ArticleBMC genomics2016
Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Distinct Denitrification Phenotypes in Closely Related Bacteria: Clues to Understanding Variations in Nitrite Accumulation Among Stutzerimonas Strains.Environmental microbiology · 2026Article
- AMicrobial genomics · 2026Article
- Niche adaptation of particle-associated ammonia-oxidizing archaea sustains nitrification under marine deoxygenation.Frontiers in microbiology · 2026Article
- Gene-Level Shift in Response to Synthetic Nitrogen Addition PromotesLife (Basel, Switzerland) · 2025Article
- Transcriptional Difference of Deep-Sea Microorganisms under Different Sampling Methods.Environmental science & technology · 2025Article
- Aquatic copper-containing nitrite reductase gene (Frontiers in microbiology · 2025Article
- Bacterial community composition and function in different habitats in Antarctic Fildes region revealed by high-throughput sequencing.Frontiers in microbiology · 2025Article
- The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.Frontiers in microbiology · 2024Article
- "Applied and environmental microbiology · 2023Article
- Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils.Microbiology spectrum · 2023Article
- Denitrification in hypersaline and coastal environments.FEMS microbiology letters · 2023Article
- In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.Environmental microbiome · 2022Article
- Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of NThe ISME journal · 2022Article
- Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece.Frontiers in microbiology · 2022Article
- Article
- Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters.The ISME journal · 2021Article
- Article
- The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks.Environmental science and pollution research international · 2020Review
- Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.Microbial ecology · 2020Article
- Genomic Insights of "Frontiers in microbiology · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset.
resultsDivision of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3' site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67% of all NirK-type denitrifiers.
conclusionThe previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome.
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