Rumen microbial community analysis and methanogenesis during adaptation to monensi

The aim of this study was to characterize the adaptation of rumen microbial populations and methane emissions to ionophores when fed to cattle over a 12 wk period. Methane emissions from ruminants contribute approximately 90% of the greenhouse gas emissions from animal agriculture (Kebreab et al. 2006). The gram-positive specific ionophore antibiotic, monensin, may lower methane production in the rumen, however the effects appear to be short term (weeks) and there is a rebound effect in which emissions return to baseline levels. We hypothesized that gram-positive bacteria, but not methanogenic archaea, adapt to monensin and that the methane emission rebound can largely be explained by adaptation of gram-positive hydrogen producing bacteria. Rumen samples were taken weekly for 12 wk from cattle fed either a high grain or a high forage diet with or without monensin (Gunn et al. 2006). Methane emissions were simultaneously measured. Microbial populations were characterized using terminal restriction fragment length polymorphisms (TRFLP) analysis. Key microbial species were quantified with real-time PCR (RT-PCR). TRFLP indicated that at the phylum level community structure was relatively stable showing no statistical difference (P < 0.05) between treatment or diet as well as no difference over time. There was a noticeable prevalence of members of the phylum Verrucomicrobia. No members of this phylum have been cultured from the rumen but may be involved in polysaccharide degradation or anaerobic methane oxidation. RT-PCR indicated that adaptation occurred partly within the hydrogen producing gram-positive bacteria on the concentrate diet and the effects on methanogens were strongly correlated with these population shifts. In the forage diet the adaptation to ionophores also occurred but modulation of gram-positive bacteria appeared to be much more subtle. The methanogenic archaea were not directly affected by monensin, the observed abundance changes were related to the decrease in the abundance of ciliate protozoa and the available hydrogen in the rumen. Methane emissions returned to baseline levels two wk earlier in grain than forage diets and this is likely the result of higher turnover rates in grain based rations. A low correlation between methane levels and temperature showed that the influence of temperature on the data was not large but could not exclude it.