Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.

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Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Multiple natural and anthropogenic processes alter the carbonate chemistry of the coastal zone in ways that either exacerbate or mitigate ocean acidification effects. Freshwater inputs and multiple acid-base reactions change carbonate chemistry conditions, sometimes synergistically. The shallow nature of these systems results in strong benthic-pelagic coupling, and marine invertebrates at different life history stages rely on both benthic and pelagic habitats. Carbonate chemistry in coastal systems can be highly variable, responding to processes with temporal modes ranging from seconds to centuries. Identifying scales of variability relevant to levels of biological organization requires a fuller characterization of both the frequency and magnitude domains of processes contributing to or reducing acidification in pelagic and benthic habitats. We review the processes that contribute to coastal acidification with attention to timescales of variability and habitats relevant to marine bivalves.

Ocean Acidification in the Coastal Zone from an Organism's Perspective: Multiple System Parameters, Frequency Domains, and Habitats

The fresh water discharged by large rivers such as the Amazon is transported hundreds to thousands of kilometers away from the coast by surface plumes. The nutrients delivered by these river plumes contribute to enhanced primary production in the ocean, and the sinking flux of this new production results in carbon sequestration. Here, we report that the Amazon River plume supports N2 fixation far from the mouth and provides important pathways for sequestration of atmospheric CO2 in the western tropical North Atlantic (WTNA). We calculate that the sinking of carbon fixed by diazotrophs in the plume sequesters 1.7 Tmol of C annually, in addition to the sequestration of 0.6 Tmol of C yr−1 of the new production supported by NO3 delivered by the river. These processes revise our current understanding that the tropical North Atlantic is a source of 2.5 Tmol of C to the atmosphere [Mikaloff-Fletcher SE, et al. (2007) Inverse estimates of the oceanic sources and sinks of natural CO2 and the implied oceanic carbon transport. Global Biogeochem Cycles 21, doi:10.1029/2006GB002751]. The enhancement of N2 fixation and consequent C sequestration by tropical rivers appears to be a global phenomenon that is likely to be influenced by anthropogenic activity and climate change.

/pdf/amazon-river-enhances-diazotrophy-and-carbon-sequestration-40jyz5i9lm.pdf

Amazon River enhances diazotrophy and carbon sequestration in the tropical North Atlantic Ocean.

Microbial dinitrogen (N2) fixation, the nitrogenase enzyme-catalysed reduction of N2 gas into biologically available ammonia, is the main source of new nitrogen (N) in the ocean. For more than 50 years, oceanic N2 fixation has mainly been attributed to the activity of the colonial cyanobacterium Trichodesmium1,2. Other smaller N2-fixing microorganisms (diazotrophs)—in particular the unicellular cyanobacteria group A (UCYN-A)—are, however, abundant enough to potentially contribute significantly to N2 fixation in the surface waters of the oceans3,​4,​5,​6. Despite their abundance, the contribution of UCYN-A to oceanic N2 fixation has so far not been directly quantified. Here, we show that in one of the main areas of oceanic N2 fixation, the tropical North Atlantic7, the symbiotic cyanobacterium UCYN-A contributed to N2 fixation similarly to Trichodesmium. Two types of UCYN-A, UCYN-A1 and -A2, were observed to live in symbioses with specific eukaryotic algae. Single-cell analyses showed that both algae–UCYN-A symbioses actively fixed N2, contributing ∼20% to N2 fixation in the tropical North Atlantic, revealing their significance in this region. These symbioses had growth rates five to ten times higher than Trichodesmium, implying a rapid transfer of UCYN-A-fixed N into the food web that might significantly raise their actual contribution to N2 fixation. Our analysis of global 16S rRNA gene databases showed that UCYN-A occurs in surface waters from the Arctic to the Antarctic Circle and thus probably contributes to N2 fixation in a much larger oceanic area than previously thought. Based on their high rates of N2 fixation and cosmopolitan distribution, we hypothesize that UCYN-A plays a major, but currently overlooked role in the oceanic N cycle.

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle

Oscillating diurnal rhythms of gene transcription, metabolic activity, and behavior are found in all three domains of life. However, diel cycles in naturally occurring heterotrophic bacteria and archaea have rarely been observed. Here, we report time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations sampled in situ over 3 days. As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. Furthermore, diel oscillations in different heterotrophic bacterial groups suggested population-specific timing of peak transcript expression in a variety of metabolic gene suites. These staggered multispecies waves of diel gene transcription may influence both the tempo and the mode of matter and energy transformation in the sea.

/pdf/multispecies-diel-transcriptional-oscillations-in-open-ocean-2pzjnmyh0o.pdf

Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection.

[1] Nitrogen fixation is assumed to be most important in oligotrophic subtropical regions of the oceans. Here we show that nitrogen fixation can also be pronounced in the upwelling region off Vietnam. We compare nitrogen fixation rates and other hydro-chemical variables from the monsoon season with the intermonsoon season and find that nitrogen fixation rates are app. 10 times higher during the monsoon season. However, this was not the case in the actual upwelling region – a 40–50 km wide strip along the coast – but further offshore, where the Mekong plume was noticeable. Therefore, we hypothesize that the stability of the water column, micronutrients and/or trace metals in the Mekong river plume may be responsible for enhanced cyanobacterial growth. These cyanobacteria may be either Trichodesmium, unicellular, or diatom-associated symbionts, the latter are known from other river plumes like the Amazon.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005GL025569

Riverine influence on nitrogen fixation in the upwelling region off Vietnam, South China Sea

The influence of the Mekong River (South China Sea) on N2 fixation and phytoplankton distribution was investigated during the lowest- and highest-discharge seasons (April 2007 and September 2008, respectively). The river plays an essential role in providing nutrients (nitrate, phosphate, silicate) for the adjacent sea and creates different salinity and nutrient gradients over different seasons. River water (salinity 0), mesohaline waters (salinity 14–32), a transition zone with salinities between 32 and 33.5, and marine waters (salinity above 33.5) were sampled at different spatial resolutions in both cruises. High N2 fixation rates were measured during both seasons, with rates of up to 5.05 nmol N L21 h21 in surface waters under nitrogen-replete conditions, increasing to 22.77 nmol N L21 h21 in nitrogen-limited waters. Asymbiotic diatoms were found only close to the river mouth, and symbiotic diatoms, which potentially hosted diazotrophs, were most abundant in waters where N2 fixation rates were highest, nitrate concentrations were at the detection limit, and phosphate and silicate were still available. Filamentous cyanobacteria like Trichodesmium were present only in marine waters with salinities above 33.5. Overall, N2 fixation accounts for 1–47% of the nitrogen demand of primary production.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2010.55.4.1668

The Mekong River plume fuels nitrogen fixation and determines phytoplankton species distribution in the South China Sea during low- and high-discharge season

Recent observations of N2 fixation rates (NFR) and the presence of nitrogenase (nifH) genes from heterotrophic N2-fixing (diazotrophic) prokaryotes in unusual habitats challenge the paradigm that pelagic marine N2 fixation is constrained to cyanobacteria in warm, oligotrophic, surface waters. Here, we compare NFR and diazotrophic diversity (assessed via high-throughput nifH sequencing) from a region known to be dominated by cyanobacterial diazotrophs (the North Pacific Subtropical Gyre, NPSG) to two regions dominated by heterotrophic diazotrophs: the Eastern South Pacific (ESP, from the Chilean upwelling system to the subtropical gyre) and the Pacific Northwest coastal upwelling system (PNW). We observed distinct biogeographical patterns among the three regions. Diazotrophic community structure differed strongly between the NPSG, dominated by cyanobacterium UCYN-A, and the ESP, dominated by heterotrophic nifH group 1J/1K, yet surface NFR were similar in magnitude (up to 5.1 nmol N L−1 d−1). However, while diverse, predominantly heterotrophic nifH genes were recovered from the PNW and the mesopelagic of the NPSG, NFR were undetectable in both of these environments (although glucose amendments stimulated low rates in the deep NPSG). Our work suggests that while diazotrophs may be nearly omnipresent in marine waters, the activity of this functional group is regionally restricted. Further, we show that the detection limits of the 15N2 fixation assay suggest that many of the low NFR reported for the mesopelagic (often < 0.1 nmol N L−1 d−1 in the literature) are not indicative of active diazotrophy, highlighting the challenges of assessing the ecosystem significance of heterotrophic diazotrophs.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.10542

Diversity and activity of nitrogen-fixing communities across ocean basins

Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed 'diazotrophs') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.

https://escholarship.org/content/qt7th6b8rt/qt7th6b8rt.pdf

Deniz Bombar

Papers

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection.

Riverine influence on nitrogen fixation in the upwelling region off Vietnam, South China Sea

The Mekong River plume fuels nitrogen fixation and determines phytoplankton species distribution in the South China Sea during low- and high-discharge season

Diversity and activity of nitrogen-fixing communities across ocean basins

Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria