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Abstract. Marine diazotrophs convert dinitrogen (N2) gas intobioavailable nitrogen (N), supporting life in the global ocean. In 2012, thefirst version of the global oceanic diazotroph database (version 1) waspublished. Here, we present an updated version of the database (version 2),significantly increasing the number of in situ diazotrophic measurements from13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cellabundance, and nifH gene copy abundance have increased by 184 %, 86 %, and809 %, respectively. Version 2 includes two new data sheets for the nifH genecopy abundance of non-cyanobacterial diazotrophs and cell-specific N2fixation rates. The measurements of N2 fixation rates approximatelyfollow a log-normal distribution in both version 1 and version 2. However,version 2 considerably extends both the left and right tails of thedistribution. Consequently, when estimating global oceanic N2 fixationrates using the geometric means of different ocean basins, version 1 andversion 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; rangesbased on one geometric standard error). In contrast, when using arithmeticmeans, 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 areestimated 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 theIndian Ocean to be 35±14 Tg N yr−1, which could not be estimatedusing version 1 due to limited data availability. Furthermore, a comparisonof N2 fixation rates obtained through different measurement methods atthe same months, locations, and depths reveals that the conventional15N2 bubble method yields lower rates in 69 % cases compared tothe new 15N2 dissolution method. This updated version of thedatabase can facilitate future studies in marine ecology andbiogeochemistry. The database is stored at the Figshare repository(https://doi.org/10.6084/m9.figshare.21677687; Shao etal., 2022).

Marine dissolved organic carbon and nitrogen (DOC and DON) are major global carbon and nutrient reservoirs, and their characterization relies on extraction methods for preconcentration and salt removal. Existing methods optimize for capturing and describing DOC. Here, we report an optimized analytical strategy to recover marine DON for subsequent molecular characterization. Retention efficiencies between 5% and 95% are reported for seven solid phase extraction (SPE) sorbents, with PPL recovering 23% of marine DON compared to 95% recovered with C18. Additional comparisons of the effect of varying sample volumes and elution speed, and the resulting molecular composition of DON extracts, were investigated using C18 and PPL sorbents. Sample volumes > 200 mL decreased DON retention efficiency independent of SPE sorbent, and gravity elution recovered 1.7‐ to 4.2‐fold more DON compared to vacuum elution. Characterization of extracted DON by negative‐ion electrospray ionization Fourier transform‐ion cyclotron resonance mass spectrometry (FT‐ICR MS) highlights compositional differences between DON species recovered by each method. DON isolated with optimized methods includes low molecular weight (< 600 Da) peptide‐like compounds with low O:C ratios (0.2 to 0.5) that are not detected by other SPE sorbents (e.g., PPL). The majority of additional DON isolated with this approach was undetectable by direct infusion negative mode FT‐ICR MS analysis. [ABSTRACT FROM AUTHOR]

The availability of nitrogen (N) in ocean surface waters affects rates of photosynthesis and marine ecosystem structure. In spite of low dissolved inorganic N concentrations, export production in oligotrophic waters is comparable to more nutrient replete regions. Prior observations raise the possibility that di-nitrogen (N2) fixation supplies a significant fraction of N supporting export production in the Gulf of Mexico. In this study, geochemical tools were used to quantify the relative and absolute importance of both subsurface nitrate and N2 fixation as sources of new N fueling export production in the oligotrophic Gulf of Mexico in May 2017 and May 2018. Comparing the isotopic composition ("δ15N") of nitrate with the δ15N of sinking particulate N collected during five sediment trap deployments each lasting two to four days indicates that N2 fixation is typically not detected and that the majority (≥80%) of export production is supported by subsurface nitrate. Moreover, no gradients in upper ocean dissolved organic N and suspended particulate N concentration and/or δ15N were found that would indicate significant N2 fixation fluxes accumulated in these pools, consistent with low Trichodesmium spp. abundance. Finally, comparing the δ15N of sinking particulate N captured within vs. below the euphotic zone indicates that during late spring regenerated N is low in δ15N compared to sinking N. [ABSTRACT FROM AUTHOR]

The highly stratified, oligotrophic regions of the oceans are predominantly nitrogen limited in the surface ocean and light limited at the deep chlorophyll maximum (DCM). Hence, determining light and nitrogen co-limitation patterns for diverse phytoplankton taxa is crucial to understanding marine primary production throughout the euphotic zone. During two cruises in the deep-water Gulf of Mexico, we measured primary productivity (H13CO3−), nitrate uptake (15NO3−) and ammonium uptake (15NH4+) throughout the water column. Primary productivity declined with depth from the mixed layer to the DCM, averaging 27.1 mmol C m−2 d−1. The fraction of growth supported by NO3− was consistently low, with upper euphotic zone values ranging from 0.01 to 0.14 and lower euphotic zone values ranging from 0.03 to 0.44. Nitrate uptake showed strong diel patterns (maximum during the day), whereas ammonium uptake exhibited no diel variability. To parameterize taxon-specific phytoplankton nutrient and light utilization, we used a data assimilation approach (Bayesian Markov Chain Monte Carlo) including primary productivity, nutrient uptake and taxon-specific growth rate measurements. Parameters derived from this analysis define distinct niches for five phytoplankton taxa (Prochlorococcus , Synechococcus , diatoms, dinoflagellates and prymnesiophytes) and may be useful for constraining biogeochemical models of oligotrophic open-ocean systems. [ABSTRACT FROM AUTHOR]

We used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic bluefin tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show extensive nutrient regeneration fueling primary productivity (mostly by cyanobacteria and other picophytoplankton) in the upper euphotic zone. The food web is dominated by the microbial loop (>70% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). By contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <10% of the net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on podonid cladocerans and other suspension-feeding zooplankton, which in turn derive much of their nutrition from nano- and micro-phytoplankton (mixotrophic flagellates, and to a lesser extent, diatoms). This allows ABT larvae to maintain a comparatively low trophic level (~4.2 for preflexion and postflexion larvae), which increases trophic transfer from phytoplankton to larval fish. [ABSTRACT FROM AUTHOR]

Biomass and composition of the phytoplankton community were investigated in the deep-water Gulf of Mexico (GoM) at the edges of Loop Current anticyclonic eddies during May 2017 and May 2018. Using flow cytometry, high-performance liquid chromatography pigments and microscopy, we found euphotic zone integrated chlorophyll a of ~10 mg m−2 and autotrophic carbon ranging from 463 to 1268 mg m−2, dominated by picoplankton (<2 μm cells). Phytoplankton assemblages were similar to the mean composition at the Bermuda Atlantic Time-series Study site, but differed from the Hawaii Ocean Times-series site. GoM phytoplankton biomass was ~2-fold higher at the deep chlorophyll maximum (DCM) relative to the mixed layer (ML). Prochlorococcus and prymnesiophytes were the dominant taxa throughout the euphotic zone; however, other eukaryotic taxa had significant biomass in the DCM. Shallower DCMs were correlated with more prymnesiophytes and prasinophytes (Type 3) and reduced Prochlorococcus. These trends in ML and DCM taxonomic composition likely reflect relative nutrient supply—with ML populations relying on remineralized ammonium as a nitrogen source, and the taxonomically diverse DCM populations using more nitrate. These spatially separated phytoplankton communities represent different pathways for primary production, with a dominance of picoplankton in the ML and more nano- and microplankton at the DCM. [ABSTRACT FROM AUTHOR]

Dinitrogen (N2) fixation is an important source of biologically reactive nitrogen (N) to the global ocean. The magnitude of this flux, however, remains uncertain, in part because N2 fixation rates have been estimated following divergent protocols and because associated levels of uncertainty are seldom reported—confounding comparison and extrapolation of rate measurements. A growing number of reports of relatively low but potentially significant rates of N2 fixation in regions such as oxygen minimum zones, the mesopelagic water column of the tropical and subtropical oceans, and polar waters further highlights the need for standardized methodological protocols for measurements of N2 fixation rates and for calculations of detection limits and propagated error terms. To this end, we examine current protocols of the 15N2 tracer method used for estimating diazotrophic rates, present results of experiments testing the validity of specific practices, and describe established metrics for reporting detection limits. We put forth a set of recommendations for best practices to estimate N2 fixation rates using 15N2 tracer, with the goal of fostering transparency in reporting sources of uncertainty in estimates, and to render N2 fixation rate estimates intercomparable among studies. [ABSTRACT FROM AUTHOR]