ArticleDatabase : the journal of biological databases and curation2014
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed.
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- Nitrogen Fixation Associated withEnvironmental science & technology · 2026Article
- Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome.The New phytologist · 2026Article
- Long-Term Excess Nitrogen Fertilizer Reduces Sorghum Yield by Affecting Soil Bacterial Community.Plants (Basel, Switzerland) · 2025Article
- Experimental warming alters free-living nitrogen fixation in a humid tropical forest.The New phytologist · 2025Article
- Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions.Rice (New York, N.Y.) · 2025Article
- Diverse community of rhizobia-diatom symbioses fixes nitrogen in the South Pacific gyre.ISME communications · 2025Article
- NifFinder: improved Nif protein prediction using SWeeP vectors and neural networks.Bioinformatics advances · 2025Article
- Molecular characterization of heavy metal-tolerant bacteria and their potential for bioremediation and plant growth promotion.Frontiers in microbiology · 2025Article
- Introduction ofFrontiers in microbiology · 2025Article
- Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing SoilMicroorganisms · 2024Article
- Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.International journal of molecular sciences · 2024Review
- Enhancing soil health, microbial count, and hydrophilic methomyl and hydrophobic lambda-cyhalothrin remediation with biochar and nano-biochar.Scientific reports · 2024Article
- NFNAR genomics and bioinformatics · 2024Article
- Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.mSystems · 2024Article
- Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.PloS one · 2024Article
- Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.Frontiers in microbiology · 2024Article
- Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities.FEMS microbiology ecology · 2023Article
- Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series.Science advances · 2023Article
36 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.
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