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Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

1
Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey
2
Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
3
Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
*
Author to whom correspondence should be addressed.
Microorganisms 2018, 6(1), 15; https://doi.org/10.3390/microorganisms6010015
Received: 8 December 2017 / Revised: 1 February 2018 / Accepted: 12 February 2018 / Published: 14 February 2018
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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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. View Full-Text
Keywords: ruminant microbiome; plant fiber fermentation; anaerobic digestion; bioaugmentation; hydrolytic bacteria; methanogenic archaea; mcrA gene; 16S rRNA gene; 454 amplicon sequencing ruminant microbiome; plant fiber fermentation; anaerobic digestion; bioaugmentation; hydrolytic bacteria; methanogenic archaea; mcrA gene; 16S rRNA gene; 454 amplicon sequencing
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Ozbayram, E.G.; Ince, O.; Ince, B.; Harms, H.; Kleinsteuber, S. Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters. Microorganisms 2018, 6, 15.

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