Investigation of rumen methanogens in New Zealand livestock : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand.
Methane emitted by farmed ruminants contributes 30.3% to New Zealand’s anthropogenic greenhouse gas inventory. Methanogens living in the rumen produce methane from H2 and CO2 as a byproduct of feed fermentation. The use of vaccines and small molecule inhibitors against the methanogens are promising methods to reduce methane emissions from extensively-grazed ruminants in New Zealand. Knowledge of the methanogens present in New Zealand ruminants is an important first step for successful vaccine and inhibitor development to target all methanogens.
In this study, the methanogen diversity of farmed ruminants (sheep [Ovis aries], cattle [Bos taurus] and red deer [Cervus elaphus]) was investigated using molecular ecological techniques. Ruminants fed different diets had largely similar rumen methanogen communities. The major methanogen groups identified were from the Methanobrevibacter ruminantium clade (Mbb. ruminantium and closely-related species), Methanobrevibacter gottschalkii clade (Mbb. gottschalkii and closely-related species), Methanosphaera spp., and the putative methanogens belonging to the group designated Rumen Cluster C. A total of 37.5 - 57% of 16S rRNA genes in the rumen of a group of cows originated from members of Rumen Cluster C. Chloroform treatment of cows increased the abundance of Rumen Cluster C to 82% - 93% of archaeal 16S rRNA genes. In parallel, a total of 22% of mcrA genes belonged to an unassigned group of archaea, and chloroform treatment increased the unassigned group of archaea to 92% of all mcrA genes. This suggested that Rumen Cluster C archaea contain the gene mcrA.
No members of the Rumen Cluster C group have previously been cultured, and currently there is no reported rumen isolate of Methanosphaera spp. A strain of Methanosphaera sp. was isolated from a sheep rumen and initial characterization suggests that this may be a new species. Three enrichment cultures were obtained containing members of Rumen Cluster C as the only archaea. Initial studies of these enrichment cultures showed that these three isolates were from three different sub-groups of Rumen Cluster C and that they produced methane.
The investigation of methanogen diversity in New Zealand farmed ruminants and isolation of previously uncultured rumen methanogens reported here in this thesis will significantly aid the development of methane reduction strategies for farmed ruminants in New Zealand.