The molecular dynamics of core genes mount the relationship between groups of diazotrophs

Abstract

Abstract Background: Biological Nitrogen Fixation (BNF) occurs in diazotroph Archaea and Bacteria through the action of the Nitrogenase Enzymatic Complex (NEC) of nitrogenase-dependent molybdenum (Mo-nitrogenase) encoded by the nif genes. Due to several factors, for example, Horizontal Gene Transfer (HGT) and gene duplications, these genes are distributed in great diversity becoming complex to relate groups and to find in silico potential diazotrophs. Raymond et al. in 2004 and Dos Santos et al. in 2012 proposed the Mo-nitrogenase classification and established the minimum Nif set in NifH, NifD, NifK, NifE, NifN and NifB, respectively, directing the field in the classification and prediction of N2-fixing organisms. Here, we proposed to build potential groups of diazotrophs with the minimum cluster (core) of Mo-nitrogenase, evaluating whether the inheritance of Mo-nitrogenase is related to the acquisition, subtraction, or replacement of accessory nif and the impacts of these relationships on the maintenance of NEC. Results: We obtained 662 diazotrophic genomes which 52 belong to potential diazotroph species within the nif core. We identified genomic duplication of nif core in Aulosira laxa NIES-50, Azoarcus sp KH32C, Calothrix brevissima NIES-22, Nostoc carneum NIES -2107, Tolypothrix tenuis PCC 7101 and Trichormus variabilis ATCC 29413 suggesting the existence of more than one nif cluster in these species probably related with the different acquisition of Mo-nitrogenase clusters. The SWeeP method applied to the vectorial projection of diazotrophic genomes was crucial to make possible the classification of these 662 genomes into 10 consistent groups. Conclusions: We suggest the classification of Mo-nitrogenase in a context more involved with molecular dynamics in relation to the proposal in Raymond et al. This fact is reinforced because we observed a significant relationship between the groups obtained with molecular composition of nif genes, such as in Azoarcus spp, Azospira spp., gram-positive and some cyanobacteria species. We hope the findings are helpful to understand the molecular BNF evolution.