The marine nitrogen cycle: new developments and global change

BACKGROUND Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. RESULTS Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. CONCLUSIONS This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.

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Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments.

The filamentous diazotrophic cyanobacterium Trichodesmium is responsible for a significant fraction of marine di-nitrogen (N2) fixation. Growth and distribution of Trichodesmium and other diazotrophs in the vast oligotrophic subtropical gyres is influenced by iron (Fe) and phosphorus (P) availability, while reciprocally influencing the biogeochemistry of these nutrients. Here we use observations across natural inverse gradients in Fe and P in the North Atlantic subtropical gyre (NASG) to demonstrate how Trichodesmium acclimates in situ to resource availability. Transcriptomic analysis identified progressive upregulation of known iron-stress biomarker genes with decreasing Fe availability, and progressive upregulation of genes involved in the acquisition of diverse P sources with decreasing P availability, while genes involved in N2 fixation were upregulated at the intersection under moderate Fe and P availability. Enhanced N2 fixation within the Fe and P co-stressed transition region was also associated with a distinct, consistent metabolic profile, including the expression of alternative photosynthetic pathways that potentially facilitate ATP generation required for N2 fixation with reduced net oxygen production. The observed response of Trichodesmium to availability of both Fe and P supports suggestions that these biogeochemically significant organisms employ unique molecular, and thus physiological responses as adaptations to specifically exploit the Fe and P co-limited niche they construct.

Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability.

Abstract. Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022). 

pdf/global-oceanic-diazotroph-database-version-2-and-elevated-t75ndvo6uh.pdf

Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation

Mutualism between Synechococcus and heterotrophic bacteria has been found to support their prolonged survival in nutrient-depleted conditions. However, environmental interference on the fate of their mutualism is not understood. Here, we show that exogenous nutrients disrupt their established mutualism. Once the exogenous nutrients were exhausted, Synechococcus and heterotrophic bacteria gradually reestablished their metabolic mutualism during 450 days of culture, which revived unhealthy Synechococcus cells. Using metagenomics, metatranscriptomics, and the 15N tracer method, we reveal that the associated bacterial nitrogen fixation triggered the reestablishment of the mutualism and revival of Synechococcus health. During this process, bacterial community structure and functions underwent tremendous adjustments to achieve the driving effect, and a cogeneration of nitrogen, phosphorus, iron, and vitamin by the heterotrophic bacteria sustained Synechococcus’s prolonged healthy growth. Our findings suggest that Synechococcus and heterotrophic bacteria may have an inherent tendency toward mutualism despite environmental interference. This may exhibit their coevolutionary adaptations in nutrient-deficient environments.

Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference

Nitrogen availability limits marine productivity across large ocean regions Diazotrophs can supply new nitrogen to the marine environment via nitrogen (N2) fixation, relieving nitrogen limitation The distributions of diazotrophs and N2 fixation have been hypothesized to be generally controlled by temperature, phosphorus, and iron availability in the global ocean However, even in the North Atlantic where most research on diazotrophs and N2 fixation has taken place, environmental controls remain contentious Here we measure diazotroph composition, abundance, and activity at high resolution using newly developed underway sampling and sensing techniques We capture a diazotrophic community shift from Trichodesmium to UCYN-A between the oligotrophic, warm (25–29 °C) Sargasso Sea and relatively nutrient-enriched, cold (13–24 °C) subpolar and eastern American coastal waters Meanwhile, N2 fixation rates measured in this study are among the highest ever recorded globally and show significant increase with phosphorus availability across the transition from the Gulf Stream into subpolar and coastal waters despite colder temperatures and higher nitrate concentrations Transcriptional patterns in both Trichodesmium and UCYN-A indicate phosphorus stress in the subtropical gyre Over this iron-replete transect spanning the western North Atlantic, our results suggest that temperature is the major factor controlling the diazotrophic community structure while phosphorous drives N2 fixation rates Overall, the occurrence of record-high UCYN-A abundance and peak N2 fixation rates in the cold coastal region where nitrate concentrations are highest (~200 nM) challenges current paradigms on what drives the distribution of diazotrophs and N2 fixation

/pdf/new-insights-into-the-distributions-of-nitrogen-fixation-and-3kl0e0e6uw.pdf

New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods.

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. Mesoscal eddies influence the distribution of marine diazotrophs in the North Atlantic, highlighting the potential role of particle-associated non-cyanobacterial diazotrophs (NCDs) on their contribution to nitrogen and carbon cycles.

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

This study aimed to improve the understanding of the nutrient modulation of Ostreopsis cf. ovata toxin content. During the 2018 natural bloom in the NW Mediterranean, the total toxin content (up to ca. 57.6 ± 7.0 pg toxin cell−1) varied markedly. The highest values often coincided with elevated O. cf. ovata cell abundance and with low inorganic nutrient concentrations. The first culture experiment with a strain isolated from that bloom showed that cell toxin content was higher in the stationary than in the exponential phase of the cultures; phosphate- and nitrate-deficient cells exhibited similar cell toxin variability patterns. The second experiment with different conditions of nitrogen concentration and source (nitrate, urea, ammonium, and fertilizer) presented the highest cellular toxin content in the high-nitrogen cultures; among these, urea induced a significantly lower cellular toxin content than the other nutrient sources. Under both high- and low-nitrogen concentrations, cell toxin content was also higher in the stationary than in the exponential phase. The toxin profile of the field and cultured cells included ovatoxin (OVTX) analogues -a to -g and isobaric PLTX (isoPLTX). OVTX-a and -b were dominant while OVTX-f, -g, and isoPLTX contributed less than 1-2%. Overall, the data suggest that although nutrients determine the intensity of the O. cf. ovata bloom, the relationship of major nutrient concentrations, sources and stoichiometry with cellular toxin production is not straightforward.

/pdf/progress-on-the-link-between-nutrient-availability-and-toxin-2zhagupy.pdf

Progress on the Link between Nutrient Availability and Toxin Production by Ostreopsis cf. ovata: Field and Laboratory Experiments

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New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods.

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

Progress on the Link between Nutrient Availability and Toxin Production by Ostreopsis cf. ovata: Field and Laboratory Experiments