US 20120231513A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0231513 A1 Stephen et al. (43) Pub. Date: Sep. 13, 2012

(54) SYSTEMIS AND METHODS FORCULTURING Publication Classification ALGAE WITH BVALVES (51) Int. Cl. (76) Inventors: David Stephen, Davis, CA (US); f (E,O CR Gaye Elizabeth Morgenthaler, CI2M I/00 CR Woodside, CA (US); Benjamin AOIG L/00 C Chiau-pin Wu, San Ramon, CA CI2N I/2 CR (US); David Vancott Jones, ( .01) Woodside, CA (US) CIIB I/O (2006.01) (21) Appl. No.: 13/263,980 (52) U.S. Cl...... 435/134:435/257.1:554/8; 435/289.1; 47/1.4; 119/242 (22) PCT Fled: Apr. 16, 2010 (86) PCT NO.: PCT/US2O1 O/O31340 (57) ABSTRACT Provided herein are systems and methods for extracting lipids (2),S371 (4) (c)(1), Date: Dec. 19, 2011 and/ord/or producing biofuel from algae in marine and freshfreshwater s e - 19 environments, wherein algae and bivalves are co-cultured in a O O system of enclosures comprising water that comprises Related U.S. Application Data recycled nutrients that are essential for algal growth. The (60) Provisional application No. 61/170,524, filed on Apr. system also include enclosures for culturing fishes which are 17, 2009. used to harvest the algae.

A. * Water Source

& - / y / Algae culture A - R. <1 0-201m + c 10. y Algae harvested 4. 3. v. 7 by fishes '. 20M 7 Planktivorous w y X y Fishes

CO d Fish processing 2 S nutrient enriched Water Controlled feeding of & bivalves with algae & S. Effluent water containing s y sy, particulate wastes, A s f 8. unused plankton in size range of y <10-20um Lipids to Bivalves Culture w ------Biofuel

^ y Harwested Bivalves Patent Application Publication Sep. 13, 2012 Sheet 1 of 2 US 2012/0231513 A1

Figure 1: Schematic of Water Flow and Trophic Level Association in Molluscan Bivalve enhanced Microalgae Production Systems for Feeding Planktivorous Fish: Applications Bioremediation of Eutrophic Zones in Marine and Freshwater Environments Carbon Recycling and Cathon Capture in Marine and Freshwater Environments Production of Fish and by products - Fish Meal, Fish Lipids and Biofuels in Marine and Freshwater Environments,

Water Source from Natural Eutrophic Zones or Natural Water Bodies (Anthropogenic Nutrient Enrichment) With high primary production (microalgae or phytoplankton) And high Secondary production (Zooplankton) or Containments such as Ponds and Tanks Operated for Specific Applications

Cultivation of Zooplankton Filter Feeding Fish Marine Environment Ex. Atlantic IIerring Clupeg harengus D Treshwater Environment Ex. Indian Major Carp Catia Cata

Vicroalgae Concentrated E?luent

Cultivation of Molluscan Bivalves Marine Environment Ex. Marine Mussels Mytilus edulis Oysters Crassostrea spp Freshwater Env. EX. Freshwater MusScls Lanelliders marginalis

Water is enriched with dissolved metabolic wastes and Carbon Dioxide from two processes in the Bivalves: Respiration and Shell Formation. Controlled Controlled Inoculation Additional Carbon Dioxide Feeding a a Diffusion From Fossil Fuc Combustion Plants (Carbon

Recycling and Carbon Capture) Intensive Micro

Algae Cultivation

IIarvests Water enriched with dissolved metabolic wastes

Cultivation of Phytoplankton Filter Feeding Fish Marine Environment Ex. Gulf Menhaden Brevoortia patronius. Indian Oil Sardine Sardinella longiceps Freshwater Environcment Ex. Chinesc Silver Carp Hypophtalmichthysmolitrix

Solid Waste Removal IIarvested Fish and Bivalves to Seafood Market

Harvested Fish: Processed to Fish Meal Lipids and Biofuels Nutrient Poor Effluent ------. Discharged Patent Application Publication Sep. 13, 2012 Sheet 2 of 2 US 2012/0231513 A1

Figure 2

( ^: Water s Source & Y&

A. s y, A. A. A. x A. x ? x, / Algae Culture A.A 2. c x SS A. 31) H. s.1 '. x Aldaehgae harveste ted x -: es ^ sk \, <10-20m20M >10- / ) by fishes Planktivorous \ / Fishes \ / Yx / s w A. N: * c ssc, \, ^ Fish processings CO2 and S nutrient enriched water Controlled feeding of X bivalves with algae 8. & Effluent water containing N& a sets particulate wastes, is a X unused plankton in size range of 3. <10-20m Lipids to Bivalves Culture k& ------Biofuel

X & w -- -

a y Harvested Bivalves US 2012/0231513 A1 Sep. 13, 2012

SYSTEMS AND METHODS FOR CULTURING ther comprising harvesting the algae by feeding the algae to ALGAE WITH BVALVES the planktivorous fishes; extracting lipids from the planktivo rous fishes; and polishing the lipids to form biofuel. Also provided herein are methods for extracting lipids from plank 0001. This application claims the benefit of U.S. Provi tivorous fishes for other uses, such as for human consump sional Application No. 61/170,524, filed Apr. 17, 2009, which tion. is incorporated by reference in its entirety. 0006. In certain embodiments, the bivalves are cultured in a bivalves enclosure separately from the algae cultured in a 1. INTRODUCTION growth enclosure. Water in the bivalves enclosure that has an 0002 Provided herein are systems and methods for increased level dissolved nutrient(s) relative to the water from extracting lipids and/or producing biofuels from algae in the source is flowed into the growth enclosure to sustain algae marine and freshwater environments. growth. Water from the growth enclosure and/or the fish enclosure are recirculated to the bivalves enclosure. In one 2. BACKGROUND OF THE INVENTION embodiment, the effluent from the fish enclosure is flowed to the bivalves enclosure at a rate that allows the bivalves to feed 0003. The United States presently consumes about 42 bil on plankton that are not consumed by the plantivorous fishes. lion gallons per year of diesel for transportation. In 2007, a The residual plankton are generally of a size class that are not nascent biodiesel industry produced 250 million gallons of a effectively retained or consumed by the planktivorous fish, bio-derived diesel substitute produced from mostly soybean e.g., less than 20 Lim, about 10-20 Lim, less than 10 Lim, about oil in the U.S. Biodiesel are fatty acid methyl esters (FAME) 2-10 um, less than 2 Lim, and between 0.2-2 um. made typically by the base-catalyzed transesterification of 0007. In another embodiment, the bivalves provided triglycerides, such as vegetable oil and animal fats. Although herein are used to condition water obtained from a source similar to petroleum diesel in many physicochemical proper prior to using the water to culture the algae in the system. The ties, biodiesel is chemically different and can be used alone methods comprise flowing water from a source into the (B100) or may be blended with petrodiesel at various con bivalves enclosure, prior to flowing into the growth enclosure, centrations in most modern diesel engines. However, a prac such that the level of dissolved inorganic nutrient(s) is tical and affordable feedstock for use in biodiesel has yet to be increased relative to the water from the source. The methods developed that would allow significant displacement of pet can further comprise removing Zooplankton in water from the rodiesel. For example, the price of soybean oil has risen source, prior to flowing the water from the source into the significantly in response to the added demand from the bivalves enclosure. The removal of Zooplankton can be biodiesel industry, thus limiting the growth of the biodiesel accomplished by filtration or by allowing the water to flow industry to less than 1% of the diesel demand. through an enclosure comprising Zooplankton-feeding organ 0004. It has been proposed to use algae as a feedstock for isms, at a rate that allows the organisms to feed on the Zoop producing biofuel, such as biodiesel. Some algae strains can lankton present in the water from the source. Zooplanktivo produce up to 50% of their dried body weight in triglyceride rous fish, such as but not limited to. Clupea harengus oils. Algae do not need arable land, and can be grown with (Atlantic herring, seawater) and Catla catla (Indian major impaired water, neither of which competes with terrestrial carp, freshwater) can be used. food crops. Moreover, the oil production per acre can be 0008. The systems provided herein generally comprise a nearly 40 times that of a terrestrial crop, such as soybeans. source of water; a growth enclosure for culturing algae and a Although the development of algae presents a feasible option bivalves enclosure for culturing bivalves, wherein the growth for biofuel production, there is a need to reduce the cost of enclosure and the bivalves enclosure are in fluid communica producing the biofuel from algae. The fall in oil price in late tion; means to regulate the rate, direction, or both the rate and 2008 places an even greater pressure on the fledgling biofuel direction, of fluid flow between the growth enclosure and the industry to develop inexpensive and efficient processes. Pro bivalves enclosure. Each of the enclosures can have a plural vided herein is a cost-efficient approach for growing algae in ity of inlets and outlets to allow passage of fluids and matters. a large scale for production of biofuel. including algae and/or fishes, between the enclosures and other facilities of the system. The system also comprise 3. SUMMARY OF THE INVENTION means for culturing the bivalves and the algae; and means for feeding a controlled amount of the algae to the bivalves such 0005 Provided herein are methods and systems for that the amount of algae consumed by the bivalves do not extracting lipids and/or producing biofuel from algae in result in a net loss of algae in the system over a period of time. marine and freshwater environments. In one embodiment, The feeding of the bivalves can be controlled by adjusting the provided herein are methods for culturing algae comprising flow rate of an effluent from the growth enclosure to the providing a source of water and a system comprising enclo bivalves enclosure and monitoring the concentration of the sures for culturing algae and culturing bivalves; culturing algae in the effluent. The systems can further comprise means algae and bivalves in the system, whereby the level of at least for harvesting the algae by the planktivorous fishes; means for one dissolved inorganic or organic nutrient in the water in the gathering the planktivorous fishes from which lipids are system is increased relative to water from the source; and feeding the algae to the bivalves at a rate such that the amount extracted and converted to biofuel; means for extracting lipids ofalgae produced in the system is greater than when the algae from the planktivorous fishes; and means for polishing the is cultured in the system without the bivalves. The dissolved lipids to form biofuel. nutrient can be carbon dioxide, ammonia, ammonium ion, a nitrite, nitrite ion, a nitrate, nitrate ion, a phosphate, ortho 4. BRIEF DESCRIPTION OF THE DRAWINGS phosphate ion, minerals, proteins, carbohydrates, or lipids. 0009 FIG. 1 shows an exemplary schematic of water flow Also provided herein are methods for producing biofuel fur and trophic level associations in the bivalves-enhanced algae US 2012/0231513 A1 Sep. 13, 2012

culture system provided herein, which includes bivalves that The bicarbonate-carbonate buffer system is important in Supply carbon dioxide, and dissolved inorganic and organic freshwater and marine cultures for controlling pH and can be nutrients, and filter plankton of a size Smaller than those used to provide CO for photosynthesis. When CO is dis grazed by planktivorous fishes. solved in water, it forms weak carbonic acid which then 0010 FIG. 2 shows another exemplary schematic of a dissociate by losing hydrogen ions to form bicarbonate systems provided herein, wherein algae less than 10 to 20 (HCO) and carbonate (CO) ions. Uptake of CO., for micrometers are not efficiently consumed by the planktivous photosynthesis and its release by respiration are major pro fishes and are flowed into the bivalves enclosure for removal cesses by which organisms alter the concentration of CO. The bicarbonate-carbonate buffer system in water can pro by the bivalves. vide CO for photosynthesis through the following reactions: 5. DETAILED DESCRIPTION OF THE 2HCO, ( ) HCO3 +HO+CO, INVENTION HCO, ( ) OH+CO, 0011 Provided herein are systems and methods for grow ing algae for extracting lipids and/or production of biofuel. The methods provided herein comprise growing algae in a 0015. As a result of CO fixation, hydroxyl groups are system that comprises bivalves. The algae, fishes, and produced which lead to a gradual increase in pH in the water. bivalves are cultured under conditions that promote nutrient Sparging CO directly into the algal culture is commonly recycling, resulting in gains in algal biomass as well as fish used to control pH and provide carbon nutrition. However, for and bivalves biomass. Unlike aquaculture operations where shallow Suspensions at near neutral pH, the residence time of algae is grown as feed for marine invertebrate larvae, the the CO bubbles are insufficient for dissolution, resulting in algae provided herein are cultured to accumulate lipids for continuous loss to the atmosphere. Certain methods provided use as energy feedstocks. The algae are harvested by fish, and herein can reduce the operating cost of an algae facility by the lipids extracted from fish are used to make biofuel. The providing a Supplementary source of CO for the algal cul bivalves cultured in the operation can optionally be sold, as ture. The bivalves are particularly beneficial when carbon animal feed or human food depending on the species and the dioxide is a limiting factor at times in primary production, market. Depending on the location of the system, the methods Such as, in eutrophic water where nitrogen and phosphorous provided herein can also be used to remediate eutrophic is not limiting. Zones, and enable carbon capture. 0016 Precipitation and dissolution of calcium carbonate 0012. Using algae to produce energy feedstock at an in the shells and structural components of bivalves plays a industrial scale requires a cost-effective and Sustainable Sup role in the cycling of inorganic carbon. When calcium car ply of nutrients. The scale of algae culture required dwarfs bonate is precipitated, CO is generated rather than con those of existing culture systems that are designed to produce Sumed. Calcification induces shifts in the seawater carbonate nutritional Supplement, fine chemicals, or aquaculture feed. equilibrium to generate dissolved CO from inorganic car The costs of carbon, nitrogen and phosphorous must be care bon. The deposition of one mole of calcium carbonate fully managed, and any savings and recycling of these nutri (Ca+2 HCO->CaCO+HO+CO) releases nearly one mole of CO in freshwater and 0.6 mole CO in seawater ents can be significant for a culture system at this scale. The (Ware et al., 1991, Coral Reefs 11:1270-120). The water culture system must also be efficient in yielding algal biom becomes more acidic due to the removal of bicarbonate and ass, and remain stable despite seasonal and other environ carbonate ions. The increase in partial pressure of CO2 from mental changes. The bivalves in the algae culture systems biogenic calcification has been studied (Berger et al., 1982, provide various benefits in these respects, and generally pro Naturwissenschaften 69:87-88), and it has been confirmed mote the efficient turnover of nutrients within the system. that calcification and respiration of invasive bivalves is a Without being bound by any theory, the bivalves that are biogenic source of CO (Chauvaud et al., 2003, Limnol. cultured in the system serve as a Supplementary source of Oceangr. 48:2086-2092). carbon dioxide, nitrogen and/or phosphorous. 0017 Calcium is a necessary component for shell secre 0013 Carbon nutrition is a significant component in the tion and formation. Many organisms do not survive when the operating cost of a commercial algal culture facility. Photo level of calcium in the water column falls below a threshold synthetic algae take up dissolved CO (inorganic carbon) and which is about 5 mg/l. Depending in part on the species being inorganic nutrients, and produce organic carbon in the form of used, the minimum concentration of calcium required ranges algal biomass. For high rates of autotrophic production, from about 25 to 150 mg/l. Calcifying organisms, such as atmospheric CO alone cannot satisfy the requirement. The bivalves, exert a variable degree of control over the process of diffusion rate of CO from atmosphere into open ponds have calcification. Growth of the shell of bivalves is governed by been estimated to sustain productivities at about 10 g dry the synthesis of an organic matrix and CaCO crystal growth weight perm per day. In one embodiment, bivalves contrib on the matrix. The amount of calcium in the shell is a function ute carbon dioxide to the system, which carbon dioxide is of the calcium level in ambient water, the amount of water produced as a result of respiration and formation of bivalves pumped across the animal's tissues, the local pH and buffer shells. ing capacity, the metabolism of the animal, and temperature 0014. In surface seawater with a pH of about 8.1, about that controls the rate of the physiologic processes. 90% of the inorganic carbon is bicarbonate ion, 9% is car 0018 Nitrogen is an element that is after carbon the most bonate ion, and only 1% is dissolved CO. The equilibrium is important and often limiting element to aquatic organisms. governed by a series of reactions: Compared to carbon that has one inorganic form, nitrogen exists in several forms in the environment, i.e., ammonium, nitrite, nitrate, dissolved nitrogen gas. Nitrogen also exists as US 2012/0231513 A1 Sep. 13, 2012 dissolved organic nitrogen and particulate organic nitrogen in which favors the release of soluble inorganic phosphate from the system. Input of nitrogen from fixation of atmospheric Fe(III)-bound phosphate complexes. The released dissolved nitrogen by bacteria is not sufficient to Support the needs of a phosphate can be used by the algae of the system. growing algal culture. Phosphorous is essential for the meta 0021. In certain embodiments, the algae produced in the bolic process of energy transfer in both photosynthesis and culture system are harvested by planktivorous fishes, such as respiration. In aquatic environments, phosphorous is found in but not limited to Brevoortia patronus (Gulf menhaden), Sar the water column as dissolved inorganic phosphorous (usu dinella longiceps (Indian oil sardine), and Hypophalmichthys ally orthophosphate), as dissolved organic phosphorous, and molitrix (Chinese silver carp). As prey size is a major factor as particulate organic phosphorous. Phosphate release from affecting planktivore predation, the age or ontogenetic form sediments is affected by adsorption-desorption equilibrium of the fishes are selected Such that the eyesight, locomotion, of phosphate with iron hydroxides. When the sediments are mouth dimensions, dentition, and gut dimension permit the anoxic, the strongly reducing environment is conducive to fishes to ingest efficiently the dominant species of algae cul release of phosphate into water. Traditional fishery practices tured in the system. However, there are smaller plankton in address the shortfall by adding fertilizers and/or manure to the the water that pass through the gills of the selected plantivo Water. rous fishes, and thus remain in the water. The plankton in this 0019. Bivalves filter water continuously at a high rate (up size class includes phytoplankton, Zooplankton and bacteria. to 8 gallons per hour), and can thus recycle nutrients that are A growing abundance of Such smaller residual plankton, if limiting in the system, thereby increasing primary produc left unchecked in the water of the system, can compete with tion. Bivalves process nutrient materials by consuming other algae for nutrients and light, and can also encourage the pelagic or Suspended particulate organic matters, and excret expansion of a Zooplankton population in the system. The ing dissolved organic and inorganic matters. Particulate occurrence of such events can make the system less efficient, organic matters include phytoplankton, Zooplankton, bacte destabilize the system by changing the trophic structure, and ria, and detritus. Suspended organic detritus often has bacte lead to a collapse of the algae culture. The removal of plank ria attached, and these bacteria are decomposing as well as ton in this size class from the water by the bivalves can assimilating the carbon in the detritus. Dissolved inorganic prevent accumulation or overgrowth of Such plankton, and matters include but is not limited to ammonia and orthophos thus maintain stability of the systems provided herein. In phates. Dissolved organic matters, include but is not limited another embodiment, the bivalves stabilize the systems pro to amino acids, proteins, carbohydrates, and lipids. In one vided herein by filtering plankton that are too small to be embodiment, dissolved organic and inorganic materials pro harvested efficiently by the fishes in the system. duced by bivalves provided herein and released in the water of 0022 Algae inhabit all types of aquatic environment, the system are readily taken up by the algae for growth. including but not limited to freshwater, marine, and brackish Exemplary species of bivalves include but are not limited to environment. Accordingly, in certain embodiments, provided Mytilus edulis (marine mussels), Crassostrea species (oys hereinare selected species of algae and bivalves in any of such ters), Lamellidens marginalis (freshwater mussels). aquatic environments. The algal culture can comprise a popu 0020. A number of feeding mechanisms have evolved in lation of algae of one or more species, and the population of bivalves. Filter-feeding bivalves pump large volume of water bivalves can comprise a single species of bivalves or multiple and filter this water to remove suspended particulate materi species. The term "algal composition” refers to any compo als. A variety of particles of different qualitative nutrient sition that comprises algae and is not limited to the culture in values in the water are pumped through the bivalve gills which the algae are cultivated. It is contemplated that an algal acting as filters. Usually water enters the mantle cavity composition can be prepared by mixing different algae from through the inhalant siphon, moves over the gills, and leaves a plurality of algal cultures. As used herein, the term “growth through the exhalent siphon. Particles that are too large are enclosure” refers to a water enclosure in which the algae are rejected as pseudofeces and particles that are too small pass grown. The majority of algal growth takes place in the growth through the gills. The rejected particles are wrapped in enclosure which is designed and equipped to optimize algal mucus, and are expelled without having passed through the growth. In addition, the systems provided herein can com digestive tract. The pseudofeces sink and become available as prise, independently and optionally, enclosures for culturing nutrients for use by benthic organisms and bacteria. Bivalves, fishes that harvest the algae, enclosures for culturing bivalves, and pseudofeces-producing bivalves in particular, are very enclosures for preparing a starter algal culture, enclosures in efficient in the transfer of suspended particulate matters from which Zooplankton is removed, bivalves husbandry units, and the pelagic environment to the benthic environment. Deposit biomass storage units. The bivalves husbandry units provide feeding bivalves generally inhabit muddy benthic environ the environments in which the bivalves are stocked, bred, ment, remove deposited sediments from the benthic environ incubated, or maintained. ment to extract organic matter, and release inorganic wastes. 0023 The algae and the bivalves that are used in the meth In coastal water, a sizeable proportion of nutrients for primary ods provided herein are described in Section 5.1 and 5.2 production is provided by mineralization of particulate matter respectively. As used herein the term “system” refers to the by benthic organisms. Depending on the environment, filter installations for practicing the methods provided herein. The feeding bivalves and/or deposit-feeding bivalves can be used methods and systems provided herein for culturing algae are in the systems provided herein. Feces and pseudofeces, pro described in Section 5.3. Technical and scientific terms used duced by the bivalves falls to and enrich the sediments sur herein have the meanings commonly understood by one of rounding the bivalves where benthic organisms, mostly bac ordinary skill in the art, unless otherwise defined. Reference teria, decompose the organic matters and release inorganic is made herein to various methodologies known to those of nutrients which can be used by the algae in the system. Meta skill in the art. Publications and other materials setting forth bolic activities of the benthic organisms consume oxygen and Such known methodologies to which reference is made are Sustain a hypoxic, reducing environment in the sediment incorporated herein by reference in their entireties as though US 2012/0231513 A1 Sep. 13, 2012 set forth in full. The practice of the methods and systems ments, and may contain a mixture of prokaryotic and eukary provided herein will employ, unless otherwise indicated, otic organisms, wherein some of the minor species may be techniques of chemistry, biology, and the aquaculture indus unidentified. Freshwater filtrates from rivers, lakes; seawater try, which are within the skill of the art. Such techniques are filtrates from coastal areas, oceans; water in hot springs or explained fully in the literature, e.g., Estuarine and Marine thermal vents; and lake, marine, or estuarine sediments, can Bivalve Mollusk Culture, Menzel B. 1991, CRC press, Boca be used to source the algae. The samples may also be col Raton, Fla., USA; Handbook of Microalgal Culture, edited by lected from local or remote bodies of water, including surface Amos Richmond, 2004, Blackwell Science; Limnology: as well as Subterranean water. Lake and River Ecosystems, Robert G. Wetzel, 2001, Aca 0028 Endemic or indigenous species are generally pre demic Press, each of which are incorporated by reference in ferred over introduced species where an open farming system their entireties. is used. Endemic or indigenous species may be enriched or 0024. As used herein, “a” or “an” means at least one, isolated from water samples obtained locally (relative to the unless clearly indicated otherwise. The term “about as used site of the culture system). It can also be beneficial to deploy herein, unless otherwise indicated, refers to a value that is no algae and fishes from a local aquatic trophic system in the more than 20% above or below the value being modified by harvesting methods provided herein. Depending on the loca the term. For clarity of disclosure, and not by way of limita tion of the algae culture system, algae obtained from tropical, tion, the detailed description is divided into the subsections Subtropical, temperate, polar or other climatic regions can be which follow. used. 0029. According to certain embodiments provided herein, 5.1. Algae one or more species of algae will be present in the algal 0025. As used herein the term “algae' refers to any organ culture, or the algal composition that is to be harvested by isms with chlorophyll and a thallus not differentiated into fish. In one embodiment, the algal culture is a monoculture, roots, stems and leaves, and encompasses prokaryotic and wherein only one species of algae is grown. However, in eukaryotic organisms that are photoautotrophic or photoaux many open systems, it may be difficult to avoid the presence otrophic. The terms “microalgae and “phytoplankton, used of other algae in the water. Accordingly, a monoculture may interchangeably herein, refer to any microscopic algae, pho comprise about 0.1% to 2% of algae species other than the toautotrophic or photoauxotrophic protozoa, and cyanobac intended species. In another embodiments, the algal culture is teria (formerly classified as Cyanophyceae). The use of the a mixed culture that comprises one or several species of algae, term "algal also relates to microalgae and thus encompasses i.e., the algal culture is not a monoculture. In certain embodi the meaning of “microalgal. These microscopic aquatic ments, especially when an open system is in use, the compo organisms are also encompassed by the term "plankton.” sition of algae in the algal culture can change seasonally; the While the term plankton includes both phytoplankton and body of water can comprise Zooplankton. The algae in an Zooplankton, it is contemplated that certain embodiments algal culture provided herein may not all be cultivable under provided herein can be practiced without isolation of the laboratory conditions. Not all the algae in an algal culture phytoplankton or removal of the Zooplankton. The culturing provided herein have to be taxonomically classified or char and harvesting methods provided herein are applicable to a acterized in order to be utilized in certain embodiments pro body of water comprising plankton and fishes. vided herein. Algal cultures and algal compositions can gen 0026. The algae that are cultured or harvested by the meth erally be distinguished by the relative proportions of the ods provided herein are grown using Solar power as its energy major groups of algae that are present. Source, although algae can also be grown under artificial light 0030 Chlorophylla is a commonly used indicator of algal and be similarly harvested. The algae provided herein can be biomass. However, it is subjected to variability of cellular a naturally occurring species. The algae can be a transgenic chlorophyll content (0.1 to 9.7% of fresh algal weight) strain, a genetically manipulated Strain, or a selected Strain, depending on algal species. An estimated biomass value can that bears certain beneficial traits, such as but not limited to, be calibrated based on the chlorophyll content of the domi increased growth rate, lipid accumulation, favorable lipid nant species within a population. Published correlation of composition, adaptation to certain environment, and robust chlorophyll a concentration and biomass value can be used in ness in changing environmental conditions. In some embodi certain embodiments provided herein. Generally, chlorophyll ments, it is desirable that the algae accumulate excess lipids a concentration is to be measured within the euphotic Zone of and/or hydrocarbons. In other embodiments, this is not a a body of water. The euphotic Zone is the depth at which the requirement since algal cells with relatively lower lipids level light intensity of the photosynthetically active spectrum (400 but higher carbohydrate level can also be useful, because the 700 nm) equals 1% of the subsurface light intensity. carbohydrates can be converted to lipids metabolically by the 0031. A mixed algal culture provided herein comprises harvesting fish. one or several dominant species of macroalgae and/or 0027 Algae, including microalgae, inhabit all types of microalgae. Microalgal species can be identified by micros aquatic environment, including but not limited to freshwater copy and enumerated by counting or flow cytometry, which (less than about 0.5 parts per thousand (ppt) salts), brackish are techniques well known in the art. A dominant species is (about 0.5 to about 31 ppt salts), marine (about 31 to about 38 one that ranks high in the number of algal cells, e.g., the top ppt salts), and briny (greater than about 38 ppt salts) environ one to five species with the highest number of cells relative to ment. As certain embodiments provided herein can be prac other species. The one or several dominant algae species may ticed in any of such aquatic environments, freshwater species, constitute greater than about 10%, about 20%, about 30%, marine species, and/or species that thrive in varying and/or about 40%, about 50%, about 60%, about 70%, about 80%, intermediate salinities or nutrient levels, can be used. The about 90%, about 95%, about 97%, about 98% of the algae algae used in the algal culture can be obtained initially from present in the culture. In certain embodiments, several domi environmental samples of natural or man-made environ nant algae species may each independently constitute greater US 2012/0231513 A1 Sep. 13, 2012

than about 10%, about 20%, about 30%, about 40%, about coccales, Nostocales, Oscillatoriales, Pseudanabaenales, 50%, about 60%, about 70%, about 80% or about 90% of the Synechococcales, and Synechococcophycideae. Non-limit algae present in the culture. Many other minor species of ing examples include Gleocapsa, Pseudoanabaena, Oscilla algae may also be present in Such culture but they may con toria, Microcystis, Synechococcus and Arthrospira species. stitute in aggregate less than about 50%, about 40%, about 0036. In certain embodiments, the algal culture or the algal 30%, about 20%, about 10%, or about 5% of the algae composition to be harvested comprises algae from one or present. In various embodiments, one, two, three, four, or five dominant species of algae are present in a culture. Accord more of the following taxonomic classes: Euglenophyceae, ingly, a mixed algal culture or an algae composition can be Dinophyceae, and Ebriophyceae. Non-limiting examples described and distinguished from other cultures or composi include Euglena species and the freshwater or marine tions by the dominant species of algae present. The compo dinoflagellates. sition and culture can be further described by the percentages 0037. In certain embodiments, the algal culture or the algal of cells that are of dominant species relative to minor species, composition to be harvested comprises green algae from one or the percentages of each of the dominant species. The iden or more of the following taxonomic classes: Micromonado tification of dominant species can also be limited to species phyceae, Charophyceae, Ulvophyceae and Chlorophyceae. within a certain size class, e.g., from about 200 to 2000 um, Non-limiting examples include species of Borodinella, Chlo about 20 to 200 um, about 2 to 20 um, or below 2 Lim. It is to rella (e.g., C. ellipsoidea), Chlamydomonas, Dunaliella (e.g., be understood that mixed algal cultures or compositions hav D. Salina, D. bardawil), Franceia, Haematococcus, Oocystis ing the same genus or species of algae may be different by (e.g., O. parva, O. pustilla), Scenedesmus, Stichococcus, virtue of the relative abundance of the various genus and/or Ankistrodesmus (e.g., A. falcatus), Chlorococcum, species present. Monoraphidium, Nannochloris and Botryococcus (e.g., B. 0032. It is contemplated that many different algal cultures braunii). In certain embodiments, Chlamydomonas rein or bodies of water which comprise plankton, can be cultured hardtii are less preferred. and/or harvested efficiently by the methods provided herein. Microalgae are preferably used in certain embodiments pro 0038. In certain embodiments, the algal culture or the algal vided herein; while macroalgae can be less preferred in cer composition to be harvested comprises golden-brown algae tain embodiments. In specific embodiments, algae of a par from one or more of the following taxonomic classes: ticular taxonomic group, genera or species, may be less Chrysophyceae and Synurophyceae. Non-limiting examples preferred. Such algae, including one or more that are listed include Boekelovia species (e.g. B. hooglandii) and below, may be specifically excluded as a dominant species in Ochromonas species. a culture. However, it should also be understood that in certain 0039. In certain embodiments, the algal culture or the algal embodiments, such algae may be present as a contaminant composition to be harvested comprises freshwater, brackish, especially in an open system, or as a non-dominant group or or marine diatoms from one or more of the following taxo minor species. Such algae may be present in negligent num nomic classes: Bacillariophyceae, Coscinodiscophyceae, and bers, or substantially diluted given the volume of the culture. Fragilariophyceae. Preferably, the diatoms are photoau The presence of Such algal genus or species in a culture or a totrophic or auxotrophic. Non-limiting examples include body of water comprising plankton is distinguishable from Achnanthes (e.g., A. Orientalis), Amphora (e.g., A. coffeifor cultures or other bodies of water where such genus or species mis Strains, A. delicatissima), Amphiprora (e.g., A. hyaline), are dominant, or constitute the bulk of the algae. Amphipleura, Chaetoceros (e.g., C. muelleri, C. gracilis), 0033. In certain embodiments, an algal composition com Caloneis, Camphyllodiscus, Cyclotella (e.g., C. cryptica, C. prising a combination of different groups of algae can be meneghiniana), Cricosphaera, Cymbella, Diplomeis, Ento used. The algal composition can be prepared by mixing a moneis, Fragilaria, Hantschia, Gyrosigma, Melosira, Nav plurality of different algal cultures. The different groups of icula (e.g., N. acceptata, N. biskanterae, N. pseudotenel algae can be present in defined proportions. The combination loides, N. saprophila), Nitzschia (e.g., N. dissipata, N. and proportion of different algae in the algal composition can communis, N. inconspicua, N. pusilla strains, N. micro be designed to enhance the growth and/or accumulation of cephala, N. intermedia, N. hantzschiana, N. alexandrina, N. lipids of certain groups or species of fish. quadrangula), Phaeodactylum (e.g., P tricornutum), Pleuro 0034. In certain embodiments, one or more species of sigma, Pleurochrysis (e.g., P. carterae, P. dentata), Selenas algae belonging to the following phyla can be cultured and/or trum, Surirella and Thalassiosira (e.g., T. Weissflogii). harvested by the methods provided herein: Cyanobacteria, 0040. In certain embodiments, the algal culture or the algal Cyanophyta, Prochlorophyta, Rhodophyta, Glaucophyta, composition to be harvested comprises planktons that are Chlorophyta, Dinophyta, Cryptophyta, Chrysophyta, Pryn characteristically small with a diameter in the range of 1 to 10 nesiophyta (Haptophyta), Bacillariophyta, Xanthophyta, rpm, or 2 to 4 Lum. Many of Such algae are members of Eustigmatophyta, Rhaphidophyta, and Phaeophyta. In cer Eustigmatophyta. Such as but not limited to Nannochloropsis tain embodiments, algae in multicellular or filamentous species (e.g. N. Salina). forms, such as seaweeds or macroalgae, many of which 0041. In certain embodiments, the algal culture or the algal belong to the phyla Phaeophyta or Rhodophyta, are less pre composition to be harvested comprises one or more algae ferred. In many embodiments, algae that are microscopic, are from the following groups: Coelastrum, Chlorosarcina, preferred. Many such microalgae occurs in unicellular or Micractinium, Porphyridium, Nostoc, Closterium, Elakato colonial form. thrix, Cyanosarcina, Trachelamonas, Kirchneriella, Cart 0035. In certain embodiments, the algal culture or the algal eria, Crytomonas, Chlamydamonas, Planktothrix, Ana composition to be harvested by the methods provided herein baena, Hymenomonas, Isochrysis, Pavlova, Monodus, comprises cyanobacteria (also known as blue-green algae) Monallanthus, Platymonas, Pyramimonas, Stephanodiscus, from one or more of the following taxonomic groups: Chroo Chroococcus, Staurastrum, Netrium, and Tetraselmis. US 2012/0231513 A1 Sep. 13, 2012

0042. In certain embodiments, any of the above-men same climatic region, same salinity environment, or same tioned genus and species of algae may independently be less ecosystem, as the algae are used. preferred as a dominant species in, or excluded from, an algal 0046 Bivalves use several mechanisms for feeding. Some composition provided herein. species can use more than one mechanism to feed, depending on the conditions of the environment. In one embodiment, the 5.2 Bivalves population of bivalves comprises exclusively or predomi nantly filter feeding species. In another embodiment, the 0043. As used herein, the term bivalves refers to any population of bivalves comprises exclusively or predomi exoskeleton-bearing invertebrate animals of the class nantly deposit feeding species. In yet another embodiment, Bivalvia in phylum Mollusca. The term is not limited to the population of bivalves comprises exclusively or predomi species that are consumed by humans as food. When referring to a plurality of organisms, the term “bivalve' is used inter nantly species that contains photoautotrophic symbionts changeably with the term “bivalves’ regardless of whether (Zooxanthellae) and/or chemotrophic symbionts. The one or more than one species are present, unless clearly chemotrophic symbionts are mostly bacteria that reside in indicated otherwise. In certain embodiments, bivalves useful extracellular or intracellular locations. The chemotrophic for the methods and systems provided herein can be obtained symbionts include lithotrophic and methanotrophic organ from hatcheries or collected from the wild. The bivalves may isms. In a preferred embodiment, the major species of be spats, larvae, trochophores, Veligers, pediveligers, juve bivalves in the population are not phytoplanktivores that niles, or mature bivalves. The bivalves may reproduce in an would consume significant amounts of the growing algae. In enclosure within the system but not necessarily in the same certain mixed bivalves population provided herein, filter enclosure as the algae culture. Any bivalves aquaculture tech feeding and deposit feeding species are both present. In addi niques known in the art can be used to stock, maintain, repro tion to filter feeding and deposit feeding species, species that duce, and harvest the bivalves useful for the methods and contain photoautotrophic and/or chemoautotrophic sym systems provided herein. bionts are also present in a mixed bivalves population pro 0044 According to certain embodiments provided herein, vided herein. the algae reside in the same body of water as a population of 0047 Bivalves from different taxonomic groups can be bivalves. In one embodiment, the bivalves population com used in the enclosure. It should be understood that, in various prises only one species of bivalves. In another embodiment, embodiments, bivalves within a taxonomic group. Such as a the bivalves population is mixed and thus comprises one or family or a genus, can be used interchangeably in various several major species of bivalves. A major species is one that methods provided herein. Certain embodiments provided ranks high in the head count, e.g., the top one to five species herein are described below using common names of bivalves with the highest head count relative to other species. The one groups and bivalves, as well as the Scientific names of exem or several major bivalves species may constitute greater than plary species. Databases, such as the Ocean Biogeographic about 10%, about 20%, about 30%, about 40%, about 50%, Information System by World Wide Web electronic publica about 60%, about 70%, about 75%, about 80%, about 90%, tion, www.iobis.org, version (03/2009), provide additional about 95%, about 97%, about 98% of the bivalves present in useful bivalves species within each of the taxonomic groups the population. In certain embodiments, several major that are useful in certain embodiments provided herein. It is bivalves species may each constitute greater than about 10%, contemplated that one of ordinary skill in art could, consistent about 20%, about 30%, about 40%, about 50%, about 60%, with the scope of certain embodiments provided herein, use about 70%, or about 80% of the bivalves present in the popu the databases to specify other species within each of the lation. In various embodiments, one, two, three, four, five described taxonomic groups for use in the methods provided major species of bivalves are present in a population. Accord herein. ingly, a mixed bivalves population or culture can be described 0048. The selection of bivalves for use in the methods and distinguished from other populations or cultures by the provided hereindepends on a number of factors. Some of the major species of bivalves present. The population or culture most important factors are the compatibility of the cultured can be further described by the percentages of the major and algae and the bivalves. Preferably, the algae culture grows minor species, or the percentages of each of the major species. well using the carbon dioxide and metabolic waste produced It is to be understood that mixed cultures having the same by the selected bivalves, thereby reducing the need to add genus or species may be different by virtue of the relative CO and to fertilize the water. Preferably, the population of abundance of the various genus and/or species present. bivalves is self-sustaining and does not require extensive 0045 Bivalves inhabits most types of aquatic environ husbandry efforts to promote reproduction and rear the lar ment, including but not limited to freshwater, marine, brack vae. The methods provided herein can employ species of ish, and briny environment. In certain embodiments, as the bivalves that are used as human food, to offset the cost of methods and systems provided herein can be practiced in any operating the algae culture. of Such aquatic environments, any freshwater species, Steno 0049. A representative group of bivalves that are useful in haline species, euryhaline species, marine species, species certain embodiments provided herein is the mollusks. Mol that grow in brine, and/or species that thrive in varying and/or lusks in the classes, Bivalvia and Gastropoda, are of particular intermediate salinities, can be used. Bivalves from tropical, interest. Within the class of bivalves are several orders which Subtropical, temperate, polar, and/or other climatic regions include many ecologically and commercially important spe can be used. Bivalves that live within the following tempera cies, such as but not limited to, Mytiloida (Mytilidae (sea ture ranges can be used: below 10°C., 9° C. to 18°C., 15° C. mussels)); Ostreoida (Pectimidae, Ostreidae, Unionoida to 25° C., 20° C. to 32° C. In one embodiment, bivalves (freshwater mussels); Myoida, Pterioida (Pteriidae, pearl indigenous to the region at which the methods provided oysters), and Veneroida (Tridacnidae, Lucimidae). Within herein are practiced, are used. Preferably, bivalves from the Gastropoda are Subclasses of organisms that produce pearl, US 2012/0231513 A1 Sep. 13, 2012

e.g., Patellogastropoda, Vetigastropoda, Littprinoida, Ton dently the rate, direction, or both the rate and direction, of nida, Muricoida and Pulmonata. fluid flow between each of the bivalves enclosure, the growth 0050. The bivalves used in the methods provided herein enclosure and the fish enclosure are also provided. are preferably sessile or sedentary and of commercial value, 0053. The bivalves, growth, and fish enclosures can be but including but not limited to oysters, mussels, Scallops, and not limited to raceways, rectangular tanks, circular tanks, clams. Exemplary species includebut are not limited to, Cras partitioned tanks, plastic bags, earthen ponds, lined ponds, Sostrea species such as C. gigas, C. virginica, C. ariakensis, channels, and artificial streams. The enclosures of the sys C. rivularis, C. angulata, C. eradelie, C. commercialis, Sac tems provided herein are connected by channels, hoses, and costrea species such as S. glomerata, S. cucculata and S. pipes. The rate, direction, or both rate and direction of flow is commercialis, Mercenaria species such as M. mercenaria and controlled by pumps, valves, and gates. The bivalves enclo M. campechensis, Ostrea species such as O. edulis, O. chil Sure may comprise embedded, Submerged or floating Sub ensis, and O. lurida, Arca transversa, Panope generosa, Sax strates, such as ropes, racks, and tubes. Preferably, the odomus nuttili, Mytilus species such as M. edulis (blue mus bivalves enclosure comprises a sedimentary bottom and a sel), M. coruscus, M. chilensis, M. trossulus, and M. benthic community of organisms, such that solid wastes pro galloprovincialis (Mediterranean mussel), Aulacomya ater; duced by the bivalves can be remineralized by the benthic Choromytilus chorus, Tapes semidecussatus, Perna species organisms and bacteria. The enclosures provided herein can Such as P viridis, P canaliculus, Venerupis species such as V. be set up according to knowledge known in the art, see, for decussata, V. semidecussata, Sinonovacula constricta (Razor example, Chapters 13 and 14 in Aquaculture Engineering, clam), Spisula solidissima (Surf clams), Amusium balloti, Odd-Ivar Lekang, 2007, Blackwell Publishing Ltd., respec Argopecten irradians (bay Scallops), Pectan species such as tively, for description of closed production systems and open P alba, P. vessonsis, P. maximus, Pinctada species such as P farming systems. margaritifera, P radiate, P. maxima, Pficata, P albina, 0054 The mode of algal culture can be a batch culture, a Hyriopsis species, such as H. cumingii, H. Schlegelii, Tridac continuous culture, or a semi-continuous culture. A batch nidae species, such as Tridacna gigas (giant clam), Lamel culture comprises providing a single inoculation of algal cells lidens species, such as L. marginalis (freshwater mussels), L. in a volume of water in the growth enclosure followed by a corrianus, and Chlamys species such as C. farreri, C. Oper growing period and finally harvesting the algal population cularis, C. prpuratus and C. varia. when it reaches a desirable density. Typically, the growth of 0051 Although native species are preferably used, non algae is characterized by a lag phase, a growth phase, and a native species that has already invaded a particular body of stationary phase. The lag phase is attributed to physiological water can also be used, e.g., Dreissena species such as D. adaptation of the algal metabolism to growth. Cultures inocu polymorpha (Zebra mussels), D. bugenesis (quagga mussels) lated with exponentially growing algae have short lag phases and D. rostiformis, Corbiucla species such as C. fluminea and are thus desirable. Cell density increases as a function of (Asian clam). time exponentially in the growth phase. The growth rate decreases as nutrient levels, carbon dioxide, unfavorable pH, 5.3 Methods and Systems or other environmental factors become limiting in a stationary 0052 Provided herein are methods and systems for grow phase culture. When a growing algae culture has outgrown ing algae to extract lipids and/or produce biofuel. According the maximum carrying capacity of an enclosure, the culture to certain embodiments provided herein, the algae as can be transferred to one or several growth enclosures with a described in Section 5.1 and the bivalves as described in lower loading density. The initial algal culture is thereby Section 5.2 are cultured for a period of time in a circulating diluted allowing the algae to grow without being limited by body of water in the systems. The algae are cultured in the the capacity of an enclosure. In a continuous culture, water same body of water as the bivalves in the system, wherein at with nutrients and gases is continuously allowed into the least one dissolved inorganic or organic nutrients provided by growth enclosure to replenish the culture, and excess water is the bivalves enable the algae to grow more efficiently than in continuously removed while the algae in the water are har the absence of the bivalves. For example, the algae culture Vested. The culture in the growth enclosure is maintained at a may require less carbon dioxide, nitrogen fertilizer, and/or particular range of algal density or growth rate. In a semi phosphorous fertilizer. The dissolved inorganic nutrient can continuous culture, growing algae in an enclosure is har be carbon dioxide, ammonia, ammonium ion, a nitrite, nitrite vested periodically followed by replenishment to about the ion, a nitrate, nitrate ion, a phosphate, or orthophosphate ion. original Volume of water and concentrations of nutrient and Organic nutrients include amino acids, proteins, lipids, and gases. Preferably, the water in the system is recycled to the carbohydrates. However, it is not required that the bivalves bivalves enclosure. In a preferred embodiment, the algae and the algae be cultured together in the same enclosure or culture is a continuous culture, maintained in open air. throughout the entire culturing process. In one embodiment, 0055 Most natural freshwater sources (rivers, lakes, the bivalves and the algae reside in the same enclosure but the springs) and municipal water Supply can be used as a source bivalves reside in a Zone within the enclosure, such as the of water for used in the systems provided herein. Seawater, benthic layer. In other embodiments, the bivalves and algae saline, and brackish water from inland, coastal or estuarine are cultured separately. The systems provided herein can regions, irrigation water, agricultural wastewater, industrial comprise a source of water, a plurality of enclosures and wastewater, or municipal wastewater can also be used in the means for growing algae, bivalves, and/or fishes, particularly, systems provided herein. Depending on the Source of water, it a growth enclosure for culturing algae, a fish enclosure for may be necessary to provide additional nutrients if the source culturing planktivorous fishes, and a bivalves enclosure for is oligotrophic. In some embodiments, the Source of water is culturing bivalves. The growth enclosure, the fish enclosure, eutrophic, in which case, the water comprises a plurality of and the bivalves enclosure are each in fluid communication algae, planktonic animals, and bacteria, and certain nutrients. with the other enclosures, and means to regulate indepen Algae from the water can be used to inoculate the growth US 2012/0231513 A1 Sep. 13, 2012 enclosure. Zooplankton that consumes algae can be removed 10,000 lux, preferably 2500 to 5000 lux. The photoperiod by filtration or by flowing the water through an enclosure (light: dark in number of hours) ranges from about 12:12, comprising Zooplantivorous fishes. about 14:10, about 16:8, about 18:6, about 20:4, about 22:2, 0056. The water for growing algae can comprise carbon and up to 24:0. The light intensity and photoperiod depend on dioxide, either dissolved or as bubbles, at a concentration the geographic location of the growth enclosures and the from about 0.05% to 1% and up to 5% volume of the air season, and may be manipulated by artificial illumination or introduced into the culture. The addition of carbon dioxide shading. Mixing of water in the growth enclosure ensures that promotes photosynthesis, and helps to maintain the pH of the all algal cells are equally exposed to light and nutrients. culture below pH 9. Sources of carbon dioxide include, but is Mixing is also necessary to prevent sedimentation of the algae not limited to, synthetic fuel plants, gasification powerplants, to the bottom or to a depth where light penetration becomes oil recovery plants, ammonia plants, ethanol plants, oil refin limiting. Mixing also prevent thermal stratification of outdoor ery plants, anaerobic digestion units, cement plants, and fossil cultures. Mixing can be provided in part by the siphoning steam plants. The use of Such carbon Source in the culturing action of bivalves or by the presence of swimming fish in the process enables carbon capture by the methods provided growth enclosure. Where additional mixing is required, it can herein. For example, the water can be supplemented with fly be provided by any means, mechanical or otherwise, includ ashes collected from gaseous output of coal-burning power ing but not limited to, paddle wheels and jet pumps. generation plants. The chemical composition of fly ashes 0060 Means and techniques for bivalves culture are well depends on the source, e.g., anthracite, bituminous, and lig known in the art and can be adapted to for use in certain nite coal. Fly ashes range in size from 0.5um to 100 um, and embodiments provided herein without undue experimenta comprise silicon dioxide, calcium oxide, iron oxide, alumi tion. For example, the bottom technique involves scattering num oxide. Silicon is required for the growth of algae, such as on the bottom of the water spat-laden cultch. Stake culture the diatoms. However, according to certain embodiments pro involves attaching spat-laden shells to bamboo, wooden, vided herein, the amount of carbon dioxide required to be cement, or PVC pipe stakes and driving the stakes into the added to the algae culture can be reduced by the presence of bottom or laid out horizontally. Spat may be allowed to settle a population of growing bivalves. The growth enclosures can directly on the stakes. This technique is particularly useful in also be fertilized regularly according to conventional prac areas with soft bottoms that would not allow bottom culture. tices. Nutrients can be provided in the form of fertilizers, Umbrella culture uses bivalves that have been attached to including inorganic fertilizers, such as but not limited to, ropes and Suspended from a central post radiating to anchors ammonium sulfate, urea, calcium Superphosphate, and vari like spokes on a wheel, thus taking the shape of an umbrella. ous N/P/K fertilizers (16:20:20, or 14:14:14); such as but not Rack culture is accomplished by constructing racks of treated limited to, manure and agricultural waste. Less fertilizer is lumber, steel rebar, or concrete blockS. Ropes, sticks, or nylon required in the systems provided herein than a system without mesh bags with bivalves attached or contained are placed on bivalves because the bivalves excrete dissolved and solid the racks for growout. The mesh bag technique is used quite metabolic waste in the bivalves enclosure. extensively in areas that are too shallow for raft culture and 0057 Means for culturing bivalves, algae and fishes are too soft for bottom culture. Raft culture incorporates floating installed in the bivalves enclosure, the growth enclosures, and structures to suspend bivalves off the bottom. The rafts can be the fish enclosures, and generally include equipment to moni made of logs, bamboo, Styrofoam, or 55-gallon drums. Raft tor and adjust the pH, salinity, temperature and/or dissolved materials are lashed together to allow flexing with wave gas in the water. The pH of the water is preferably kept within action. Rafts are anchored to the bottom securely. Strings, the ranges of from about pH6.5 to pH9, and more preferably ropes, nets (pearl nets, lantern nets), trays, and bags of from about 8.2 to about 8.7. The salinity of seawater ranges bivalves are suspended below the raft. The long line technique preferably from about 12 to about 40 g/L and more preferably also involves suspending bivalves off the bottom, wherein from 20 to 24 g/L. The temperature for seawater-based cul spat-laden cultch are attached to polypropylene rope and ture ranges preferably from about 16° C. to about 27°C. or strung betweenwooden, metal, or PVC plastic stakes inserted from about 18°C. to about 24° C. into the Substrate. Other techniques known in the art can also 0058 According to the methods provided herein, a starter be applied, see, for example, U.S. Pat. Nos. 3,811.411, 4,896, culture of algae can be used to seed a growth enclosure. A 626, 5,511,514 and 5,836,266. The bivalves can be fed with starter culture can also be used to inoculate a growth enclo algae produced in the growth enclosure by flowing an effluent Sure periodically to maintain a stable population of the from the growth enclosure. The amount of algae allowed to desired species. The starter culture is grown in water enclo flow into the bivalves enclosure is monitored and controlled Sures typically smaller than the growth enclosure, referred to so that the yield of the system is not affected by over-con herein as "inoculation enclosures.” The inoculation enclo Sumption by the bivalves. The amount of algae can be con Sures can be, but not limited to, one or more flasks, carboys, trolled by adjusting the flow rate of the effluent, the concen cylinders, plastic bags, chambers, indoor tanks, outdoor tration of algae in the effluent, or the amount of time that the tanks, indoor ponds, and outdoor ponds, or a combination flow is established. In addition, the bivalves can also be fed thereof. One or more inoculation enclosures can be tempo with algae present in the source of the water, or the residual rarily or permanently connected to one or more growth enclo algae that are not consumed by planktivorous fishes provided Sures and to each other with means for regulating fluid flow herein. and flow direction, e.g., gate, valve. Typically, the Volume of 0061. In addition to algae and bivalves, the bivalves and an inoculation enclosure ranges from 1 to 10 liters, 5 to 50 growth enclosure may comprise other aquatic life, such as liters, 25 to 150 liters, 100 to 500 liters. In certain embodi fishes, bacteria, Zooplankton, aquatic plants, insects, worms, ments, the inoculation enclosure does not comprise fish. and nematodes. These bacteria, plants, and animals constitute 0059 For productive growth in an enclosure, the algae are various trophic levels of an ecological system and lend sta exposed to light of an intensity that ranges from 1000 to bility to an algal culture grown in an open pond. However, US 2012/0231513 A1 Sep. 13, 2012

Zooplankton grazing on microalgae compete with bivalves genus, can be used interchangeably in various methods pro for food and are generally undesirable in the growth enclo vided herein. Certain embodiments provided herein sure. They can be removed from the water by sand filtration or described below using common names of fish groups and controlled by keeping Zooplanktivorous fishes in an enclo fishes, as well as the Scientific names of exemplary species. Sure. The numbers and species of planktons, including Zoop Databases, such as FishBase by Froese, R. and D. Pauly (Ed.), lanktons, can be assessed by counting under a microscope World Wide Web electronic publication, www.fishbase.org, using, for example, a Sedgwick-Rafter cell. version (06/2008), provide additional useful fish species 0062. In various embodiments, the algae are concentrated within each of the taxonomic groups that are useful in certain so that the number of algal cells per unit volume increases by embodiments provided herein. It is contemplated that one of two, five, 10, 20, 25, 30, 40, 50, 75, 100-fold, or more. For ordinary skill in art could, consistent with the scope of certain example, the starting concentration of an algal culture can embodiments provided herein, use the databases to specify range from about 0.05 g/L, about 0.1 g/L, about 0.2 g/L, about other species within each of the described taxonomic groups 0.5 g/L to about 1.0 g/L. After the concentration step, the for use in the methods provided herein. concentration of algae in analgal composition can range from 0065. In certain embodiments, the fishes used comprise at least about 0.2 g/L, about 0.5g/L, about 1.0 g/L, about 2.0 fishes in the order Clupeiformes, i.e., the clupeids, which g/L, about 5 g/L to about 10 g/L. An alternative system to include the following families: Chirocentridae, Clupeidae assess algal concentration that measures chlorophyll-acon (menhadens, shads, herrings, sardines, hillsa), Denticipitidae, centration (ug/L) can be used similarly. The concentration of Engraulidae (anchovies). Exemplary members within the algae can be increased progressively by concentrating the order Clupeiformes include but not limited to, the menhadens algae in multiple stages. Starting in the growth enclosure, the (Brevoortia species), e.g., Ethmidium maculatum, Brevoortia algal culture is concentrated to provide an algal composition aurea, Brevoortia gunteri, Brevoortia Smithi, Brevoortia pec comprising algae at a density or concentration that is higher tinata, Gulf menhaden (Brevoortia patronus), and Atlantic than that of the algal culture in the growth enclosure. The menhaden (Brevoortia tyrannus); the shads, e.g., Alosa alosa, concentrated algal composition can be subjected to another Alosa alabamae, Alosa fallax, Alosa mediocris, Alosa round of concentration using the same or a different tech sapidissima, Allos pseudoharengus, Alosa chrysochloris, nique. Although it is desirable to remove as much water as Dorosoma petenense; the herrings, e.g., Etrumeus teres, possible from the algae before processing, it should be under Harengula thrissina, Pacific herring (Clupea palasii pal stood that the concentration step does not require that the lasii), Alosa aestivalis, Ilisha africana, Ilisha elongata, Ilisha algae be dried, dewatered, or reduced to a paste or any semi megaloptera, Ilisha melastoma, Ilisha pristigastroides, Pel Solid state. The resulting concentrated algae composition can lona ditchela, Opisthopterus tardoore, Nematalosa come, be a solid, a semi-solid (e.g., paste), or a liquid (e.g., a sus Alosa aestivalis, Alosa chrysochloris, freshwater herring pension). It can be stored for future use, used to make biofuel, (Alosa pseudoharengus), Arripis georgianus, Alosa or used as feed for the bivalves. chrysochloris, Opisthonema libertate, Opisthonema ogli 0063. The choice of fish for use in the harvesting methods num, Atlanticherring (Clupea harengus), Balticherring (Clu provided herein depends on a number of factors, such as the pea harengus membras); the Sardines, e.g., Ilisha species, palatability and nutritional value of the cultured algae as food Sardinella species, Amblygaster species, Opisthopterus for the fishes, the lipid composition and content of the fish, the equatorialis, Sardinella aurita, Pacific sardine (Sardinops feed conversion ratio, the fish growth rate, and the environ sagax), Harengula clupeola, Harengula humeralis, Haren mental requirements that encourages feeding and growth of gula thrissina, Harengulajaguana, Sardinella albella, Sar the fish. For example, it is preferable that the selected fishes dinella janeiro, Sardinellafimbriata, oil sardine (Sardinella will feed on the cultured algae until satiation, and convert the longiceps), and European pilchard (Sardina pilchardus); the algal biomass into fish biomass rapidly and efficiently. Gut hilsas, e.g., Tenuolosa species, and the anchovies, e.g., content analysis can reveal the dimensions of the plankton Anchoa species (A. hepsetus, A. mitchillis), Engraulis spe ingested by the planktivore and the preference of the plank cies, Thryssa species, anchoveta (Engraulis ringens), Euro tivore for certain species of algae. Knowing the average pean anchovy (Engraulis encrasicolus), Engraulis eurystole, dimensions of ingested plankton, the preference and effi Australian anchovy (Engraulis australis), and Setipinna ciency of the planktivore towards a certain size class of plank phasa, Coilia dussumieri. ton can be determined. The size preference of a planktivore 0066. In a preferred embodiment, the fishes used are shin can be used to match the dimensions of algae in the algal ers. A variety of shiners that inhabit the Gulf of Mexico, composition to improve efficiency, e.g., sizes of algae being particularly Northern Gulf of Mexico, can be used. Examples greater than about 20 Lum, about 20-200 um. It may also be of shiners include but are not limited to, members of Luxilus, preferable to deploy combinations of algae and fishes that are Cyprinella and Notropis genus, Alabama shiner (Cyprinella parts of a naturally occurring trophic system. Many trophic callistia). Altamaha shiner (Cyprinella xaenura), Ameca systems are known in the art and can be used to guide the shiner (Notropis anecae), Ameca shiner (Notropis anecae), selection of algae and fishes for use in certain embodiments Apalachee shiner (Pteronotropis grandipinnis), Arkansas provided herein. Rivershiner (Notropis girardi). Aztec shiner (Aztecula Sallaei 0064. The selected fishes should grow well in water of a old), Balsas shiner (Hybopsis boucardi), Bandfin shiner salinity which is similar to that of the algal culture, so as to (Luxilus zonistius), Bannerfin shiner (Cyprinella leedsi), reduce the need to change water when the algae is brought to Beautiful shiner (Cyprinella formosa), Bedrock shiner (Not the fishes. For an open pond system, it may be preferable to ropis rupestris), Bigeye shiner (Notropis boops), Bigmouth use endemic species of fishes. Fishes from different taxo shiner (Hybopsis dorsalis), Blackchin shiner (Notropis het nomic groups can be used in the growth enclosure or fish erodon), Blackmouth Shiner (Notropis melanostomus), Blac enclosure. It should be understood that, in various embodi knose shiner (Can Quebec Notropis heterolepis), Blacknose ments, fishes within a taxonomic group. Such as a family or a shiner (Notropis heterolepis), Blackspot shiner (Notropis US 2012/0231513 A1 Sep. 13, 2012

atrocaudalis), Blacktail shiner (Cyprinella venusta), Black nis), Sand shiner (Notropis stramineus), Sandbar shiner (Not tip shiner (Lythrurus atrapiculus), Bleeding shiner (Luxilus ropis scepticus), Satinfin shiner (Cyprinella analostana), zonatus), Blue Shiner (Cyprinella caerulea), Bluehead Scarlet shiner (Lythrurus fasciolaris), Sharpnose Shiner (Not Shiner (Pteronotropis hubbsi), Bluenose Shiner (Pteronotro ropis Oxyrhynchus). Notropis atherinoides, Notropis hudso pis welaka), Bluestripe Shiner (Cyprinella callitaenia), nius, Richardsonius balteatus, Pomoxis nigromaculatus, Bluntface shiner (Cyprinella camura), Bluntnose shiner Cymatogaster aggregata, Shiner Mauritania (Selene dorsa (Notropis simus), Bluntnosed shiner (Selene setapinnis), lis), Silver shiner (Notropis photogenis), Silver shiner (Rich Bridle shiner (Notropis bifrenatus), Broadstripe shiner (Not ardsonius balteatus), Silver shiner (Richardsonius baltea ropis euryzomus), Burrhead shiner (Notropis asperifrons), tus), Silver shiner (Notropis photogenis), Silverband shiner Cahaba Shiner (Notropis cahabae), Cape Fear Shiner (Not (Notropis shunardi), Silverside shiner (Notropis candidus), ropis mekistocholas), Cardinal shiner (Luxilus cardinalis), Silverstripe shiner (Notropis stilbius), Skygazer shiner (Not Carmine shiner (Notropis percobromus), Channel shiner ropis uranoscopus), Smalleye Shiner (Notropis buccula), (Notropis wicklifi), Chemyfin shiner (Lythrurus roseipinnis), Soto la Marina shiner (Notropis aguirrepequenoi), Spotfin Chihuahua shiner (Notropis chihuahua), Chub shiner (Not shiner (Cyprinella spiloptera), Spottail shiner (Notropis hud ropis potteri), Coastal shiner (Notropis petersoni), Colorless sonius), Steelcolor shiner (Cyprinella whipplei), Striped Shiner (Notropis perpallidus), Comely shiner (Notropis shiner (Luxilus chrysocephalus), Swallowtail shiner (Notro amoenus), Common emerald shiner (Notropis atherinoides), pis procne), Taillight shiner (Notropis maculatus), Tallapoosa Common shiner (Luxilus cornutus), Conchos shiner (Cyp shiner (Cyprinella gibbsii), Tamaulipas shiner (Notropis bray rinella panarcy's), Coosa shiner (Notropis xaenocephalus), toni), Telescope shiner (Notropis telescopus), Tennessee Crescent shiner (Luxilus cerasinus), Cuatro Cienegas shiner shiner (Notropis leuciodus), Tepehuan shiner (Cyprinella (Cyprinella xanthicara). Durango shiner (Notropis aulidion), alvarezdelvillari), Texas Shiner (Notropis amabilis), Topeka Dusky shiner (Notropis cummingsae), DuskyStripe shiner shiner (Notropis topeka), Tricolor shiner (Cyprinella (Luxilus pilsbryi), Edwards Plateau shiner (Cyprinella trichroistia), Turquoise Shiner (Erimonax monachus), War lepida), Emerald shiner (Notropis atherinoides), Fieryblack paint shiner (Luxilus coccogenis), Warrior shiner (Lythrurus shiner (Cyprinella pyrrhomelas), Flagfin shiner (Notropis alegnotus), Wedgespot shiner (Notropis greenei), Weed signipinnis), Fluvial shiner (Notropis edwardraneyi), Ghost shiner (Notropis texanus), White shiner (Luxilus albeolus), shiner (Notropis buchanani), Gibbous shiner (Cyprinella Whitefinishiner (Cyprinella nivea), Whitemouth shiner (Not garmani), Golden shiner (Notemigonus Crysoleucas), Golden ropis alborus), Whitetail shiner (Cyprinella galactura), shiner minnow (Notemigonus Crysoleucas), Greenfin shiner Yazoo shiner (Notropis rafinesquei), Yellow shiner (Cymato (Cyprinella chloristia), Greenhead shiner (Notropis chloro gaster aggregata), Yellow shiner (Notropis calientis), and cephalus), Highfin shiner (Notropis altipinnis), Highland Yellowfin shiner (Notropis lutipinnis). shiner (Notropis micropteryx), Highscale shiner (Notropis 0067. Other exemplary fish species that can be used to hypsilepis), Ironcolor shiner (Notropis chalybaeus), Kiami harvest algae include: Brevoortia species such as B. patronus chishiner (Notropis Ortenburgeri), Lake emerald shiner (Not and B. tyrannus, Hyporhamphus unifasciatus, Sardinella ropis atherinoides), Lake shiner (Notropis atherinoides), aurita, Adinia xenica, Diplodus holbrooki, Dorosoma peten Largemouth shiner (Cyprinella bocagrande), Longnose ense, Lagodon rhombodides, Microgobius gulosus, Mugil shiner (Notropis longirostris), Mexican red shiner (Cyp species Such as Mugil cephalus, Mugil cephalus, Mugil rinella rutila), Mimic shiner (Notropis volucellus), Mirror curema, Sphoeroides species such as Sphoeroides maculatus, shiner (Notropis spectrunculus), Mountain shiner (Lythrurus Sphoeroides nephelus, Sphoeroides parvus, Sphoeroides lirus), Nazas shiner (Notropis nazas), New Rivershiner (Not Spengleri, Aluterus Schoepfi, Anguilla rostrata, Arius felis, ropis scabriceps), Ocmulgee shiner (Cyprinella callisema), Bairdella chrysoura, Bairdeiella chrysoura, Chasmodies Orangefin shiner (Notropis ammophilus), Orangetail shiner species such as Chasmodes saburrae and Chasmodies sabur (Pteronotropis merlini), Ornate shiner (Cyprinella ornata), rae, Diplodus holbrooki, Heterandria formosa, Hybopsis Ouachita Mountain Shiner (Lythrurus Snelsoni), Ouachita winchelli, Ictalurus species such as Ictalurus serracantus and shiner (Lythrurus Snelsoni), Ozark shiner (Notropis Ozarca Ictalurus punctatus, Leiostomus xanthurus, Micropogonias nus), Paleband shiner (Notropis albizonatus), Pallid shiner undulatus, Monacanthus ciliatus, Notropis texanus, Opistho (Hybopsis amnis), Peppered shiner (Notropis perpallidus), nema oglinum, Orthopristis chrysoptera, Stephanolepis his Phantom shiner (Notropis orca), Pinewoods shiner (Lythru pidus, Syndousfoetens, Syngnathus species such as Syng rus matutinus), Plateau shiner (Cyprinella lepida), Popeye nathus scovelli, Trinectes maculatus, Archosargus shiner (Notropisariomimus), Pretty shiner (Lythrurus bellus), probatocephalus, Carpiodes species such as C. Cyprinus and Proserpine shiner (Cyprinella proserpina), Pugnose shiner C. velifer; Dorosoma Cepedianum, Erimyzon species such as (Notropis anogenus), Pygmy shiner (Notropis tropicus), Erimyzon Oblongus, Erimyzon Sucetta, and Erimyzon tenuis, Rainbow shiner (Notropis chrosomus), Red River shiner Floridichthys carpio, Microgobius gulosus, Monacanthus (Notropis bairdi), Red shiner (Cyprinella lutrensis), Redfin ciliatus, Moxostoma poecilurum, and Orthopristis chrysoph shiner (Lythrurus umbratilis), Redlip shiner (Notropis chiliti tera. cus), Redside shiner (Richardsonius balteatus), Ribbon 0068 Transgenic fish and genetically improved fish can shiner (Lythrurusfumeus), Rio Grande bluntnose shiner (Not also be used in the culturing and/or harvesting methods pro ropis simus), Rio Grande shiner (Notropisjemezanus), River vided herein. The term “genetically improved fish' refers shiner (Notropis blennius), Rocky shiner (Notropis Suttkusi), herein to a fish that is genetically predisposed to having a Rosefinishiner (Lythrurus ardens), Rosyface shiner (Notropis higher growth rate and/or a lipid content that is higher than a rubellus), Rough shiner (Notropis baileyi), Roughhead wild type fish, when they are cultured under the same condi Shiner (Notropis semperasper), Sabine shiner (Notropis sabi tions. Such fishes can be obtained by traditional breeding nae), Saffron shiner (Notropis rubricroceus), Sailfin shiner techniques or by transgenic technology. Over-expression or (Notropis hypselopterus), Salado Shiner (Notropis salado ectopic expression of a piscine growth hormone transgene in US 2012/0231513 A1 Sep. 13, 2012

a variety of fishes resulted in enhanced growth rate. For environmental factors. If higher EPA and/or DHA concentra example, the growth hormone genes of Chinook salmon, tions are desired, several established methods could be Sockeye salmon, Tilapia, Atlantic salmon, grass carp, and employed, including chromatography, fractional or molecu mud loach have been used in creating transgenic fishes lar distillation, enzymatic splitting, low-temperature crystal (Zbikowska, Transgenic Research, 12:379-389, 2003: Guan lization, Supercritical fluid extraction, or urea complexation. et al., Aquaculture, 284:217-223, 2008). Transgenic carp or These methods can further concentrate the EPA and/or DHA transgenic tilapia comprising an ectopically-expressed pis to nearly pure EPA and/or DHA. cine growth hormone transgene are particularly useful in the 0073. In certain embodiments, EPA- and/or DHA-con harvesting methods provided herein. taining lipids may be separated and concentrated by short 0069. Examples of means and methods for processing lip path distillation, or molecular distillation. The lipids are first ids. Such as algal oil and fish lipids into biofuel. Such as transesterified, either acid- or base-catalyzed, with ethanol to biodiesel, can be found in the following patent publications, produce a mixture of fatty acid ethyl esters (FAEE). The the entire contents of each of which are incorporated by FAEE are then fractionated in the short-path distillation to reference herein: U.S. Patent Publication No. 2007/0010682, remove the short chain FAEE, C-14 to C-18. The concentrate entitled “Process for the Manufacture of Diesel Range of FAEE from C-20 to C-22 is where the EPA and/or DHA Hydrocarbons.” U.S. Patent Publication No. 2007/0131579, can be found. A second distillation of the concentrate can entitled “Process for Producing a Saturated Hydrocarbon result in a final Omega-3 content of up to 70%. The concen Component.” U.S. Patent Publication No. 2007/0135316, tration of the EPA and/or DHA in the final product will entitled “Process for Producing a Saturated Hydrocarbon depend on the initial lipid profile of the fish oil. The FAEE can Component.” U.S. Patent Publication No. 2007/0135663, be used as a consumer product at this stage (fish oil capsules). entitled “Base Oil: U.S. Patent Publication No. 2007/ In some countries, the FAEE are required to be reconverted to 0135666, entitled “Process for Producing a Branched Hydro triglycerides through a glycerolysis reaction before they can carbon Component.” U.S. Patent Publication No. 2007/ be sold as a consumer product. In order to obtain pure EPA 0135669, entitled “Process for Producing a Hydrocarbon and/or DHA, an additional purification step is required using Component:” and U.S. Patent Publication No. 2007/ chromatography, enzymatic transesterification, ammonia 0299291, entitled “Process for the Manufacture of Base Oil.” complexation, or Supercritical fluid extraction. 0070. In certain embodiments, the extraction of lipids 0074 All references cited herein are incorporated herein from the fishes can comprise heating the fish to a temperature by reference in their entirety and for all purposes to the same between 70° C. to 100° C., pressing the fishes to release the extent as if each individual publication or patent or patent lipids, and collecting the lipids. Separation of the lipids from application was specifically and individually indicated to be an aqueous phase and/or a solid phase can be included in the incorporated by reference in its entirety for all purposes. extraction step. The entire fish or a portion thereof can be used 0075. Many modifications and variations of this invention to extract lipids. If lipid concentrates are desired, several can be made without departing from its spirit and scope, as established methods could be employed, including chroma will be apparent to those skilled in the art. The specific tography, fractional or molecular distillation, enzymatic split embodiments described herein are offered by way of example ting, low-temperature crystallization, Supercritical fluid only, and the invention is to be limited only by the terms of the extraction, or urea complexation. appended claims along with the full scope of equivalents to 0071. In certain embodiments, the processing step which such claims are entitled. involves heating the fishes to greater than about 70° C., 80° What is claimed: C., 90° C. or 100° C., typically by a steam cooker, which 1. A method for culturing algae comprising coagulates the protein, ruptures the fat deposits and liberates (i) providing a source of water and a system comprising lipids and oil and physico-chemically bound water, and; enclosures and water for culturing algae and culturing grinding, pureeing and/or pressing the fish by a continuous bivalves; press with rotating helical screws. The fishes can be subjected (ii) culturing the bivalves that increase the level of at least to gentle pressure cooking and pressing which use signifi one dissolved nutrient in the water in the system relative cantly less energy than that is required to obtain lipids from to the water from the source: algae. The coagulate may alternatively be centrifuged. This (iii) culturing the algae in the water in the system; and step removes a large fraction of the liquids (press liquor) from (iv) feeding the algae to the bivalves at a rate such that the the mass, which comprises an oily phase and an aqueous amount of algae produced in the system is greater than fraction (Stickwater). The separation of press liquor can be when the algae is cultured in the system without the carried out by centrifugation after the liquor has been heated bivalves. to 90° C. to 95° C. Separation of stickwater from oil can be 2. The method of claim 1, wherein the bivalves are cultured carried out in vertical disc centrifuges. The lipids in the oily in a bivalves enclosure separately from the algae cultured in a phase (fish oil) may be polished by treating with hot water growth enclosure; which extracts impurities from the lipids. the step of culturing the algae comprises flowing an efflu 0072. In certain embodiments, the extracted fish lipids are ent from the bivalves enclosure to the growth enclosure, not limited to use as biofuels. In one embodiment, the said effluent from the bivalves enclosure having a level extracted fish lipids can be used to obtain omega 3 fatty acids, of at least one dissolved nutrient that is increased relative Such as eicosahexaenoic acid (EPA) and/or docosahexaenoic to the water from the source; and acid (DHA) and/or derivatives thereof including, but not lim the step of culturing the bivalves comprises recirculating ited to esters, glycerides, phospholipids, sterols, and/or mix an effluent from the growth enclosure to the bivalves tures thereof. In one embodiment, the extracted fish lipids enclosure. contain EPA and/or DHA ranging from 1 to 50%, depending 3. The method of claim 1, further comprising flowing water on the fish species, age, location, and a host of ecological and from the source into the bivalves enclosure prior to the growth US 2012/0231513 A1 Sep. 13, 2012

enclosure, such that the level of at least one dissolved inor growth enclosure, such that the level of at least one dissolved ganic nutrient is increased relative to the water from the inorganic nutrient is increased relative to the water from the SOUC. SOUC. 4. The method of claim 3, further comprising removing 12. The method of claim 11, further comprising removing Zooplankton in the water from the source prior to flowing the Zooplankton in water from the source prior to flowing the water from the source into the bivalves enclosure. water from the source into the bivalves enclosure. 5. The method of claim 1, wherein the dissolved inorganic 13. The method of claim 7, wherein the dissolved inorganic nutrient is carbon dioxide, ammonia, ammonium ion, a nutrient is carbon dioxide, ammonia, ammonium ion, a nitrite, nitrite ion, a nitrate, nitrate ion, a phosphate, or ortho nitrite, nitrite ion, a nitrate, nitrate ion, a phosphate, or ortho phosphate ion. phosphate ion. 6. The method of claim 1, wherein the bivalves are Mytilus 14. The method of claim 7, wherein the bivalves are Myti edulis and/or Crassostrea virginica. lus edulis and/or Crassostrea virginica. 15. The method of claim 7, wherein the planktivorous 7. A method for producing biofuel comprising fishes are Brevoortia patronus and/or Clupea harengus. (i) providing a source of water and a system comprising 16. A method for extracting lipids from planktivorous enclosures and water for culturing algae, culturing fishes comprising planktivorous fishes, and culturing bivalves, (i) providing a source of water and a system comprising (ii) culturing the bivalves that increase the level of at least enclosures and water for culturing algae, culturing one dissolved nutrient in the water in the system relative planktivorous fishes, and culturing bivalves, to the water from the source: (ii) culturing the bivalves that increase the level of at least (iii) culturing the algae in the water in the system; one dissolved nutrient in the water in the system relative (iv) feeding the algae to the bivalves at a rate such that the to the water from the source: amount of algae produced in the system is greater than (iii) culturing the algae in the water in the system; when the algae is cultured in the system without the (iv) feeding the algae to the bivalves at a rate such that the bivalves; amount of algae produced in the system is greater than (v) harvesting the algae by feeding the algae to the plank when the algae is cultured in the system without the tivorous fishes; bivalves; (vi) extracting lipids from the planktivorous fishes; and (v) harvesting the algae by feeding the algae to the plank (vii) polishing the lipids to form biofuel. tivorous fishes; and 8. The method of claim 7, wherein the bivalves are cultured (vi) extracting lipids from the planktivorous fishes. in a bivalves enclosure separately from the algae cultured in a 17. The method of claim 16, wherein the bivalves are growth enclosure; cultured in a bivalves enclosure separately from the algae the step of culturing the algae comprises flowing an efflu cultured in a growth enclosure; ent from the bivalves enclosure to the growth enclosure, the step of culturing the algae comprises flowing an efflu said effluent from the bivalves enclosure having a level ent from the bivalves enclosure to the growth enclosure, of at least one dissolved nutrient that is increased relative said effluent from the bivalves enclosure having a level to the water from the source; and of at least one dissolved nutrient that is increased relative the step of culturing the bivalves comprises recirculating to the water from the source; and an effluent from the growth enclosure to the bivalves the step of culturing the bivalves comprises recirculating enclosure. an effluent from the growth enclosure to the bivalves enclosure. 9. The method of claim 7, wherein the bivalves are cultured 18. The method of claim 16, wherein the bivalves are in a bivalves enclosure separately from the algae cultured in a cultured in a bivalves enclosure separately from the algae growth enclosure; cultured in a growth enclosure; the fishes are cultured in a fish enclosure separately from the fishes are cultured in a fish enclosure separately from the bivalves or the algae: the bivalves or the algae: the step of culturing the algae comprises flowing an efflu the step of culturing the algae comprises flowing an efflu ent from the bivalves enclosure to the growth enclosure, ent from the bivalves enclosure to the growth enclosure, said effluent from the bivalves enclosure having a level said effluent from the bivalves enclosure having a level of at least one dissolved inorganic nutrient that is of at least one dissolved inorganic nutrient that is increased relative to the water from the source; and increased relative to the water from the source; and the step of culturing the bivalves comprises flowing an the step of culturing the bivalves comprises flowing an effluent from the growth enclosure to the bivalves enclo effluent from the growth enclosure to the bivalves enclo sure and flowing an effluent from the fish enclosure to sure and flowing an effluent from the fish enclosure to the bivalves enclosure. the bivalves enclosure. 10. The method of claim 9, wherein the step of culturing the 19. The method of claim 16, wherein the step of culturing bivalves comprises flowing the effluent from the fish enclo the bivalves comprises flowing the effluent from the fish sure to the bivalves enclosure at a rate effective for the enclosure to the bivalves enclosure at a rate effective for the bivalves to feed on residual plankton in the effluent from the bivalves to feed on residual plankton in the effluent from the fish enclosure, as indicated by a lower number of plankton in fish enclosure, as indicated by a lower number of plankton in the effluent from the bivalves enclosure than the number of the effluent from the bivalves enclosure than the number of plankton in the effluent from the fish enclosure. plankton in the effluent from the fish enclosure. 11. The method of claim 7, further comprising flowing 20. The method of claim 16, further comprising flowing water from the source into the bivalves enclosure prior to the water from the source into the bivalves enclosure prior to the US 2012/0231513 A1 Sep. 13, 2012

growth enclosure, such that the level of at least one dissolved (v) means for culturing the algae in the effluent from the inorganic nutrient is increased relative to the water from the bivalves enclosure; and SOUC. (vi) means for feeding a controlled amount of the algae to 21. The method of claim 20, further comprising removing the bivalves Such that the amount of algae produced in Zooplankton in water from the source prior to flowing the the system is greater than when the algae is cultured in water from the source into the bivalves enclosure. the system without the bivalves. 28. A system for producing biofuel comprising 22. The method of claim 16, wherein the dissolved inor (i) a source of water, ganic nutrient is carbon dioxide, ammonia, ammonium ion, a (ii) a growth enclosure for culturing algae, a fish enclosure nitrite, nitrite ion, a nitrate, nitrate ion, a phosphate, or ortho for culturing planktivorous fishes, and a bivalves enclo phosphate ion. sure for culturing bivalves, wherein the growth enclo 23. The method of claim 16, wherein the bivalves are Sure, the fish enclosure, and the bivalves enclosure are Mytilus edulis and/or Crassostrea virginica. each in fluid communication with the other enclosures; 24. The method of claim 16, wherein the planktivorous (iii) means to regulate independently the rate, direction, or fishes are Brevoortia patronus and/or Clupea harengus. both the rate and direction, offluid flow between each of 25. The method of claim 16, further comprising processing the bivalves enclosure, the growth enclosure and the fish the lipids to form EPA- and/or DHA-containing products for enclosure; human consumption or animal feeds. (iv) means for culturing the bivalves that increase the level 26. The method of claim 16, wherein said extracting step of at least one dissolved inorganic nutrient in an effluent comprises a processing technique selected from chromatog from the bivalves enclosure relative to the water from the raphy, fractional or molecular distillation, enzymatic split Source; ting, low-temperature crystallization, Supercritical fluid (v) means for culturing the algae in the effluent from the extraction, or urea complexation. bivalves enclosure; and (vi) means for feeding a controlled amount of the algae to 27. A system for culturing algae comprising: the bivalves Such that the amount of algae produced in (i) a source of water, the system is greater than when the algae is cultured in (ii) a growth enclosure for culturing algae and a bivalves the system without the bivalves; enclosure for culturing bivalves, wherein the growth (viii) means for harvesting the algae by the planktivorous enclosure and the bivalves enclosure are in fluid com fishes; munication; (ix) means for gathering the planktivorous fishes from (iii) means to regulate the rate, direction, or both the rate which lipids are extracted and converted to biofuel. and direction, of fluid flow between the growth enclo 29. The system of claim 28, further comprising (x) means sure and the bivalves enclosure; for extracting lipids from the planktivorous fishes; and (xi) (iv) means for culturing the bivalves that increase the level means for polishing the lipids to form biofuel. of at least one dissolved nutrient in an effluent from the bivalves enclosure relative to the water from the source: c c c c c