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DNA Res. 2015 Dec;22(6):413-24. doi: 10.1093/dnares/dsv023. Epub 2015 Oct 1.

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance.

Author information

1
Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan.
2
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Tokyo 152-8550, Japan.
3
Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
4
Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan.
5
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan.
6
Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan Principles of Informatics Research Division, National Institute of Informatics, Hitotsubashi, Tokyo 101-8430, Japan.
7
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Tokyo 152-8550, Japan Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Tokyo 152-8550, Japan.
8
Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan mtsuda@ige.tohoku.ac.jp.

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.

KEYWORDS:

metagenome; phage; recalcitrant aromatic compounds; robustness; soil microbiome

PMID:
26428854
PMCID:
PMC4675710
DOI:
10.1093/dnares/dsv023
[Indexed for MEDLINE]
Free PMC Article

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