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

Hiromi Kato, Hiroshi Mori, Fumito Maruyama, Atsushi Toyoda, Kenshiro Oshima, Ryo Endo, Genki Fuchu, Masatoshi Miyakoshi, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Masahira Hattori, Asao Fujiyama, Ken Kurokawa, Masataka Tsuda

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)413-424
Number of pages12
JournalDNA Research
Volume22
Issue number6
DOIs
Publication statusPublished - 2015 Jun 17
Externally publishedYes

Fingerprint

Metagenomics
Microbiota
Soil
Burkholderia
Gene Pool
Environmental Biodegradation
Bacteriophages
Genes
Mycobacterium

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Kato, H., Mori, H., Maruyama, F., Toyoda, A., Oshima, K., Endo, R., ... Tsuda, M. (2015). Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Research, 22(6), 413-424. https://doi.org/10.1093/dnares/dsv023

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. / Kato, Hiromi; Mori, Hiroshi; Maruyama, Fumito; Toyoda, Atsushi; Oshima, Kenshiro; Endo, Ryo; Fuchu, Genki; Miyakoshi, Masatoshi; Dozono, Ayumi; Ohtsubo, Yoshiyuki; Nagata, Yuji; Hattori, Masahira; Fujiyama, Asao; Kurokawa, Ken; Tsuda, Masataka.

In: DNA Research, Vol. 22, No. 6, 17.06.2015, p. 413-424.

Research output: Contribution to journalArticle

Kato, H, Mori, H, Maruyama, F, Toyoda, A, Oshima, K, Endo, R, Fuchu, G, Miyakoshi, M, Dozono, A, Ohtsubo, Y, Nagata, Y, Hattori, M, Fujiyama, A, Kurokawa, K & Tsuda, M 2015, 'Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance', DNA Research, vol. 22, no. 6, pp. 413-424. https://doi.org/10.1093/dnares/dsv023
Kato, Hiromi ; Mori, Hiroshi ; Maruyama, Fumito ; Toyoda, Atsushi ; Oshima, Kenshiro ; Endo, Ryo ; Fuchu, Genki ; Miyakoshi, Masatoshi ; Dozono, Ayumi ; Ohtsubo, Yoshiyuki ; Nagata, Yuji ; Hattori, Masahira ; Fujiyama, Asao ; Kurokawa, Ken ; Tsuda, Masataka. / Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. In: DNA Research. 2015 ; Vol. 22, No. 6. pp. 413-424.
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