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Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters

  • Environmental biotechnology
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Abstract

Droplet digital PCR (ddPCR) is a new DNA quantification platform without an external DNA calibrator. This study examined methanogen communities in four full-scale anaerobic digesters treating municipal sewage sludge, using ddPCR with taxon-specific primer/TaqMan probe sets (5 orders, 11 families, and 13 genera), many of which were developed in this study. Total methanogen abundance was positively correlated with hydraulic retention time (HRT) and temperature (p < 0.05), though the effect of HRT was stronger (r = 0.864 vs. 0.682, respectively). Moreover, total abundance was strongly correlated with biogas production rate (r = 0.896). HRT was positively correlated with seven methanogenic taxa, while temperature was positively or negatively correlated with 13 taxa (p < 0.05). For instance, the predominant genera Methanosaeta and Methanosarcina were negatively and positively associated, respectively, with temperature only (p < 0.05). Redundancy analysis and principal component analysis using the absolute-abundance dataset indicated that only temperature explained the variability in the methanogen communities at all classification levels. Therefore, HRT was the most important operational factor to influence net methanogen abundance and activity, while temperature governed the composition of the methanogen community. ddPCR enabled absolute quantification of methanogens without the external DNA standards and linked methanogen communities and operational factors, suggesting that it is a promising tool for analyzing the microbial ecology of anaerobic digestion.

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Acknowledgments

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (NRF-2012R1A2A2A03046724).

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The authors declare that they have no conflict of interest.

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  1. Department of Environmental Science and Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 120-750, Republic of Korea

    Tae Gwan Kim, So-Yeon Jeong & Kyung-Suk Cho

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  1. Tae Gwan Kim
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  2. So-Yeon Jeong
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Correspondence to Kyung-Suk Cho.

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Kim, T.G., Jeong, SY. & Cho, KS. Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters. Appl Microbiol Biotechnol 99, 445–458 (2015). https://doi.org/10.1007/s00253-014-6007-x

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  • DOI: https://doi.org/10.1007/s00253-014-6007-x

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