title: Phylogenetic identification of methanogens assimilating acetate-derived carbon in dairy and swine manures.
abstract: In order to develop approaches for reducing the carbon footprint of the swine and dairy industries, it is important first to identify the methanogenic communities that drive methane emissions from stored manure. In this study, the metabolically active methanogens in substrate-starved manure samples taken from two dairy and one swine manure storage tanks were identified using [(13)C]-acetate and DNA stable-isotope probing (DNA-SIP). Molecular analysis of recovered genomic [(13)C]-DNA revealed that two distinct clusters of unclassified methanogen populations affiliated with the Methanoculleus genus, and the populations affiliated with Methanoculleus chikugoensis assimilated acetate-derived carbon (acetate-C) in swine and dairy starved manure samples, respectively. Furthermore, carbon flow calculations indicated that these populations were the primary contributors to methane emissions during these anoxic SIP incubations. Comparative analysis of mcrA gene abundance (coding for a key enzyme of methanogenesis) for Methanoculleus spp. in fresh feces and a wider range of stored dairy or swine manure samples, by real-time quantitative PCR using newly designed specific primers, demonstrated that the abundance of this genus significantly increased during storage. The findings supported the involvement of these particular methanogen populations as methane emitters from swine and dairy manure storage tanks. The study revealed that the ability to assimilate acetate-C for growth in manure differed within the Methanoculleus genus.
authors.affiliation: Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College, Sherbrooke, QC, Canada J1M 0C8.
authors.forename: Maialen
authors.initials: M
authors.lastname: Barret
authors.affiliation: Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College, Sherbrooke, QC, Canada J1M 0C8.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Gagnon
authors.affiliation: Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College, Sherbrooke, QC, Canada J1M 0C8.
authors.forename: Bruno
authors.initials: B
authors.lastname: Morissette
authors.affiliation: Atlantic Food and Horticulture Research Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada B4N 1J5.
authors.forename: Martin L
authors.initials: ML
authors.lastname: Kalmokoff
authors.affiliation: Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, Canada N5V 4T3.
authors.forename: Edward
authors.initials: E
authors.lastname: Topp
authors.affiliation: Bureau of Nutritional Sciences, Health Products and Foods Branch, Banting Research Centre, Ottawa, ON Canada K1A 0L2.
authors.forename: Stephen P J
authors.initials: SP
authors.lastname: Brooks
authors.affiliation: Bureau of Nutritional Sciences, Health Products and Foods Branch, Banting Research Centre, Ottawa, ON Canada K1A 0L2.
authors.forename: Fernando
authors.initials: F
authors.lastname: Matias
authors.affiliation: Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada N2L 3G1.
authors.forename: Josh D
authors.initials: JD
authors.lastname: Neufeld
authors.affiliation: Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College, Sherbrooke, QC, Canada J1M 0C8. Electronic address: Guylaine.Talbot@agr.gc.ca.
authors.forename: Guylaine
authors.initials: G
authors.lastname: Talbot
mesh_terms: D000085:Acetates / Q000378:metabolism*; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D002417:Cattle; D019605:Euryarchaeota / Q000201:enzymology / Q000235:genetics*; D018628:Gene Dosage; D005798:Genes, Bacterial; D007700:Kinetics; D008372:Manure / Q000382:microbiology*; D053858:Metabolic Networks and Pathways; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D034421:Sus scrofa
chemical_list: D000085:Acetates; D001426:Bacterial Proteins; D008372:Manure; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase
keywords: DNA stable-isotope probing; Methanoculleus spp.; Methanogenesis; Methyl coenzyme M reductase