ArticleBMC genomics2025
Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Genomic and secondary metabolites of the marine cyanobacterium Capilliphycus salinus ALCB114379.Journal of phycology · 2026Article
- A 'Genome-First' Framework for Next-Generation Bioinputs: From Functional Mining to Rational Synthetic Microbial Communities.Environmental microbiology · 2026Review
- Isolation of N-Fixing Bacteria from Warm-Season Pasture Grasses and the Evaluation of Nitrogen Effects on the Bacterial Communities Present inMicroorganisms · 2026Article
- Metabolic potential structures gill symbiont communities in two common shipworm species.The ISME journal · 2026Article
- Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats.ISME communications · 2026Article
- Article
- Nitrogen-fixing microbes gain genes in diverse types of living environments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Supplementation with Mo, Co, and Ni Enhances the Effectiveness of Co-Inoculation with the RhizobacteriaMicroorganisms · 2025Article
- Nitrogen-fixing Ability of a Thermophilic Sulfate-reducing Bacterium in the Genus Thermodesulfovibrio Isolated from a Terrestrial Hot Spring in Japan.Microbes and environments · 2025Article
- NifFinder: improved Nif protein prediction using SWeeP vectors and neural networks.Bioinformatics advances · 2025Article
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Abstract
backgroundDiazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.
resultsIn a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS³G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k = 10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.
conclusionsThis study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N₂-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.
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