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ABSTRACT Dinitrogen (N₂) fixation provides bioavailable nitrogen to the biosphere. However, in some habitats (e.g., sediments), the metabolic pathways of organisms carrying out N₂fixation are unclear. We present metabolic models representing various chemotrophic N₂fixers, which simulate potential pathways of electron transport and energy flow, resulting in predictions of whole-cell stoichiometries. By balancing mass, electrons, and energy for metabolic half-reactions, we quantify the electron usage for nine N₂fixers. Our results demonstrate that all modeled organisms fix sufficient N₂for growth. Aerobic organisms allocate more electrons to N₂fixation and growth, yielding more biomass and fixing more N₂, while methanogens using acetate and organisms using sulfate allocate fewer electrons. This work can be applied to investigate the depth distribution of N₂fixers based on nutrient availability, complementing field measurements of biogeochemical processes and microbial communities.IMPORTANCEN₂fixation is an important process in the global N cycle. Researchers have developed models for heterotrophic and photoautotrophic N₂fixers, but there is a lack of modeling studies on chemoautotrophic N₂fixers. Here, we built nine biochemical models for different chemoautotrophic N₂fixers by combining different types of half-chemical reactions. We include three sulfide oxidizers using different electron acceptors (O₂, NO₃⁻, and Fe³⁺), contributing to the sulfur, nitrogen, and iron cycles in the sediment. We have two methanogens using different substrates (H₂and acetate) and four methanotrophs using different electron acceptors (O₂, NO₃⁻, Fe³⁺, and SO₄²⁻). By modeling these methane producers and users in the sediment and their N₂-fixing metabolic pathways, our work can provide insight for future carbon cycle studies. This study outlines various metabolic pathways that can facilitate N₂fixation, with implications for where in the environment they might occur. 

ABSTRACT Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality. 

We conducted a cross-ecoregion study to test the hypothesis that N-fixation and denitrification would co-occur in streams and rivers across a range of reactive N concentrations. Between 2017 and 2019, we sampled 30 streams in 13 ecoregions, using chambers to quantify N-fixation using acetylene reduction and denitrification using acetylene block. 25 of the study streams were part of the National Ecological Observatory Network or the StreamPULSE network, which provided data on water temperature, light, nutrients, discharge and metabolism. Although N-fixation and denitrification occur under contrasting environmental conditions, we found that they co-occurred in ca. 40% of stream ecosystems surveyed, and microbes capable of carrying out each process were found in all surveyed streams. This dataset includes the chamber data used to calculate nitrogen fixation and denitrification rates, stream substrate information used to scale rates from substrate to whole-reach scale, and a variety of reach-to-landscape scale covariates used to evaluate predictors of rates across the study streams. 

Biological nitrogen fixation is a key driver of global primary production and climate. Decades of effort have repeatedly updated nitrogen fixation estimates for terrestrial and open ocean systems, yet other aquatic systems in between have largely been ignored. Here we present an evaluation of nitrogen fixation for inland and coastal waters. We demonstrate that water column and sediment nitrogen fixation is ubiquitous across these diverse aquatic habitats, with rates ranging six orders of magnitude. We conservatively estimate that, despite accounting for less than 10% of the global surface area, inland and coastal aquatic systems fix 40 (30 to 54) teragrams of nitrogen per year, equivalent to 15% of the nitrogen fixed on land and in the open ocean. Inland systems contribute more than half of this biological nitrogen fixation. 

Biological nitrogen fixation is the conversion of dinitrogen (N2) gas into bioavailable nitrogen by microorganisms with consequences for primary production, ecosystem function, and global climate. Here we present a compiled dataset of 4793 nitrogen fixation (N2-fixation) rates measured in the water column and benthos of inland and coastal systems via the acetylene reduction assay, 15N2 labeling, or N2/Ar technique. While the data are distributed across seven continents, most observations (88%) are from the northern hemisphere. 15N2 labeling accounted for 67% of water column measurements, while the acetylene reduction assay accounted for 81% of benthic N2-fixation observations. Dataset median area-, volume-, and mass-normalized N2-fixation rates are 7.1 μmol N2-N m−2 h−1, 2.3 × 10−4 μmol N2-N L−1 h−1, and 4.8 × 10−4 μmol N2-N g−1 h−1, respectively. This dataset will facilitate future efforts to study and scale N2-fixation contributions across inland and coastal aquatic environments. 

Great Lakes coastlines are mosaics of wetland, stream, and lake habitats, characterized by a high degree of spatial heterogeneity that may facilitate the co-occurrence of seemingly incompatible biogeochemical processes due to variation in environmental factors that favor each process. We measured nutrient limitation and rates of N2 fixation and denitrification along transects in 5 wetland - stream - lake ecotones with different nutrient loading in Lakes Superior and Huron and hypothesized that rates of both processes would be related to nutrient limitation status, habitat type, and environmental characteristics including temperature, nutrient concentrations, and organic matter quality. This data package includes information on sampling sites, dates and locations; rates of N fixation and denitrification measured at each site, date and transect location; and biomass information from nutrient diffusing substrates deployed on the study transects. 

We hypothesized that environmental variation at the patch scale (1 - 10’s m) would facilitate the co-occurrence of N2 fixation and denitrification through the formation of hot spots in streams. We measured rates of N2 fixation and denitrification and relative abundances of the genes nifH and nirS in patches determined by channel geomorphic units and substrate type in 4 Idaho and 3 Michigan streams encompassing a gradient of N and P concentrations. This data package includes patch-level measurements of N2 fixation and denitrification rates, relative gene abundances of nifH and nirS, and environmental covariates (nutrient concentrations, water temperature, surface and subsurface dissolved oxygen concentrations, organic matter content) that were used to explore the factors that could predict process rates and relative gene abundances across patches and streams.