Nitrogen fixation in denitrified marine waters

Cold seep nitrogen fixation and its potential relationship with sulfur cycling

Dinitrogen (N2) fixation is a crucial source of bioavailable nitrogen in carbon-dominated cold seep systems. Previous studies have shown that diazotrophy is not necessarily dependent on sulfate-dependent anaerobic oxidation of methane for energy, and diverse catabolism can fuel the high-energy-demanding process in sediments. However, it remains unclear whether diazotroph can obtain energy by sulfur oxidation in sulfur-rich cold seep water column. Here, field investigations and in situ experiments were conducted in Haima cold seep to examine the effects of diverse sources of dissolved organic matter (DOM) on N2 fixation, specifically containing sulfur, carbon, nitrogen, and phosphorus. We found that active N2 fixation occurred in the water column above the Haima cold seep, with the Dechloromonas genus dominating the diazotroph community as revealed by nifH gene using high-throughput sequencing. In situ experiments showed an increased rate of N2 fixation (1.15- to 12.70-fold compared to that in control group) and a greater relative abundance of the Dechloromonas genus following enrichment with sulfur-containing organic matter. Furthermore, metagenomic assembly and binning revealed that Dechloromonas sp. carried genes related to N2 fixation (nifDHK) and sulfur compound oxidation (fccAB and soxABCXYZ), implying that the genus potentially serves as a multifunctional mediator for N2 fixation and sulfur cycling. Our results provide new insights regarding potential coupling mechanism associated with sulfur-driven N2 fixation in methane- and sulfide-rich environments.

IMPORTANCE

N2 fixation is an important source of biologically available in carbon-dominated cold seep systems as little nitrogen is released by hydrocarbon seepage, thereby promoting biological productivity and the degradation of non-nitrogenous organic matter. Cold seeps are rich in diverse sources of dissolved organic matter (DOM) derived from the sinking of photosynthetic products in euphotic layer and the release of chemosynthesis products on the seafloor. However, it remains unclear whether N2 fixation is coupled to the metabolic processes of DOM, as determined by e.g., carbon, nitrogen, phosphorus, and sulfur content, for energy acquisition in sulfur-rich cold seeps. In this study, diazotroph community structure and its response to DOM compositions were revealed. Moreover, the metagenomics analysis suggested that Dechloromonas genus plays a dominant role in potential coupling N2 fixation and sulfur oxidation. Our study highlighted that sulfur oxidation in deep-sea cold seeps may serve as an energy source to drive N2 fixation.

Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni

The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.

Feammox bacterial biofilm formation in HFMB

Nitrogen pollution has been increasing with the development of industrialization. Consequently, the excessive deposition of reactive nitrogen in the environment has generated the loss of biodiversity and eutrophication of different ecosystems. In 2005, a Feammox process was discovered that anaerobically metabolizes ammonium. Feammox with the use of hollow fiber membrane bioreactors (HFMB), based on the formation of biofilms of bacterial communities, has emerged as a possible efficient and sustainable method for ammonium removal in environments with high iron concentrations. This work sought to study the possibility of implementing, at laboratory scale, an efficient method by evaluating the use of HFMB. Samples from an internal circulation reactor (IC) incubated in culture media for Feammox bacteria. The cultures were enriched in a batch reactor to evaluate growth conditions. Next, HFMB assembly was performed, and Feammox parameters were monitored. Also, conventional PCR and scanning electron microscopy (SEM) analysis were performed to characterize the bacterial communities associated with biofilm formation. The use of sodium acetate presented the best performance for Feammox activity. The HFMB operation showed an ammonium (NH4+) removal of 50%. SEM analysis of the fibers illustrated the formation of biofilm networks formed by bacteria, which were identified as Albidiferax ferrireducens, Geobacter spp, Ferrovum myxofaciens, Shewanella spp., and Anammox. Functional genes Archaea/Bacteria ammonia monooxygenase, nrxA, hzsB, nirS and nosZ were also identified. The implementation of HFMB Feammox could be used as a sustainable tool for the removal of ammonium from wastewater produced because of anthropogenic activities.

Unsolved mysteries in marine nitrogen fixation

Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.

Distribution of the N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa in the Mexican Pacific upwelling system under two contrasting El Niño Southern Oscillation conditions

The unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is a key diazotroph in the global ocean owing to its high N2 fixation rates and wide distribution in marine environments. Nevertheless, little is known about UCYN-A in oxygen-deficient zones (ODZs), which may be optimal environments for marine diazotrophy. Therefore, the distribution and diversity of UCYN-A were studied in two consecutive years under contrasting phases (La Niña vs. El Niño) of El Niño Southern Oscillation (ENSO) along a transect in the ODZ of the Mexican Pacific upwelling system. Of the three UCYN-A sublineages found, UCYN-A1 and UCYN-A3 were barely detected, whereas UCYN-A2 was dominant in all the stations and showed a wide distribution in both ENSO phases. The presence of UCYN-A was associated with well-oxygenated waters, but it was also found for the first time under suboxic conditions (<20 μM) at the bottom of a shallow coastal station, within the oxygen-poor and nutrient-rich Subsurface Subtropical water mass. This study contributes to the understanding of UCYN-A distribution under different oceanographic conditions associated with ENSO phases in upwelling systems, especially because of the current climate change and increasing deoxygenation in many areas of the world's oceans.

Seasonal dynamics of bacterial community and co-occurrence with eukaryotic phytoplankton in the Pearl River Estuary

In this study, we investigated the taxonomic composition of the bacteria and phytoplankton communities in the Pearl River Estuary (PRE) through Illumina sequencing of the V3-V4 region of the 16 S rRNA gene. Furthermore, their relationships as well as recorded environmental variables were explored by co-occurrence networks. Bacterial community composition was different in two size fractions, as well as along the salinity gradient across two seasons. Free-living (FL) communities were dominated by pico-sized Cyanobacteria (Synechococcus CC9902) while Exiguobacterium, Halomonas and Pseudomonas were predominantly associated with particle-associated (PA) lifestyle, and Cyanobium PCC-6307 exhibited seasonal shifts in lifestyles in different seasons. In wet season, bacterial community composition was characterized by abundance of Cyanobacteria, Actinobacteria, and Bacteroidetes, which were tightly linked with high riverine inflow. While in dry season, Proteobacteria increased in prevalence, especially for Psychrobacter, NOR5/OM60 clade and Pseudomonas, which were thrived in lower water temperature and higher salinity. Moreover, we discovered that differences between PA and FL composition were more significant in the wet season than in the dry season, which may be due to better nutritional conditions of particles (indicated by POC%) in the wet season and then attract more diverse PA populations. Based on the analysis of plastidial 16 S rRNA genes, abundant small-sized mixotrophic phytoplankton (Dinophyceae, Euglenida and Haptophyta) were identified in the PRE. The complexity of co-occurrence network increased from FL to PA fractions in both seasons, which suggested that suspended particles can provide ecological niches for particle-associated colonizers contributing to the maintenance of a more stable community structure. In addition, the majority of phytoplankton species exhibited positive co-occurrences with both other phytoplankton species and bacterial counterparts, indicating the mutual cooperation between phytoplankton assemblages and specific bacterial populations e likely benefited from phytoplankton-derived organic compounds. This study enhances our understanding of the seasonal and spatial dynamics of bacterial communities and their potential relationship with phytoplankton assembly in estuarine waters.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika

The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika - a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.

Prokaryote Distribution Patterns along a Dissolved Oxygen Gradient Section in the Tropical Pacific Ocean

Oceanic oxygen levels are decreasing significantly in response to global climate change; however, the microbial diversity and ecological functional responses to dissolved oxygen (DO) in the open ocean are largely unknown. Here, we present prokaryotic distribution coupled with physical and biogeochemical variables and DO gradients from the surface to near the bottom of a water column along an approximately 12,000-km transect from 13° N to 18° S in the Tropical Pacific Ocean. Nitrate (11.42%), temperature (10.90%), pH (10.91%), silicate (9.34%), phosphate (4.25%), chlorophyll a (3.66%), DO (3.50%), and salinity (3.48%) significantly explained the microbial community variations in the studied area. A distinct microbial community composition broadly corresponding to the water masses formed vertically. Additionally, distinct ecotypes of Thaumarchaeota and Nitrospinae belonging to diverse phylogenetic clades that coincided with specific vertical niches were observed. Moreover, the correlation analysis revealed large-scale natural feedback in which chlorophyll a (organic matter) promoted Thaumarchaeotal biomass at depths that subsequently coupled with Nitrospina, produced and replenished nitrate for phytoplankton productivity at the surface. Low DO also favored Thaumarchaeota growth and fueled nitrate production.

Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch

Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.

Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula

Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.

Nitrogen fixation: a poorly understood process along the freshwater-marine continuum

Although N₂ fixation is a major component of the global N cycle and has been extensively studied in open-ocean and terrestrial ecosystems, rates and ecological dynamics remain virtually unknown for the inland and coastal aquatic ecosystems (lakes, wetlands, rivers, streams, estuaries) that connect terrestrial and marine biomes. This is due to the diversity of these habitats, as well as the traditional paradigm that N₂ fixation rates were low to nonexistent, and therefore not important, in these ecosystems. We identify three major research themes to advance understanding of aquatic N₂ fixation: 1) the biological diversity of diazotrophs and variability of N₂ fixation rates, 2) the ecological stoichiometry of N₂ fixation, and 3) the upscaling of N₂ fixation rates from genes to ecosystems. Coordinating research across these areas will advance limnology and oceanography by fully integrating N₂ fixation into ecological dynamics of aquatic ecosystems from local to global scales.

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities

Native C4 grasses have become the preferred species for native perennial pastures and bioenergy production due to their high productivity under low soil nitrogen (N) status. One reason for their low N requirement is that C4 grasses may benefit from soil diazotrophs and promote biological N fixation. Our objective was to evaluate the impact of N fertilization rates (0, 67, and 202 kg N ha-1) and grass species (switchgrass [Panicum virgatum] and big bluestem [Andropogon gerardii]) on the abundance, activity, diversity, and community composition of soil diazotrophs over three agricultural seasons (grass green-up, initial harvest, and second harvest) in a field experiment in East Tennessee, United States. Nitrogen fertilization rate had a stronger influence on diazotroph population size and activity (determined by nifH gene and transcript abundances) and community composition (determined by nifH gene amplicon sequencing) than agricultural season or grass species. Excessive fertilization (202 kg N ha-1) resulted in fewer nifH transcripts compared to moderate fertilization (67 kg N ha-1) and decreased both richness and evenness of diazotrophic community, reflecting an inhibitory effect of high N application rates on soil diazotrophic community. Overall, cluster I and cluster III diazotrophs were dominant in this native C4 grass system. Diazotroph population size and activity were directly related to soil water content (SWC) based on structural equation modeling. Soil pH, SWC, and C and N availability were related to the variability of diazotrophic community composition. Our results revealed relationships between soil diazotrophic community and associated soil properties, adding to our understanding of the response of soil diazotrophs to N fertilization and grass species in native C4 grass systems.

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2–2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180–2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.

Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.

Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean

Despite the increasing reports of non-cyanobacterial diazotrophs (NCDs) in pelagic waters, only one NCD (GammaA) has been relatively well described, whose genome and physiology are still unclear. Here we present a comprehensive analysis of the biogeography and ecophysiology of a widely distributed NCD, Gamma4. Gamma4 was the most abundant Gammaproteobacterial NCD along transects across the subtropical North Pacific. Using quantitative PCR, Gamma4 was detectable throughout the surface waters of North Pacific (7°N-55°N, 138°E-80°W), whereas GammaA was detected at <2/3 of the stations. Gamma4 was abundant during autumn-winter and positively correlated with chlorophyll a, while GammaA thrived during spring-summer and was positively correlated with temperature. Environmental clones affiliated with Gamma4 were widely detected in pelagic waters, oxygen minimum zones and even dinoflagellate microbiomes. By analysing the metabolic potential of a genome of Gamma4 reconstructed from the Tara Oceans dataset, we suggest that Gamma4 is a versatile heterotrophic NCD equipped with multiple strategies in scavenging phosphate (and iron) and for respiratory protection of nitrogenase. The transcription of nitrogenase genes is putatively regulated by Fnr-NifL-NifA and GlnD-GlnK systems that respond to intracellular oxygen and glutamate concentration. These results provide important implications for the potential life strategies of pelagic NCDs.

Quantitative models of nitrogen-fixing organisms

Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.

Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans

During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N₂ production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N₂ O and N₂ production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N₂ production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.

Revisiting the distribution of oceanic N2 fixation and estimating diazotrophic contribution to marine production

Marine N₂ fixation supports a significant portion of oceanic primary production by making N₂ bioavailable to planktonic communities, in the process influencing atmosphere-ocean carbon fluxes and our global climate. However, the geographical distribution and controlling factors of marine N₂ fixation remain elusive largely due to sparse observations. Here we present unprecedented high-resolution underway N₂ fixation estimates across over 6000 kilometers of the western North Atlantic. Unexpectedly, we find increasing N₂ fixation rates from the oligotrophic Sargasso Sea to North America coastal waters, driven primarily by cyanobacterial diazotrophs. N₂ fixation is best correlated to phosphorus availability and chlorophyll-a concentration. Globally, intense N₂ fixation activity in the coastal oceans is validated by a meta-analysis of published observations and we estimate the annual coastal N₂ fixation flux to be 16.7 Tg N. This study broadens the biogeography of N₂ fixation, highlights the interplay of regulating factors, and reveals thriving diazotrophic communities in coastal waters with potential significance to the global nitrogen and carbon cycles.

The geographical distribution and controlling factors of marine N₂ fixation are understudied. Here the authors find increasing rates of N₂ fixation from the Sargasso Sea to the coastal waters of North America, driven primarily by cyanobacterial diazotrophs and best correlated with phosphorus availability and chlorophyll-a concentrations.

A quantitative model of nitrogen fixation in the presence of ammonium

Nitrogen fixation provides bioavailable nitrogen, supporting global ecosystems and influencing global cycles of other elements. It provides an additional source of nitrogen to organisms at a cost of lower growth efficiency, largely due to respiratory control of intra-cellular oxygen. Nitrogen-fixing bacteria can, however, utilize both dinitrogen gas and fixed nitrogen, decreasing energetic costs. Here we present an idealized metabolic model of the heterotrophic nitrogen fixer Azotobacter vinelandii which, constrained by laboratory data, provides quantitative predictions for conditions under which the organism uses either ammonium or nitrogen fixation, or both, as a function of the relative supply rates of carbohydrate, fixed nitrogen as well as the ambient oxygen concentration. The model reveals that the organism respires carbohydrate in excess of energetic requirements even when nitrogen fixation is inhibited and respiratory protection is not essential. The use of multiple nitrogen source expands the potential niche and range for nitrogen fixation. The model provides a quantitative framework which can be employed in ecosystem and biogeochemistry models.

Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters

Putative heterotrophic bacteria carrying out N₂-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O₂-inhibited N₂-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N₂-fixation. First, water enriched with natural particles or sediment showed higher N₂-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N₂-fixation, and indicates that resuspension of sediment material can elevate pelagic N₂-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by “pioneer” bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N₂-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.

Global Marine N2 Fixation Estimates: From Observations to Models

Fixed nitrogen (N) limits productivity across much of the low-latitude ocean. The magnitude of its inventory results from the balance of N input and N loss, the latter largely occurring in regionally well-defined low-oxygen waters and sediments (denitrification and anammox). The rate and distribution of N input by biotic N₂ fixation, the dominant N source, is not well known. Here we compile N₂ fixation estimates from experimental measurements, tracer-based geochemical and modeling approaches, and discuss their limitations and uncertainties. The lack of adequate experimental data coverage and the insufficient understanding of the controls of marine N₂ fixation result in high uncertainties, which make the assessment of the current N-balance a challenge. We suggest that a more comprehensive understanding of the environmental and ecological interaction of marine N₂ fixers is required to advance the field toward robust N₂ fixation rates estimates and predictions.

In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre

Major advances in understanding the diversity, distribution, and activity of marine N2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-A1 were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N2 in the presence of nitrate. Net growth rates for UCYN-A1, UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 ± 0.5 d-1), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-A1 and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-A1. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models.

Metabolic versatility of a novel N2 -fixing Alphaproteobacterium isolated from a marine oxygen minimum zone

The N₂ -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula (Rhodobacteraceae, Alphaproteobacteria) and its capability to fix N₂ was confirmed in laboratory experiments. Genome sequencing revealed that it is a strict heterotroph with a high versatility in substrate utilization and energy acquisition mechanisms. Pathways for sulfide oxidation and nitrite reduction to nitrous oxide are encoded in the genome and might explain the presence throughout the Peruvian OMZ. The genome further indicates that this novel organism could be in direct interaction with other microbes or particles. NanoSIMS analyses were used to compare the metabolic potential of S. castanea with single-cell activity in situ; however, N₂ fixation by this diazotroph could not be detected at the isolation site. While the biogeochemical impact of S. castanea is yet to be resolved, its abundance and widespread distribution suggests that its potential to contribute to the marine N input could be significant at a larger geographical scale.

Nitrogen fixation in two coastal upwelling regions of the Taiwan Strait

Recent studies have demonstrated that dinitrogen fixation can be important in nutrient-rich coastal upwelling regions. During a cruise to the Taiwan Strait in summer 2015, we found that the nitrogen fixation rate in surface waters ranged from below detection limits to 7.51 nmol N L⁻¹ d⁻¹. Higher rates accompanied by low N:P ratios (1–10.4:1) associated with low temperatures occurred in the surface water where the Pingtan and the Dongshan upwelling regions met (the NE area). In contrast, insignificant rates were observed in the southwest area of the Dongshan upwelling region (the SW area) with sufficient N and deficient P, and therefore high N:P ratios (e.g., >43 at station C2) due largely to the influence of the Pearl River plume. Diatom-associated symbionts (het-1; 10⁴–10⁶ copies L⁻¹) that are efficient in organic matter export were found to dominate the other diazotrophic groups that were surveyed, which may represent a direct relationship between new nitrogen input and export in the upwelling regions. Our results suggest a hydrographical influence on the diazotroph community and N₂ fixation in coastal upwelling regions.

Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments

Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N₂) fixation. Other potentially N₂-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N₂ fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N₂ fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L⁻¹ d⁻¹). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that nifH transcription data for NCDs have been reported in only a few studies where N₂ fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.

Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day^-1) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day^-1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N₂-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters

Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N₂) fixation through the activity of “diazotrophic” bacterioplankton. Here, we investigated N₂ fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N₂ fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L^-1 d^-1. Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N₂ fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N₂ fixing assemblages as a potentially significant source of dissolved N within the water column.

Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis

The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection

The nitrogen input through biological N₂ fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N₂-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N₂ at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N₂ fixation on local and global scales.

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas

Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments.

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome

Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.

Expanding the World of Marine Bacterial and Archaeal Clades

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.

Nitrogen and Oxygen Isotopic Studies of the Marine Nitrogen Cycle

The marine nitrogen cycle is a complex web of microbially mediated reactions that control the inventory, distribution, and speciation of nitrogen in the marine environment. Because nitrogen is a major nutrient that is required by all life, its availability can control biological productivity and ecosystem structure in both surface and deep-ocean communities. Stable isotopes of nitrogen and oxygen in nitrate and nitrite have provided new insights into the rates and distributions of marine nitrogen cycle processes, especially when analyzed in combination with numerical simulations of ocean circulation and biogeochemistry. This review highlights the insights gained from dual-isotope studies applied at regional to global scales and their incorporation into oceanic biogeochemical models. These studies represent significant new advances in the use of isotopic measurements to understand the modern nitrogen cycle, with implications for the study of past ocean productivity, oxygenation, and nutrient status.

Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific)

Dinitrogen (N2) fixation was investigated together with organic matter composition in the mesopelagic zone of the Bismarck (Transect 1) and Solomon (Transect 2) Seas (Southwest Pacific). Transparent exopolymer particles (TEP) and the presence of compounds sharing molecular formulae with saturated fatty acids and sugars, as well as dissolved organic matter (DOM) compounds containing nitrogen (N) and phosphorus (P) were higher on Transect 1 than on Transect 2, while oxygen concentrations showed an opposite pattern. N2 fixation rates (up to ~1 nmol N L-1 d-1) were higher in Transect 1 than in Transect 2, and correlated positively with TEP, suggesting a dependence of diazotroph activity on organic matter. The scores of the multivariate ordination of DOM molecular formulae and their relative abundance correlated negatively with bacterial abundances and positively with N2 fixation rates, suggesting an active bacterial exploitation of DOM and its use to sustain diazotrophic activity. Sequences of the nifH gene clustered with Alpha-, Beta-, Gamma- and Deltaproteobacteria, and included representatives from Clusters I, III and IV. A third of the clone library included sequences close to the potentially anaerobic Cluster III, suggesting that N2 fixation was partially supported by presumably particle-attached diazotrophs. Quantitative polymerase chain reaction (qPCR) primer-probe sets were designed for three phylotypes and showed low abundances, with a phylotype within Cluster III at up to 103 nifH gene copies L-1. These results provide new insights into the ecology of non-cyanobacterial diazotrophs and suggest that organic matter sustains their activity in the mesopelagic ocean.

The cyanobacterium Mastigocladus fulfills the nitrogen demand of a terrestrial hot spring microbial mat

Cyanobacteria from Subsection V (Stigonematales) are important components of microbial mats in non-acidic terrestrial hot springs. Despite their diazotrophic nature (N2 fixers), their impact on the nitrogen cycle in such extreme ecosystems remains unknown. Here, we surveyed the identity and activity of diazotrophic cyanobacteria in the neutral hot spring of Porcelana (Northern Patagonia, Chile) during 2009 and 2011-2013. We used 16S rRNA and the nifH gene to analyze the distribution and diversity of diazotrophic cyanobacteria. Our results demonstrate the dominance of the heterocystous genus Mastigocladus (Stigonematales) along the entire temperature gradient of the hot spring (69-38 °C). In situ nitrogenase activity (acetylene reduction), nitrogen fixation rates (cellular uptake of (15)N2) and nifH transcription levels in the microbial mats showed that nitrogen fixation and nifH mRNA expression were light-dependent. Nitrogen fixation activities were detected at temperatures ranging from 58 °C to 46 °C, with maximum daily rates of 600 nmol C2H4 cm(-2) per day and 94.1 nmol N cm(-2) per day. These activity patterns strongly suggest a heterocystous cyanobacterial origin and reveal a correlation between nitrogenase activity and nifH gene expression during diurnal cycles in thermal microbial mats. N and C fixation in the mats contributed ~3 g N m(-2) per year and 27 g C m(-2) per year, suggesting that these vital demands are fully met by the diazotrophic and photoautotrophic capacities of the cyanobacteria in the Porcelana hot spring.

Nitrate and Nitrite Variability at the Seafloor of an Oxygen Minimum Zone Revealed by a Novel Microfluidic In-Situ Chemical Sensor

Microfluidics, or lab-on-a-chip (LOC) is a promising technology that allows the development of miniaturized chemical sensors. In contrast to the surging interest in biomedical sciences, the utilization of LOC sensors in aquatic sciences is still in infancy but a wider use of such sensors could mitigate the undersampling problem of ocean biogeochemical processes. Here we describe the first underwater test of a novel LOC sensor to obtain in situ calibrated time-series (up to 40 h) of nitrate+nitrite (ΣNO_x) and nitrite on the seafloor of the Mauritanian oxygen minimum zone, offshore Western Africa. Initial tests showed that the sensor successfully reproduced water column (160 m) nutrient profiles. Lander deployments at 50, 100 and 170 m depth indicated that the biogeochemical variability was high over the Mauritanian shelf: The 50 m site had the lowest ΣNO_x concentration, with 15.2 to 23.4 μM (median=18.3 μM); while at the 100 site ΣNO_x varied between 21.0 and 30.1 μM over 40 hours (median = 25.1μM). The 170 m site had the highest median ΣNO_x level (25.8 μM) with less variability (22.8 to 27.7 μM). At the 50 m site, nitrite concentration decreased fivefold from 1 to 0.2 μM in just 30 hours accompanied by decreasing oxygen and increasing nitrate concentrations. Taken together with the time series of oxygen, temperature, pressure and current velocities, we propose that the episodic intrusion of deeper waters via cross-shelf transport leads to intrusion of nitrate-rich, but oxygen-poor waters to shallower locations, with consequences for benthic nitrogen cycling. This first validation of an LOC sensor at elevated water depths revealed that when deployed for longer periods and as a part of a sensor network, LOC technology has the potential to contribute to the understanding of the benthic biogeochemical dynamics.

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water

The ability to reduce atmospheric nitrogen (N₂) to ammonia, known as N₂ fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N₂-fixing heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N₂ fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas stutzeri strain BAL361 and Raoultella ornithinolytica strain BAL286, which are gammaproteobacteria, and Rhodopseudomonas palustris strain BAL398, an alphaproteobacterium. Genome sequencing revealed that all were metabolically versatile and that the gene clusters encoding the N₂ fixation complex varied in length and complexity between isolates. All three isolates could sustain growth by N₂ fixation in the absence of reactive N, and this fixation was stimulated by low concentrations of oxygen in all three organisms (≈4 to 40 µmol O₂ liter⁻¹). P. stutzeri BAL361 did, however, fix N at up to 165 µmol O₂ liter⁻¹, presumably accommodated through aggregate formation. Glucose stimulated N₂ fixation in general, and reactive N repressed N₂ fixation, except that ammonium (NH₄⁺) stimulated N₂ fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations between nitrogenase reductase gene expression and ethylene (C₂H₄) production indicated tight posttranscriptional-level control. The N₂ fixation rates obtained suggested that, given the right conditions, these heterotrophic diazotrophs could contribute significantly to in situ rates.

The biological process of importing atmospheric N₂ is of paramount importance in terrestrial and aquatic ecosystems. In the oceans, a diverse array of prokaryotes seemingly carry the genetic capacity to perform this process, but lack of knowledge about their autecology and the factors that constrain their N₂ fixation hamper an understanding of their ecological importance in marine waters. The present study documents a high variability of genomic and ecophysiological properties related to N₂ fixation in three heterotrophic isolates obtained from estuarine surface waters and shows that these organisms fix N₂ under a surprisingly broad range of conditions and at significant rates. The observed intricate regulation of N₂ fixation for the isolates indicates that indigenous populations of heterotrophic diazotrophs have discrete strategies to cope with environmental controls of N₂ fixation. Hence, community-level generalizations about the regulation of N₂ fixation in marine heterotrophic bacterioplankton may be problematic.

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes

Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK, and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes) correlated with coupled nitrification-denitrification (Dn), and the denitrification of the overlying water NO₃^- (Dw) correlated with the nirS/nirK ratio. The number of core nirS, nirK, and nosZ operational taxonomical units (OTUs) was low (6, 7, and 3, respectively), and most of these core OTUs were shared among the lakes. Dominant nirK sequences matched best with those of the order Rhizobiales, which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant nirS sequences were affiliated with the order Burkholderiales. Over half of the nosZ sequences belonged to a single OTU of the order Burkholderiales, but coupled nitrification–denitrification rate correlated with another dominant nosZ OTU assigned to the order Rhodospirillales. The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same Alpha- and Betaproteobacteria denitrifier clusters were present in different lakes and seasons.

Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype

Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic γ-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several γ-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism.

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.

Light-limited growth rate modulates nitrate inhibition of dinitrogen fixation in the marine unicellular cyanobacterium Crocosphaera watsonii

Biological N₂ fixation is the dominant supply of new nitrogen (N) to the oceans, but is often inhibited in the presence of fixed N sources such as nitrate (NO₃⁻). Anthropogenic fixed N inputs to the ocean are increasing, but their effect on marine N₂ fixation is uncertain. Thus, global estimates of new oceanic N depend on a fundamental understanding of factors that modulate N source preferences by N₂-fixing cyanobacteria. We examined the unicellular diazotroph Crocosphaera watsonii (strain WH0003) to determine how the light-limited growth rate influences the inhibitory effects of fixed N on N₂ fixation. When growth (µ) was limited by low light (µ = 0.23 d⁻¹), short-term experiments indicated that 0.4 µM NH₄⁺ reduced N₂-fixation by ∼90% relative to controls without added NH₄⁺. In fast-growing, high-light-acclimated cultures (µ = 0.68 d⁻¹), 2.0 µM NH₄⁺ was needed to achieve the same effect. In long-term exposures to NO₃⁻, inhibition of N₂ fixation also varied with growth rate. In high-light-acclimated, fast-growing cultures, NO₃⁻ did not inhibit N₂-fixation rates in comparison with cultures growing on N₂ alone. Instead NO₃⁻ supported even faster growth, indicating that the cellular assimilation rate of N₂ alone (i.e. dinitrogen reduction) could not support the light-specific maximum growth rate of Crocosphaera. When growth was severely light-limited, NO₃⁻ did not support faster growth rates but instead inhibited N₂-fixation rates by 55% relative to controls. These data rest on the basic tenet that light energy is the driver of photoautotrophic growth while various nutrient substrates serve as supports. Our findings provide a novel conceptual framework to examine interactions between N source preferences and predict degrees of inhibition of N₂ fixation by fixed N sources based on the growth rate as controlled by light.

The contamination of commercial 15N2 gas stocks with 15N-labeled nitrate and ammonium and consequences for nitrogen fixation measurements

We report on the contamination of commercial 15-nitrogen (¹⁵N) N₂ gas stocks with ¹⁵N-enriched ammonium, nitrate and/or nitrite, and nitrous oxide. ¹⁵N₂ gas is used to estimate N₂ fixation rates from incubations of environmental samples by monitoring the incorporation of isotopically labeled ¹⁵N₂ into organic matter. However, the microbial assimilation of bioavailable ¹⁵N-labeled N₂ gas contaminants, nitrate, nitrite, and ammonium, is liable to lead to the inflation or false detection of N₂ fixation rates. ¹⁵N₂ gas procured from three major suppliers was analyzed for the presence of these ¹⁵N-contaminants. Substantial concentrations of ¹⁵N-contaminants were detected in four Sigma-Aldrich ¹⁵N₂ lecture bottles from two discrete batch syntheses. Per mole of ¹⁵N₂ gas, 34 to 1900 µmoles of ¹⁵N-ammonium, 1.8 to 420 µmoles of ¹⁵N-nitrate/nitrite, and ≥21 µmoles of ¹⁵N-nitrous oxide were detected. One ¹⁵N₂ lecture bottle from Campro Scientific contained ≥11 µmoles of ¹⁵N-nitrous oxide per mole of ¹⁵N₂ gas, and no detected ¹⁵N-nitrate/nitrite at the given experimental ¹⁵N₂ tracer dilutions. Two Cambridge Isotopes lecture bottles from discrete batch syntheses contained ≥0.81 µmoles ¹⁵N-nitrous oxide per mole ¹⁵N₂, and trace concentrations of ¹⁵N-ammonium and ¹⁵N-nitrate/nitrite. ¹⁵N₂ gas equilibrated cultures of the green algae Dunaliella tertiolecta confirmed that the ¹⁵N-contaminants are assimilable. A finite-differencing model parameterized using oceanic field conditions typical of N₂ fixation assays suggests that the degree of detected ¹⁵N-ammonium contamination could yield inferred N₂ fixation rates ranging from undetectable, <0.01 nmoles N L⁻¹ d⁻¹, to 530 nmoles N L⁻¹ d⁻¹, contingent on experimental conditions. These rates are comparable to, or greater than, N₂ fixation rates commonly detected in field assays. These results indicate that past reports of N₂ fixation should be interpreted with caution, and demonstrate that the purity of commercial ¹⁵N₂ gas must be ensured prior to use in future N₂ fixation rate determinations.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.

Significant N₂ fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries

Nitrogen (N) fixation is fueling planktonic production in a multitude of aquatic environments. In meso- and poly-haline estuaries, however, the contribution of N by pelagic N₂ fixation is believed to be insignificant due to the high input of N from land and the presumed absence of active N₂-fixing organisms. Here we report N₂ fixation rates, nifH gene composition and nifH gene transcript abundance for key diazotrophic groups over 1 year in two contrasting, temperate, estuarine systems: Roskilde Fjord (RF) and the Great Belt (GB) strait. Annual pelagic N₂ fixation rates averaged 17 and 61 mmol N m(-2) per year at the two sites, respectively. In RF, N₂ fixation was mainly accompanied by transcripts related to heterotrophic (for example, Pseudomonas sp.) and photoheterotrophic bacteria (for example, unicellular diazotrophic cyanobacteria group A). In the GB, the first of two N₂ fixation peaks coincided with a similar nifH-expressing community as in RF, whereas the second peak was synchronous with increased nifH expression by an array of diazotrophs, including heterotrophic organisms as well as the heterocystous cyanobacterium Anabaena. Thus, we show for the first time that significant planktonic N₂ fixation takes place in mesohaline, temperate estuaries and that the importance of heterotrophic, photoheterotrophic and photosynthetic diazotrophs is clearly variable in space and time.

Facets of diazotrophy in the oxygen minimum zone waters off Peru

Nitrogen fixation, the biological reduction of dinitrogen gas (N2) to ammonium (NH4(+)), is quantitatively the most important external source of new nitrogen (N) to the open ocean. Classically, the ecological niche of oceanic N2 fixers (diazotrophs) is ascribed to tropical oligotrophic surface waters, often depleted in fixed N, with a diazotrophic community dominated by cyanobacteria. Although this applies for large areas of the ocean, biogeochemical models and phylogenetic studies suggest that the oceanic diazotrophic niche may be much broader than previously considered, resulting in major implications for the global N-budget. Here, we report on the composition, distribution and abundance of nifH, the functional gene marker for N2 fixation. Our results show the presence of eight clades of diazotrophs in the oxygen minimum zone (OMZ) off Peru. Although proteobacterial clades dominated overall, two clusters affiliated to spirochaeta and archaea were identified. N2 fixation was detected within OMZ waters and was stimulated by the addition of organic carbon sources supporting the view that non-phototrophic diazotrophs were actively fixing dinitrogen. The observed co-occurrence of key functional genes for N2 fixation, nitrification, anammox and denitrification suggests that a close spatial coupling of N-input and N-loss processes exists in the OMZ off Peru. The wide distribution of diazotrophs throughout the water column adds to the emerging view that the habitat of marine diazotrophs can be extended to low oxygen/high nitrate areas. Furthermore, our statistical analysis suggests that NO2(-) and PO4(3-) are the major factors affecting diazotrophic distribution throughout the OMZ. In view of the predicted increase in ocean deoxygenation resulting from global warming, our findings indicate that the importance of OMZs as niches for N2 fixation may increase in the future.

Benthic N2 fixation in coral reefs and the potential effects of human-induced environmental change

Tropical coral reefs are among the most productive and diverse ecosystems, despite being surrounded by ocean waters where nutrients are in short supply. Benthic dinitrogen (N2) fixation is a significant internal source of "new" nitrogen (N) in reef ecosystems, but related information appears to be sparse. Here, we review the current state (and gaps) of knowledge on N2 fixation associated with coral reef organisms and their ecosystems. By summarizing the existing literature, we show that benthic N2 fixation is an omnipresent process in tropical reef environments. Highest N2 fixation rates are detected in reef-associated cyanobacterial mats and sea grass meadows, clearly showing the significance of these functional groups, if present, to the input of new N in reef ecosystems. Nonetheless, key benthic organisms such as hard corals also importantly contribute to benthic N2 fixation in the reef. Given the usually high coral coverage of healthy reef systems, these results indicate that benthic symbiotic associations may be more important than previously thought. In fact, mutualisms between carbon (C) and N2 fixers have likely evolved that may enable reef communities to mitigate N limitation. We then explore the potential effects of the increasing human interferences on the process of benthic reef N2 fixation via changes in diazotrophic populations, enzymatic activities, or availability of benthic substrates favorable to these microorganisms. Current knowledge indicates positive effects of ocean acidification, warming, and deoxygenation and negative effects of increased ultraviolet radiation on the amount of N fixed in coral reefs. Eutrophication may either boost or suppress N2 fixation, depending on the nutrient becoming limiting. As N2 fixation appears to play a fundamental role in nutrient-limited reef ecosystems, these assumptions need to be expanded and confirmed by future research efforts addressing the knowledge gaps identified in this review.

Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea

Nitrogenase genes (nifH) from heterotrophic dinitrogen (N2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79 μmol O2 L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6 × 10(5) and 5.8 × 10(5) nifH gene copies L(-1) within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15 μmol O2 L(-1) and 186-194 μmol O2 L(-1) in the absence of combined N.

Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae

Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4X^T. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4X^T displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C_15∶0, C_16∶1ω5c, summed feature 3 (containing C_16∶1ω6c and/or C_16∶1ω7c) and summed feature 4 (comprising anteiso-C_17∶1B and/or iso-C_17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4X^T actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4X^T is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4X^T ( = CCTCC AB 2013049^T = NRRL B-59974^T).