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Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters

  • Environmental biotechnology
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Abstract

While the use of anaerobic digestion to generate methane as a source of bioenergy is increasing worldwide, our knowledge of the microbial communities that perform biomethanation is very limited. Using next-generation sequencing, bacterial population profiles were determined in three full-scale mesophilic anaerobic digesters operated on dairy farms in the state of Vermont (USA). To our knowledge, this is the first report of a metagenomic analysis on the bacterial population of anaerobic digesters using dairy manure as their main substrate. A total of 20,366 non-chimeric sequence reads, covering the V1-V2 hypervariable regions of the bacterial 16S rRNA gene, were assigned to 2,176 operational taxonomic units (OTUs) at a genetic distance cutoff value of 5 %. Based on their limited sequence identity to validly characterized species, the majority of OTUs identified in our study likely represented novel bacterial species. Using a naïve Bayesian classifier, 1,624 anaerobic digester OTUs could be assigned to 16 bacterial phyla, while 552 OTUs could not be classified and may belong to novel bacterial taxonomic groups that have yet to be described. Firmicutes, Bacteroidetes, and Chloroflexi were the most highly represented bacteria overall, with Bacteroidetes and Chloroflexi showing the least and the most variation in abundance between digesters, respectively. All digesters shared 132 OTUs, which as a “core” group represented 65.4 to 70.6 % of sequences in individual digesters. Our results show that bacterial populations from microbial communities of anaerobic manure digesters can display high levels of diversity despite sharing a common core substrate.

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Acknowledgments

Funding for this project was provided through a VT-REAP grant from the Vermont Agency of Agriculture, Food and Markets. The authors would also like to thank the Vermont dairy farm owners involved in this study for their collaboration: Eugene and Marie Audet (Blue Spruce Farms), Brian and Bill Rowell (Green Mountain Dairy), as well as Reg and Mike Chaput (Chaput Family Farms).

Conflict of interest

The authors declare that they have no conflict of interest.

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  1. Department of Animal Science, The University of Vermont, 570 Main Street, Burlington, VT, 05405, USA

    Benoit St-Pierre & André-Denis G. Wright

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  1. Benoit St-Pierre
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  2. André-Denis G. Wright
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Correspondence to André-Denis G. Wright.

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St-Pierre, B., Wright, AD.G. Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters. Appl Microbiol Biotechnol 98, 2709–2717 (2014). https://doi.org/10.1007/s00253-013-5220-3

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  • DOI: https://doi.org/10.1007/s00253-013-5220-3

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