Description: Marine diazotrophs convert dinitrogen (N-2) 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 N-2 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 N-2 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 N-2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43-57 versus 45-63 TgNyr (-1); ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223 +/- 30 TgNyr (-1) (mean +/- standard error; same hereafter) compared to version 1 (74 +/- 7 TgNyr (-1)). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88 +/- 23 versus 20 +/- 2 TgNyr 1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40 +/- 9 versus 10 +/- 2 TgNyr (-1)). Moreover, version 2 estimates the N-2 fixation rate in the Indian Ocean to be 35 +/- 14 TgNyr (-1), which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N-2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional N-15(2) bubble method yields lower rates in 69% cases compared to the new N-15(2) 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).

Description: In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S–50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.

Description: Biogeochemical cycling of carbon (C) and nitrogen (N) in the ocean depends on both the composition and activity of underlying biological communities and on abiotic factors. The Southern Ocean is encircled by a series of strong currents and fronts, providing a barrier to microbial dispersion into adjacent oligotrophic gyres. Our study region straddles the boundary between the nutrient-rich Southern Ocean and the adjacent oligotrophic gyre of the South Indian Ocean, providing an ideal region to study changes in microbial productivity. Here, we measured the impact of C- and N- uptake on microbial community diversity, contextualized by hydrographic factors and local physico-chemical conditions across the Southern Ocean and South Indian Ocean. We observed that contrasting physico-chemical characteristics led to unique microbial diversity patterns, with significant correlations between microbial alpha diversity and primary productivity (PP). However, we detected no link between specific PP (PP normalized by chlorophyll a concentration) and microbial alpha and beta diversity. Prokaryotic alpha and beta diversity were correlated with biological N2 fixation, itself a prokaryotic process, and we detected measurable N2 fixation to 60° S. While regional water masses have distinct microbial genetic fingerprints in both the eukaryotic and prokaryotic fractions, PP and N2 fixation vary more gradually and regionally. This suggests that microbial phylogenetic diversity is more strongly bounded by physical oceanographic features, while microbial activity responds more to chemical factors. We conclude that concomitant assessments of microbial diversity and activity is central in understanding the dynamics and complex responses of microorganisms to a changing ocean environment.

Description: Plankton networks driving carbon export in the oligotrophic ocean Nature 532, 7600 (2016). doi:10.1038/nature16942 Authors: Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stephane Audic, Léo Berline, Jennifer R. Brum, Luis Pedro Coelho, Julio Cesar Ignacio Espinoza, Shruti Malviya, Shinichi Sunagawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Julie Poulain, Sarah Searson, Lars Stemmann, Fabrice Not, Pascal Hingamp, Sabrina Speich, Mick Follows, Lee Karp-Boss, Emmanuel Boss, Hiroyuki Ogata, Stephane Pesant, Jean Weissenbach, Patrick Wincker, Silvia G. Acinas, Peer Bork, Colomban de Vargas, Daniele Iudicone, Matthew B. Sullivan, Jeroen Raes, Eric Karsenti, Chris Bowler & Gabriel Gorsky The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure

Description: Abstract: We investigated the bacterial community structure in surface waters along a 2500 km transect in the eastern Indian Ocean. Using high throughput sequencing of the 16S rRNA gene we measured a significant latitudinal increase in bacterial richness from 800 to 1400 OTUs (42% increase; r2=0.65; p〈0.001) from the tropical Timor Sea to the colder temperate waters. Total dissolved inorganic nitrogen, chl a, phytoplankton community structure and primary productivity strongly correlated with bacterial richness (all p〈0.01). Our data suggest that primary productivity drives greater bacterial richness. Because, N2-fixation accounts for up to 50% of new production in this region we tested whether higher N2-fixation rates are linked to a greater nifH diversity. The nifH diversity was dominated by heterotrophic Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. We did not found any mechanistic links between nifH amplicon data, bacterial richness and primary productivity due to the overall low nifH evenness in this region. Scientific statement: Geographic gradients of marine microbial diversity is currently thought to be explained by two mechanisms, 1) diversity increases with increased productivity, and 2) it increases with increasing temperature. However, conclusive evidence for these mechanisms has been lacking from studies that span gradients in both, and it is unclear which organisms are responsible for the changes in diversity along these gradients. Here we present the first analysis of bacterial richness along the West Australian boundary current, the Leeuwin Current. Our analysis of bacterial richness along a latitudinal gradient in the eastern Indian Ocean shows support for the productivity mechanism rather than the temperature mechanism. Further, we show that bacterial richness increases towards the productive temperate waters are driven by productive eukaryotes (NO3- based) and heterotrophic N2-fixers.

Description: Our data, as part of the OISO (Ocean Indien Service d'Observation) campaign, contributes to a better understanding of the physical and biological factors controlling N2 fixation in the Southern Indian Ocean and the French Southern and Antarctic lands during Austral summer January and February 2017. We measured N2 and C fixation as well as NH4+ and NO3- assimilation in 3-6 replicates per station. Additionally, we measured diagnostic pigment concentrations to evaluate phtosynthetic community composition. For pigment analysis 4L water was filtered through 25mm Whatman GF/F filters (pressure drop 〈10kPa). Samples were stored at -80°C until analysis. Pigments were analysed using High Performance Liquid Chromatography (HPLC). Pigment concentration were calculated according to Kilias et al (2013, doi:10.1111/jpy.12109). N2 fixation experiments were carried out in three to six replicates for each station. Incubations were done in pre-acid washed polycarbonate bottles on deck with ambient light conditions. All polycarbonate incubation bottles were rinsed with deionized water, and seawater prior to incubation. We used the combination of the bubble approach (Montoya et al., 1996) and the dissolution method (Mohr et al., 2010, doi:10.1371/journal.pone.0012583) proposed by Klawonn et al. (2015, doi:10.3389/fmicb.2015.00769). Bottles were filled up to capacity to avoid air contamination. Incubations were initialized by adding a 10 ml 15-15N gas bubble. Bottles were gently rocked for 15 minutes. Finally, the remaining bubble was removed to avoid equilibration between gas and aqueous phase. after 24 hours a water subsample was taken to a 12 ml exetainer and preserved with 100 µl HgCl2 solution for later determination of exact 15N-15N concentration. Natural 15N2 was determined using Membrane Inlet Mass Spectrometry (MIMS; GAM200, IPI) for each station. Analysis of 15N2 incorporated was carried out by the Isotopic Laboratory at the UC Davis, California campus. We used stable isotope tracers (15N) to measure dissolved inorganic nitrogen (DIN) assimilation rates. Experiments were initiated by adding a known concentration of 0.05 of K15NO3 and 15NH4Cl for oligotrophic waters of the IO and 0.625 µmol L-1 for HNLC regions in the ACC and PF (Knap et al., 1994, Waite et al., 2007, doi:10.1016/j.dsr2.2006.12.010) to one litre polycarbonate bottles. For C assimilation experiments, we added 20 µmol L-1 of NaH13CO3 to one of each of N2 fixation, NH4+ and NO3- assimilation experiment bottles. For incubation, we followed the same procedure as for N2 fixation experiments. Findings reveal that N2 fixation occurs throughout the whole sampling area up to 55°S latitude. In addition, variations of N2 fiaxation rates between replicates were relatively high indicating a great heterogeneity of the French Southern and Antarctic waters. References: Montoya 1996: Montoya, Joseph P., et al. "A Simple, High-Precision, High-Sensitivity Tracer Assay for N (inf2) Fixation." Applied and environmental microbiology 62.3 (1996): 986-993. Knap et al 1994: Knap, A., Michaels, A., Close, A., Ducklow, H. & Dickson, A. 1994. Protocols for the Joint Global Ocean Flux Study (JGOFS) Core Measurements, JGOFS, Reprint of the IOC Manuals and Guides No. 29. UNESCO, 19, 1.