NFixDB (Nitrogen Fixation DataBase) - A Comprehensive Integrated Database for Robust ‘Omics Analysis of Diazotrophs

Biological nitrogen fixation is a fundamental biogeochemical process that transforms that provides fixed biologically available nitrogen by diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which has three different gene clusters: 1) molybdenum nitrogenase ( nifDHK ) is the most abundant, followed by it’s alternatives 2) vanadium nitrogenase ( vnfDHK ), and 3) iron nitrogenase ( anfDHK ). 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 NF ix DB ( N itrogen Fix ation D ata B ase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases ( nifDHK , vnfDHK , anfDHK ) and nitrogenase-like enzymes (e.g., nflDH ) linked to ribosomal operons (16S-5.8S-23S). NF ix DB 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 operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NF ix DB to nifH databases from Buckley, Zehr, Mise, and FunGene finding extensive evidence of nifH , in addition to vnfH and nflH . NF ix DB contains more than 4,000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NF ix DB offers the first comprehensive nitrogenase database available to researchers.