstocks can be used than are required for the extraction of algal lipids for use in biodiesel production. Biogas resulting from anaerobic digestion of algal biomass can be combusted to produce electricity or alternatively, upgraded to obtain the same methane content as natural gas, enabling its use as a transport fuel or its injection into the gas grid. However, upgrading biogas to higher methane content entails significant energy and economic costs. 
         [0008]    Algal biotechnology typically also depends on the axenic cultivation of a single strain, such as  Spirulina, Nanochloropsis, Chlorella,  or  Dunaliella.  However, at large scale, aseptic conditions are difficult to maintain (Quinn et al., 2012,  Nannochloropsis production metrics in a scalable outdoor photobioreactor for commercial applications.  Biores. Technol. 117: 164-171) and ecological processes such as invasion by other algae species, decimation by grazers, fungi and/or viral infection lead to process instability (Cauchie et al., 1995,  Daphnia magna Straus living in an aerated sewage lagoon as a source of chitin: ecological aspects.  Belg. J. Zool. 125; Oswald W J, 1980,  Algal production—problems, achievements and potential. Algae biomass: production and use . [sponsored by the National Council for Research and Development, Israel and the Gesellschaft fur Strahlen-und Umweltforschung (GSF), Munich, Germany]; editors, Gedaliah Shelef, Carl J Soeder.), which also decreases economic feasibility. 
       SUMMARY 
       [0009]    The exemplary embodiments of the present disclosure pertain to methods for growth of biofilms of alkaliphilic microbial communities dominated by phototrophic bacteria for production of biomass for use as feedstocks for fuel production. 
         [0010]    According to one aspect, a fuel produced from such biomass feedstocks may be a solid (for example, dried biomass pellets or briquets), a gas (for example, methane) or a liquid (for example, ethanol or biodiesel). 
         [0011]    The exemplary methods generally comprise the following elements:
       (1) The biofilms are grown on a thin, transparent surface that is exposed to sunlight. CO2 is provided to the biofilms via the alkaline growth medium in the form of sodium and/or potassium (bi)carbonate.   (2) The biofilms comprise diverse microbial communities. To select for a microbial community with favourable properties, the sunlight is attenuated by passing it through an optical filter. The optical filter may be constructed with organic films, preferably with photovoltaic activity. One example of a suitable optical filter is an organic solar cell. By passing sunlight through an optical filter such as an organic solar cell with an organic film having photovoltaic activity, only parts of the solar spectrum are made available to phototrophic microbes. At the same time, the organic photovoltaic activity in the optical filter can use the absorbed photon energy to produce electricity which can be used to operate pumps and other equipment needed to run the overall process, or alternatively, stored in in a battery.   (3) Additional ecologically selective pressure is applied to the biofilms by preventing accumulation of reduced chemical compounds such as sulfide (HS − ). This may be done by adding nitrate to the growth medium and/or by pumping the growth medium along the biofilms.   (4) The biofilms are harvested periodically by pigging, wiping or by applying a water jet. During harvesting, surface roughness, for example in the form of etched grooves on the transparent surface, ensures that sufficient biomass is left behind for effective regrowth of the biofilms.   (5) The productivity of the biofilms is monitored online by quantification of oxygen production.   (6) The (bi)carbonate in the growth medium is regenerated by capturing CO 2 , either from a stack gas or directly from the atmosphere. Regeneration takes place in a separate process module.       
 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES: 
         [0018]    The present disclosure will be described in conjunction with reference to the following drawings in which: 
           [0019]      FIG. 1A  is a side view and  FIG. 1B  is a front view of an example of a photobioreactor according to one embodiment of the present invention; 
           [0020]      FIG. 2  is a close-up cross-sectional view of the photobioreactor illustrated in  FIG. 1 ; 
           [0021]      FIG. 2  is an exemplary illustration of an exemplary process scheme according to one embodiment of the present disclosure; 
           [0022]      FIG. 3  is a chart showing the phototrophic microbial productivity in an exemplary bioreactor with an interior depth of 1.6 mm (open circles), 3.5 mm (closed circles) and 7.0 mm (triangles); 
           [0023]      FIG. 4A  is a pie chart showing distribution of microbial species within a community maintained in a photobioreactor exposed to blues light waves only, while  FIG. 4B  is a pie chart showing distribution of microbial species within a community maintained in a photobioreactor exposed to white light waves comprising a full solar spectrum, and  FIG. 4C  is a pie chart showing distribution of microbial species within a community maintained in a photobioreactor exposed to red light waves only; 
           [0024]      FIG. 5  is a chart showing the phototrophic microbial productivity in an exemplary bioreactor exposed to red (open triangles) or blue (closed squares) light waves only as compared to white light waves comprising a full solar spectrum (closed circles); 
           [0025]      FIG. 6A  is a pie chart showing distribution of microbial species within a community maintained in a photobioreactor without regular nutrient media refreshing and regular microbial harvesting, while  FIG. 6B  is a pie chart showing distribution of microbial species within a community maintained in a photobioreactor with regular nutrient media refreshing and regular microbial harvesting; and 
           [0026]      FIG. 7  is a chart showing recovery of phototrophic microbial productivity in an exemplary bioreactor having etched surfaces for supporting microbial growth (open circles) in comparison to phototrophic microbial productivity in an exemplary bioreactor that did not have etched surfaces (closed circles); 
       
    
    
     DETAILED DESCRIPTION 
       [0027]    The embodiments of the present disclosure generally pertain to integrated systems and processes for the cultivation of biofilms of alkaliphilic microbial communities comprising phototrophic microorganisms for production of biomass for use as feedstocks for fuel production. According to one aspect, a fuel produced from such biomass feedstocks may be a solid (for example, dried biomass pellets) or a gas (for example, methane) or a liquid (for example, ethanol or biodiesel). 
         [0028]    Some embodiments pertain to photobioreactors for culturing and maintaining therein said biofilms comprising microbial communities. It is to be noted that the microbial communities will not proliferate within the photobioreactors in the form of suspended cells. 
         [0029]    An example of a method according to the present disclosure generally comprise the following steps:
       (1) The biofilms are grown on a thin, transparent surface that is exposed to sunlight. CO 2  is provided to the biofilms via the alkaline growth medium in the form of sodium and/or potassium (bi)carbonate.   (2) The biofilms comprise diverse microbial communities. To select a suitable microbial community having favourable properties for biomass production, the sunlight is attenuated by passage through an optical filter. The optical filter may be constructed with organic films, and preferably, may have photovoltaic activity. One example of a suitable optical filter is an organic solar cell. By passing sunlight through an organic solar cell with an organic film having photovoltaic activity, only parts of the solar spectrum are made available to the underlying phototrophic microbes. Examples of suitable optical filters include filters that filter out blue light, or red light, or green light, and other light spectra At the same time, the organic photovoltaic activity in the optical filter can use the absorbed photon energy to produce electricity which can be used to operate pumps and other equipment needed to run the overall process, or alternatively, stored in in a battery.   (3) Additional ecologically selective pressure may be applied to the biofilms by preventing accumulation of reduced chemical compounds such as sulfide (HS − ). This may be done by adding nitrate to the growth medium and/or by pumping the growth medium along the biofilms.   (4) The biofilms are harvested periodically by pigging, wiping or by applying a water jet to the biofilms. During harvesting, surface roughness, for example in the form of etched grooves on the transparent surface, will ensure that sufficient biomass is left behind for effective regrowth of the biofilms.   (5) The productivity of the biofilms is monitored online by quantification of oxygen production.   (6) The (bi)carbonate in the growth medium is regenerated by capturing CO 2 , either from a stack gas or directly from the atmosphere. Regeneration takes place in a separate process module.       
 
         [0036]    An example of a photobioreactor  10  according to the present disclosure, is shown in  FIGS. 1A, 1B, and 2 . In this example, the dimensions of the photobioreactor 10 are 1 m high by 1 m wide by 5 mm wide.  FIG. 1A  shows a side view of the photobioreactor  10  which  FIG. 1B  shows a front view. The photobioreactor comprises two outer walls  35   a ,  35   b . An organic solar cell  40  about 1-mm thick, is positioned and secured directly adjacent a first outer wall  35   a . A transparent sheet material  15  having etched grooves  17  is spaced about 1 mm away from the underside of the organic solar cell  40  and secured in place. The transparent sheet material  15  may be a synthetic polymer such as a polycarbonate resin or alternatively glass or other such sheet materials. This photoreactor  10  has one inlet port  30  receiving therethrough nutrient media and for maintaining nutrient media  50  at a selected level in the photobioreactor  10 . One or more outlet ports  20  are provided near the top of the photobioreactor  10  for egress of nutrient media and for periodic harvesting of microbial biomass. The photobioreactor  10  is additionally equipped with piping (not shown) for egress of gases from the top of the photobioreactor  10 , with a volumetric gas flow meter, and oxygen egress port, and optionally, a CO 2 -capturing device. 
         [0037]    The outer-facing surface of the transparent sheet material  15  (i.e., the face facing the second outer wall  35   b ) is seeded with a sample of a naturally occurring microbial population collected from a natural habitat, for example, from an alkaline soda lake. Then a selected growth medium containing &gt;0.5 mol/L sodium and/or potassium (bi)carbonate at pH&gt;9 as well as other nutrients suitable to support microbial growth and development. It is to be noted that the photobioreactor modules may be planar and may be mounted vertically or near-vertical, for example at angles of 30° or greater to enable the spontaneous outgassing of the oxygen produced by the biofilms, as oxygen bubbles that collect at the top of the module. A module width of 3.5 mm is ideal to enable the effective outgassing of the produced oxygen ( FIG. 3 ). During outgassing in smaller module widths, gas bubbles may prevent proper affixing of the biofilms to the walls of transparent grooved sheet material and thereby result in lower phototrophic microbial productivity. Larger module widths may also result in lower productivity. However, the dimensions of the photobioreactor may vary in the ranges of 0.5 m to 3.5 m high, 0.5 m to 3.5 m wide, and 2.5 mm to 100 mm wide. It is to be noted that such structures are commonly referred to as “rectangular parellelepipeds”. 
         [0038]    As the biofilms develop and produce gases, the gases will flow into the egress piping for separation of 0 2  and CO 2 . In a later step, CO 2  may be absorbed from a flue gas or directly from the atmosphere. 
         [0039]    Because the CO 2  absorption stage is separate and no gas is provided to the photobioreactor module, the productivity of the photobioreactor can be monitored and quantified online, for example volumetrically as taught by Veiga et al. (1990,  A new device for measurement and control of gas production by bench scale anaerobic digesters.  Water Res. 24:12, 1551-1554). Oxygen production may be quantified for a single photobioreactor module, or for multiple connected modules. Both the front and back of the module may consist of surfaces as depicted in  FIG. 1 . Alternatively, only a single side of the module may be transparent. In any case, the transparent surface area of the module is typically arranged such that the sunlight shines onto it at an angle so that ideally, the photosynthetically active radiation remains below 600 μmol/m 2  surface/s, to limit photoinhibition. That means that the amount of module surface area will be larger than its footprint (typically 2-5×). The modules are also engineered in such a way that rainwater can be collected, stored, and used for the makeup of fresh medium that is lost from the process during biomass harvesting. The module may be seeded with one or more natural microbial communities collected from suitable natural habitats, for example from alkaline soda lakes. 
         [0040]    Studies of alkaline soda lakes in Africa and Siberia have shown that both microalgae and cyanobacteria are highly active in such lakes (Seckbach, 2007, Algae and Cyanobacteria in Extreme Environments, Springer; Schragerl et al., 2008,  Phytoplankton community relationship to environmental variables in three Kenyan Rift Valley saline - alkaline lakes . Marine and Freshwater Res. 59:125-136) and as such these ecosystems are among the most productive in the world (Melack, 1981,  Photosynthetic activity of phytoplankton in tropical African soda lakes.  Hydrobiologia 81:71-85.). Alkaline soda lakes typically have moderate to high salt concentrations (sodium carbonate up to saturation) and pHs ranging from 9 to 11 with diverse microbial communities (Sorokin et al., 2014,  Microbial diversity and biogeochemical cycling in soda lakes . Extremophiles 18:791-809.). Many small alkaline lakes harbouring active photosynthetic microbial mats adapted to high pH and alkalinity have been discovered on the Cariboo Plateau in British Columbia, Canada (Brady et al., 2013,  Isotopic biosignatures in carbonate - rich, cyanobacteria dominated mats of the Cariboo Plateau, B.C.  Geobiology 11:437-456). The pHs of the Cariboo lakes show little variation seasonally and over successive years with mean values ranging between 10.1 to 10.2±0.1. The lakes are dominated by Na +  ions with Na +  concentrations ranging from 6,508 to 32,600 mg L −1  and are poor in Ca 2+  ions (&lt;10 mg L −1 ) and Mg 2+  ions (&lt;96 mg L −1 ). The maximum dissolved inorganic carbon concentration observed is 9,200 mg L −1 . 
         [0041]    Multiple different types of microbial phototrophs may be active at the same time in a microbial community, and may compete for space, nutrients, and light. These different types of phototrophs typically have different properties with respect to their density, biofilm structural strength, productivity, and lipid content. Different types of phototrophs use different parts of the solar spectrum. For example, cyanobacteria mainly use red light whereas diatoms also use blue light. These different phototrophs may also interact in antagonistic ways, resulting in a loss of productivity. To select for a specific type of desired phototroph, the sunlight is attenuated by the addition of an optic filter on the outside transparent wall of a photobioreactor module as shown in  FIGS. 4A, 4C . This filter preferentially transmits light either above or below 625 nm. 
         [0042]    The most productive microbial community was grown under red light (&gt;625 nm, as opposed to white or blue;  FIG. 5 ) and was dominated by oxygenic phototrophs closely related to  Lyngbya sp.    
         [0043]    This microbial community also contained members of the genera  Marinicella  and  Rhodobaca  (phylum Proteobacteria), the family Saprospiraceae (phylum Bacteroidetes) and order  Oceanospirillales  (phylum Proteobacteria) (Table 1). The addition of an optic filter transmitting light below 625 nm selects for a phototrophic microbial community dominated by diatoms ( FIG. 4A ) that is less productive than either the red light wave community or the full spectrum white light wave community ( FIG. 5 ). The less productive blue light microbial community was dominated by the Eukaryote genus  Nitzschia  (phylum Bacillariophyta) with lower amounts of the bacterial genera  Marinicella, Alcanivorax , and  Rhodobaca  (phylum Proteobacteria) and family Saprospiraceae (phylum Bacteroidetes) (Table 1). The full spectrum white light microbial community was a mixture of the microbial communities found in the blue and red light microbial communities (Table 1). 
         [0044]    Preferentially, the filter consists of a semi-transparent photovoltaic device that converts the energy in the solar spectrum not used by the desired microbial phototrophs into electricity. Organic and dye-based photovoltaics are energy conversion technologies that rely on organic materials to convert sunlight into electricity. These organic materials are highly soluble in organic solvents which allows for room temperature solution deposition, thus enabling the fabrication of solar cell devices onto a range of substrates/surfaces including foils and plastic films that are light weight and flexible. In addition these cells can be color-tuned and made semi-transparent. Thus, the type and amount of transmitted light can be finely adjusted. The electricity so produced may be used to power pumps and other equipment needed to run the photobioreactor. Thus, the filter differs from ones previously disclosed that reflect light (for example, such as those disclosed in US Pub. Pat. Appl. No. 2014/0154769 A1). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 1 
               
               
                   
               
               
                 Summary of the composition of microbial communities grown in biofilms under 
               
               
                 red, white, or blue wavelength light. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 Red 
                 White 
                 Blue 
                 Kingdom 
                 Phylum 
                 Class 
                 Order 
               
               
                   
               
               
                 0.28 
                 0.57 
                 0.02 
                 Bacteria 
               
               
                 0.00 
                 0.06 
                 0.02 
                 Bacteria 
                 BD1-5 
               
               
                 0.22 
                 0.17 
                 0.10 
                 Bacteria 
                 Bacteroidetes 
               
               
                 0.06 
                 0.00 
                 0.00 
                 Bacteria 
                 Bacteroidetes 
                 Bacteroidia 
                 Bacteroidales 
               
               
                 0.00 
                 0.00 
                 0.02 
                 Bacteria 
                 Bacteroidetes 
                 Bacteroidia 
                 Bacteroidales 
               
               
                 0.23 
                 0.11 
                 0.00 
                 Bacteria 
                 Bacteroidetes 
                 Cytophagia 
               
               
                 0.06 
                 0.00 
                 0.00 
                 Bacteria 
                 Bacteroidetes 
                 Cytophagia 
                 Cytophagales 
               
               
                 0.05 
                 0.06 
                 0.02 
                 Bacteria 
                 Bacteroidetes 
                 Cytophagia 
                 Order_III 
               
               
                 0.05 
                 0.17 
                 0.02 
                 Bacteria 
                 Bacteroidetes 
                 Cytophagia 
                 Order_III 
               
               
                 0.67 
                 1.20 
                 0.25 
                 Bacteria 
                 Bacteroidetes 
                 Cytophagia 
                 Order_III 
               
               
                 0.28 
                 0.29 
                 0.00 
                 Bacteria 
                 Bacteroidetes 
                 Flavobacteriia 
                 Flavobacteriales 
               
               
                 0.45 
                 0.06 
                 0.41 
                 Bacteria 
                 Bacteroidetes 
                 Flavobacteriia 
                 Flavobacteriales 
               
               
                 0.67 
                 0.34 
                 0.00 
                 Bacteria 
                 Bacteroidetes 
                 Flavobacteriia 
                 Flavobacteriales 
               
               
                 0.13 
                 0.46 
                 0.08 
                 Bacteria 
                 Bacteroidetes 
                 Flavobacteriia 
                 Flavobacteriales 
               
               
                 3.05 
                 2.35 
                 0.83 
                 Bacteria 
                 Bacteroidetes 
                 Sphingobacteriia 
                 Sphingobacteriales 
               
               
                 0.02 
                 0.00 
                 0.00 
                 Bacteria 
                 Candidate_division_OD1 
               
               
                 0.00 
                 0.00 
                 0.02 
                 Bacteria 
                 Candidate_division_SR1 
               
               
                 0.02 
                 0.00 
                 0.00 
                 Bacteria 
                 Candidate_division_WS6 
               
               
                 0.13 
                 0.00 
                 0.04 
                 Bacteria 
                 Chlamydiae 
                 Chlamydiae 
                 Chlamydiales 
               
               
                 0.03 
                 0.00 
                 0.00 
                 Bacteria 
                 Chlamydiae 
                 Chlamydiae 
                 Chlamydiales 
               
               
                 0.03 
                 0.00 
                 0.00 
                 Bacteria 
                 Chloroflexi 
                 Anaerolineae 
                 Anaerolineales 
               
               
                 0.00 
                 0.06 
                 0.00 
                 Bacteria 
                 Chloroflexi 
                 Thermomicrobia 
                 Sphaerobacterales 
               
               
                 1.80 
                 39.41 
                 93.09 
                 Eukaryote 
                 Bacillariophyta 
                 Bacillariophyceae 
                 Bacillariales 
               
               
                 0.75 
                 0.86 
                 0.00 
                 Bacteria 
                 Cyanobacteria 
                 Cyanobacteria 
               
               
                 0.52 
                 2.01 
                 0.00 
                 Bacteria 
                 Cyanobacteria 
                 Cyanobacteria 
                 SubsectionI 
               
               
                 0.06 
                 0.00 
                 0.00 
                 Bacteria 
                 Cyanobacteria 
                 Cyanobacteria 
                 SubsectionIII 
               
               
                 74.43  
                 39.19 
                 0.04 
                 Bacteria 
                 Cyanobacteria 
                 Cyanobacteria 
                 SubsectionIII 
               
               
                 0.20 
                 0.11 
                 0.00 
                 Bacteria 
                 Deinococcus-Thermus 
                 Deinococci 
                 Deinococcales 
               
               
                 0.00 
                 0.06 
                 0.00 
                 Bacteria 
                 Firmicutes 
                 Clostridia 
                 Clostridiales 
               
               
                 0.06 
                 0.06 
                 0.08 
                 Bacteria 
                 Gemmatimonadetes 
                 Gemmatimonadetes 
                 BD2-11_terrestrial_group 
               
               
                 0.05 
                 0.00 
                 0.02 
                 Bacteria 
                 Lentisphaerae 
                 SS1-B-03-39 
               
               
                 0.14 
                 0.00 
                 0.10 
                 Bacteria 
                 Planctomycetes 
                 Phycisphaerae 
                 Phycisphaerales 
               
               
                 0.17 
                 0.63 
                 0.27 
                 Bacteria 
                 Planctomycetes 
                 Phycisphaerae 
                 Phycisphaerales 
               
               
                 0.08 
                 0.00 
                 0.08 
                 Bacteria 
                 Proteobacteria 
               
               
                 0.00 
                 0.11 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
               
               
                 0.05 
                 0.06 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Caulobacterales 
               
               
                 0.06 
                 0.17 
                 0.02 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Caulobacterales 
               
               
                 0.33 
                 0.17 
                 0.06 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 DB1-14 
               
               
                 1.45 
                 0.98 
                 0.42 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rhizobiales 
               
               
                 0.03 
                 0.06 
                 0.06 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rhizobiales 
               
               
                 0.23 
                 0.17 
                 0.04 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rhodobacterales 
               
               
                 2.31 
                 2.18 
                 0.50 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rhodobacterales 
               
               
                 0.34 
                 0.69 
                 0.08 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rhodobacterales 
               
               
                 0.11 
                 0.23 
                 0.02 
                 Bacteria 
                 Proteobacteria 
                 Alphaproteobacteria 
                 Rickettsiales 
               
               
                 0.03 
                 0.00 
                 0.06 
                 Bacteria 
                 Proteobacteria 
                 Deltaproteobacteria 
                 Bdellovibrionales 
               
               
                 0.09 
                 0.00 
                 0.12 
                 Bacteria 
                 Proteobacteria 
                 Deltaproteobacteria 
                 Bdellovibrionales 
               
               
                 0.02 
                 0.00 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Deltaproteobacteria 
                 Bdellovibrionales 
               
               
                 0.02 
                 0.11 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Deltaproteobacteria 
                 Desulfuromonadales 
               
               
                 0.73 
                 0.40 
                 0.12 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
               
               
                 0.97 
                 0.11 
                 0.15 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Alteromonadales 
               
               
                 0.00 
                 0.00 
                 0.04 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Alteromonadales 
               
               
                 0.25 
                 0.17 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Alteromonadales 
               
               
                 0.02 
                 0.00 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Chromatiales 
               
               
                 0.06 
                 0.00 
                 0.02 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Incertae_Sedis 
               
               
                 0.77 
                 0.34 
                 0.35 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Incertae_Sedis 
               
               
                 0.02 
                 0.00 
                 0.02 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 HOC36 
               
               
                 0.03 
                 0.00 
                 0.04 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.31 
                 0.17 
                 0.56 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.02 
                 0.06 
                 0.04 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 2.09 
                 0.52 
                 0.04 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.42 
                 0.34 
                 0.06 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.05 
                 0.00 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.00 
                 0.00 
                 0.06 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 0.03 
                 0.00 
                 0.00 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Oceanospirillales 
               
               
                 4.02 
                 3.16 
                 1.27 
                 Bacteria 
                 Proteobacteria 
               
               
                 0.03 
                 0.00 
                 0.10 
                 Bacteria 
                 Proteobacteria 
                 Gammaproteobacteria 
                 Pseudomonadales 
               
               
                 0.03 
                 0.00 
                 0.00 
                 Bacteria 
                 Spirochaetae 
                 Spirochaetes 
                 Spirochaetales 
               
               
                 0.16 
                 0.00 
                 0.00 
                 Bacteria 
                 Spirochaetae 
                 Spirochaetes 
                 Spirochaetales 
               
               
                 0.03 
                 0.11 
                 0.00 
                 Bacteria 
                 Verrucomicrobia 
                 Opitutae 
               
               
                 0.17 
                 0.06 
                 0.00 
                 Bacteria 
                 Verrucomicrobia 
                 Opitutae 
                 BC-COM435 
               
               
                 0.03 
                 1.09 
                 0.19 
                 Bacteria 
                 Verrucomicrobia 
                 Opitutae 
                 Puniceicoccales 
               
               
                 0.00 
                 0.06 
                 0.04 
                 Bacteria 
                 Verrucomicrobia 
                 Opitutae 
                 Puniceicoccales 
               
               
                 0.00 
                 0.06 
                 0.00 
                 Bacteria 
                 Verrucomicrobia 
                 Opitutae 
                 Puniceicoccales 
               
               
                 0.00 
                 0.17 
                 0.06 
                 Bacteria 
                 Verrucomicrobia 
                 Verrucomicrobiae 
                 Verrucomicrobiales 
               
               
                   
               
             
          
           
               
                   
                 Red 
                 White 
                 Blue 
                 Family 
                 Genus 
               
               
                   
                   
               
               
                   
                 0.28 
                 0.57 
                 0.02 
               
               
                   
                 0.00 
                 0.06 
                 0.02 
               
               
                   
                 0.22 
                 0.17 
                 0.10 
               
               
                   
                 0.06 
                 0.00 
                 0.00 
               
               
                   
                 0.00 
                 0.00 
                 0.02 
                 ML635J-40 
               
               
                   
                 0.23 
                 0.11 
                 0.00 
               
               
                   
                 0.06 
                 0.00 
                 0.00 
               
               
                   
                 0.05 
                 0.06 
                 0.02 
               
               
                   
                 0.05 
                 0.17 
                 0.02 
                 F1-37X2 
               
               
                   
                 0.67 
                 1.20 
                 0.25 
                 ML310M-34 
               
               
                   
                 0.28 
                 0.29 
                 0.00 
                 Cryomorphaceae 
                 
                   Brumimicrobium 
                 
               
               
                   
                 0.45 
                 0.06 
                 0.41 
                 Cryomorphaceae 
                 
                   Fluviicola 
                 
               
               
                   
                 0.67 
                 0.34 
                 0.00 
                 Cryomorphaceae 
                 
                   Owenweeksia 
                 
               
               
                   
                 0.13 
                 0.46 
                 0.08 
                 Flavobacteriaceae 
                 
                   Psychroflexus 
                 
               
               
                   
                 3.05 
                 2.35 
                 0.83 
                 Saprospiraceae 
               
               
                   
                 0.02 
                 0.00 
                 0.00 
               
               
                   
                 0.00 
                 0.00 
                 0.02 
               
               
                   
                 0.02 
                 0.00 
                 0.00 
               
               
                   
                 0.13 
                 0.00 
                 0.04 
               
               
                   
                 0.03 
                 0.00 
                 0.00 
                 Waddliaceae 
                 
                   Waddlia 
                 
               
               
                   
                 0.03 
                 0.00 
                 0.00 
                 Anaerolineaceae 
               
               
                   
                 0.00 
                 0.06 
                 0.00 
                 Sphaerobacteraceae 
                 
                   Nitrolancea 
                 
               
               
                   
                 1.80 
                 39.41 
                 93.09 
                 Bacillariaceae 
                 
                   Nitzschia 
                 
               
               
                   
                 0.75 
                 0.86 
                 0.00 
               
               
                   
                 0.52 
                 2.01 
                 0.00 
                 FamilyI 
                 
                   Cyanobacterium 
                 
               
               
                   
                 0.06 
                 0.00 
                 0.00 
                 FamilyI 
               
               
                   
                 74.43  
                 39.19 
                 0.04 
                 FamilyI 
                 
                   Lyngbya 
                 
               
               
                   
                 0.20 
                 0.11 
                 0.00 
                 Trueperaceae 
                 
                   Truepera 
                 
               
               
                   
                 0.00 
                 0.06 
                 0.00 
               
               
                   
                 0.06 
                 0.06 
                 0.08 
               
               
                   
                 0.05 
                 0.00 
                 0.02 
               
               
                   
                 0.14 
                 0.00 
                 0.10 
                 Phycisphaeraceae 
                 SM1A02 
               
               
                   
                 0.17 
                 0.63 
                 0.27 
                 Phycisphaeraceae 
                 Urania-1B-19 
               
               
                   
                 0.08 
                 0.00 
                 0.08 
               
               
                   
                 0.00 
                 0.11 
                 0.00 
               
               
                   
                 0.05 
                 0.06 
                 0.00 
                 Hyphomonadaceae 
                 
                   Glycocaulis 
                 
               
               
                   
                 0.06 
                 0.17 
                 0.02 
                 Hyphomonadaceae 
                 
                   Oceanicaulis 
                 
               
               
                   
                 0.33 
                 0.17 
                 0.06 
               
               
                   
                 1.45 
                 0.98 
                 0.42 
                 Bradyrhizobiaceae 
                 
                   Salinarimonas 
                 
               
               
                   
                 0.03 
                 0.06 
                 0.06 
                 Phyllobacteriaceae 
                 
                   Pseudaminobacter 
                 
               
               
                   
                 0.23 
                 0.17 
                 0.04 
                 Rhodobacteraceae 
               
               
                   
                 2.31 
                 2.18 
                 0.50 
                 Rhodobacteraceae 
                 
                   Rhodobaca 
                 
               
               
                   
                 0.34 
                 0.69 
                 0.08 
                 Rhodobacteraceae 
                 
                   Rhodovulum 
                 
               
               
                   
                 0.11 
                 0.23 
                 0.02 
               
               
                   
                 0.03 
                 0.00 
                 0.06 
                 Bacteriovoracaceae 
                 
                   Bacteriovorax 
                 
               
               
                   
                 0.09 
                 0.00 
                 0.12 
                 Bacteriovoracaceae 
                 
                   Peredibacter 
                 
               
               
                   
                 0.02 
                 0.00 
                 0.00 
                 Bdellovibrionaceae 
                 
                   Bdellovibrio 
                 
               
               
                   
                 0.02 
                 0.11 
                 0.00 
                 GR-WP33-58 
               
               
                   
                 0.73 
                 0.40 
                 0.12 
               
               
                   
                 0.97 
                 0.11 
                 0.15 
                 Alteromonadaceae 
                 
                   Marinobacter 
                 
               
               
                   
                 0.00 
                 0.00 
                 0.04 
                 Alteromonadaceae 
                 
                   Simiduia 
                 
               
               
                   
                 0.25 
                 0.17 
                 0.00 
                 Idiomarinaceae 
                 
                   Aliidiomarina 
                 
               
               
                   
                 0.02 
                 0.00 
                 0.00 
                 Ectothiorhodospiraceae 
                 
                   Ectothiorhodospira 
                 
               
               
                   
                 0.06 
                 0.00 
                 0.02 
                   
                 
                   Alkalimonas 
                 
               
               
                   
                 0.77 
                 0.34 
                 0.35 
                   
                 
                   Methylonatrum 
                 
               
               
                   
                 0.02 
                 0.00 
                 0.02 
               
               
                   
                 0.03 
                 0.00 
                 0.04 
               
               
                   
                 0.31 
                 0.17 
                 0.56 
                 Alcanivoracaceae 
                 
                   Alcanivorax 
                 
               
               
                   
                 0.02 
                 0.06 
                 0.04 
                 Halomonadaceae 
                 
                   Halomonas 
                 
               
               
                   
                 2.09 
                 0.52 
                 0.04 
                 ML617.5J-3 
               
               
                   
                 0.42 
                 0.34 
                 0.06 
                 OM182_clade 
               
               
                   
                 0.05 
                 0.00 
                 0.00 
                 Oceanospirillaceae 
                 
                   Marinospirillum 
                 
               
               
                   
                 0.00 
                 0.00 
                 0.06 
                 Oceanospirillaceae 
                 
                   Nitrincola 
                 
               
               
                   
                 0.03 
                 0.00 
                 0.00 
                 Oceanospirillaceae 
                 
                   Pseudospirillum 
                 
               
               
                   
                 4.02 
                 3.16 
                 1.27 
                 Incertae_Sedis 
                 
                   Marinicella 
                 
               
               
                   
                 0.03 
                 0.00 
                 0.10 
                 Pseudomonadaceae 
                 
                   Pseudomonas 
                 
               
               
                   
                 0.03 
                 0.00 
                 0.00 
                 PL-11B10 
               
               
                   
                 0.16 
                 0.00 
                 0.00 
                 Spirochaetaceae 
                 
                   Spirochaeta 
                 
               
               
                   
                 0.03 
                 0.11 
                 0.00 
               
               
                   
                 0.17 
                 0.06 
                 0.00 
               
               
                   
                 0.03 
                 1.09 
                 0.19 
                 Puniceicoccaceae 
               
               
                   
                 0.00 
                 0.06 
                 0.04 
                 Puniceicoccaceae 
                 
                   Coraliomargarita 
                 
               
               
                   
                 0.00 
                 0.06 
                 0.00 
                 Puniceicoccaceae 
                 marine_group 
               
               
                   
                 0.00 
                 0.17 
                 0.06 
                 Verrucomicrobiaceae 
                 
                   Haloferula 
                 
               
               
                   
                   
               
             
          
         
       
     
         [0045]    Microbial communities growing in biofilms contain oxygenic phototrophic microbes that contribute to productivity. However, biofilms also contain other microbes that might negatively affect productivity. For example, sulfate-reducing bacteria may be present. When parts of the biofilms become anoxic (for example, at night when no oxygen is produced), sulfate-reducing bacteria produce sulfide which is toxic to the oxygenic phototrophic microbes. To limit toxic effects of anoxic conditions inside biofilms, the oxic medium is pumped along the biofilms with a pump (typically 1 to 4 volume changes/day). Flow can be applied continuously or periodically and has the additional benefits of: (i) cooling the biofilms when their temperature becomes too high because of the exposure to sunlight during the day, and (ii) removal of excess oxygen thereby preventing inhibition of the biofilms&#39; biological activities. In the absence of sufficient flow, a microbial community with low productivity is selected ( FIGS. 6A, 6B ). In addition, a dissolved redox buffer (e.g. nitrate or iron(II/III), 5-25 mM) is added to the medium to select for anaerobic bacteria that may out compete sulfate reducers for substrates and/or re-oxidize any sulfide that is still produced. 
         [0046]    Additional measures to select for biomass with favourable properties or to reduce process costs can be implemented. For example, a nitrogen source may be omitted from the growth medium to stimulate nitrogen fixation. 
         [0047]    The biofilms are harvested periodically, for example by applying mechanical or hydraulic force, for example by “pigging” (as is done for pipelines), mechanical wiping, or by application of hydraulic shear with a water jet. To enable effective and rapid re-growth of the biofilms after harvesting, macroscopic structural features (&gt;50 μm in size) are present on the transparent walls of the photobioreactor. These features are macroscopic. In one embodiment of the method disclosed herein, the structural features are present in the form of grooves ( 17  in  FIG. 2 ). Because of these features, some of the microorganisms remain attached to the surface during harvesting and act as seed for reestablishment and development of a new biofilm ( FIG. 7 ). 
         [0048]    The harvested microbial biomass may be dried and then compressed to form combustible additionally comprising the steps of drying the harvested microbial biomass, and compressing the dried microbial biomass to form a plurality of combustible pellets or briquets or other such materials. Alternatively, the harvested biomass may be extruded through suitable dies to form elongate strands to form pellets that may then dried to a combustible material form. 
         [0049]    Alternatively, the harvested microbial biomass may be used as a feedstock for a fermentation process for production of a fuel ethanol therefrom. Alternatively, the harvested microbial biomass may be anaerobically digested to produce one or more combustible gases therefrom.