ArticleApplied and environmental microbiology2010
Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil.
Article in Applied and environmental microbiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 62 citations in OpenAlex.
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- Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments.Microorganisms · 2020Article
- Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition.Applied and environmental microbiology · 2019Article
- Metagenomic Approaches for Understanding New Concepts in Microbial Science.International journal of genomics · 2018Review
- Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.Applied and environmental microbiology · 2017Article
- AcidotolerantFrontiers in microbiology · 2017Article
- Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen.Frontiers in microbiology · 2016Article
- Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.Frontiers in microbiology · 2015Review
- Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening.Microbial biotechnology · 2015Review
- Denitrification activity of a remarkably diverse fen denitrifier community in finnish lapland is N-oxide limited.PloS one · 2015Article
- Article
- A fragrant neighborhood: volatile mediated bacterial interactions in soil.Frontiers in microbiology · 2015Article
- Efficient PCR-based amplification of diverse alcohol dehydrogenase genes from metagenomes for improving biocatalysis: screening of gene-specific amplicons from metagenomes.Applied and environmental microbiology · 2014Article
- Actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in N2O-metabolizing palsa peat.Applied and environmental microbiology · 2012Article
- Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra.The ISME journal · 2012Article
- Biocatalysts and small molecule products from metagenomic studies.Current opinion in chemical biology · 2012Review
- Emission of methane by Eudrilus eugeniae and other earthworms from Brazil.Applied and environmental microbiology · 2012Article
- The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders.The ISME journal · 2011Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phenoxyalkanoic acid (PAA) herbicides are widely used in agriculture. Biotic degradation of such herbicides occurs in soils and is initiated by alpha-ketoglutarate- and Fe2+-dependent dioxygenases encoded by tfdA-like genes (i.e., tfdA and tfdAalpha). Novel primers and quantitative kinetic PCR (qPCR) assays were developed to analyze the diversity and abundance of tfdA-like genes in soil. Five primer sets targeting tfdA-like genes were designed and evaluated. Primer sets 3 to 5 specifically amplified tfdA-like genes from soil, and a total of 437 sequences were retrieved. Coverages of gene libraries were 62 to 100%, up to 122 genotypes were detected, and up to 389 genotypes were predicted to occur in the gene libraries as indicated by the richness estimator Chao1. Phylogenetic analysis of in silico-translated tfdA-like genes indicated that soil tfdA-like genes were related to those of group 2 and 3 Bradyrhizobium spp., Sphingomonas spp., and uncultured soil bacteria. Soil-derived tfdA-like genes were assigned to 11 clusters, 4 of which were composed of novel sequences from this study, indicating that soil harbors novel and diverse tfdA-like genes. Correlation analysis of 16S rRNA and tfdA-like gene similarity indicated that any two bacteria with D>20% of group 2 tfdA-like gene-derived protein sequences belong to different species. Thus, data indicate that the soil analyzed harbors at least 48 novel bacterial species containing group 2 tfdA-like genes. Novel qPCR assays were established to quantify such new tfdA-like genes. Copy numbers of tfdA-like genes were 1.0x10(6) to 65x10(6) per gram (dry weight) soil in four different soils, indicating that hitherto-unknown, diverse tfdA-like genes are abundant in soils.
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