Comparison of rumen and manure microbiomes and implications for the inoculation of anaerobic digesters

Emine Gozde Ozbayram, Orhan Ince, Bahar Ince, Hauke Harms, Sabine Kleinsteuber*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

82 Citations (Scopus)

Abstract

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

Original languageEnglish
Article number15
JournalMicroorganisms
Volume6
Issue number1
DOIs
Publication statusPublished - 2018

Bibliographical note

Publisher Copyright:
© 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Funding

Acknowledgments: Emine Gozde Ozbayram was supported by the Research Fellowship Programme of the Scientific and Technological Research Council of Turkey (grant no. 2214A). The authors are grateful to Alexander Starke and Matthias Kaiser from the Veterinary Faculty of Leipzig University for providing access to fistulated cows and support in rumen and manure sampling. The authors also would like to acknowledge Ute Lohse (UFZ) for technical assistance in pyrosequencing and Denny Popp (UFZ) and Canan Karakoç (UFZ) for their valuable help in sequence data analysis.

FundersFunder number
Türkiye Bilimsel ve Teknolojik Araştirma Kurumu2214A

    Keywords

    • 16S rRNA gene
    • 454 amplicon sequencing
    • Anaerobic digestion
    • Bioaugmentation
    • Hydrolytic bacteria
    • McrA gene
    • Methanogenic archaea
    • Plant fiber fermentation
    • Ruminant microbiome

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