Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
- Weibing Shi1,2,
- Christina D. Moon3,
- Sinead C. Leahy3,
- Dongwan Kang1,2,
- Jeff Froula1,2,
- Sandra Kittelmann3,
- Christina Fan1,2,
- Samuel Deutsch1,2,
- Dragana Gagic3,
- Henning Seedorf3,
- William J. Kelly3,
- Renee Atua3,
- Carrie Sang3,
- Priya Soni3,
- Dong Li3,
- Cesar S. Pinares-Patiño3,
- John C. McEwan3,
- Peter H. Janssen3,
- Feng Chen1,2,
- Axel Visel1,2,4,
- Zhong Wang1,2,4,
- Graeme T. Attwood3 and
- Edward M. Rubin1,2
- 1Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA;
- 2Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
- 3AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
- 4School of Natural Sciences, University of California, Merced, California 95343, USA
- Corresponding author: emrubin{at}lbl.gov
Abstract
Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.168245.113.
- Received October 11, 2013.
- Accepted May 13, 2014.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
