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J Gen Appl Microbiol. 2019 Mar 8. doi: 10.2323/jgam.2018.10.003. [Epub ahead of print]

Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis.

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Life Sciences and Bioengineering, Graduate School of Life and Environmental Science, University of Tsukuba.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
National Institute of Technology and Evaluation (NITE).
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
Department of Bioengineering, Nagaoka University of Technology.
Taisei Corporation.
Biotechnology Research Center, The University of Tokyo.


Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.


Rhodococcus jostii RHA1; bioremediation; chlorinated ethylenes; metagenomics; metatranscriptomics; next-generation sequencing

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