ArticlePloS one2012
Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Article
- Different microbial communities in paddy soils under organic and nonorganic farming.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation.Scientific reports · 2022Article
- Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic.Environmental microbiome · 2022Article
- Factors Driving Bacterial Microbiota of Eggs from Commercial Hatcheries of European Seabass and Gilthead Seabream.Microorganisms · 2021Article
- A NewFrontiers in microbiology · 2021Article
- Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone.Frontiers in microbiology · 2021Article
- Biphenyl 2,3-Dioxygenase inFrontiers in microbiology · 2021Article
- Effect of Co-contamination by PAHs and Heavy Metals on Bacterial Communities of Diesel Contaminated Soils of South Shetland Islands, Antarctica.Microorganisms · 2020Article
- Rhizodegradation of PAHs differentially altered by C3 and C4 plants.Scientific reports · 2020Article
- Differences in microbiome and virome between cattle and horses in the same farm.Asian-Australasian journal of animal sciences · 2020Article
- Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens.mSystems · 2020Article
- Alterations in the Gut Microbiota of Zebrafish (Frontiers in public health · 2020Article
- Characterization of the Belowground Microbial Community in a Poplar-Phytoremediation Strategy of a Multi-Contaminated Soil.Frontiers in microbiology · 2020Article
- Inverted Regulation of Multidrug Efflux Pumps, Acid Resistance, and Porins in Benzoate-Evolved Escherichia coli K-12.Applied and environmental microbiology · 2019Article
- Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.The ISME journal · 2019Article
- Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil.Scientific reports · 2019Article
- Comparative Genomics ofFrontiers in microbiology · 2019Article
- Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier.Frontiers in microbiology · 2017Article
- Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.International journal of molecular sciences · 2016Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. In order to avoid biases of culture-based approaches, stable isotope probing was applied in combination with sequence analysis of 16 S rRNA gene pyrotags amplified from (13)C-enriched DNA fractions. Special attention was paid to pyrosequencing data analysis in order to eliminate the errors caused by either generation of amplicons (random errors caused by DNA polymerase, formation of chimeric sequences) or sequencing itself. Therefore, sample DNA was amplified, sequenced, and analyzed along with the DNA of a mock community constructed out of 8 bacterial strains. This warranted that appropriate tools and parameters were chosen for sequence data processing. (13)C-labeled metagenomes isolated after the incubation of soil samples with all three studied aromatics were largely dominated by Proteobacteria, namely sequences clustering with the genera Rhodanobacter Burkholderia, Pandoraea, Dyella as well as some Rudaea- and Skermanella-related ones. Pseudomonads were mostly labeled by (13)C from naphthalene and benzoate. The results of this study show that many biphenyl/benzoate-assimilating bacteria derive carbon also from naphthalene, pointing out broader biodegradation abilities of some soil microbiota. The results also demonstrate that, in addition to traditionally isolated genera of degradative bacteria, yet-to-be cultured bacteria are important players in bioremediation. Overall, the study contributes to our understanding of biodegradation processes in contaminated soil. At the same time our results show the importance of sequencing and analyzing a mock community in order to more correctly process and analyze sequence data.
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