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Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase () is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase () and (iii) iron nitrogenase (). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (, , ) and nitrogenase-like enzymes (e.g. ) linked to ribosomal RNA operons (16S-5S-23S). NFDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFDB to databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of , in addition to and . NFDB contains >4000 verified sequences contained on 50 unique phyla of bacteria and archaea. NFDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155484 | PMC |
| http://dx.doi.org/10.1093/nargab/lqae063 | DOI Listing |
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