ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
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- Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins.Toxics · 2024Article
- Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture.Frontiers in microbiology · 2024Review
- Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Reconstruction of a Soil Microbial Network Induced by Stress Temperature.Microbiology spectrum · 2022Article
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- Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds.Frontiers in microbiology · 2020Article
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- Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-TolerantFrontiers in microbiology · 2019Article
- Latent environment allocation of microbial community data.PLoS computational biology · 2018Article
- The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.Frontiers in bioengineering and biotechnology · 2018Article
- 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.Frontiers in microbiology · 2018Article
- Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.Nucleic acids research · 2017Article
- Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics.Journal of environmental engineering (New York, N.Y.) · 2016Article
- Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales.Frontiers in microbiology · 2016Article
- Complete Genome Sequence of a Phenanthrene Degrader, Burkholderia sp. HB-1 (NBRC 110738).Genome announcements · 2015Article
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Soil microbial communities have great potential for bioremediation of recalcitrant aromatic compounds. However, it is unclear which taxa and genes in the communities, and how they contribute to the bioremediation in the polluted soils. To get clues about this fundamental question here, time-course (up to 24 weeks) metagenomic analysis of microbial community in a closed soil microcosm artificially polluted with four aromatic compounds, including phenanthrene, was conducted to investigate the changes in the community structures and gene pools. The pollution led to drastic changes in the community structures and the gene sets for pollutant degradation. Complete degradation of phenanthrene was strongly suggested to occur by the syntrophic metabolism by Mycobacterium and the most proliferating genus, Burkholderia. The community structure at Week 24 (∼12 weeks after disappearance of the pollutants) returned to the structure similar to that before pollution. Our time-course metagenomic analysis of phage genes strongly suggested the involvement of the 'kill-the-winner' phenomenon (i.e. phage predation of Burkholderia cells) for the returning of the microbial community structure. The pollution resulted in a decrease in taxonomic diversity and a drastic increase in diversity of gene pools in the communities, showing the functional redundancy and robustness of the communities against chemical disturbance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.