Cyanobacterial hydrogenases: diversity, regulation and applications

Regulation of organic acid and hydrogen production by NADH/NAD+ ratio in Synechocystis sp. PCC 6803

Cyanobacteria serve as useful hosts in the production of substances to support a low-carbon society. Specifically, the unicellular cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) can produce organic acids, such as acetate, lactate, and succinate, as well as hydrogen, under dark, anaerobic conditions. The efficient production of these compounds appears to be closely linked to the regulation of intracellular redox balance. Notably, alterations in intracellular redox balance have been believed to influence the production of organic acids and hydrogen. To achieve these alterations, genetic manipulations involved overexpressing malate dehydrogenase (MDH), knocking out d-lactate dehydrogenase (DDH), or knocking out acetate kinase (AK), which subsequently modified the quantities and ratios of organic acids and hydrogen under dark, anaerobic conditions. Furthermore, the mutants generated displayed changes in the oxidation of reducing powers and the nicotinamide adenine dinucleotide hydrogen (NADH)/NAD+ ratio when compared to the parental wild-type strain. These findings strongly suggest that intracellular redox balance, especially the NADH/NAD+ ratio, plays a pivotal role in the production of organic acids and hydrogen in Synechocystis 6803.

Electron transport in cyanobacterial thylakoid membranes: Are cyanobacteria simple models for photosynthetic organisms?

Cyanobacteria are structurally the simplest oxygenic phototrophs, which makes it difficult to understand the regulation of photosynthesis because the photosynthetic and respiratory processes share the same thylakoid membranes and cytosolic space. This review aimed to summarise the molecular mechanisms and in vivo activities of electron transport in cyanobacterial thylakoid membranes based on the latest progress in photosynthesis research in cyanobacteria. Photosynthetic linear electron transport for CO2 assimilation has the dominant electron flux in the thylakoid membranes. The capacity of O2 photoreduction in cyanobacteria is comparable to the photosynthetic CO2 assimilation, which is mediated by flavodiiron proteins. Additionally, cyanobacterial thylakoid membranes harbour the significant electron flux of respiratory electron transport through a homologue of respiratory complex I, which is also recognized as the part of cyclic electron transport chain if it is coupled with photosystem I in the light. Further, O2-independent alternative electron transports through hydrogenase and nitrate reductase function with reduced ferredoxin as the electron donor. Whereas all these electron transports are recently being understood one by one, the complexity as the whole regulatory system remains to be uncovered in near future.

Photobiohydrogen Production and Strategies for H2 Yield Improvements in Cyanobacteria

Hydrogen gas (H2) is one of the potential future sustainable and clean energy carriers that may substitute the use of fossil resources including fuels since it has a high energy content (heating value of 141.65 MJ/kg) when compared to traditional hydrocarbon fuels [1]. Water is a primary product of combustion being a most significant advantage of H2 being environmentally friendly with the capacity to reduce global greenhouse gas emissions. H2 is used in various applications. It generates electricity in fuel cells, including applications in transportation, and can be applied as fuel in rocket engines [2]. Moreover, H2 is an important gas and raw material in many industrial applications. However, the high cost of the H2 production processes requiring the use of other energy sources is a significant disadvantage. At present, H2 can be prepared in many conventional ways, such as steam reforming, electrolysis, and biohydrogen production processes. Steam reforming uses high-temperature steam to produce hydrogen gas from fossil resources including natural gas. Electrolysis is an electrolytic process to decompose water molecules into O2 and H2. However, both these two methods are energy-intensive and producing hydrogen from natural gas, which is mostly methane (CH4) and in steam reforming generates CO2 and pollutants as by-products. On the other hand, biological hydrogen production is more environmentally sustainable and less energy intensive than thermochemical and electrochemical processes [3], but most concepts are not yet developed to production scale.

Flv3A facilitates O2 photoreduction and affects H2 photoproduction independently of Flv1A in diazotrophic Anabaena filaments

The model heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a typical example of a multicellular organism capable of simultaneously performing oxygenic photosynthesis in vegetative cells and O₂ -sensitive N₂ -fixation inside heterocysts. The flavodiiron proteins have been shown to participate in photoprotection of photosynthesis by driving excess electrons to O₂ (a Mehler-like reaction). Here, we performed a phenotypic and biophysical characterization of Anabaena mutants impaired in vegetative-specific Flv1A and Flv3A in order to address their physiological relevance in the bioenergetic processes occurring in diazotrophic Anabaena under variable CO₂ conditions. We demonstrate that both Flv1A and Flv3A are required for proper induction of the Mehler-like reaction upon a sudden increase in light intensity, which is likely important for the activation of carbon-concentrating mechanisms and CO₂ fixation. Under ambient CO₂ diazotrophic conditions, Flv3A is responsible for moderate O₂ photoreduction, independently of Flv1A, but only in the presence of Flv2 and Flv4. Strikingly, the lack of Flv3A resulted in strong downregulation of the heterocyst-specific uptake hydrogenase, which led to enhanced H₂ photoproduction under both oxic and micro-oxic conditions. These results reveal a novel regulatory network between the Mehler-like reaction and the diazotrophic metabolism, which is of great interest for future biotechnological applications.

Engineering cyanobacterial chassis for improved electron supply toward a heterologous ene-reductase

Cyanobacteria are noteworthy hosts for industrially relevant redox reactions, owing to a light-driven cofactor recycling system using water as electron donor. Customizing Synechocystis sp. PCC 6803 chassis by redirecting electron flow offers a particularly interesting approach to further improve light-driven biotransformations. Therefore, different chassis expressing the heterologous ene-reductase YqjM (namely ΔhoxYH, Δflv3, ΔndhD2 and ΔhoxYHΔflv3) were generated/evaluated. The results showed the robustness of the chassis, that exhibited growth and oxygen evolution rates similar to Synechocystis wild-type, even when expressing YqjM. By engineering the electron flow, the YqjM light-driven stereoselective reduction of 2-methylmaleimide to 2-methylsuccinimide was significantly enhanced in all chassis. In the best performing chassis (ΔhoxYH, lacking an active bidirectional hydrogenase) a 39 % increase was observed, reaching an in vivo specific activity of 116 U g_DCW^-1 and an initial reaction rate of 16.7 mM h^-1. In addition, the presence of the heterologous YqjM mitigated substrate toxicity, and the conversion of 2-methylmaleimide increased oxygen evolution rates, in particular at higher light intensity. In conclusion, this work demonstrates that rational engineering of electron transfer pathways is a valid strategy to increase in vivo specific activities and initial reaction rates in cyanobacterial chassis harboring oxidoreductases.

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H₂O₂ and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H₂O₂-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H₂O₂. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H₂O₂-consumption assays. Furthermore, an entrance channel for H₂O₂ was identified and key residues implicated in H₂O₂ activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

The DNA binding and H₂O₂ sensing mechanisms are revealed for RexT, a transcriptional regulator found in cyanobacteria of the Nostocales order.

Expression and activity of heterologous hydroxyisocaproate dehydrogenases in Synechocystis sp. PCC 6803 ΔhoxYH

Exploiting light to drive redox reactions is currently a hot topic since light is considered as an environmentally friendly source of energy. Consequently, cyanobacteria, which can use light e.g., for generating NADPH, are in the focus of research. Previously, it has been shown that various heterologous redox enzymes could be expressed in these microorganisms. Here we demonstrated the successful inducer-free expression of α-keto-acid dehydrogenases (L-HicDH and D-HicDH) from Lactobacillus confusus DSM 20196 and Lactobacillus paracasei DSM 20008 in Synechocystis sp. PCC 6803 ΔhoxYH mutant using replicative plasmids. While the L-HicDH showed poor activity limited by the amount of expressed enzyme, the D-HicDH was applied both in vivo and in vitro, transforming the selected α-keto acids to the corresponding optically pure (R)-α-hydroxy acids (ee >99%) in up to 53% and 90% conversion, respectively.

Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation

The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.

Electron & Biomass Dynamics of Cyanothece Under Interacting Nitrogen & Carbon Limitations

Marine diazotrophs are a diverse group with key roles in biogeochemical fluxes linked to primary productivity. The unicellular, diazotrophic cyanobacterium Cyanothece is widely found in coastal, subtropical oceans. We analyze the consequences of diazotrophy on growth efficiency, compared to NO₃^–-supported growth in Cyanothece, to understand how cells cope with N₂-fixation when they also have to face carbon limitation, which may transiently affect populations in coastal environments or during blooms of phytoplankton communities. When grown in obligate diazotrophy, cells face the double burden of a more ATP-demanding N-acquisition mode and additional metabolic losses imposed by the transient storage of reducing potential as carbohydrate, compared to a hypothetical N₂ assimilation directly driven by photosynthetic electron transport. Further, this energetic burden imposed by N₂-fixation could not be alleviated, despite the high irradiance level within the cultures, because photosynthesis was limited by the availability of dissolved inorganic carbon (DIC), and possibly by a constrained capacity for carbon storage. DIC limitation exacerbates the costs on growth imposed by nitrogen fixation. Therefore, the competitive efficiency of diazotrophs could be hindered in areas with insufficient renewal of dissolved gases and/or with intense phytoplankton biomass that both decrease available light energy and draw the DIC level down.

A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers

Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. Anabaena sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, iAnC892, for this organism using annotations and content obtained from multiple databases. iAnC892 describes both the vegetative and heterocyst cell types found in the filaments of Anabaena sp. ATCC 33047. iAnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of iAnC892 reaction content with the GSM of Anabaena sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to iAnC892. iAnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N₂ fixation. When used alongside the strain design algorithm, OptForce, iAnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors.

Green technology for sustainable biohydrogen production (waste to energy): A review

Perceiving and detecting a sustainable source of energy is very critical issue for current modern society. Hydrogen on combustion releases energy and water as a byproduct and has been considered as an environmental pollution free energy carrier. From the last decade, most of the researchers have recommended hydrogen as one of the cleanest fuels and its demand is rising ever since. Hydrogen having the highest energy density is more advantageous than any other fuel. Hydrogen obtained from the fossil fuels produces carbon dioxide as a byproduct and creates environment negative effect. Therefore, biohydrogen production from green algae and cyanobacteria is an attractive option that generates a benign renewable energy carrier. Microalgal feedstocks show a high potential for the generation of fuel such as biohydrogen, bioethanol and biodiesel. This article has reviewed the different methods of biohydrogen production while also trying to find out the most economical and ecofriendly method for its production. A thorough review process has been carried out to study the methods, enzymes involved, factors affecting the rate of hydrogen production, dual nature of algae, challenges and commercialization potential of algal biohydrogen.

Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy

Volcanic and geothermal areas are hot and often acidic environments that emit geothermal gasses, including H₂, CO and CO₂. Geothermal gasses mix with air, creating conditions where thermoacidophilic aerobic H₂- and CO-oxidizing microorganisms could thrive. Here, we describe the isolation of two Kyrpidia spormannii strains, which can grow autotrophically by oxidizing H₂ and CO with oxygen. These strains, FAVT5 and COOX1, were isolated from the geothermal soils of the Favara Grande on Pantelleria Island, Italy. Extended physiology studies were performed with K. spormannii FAVT5, and showed that this strain grows optimally at 55°C and pH 5.0. The highest growth rate is obtained using H₂ as energy source (μ_max 0.19 ± 0.02 h^–1, doubling time 3.6 h). K. spormannii FAVT5 can additionally grow on a variety of organic substrates, including some alcohols, volatile fatty acids and amino acids. The genome of each strain encodes for two O₂-tolerant hydrogenases belonging to [NiFe] group 2a hydrogenases and transcriptome studies using K. spormannii FAVT5 showed that both hydrogenases are expressed under H₂ limiting conditions. So far no Firmicutes except K. spormannii FAVT5 have been reported to exhibit a high affinity for H₂, with a K_s of 327 ± 24 nM. The genomes of each strain encode for one putative CO dehydrogenase, belonging to Form II aerobic CO dehydrogenases. The genomic potential and physiological properties of these Kyrpidia strains seem to be quite well adapted to thrive in the harsh environmental volcanic conditions.

Ferredoxin-mediated reduction of 2-nitrothiophene inhibits photosynthesis: mechanism and herbicidal potential

Searching for compounds that inhibit the growth of photosynthetic organisms highlighted a prominent effect at micromolar concentrations of the nitroheteroaromatic thioether, 2-nitrothiophene, applied in the light. Since similar effects were reminiscent to those obtained also by radicals produced under excessive illumination or by herbicides, and in light of its redox potential, we suspected that 2-nitrothiophene was reduced by ferredoxin, a major reducing compound in the light. In silico examination using docking and tunneling computing algorithms of the putative interaction between 2-nitrothiophene and cyanobacterial ferredoxin has suggested a site of interaction enabling robust electron transfer from the iron-sulfur cluster of ferredoxin to the nitro group of 2-nitrothiophene. ESR and oximetry analyses of cyanobacterial cells (Anabaena PCC7120) treated with 50 μM 2-nitrothiophene under illumination revealed accumulation of oxygen radicals and peroxides. Gas chromatography mass spectrometry analysis of 2-nitrothiophene-treated cells identified cytotoxic nitroso and non-toxic amino derivatives. These products of the degradation pathway of 2-nitrohiophene, which initializes with a single electron transfer that forms a short-live anion radical, are then decomposed to nitrate and thiophene, and may be further reduced to a nitroso hydroxylamine and amino derivatives. This mechanism of toxicity is similar to that of nitroimidazoles (e.g. ornidazole and metronidazole) reduced by ferredoxin in anaerobic bacteria and protozoa, but differs from that of ornidazole in planta.

Overproduction of the Flv3B flavodiiron, enhances the photobiological hydrogen production by the nitrogen-fixing cyanobacterium Nostoc PCC 7120

Background

The ability of some photosynthetic microorganisms, particularly cyanobacteria and microalgae, to produce hydrogen (H₂) is a promising alternative for renewable, clean-energy production. However, the most recent, related studies point out that much improvement is needed for sustainable cyanobacterial-based H₂ production to become economically viable. In this study, we investigated the impact of induced O₂-consumption on H₂ photoproduction yields in the heterocyte-forming, N₂-fixing cyanobacterium Nostoc PCC7120.

Results

The flv3B gene, encoding a flavodiiron protein naturally expressed in Nostoc heterocytes, was overexpressed. Under aerobic and phototrophic growth conditions, the recombinant strain displayed a significantly higher H₂ production than the wild type. Nitrogenase activity assays indicated that flv3B overexpression did not enhance the nitrogen fixation rates. Interestingly, the transcription of the hox genes, encoding the NiFe Hox hydrogenase, was significantly elevated, as shown by the quantitative RT-PCR analyses.

Conclusion

We conclude that the overproduced Flv3B protein might have enhanced O₂-consumption, thus creating conditions inducing hox genes and facilitating H₂ production. The present study clearly demonstrates the potential to use metabolic engineered cyanobacteria for photosynthesis driven H₂ production.

The Draft Genome of a Hydrogen-producing Cyanobacterium, Arthrospira platensis NIES-46

Arthrospira is an economically important cyanobacterium that contains many useful products, including proteins, vitamins, lipids, and pigments, and it is distributed in several alkaline soda lakes. Arthrospira platensis NIES-46 produces large amounts of hydrogen. In this study, we sequenced the NIES-46 draft genome and performed comparative analyses among Arthrospira species to elucidate the genomic background of this strain. The genome consists of 5.7 Mbp with a GC% of 44.5% and encodes 5,008 proteins. Our phylogenetic analysis using multiple orthologous proteins shows that Arthrospira is divided into two clades and that NIES-46 is closely related to A. platensis NIES-39. The genome structure and protein functions are highly conserved between A. platensis NIES-39 and NIES-46, suggesting that these two strains have recently diverged. Genes involved in hydrogen production are well-conserved among Arthrospira species, indicating conserved abilities to produce hydrogen.

Effects of the Photosystem II Inhibitors CCCP and DCMU on Hydrogen Production by the Unicellular Halotolerant Cyanobacterium Aphanothece halophytica

The unicellular halotolerant cyanobacterium Aphanothece halophytica is a potential dark fermentative producer of molecular hydrogen (H₂) that produces very little H₂ under illumination. One factor limiting the H₂ photoproduction of this cyanobacterium is an inhibition of bidirectional hydrogenase activity by oxygen (O₂) obtained from splitting water molecules via photosystem II activity. The present study aimed to investigate the effects of the photosystem II inhibitors carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) on H₂ production of A. halophytica under light and dark conditions and on photosynthetic and respiratory activities. The results showed that A. halophytica treated with CCCP and DCMU produced H₂ at three to five times the rate of untreated cells, when exposed to light. The highest H₂ photoproduction rates, 2.26 ± 0.24 and 3.63 ± 0.26  μmol H₂g⁻¹ dry weight h⁻¹, were found in cells treated with 0.5 μM CCCP and 50 μM DCMU, respectively. Without inhibitor treatment, A. halophytica incubated in the dark showed a significant increase in H₂ production compared with cells that were incubated in the light. Only CCCP treatment increased H₂ production of A. halophytica during dark incubation, because CCCP functions as an uncoupling agent of oxidative phosphorylation. The highest dark fermentative H₂ production rate of 39.50 ± 2.13  μmol H₂g⁻¹ dry weight h⁻¹ was found in cells treated with 0.5 μM CCCP after 2 h of dark incubation. Under illumination, CCCP and DCMU inhibited chlorophyll fluorescence, resulting in a low level of O₂, which promoted bidirectional hydrogenase activity in A. halophytica cells. In addition, only CCCP enhanced the respiration rate, further reducing the O₂ level. In contrast, DCMU reduced the respiration rate in A. halophytica.

Hydrogen Dynamics in Trichodesmium Colonies and Their Potential Role in Mineral Iron Acquisition

N2-fixing cyanobacteria mediate H2 fluxes through the opposing processes of H2 evolution, which is a by-product of the N2 fixation reaction, and H2 uptake, which is driven by uptake hydrogenases. Here, we used microelectrodes to characterize H2 and O2 dynamics in single natural colonies of the globally important N2 fixer Trichodesmium collected from the Gulf of Eilat. We observed gradually changing H2 dynamics over the course of the day, including both net H2 evolution and net H2 uptake, as well as large differences in H2 fluxes between individual colonies. Net H2 uptake was observed in colonies amended with H2 in both light and dark. Net H2 evolution was recorded in the light only, reflecting light-dependent N2 fixation coupled to H2 evolution. Both net H2 evolution and H2 uptake rates were higher before 2 pm than later in the day. These pronounced H2 dynamics in the morning coincided with strong net O2 uptake and the previously reported diel peak in N2 fixation. Later in the afternoon, when photosynthesis rates determined by O2 measurements were highest, and N2 fixation rates decrease according to previous studies, the H2 dynamics were also less pronounced. Thus, the observed diel variations in H2 dynamics reflect diel changes in the rates of O2 consumption and N2 fixation. Remarkably, the presence of H2 strongly stimulated the uptake of mineral iron by natural colonies. The magnitude of this effect was dependent on the time of day, with the strongest response in incubations that started before 2 pm, i.e., the period that covered the time of highest uptake hydrogenase activity. Based on these findings, we propose that by providing an electron source for mineral iron reduction in N2-fixing cells, H2 may contribute to iron uptake in Trichodesmium colonies.

An efficient method for DNA extraction from cyanobacteria isolated from hypersaline and marine environments

Cyanobacteria are ancient organisms surviving on the earth due to their simple nutritional requirements and ability to produce distinct secondary metabolites that can combat detrimental environmental impacts. In order to understand these abilities of cyanobacteria at the molecular level, it is necessary to extract high-quality genomic DNA. However, the presence of secondary metabolites and exopolysaccharides hinders the DNA extraction from these organisms, especially from hypersaline environments. Here we have developed and compared a new method with two known methods of DNA extraction from environmental isolates. The results clearly indicate that the new optimized method yielded large amount of DNA with high purity. Additionally, the extracted DNA showed reduced degradation and excellent overall quality, which can be used directly for downstream purposes such as PCR and sequencing.

Metalloproteins in the Biology of Heterocysts

Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.

Selenium versus sulfur: Reversibility of chemical reactions and resistance to permanent oxidation in proteins and nucleic acids

This review highlights the contributions of Jean Chaudière to the field of selenium biochemistry. Chaudière was the first to recognize that one of the main reasons that selenium in the form of selenocysteine is used in proteins is due to the fact that it strongly resists permanent oxidation. The foundations for this important concept was laid down by Al Tappel in the 1960's and even before by others. The concept of oxygen tolerance first recognized in the study of glutathione peroxidase was further advanced and refined by those studying [NiFeSe]-hydrogenases, selenosubtilisin, and thioredoxin reductase. After 200 years of selenium research, work by Marcus Conrad and coworkers studying glutathione peroxidase-4 has provided definitive evidence for Chaudière's original hypothesis (Ingold et al., 2018) [36]. While the reaction of selenium with oxygen is readily reversible, there are many other examples of this phenomenon of reversibility. Many reactions of selenium can be described as "easy in - easy out". This is due to the strong nucleophilic character of selenium to attack electrophiles, but then this reaction can be reversed due to the strong electrophilic character of selenium and the weakness of the selenium-carbon bond. Several examples of this are described.

Modulation of Intracellular O2 Concentration in Escherichia coli Strains Using Oxygen Consuming Devices

The use of cell factories for the production of bulk and value-added compounds is nowadays an advantageous alternative to the traditional petrochemical methods. Nevertheless, the efficiency and productivity of several of these processes can improve with the implementation of micro-oxic or anoxic conditions. In the industrial setting, laccases are appealing catalysts that can oxidize a wide range of substrates and reduce O₂ to H₂O. In this work, several laccase-based devices were designed and constructed to modulate the intracellular oxygen concentration in bacterial chassis. These oxygen consuming devices (OCDs) included Escherichia coli's native laccase (CueO) and three variants of this protein obtained by directed evolution. The OCDs were initially characterized in vitro using E. coli DH5α protein extracts and subsequently using extracts obtained from other E. coli strains and in vivo. Upon induction of the OCDs, no major effect on growth was observed in four of the strains tested, and analysis of the cell extract protein profiles revealed increased levels of laccase. Moreover, oxygen consumption associated with the OCDs occurred under all of the conditions tested, but the performance of the devices was shown to be strain-dependent, highlighting the importance of the genetic background even in closely related strains. One of the laccase variants showed 13- and 5-fold increases in oxidase activity and O₂ consumption rate, respectively. Furthermore, it was also possible to demonstrate O₂ consumption in vivo using l-DOPA as the substrate, which represents a proof of concept that these OCDs generate an intracellular oxygen sink, thereby manipulating the redox status of the cells. In addition, the modularity and orthogonality principles used for the development of these devices allow easy reassembly and fine-tuning, foreseeing their introduction into other chassis/systems.

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.

Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph

Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N₂ fixation is energetically highly expensive, and an energy-generating process such as photosynthesis can meet the energy demand of N₂ fixation. However, synthesis and expression of nitrogenase are exquisitely sensitive to the presence of oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N₂. Here, we demonstrate a feasible way to engineer nitrogenase activity in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. In addition, we have identified the minimal nif cluster required for such activity in Synechocystis 6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels of nif genes. Importantly, the O₂ tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineered Synechocystis 6803 strains that, remarkably, have more than 30% of the N₂ fixation activity of Cyanothece 51142, the highest such activity established in any nondiazotrophic oxygenic photosynthetic organism. This report establishes a baseline for the ultimate goal of engineering nitrogen fixation ability in crop plants.

Application of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes and the widespread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow to crop plants the ability to fix atmospheric N₂in situ. One long-term approach is to transfer all nif genes from a prokaryote to plant cells and to express nitrogenase in an energy-producing organelle, chloroplast, or mitochondrion. In this context, Synechocystis 6803, the nondiazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.

Edwardsiella tarda Sip2: A Serum-Induced Protein That Is Essential to Serum Survival, Acid Resistance, Intracellular Replication, and Host Infection

Edwardsiella tarda is a broad-host pathogen that can infect mammals, reptiles, and fish. E. tarda exhibits a remarkable ability to survive in host serum and replicate in host phagocytes, but the underlining mechanism is unclear. In this study, in order to identify E. tarda proteins involved in serum resistance, iTRAQ proteomic analysis was performed to examine the whole-cell protein profiles of TX01, a pathogenic E. tarda isolate, in response to serum treatment. Of the differentially expressed proteins identified, one (named Sip2) possesses a conserved hydrogenase domain and is homologous to the putative hydrogenase accessory protein HypB. When Sip2 was expressed in Escherichia coli, it significantly enhanced the survival of the host cells in serum. Compared to TX01, the sip2 knockout, TX01Δsip2, was dramatically reduced in the ability of hydrogenase activity, serum resistance, intracellular replication, dissemination in fish tissues, and causing mortality in infected fish. The lost virulence capacities of TX01Δsip2 were restored by complementation with the sip2 gene. Furthermore, TX01Δsip2 was significantly reduced in the capacity to grow under low pHs and iron-depleted conditions, and was unable to maintain its internal pH in acidic environment. Taken together, these results indicate that Sip2 is a novel serum-induced protein that is essential to serum resistance, cellular and tissue infection, and coping with acidic stress via its ability to modulate intracellular pH.

Phenotypic and genotypic characterisation of an unique indigenous hypersaline unicellular cyanobacterium, Euhalothece sp.nov

A novel halotolerant species of cyanobacterium of the order Chroococcales was isolated from hypersaline estuary in Kwa-Zulu Natal, South Africa. A comprehensive polyphasic approach viz., cell morphology, pigment composition and complete genome sequence analysis was conducted to elucidate the taxonomic position of the isolated strain. The blue-green oval to rod-shaped cells were 14-18 μm in size, and contained a high amount of phycocyanin pigments. The strain was moderate thermotolerant/alkalitolerant halophile with the optimum conditions for growth at 35 °C, pH 8.5 and 120 g/l of NaCl. Based on 16S rRNA gene sequence phylogeny, the strain was related to members of the 'Euhalothece' subcluster (99%). The whole genome sequence was determined, and the annotated genes showed a 90% sequence similarity to the gas-vacuolate, spindle-shaped Dactylococcopsis salina PCC 8305. The size of the genome was determined to be 5,113,178 bp and contained 4332 protein-coding genes and 69 RNA genes with a G + C content of 46.7%. Genes encoding osmoregulation, oxidative stress, heat shock, persister cells, and UV-absorbing secondary metabolites, among others, were identified. Based on the phylogenetic analysis of the 16S rRNA gene sequences, physiological data, pigment compositions and genomic data, the strain is considered to represent a novel species of Euhalothece.

Rewiring of Cyanobacterial Metabolism for Hydrogen Production: Synthetic Biology Approaches and Challenges

With the demand for renewable energy growing, hydrogen (H₂) is becoming an attractive energy carrier. Developing H₂ production technologies with near-net zero carbon emissions is a major challenge for the "H₂ economy." Certain cyanobacteria inherently possess enzymes, nitrogenases, and bidirectional hydrogenases that are capable of H₂ evolution using sunlight, making them ideal cell factories for photocatalytic conversion of water to H₂. With the advances in synthetic biology, cyanobacteria are currently being developed as a "plug and play" chassis to produce H₂. This chapter describes the metabolic pathways involved and the theoretical limits to cyanobacterial H₂ production and summarizes the metabolic engineering technologies pursued.

Microalgal hydrogen production - A review

Bio-hydrogen from microalgae including cyanobacteria has attracted commercial awareness due to its potential as an alternative, reliable and renewable energy source. Photosynthetic hydrogen production from microalgae can be interesting and promising options for clean energy. Advances in hydrogen-fuel-cell technology may attest an eco-friendly way of biofuel production, since, the use of H₂ to generate electricity releases only water as a by-product. Progress in genetic/metabolic engineering may significantly enhance the photobiological hydrogen production from microalgae. Manipulation of competing metabolic pathways by modulating the certain key enzymes such as hydrogenase and nitrogenase may enhance the evolution of H₂ from photoautotrophic cells. Moreover, biological H₂ production at low operating costs is requisite for economic viability. Several photobioreactors have been developed for large-scale biomass and hydrogen production. This review highlights the recent technological progress, enzymes involved and genetic as well as metabolic engineering approaches towards sustainable hydrogen production from microalgae.

Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

The first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro, with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.

A tight tunable range for Ni(II) sensing and buffering in cells

The metal affinities of metal-sensing transcriptional regulators co-vary with cellular metal concentrations over more than 12 orders of magnitude. To understand the cause of this relationship, we determined the structure of the Ni(II) sensor InrS and then created cyanobacteria (Synechocystis PCC 6803) in which transcription of genes encoding a Ni(II) exporter and a Ni(II) importer were controlled by InrS variants with weaker Ni(II) affinities. Variant strains were sensitive to elevated nickel and contained more nickel, but the increase was small compared with the change in Ni(II) affinity. All of the variant sensors retained the allosteric mechanism that inhibits DNA binding following metal binding, but a response to nickel in vivo was observed only when the sensitivity was set to respond in a relatively narrow (less than two orders of magnitude) range of nickel concentrations. Thus, the Ni(II) affinity of InrS is attuned to cellular metal concentrations rather than the converse.

The NiFe Hydrogenases of the Tetrachloroethene-Respiring Epsilonproteobacterium Sulfurospirillum multivorans: Biochemical Studies and Transcription Analysis

The organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans is able to grow with hydrogen as electron donor and with tetrachloroethene (PCE) as electron acceptor; PCE is reductively dechlorinated to cis-1,2-dichloroethene. Recently, a genomic survey revealed the presence of four gene clusters encoding NiFe hydrogenases in its genome, one of which is presumably periplasmic and membrane-bound (MBH), whereas the remaining three are cytoplasmic. To explore the role and regulation of the four hydrogenases, quantitative real-time PCR and biochemical studies were performed with S. multivorans cells grown under different growth conditions. The large subunit genes of the MBH and of a cytoplasmic group 4 hydrogenase, which is assumed to be membrane-associated, show high transcript levels under nearly all growth conditions tested, pointing toward a constitutive expression in S. multivorans. The gene transcripts encoding the large subunits of the other two hydrogenases were either not detected at all or only present at very low amounts. The presence of MBH under all growth conditions tested, even with oxygen as electron acceptor under microoxic conditions, indicates that MBH gene transcription is not regulated in contrast to other facultative hydrogen-oxidizing bacteria. The MBH showed quinone-reactivity and a characteristic UV/VIS spectrum implying a cytochrome b as membrane-integral subunit. Cell extracts of S. multivorans were subjected to native polyacrylamide gel electrophoresis (PAGE) and hydrogen oxidizing activity was tested by native staining. Only one band was detected at about 270 kDa in the particulate fraction of the extracts, indicating that there is only one hydrogen-oxidizing enzyme present in S. multivorans. An enrichment of this enzyme and SDS PAGE revealed a subunit composition corresponding to that of the MBH. From these findings we conclude that the MBH is the electron-donating enzyme system in the PCE respiratory chain. The roles for the other three hydrogenases remain unproven. The group 4 hydrogenase might be involved in hydrogen production upon fermentative growth.

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.

Increased heterocyst frequency by patN disruption in Anabaena leads to enhanced photobiological hydrogen production at high light intensity and high cell density

The effects of increasing the heterocyst-to-vegetative cell ratio on the nitrogenase-based photobiological hydrogen production by the filamentous heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 were studied. Using the uptake hydrogenase-disrupted mutant (ΔHup) as the parent, a deletion-insertion mutant (PN1) was created in patN, known to be involved in heterocyst pattern formation and leading to multiple singular heterocysts (MSH) in Nostoc punctiforme strain ATCC 29133. The PN1 strain showed heterocyst differentiation but failed to grow in medium free of combined-nitrogen; however, a spontaneous mutant (PN22) was obtained on prolonged incubation of PN1 liquid cultures and was able to grow robustly on N₂. The disruption of patN was confirmed in both PN1 and PN22 by PCR and whole genome resequencing. Under combined-nitrogen limitation, the percentage of heterocysts to total cells in the PN22 filaments was 13-15 and 16-18% under air and 1% CO₂-enriched air, respectively, in contrast to the parent ΔHup which formed 6.5-11 and 9.7-13% heterocysts in these conditions. The PN22 strain exhibited a MSH phenotype, normal diazotrophic growth, and higher H₂ productivity at high cell concentrations, and was less susceptible to photoinhibition by strong light than the parent ΔHup strain, resulting in greater light energy utilization efficiency in H₂ production on a per unit area basis under high light conditions. The increase in MSH frequency shown here appears to be a viable strategy for enhancing H₂ productivity by outdoor cultures of cyanobacteria in high-light environments.

Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey

Microbial Molecular hydrogen (H₂) cycling plays an important role in several ecological niches. Hydrogenases (H₂ases), enzymes involved in H₂ metabolism, are of great interest for investigating microbial communities, and producing BioH₂. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H₂ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H₂ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H₂ase. The [NiFe] H₂ases were found to be the only enzymes present in this phylum. Fifty-five strains were found to be potentially able produce the bidirectional Hox enzyme and 33 to produce the uptake (Hup) enzyme. H₂ metabolism in Cyanobacteria has a broad ecological distribution, since only the genomes of strains collected from the open ocean do not possess hox genes. In addition, the presence of H₂ase was found to increase in the late branching clades of the phylogenetic tree of the species. Surprisingly, five cyanobacterial genomes were found to possess homologs of oxygen tolerant H₂ases belonging to groups 1, 3b, and 3d. Overall, these data show that H₂ases are widely distributed, and are therefore probably of great functional importance in Cyanobacteria. The present finding that homologs to oxygen-tolerant H₂ases are present in this phylum opens new perspectives for applying the process of photosynthesis in the field of H₂ production.

Carotenoid Biosynthesis in Calothrix sp. 336/3: Composition of Carotenoids on Full Medium, During Diazotrophic Growth and After Long-Term H2 Photoproduction

The carotenoid composition of the filamentous heterocystous N₂-fixing cyanobacterium Calothrix sp. 336/3 was investigated under three conditions: in full medium (non-diazotrophic growth); in the absence of combined nitrogen (diazotrophic growth); and after long-term H₂ photoproduction (diazotrophic medium and absence of nitrogen in the atmosphere). Anabaena sp. PCC 7120 and its ΔhupL mutant with disrupted uptake hydrogenase were used as reference strains. Analysis of identified carotenoids and enzymes involved in carotenogenesis showed the presence of three distinct biosynthetic pathways in Calothrix sp. 336/3. The first one is directed towards biosynthesis of myxoxanthophylls, such as myxol 2'-methylpentoside and 2-hydroxymyxol 2'-methylpentoside. The second pathway results in production of hydroxylated carotenoids, such as zeaxanthin, caloxanthin and nostoxanthin, and the last pathway is responsible for biosynthesis of echinenone and hydroxylated forms of ketocarotenoids, such as 3'-hydroxyechinenone and adonixanthin. We found that carotenogenesis in filamentous heterocystous cyanobacteria varies depending on the nitrogen status of the cultures, with significant accumulation of echinenone during diazotrophic growth at the expense of β-carotene. Under the severe N deficiency and high CO₂ supply, which leads to efficient H₂ photoproduction, cyanobacteria degrade echinenone and β-carotene, and accumulate glycosylated and hydroxylated carotenoids, such as myxol (or ketomyxol) 2'-methylpentosides, 3'-hydroxyechinenone and zeaxanthin. We suggest that the stability of the photosynthetic apparatus in Calothrix sp. 336/3 cells under N deficiency and high carbon conditions, which also appeared as the partial recovery of the pigment composition by the end of the long-term (∼1 month) H₂ photoproduction process, might be mediated by a high content of hydroxycarotenoids.

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica 'Solar Lake'), a Model Anoxygenic Photosynthetic Cyanobacterium

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth's biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica 'Solar Lake', a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating redox gradients and nitrogen availability that occur in benthic mats over a diel cycle. Such dynamic geochemical conditions likely also challenged Proterozoic cyanobacteria, modulating oxygen production. The genetic repertoire that underpins flexible oxygenic/anoxygenic photosynthesis in cyanobacteria provides a foundation to explore the regulation, evolutionary context, and biogeochemical implications of these co-occurring metabolisms in Earth history.