1887

Abstract

Structures of free-living and protozoa-associated methanogen (PAM) communities from forage-fed cattle were investigated by comparative sequence analysis of 16S rRNA and methyl coenzyme M reductase () gene clone libraries. The free-living and protozoa-associated communities were composed of the same three genera [namely , and rumen cluster C (RCC), which is distantly related to ]; however, the distribution of the methanogen genera differed between the two communities. Despite previous reports of potential bias for the degenerate primer set, the 16S rRNA ( = 100 clones) and ( = 92 clones) gene libraries exhibited a similar distribution pattern for the three methanogenic genera. RCC was more abundant in the free-living community and represented 72 and 42 % of the 16S rRNA and gene sequences, respectively, versus 54 and 13 % of the 16S rRNA and gene sequences from the PAM community, respectively. The majority of RCC sequences from the free-living and protozoa-associated communities belonged to different species-level operational taxonomic units. species were more abundant in the PAM community and represented 42 and 79 % of clones for the 16S rRNA and gene libraries, respectively, versus 9 and 27 % of 16S rRNA and gene clones from the free-living community, respectively. species were predominantly free-living. Primers for quantitative PCR were designed to target specific methanogen groups and used to assess the effect of a high-grain diet on methanogen species composition. Switching the ruminant diet from forage to high-grain resulted in reduced protozoal diversity, along with a profound overall reduction in the relative abundance of RCC and an increase in the relative abundance of free-living spp. It was unclear whether the reduced abundance of RCC in grain-fed animals was due to the loss of symbiotic protozoa species or due to broader changes in the rumen environment that affected both RCC and protozoa. Importantly, results from this study emphasize the need to consider the different methanogen communities when developing strategies for mitigating methane emissions in ruminants.

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2012-07-01
2020-07-12
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