Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean

High metabolic versatility and phenotypic heterogeneity in a marine non-cyanobacterial diazotroph

Marine non-cyanobacterial diazotrophs (NCDs) are widespread in the oceans, but the processes controlling nitrogen fixation in cell populations remain understudied. In this study, we combined high-throughput sequencing, genetic and physiological characterization, and single-cell quantification of nitrogenase expression to investigate the growth strategies of the marine NCD Vibrio diazotrophicus. We demonstrate that this marine NCD is highly versatile, capable of utilizing a broad range of organic and inorganic nitrogen sources. Quantitative fluorescence microscopy revealed intense posttranscriptional regulation of nitrogenase expression and that V. diazotrophicus regulates both the proportion of cells and their nitrogenase expression levels based on ammonium concentration in an NtrC-dependent manner. We also found that this phenotypic heterogeneity in nitrogenase expression is more widespread among marine NCDs, suggesting it is a conserved trait. These findings help explain their high abundance in the oceans and deepen our understanding of their ecological importance.

Unveiling the contribution of particle-associated non-cyanobacterial diazotrophs to N2 fixation in the upper mesopelagic North Pacific Gyre

Dinitrogen (N2) fixation supports marine life through the supply of reactive nitrogen. Recent studies suggest that particle-associated non-cyanobacterial diazotrophs (NCDs) could contribute significantly to N2 fixation contrary to the paradigm of diazotrophy as primarily driven by cyanobacterial genera. We examine the community composition of NCDs associated with suspended, slow, and fast-sinking particles in the North Pacific Subtropical Gyre. Suspended and slow-sinking particles showed a higher abundance of cyanobacterial diazotrophs than fast-sinking particles, while fast-sinking particles showed a higher diversity of NCDs including Marinobacter, Oceanobacter and Pseudomonas. Using single-cell mass spectrometry we find that Gammaproteobacteria N2 fixation rates were higher on suspended and slow-sinking particles (up to 67 ± 48.54 fmol N cell⁻¹ d⁻¹), while putative NCDs' rates were highest on fast-sinking particles (121 ± 22.02 fmol N cell⁻¹ d⁻¹). These rates are comparable to previous diazotrophic cyanobacteria observations, suggesting that particle-associated NCDs may be important contributors to pelagic N2 fixation.

Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters

Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters.

IMPORTANCE

Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.

Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed

Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.

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.

Fronts divide diazotroph communities in the Southern Indian Ocean

Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well-explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here, we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multifrontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving high N2 fixation rates (up to 13.96 nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.

Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy

Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.

Isolation and biogeography of the oligotrophic ocean diazotroph, Crocosphaera waterburyi nov. sp

Marine N2-fixing cyanobacteria, including the unicellular genus Crocosphaera, are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen and carbon, which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one pelagic, oligotrophic, phycoerythrin-rich species, Crocosphaera watsonii, has ever been identified and characterized as widespread. Herein, we present a new species, named Crocosphaera waterburyi, enriched from the North Pacific Ocean. C. waterburyi was found to be phenotypically and genotypically distinct from C. watsonii, active in situ, distributed globally, and preferred warmer temperatures in culture and the ocean. Additionally, C. waterburyi was detectable in 150- and 4000-meter sediment export traps, had a relatively larger biovolume than C. watsonii, and appeared to aggregate in the environment and laboratory culture. Therefore, it represents an additional, previously unknown link between atmospheric CO2 and N2 gas and deep ocean carbon and nitrogen export and sequestration.

Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities

We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.

Better together? Lessons on sociality from Trichodesmium

The N2-fixing cyanobacterium Trichodesmium is an important player in the oceanic nitrogen and carbon cycles. Trichodesmium occurs both as single trichomes and as colonies containing hundreds of trichomes. In this review, we explore the benefits and disadvantages of colony formation, considering physical, chemical, and biological effects from nanometer to kilometer scale. Showing that all major life challenges are affected by colony formation, we claim that Trichodesmium's ecological success is tightly linked to its colonial lifestyle. Microbial interactions in the microbiome, chemical gradients within the colony, interactions with particles, and elevated mobility in the water column shape a highly dynamic microenvironment. We postulate that these dynamics are key to the resilience of Trichodesmium and other colony formers in our changing environment.

Microalgal and Nitrogen-Fixing Bacterial Consortia: From Interaction to Biotechnological Potential

Microalgae are used in various biotechnological processes, such as biofuel production due to their high biomass yields, agriculture as biofertilizers, production of high-value-added products, decontamination of wastewater, or as biological models for carbon sequestration. The number of these biotechnological applications is increasing, and as such, any advances that contribute to reducing costs and increasing economic profitability can have a significant impact. Nitrogen fixing organisms, often called diazotroph, also have great biotechnological potential, mainly in agriculture as an alternative to chemical fertilizers. Microbial consortia typically perform more complex tasks than monocultures and can execute functions that are challenging or even impossible for individual strains or species. Interestingly, microalgae and diazotrophic organisms are capable to embrace different types of symbiotic associations. Certain corals and lichens exhibit this symbiotic relationship in nature, which enhances their fitness. However, this relationship can also be artificially created in laboratory conditions with the objective of enhancing some of the biotechnological processes that each organism carries out independently. As a result, the utilization of microalgae and diazotrophic organisms in consortia is garnering significant interest as a potential alternative for reducing production costs and increasing yields of microalgae biomass, as well as for producing derived products and serving biotechnological purposes. This review makes an effort to examine the associations of microalgae and diazotrophic organisms, with the aim of highlighting the potential of these associations in improving various biotechnological processes.

Natural iron fertilization by shallow hydrothermal sources fuels diazotroph blooms in the ocean

Iron is an essential nutrient that regulates productivity in ~30% of the ocean. Compared with deep (>2000 meter) hydrothermal activity at mid-ocean ridges that provide iron to the ocean's interior, shallow (<500 meter) hydrothermal fluids are likely to influence the surface's ecosystem. However, their effect is unknown. In this work, we show that fluids emitted along the Tonga volcanic arc (South Pacific) have a substantial impact on iron concentrations in the photic layer through vertical diffusion. This enrichment stimulates biological activity, resulting in an extensive patch of chlorophyll (360,000 square kilometers). Diazotroph activity is two to eight times higher and carbon export fluxes are two to three times higher in iron-enriched waters than in adjacent unfertilized waters. Such findings reveal a previously undescribed mechanism of natural iron fertilization in the ocean that fuels regional hotspot sinks for atmospheric CO₂.