ArticleApplied and environmental microbiology2014
Refined NrfA phylogeny improves PCR-based nrfA gene detection.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 206 citations in OpenAlex.
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- Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition.Journal of microbiology (Seoul, Korea) · 2025Article
- Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification.The ISME journal · 2025Article
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- Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela.FEMS microbiology letters · 2024Article
- Spatiotemporal patterns and co-occurrence patterns of dissimilatory nitrate reduction to ammonium community in sediments of the Lancang River cascade reservoirs.Frontiers in microbiology · 2024Article
- Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.Nature communications · 2023Article
- Integrative knowledge-based nitrogen management practices can provide positive effects on ecosystem nitrogen retention.Nature food · 2023Article
- Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia.The ISME journal · 2023Article
- Pangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal.Archives of microbiology · 2023Article
- Nitrogen removal in freshwater sediments of riparian zone: N-loss pathways and environmental controls.Frontiers in microbiology · 2023Article
- In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary.Ecosphere (Washington, D.C) · 2022Article
- Effects of sulphur amino acids on the size and structure of microbial communities of aerobic granular sludge bioreactors.Amino acids · 2022Article
- Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method.mSphere · 2022Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new nrfA-containing isolates. nrfA amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
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