ArticleScientific reports2016
Design and evaluation of primers targeting genes encoding NO-forming nitrite reductases: implications for ecological inference of denitrifying communities.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 41 citations in OpenAlex.
- Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.ISME communications · 2025Article
- Aquatic copper-containing nitrite reductase gene (Frontiers in microbiology · 2025Article
- Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles.ISME communications · 2024Article
- Resistance and Resilience of Soil Nitrogen Cycling to Drought and Heat Stress in Rehabilitated Urban Soils.Frontiers in microbiology · 2021Article
- Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes.Microbial ecology · 2020Article
- Habitat diversity and type govern potential nitrogen loss by denitrification in coastal sediments and differences in ecosystem-level diversities of disparate N2O reducing communities.FEMS microbiology ecology · 2020Article
- The Structure and Diversity of Nitrogen Functional Groups from Different Cropping Systems in Yellow River Delta.Microorganisms · 2020Article
- Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types.Microbes and environments · 2020Article
- Denitrification Aligns with NScientific reports · 2019Article
- Diversity of tryptophan halogenases in sponges of the genus Aplysina.FEMS microbiology ecology · 2019Article
- Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils.Scientific reports · 2018Article
- Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase GenesApplied and environmental microbiology · 2018Article
- Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell.Frontiers in microbiology · 2018Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detection of NO-forming nitrite reductase genes (nir) has become the standard when studying denitrifying communities in the environment, despite well-known amplification biases in available primers. We review the performance of 35 published and 121 newly designed primers targeting the nirS and nirK genes, against sequences from complete genomes and 47 metagenomes from three major habitats where denitrification is important. There were no optimal universal primer pairs for either gene, although published primers targeting nirS displayed up to 75% coverage. The alternative is clade-specific primers, which show a trade-off between coverage and specificity. The test against metagenomic datasets showed a distinct performance of primers across habitats. The implications of clade-specific nir primers choice and their performance for ecological inference when used for quantitative estimates and in sequenced-based community ecology studies are discussed and our phylogenomic primer evaluation can be used as a reference along with their environmental specificity as a guide for primer selection. Based on our results, we also propose a general framework for primer evaluation that emphasizes the testing of coverage and phylogenetic range using full-length sequences from complete genomes, as well as accounting for environmental range using metagenomes. This framework serves as a guideline to simplify primer performance comparisons while explicitly addressing the limitations and biases of the primers evaluated.
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