AU2015203364A1 - Efficient light harvesting - Google Patents

Abstract

Various aspects provide for genetically modifying photosynthetic cells. In some cases, an integrated light harvesting efficiency of photosynthetic cells may be increased by reducing the amount of incident light that is absorbed but not used for photosynthesis. In some cases, an increased transparency may be associated with an increased light harvesting efficiency when absorption due to non-photosynthetic processes is reduced. A reduced capacity of various light-harvesting antenna apparatus may increase transparency. In some cases, a capacity of an organism to adapt to varying light levels may be reduced, and in certain cases, a modified organism may have a reduced ability to acclimate to a low light irradiance. WO 2010/129041 PCT/US2010/001315 Start Choose Organism Mutate Organism - - - -, Compare properties Determine Growth Rate 1150 ~ ~ ~ - Select Organisms End

Description

WO 2010/129041 PCT/US2010/001315 EFFICIENT LIGHT HARVESTING BACKGROUND 1. Technical Field [00011 The present invention relates to improving the efficiency with which photosynthetic organisms use light. 2. Description of Related Art [0002] Photosynthetic organisms use energy from light to form chemical bonds. Energy embodied within the chemical bonds may be used at a later date. As such, chemical bonds provide a storage mechanism for the energy associated with incident light. [0003] A supply of light is often finite in a given period of time. For a given fluence of incident light, photosynthetic organisms may use some of the light to perform photosynthesis. Some of the light may not be used for photosynthesis. Some light may be converted to heat. Some light may be absorbed and reemitted (e.g., fluoresced). Some light may damage the organism. Light that is not used for photosynthesis may not be converted into stored chemical energy within the organism, and so the energy associated with this unconverted light may not be available for subsequent use. Improving the WO 2010/129041 PCT/US2010/001315 conversion of incident light to biomass (e.g., increasing the percentage of incident energy converted to chemical bonds) may increase the efficiency of biomass production, which may increase the amount of incident solar energy available for subsequent use. 2 WO 2010/129041 PCT/US2010/001315 SUMMARY OF THE INVENTION [00041 Various aspects provide for selecting a natural and/or wild type photosynthetic organism. Cells of the wild type organism may have a first transparency associated with light transmission through the cells. The organism may be subject to mutagenesis to create one or more mutated photosynthetic organisms. Transparencies of the cells of the mutated organisms may be determined, and a mutated organism having a transparency greater than that of the wild type organism may be selected. [00051 In some cases, growth rates may be measured. A mutated organism and/or a plurality of mutated organisms (e.g., a suspension of organisms) may have a higher growth rate than a similar wild type. In some cases, more transparent organisms or cells may have a higher overall growth rate. Growth rate may be measured in terms of total biomass (e.g., dry matter) and/or quantities of certain components or chemicals (carbohydrates, proteins, lipids, nucleic acids, and the like). Growth rate may include or be normalized to a quantity of incident radiation (e.g., light or sunlight). [00061 Organisms may include crops such as com, rice, wheat, sugarcane, and the like. Organisms may include trees, such as poplar, conifers, jatropha, palm, and the like. Organisms may include grasses such as prairie 3 WO 2010/129041 PCT/US2010/001315 grasses, switchgrass, Miscanthus, and the like. Organisms may include single cell organisms such as algae, diatoms, cyanobacteria, and the like. 100071 In some cases, mutated organisms may be identified optically, for example using fluorescence. In certain cases, a more transparent organism may have a paler green color than a less transparent version. Organisms may be identified using various responses, such as a photosystem I response, photosystem II response, nonphotochemical quenching, photosynthetic rate, irradiance threshold, and the like. [0008] In some embodiments, an organism may be modified to reduce a sensitivity of one or more light harvesting apparatus and/or mechanisms. In some cases, a light harvesting antenna (e.g., associated with photosystem II) may be modified to have a reduced effectiveness or efficiency as compared to an unmodified (e.g., wild type) organism. In some cases, modification of an organism may result in a modified organism having a reduced ability to adapt to changing light conditions. In certain examples, this reduced ability may be manifest as a reduced ability to adapt to low light conditions. Certain cells and/or organisms may be described as being "locked" into an acclimation state associated with high irradiance levels, despite exposure to low irradiance levels. [0009] Organisms may be mutated (e.g., using mutagenesis) to create one or more mutated versions of the organism. Mutated versions may be 4 WO 2010/129041 PCT/US2010/001315 screened for one or more properties. In some cases, a plurality of mutated organisms (e.g., a suspension of algae or diatoms) may have an increased transparency and a higher growth rate than an otherwise equivalent plurality of wild type organisms. 5 WO 2010/129041 PCT/US2010/001315 BRIEF DESCRIPTION OF THE DRAWINGS [00101 FIG. 1 illustrates an exemplary saturation response of a photosynthetic cell, according to some embodiments. [0011] FIGS 2A and 2B illustrate variations in light intensity for exemplary pluralities of photosynthetic cells. [00121 FIG. 3A illustrates an exemplary suspension. [00131 FIG. 3B is a schematic illustration of an exemplary variation in light intensity with depth through a plurality of cells (e.g., within a suspension). [0014] FIG. 4 is a schematic illustration of an effect of increased transparency, according to some embodiments. 100151 FIG. 5 illustrates a schematic comparison of two photosynthetic rate responses, according to some embodiments. [00161 FIG. 6 illustrates a schematic comparison of light loss as a function of light intensity, according to some embodiments. [00171 FIG. 7 illustrates a schematic comparison of photochemical responses, according to some embodiments. [00181 FIG. 8 illustrates a schematic comparison of transparency as a function of cell density, according to some embodiments. [0019] FIG. 9 illustrates a schematic comparison of the transition thresholds of modified and unmodified cells, according to some embodiments. 6 WO 2010/129041 PCT/US2010/001315 100201 FIG. 10 illustrates a schematic comparison of maximum photosynthetic rates, according to certain embodiments. 100211 FIG. 11 illustrates an exemplary method. [00221 FIGS. 12A, 12B, and 12C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 1 of growth. [00231 FIGS. 13A, 13B, and 13C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 2 of growth. [00241 FIGS. 14A, 14B, and 14C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 4 of growth. 100251 FIGS. 15A, 15B, and 15C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 7 of growth. [00261 FIG. 16 illustrates a comparison of irradiance vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. [00271 FIG. 17 illustrates a comparison of measured Ek vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. 100281 FIG. 18 illustrates a comparison of measured Pmax vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. 7 WO 2010/129041 PCT/US2010/001315 DETAILED DESCRIPTION OF THE INVENTION 100291 Many organisms include cells, organelles, membranes, and the like that perform photosynthesis. A photosynthetic cell may be modified to change (e.g., increase or decrease) its transparency to light. Modification of a cell may include mutating the cell, and may include performing PCR Mutagenesis, Transposon Mutagenesis, Site-directed Mutagenesis, Directed Mutagenesis, RandomMutagenesis, Insertional Mutagenesis, Targeted Mutagenesis, and the like on the cell. [00301 Transparency may be changed by modifying the size of a light harvesting antenna (LHA). In some cases, LHA associated with Photosystem II (PSII) may be modified in a manner that increases transparency. A reduced transparency of a first cell may result in a greater amount of light passing through the first cell to a second cell. The second cell may productively utilize a portion of light that might have been dissipated by the first cell were it not to pass through the first cell. [00311 A plurality of cells having increased transparency may have a higher overall photochemical efficiency than a similar plurality having reduced (e.g., native) transparency. A light harvesting efficiency of a population of photosynthetic cells may be increased by reducing the total amount of incident light absorbed, scattered, converted, or otherwise consumed by non 8 WO 2010/129041 PCT/US2010/001315 photosynthetic reactions. In some cases, an overall or integrated growth rate of the group of more transparent cells may be as great as, or even greater than, the growth rate of the group of less transparent cells. In some cases, a more transparent cell may be less susceptible to damage, particularly under bright light conditions. A more transparent cell may be more robust to changing light conditions (e.g., passing from a low light condition to a high light condition). [00321 An efficiency with which light is harvested by a group of photosynthetic cells may increase the amount of incident energy that is converted to chemical bonds. An increase in light harvesting efficiency may be manifest in a reduction in the incident energy needed to create biomass, which may be manifest as a concomitant reduction in the energy needed to produce biomass-derived products, such as biochemicals, biofuels, ethanol, esters, alkanes, nutrients, food, supplements, and/or other products derived from photosynthetic organisms. [00331 Many photosynthetic cells have a finite capacity to utilize incident light for photosynthesis. A low intensity light may be efficiently utilized (e.g., substantially converted to chemical energy, or converted as efficiently as quantum or physiological limits allow). A more intense light may "overpower" the organism's photosynthesis capabilities, resulting in a substantial portion of the incident light not being used for photosynthesis. Such unused light may be 9 WO 2010/129041 PCT/US2010/001315 absorbed, create heat, damage the organism, or may otherwise be "wasted." In some cases, high intensity light may damage a cell in a way that results in decreased photosynthetic efficiency, decreased growth rate, or even death of the cell. 100341 FIG. 1 illustrates an exemplary saturation response of a photosynthetic cell, according to some embodiments. FIG. 1 illustrates a schematic response 100 describing photosynthetic rate 110 as a function of light intensity 120. Photosynthetic rate 110 may represent or be represented by photosynthetic productivity, photosynthetic efficiency, electron transport rates, lipid productivity, biomass productivity, oxygen production, C02 sequestration, and the like. Photosynthetic rate 110 may be associated with Photosystem I and/or II production. In some cases, photosynthetic rate 110 may represent an electron transport rate associated with PSII. [00351 Response 100 may include a substantially "linear" regime 130 and a saturation regime 140. Linear regime 130 and saturation regime 140 may be separated by a threshold 150. Threshold 150 may be broad or narrow, and may be empirically associated with a transition between regimes. Threshold 150 may vary among diverse photosynthetic organisms - trees, grasses, corn, sugarcane, algae, diatoms, rhizomes such as switchgrass (Panicum), prairie grass (e.g., Miscanthus), and the like. For some algae (e.g., Nannochloropsis), a threshold 10 WO 2010/129041 PCT/US2010/001315 150 may be near 200 jimol quanta/mA2-sec. In some cases, a relatively "maximum" photosynthetic rate Pmax 152 may be defined. Threshold 150 may be associated with a light intensity such as Ek 154, which may represent an irradiance level at which an optimum photosynthetic rate is achieved. [00361 Linear regime 130 may be associated with a region of light intensity in which photosynthetic rate 110 is approximately linearly dependent upon light intensity 120. A linear regime 130 may be characterized as a "light limited" regime, in that photosynthetic productivity is ostensibly limited by the available light, not by the cell per se. In some cases, an organism may be characterized by a slope 132 associated with linear regime 130. For some organisms, slope 132 of the photosynthetic rate vs. intensity response may be associated with a quantum yield of Photosystem II photochemistry. Slope 132 may be characterized by one or more metrics, (e.g., moles of 02 evolved per number of incident photons, mass of C02 converted to biomass per input energy, and the like). [00371 Saturation regime 140 may be characterized by a photosynthetic rate below what would be expected based on an extrapolation of the response in linear regime 130 (to higher intensities). For example, an observed photosynthetic rate 160 at intensity 162 may be below an extrapolated photosynthetic rate 164 (based on extrapolating from linear regime 130, e.g. using l 1 WO 2010/129041 PCT/US2010/001315 slope 132). An organism receiving an intensity in saturation regime 140 (e.g., at intensity 162) may use a relatively smaller percentage of the incident light for photosynthesis, as compared to an organism in linear regime 130. Such an exposure may overwhelm the photosynthetic capabilities of the organism, resulting in a relatively larger amount of the light not being utilized for photosynthesis. Such an exposure may be characterized by a lost productivity 170, which may be associated with a difference between actual photosynthetic rate and a photosynthetic rate that might be expected based on a productivity response at lower intensities (e.g., in a light limited regime). [00381 Photosynthetic cells may be exposed to a wide range of light intensities. In some cases, a single organism may have some cells that are exposed to bright light, while other cells are exposed to weaker light. In some cases, single cells or single celled organisms (e.g., algae, diatoms, and the like) may be exposed to a range of light intensities. For example, algae in water may circulate from the surface (where light is intense) to a depth beneath the surface at which light is faint. Certain embodiments include maximizing a number of organisms exposed to an intensity near (or below) threshold 150. [00391 FIGS 2A and 2B illustrate variations in light intensity for exemplary pluralities of photosynthetic cells. FIG. 2A illustrates a tree 200 having some cells 210 exposed to bright light, and other cells 220 exposed to 12 WO 2010/129041 PCT/US2010/001315 weaker light. In some cases, cells 210 may at least partially shade cells 220. Exemplary organisms include firs, pines, poplars, and other plants. [00401 FIG. 2B illustrates a plurality of photosynthetic organisms having cells exposed to a different light intensities. Crop 230 may include one or more plants for which some cells 240 are exposed to more intense light, and other cells 250 are exposed to less intense light. Exemplary crops 230 include corn, oats, wheat, barley, rice, sugarcane, beets, bamboo, palm, jatropha, various grasses such as prairie grasses, halophytes (e.g., Spartina, Salicornia, and the like) and/or other plants. [00411 FIG. 3A illustrates an exemplary suspension. In this example, an exemplary pond 300 has sides and a bottom, and is sufficiently deep to contain a suspension 310 at a depth 320. Suspension 310 may be characterized by a surface that "faces" a source of light. In FIG. 3A, a top surface of the suspension 310 faces light 330 (e.g., sunlight) arriving in an incident direction. The facing surface (e.g., the top surface) of suspension 310 may be characterized by an area 340. Suspension 310 may include a liquid 350 and a suspended phase 360. [0042] Liquid 350 may include aqueous media such as water, seawater, fresh water, brackish water, growth media, and the like. Suspended phase 360 may include suspended photosynthetic organisms, such as algae, diatoms, and 13 WO 2010/129041 PCT/US2010/001315 the like. Exemplary algae may include members of the genus Nannochloropsis. Exemplary diatoms may include members of the genera Navicula, Amphora, Thallasiosira, Chaetoceros, Nitzschia, Cyclotella, Skeletonema, Phaeodactylum, Achnanthes, Coscinodiscus, Cylindrotheca, Pseudo-Nitzschia, Thalassionema, Hantzschia, Cymbella, and/or Psammodictyon. Liquid 350 may include an aqueous liquid, such as water, seawater, synthetic seawater, brackish water, growth media, and the like. [00431 FIG. 3B is a schematic illustration of an exemplary variation in light intensity with depth through a plurality of cells (e.g., within a suspension). FIG. 3B illustrates a relationship 370 between light intensity 120 and depth 320 under a set of conditions. For example, relationship 370 may represent a measured light intensity at various depths within suspension 310, at a particular incident light intensity, for a given concentration of certain organisms in a liquid having a certain composition. A first intensity 380 may be associated with a shallow depth 382 (e.g., at or near the top surface), and may be a relatively brighter light condition. A second intensity 390 may be a lower intensity of light at a deeper depth 392. [0044] The light intensity within the suspension may scale with the incident light intensity. For example, first intensity 380 at mid-day on a sunny day in the tropics may correspond to an intensity in a saturation regime 140 (FIG. 14 WO 2010/129041 PCT/US2010/001315 1) (e.g., intensity 162, FIG. 1), and second intensity 390 and may correspond to an intensity corresponding to a "light limited" regime of some organisms, such as intensity 130 (FIG. 1). On a less-bright day (e.g., a cloudy day), first intensity 380 may correspond to an intensity associated with threshold 150 (FIG. 1) or even a linear regime 130, and second intensity 390 may correspond to a light level below which photosynthesis may not occur. In some cases, second intensity 390 may correspond to a relatively dark "repair" intensity at which a photosynthetic cell may repair damage to itself. On a particular day and time, some cells may be "overexposed" to light, some cells may be "underexposed" to light, and some cells may receive an optimal amount of light (e.g., an intensity at or near threshold 150). 100451 Many photosynthetic organisms adapt or acclimate to different light conditions. In some cases, a cell residing for significant time (e.g., hours or days) at a weak intensity may adapt to those weak light conditions, and may increase its sensitivity to light. A cell residing at a high intensity (e.g., intensity 380 on a sunny day) may adapt to bright light conditions, and may decrease its sensitivity to light. In some cases, sensitivity may be adjusted by adjusting one or more light harvesting antennae (LHA). Sensitivity may be adjusted by adjusting a violaxanthin-chlorophyll-a protein (VCP). 15 WO 2010/129041 PCT/US2010/001315 [0046] A cell that has adapted to weak-light conditions may have a "sensitized" LHA. Exposing such a "sensitized" cell to bright light may saturate or "overpower" the LHA, which may result in a substantial portion of the incident bright light not being used for photosynthesis. In some cases, bright light may result in an increased amount of non-photochemical quenching (NPQ), and/or an increased ratio of NPQ to photosynthetic absorption. In some cases, cells that are adapted to weak intensity may be damaged by a high intensity. [00471 A cell that has acclimated to intense light may not harvest as much weak light as a cell that has acclimated to weak light. In some cases, a cell may "reduce the gain" of a light harvesting antenna in response to intense light, which may allow for a relatively larger fraction of light to pass through the cell without being absorbed by the antenna. In some cases, a reduction in LHA sensitivity may be manifest as a reduced slope 132 (FIG. 1) as compared to the slope characterizing a cell having a standard LHA (e.g., a wild type). [0048] Cells nearer to an incident light source (e.g., at the top of a tree or top of a suspension) may absorb some incident light, and a portion of the incident light may pass through the cells to the "shaded" cells beneath or behind the nearer cells. Light that has passed through a first cell may be absorbed by a second cell. In some embodiments, an overall efficiency of a plurality of photosynthetic cells may be increased by reducing the amount of light absorbed 16 WO 2010/129041 PCT/US2010/001315 each individual cell, and more particularly, by minimizing an amount of light that is absorbed via non-photosynthetic processes (e.g., NPQ). In some embodiments, a plurality of cells are engineered to have an increased transparency via a reduced LHA sensitivity. By minimizing the scattering and/or absorption of light via non-photosynthetic mechanisms (e.g., NPQ dissipation of light as heat, ionization, damage, and the like), light that is not used for photosynthesis by a first cell may pass through the first cell be available for use by a second cell. [0049] In some cases, a reduction in each individual cell's ability to harvest light may result in an increase in the overall efficiency of a population of the cells. A reduction in light harvesting efficiency results in greater transmittance of light through a cell, which increases the light available to other cells. A reduction in LHA efficiency may be manifest as an increased transparency of the cell (and/or a plurality of such cells). [00501 FIG. 4 is a schematic illustration of an effect of increased transparency, according to some embodiments. FIG. 4 illustrates two variations in measured light intensity 120 as a function of depth 410 in two suspensions, and may be determined by measuring an intensity of light at various depths (or distances from the surface facing the light) of the suspension. A first organism WT 420 may be a native, wild type, or other unmodified organism. A second 17 WO 2010/129041 PCT/US2010/001315 organism PGM 430 may include a modified transparency, and in some cases, may be characterized by an increased transparency as compared to WT 420. A suspension of PGM 430 cells may attenuate light less than a corresponding suspension of WT 420 cells, as illustrated in FIG. 4. [00511 In some embodiments, transparency may be increased by reducing a size and/or number of LHA. In some cases, transparency may be increased by decreasing an amount of chlorophyll in the cell (e.g., an amount of chlorophyll associated with one or more LHA). In some cases, a transparency may be increased by decreasing an amount of chlorophyll in apparatus associated with Photosystem I. In some cases, a transparency may be increased by decreasing an amount of chlorophyll in apparatus associated with Photosystem II (PSII). In some cases a transparency may be increased by decreasing an amount of carotenoid (e.g., Violaxanthin) with and/or within a LHA. [0052] FIG. 5 illustrates a schematic comparison of two photosynthetic rate responses, according to some embodiments. FIG. 5 is a schematic graph of photosynthetic rate 110 as a function of incident light intensity 120. In some embodiments, Photosynthetic rate 110 is associated with a Photosystem II electron transport rate. FIG. 5 compares responses for two organisms, a wild type organism WT 420 and a modified organism PGM 430. In some 18 WO 2010/129041 PCT/US2010/001315 embodiments, PGM 430 may reach a higher photosynthetic rate 110 than WT 420, at one or more light intensities. In some cases, PGM 430 has a higher maximum photosynthetic rate than does WT 420. PGM 430 may have a linear regime characterized by a slope 532 that is lower than the corresponding slope 522 of WT 420. In some cases, PGM 430 may have a threshold 550 that is higher than the corresponding threshold 560 of WT 420. PGM 430 may have a higher slope at high light intensities (e.g., above threshold 540) than does WT 420. At some particularly high light intensities, the photosynthetic rate of WT 420 may decrease with increasing intensity, whereas the photosynthetic rate of PGM 430 at those intensities may not decrease as much or at all. [00531 FIG. 6 illustrates a schematic comparison of light loss as a function of light intensity, according to some embodiments. Light loss 600 may characterize an amount of light incident on a cell that is not used for photosynthesis. Light loss 600 may be associated with various dissipation mechanisms, such as NPQ a conversion of light to heat, photoinduced ionization, and the like. In some embodiments, an unmodified organism WT 420 may lose or otherwise dissipate more light than a modified organism PGM 430, particularly at high light intensities. [00541 FIG. 7 illustrates a schematic comparison of photochemical responses, according to some embodiments. Photochemical response 700 may 19 WO 2010/129041 PCT/US2010/001315 include a response such as a Photosystem I electron transport rate. In some embodiments, WT 420 and PGM 430 may have similar photochemical responses 700. In some cases, a WT 420 and a PGM 430 may display similar first photochemical responses (e.g., PS I electron transport rate) while having different second photochemical responses (e.g., PS II electron transport rate). [00551 In some embodiments, PGM 430 may display a different photochemical response 700 as compared to WT 420 (e.g., higher slope and/or higher maximum). In some cases, this difference may increase with time (e.g., exposure time, growth time, replications, and the like). This difference may vary with irradiant intensity. [0056] FIG. 8 illustrates a schematic comparison of transparency as a function of cell density, according to some embodiments. Transparency 800 may be measured as a function of incident light intensity, depth, cell density (e.g., number of cells per volume of liquid), and the like. Transparency may be measured using an apparatus having a defined path length and light intensity. Transparency may be measured by measuring light intensity at one or more points within a suspension as a function of incident intensity. Cell density measurements (e.g., cell counting over a volume) may be used to differentiate among factors affecting transparency (e.g., cell transparency vs. number of cells). In some cases, cell density 810 may include a response associated with cell 20 WO 2010/129041 PCT/US2010/001315 replication (e.g., new cells growing) and/or adapting to light conditions (e.g., cell density). In some cases, cell density 810 may include a response associated with cells adapting to light (e.g., high cell densities and corresponding decreased mean intensities may result in adaptation of LHA apparatus). 10057] At one or more cell densities 810, modified organism PGM 430 may have an increased transparency as compared to unmodified organism WT 420. Increased transparency may be manifest as an increased measured light intensity at a point within a suspension of modified organisms, as compared to an equivalent measurement (e.g., at equal cell density) within a suspension of unmodified organisms. 100581 FIG. 9 illustrates a schematic comparison of transition thresholds of modified and unmodified cells, according to some embodiments. FIG. 9 schematically compares a response of a modified organism PGM 430 to that of an unmodified organism WT 420. An exemplary transition is shown as threshold 150 in FIG. 9, although other transitions (e.g., Ek) may be used. In some cases, a transition may characterize an irradiance level for optimal photosynthetic productivity. In some cases, increasing cell density may be associated with growth of cells. 100591 FIG. 10 illustrates a schematic comparison of maximum photosynthetic rates, according to certain embodiments. FIG. 10 schematically 21 WO 2010/129041 PCT/US2010/001315 compares a response of a modified organism PGM 430 to that of an unmodified organism WT 420. In this example, extracted values of Pmax 152 are shown as a function of cell density 810. [00601 FIG. 11 illustrates an exemplary method. A starting (e.g., native or wild type) organism is chosen in step 1110. In step 1120, the organism is mutated (e.g., using mutagenesis) to create one or more mutated organisms. One or more properties of the organisms may be compared in step 1130, which may include selecting one or more mutated organisms. Selecting may include using fluorescence activated cell sorting to select cells based on certain optical properties. Certain embodiments include screening based on phenotypes. In some cases, a specific genetic sequence may be modified (e.g., a genetic sequence that reduces an efficacy of a light harvesting antenna may be incorporated into an organism). [0061] Properties to be screened for and compared may include transparency, threshold, Pmax, PSII properties, PSI properties, NPQ and the like. In some cases, properties may include optical properties, and may include properties that may be rapidly screened for and/or measured. In some cases, organisms may be selected using quickly screenable properties (e.g., transparency). A selected subset may be further screened for properties that may take longer to evaluate (e.g., growth rates). 22 WO 2010/129041 PCT/US2010/001315 [00621 In optional step 1140, growth rates may be compared. One or more mutated organisms may be selected in step 1150. In some cases, a selected organism may have a higher growth rate than the wild type equivalent, and may also have certain properties (e.g., as determined in step 1130) that distinguish it from the wild type organism. A selected mutated organism may have an increased transparency, a higher PSI1 ETR, a lower NPQ a paler color, a different fluorescence spectrum and/or intensity, and the like. [00631 In some embodiments, cells may be subjected to mutagenesis, and the mutated cells may be grown. Mutated cells having increased transparency as compared to native cells may be selected. In some cases, cells having increased transparency may be further selected based on growth rates (e.g., choosing those cultures with the highest growth rates). In certain cases, cultures having high growth rates under high light conditions and high cellular densities are selected. [00641 EXAMPLE 1 Random Mutagenesis Using ICR-191 Nannochloropsis sp. (e.g., Oceanica) were mutated and their properties measured. ICR-191 was prepared as a stock solution at a concentration of 1mg/ml in 0.IN filter sterilized HCI. Cells were grown to mid-log phase and diluted to 106cells/ml. To 20ml of the diluted culture 40d of the ICR-191 stock was added. Flasks were placed on a shaker and illuminated at 50 pmol quanta m- 2 s~'. Following 7 days of growth cells were 23 WO 2010/129041 PCT/US2010/001315 washed twice with growth medium and then plated on agar plates. After 3-4 weeks of growth on plates relatively pale green colonies were selected, re-suspended in medium and then re-plated on fresh agar plates. [00651 Fluorescence and Spectroscopic analysis of photosynthetic function Pulse amplitude modulated (PAM) fluorescence was recorded at the growth temperature of the culture using a Dual-PAM (Walz, Effeltrich, Germany). Samples were illuminated with visible light using the red LED built into the Dual-PAM. Samples were dark adapted in the sample chamber for a minimum of 10 min prior to all measurements. The actual photochemical efficiency of PSII at any given actinic irradiance was calculated as Fm'-Fs/Fm'. The relative PSII ETR was calculated as the product of the actual photochemical efficiency of PSII and the actinic irradiance. NPQ was measured as Fm-Fm'/Fm'. In addition to PSII ETR, simultaneous measurements of PSI ETR were made. The photochemical efficiency of PSI at any given actinic irradiance was calculated as I-(Y(ND)+Y(NA)). PSI ETR was then calculated as the product of Y(1) and the actinic irradiance. [00661 FIGS. 12A, 12B, and 12C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 1 of growth. FIG. 12A illustrates PSII electron transport rate (ETR) data as a function of irradiance. FIG. 12B illustrates NPQ as a function of irradiance. FIG. 12C illustrates PSI ETR as a function of irradiance. 24 WO 2010/129041 PCT/US2010/001315 100671 FIGS. 13A, 13B, and 13C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 2 of growth. FIG. 13A illustrates PSII electron transport rate (ETR) data as a function of irradiance. FIG. 13B illustrates NPQ as a function of irradiance. FIG. 13C illustrates PSI ETR as a function of irradiance. [00681 FIGS. 14A, 14B, and 14C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 4 of growth. FIG. 14A illustrates PSII electron transport rate (ETR) data as a function of irradiance. FIG. 14B illustrates NPQ as a function of irradiance. FIG. 14C illustrates PSI ETR as a function of irradiance. [00691 FIGS. 15A, 15B, and 15C illustrate experimental results for wild type (annotated WT) and mutated (annotated 979) samples after day 7 of growth. FIG. 15A illustrates PSII electron transport rate (ETR) data as a function of irradiance. FIG. 15B illustrates NPQ as a function of irradiance. FIG. 15C illustrates PSI ETR as a function of irradiance. [0070] FIG. 16 illustrates a comparison of irradiance vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. In this example, "irradiance" generally describes a measured light intensity at a point within the suspension for a given incident intensity. Samples were measured at different lengths of growth time, generally corresponding to the days shown in 25 WO 2010/129041 PCT/US2010/001315 FIGS. 12-15. Mutated sample 979 generally resulted in a more intense measured light intensity (higher irradiance) at a given cell density, as compared to the wild type sample WT. 100711 FIG. 17 illustrates a comparison of measured Ek vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. In this example, Ek was estimated using the PSII ETR results of FIGS. 12-15. Mutated sample 979 generally displayed a higher Ek at a given cell density. [0072] FIG. 18 illustrates a comparison of measured Pmax vs. cell density for wild type (annotated WT) and mutated (annotated 979) samples. In this example, Pmax is the maximum observed photosynthetic rate, and was estimated using the PSII ETR results of FIGS. 12-15. Mutated sample 979 generally displayed a higher Pmax at a given cell density. 100731 Some embodiments include sensors to sense various parameters (e.g., light intensity, concentration, depth, photosynthetic rate, clarity, pH, mass, dielectric constant, transparency, opacity, time, date, and other characteristics). Apparatus may monitor various sensors, and systems may be actuated by automated controls (solenoid, pneumatic, piezoelectric, and the like). Some embodiments include a computer readable storage medium coupled to a processor and memory. Executable instructions stored on the computer readable storage medium may be executed by the processor to perform various methods 26 WO 2010/129041 PCT/US2010/001315 described herein. Sensors and actuators may be coupled to the processor, providing input and receiving instructions associated with various methods. Certain instructions provide for closed-loop control of various parameters via coupled sensors providing input and coupled actuators receiving instructions to adjust parameters. Certain embodiments include materials. A biofuel may be synthesized from a carbohydrate, a lipid, and/or other biomass, which may be derived from cells and methods according to various embodiments. [00741 The above description is illustrative and not restrictive. Many variations of the invention will become apparent to those of skill in the art upon review of this disclosure. The scope of the invention should, therefore, be determined not with reference to the above description, but instead should be determined with reference to the appended claims along with their full scope of equivalents. 27

Claims (27)

1. A method for selecting a photosynthetic organism, the method comprising: choosing a first photosynthetic organism having a first transparency associated with light transmission through the first photosynthetic organism; subjecting the first photosynthetic organism to mutagenesis to create one or more second photosynthetic organisms; determining a second transparency associated with light transmission through at least one of the second photosynthetic organisms; and selecting one or more second photosynthetic organisms for which the second transparency is greater than the first transparency.

2. The method of claim 1, further comprising: determining a first growth rate of the first photosynthetic organism; determining a second growth rate of at least one of the second photosynthetic organisms; and selecting one or more second photosynthetic organisms having a second growth rate larger than the first growth rate. 28 WO 2010/129041 PCTIUS2010/001315

3. The method of claim 2, wherein at least one of the second photosynthetic organisms having a second growth rate larger than the first growth rate has a second transparency greater than the first transparency.

4. The method of claim 2, wherein one or more growth rates include a measurement of total biomass.

5. The method of claim 2, wherein one or more growth rates include a measurement of lipid production.

6. The method of claim 1, wherein the first photosynthetic organism includes any of a crop, a grass, a tree, a rhizome, a diatom, a cyanobacterium, and an alga.

7. The method of claim 1, wherein the first photosynthetic organism includes an alga.

8. The method of claim 1, wherein the first photosynthetic organism includes a member of the genus Nannochloropsis. 29 WO 2010/129041 PCT/US2010/001315

9. The method of claim 1, wherein the transparency is determined in the visible light regime.

10. The method of claim 1, wherein a color of the first photosynthetic organism is a first green, and at least one of the selected second photosynthetic organisms is a paler green than the first green.

11. The method of claim 1, wherein at least one of the selected second photosynthetic organisms has a less effective light harvesting antenna than does the first photosynthetic organism.

12. The method of claim 1, wherein at least one of the second photosynthetic organisms has a higher PSII electron transport rate than the first photosynthetic organism at a first irradiance.

13. The method of claim 12, wherein the first irradiance is associated with a saturation regime of the first photosynthetic organism. 30 WO 2010/129041 PCT/US2010/001315

14. The method of claim 1, wherein at least one of the second photosynthetic organisms has a lower value associated with nonphotochemical quenching than does the first photosynthetic organism at a first irradiance.

15. The method of claim 1, wherein at least one of the second photosynthetic organisms has a higher threshold irradiance than does the first photosynthetic organism.

16. The method of claim 1, wherein at least one of the second photosynthetic organisms has a higher maximum photosynthetic rate than does the first photosynthetic organism. 31 WO 2010/129041 PCT/US2010/001315

17. A method of increasing a light harvesting efficiency of a photosynthetic organism, the method comprising: selecting a first photosynthetic organism; subjecting the first photosynthetic organism to mutagenesis to create one or more second photosynthetic organisms; determining a first sensitivity associated with a light harvesting apparatus of the first photosynthetic organism; determining a second sensitivity associated with a light harvesting apparatus of at least one second photosynthetic organism; and selecting a second photosynthetic organism for which the second sensitivity is less than the first sensitivity.

18. The method of claim 17, wherein the first photosynthetic organism includes an algae.

19. The method of claim 18, wherein the algae includes a member of the genus Nannochloropsis. 32 WO 2010/129041 PCT/US2010/001315

20. The method of claim 17, wherein the sensitivity includes an ability to adapt to changing light levels, and the second photosynthetic organism has a reduced ability to adapt to changing light levels than does the first photosynthetic organism.

21. The method of claim 20, wherein a difference between the first and second sensitivities increases with a decrease in irradiant intensity.

22. A plurality of genetically modified photosynthetic cells, the plurality having: a greater transparency than a substantially equivalent plurality of non genetically modified versions of the photosynthetic cells; and a greater integrated growth rate than that of a substantially equivalent plurality of non-genetically modified versions of the photosynthetic cells.

23. The plurality of claim 22, wherein the cells are a part of the same organism.

24. The plurality of claim 23, wherein the organism includes any of a crop, a tree, and a grass. 33 WO 2010/129041 PCT/US2010/001315

25. The plurality of claim 22, wherein the cells include algal cells.

26. The plurality of claim 22, wherein the cells include diatoms.

27. The plurality of claim 22, wherein the cells include cyanobacteria. 34