Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Abstract

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Coastal N2 Fixation Rates Coincide Spatially With Nitrogen Loss in the Humboldt Upwelling System off Peru

“…Our measured rates may however be underestimated compared to in situ rates due to incubation artifacts, in particular, elevated incubation compared to in situ temperature as well as potential O 2 contamination. Higher incubation temperatures (22.91 ± 1.36°C) relative to in situ conditions (15.21 ± 1.46°C) may have been on the upper end of thermal tolerances for N 2 fixers associated with cool upwelled waters (3–18°C) such as the Gamma4 γ‐proteobacteria abundantly observed from the ETSP (Cheung et al., 2021; Löscher et al., 2014; Turk‐Kubo et al., 2014, 2022). Dissolved O 2 concentrations in the incubation bottles may have been higher than in situ because even though we overflowed the bottles with samples to minimize atmospheric contact with the sample, we cannot not completely exclude potential O 2 contamination when filling incubation bottles or during the introduction of isotope‐enriched waters.…”

Diazotrophy in the Indian Ocean: Current understanding and future perspectives

“…Just as in the other sub-basins where NCDs dominate, it is yet unclear if and how these diazotrophs contribute to fixed nitrogen inputs and how they obtain energy to fix N 2 . Recent analyses of NCDs metagenome assembled genomes show a variety of possible energy obtaining metabolisms, including anoxygenic photosynthesis, dissimilatory sulfate reduction, thiosulfate oxidation, dissimilatory nitrate reduction and denitrification (Turk-Kubo et al 2022).…”

“…N 2 fixation is carried out by diazotrophs: prokaryotes including filamentous and unicellular cyanobacteria, and non‐cyanobacterial diazotrophs (NCDs) that may comprise a diverse suite of metabolisms including chemoorganoheterotrophy and chemolithoautotrophy, among others (Turk‐Kubo et al 2022). Due to the high energy demand of this process, N 2 fixation is usually inhibited in the presence of more readily available reactive nitrogen compounds such as ammonium and nitrate (Zehr and Capone 2020).…”

Heterogeneous Diazotroph Communities in the Subtropical‐Subantarctic Transition and Aphotic Zones Off the Coast of Patagonia, Eastern South Pacific Ocean

“…Only 5 ASVs (ASV033n, 065n, 155n, 169n, and 186n) were classified as cyanobacteria, which were a minor component of the diazotrophic communities; in other words, nifH from non-cyanobacterial diazotrophs dominated all samples. Among the 10 most abundant nifH amino acid sequence groups, 3 ASVs (ASV014n,018n and 021n) showed low similarity to sequences in the marine NCD database (Turk-Kubo et al, 2022) (up to 92%, 89%, and 90%, respectively), and all others had high similarity (>97%). The nifH amino acid sequences of those ASVs were similar to Antarc-Shio-SV002, PM-RGC_gene_1205376, and PM-RGC_gene_1229881 retrieved from polar regions, EVHVF (Burkholderia vietnamiensis), and BT5667A01 (Alphaproteobacteria) from marine aphotic zones, BAL354 (Pseudomonas) from estuarine surface waters, and NB3 (Pelobacter) from marine sediment.…”

“…However, recent studies indicate that N 2 fixation also occurs in subtropical‐subarctic transition regions (Gradoville et al., 2020; Sato et al., 2021; Shiozaki et al., 2017), N‐rich environments (Knapp, 2012; Mills et al., 2020), polar regions (Blais et al., 2012; Shiozaki, Fujiwara, et al., 2018, 2020), and aphotic zones (Benavides et al., 2018; Moisander et al., 2017). Moreover, diazotrophs include not only cyanobacteria but also a wide variety of non‐cyanobacteria, which can adapt to various environments due to their diverse metabolic functions (Delmont et al., 2018, 2022; Shiozaki et al., 2023; Turk‐Kubo et al., 2022). These recently identified regions of N 2 fixation may hold the answer to unraveling the enigmas surrounding the marine N cycle (Shao et al., 2023; Zehr & Capone, 2020), wherein the estimated N gain through N 2 fixation is much smaller than the N loss through denitrification (Codispoti, 2007).…”