Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.

Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium1 and a terrestrial cyanobacterium2. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps3 from marine photoheterotrophs have thus far failed4-6. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.

Growth, calcification, and photobiology of the threatened coral Acropora cervicornis in natural versus artificial light.

Land-based coral culture is of increasing interest for conservation and educational display. Shallow water corals generate most of their energy from photosynthesis, and light is a critical abiotic factor in their husbandry. We compared growth, calcification, and photobiology in the coral Acropora cervicornis between natural and artificial (light-emitting diode; LED) light to better understand the impact of light source on coral performance. One tank of a greenhouse recirculating system at The Florida Aquarium's Center for Conservation was used to culture replicate coral colonies. Half of the tank and corals were covered to block sunlight and illuminated with a commercial reef aquarium LED fixture, while the other half was exposed to natural sunlight. Treatments were matched in terms of maximum photosynthetically active radiation and spectral measurements characterized both light regimes. Coral growth and calcification were tracked over a period of 19 weeks by repeated measurements of total linear extension (TLE) and buoyant weight. For the first 5 weeks, photosynthetic yield was measured weekly using a pulse-amplitude-modulated fluorometer. Calcification was significantly higher under LED lighting relative to natural light, but TLE did not differ. Photobiology data suggest that corals in both treatments were acclimated to the same light level, but photosynthetic efficiency was ultimately greater in the natural light treatment. More consistent light delivery and different spectral composition under LED treatment conditions may explain the incongruity between calcification and photosynthetic efficiency. This experiment informs husbandry of shallow-water scleractinian corals maintained in both natural sunlight and enclosed structures.

TOR kinase activity in Chlamydomonas reinhardtii is modulated by cellular metabolic states.

Target of rapamycin (TOR) kinase is a sensor and a central integrator of internal and external metabolic cues. However, in algae and in higher plants, the components of TOR kinase signaling are yet to be characterized. Here, we establish an assay system to study TOR kinase activity in Chlamydomonas reinhardtii using the phosphorylation status of its putative downstream target, CrS6K. Using this assay, we probe the modulation of cellular TOR kinase activity under various physiological states such as photoautotrophy, heterotrophy, mixotrophy, and nitrogen (N) starvation. Importantly, we uncover that excess acetate in the medium leads to high cellular reactive oxygen species levels, triggering autophagy and a concomitant drop in TOR kinase activity in a dose-dependent manner, thus leading to a N-starvation-like cellular phenotype, even when nitrogen is present.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses.

The discovery of eukaryotic giant viruses has transformed our understanding of the limits of viral complexity, but the extent of their encoded metabolic diversity remains unclear. Here we generate 501 metagenome-assembled genomes of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from environments around the globe, and analyze their encoded functional capacity. We report a remarkable diversity of metabolic genes in widespread giant viruses, including many involved in nutrient uptake, light harvesting, and nitrogen metabolism. Surprisingly, numerous NCLDV encode the components of glycolysis and the TCA cycle, suggesting that they can re-program fundamental aspects of their host's central carbon metabolism. Our phylogenetic analysis of NCLDV metabolic genes and their cellular homologs reveals distinct clustering of viral sequences into divergent clades, indicating that these genes are virus-specific and were acquired in the distant past. Overall our findings reveal that giant viruses encode complex metabolic capabilities with evolutionary histories largely independent of cellular life, strongly implicating them as important drivers of global biogeochemical cycles.

Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria.

The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Rímov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Rímov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

A Dual Role for Ca2+ in Expanding the Spectral Diversity and Stability of Light-Harvesting 1 Reaction Center Photocomplexes of Purple Phototrophic Bacteria.

The light-harvesting 1 reaction center (LH1-RC) complex in the purple sulfur bacterium Thiorhodovibrio ( Trv.) strain 970 cells exhibits its LH1 Q y transition at 973 nm, the lowest-energy Q y absorption among purple bacteria containing bacteriochlorophyll a (BChl a). Here we characterize the origin of this extremely red-shifted Q y transition. Growth of Trv. strain 970 did not occur in cultures free of Ca2+, and elemental analysis of Ca2+-grown cells confirmed that purified Trv. strain 970 LH1-RC complexes contained Ca2+. The LH1 Q y band of Trv. strain 970 was blue-shifted from 959 to 875 nm upon Ca2+ depletion, but the original spectral properties were restored upon Ca2+ reconstitution, which also occurs with the thermophilic purple bacterium Thermochromatium ( Tch.) tepidum. The amino acid sequences of the LH1 α- and ß-polypeptides from Trv. strain 970 closely resemble those of Tch. tepidum; however, Ca2+ binding in the Trv. strain 970 LH1-RC occurred more selectively than in Tch. tepidum LH1-RC and with a reduced affinity. Ultraviolet resonance Raman analysis indicated that the number of hydrogen-bonding interactions between BChl a and LH1 proteins of Trv. strain 970 was significantly greater than for Tch. tepidum and that Ca2+ was indispensable for maintaining these bonds. Furthermore, perfusion-induced Fourier transform infrared analyses detected Ca2+-induced conformational changes in the binding site closely related to the unique spectral properties of Trv. strain 970. Collectively, our results reveal an ecological strategy employed by Trv. strain 970 of integrating Ca2+ into its LH1-RC complex to extend its light-harvesting capacity to regions of the near-infrared spectrum unused by other purple bacteria.

Light-dependent growth kinetics enable scale-up of well-mixed phototrophic bioprocesses in different types of photobioreactors.

Scaling of phototrophic bioprocesses can be extremely challenging especially when reactor types in the considered scales differ. In this study, the mean integral photon flux density was used to transfer light-dependent growth kinetics of Nannochloropsis salina 40.85 and Nannochloropsis gaditana 2.99 grown with constant LED irradiation from flat-plate gas-lift photobioreactors (0.09 m2) to thin-layer cascade photobioreactors (8 m2). Even though completely different reactors were used, comparable growth rates were achieved on both scales with both strains by application of comparable mean light availabilities in the microalgae suspensions. In contrast, the light-dependent growth kinetics change significantly when irradiation varies dynamically (day-night cycles). The maximum intra-day growth rate of N. salina with dynamic climate simulation was doubled to 0.07 h-1 compared to constant irradiation, but tolerance of the microalgae against excessive irradiation was drastically reduced compared to constant irradiation. Because of that, predicting growth of N. salina in a physically simulated day-night climate would require the determination of the light-dependence of growth with dynamically varying conditions.

High temperature accelerates growth of aerobic anoxygenic phototrophic bacteria in seawater.

Temperature is an important controlling factor in the growth activity of all microorganisms. Aerobic anoxygenic phototrophic (AAP) bacteria actively grow in the ocean and are known as one of the main driving forces in organic matter cycling in surface seawater environments. Whether temperature change affects AAP bacteria activity from an ecological viewpoint remains an open question. To date, no known studies have reported the effect of temperature change on AAP bacteria growth in the ocean. We here show that the growth rate of AAP bacteria exceeded that of other bacterial types at high water temperatures in the absence of grazers. The slope of the regression line of the net growth rate of AAP bacteria as a function of water temperature was the same as that for non-AAP bacteria at all temperatures (10, 20, and 30°C); however, when grazers were eliminated, it was 4.7 times higher than that of non-AAP bacteria. This result suggests that AAP bacteria are more responsive to water temperature increases than other bacteria and that AAP bacteria might become more dominant than other bacteria under elevated water temperatures.

Possible nitrogen fertilization of the early Earth Ocean by microbial continental ecosystems.

While significant efforts have been invested in reconstructing the early evolution of the Earth's atmosphere-ocean-biosphere biogeochemical nitrogen cycle, the potential role of an early continental contribution by a terrestrial, microbial phototrophic biosphere has been largely overlooked. By transposing to the Archean nitrogen fluxes of modern topsoil communities known as biological soil crusts (terrestrial analogs of microbial mats), whose ancestors might have existed as far back as 3.2 Ga ago, we show that they could have impacted the evolution of the nitrogen cycle early on. We calculate that the net output of inorganic nitrogen reaching the Precambrian hydrogeological system could have been of the same order of magnitude as that of modern continents for a range of inhabited area as small as a few percent of that of present day continents. This contradicts the assumption that before the Great Oxidation Event, marine and continental biogeochemical nitrogen cycles were disconnected.

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels.

Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbour an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation-dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multitrophic level communities lend stability to ecosystem functioning. This multitrophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments.

FLUCTUATING-LIGHT-ACCLIMATION PROTEIN1, Conserved in Oxygenic Phototrophs, Regulates H+ Homeostasis and Non-Photochemical Quenching in Chloroplasts.

Plants have mechanisms allowing them to acclimate to intense light conditions, which involves the dissipation of excess light energy. These mechanisms allow plants to perform photosynthesis efficiently and, therefore, must be accurately and precisely controlled. However, how plants dissipate excess light energy has yet to be fully elucidated. Herein we report the identification of a gene, which we named Fluctuating-Light-Acclimation Protein1 (FLAP1), that is conserved in oxygenic phototrophs. We show that Arabidopsis FLAP1 is associated with chloroplast thylakoid and envelope membranes and that the flap1 mutant shows delayed non-photochemical quenching (NPQ) relaxation during induction of photosynthesis at moderate light intensity. Under fluctuating light conditions, NPQ levels in the flap1 mutant were higher than those in the wild type during the high light period, and the mutant exhibited a pale-green phenotype. These findings suggest that FLAP1 is involved in NPQ control, which is important for an acclimation response to fluctuating light.

Phototrophy and starvation-based induction of autophagy upon removal of Gcn5-catalyzed acetylation of Atg7 in Magnaporthe oryzae.

Magnaporthe oryzae, the ascomycete fungus that causes rice blast disease, initiates conidiation in response to light when grown on Prune-Agar medium containing both carbon and nitrogen sources. Macroautophagy/autophagy was shown to be essential for M. oryzae conidiation and induced specifically upon exposure to light but is undetectable in the dark. Therefore, it is inferred that autophagy is naturally induced by light, rather than by starvation during M. oryzae conidiation. However, the signaling pathway(s) involved in such phototropic induction of autophagy remains unknown. We identified an M. oryzae ortholog of GCN5 (MGG_03677), encoding a histone acetyltransferase (HAT) that negatively regulates light- and nitrogen-starvation-induced autophagy, by acetylating the autophagy protein Atg7. Furthermore, we unveiled novel regulatory mechanisms on Gcn5 at both transcriptional and post-translational levels, governing its function associated with the unique phototropic response of autophagy in this pathogenic fungus. Thus, our study depicts a signaling network and regulatory mechanism underlying the autophagy induction by important environmental clues such as light and nutrients.

Chlamydomonas reinhardtii responding to high light: a role for 2-propenal (acrolein).

High light causes photosystem II to generate singlet oxygen (1 O2 ), a reactive oxygen species (ROS) that can react with membrane lipids, releasing reactive electrophile species (RES), such as acrolein. To investigate how RES may contribute to light stress responses, Chlamydomonas reinhardtii was high light-treated in photoautotrophic and mixotrophic conditions and also in an oxygen-enriched atmosphere to elevate ROS production. The responses were compared to exogenous acrolein. Non-photochemical quenching (NPQ) was higher in photoautotrophic cells, as a consequence of a more de-epoxidized state of the xanthophyll cycle pool and more LHCSR3 protein, showing that photosynthesis was under more pressure than in mixotrophic cells. Photoautotrophic cells had lowered α-tocopherol and ß-carotene contents and a higher level of protein carbonylation, indicators of elevated 1 O2 production. Levels of glutathione, glutathione peroxidase (GPX5) and glutathione-S-transferase (GST1), important antioxidants against RES, were also increased in photoautotrophic cells. In parallel to the wild-type, the LHCSR3-deficient npq4 mutant was high light-treated, which in photoautotrophic conditions exhibited particular sensitivity under elevated oxygen, the treatment that induced the highest RES levels, including acrolein. The npq4 mutant had more GPX5 and GST1 alongside higher levels of carbonylated protein and a more oxidized glutathione redox state. In wild-type cells glutathione contents doubled after 4 h treatment, either with high light under elevated oxygen or with a non-critical dose (600 ppm) of acrolein. Exogenous acrolein also increased GST1 levels, but not GPX5. Overall, RES-associated oxidative damage and glutathione metabolism are prominently associated with light stress and potentially in signaling responses of C. reinhardtii.

Photochemical characterization of actinorhodopsin and its functional existence in the natural host.

Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes. The purified RpActR showed λmax at 534nm and underwent a photocycle characterized by the very fast formation of M intermediate. The subsequent intermediate, named P620, could be assigned to the O intermediate in other H+ pumps. In contrast to conventional O, the accumulation of P620 remains prominent, even at high pH. Flash-induced absorbance changes suggested that there exists only one kind of photocycle at any pH. However, above pH7, RpActR shows heterogeneity in the H+ transfer sequences: one first captures H+ and then releases it during the formation and decay of P620, while the other first releases H+ prior to H+ uptake during P620 formation.

The Non-Coding RNA Ncr0700/PmgR1 is Required for Photomixotrophic Growth and the Regulation of Glycogen Accumulation in the Cyanobacterium Synechocystis sp. PCC 6803.

Carbohydrate metabolism is a tightly regulated process in photosynthetic organisms. In the cyanobacterium Synechocystis sp. PCC 6803, the photomixotrophic growth protein A (PmgA) is involved in the regulation of glucose and storage carbohydrate (i.e. glycogen) metabolism, while its biochemical activity and possible factors acting downstream of PmgA are unknown. Here, a genome-wide microarray analysis of a ΔpmgA strain identified the expression of 36 protein-coding genes and 42 non-coding transcripts as significantly altered. From these, the non-coding RNA Ncr0700 was identified as the transcript most strongly reduced in abundance. Ncr0700 is widely conserved among cyanobacteria. In Synechocystis its expression is inversely correlated with light intensity. Similarly to a ΔpmgA mutant, a Δncr0700 deletion strain showed an approximately 2-fold increase in glycogen content under photoautotrophic conditions and wild-type-like growth. Moreover, its growth was arrested by 38 h after a shift to photomixotrophic conditions. Ectopic expression of Ncr0700 in Δncr0700 and ΔpmgA restored the glycogen content and photomixotrophic growth to wild-type levels. These results indicate that Ncr0700 is required for photomixotrophic growth and the regulation of glycogen accumulation, and acts downstream of PmgA. Hence Ncr0700 is renamed here as PmgR1 for photomixotrophic growth RNA 1.

The Type II NADPH Dehydrogenase Facilitates Cyclic Electron Flow, Energy-Dependent Quenching, and Chlororespiratory Metabolism during Acclimation of Chlamydomonas reinhardtii to Nitrogen Deprivation.

When photosynthetic organisms are deprived of nitrogen (N), the capacity to grow and assimilate carbon becomes limited, causing a decrease in the productive use of absorbed light energy and likely a rise in the cellular reduction state. Although there is a scarcity of N in many terrestrial and aquatic environments, a mechanistic understanding of how photosynthesis adjusts to low-N conditions and the enzymes/activities integral to these adjustments have not been described. In this work, we use biochemical and biophysical analyses of photoautotrophically grown wild-type and mutant strains of Chlamydomonas reinhardtii to determine the integration of electron transport pathways critical for maintaining active photosynthetic complexes even after exposure of cells to N deprivation for 3 d. Key to acclimation is the type II NADPH dehydrogenase, NDA2, which drives cyclic electron flow (CEF), chlororespiration, and the generation of an H(+) gradient across the thylakoid membranes. N deprivation elicited a doubling of the rate of NDA2-dependent CEF, with little contribution from PGR5/PGRL1-dependent CEF The H(+) gradient generated by CEF is essential to sustain nonphotochemical quenching, while an increase in the level of reduced plastoquinone would promote a state transition; both are necessary to down-regulate photosystem II activity. Moreover, stimulation of NDA2-dependent chlororespiration affords additional relief from the elevated reduction state associated with N deprivation through plastid terminal oxidase-dependent water synthesis. Overall, rerouting electrons through the NDA2 catalytic hub in response to photoautotrophic N deprivation sustains cell viability while promoting the dissipation of excess excitation energy through quenching and chlororespiratory processes.

[Hygienic and environmental problems of energy-saving illumination in urbanization of Crimea].

The article considers the problems offloodlights pollution in the territory of Crimea due to the work of illumination led equipment of the key elements of the international transport artery "China-Europe". There was performed a qualitative assessment of characteristics of led floodlights pollution on the example of the sea surface of the transport crossing through the Kerch Strait. Ichthyologists and oceanographers were shown to estimate the amount of phytoplankton biomass based on sunlight illumination. The excess dose of blue light in the spectrum of led lighting was established to have an impact on phytoplankton greater than solar and lunar light, creating preconditions for the increase of biological mass of phytoplankton and consequently to the formation of the "stern stock". Arising from additional phytoplankton biomass can significantly influence on the schedule offish migration in waters of the Kerch Strait, the biomass of mosquitoes and midges, which are prey for amphibians and birds. The decline of the both light pollution and its negative impact on fauna andflora requires the development of semiconductor sources of white light with a biologically adequate spectrum in the framework of the "Lighting of the lighting equipment of Crimea".

Marine phototrophic consortia transfer electrons to electrodes in response to reductive stress.

This work studies how extracellular electron transfer (EET) from cyanobacteria-dominated marine microbial biofilms to solid electrodes is affected by the availability of inorganic carbon (Ci). The EET was recorded chronoamperometrically in the form of electrical current by a potentiostat in two identical photo-electrochemical cells using carbon electrodes poised at a potential of +0.6 V versus standard hydrogen electrode under 12/12 h illumination/dark cycles. The Ci was supplied by the addition of NaHCO3 to the medium and/or by sparging CO2 gas. At high Ci conditions, EET from the microbial biofilm to the electrodes was observed only during the dark phase, indicating the occurrence of a form of night-time respiration that can use insoluble electrodes as the terminal electron acceptor. At low or no Ci conditions, however, EET also occurred during illumination suggesting that, in the absence of their natural electron acceptor, some cyanobacteria are able to utilise solid electrodes as an electron sink. This may be a natural survival mechanism for cyanobacteria to maintain redox balance in environments with limiting CO2 and/or high light intensity.

Comparison of the Photosynthetic Yield of Cyanobacteria and Green Algae: Different Methods Give Different Answers.

The societal importance of renewable carbon-based commodities and energy carriers has elicited a particular interest for high performance phototrophic microorganisms. Selection of optimal strains is often based on direct comparison under laboratory conditions of maximal growth rate or additional valued features such as lipid content. Instead of reporting growth rate in culture, estimation of photosynthetic efficiency (quantum yield of PSII) by pulse-amplitude modulated (PAM) fluorimetry is an often applied alternative method. Here we compared the quantum yield of PSII and the photonic yield on biomass for the green alga Chlorella sorokiniana 211-8K and the cyanobacterium Synechocystis sp. PCC 6803. Our data demonstrate that the PAM technique inherently underestimates the photosynthetic efficiency of cyanobacteria by rendering a high F0 and a low FM, specifically after the commonly practiced dark pre-incubation before a yield measurement. Yet when comparing the calculated biomass yield on light in continuous culture experiments, we obtained nearly equal values for both species. Using mutants of Synechocystis sp. PCC 6803, we analyzed the factors that compromise its PAM-based quantum yield measurements. We will discuss the role of dark respiratory activity, fluorescence emission from the phycobilisomes, and the Mehler-like reaction. Based on the above observations we recommend that PAM measurements in cyanobacteria are interpreted only qualitatively.