Modification of the Fe Protein of Nitrogenase in Natural Populations of Trichodesmium thiebautii

Rapid mode switching facilitates the growth of Trichodesmium: A model analysis

Trichodesmium is one of the dominant dinitrogen (N2) fixers in the ocean, influencing global carbon and nitrogen cycles through biochemical reactions. Although its photosynthetic activity fluctuates rapidly, the physiological or ecological advantage of this fluctuation is unclear. We develop a metabolic model of Trichodesmium that can perform daytime N2 fixation. We examined (1) the effect of the duration of switches between photosynthetic and non-photosynthetic cellular states and (2) the effect of the presence and absence of N2 fixation in photosynthetic states. Results show that a rapid switch between photosynthetic and non-photosynthetic states increases Trichodesmium growth rates by improving metabolic efficiencies due to an improved balance of C and N metabolism. This provides a strategy for previous paradoxical observations that all Trichodesmium cells can contain nitrogenase. This study reveals the importance of fluctuating photosynthetic activity and provides a mechanism for daytime N2 fixation that allows Trichodesmium to fix N2 aerobically in the global ocean.

Deoxygenation enhances photosynthetic performance and increases N2 fixation in the marine cyanobacterium Trichodesmium under elevated pCO2

Effects of changed levels of dissolved O₂ and CO₂ on marine primary producers are of general concern with respect to ecological effects of ongoing ocean deoxygenation and acidification as well as upwelled seawaters. We investigated the response of the diazotroph Trichodesmium erythraeum IMS 101 after it had acclimated to lowered pO₂ (~60 μM O₂) and/or elevated pCO₂ levels (HC, ~32 μM CO₂) for about 20 generations. Our results showed that reduced O₂ levels decreased dark respiration significantly, and increased the net photosynthetic rate by 66 and 89% under the ambient (AC, ~13 μM CO₂) and the HC, respectively. The reduced pO₂ enhanced the N₂ fixation rate by ~139% under AC and only by 44% under HC, respectively. The N₂ fixation quotient, the ratio of N₂ fixed per O₂ evolved, increased by 143% when pO₂ decreased by 75% under the elevated pCO₂. Meanwhile, particulate organic carbon and nitrogen quota increased simultaneously under reduced O₂ levels, regardless of the pCO₂ treatments. Nevertheless, changed levels of O₂ and CO₂ did not bring about significant changes in the specific growth rate of the diazotroph. Such inconsistency was attributed to the daytime positive and nighttime negative effects of both lowered pO₂ and elevated pCO₂ on the energy supply for growth. Our results suggest that Trichodesmium decrease its dark respiration by 5% and increase its N₂-fixation by 49% and N₂-fixation quotient by 30% under future ocean deoxygenation and acidification with 16% decline of pO₂ and 138% rise of pCO₂ by the end of this century.

Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera

In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.

Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins

Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.

Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium

Cyanobacteria of the genus Trichodesmium provide about 80 Tg of fixed nitrogen to the surface ocean per year and contribute to marine biogeochemistry, including the sequestration of carbon dioxide. Trichodesmium fixes nitrogen in the daylight, despite the incompatibility of the nitrogenase enzyme with oxygen produced during photosynthesis. While the mechanisms protecting nitrogenase remain unclear, all proposed strategies require considerable resource investment. Here we identify a crucial benefit of daytime nitrogen fixation in Trichodesmium spp. that may counteract these costs. We analysed diel proteomes of cultured and field populations of Trichodesmium in comparison with the marine diazotroph Crocosphaera watsonii WH8501, which fixes nitrogen at night. Trichodesmium's proteome is extraordinarily dynamic and demonstrates simultaneous photosynthesis and nitrogen fixation, resulting in balanced particulate organic carbon and particulate organic nitrogen production. Unlike Crocosphaera, which produces large quantities of glycogen as an energy store for nitrogenase, proteomic evidence is consistent with the idea that Trichodesmium reduces the need to produce glycogen by supplying energy directly to nitrogenase via soluble ferredoxin charged by the photosynthesis protein PsaC. This minimizes ballast associated with glycogen, reducing cell density and decreasing sinking velocity, thus supporting Trichodesmium's niche as a buoyant, high-light-adapted colony forming cyanobacterium. To occupy its niche of simultaneous nitrogen fixation and photosynthesis, Trichodesmium appears to be a conspicuous consumer of iron, and has therefore developed unique iron-acquisition strategies, including the use of iron-rich dust. Particle capture by buoyant Trichodesmium colonies may increase the residence time and degradation of mineral iron in the euphotic zone. These findings describe how cellular biochemistry defines and reinforces the ecological and biogeochemical function of these keystone marine diazotrophs.

Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics

The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle-colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium's ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A

The symbiotic cyanobacterium UCYN‐A is one of the most globally abundant marine dinitrogen (N₂)‐fixers, but cultures have not been available and its biology and ecology are poorly understood. We used cultivation‐independent approaches to investigate how UCYN‐A single‐cell N₂ fixation rates (NFRs) and nifH gene expression vary as a function of depth and photoperiod. Twelve‐hour day/night incubations showed that UCYN‐A only fixed N₂ during the day. Experiments conducted using in situ arrays showed a light‐dependence of NFRs by the UCYN‐A symbiosis, with the highest rates in surface waters (5–45 m) and lower rates at depth (≥ 75 m). Analysis of NFRs versus in situ light intensity yielded a light saturation parameter (I_k) for UCYN‐A of 44 μmol quanta m⁻² s⁻¹. This is low compared with other marine diazotrophs, suggesting an ecological advantage for the UCYN‐A symbiosis under low‐light conditions. In contrast to cell‐specific NFRs, nifH gene‐specific expression levels did not vary with depth, indicating that light regulates N₂ fixation by UCYN‐A through processes other than transcription, likely including host–symbiont interactions. These results offer new insights into the physiology of the UCYN‐A symbiosis in the subtropical North Pacific Ocean and provide clues to the environmental drivers of its global distributions.

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.

N2 fixation in free-floating filaments of Trichodesmium is higher than in transiently suboxic colony microenvironments

To understand the role of micrometer-scale oxygen (O₂ ) gradients in facilitating dinitrogen (N₂ ) fixation, we characterized O₂ dynamics in the microenvironment around free-floating trichomes and colonies of Trichodesmium erythraeum IMS101. Diurnal and spatial variability in O₂ concentrations in the bulk medium, within colonies, along trichomes and within single cells were determined using O₂ optodes, microsensors and model calculations. Carbon (C) and N₂ fixation as well as O₂ evolution and uptake under different O₂ concentrations were analyzed by stable isotope incubations and membrane inlet mass spectrometry. We observed a pronounced diel rhythm in O₂ fluxes, with net O₂ evolution restricted to short periods in the morning and evening, and net O₂ uptake driven by dark respiration and light-dependent O₂ uptake during the major part of the light period. Remarkably, colonies showed lower N₂ fixation and C fixation rates than free-floating trichomes despite the long period of O₂ undersaturation in the colony microenvironment. Model calculations demonstrate that low permeability of the cell wall in combination with metabolic heterogeneity between single cells allows for anoxic intracellular conditions in colonies but also free-floating trichomes of Trichodesmium. Therefore, whereas colony formation must have benefits for Trichodesmium, it does not favor N₂ fixation.

Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions

Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.

Molecular Ecology of nifH Genes and Transcripts Along a Chronosequence in Revegetated Areas of the Tengger Desert

The colonization and succession of diazotrophs are essential for the development of organic soil layers in desert. We examined the succession of diazotrophs in the well-established revegetated areas representing a chronosequence of 0 year (control), 22 years (restored artificially since 1981), 57 years (restored artificially since 1956), and more than 100 years (restored naturally) to determine the community assembly and active expression of diazotrophs. The pyrosequencing data revealed that Alphaproteobacteria-like diazotrophs predominated in the topsoil of our mobile dune site, while cyanobacterial diazotrophs predominated in the revegetated sites. The cyanobacterial diazotrophs were primarily composed of the heterocystous genera Anabaena, Calothrix, Cylindrospermum, Nodularia, Nostoc, Trichormus, and Mastigocladus. Almost all the nifH sequences belonged to the Cyanobacteria phylum (all the relative abundance values >99.1 %) at transcript level and all the active cyanobacterial diazotrophs distributed in the families Nostocaceae and Rivulariaceae. The most dominant active cyanobacterial genus was Cylindrospermum in all the samples. The rank abundance and community analyses demonstrated that most of the diazotrophic diversity originated from the "rare" species, and all the DNA-based diazotrophic libraries were richer and more diverse than their RNA-based counterparts in the revegetated sites. Significant differences in the diazotrophic community and their active population composition were observed among the four research sites. Samples from the 1981-revegetating site (predominated by cyanobacterial crusts) showed the highest nitrogenase activity, followed by samples from the naturally revegetating site (predominated by lichen crusts), the 1956-revegetating site (predominated by moss crusts), and the mobile dune site (without crusts). Collectively, our data highlight the importance of nitrogen fixation by the primary successional desert topsoil and suggest that the N2-fixing cyanobacteria are the key diazotrophs to the nitrogen budget and the development of topsoil in desert, which is critical for the succession of the degraded terrestrial ecosystems.

Levels of daily light doses under changed day-night cycles regulate temporal segregation of photosynthesis and N2 Fixation in the cyanobacterium Trichodesmium erythraeum IMS101

While the diazotrophic cyanobacterium Trichodesmium is known to display inverse diurnal performances of photosynthesis and N₂ fixation, such a phenomenon has not been well documented under different day-night (L-D) cycles and different levels of light dose exposed to the cells. Here, we show differences in growth, N₂ fixation and photosynthetic carbon fixation as well as photochemical performances of Trichodesmium IMS101 grown under 12L:12D, 8L:16D and 16L:8D L-D cycles at 70 μmol photons m^-2 s^-1 PAR (LL) and 350 μmol photons m^-2 s^-1 PAR (HL). The specific growth rate was the highest under LL and the lowest under HL under 16L:8D, and it increased under LL and decreased under HL with increased levels of daytime light doses exposed under the different light regimes, respectively. N₂ fixation and photosynthetic carbon fixation were affected differentially by changes in the day-night regimes, with the former increasing directly under LL with increased daytime light doses and decreased under HL over growth-saturating light levels. Temporal segregation of N₂ fixation from photosynthetic carbon fixation was evidenced under all day-night regimes, showing a time lag between the peak in N₂ fixation and dip in carbon fixation. Elongation of light period led to higher N₂ fixation rate under LL than under HL, while shortening the light exposure to 8 h delayed the N₂ fixation peaking time (at the end of light period) and extended it to night period. Photosynthetic carbon fixation rates and transfer of light photons were always higher under HL than LL, regardless of the day-night cycles. Conclusively, diel performance of N₂ fixation possesses functional plasticity, which was regulated by levels of light energy supplies either via changing light levels or length of light exposure.

Trichodesmium--a widespread marine cyanobacterium with unusual nitrogen fixation properties

The last several decades have witnessed dramatic advances in unfolding the diversity and commonality of oceanic diazotrophs and their N₂-fixing potential. More recently, substantial progress in diazotrophic cell biology has provided a wealth of information on processes and mechanisms involved. The substantial contribution by the diazotrophic cyanobacterial genus Trichodesmium to the nitrogen influx of the global marine ecosystem is by now undisputable and of paramount ecological importance, while the underlying cellular and molecular regulatory physiology has only recently started to unfold. Here, we explore and summarize current knowledge, related to the optimization of its diazotrophic capacity, from genomics to ecophysiological processes, via, for example, cellular differentiation (diazocytes) and temporal regulations, and suggest cellular research avenues that now ought to be explored.

INTERACTIVE EFFECTS OF IRRADIANCE AND CO2 ON CO2 FIXATION AND N2 FIXATION IN THE DIAZOTROPH TRICHODESMIUM ERYTHRAEUM (CYANOBACTERIA)(1)

The diazotrophic cyanobacteria Trichodesmium spp. contribute approximately half of the known marine dinitrogen (N2 ) fixation. Rapidly changing environmental factors such as the rising atmospheric partial pressure of carbon dioxide (pCO2 ) and shallower mixed layers (higher light intensities) are likely to affect N2 -fixation rates in the future ocean. Several studies have documented that N2 fixation in laboratory cultures of T. erythraeum increased when pCO2 was doubled from present-day atmospheric concentrations (∼380 ppm) to projected future levels (∼750 ppm). We examined the interactive effects of light and pCO2 on two strains of T. erythraeum Ehrenb. (GBRTRLI101 and IMS101) in laboratory semicontinuous cultures. Elevated pCO2 stimulated gross N2 -fixation rates in cultures growing at 38 μmol quanta · m(-2 ) · s(-1) (GBRTRLI101 and IMS101) and 100 μmol quanta · m(-2 ) · s(-1) (IMS101), but this effect was reduced in both strains growing at 220 μmol quanta · m(-2 ) · s(-1) . Conversely, CO2 -fixation rates increased significantly (P < 0.05) in response to high pCO2 under mid- and high irradiances only. These data imply that the stimulatory effect of elevated pCO2 on CO2 fixation and N2 fixation by T. erythraeum is correlated with light. The ratio of gross:net N2 fixation was also correlated with light and trichome length in IMS101. Our study suggests that elevated pCO2 may have a strong positive effect on Trichodesmium gross N2 fixation in intermediate and bottom layers of the euphotic zone, but perhaps not in light-saturated surface layers. Climate change models must consider the interactive effects of multiple environmental variables on phytoplankton and the biogeochemical cycles they mediate.

Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer

Bacteria belonging to the genus Bradyrhizobium are capable of establishing symbiotic relationships with a broad range of plants belonging to the three subfamilies of the family Leguminosae ( = Fabaceae), with the formation of specialized structures on the roots called nodules, where fixation of atmospheric nitrogen takes place. Symbiosis is under the control of finely tuned expression of common and host-specific nodulation genes and also of genes related to the assembly and activity of the nitrogenase, which, in Bradyrhizobium strains investigated so far, are clustered in a symbiotic island. Information about the diversity of these genes is essential to improve our current poor understanding of their origin, spread and maintenance and, in this study, we provide information on 40 Bradyrhizobium strains, mostly of tropical origin. For the nodulation trait, common (nodA), Bradyrhizobium-specific (nodY/K) and host-specific (nodZ) nodulation genes were studied, whereas for fixation ability, the diversity of nifH was investigated. In general, clustering of strains in all nod and nifH trees was similar and the Bradyrhizobium group could be clearly separated from other rhizobial genera. However, the congruence of nod and nif genes with ribosomal and housekeeping genes was low. nodA and nodY/K were not detected in three strains by amplification or hybridization with probes using Bradyrhizobium japonicum and Bradyrhizobium elkanii type strains, indicating the high diversity of these genes or that strains other than photosynthetic Bradyrhizobium must have alternative mechanisms to initiate the process of nodulation. For a large group of strains, the high diversity of nod genes (with an emphasis on nodZ), the low relationship between nod genes and the host legume, and some evidence of horizontal gene transfer might indicate strategies to increase host range. On the other hand, in a group of five symbionts of Acacia mearnsii, the high congruence between nod and ribosomal/housekeeping genes, in addition to shorter nodY/K sequences and the absence of nodZ, highlights a co-evolution process. Additionally, in a group of B. japonicum strains that were symbionts of soybean, vertical transfer seemed to represent the main genetic event. In conclusion, clustering of nodA and nifH gives additional support to the theory of monophyletic origin of the symbiotic genes in Bradyrhizobium and, in addition to the analysis of nodY/K and nodZ, indicates spread and maintenance of nod and nif genes through both vertical and horizontal transmission, apparently with the dominance of one or other of these events in some groups of strains.

Interactions between CCM and N2 fixation in Trichodesmium

In view of the current increase in atmospheric pCO(2) and concomitant changes in the marine environment, it is crucial to assess, understand, and predict future responses of ecologically relevant phytoplankton species. The diazotrophic cyanobacterium Trichodesmium erythraeum was found to respond strongly to elevated pCO(2) by increasing growth, production rates, and N(2) fixation. The magnitude of these CO(2) effects exceeds those previously seen in other phytoplankton, raising the question about the underlying mechanisms. Here, we review recent publications on metabolic pathways of Trichodesmium from a gene transcription level to the protein activities and energy fluxes. Diurnal patterns of nitrogenase activity change markedly with CO(2) availability, causing higher diel N(2) fixation rates under elevated pCO(2). The observed responses to elevated pCO(2) could not be attributed to enhanced energy generation via gross photosynthesis, although there are indications for CO(2)-dependent changes in ATP/NADPH + H(+) production. The CO(2) concentrating mechanism (CCM) in Trichodesmium is primarily based on HCO(3)(-) uptake. Although only little CO(2) uptake was detected, the NDH complex seems to play a crucial role in internal cycling of inorganic carbon, especially under elevated pCO(2). Affinities for inorganic carbon change over the day, closely following the pattern in N(2) fixation, and generally decrease with increasing pCO(2). This down-regulation of CCM activity and the simultaneously enhanced N(2) fixation point to a shift in energy allocation from carbon acquisition to N(2) fixation under elevated pCO(2) levels. A strong light modulation of CO(2) effects further corroborates the role of energy fluxes as a key to understand the responses of Trichodesmium.

The influence of pCO2 and temperature on gene expression of carbon and nitrogen pathways in Trichodesmium IMS101

Growth, protein amount, and activity levels of metabolic pathways in Trichodesmium are influenced by environmental changes such as elevated pCO(2) and temperature. This study examines changes in the expression of essential metabolic genes in Trichodesmium grown under a matrix of pCO(2) (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO(2) concentrating mechanism (bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX), energy metabolism (atpB, sod, prx, glcD), nitrogen metabolism (glnA, hetR, nifH), and inorganic carbon fixation and photosynthesis (rbcL, rca, psaB, psaC, psbA). nifH and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for glnA and hetR only when both pCO(2) and temperature were elevated. CO(2) concentrating mechanism genes were not affected by pCO(2) and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO(2) concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in Trichodesmium, CO(2) concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N(2) fixation take place, pointing at the tight and complex regulation of gene expression in Trichodesmium. Here we provide new data linking environmental changes of pCO(2) and temperature to gene expression in Trichodesmium. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity.

Combined effects of CO2 and light on the N2-fixing cyanobacterium Trichodesmium IMS101: a mechanistic view

The marine diazotrophic cyanobacterium Trichodesmium responds to elevated atmospheric CO(2) partial pressure (pCO(2)) with higher N(2) fixation and growth rates. To unveil the underlying mechanisms, we examined the combined influence of pCO(2) (150 and 900 microatm) and light (50 and 200 micromol photons m(-2) s(-1)) on Trichodesmium IMS101. We expand on a complementary study that demonstrated that while elevated pCO(2) enhanced N(2) fixation and growth, oxygen evolution and carbon fixation increased mainly as a response to high light. Here, we investigated changes in the photosynthetic fluorescence parameters of photosystem II, in ratios of the photosynthetic units (photosystem I:photosystem II), and in the pool sizes of key proteins involved in the fixation of carbon and nitrogen as well as their subsequent assimilation. We show that the combined elevation in pCO(2) and light controlled the operation of the CO(2)-concentrating mechanism and enhanced protein activity without increasing their pool size. Moreover, elevated pCO(2) and high light decreased the amounts of several key proteins (NifH, PsbA, and PsaC), while amounts of AtpB and RbcL did not significantly change. Reduced investment in protein biosynthesis, without notably changing photosynthetic fluxes, could free up energy that can be reallocated to increase N(2) fixation and growth at elevated pCO(2) and light. We suggest that changes in the redox state of the photosynthetic electron transport chain and posttranslational regulation of key proteins mediate the high flexibility in resources and energy allocation in Trichodesmium. This strategy should enable Trichodesmium to flourish in future surface oceans characterized by elevated pCO(2), higher temperatures, and high light.

Improved Method for Recovery of mRNA from Aquatic Samples and Its Application to Detection of mer Expression

Previously described methods for extraction of mRNA from environmental samples may preclude detecting transcripts from genes that were present in low abundance in aquatic bacterial communities. By combining a boiling sodium dodecyl sulfate-diethylpyrocarbonate lysis step with acid-guanidinium extraction, we improved recovery of target mRNA from both pure cultures and environmental samples. The most significant advantage of the new protocol is that it is easily adapted to yield high recovery of mRNA from 142-mm-diameter flat filters and high-capacity cartridge filters. The lysis and extraction procedures are more rapid than previously described methods, and many samples can be handled at once. RNA extracts have been shown to be free of contaminating DNA. The lysis procedure does not damage target mRNA sequences, and mRNA can be detected from fewer than 10 bacterial cells. We used the new method to examine transcripts of genes responsible for detoxification of mercurial compounds. Induction of merA (specifying mercuric reductase) transcripts in stationary-phase Pseudomonas aeruginosa containing Tn501 occurred within 60 s of HgCl(2) addition and was proportional to the amount of Hg(II) added. The new technique also allowed the detection of merA transcripts from the microbial community of a mercury-contaminated pond (Reality Lake, Oak Ridge, Tenn.). Significant differences in merA transcript abundance were observed between different locations associated with the lake. The results indicate that the new method is simple and rapid and can be applied to the study of mer gene expression of aquatic communities in their natural habitats.

Amino Acid Cycling in Colonies of the Planktonic Marine Cyanobacterium Trichodesmium thiebautii

We examined diel trends in internal pools and net efflux of free amino acids in colonies of the nonheterocystous, diazotrophic cyanobacterium Trichodesmium thiebautii, freshly collected from waters of the Caribbean and the Bahamas. The kinetics of glutamate uptake by whole colonies were also examined. While intracolonial pools of most free amino acids were relatively constant through the day, pools of glutamate and glutamine varied over the diel cycle, with maxima during the early afternoon. This paralleled the daily cycle of nitrogenase activity. We also observed a large net release of these two amino acids from intact colonies. Glutamate release was typically 100 pmol of N colony h. This is about one-fourth the concurrent rate of N(2) fixation during the day. However, while nitrogenase activity only occurs during the day, net release of glutamate and glutamine persisted into the night and may therefore account for a greater loss of recently fixed N on a daily basis. This release may be an important route of new N input into tropical, oligotrophic waters. Whole colonies also displayed saturation kinetics with respect to glutamate uptake. The K(s) for whole colonies varied from 1.6 to 3.2 muM, or about 100-fold greater than typical ambient concentrations. Thus, uptake systems appear to be adapted to the higher concentrations of glutamate found within the intracellular spaces of the colonies. This suggests that glutamate may be a vehicle for N exchange among trichomes in the colony.

Temporal Variability in Nitrogenase Gene Expression in Natural Populations of the Marine Cyanobacterium Trichodesmium thiebautii

We report a distinct diel periodicity in the abundance of nifH (dinitrogenase reductase) mRNA in natural populations of the nonheterocystous marine cyanobacterium Trichodesmium thiebautii. Our observations show that in addition to translational and posttranslational controls, Trichodesmium nitrogenase expression is also regulated at the transcriptional and/or posttranscriptional level.

NifH expression by five groups of phototrophs compared with nitrogenase activity in coastal microbial mats

Diazotrophic (nitrogen-fixing) Cyanobacteria are often structurally dominant in coastal microbial mats but diazotrophs from other bacterial lineages are also present and active. The expression of nifH by four nonheterocystous Cyanobacteria and one member of the Gammaproteobacteria was followed over a 24-h cycle using quantitative reverse transcriptase-PCR. Daily nifH expression patterns were compared with the actual nitrogenase activity (NA) of the entire mat community. Lyngbya sp. was identified as the dominant cyanobacterium but, although recognized as a diazotroph, its cell-specific and abundance-related nifH expression was low. Unexpectedly, the other three cyanobacterial phylotypes dominated community nifH expression at all stations. Also, the gammaproteobacterium showed high levels of cell-specific nifH expression but its nifH copy number was low. Its contribution to the whole community nifH expression was therefore low. These results indicate that there were varying levels of cell-specific expression of nifH in the different mat types and more so, varying contributions to the overall nifH expression by the different diazotrophs. Furthermore, NA did not follow nifH expression patterns.

Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean

Mesoscale physical processes (for example eddies, frontal meanders and planetary waves) can play important roles in controlling ocean biogeochemistry. We examined spatial variations in upper ocean (0-100 m) nutrient inventories, N(2) fixing microorganism diversity and abundance, and rates of N(2) fixation in an anticyclonic eddy near Station ALOHA (22 degrees 45' N, 158 degrees 00' W) in the North Pacific Subtropical Gyre (NPSG). In July 2005, satellite-based sea surface altimetry and ocean color observation revealed an anticyclonic eddy with enhanced chlorophyll in the upper ocean in the vicinity of Station ALOHA. Within the eddy, near-surface ocean chlorophyll concentrations were approximately 5-fold greater than in the surrounding waters. Inventories of nitrate and phosphate in the eddy were similar to the concentrations historically observed at Station ALOHA, while silicic acid inventories were significantly depleted (one-way analysis of variance, P<0.01). Quantitative PCR determinations of nifH gene copies revealed relatively high abundances of several N(2) fixing cyanobacteria, including Trichodesmium spp., Crocosphaera watsonii and Richelia intracellularis. Reverse transcriptase PCR (RT-PCR) amplified nitrogenase (nifH) gene transcripts were cloned and sequenced to examine the diversity of active N(2) fixing microorganisms; these clone libraries were dominated by sequence-types 97%-99% identical to the filamentous cyanobacteria Trichodesmium spp. Near-surface ocean rates of N(2) fixation were 2-18 times greater (averaging 8.6+/-5.6 nmol N per l per day) than previously reported measurements at Station ALOHA. These results suggest that mesoscale physical variability can play an important role in modifying the abundances of N(2) fixing microorganisms and associated rates of N(2) fixation in open ocean ecosystems.

On the role of oxygen for nitrogen fixation in the marine cyanobacterium Trichodesmium sp

The marine, non-heterocystous, filamentous cyanobacterium Trichodesmium shows a distinct diurnal pattern of nitrogenase activity. In an attempt to reveal the factors that control this pattern, a series of measurements were carried out using online acetylene reduction assay. Light response curves of nitrogenase were recorded applying various concentrations of oxygen. The effect of oxygen depended on the irradiance applied. Above a photon irradiance of 16 mumol m(-2) s(-1) nitrogenase activity was highest under anoxic conditions. Below this irradiance the presence of oxygen was required to achieve highest nitrogenase activity and in the dark 5% oxygen was optimal. At any oxygen concentration a photon irradiance of 100 mumol m(-2) s(-1) was saturating. When Trichodesmium was incubated in the dark, nitrogenase activity gradually decreased and this decline was higher at higher levels of oxygen. The activity recovered when the cells were subsequently incubated in the light. This recovery depended on oxygenic photosynthesis because it did not occur in the presence of DCMU [3-(3,4-dichlorophenyl)-1,1-dimethylurea]. Recovery of nitrogenase activity in the light was faster at low oxygen concentrations. The results showed that under aerobic conditions nitrogenase activity was limited by the availability of reducing equivalents suggesting a competition for electrons between nitrogenase and respiration.

Modeling the dynamic regulation of nitrogen fixation in the cyanobacterium Trichodesmium sp

A physiological, unbalanced model is presented that explicitly describes growth of the marine cyanobacterium Trichodesmium sp. at the expense of N(2) (diazotrophy). The model involves the dynamics of intracellular reserves of carbon and nitrogen and allows the uncoupling of the metabolism of these elements. The results show the transient dynamics of N(2) fixation when combined nitrogen (NO(3)(-), NH(4)(+)) is available and the increased rate of N(2) fixation when combined nitrogen is insufficient to cover the demand. The daily N(2) fixation pattern that emerges from the model agrees with measurements of rates of nitrogenase activity in laboratory cultures of Trichodesmium sp. Model simulations explored the influence of irradiance levels and the length of the light period on fixation activity and cellular carbon and nitrogen stoichiometry. Changes in the cellular C/N ratio resulted from allocations of carbon to different cell compartments as demanded by the growth of the organism. The model shows that carbon availability is a simple and efficient mechanism to regulate the balance of carbon and nitrogen fixed (C/N ratio) in filaments of cells. The lowest C/N ratios were obtained when the light regime closely matched nitrogenase dynamics.

Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean

Dinitrogen (N(2))-fixing microorganisms (diazotrophs) play important roles in ocean biogeochemistry and plankton productivity. In this study, we examined the presence and expression of specific planktonic nitrogenase genes (nifH) in the upper ocean (0 to 175 m) at Station ALOHA in the oligotrophic North Pacific Ocean. Clone libraries constructed from reverse-transcribed PCR-amplified mRNA revealed six unique phylotypes. Five of the nifH phylotypes grouped with sequences from unicellular and filamentous cyanobacteria, and one of the phylotypes clustered with gamma-proteobacteria. The cyanobacterial nifH phylotypes retrieved included two sequence types that phylogenetically grouped with unicellular cyanobacteria (termed groups A and B), several sequences closely related (97 to 99%) to Trichodesmium spp. and Katagnymene spiralis, and two previously unreported phylotypes clustering with heterocyst-forming nifH cyanobacteria. Temporal patterns of nifH expression were evaluated using reverse-transcribed quantitative PCR amplification of nifH gene transcripts. The filamentous and presumed unicellular group A cyanobacterial phylotypes exhibited elevated nifH transcription during the day, while members of the group B (closely related to Crocosphaera watsonii) unicellular phylotype displayed greater nifH transcription at night. In situ nifH expression by all of the cyanobacterial phylotypes exhibited pronounced diel periodicity. The gamma-proteobacterial phylotype had low transcript abundance and did not exhibit a clear diurnal periodicity in nifH expression. The temporal separation of nifH expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological responses to daily fluctuations of light in the upper ocean.

The Natural History of Nitrogen Fixation

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.

Diurnal expression of hetR and diazocyte development in the filamentous non-heterocystous cyanobacterium Trichodesmium erythraeum

The marine non-heterocystous cyanobacterium Trichodesmium fixes atmospheric N(2) aerobically in light. In situ immunolocalization/light microscopy of NifH revealed that lighter, non-granulated cell regions observed correspond to the nitrogenase-containing diazocyte clusters in Trichodesmium IMS101. The number of diazocyte clusters per trichome varied from 0 to 4 depending on trichome length. The constant percentage of diazocytes (approx. 15 %) in cultured strains and five natural populations suggests a developmentally regulated differentiation process. Real-time RT-PCR showed that ntcA, encoding the global nitrogen regulator in cyanobacteria, and hetR, the key regulatory gene in heterocyst differentiation, are both constitutively expressed during a 12 h/12 h light/dark cycle. hetR in addition showed a distinct peak in the dark (close to midnight) while nifH expression commenced 6-8 h later. The expression of all three genes was negatively affected by addition of ammonia. Some early heterocyst differentiation genes were also identified in the genome of Trichodesmium. The data suggest that hetR and ntcA may be required for development and function of diazocytes in Trichodesmium.

The nitrogen physiology of the marine N2-fixing cyanobacteria Trichodesmium spp

Trichodesmium spp. have proved to be enigmatic organisms, and their ecology and physiology are unusual among diazotrophs. Recent research shows that they can simultaneously fix N2 and take up combined nitrogen. The co-occurrence of these two processes is thought to be incompatible, but they could be obligatory in Trichodesmium spp. if only a small fraction of cells within a colony or along a filament are capable of N2 fixation. Combined nitrogen is released from cells during periods of active growth and N2 fixation, and concomitantly taken up by Trichodesmium spp. or cells living in association with colonies. Although the nitrogenase of Trichodesmium spp. is affected by high concentrations of combined nitrogen, it might be relatively less sensitive to low concentrations of combined nitrogen typical of the oligotrophic ocean and culture conditions. Nitrogenase activity and synthesis exhibits an endogenous rhythm in Trichodesmium spp. cultures, which is affected by the addition of nitrogen.

Expression of photosynthesis genes in relation to nitrogen fixation in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. IMS 101

The daily cycle of nitrogenase expression in the marine filamentous nonheterocystous cyanobacterium Trichodesmium spp. is controlled by a circadian rhythm. We evaluated the rhythm of two key photosynthesis genes, psbA of photosystem II and psaA of photosystem I, in Trichodesmium sp. IMS 101 using the 3 criteria for an endogenous rhythm. The transcript abundance of psbA and psaA transcripts oscillated with a period of ca. 24 h under a 12 h light/12 h dark regime. At 24 degrees C and 28 degrees C the cyclic pattern of transcript abundance was maintained for at least 58 h under constant light conditions, whereas the periods were about 24 h at 24 degrees C, and 26-30 h at the higher temperature. The cycles of psbA and psaA gene expression were entrained using light-dark cues. Transcription of nifHDK was initiated prior to the light period, followed by psbA and finally psaA. There was a 90 degrees (6 h) phase difference between the net accumulation of nifHDK and psbA transcripts, as well as between that of psbA and psaA transcripts. Results of inhibitor experiments indicated that psbA and psaA transcription was regulated differently by initiation and degradation during the light period. Short-term changes of light conditions resulted in significant effects on psbA transcription and nitrogenase activity, but had less of an effect on psaA and nifHDK transcription.

In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater

We developed procedures for isolating and characterizing in situ-transcribed mRNA from groundwater microorganisms catabolizing naphthalene at a coal tar waste-contaminated site. Groundwater was pumped through 0.22-microm-pore-size filters, which were then frozen in dry ice-ethanol. RNA was extracted from the frozen filters by boiling sodium dodecyl sulfate lysis and acidic phenol-chloroform extraction. Transcript characterization was performed with a series of PCR primers designed to amplify nahAc homologs. Several primer pairs were found to amplify nahAc homologs representing the entire diversity of the naphthalene-degrading genes. The environmental RNA extract was reverse transcribed, and the resultant mixture of cDNAs was amplified by PCR. A digoxigenin-labeled probe mixture was produced by PCR amplification of groundwater cDNA. This probe mixture hybridized under stringent conditions with the corresponding PCR products from naphthalene-degrading bacteria carrying a variety of nahAc homologs, indicating that diverse dioxygenase transcripts had been retrieved from groundwater. Diluted and undiluted cDNA preparations were independently amplified, and 28 of the resulting PCR products were cloned and sequenced. Sequence comparisons revealed two major groups related to the dioxygenase genes ndoB and dntAc, previously cloned from Pseudomonas putida NCIB 9816-4 and Burkholderia sp. strain DNT, respectively. A distinctive subgroup of sequences was found only in experiments performed with the undiluted cDNA preparation. To our knowledge, these results are the first to directly document in situ transcription of genes encoding naphthalene catabolism at a contaminated site by indigenous microorganisms. The retrieved sequences represent greater diversity than has been detected at the study site by culture-based approaches.

Cloning and transcriptional analysis of the nifUHDK genes of Trichodesmium sp. IMS101 reveals stable nifD, nifDK and nifK transcripts

Trichodesmium spp. are marine filamentous, non-heterocystous cyanobacteria capable of aerobic nitrogen fixation. In this study, the nitrogenase structural genes (nifHDK) and nifU gene of Trichodesmium sp. IMS101 were cloned and sequenced. The Trichodesmium sp. IMS101 nifH, nifD and nifK amino acid sequences showed only 79%, 66% and 68% identity, respectively, to those of Anabaena sp. strain PCC 7120. A potential transcription start site for nifH was found 212 bases upstream of the nifH start codon. Promoter-like nucleotide sequences upstream of the transcription start site were identified that were very similar to those identified for the nitrogenase genes of Anabaena spp. Sequence analysis revealed regions of DNA that may form stem-loop structures in the intercistronic regions downstream of nifH and nifD. RNA analysis by Northern hybridization revealed the presence of transcripts corresponding to nifH, nifHD and nifHDK. Surprisingly, Northern hybridization also revealed the presence of transcripts that corresponded to nifD, nifDK and nifK, which have not been previously reported as transcripts in contiguous nifHDK genes of cyanobacteria. Transcription of the nifHDK genes was not significantly repressed in the presence of nitrate at a final concentration of 20 mM or at oxygen concentrations of up to 40%, whereas ammonium and urea inhibited nifHDK transcription. The transcription of the nifHDK genes was not affected by darkness, which suggests that transcription of these genes in Trichodesmium is not directly regulated by light.

Whole-cell immunolocalization of nitrogenase in marine diazotrophic cyanobacteria, trichodesmium spp

The mechanism by which planktonic marine cyanobacteria of the genus Trichodesmium fix N2 aerobically during photosynthesis without heterocysts is unknown. As an aid in understanding how these species protect nitrogenase, we have developed an immunofluorescence technique coupled to light microscopy (IF-LM) with which intact cyanobacteria can be immunolabeled and the distribution patterns of nitrogenase and other proteins can be described and semiquantified. Chilled ethanol was used to fix the cells, which were subsequently made permeable to antibodies by using dimethyl sulfoxide. Use of this technique demonstrated that about 3 to 20 cells (mean +/- standard deviation, 9 +/- 4) consecutively arranged in a Trichodesmium trichome were labeled with the nitrogenase antibody. The nitrogenase-containing cells were distributed more frequently around the center of the trichome and were rarely found at the ends. On average 15% of over 300 randomly encountered cells examined contained nitrogenase. The percentage of nitrogenase-containing cells (nitrogenase index [NI]) in an exponential culture was higher early in the light period than during the rest of the light-dark cycle, while that for a stationary culture was somewhat constant at a lower level throughout the light-dark cycle. The NI was not affected by treatment of the cultures with the photosynthetic inhibitor dichloro 1,3'-dimethyl urea or with low concentrations of ammonium (NH4Cl). However, incubation of cultures with 0.5 &mgr;M NH4Cl over 2 days reduced the NI. The IF technique combined with 14C autoradiography showed that the CO2 fixation rate was lower in nitrogenase-containing cells. The results of the present study suggest that (i) the IF-LM technique may be a useful tool for in situ protein localization in cyanobacteria, (ii) cell differentiation occurs in Trichodesmium and only a small fraction of cells in a colony have the potential to fix nitrogen, (iii) the photosynthetic activity (CO2 uptake) is reduced if not absent in N2-fixing cells, and (iv) variation in the NI may be a modulator of nitrogen-fixing activity.

Circadian rhythm of nitrogenase gene expression in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. strain IMS 101

Recent studies suggested that the daily cycle of nitrogen fixation activity in the marine filamentous nonheterocystous cyanobacterium Trichodesmium sp. is controlled by a circadian rhythm. In this study, we evaluated the rhythm of nitrogen fixation in Trichodesmium sp. strain IMS 101 by using the three criteria for an endogenous rhythm. Nitrogenase transcript abundance oscillated with a period of approximately 24 h, and the cycle was maintained even under constant light conditions. The cyclic pattern of transcript abundance was maintained when the culture was grown at 24 and 28.5 degrees C, although the period was slightly longer (26 h) at the higher temperature. The cycle of gene expression could be entrained with light-dark cues. Results of inhibitor experiments indicated that transcript abundance was regulated primarily by transcription initiation, rather than by degradation. The circadian rhythm, the first conclusively demonstrated endogenous rhythm in a filamentous cyanobacterium, was also reflected in nitrogenase MoFe protein abundance and patterns of Fe protein posttranslational modification-demodification.

Regulation of nitrogen fixation by different nitrogen sources in the filamentous non-heterocystous cyanobacterium Microcoleus sp

The pattern of N2 fixation, the synthesis and activity of nitrogenase under different nitrogen sources was studied in the filamentous, non-heterocystous cyanobacterium Microcoleus sp. grown under defined culture conditions. Cells grown under a 10 h light/14 h dark (10L/14D) cycle with N2 as an inorganic nitrogen source showed highest nitrogenase activity (acetylene reduction) at the end of the light phase and then a decrease after entering the dark phase. Nitrogenase synthesis was neither suppressed after 7 days of growth with 2 mM NaNO3 or 0.2 mM (NH4)2SO4 or 0.3 mM urea nor with 20 mM NaNO3 or 3 mM (NH4)2SO4 or 4 mM urea under the 10L/14D cycle. Western immunoblots tested with polyclonal antisera against the Fe-protein revealed the following: (1) the Fe-protein was synthesized in cells grown with N2 as well as in cells grown with NaNO3 or (NH4)2SO4 under the 10L/14D cycle; (2) the Fe-protein was found in cells grown with urea under the 10L/14D cycle, but not in the darkness; (3) only one protein band, corresponding to the Fe-protein, was found in cells harvested during the light phase of the 10L/14D cycle under the tested conditions. No nitrogenase activity was observed when chloramphenicol was added to the cultures 4 h before the onset of the light period. This observation suggest de novo synthesis of nitrogenase in Microcoleus sp.

Regulation of nitrogen fixation in Azospirillum brasilense

The regulation of nitrogen fixation in Azospirillum brasilense is very complicated, and it responds to exogenous fixed nitrogen or a change of oxygen concentration. This regulation occurs at both transcriptional and posttranslational levels. Unlike regulation seen in Klebsiella pneumoniae, transcription of nifA does not require NTRB/NTRC in A. brasilense and the expression of nifHDK is controlled by posttranslational regulation of NIFA activity. Addition of NH4+ or a shift from microaerobic to anaerobic conditions also causes a rapid loss of nitrogenase activity in A. brasilense. This posttranslational regulation of nitrogenase activity involves the DRAT/DRAG regulatory system, which is similar to that of Rhodospirillum rubrum. Both DRAT and DRAG activities are regulated in vivo, but the mechanisms for their regulation are unknown.

Transcriptional and translational regulation of nitrogenase in light-dark- and continuous-light-grown cultures of the unicellular cyanobacterium Cyanothece sp. strain ATCC 51142

Cyanothece sp. strain ATCC 51142 is a unicellular, diazotrophic cyanobacterium which demonstrated extensive metabolic periodicities of photosynthesis, respiration, and nitrogen fixation when grown under N2-fixing conditions. N2 fixation and respiration peaked at 24-h intervals early in the dark or subjective-dark period, whereas photosynthesis was approximately 12 h out of phase and peaked toward the end of the light or subjective-light phase. Gene regulation studies demonstrated that nitrogenase is carefully controlled at the transcriptional and posttranslational levels. Indeed, Cyanothece sp. strain ATCC 51142 has developed an expensive mode of regulation, such that nitrogenase was synthesized and degraded each day. These patterns were seen when cells were grown under either light-dark or continuous-light conditions. Nitrogenase mRNA was synthesized from the nifHDK operon during the first 4 h of the dark period under light-dark conditions or during the first 6 h of the subjective-dark period when grown in continuous light. The nitrogenase NifH and NifDK subunits reached a maximum level at 4 to 10 h in the dark or subjective-dark periods and were shown by Western blotting and electron microscopy immunocytochemistry to be thoroughly degraded toward the end of the dark periods. An exception is the NifDK protein (MoFe-protein), which appeared not to be completely degraded under continuous-light conditions. We hypothesize that cellular O2 levels were kept low by decreasing photosynthesis and by increasing respiration in the early dark or subjective-dark periods to permit nitrogenase activity. The subsequent increase in O2 levels resulted in nitrogenase damage and eventual degradation.

Problems and Promises of Assaying the Genetic Potential for Nitrogen Fixation in the Marine Environment

Nitrogen fixation in the sea has attracted the attention of ecologists for decades. Much is known about the habitats in which it occurs and some of the factors that limit N2 fixation activity in different environments, but we still know little about the organisms that fix nitrogen, and what limits the growth and distribution of these organisms in marine environments. Molecular biology technological developments have provided tools for detecting and characterizing N2-fixing organisms in the environment. These techniques hold great promise for unraveling the mysteries and paradoxes of N2 fixation in the sea. In this review, we address the theoretical basis for the use of a molecular approach to N2 fixation, highlight the strengths and weaknesses of the approach, and provide case studies that demonstrate the potential contribution of molecular biology approaches to studies of N2 fixation in the sea.

N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation

Molecular and immunological techniques were used to examine N2 fixation in a ubiquitous heterotrophic marine bacterium, the facultative anaerobic Vibrio natriegens. When batch cultures were shifted from aerobic N-replete to anaerobic N-deplete conditions, transcriptional and post-translational regulation of N2 fixation was observed. Levels of nifHDK mRNA encoding the nitrogenase enzyme were highest at 140 min postshift and undetectable between 6 and 9 h later. Immunologically determined levels of nitrogenase enzyme (Fe protein) were highest between 6 and 15 h postshift, and nitrogenase activity peaked between 6 and 9 h postshift, declining by a factor of 2 after 12-15 h. Unlike their regulation in cyanobacteria, Fe protein and nitrogenase activity were present when nifHDK mRNA was absent in V. natriegens, indicating that nitrogenase is stored and stable under anaerobic conditions. Both nifHDK mRNA and Fe protein disappeared within 40 min after cultures were shifted from N2-fixing conditions (anaerobic, N-deplete) to non- N2-fixing conditions (aerobic, N-enriched) but reappeared when shifted to conditions favoring N2 fixation. Thus, unlike other N2-fixing heterotrophic bacteria, nitrogenase must be resynthesized after aerobic exposure in V. natriegens. Immunological detection based on immunoblot (Western) analysis and immunogold labeling correlated positively with nitrogenase activity; no localization of nitrogenase was observed. Because V. natriegens continues to fix N2 for many hours after anaerobic induction, this species may play an important role in providing "new" nitrogen in marine ecosystems.

Isolation of nifH and part of nifD by modified capture polymerase chain reaction from a natural population of the marine cyanobacterium Trichodesmium sp

A modified capture polymerase chain reaction (CPCR) technique was used to isolate the entire sequence of the nifH gene and its flanking regions from a natural population of Trichodesmium sp. A set of specific CPCR primers derived from a known 72-bp DNA segment of the nifH sequence permitted isolation of both the upstream and the downstream region of Trichodesmium sp. nifH. The 882-bp nifH gene presented here is the first full-length gene isolated from Trichodesmium sp. A sequence similar to a nif-like promoter was found in front of nifH. The nifH open reading frame of Trichodesmium sp. encoded 294 amino acids. Comparative analysis of the Trichodesmium sp. NifH sequence revealed strong similarity with 23 known NifH proteins. Amino acids postulated to be involved in binding of the 4Fe:4S cluster and those subjected to ADP-ribosylation were present. An open reading frame for the nifD gene was identified 189 bp downstream of nifH. A sequence similar to the consensus of the nif-like promoter was also found in front of nifD.

Microscale physiological and ecological studies of aquatic cyanobacteria: macroscale implications

Cyanobacteria have had a profound and unparalleled biogeochemical impact on the earth's biosphere. As the first oxygenic phototrophs, cyanobacteria were responsible for the transition from anaerobic to aerobic life. Ironically, molecular oxygen (O2) is inhibitory to critical components of cyanobacterial metabolism, including photosynthesis and nitrogen fixation. Cyanobacteria have developed a great variety of biochemical, structural, and biotic adaptations ensuring optimal growth and proliferation in diverse oxic environments to counter this difficult situation. Structurally, cyanobacteria reveal remarkable diversity, including the formation of highly differentiated, O2-deplete cells (heterocysts), multicellularity as trichomes, and aggregates, that, among N2-fixing genera, facilitate division of labor between aerobic and anaerobic processes. Cyanobacteria enjoy unique consortial and symbiotic associations with other microorganisms, higher plants, and animals, in which O2 consumption is closely coupled in time and space to its production. Because as prokaryotes they are devoid of O2-consuming organelles (e.g., mitochondria), cyanobacteria have developed alternative strategies for locally protecting O2-sensitive processes, including consortial relationships with other microorganisms. Specific organic compounds released by cyanobacteria are capable of chemotactically attracting bacterial consorts, which in turn attach to the host cyanobacteria, consume O2, and recycle inorganic nutrients within the cyanobacterial "phycosphere." Multicellularity and aggregation lead to localized O2 gradients and hypoxic/anoxic microzones in which O2-sensitive processes can coexist. Microscale partitioning of O2-producing and O2-inhibited processes promotes contiguous and effective metabolite and nutrient exchange between these processes in oxygenated waters, representing a bulk of the world's oceanic and freshwater ecosystems.

Genetic evidence of a major role for glucose-6-phosphate dehydrogenase in nitrogen fixation and dark growth of the cyanobacterium Nostoc sp. strain ATCC 29133

Heterocysts, sites of nitrogen fixation in certain filamentous cyanobacteria, are limited to a heterotrophic metabolism, rather than the photoautotrophic metabolism characteristic of cyanobacterial vegetative cells. The metabolic route of carbon catabolism in the supply of reductant to nitrogenase and for respiratory electron transport in heterocysts is unresolved. The gene (zwf) encoding glucose-6-phosphate dehydrogenase (G6PD), the initial enzyme of the oxidative pentose phosphate pathway, was inactivated in the heterocyst-forming, facultatively heterotrophic cyanobacterium, Nostoc sp. strain ATCC 29133. The zwf mutant strain had less than 5% of the wild-type apparent G6PD activity, while retaining wild-type rates of photoautotrophic growth with NH4+ and of dark O2 uptake, but it failed to grow either under N2-fixing conditions or in the dark with organic carbon sources. A wild-type copy of zwf in trans in the zwf mutant strain restored only 25% of the G6PD specific activity, but the defective N2 fixation and dark growth phenotypes were nearly completely complemented. Transcript analysis established that zwf is in an operon also containing genes encoding two other enzymes of the oxidative pentose phosphate cycle, fructose-1,6-bisphosphatase and transaldolase, as well as a previously undescribed gene (designated opcA) that is cotranscribed with zwf. Inactivation of opcA yielded a growth phenotype identical to that of the zwf mutant, including a 98% decrease, relative to the wild type, in apparent G6PD specific activity. The growth phenotype and lesion of G6PD activity in the opcA mutant were complemented in trans with a wild-type copy of opcA. In addition, placement in trans of a multicopy plasmid containing the wild-type copies of both zwf and opcA in the zwf mutant resulted in an approximately 20-fold stimulation of G6PD activity, relative to the wild type, complete restoration of nitrogenase activity, and a slight stimulation of N2-dependent photoautotrophic growth and fructose-supported dark growth. These results unequivocally establish that G6PD, and most likely the oxidative pentose phosphate pathway, represents the essential catabolic route for providing reductant for nitrogen fixation and respiration in differentiated heterocysts and for dark growth of vegetative cells. Moreover, the opcA gene product is involved by an as yet unknown mechanism in G6PD synthesis or catalytic activity.

Posttranslational modification of nitrogenase. Differences between the purple bacterium Rhodospirillum rubrum and the cyanobacterium Anabaena variabilis

In the photosynthetic bacteria Rhodospirillum rubrum and Rhodopseudomonas capsulatus post-translational regulation of nitrogenase is due to ADP-ribosylation of the Fe-protein, the dinitrogenase reductase [Burris, R. H. (1991) J. Biol. Chem. 266, 9339-9342]. This mechanism has been assumed to be responsible for nitrogenase modification in a variety of organisms. In the present study, we examined whether ADP-ribosylation holds true for the filamentous cyanobacterium Anabaena variabilis. Genes coding for the nitrogenase-modifying enzymes dinitrogenase reductase-activating glycohydrolase (DRAG) and dinitrogenase reductase ADP-ribosyl transferase (DRAT) from R. rubrum have been subcloned and overexpressed in Escherichia coli. After isolation under anaerobic conditions, both proteins were functional as determined by in-vitro assays using nitrogenase from R. rubrum as substrate. In contrast to the R. rubrum enzyme, nitrogenase from A. variabilis was not affected by DRAG or DRAT. Neither could inactive nitrogenase be restored by DRAG, nor nitrogenase activity suppressed by DRAT. Using specific antibodies against arginine-bound ADP-ribose [Meyer, T. & Hilz, H. (1986) Eur. J. Biochem. 155, 157-165], immunoblotting of the inactive, modified form of the Fe-protein from R. rubrum but not that from A. variabilis showed a strong cross reaction. Furthermore, differently to R. rubrum no ADP-ribosylated proteins could be detected at all, indicating the absence of this posttranslational modification in A. variabilis.

Modification of the Fe protein of the nitrogenase of Gloeothece (Nägeli) sp. ATCC 27152 during growth under alternating light and darkness

The Fe protein of the nitrogenase of the unicellular Cyanobacterium Gloeothece (Nägeli) sp. ATCC 27152 can be resolved by SDS-PAGE into two antigenically detectable components of approximate M_r 38500 and 40000 respectively. The larger form of this protein may be produced by modification of the smaller form. Modification of the Fe protein is promoted under conditions where O₂ (but not O₂ ^- or H₂ O₂ ) has increased access to the enzyme, but does not allow nitrogenase to function under conditions of O₂ stress. During growth of Gloeothece under alternating light and darkness, antigenically detectable Fe protein is absent throughout most of the light period. The restriction of nitrogenase activity to the period of darkness is better explained in terms of regulation of nitrogenase synthesis and degradation than by reversible modification of a constant intracellular concentration of Fe protein. However, newly synthesized Fe protein always appeared initially as its larger form, which may be catalytically inactive in aerobic cultures of Gloeothece. Conversion of this form to the smaller, assumed active, form of the Fe protein may be an additional factor in explaining the increase in nitrogenase activity that occurs during the first few hours of each dark phase.