Exploring rumen methanogen genomes to identify targets for methane mitigation strategies

Methane emissions from ruminant livestock is generated by the action of methanogenic archaea, mainly in the rumen. A variety of methanogen genera are responsible for CH4 production, including a large group that lacks cultivated representatives. To be generally effective, technologies for reducing ruminant CH4 emissions must target all rumen methanogens to prevent any unaffected methanogen from expanding to occupy the vacated niche. Interventions must also be specific for methanogens so that other rumen microbes can continue normal digestive functions. Thus a detailed knowledge of the diversity and physiology of rumen methanogens is required to define conserved features that can be targeted for methanogen inhibition. Genome sequencing projects are underway in New Zealand and Australia on several ruminal methanogen groups, including representatives of the genera Methanobrevibacter, Methanobacterium, Methanosphaera, Methanosarcina, and the uncultured group, Rumen Cluster C. The completed Methanobrevibacter ruminantium genome and draft sequences from other rumen methanogen species are beginning to allow identification of underlying cellular processes that define these organisms, and is leading to a better understanding of their lifestyles within the rumen. Although the research is mainly at the explorative stage, two types of opportunities for inhibiting methanogens are emerging, being inactivation of conserved methanogen enzymes by screening for, or designing, small inhibitors via a chemogenomics approach, and identifying surface proteins shared among rumen methanogens that can be used as antigens in an anti-methanogen vaccine. Many of the conserved enzyme targets are involved in energy generation via the methanogenesis pathway, while the majority of the conserved surface protein targets are of unknown function. An understanding of the expression and accessibility of these targets within methanogen cells and/or microbial biofilms under ruminal conditions will be required for their development as CH4 production mitigations. This paper is part of the special issue entitled: Greenhouse Gases in Animal Agriculture – Finding a Balance Between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors: K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson