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

Abstract

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 its 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 NFixDB (Nitrogen Fixation DataBase), 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). NFixDB 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 NFixDB to nifH databases from Buckley, Zehr, Mise, and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains more than 4,000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB offers the first comprehensive nitrogenase database available to researchers.