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Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing

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Abstract

The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHDα gene detected in the heavy DNA fraction of 13C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of 13C-PHE treatment and lack of PAH-RHDα gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.

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Acknowledgements

Financial support was provided by the National Natural Science Foundation of China (Nos. 41673111 & 41603072) and the Scientific and Technological Planning Project of Guangzhou, China (Nos. 201707020034 & 201510010038).

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Authors and Affiliations

  1. Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China

    Jibing Li, Longfei Jiang, Chunling Luo & Gan Zhang

  2. University of Chinese Academy of Sciences, Bei**g, 100039, China

    Jibing Li

  3. School of Environment, Tsinghua University, Bei**g, 100084, China

    Dayi Zhang

  4. Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK

    Dayi Zhang

  5. College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China

    Mengke Song & Chunling Luo

  6. School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China

    Yujie Wang

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Correspondence to Chunling Luo.

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Li, J., Zhang, D., Song, M. et al. Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing. Biodegradation 28, 423–436 (2017). https://doi.org/10.1007/s10532-017-9806-9

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