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FEMS Microbiol Ecol. 2015 Apr;91(4). pii: fiv028. doi: 10.1093/femsec/fiv028. Epub 2015 Mar 19.

Monitoring the dynamics of syntrophic β-oxidizing bacteria during anaerobic degradation of oleic acid by quantitative PCR.

Author information

1
Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98195, USA ziels@uw.edu.
2
eScience Institute, University of Washington, Box 355014, Seattle, WA 98195, USA Department of Chemical Engineering, University of Washington, Box 355014, Seattle, WA 98195, USA.
3
Department of Thematic Studies-Environmental Change, Linköping University, SE-581 83 Linköping, Sweden.
4
Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98195, USA.

Abstract

The ecophysiology of long-chain fatty acid-degrading syntrophic β-oxidizing bacteria has been poorly understood due to a lack of quantitative abundance data. Here, TaqMan quantitative PCR (qPCR) assays targeting the 16S rRNA gene of the known mesophilic syntrophic β-oxidizing bacterial genera Syntrophomonas and Syntrophus were developed and validated. Microbial community dynamics were followed using qPCR and Illumina-based high-throughput amplicon sequencing in triplicate methanogenic bioreactors subjected to five consecutive batch feedings of oleic acid. With repeated oleic acid feeding, the initial specific methane production rate significantly increased along with the relative abundances of Syntrophomonas and methanogenic archaea in the bioreactor communities. The novel qPCR assays showed that Syntrophomonas increased from 7 to 31% of the bacterial community 16S rRNA gene concentration, whereas that of Syntrophus decreased from 0.02 to less than 0.005%. High-throughput amplicon sequencing also revealed that Syntrophomonas became the dominant genus within the bioreactor microbiomes. These results suggest that increased specific mineralization rates of oleic acid were attributed to quantitative shifts within the microbial communities toward higher abundances of syntrophic β-oxidizing bacteria and methanogenic archaea. The novel qPCR assays targeting syntrophic β-oxidizing bacteria may thus serve as monitoring tools to indicate the fatty acid β-oxidization potential of anaerobic digester communities.

KEYWORDS:

Syntrophomonas; Syntrophus; anaerobic digestion; high-throughput sequencing; long-chain fatty acids (LCFA); methanogenesis; quantitative PCR (qPCR); syntrophy; β-oxidization

PMID:
25873606
DOI:
10.1093/femsec/fiv028
[Indexed for MEDLINE]

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