Structure of the Archaeal Community of the Rumen

Abstract

Members of the domain Archaea contribute about 0.3 to 3.3% of the microbial small subunit (16S and 18S) rRNA in the rumen (22,39,60). Archaea have a range of different metabolisms and are found in many habitats (6), but those known to exist in the rumen are strictly anaerobic methanogens. Yanagita et al. (59) observed that 2.8 to 4.0% of ruminal microorganisms displayed autofluorescence characteristic of F 420 , a methanogen cofactor, able to be seen under UV illumination during microscopy. Taken together with the small subunit rRNA abundance data, this suggests that a large part of the archaeal population is made up of methanogens. Most species of methanogens can grow using H 2 and often formate as their energy sources and use the electrons derived from H 2 (or formate) to reduce CO 2 to CH 4 . Some species can grow with methyl groups, oxidizing some to CO 2 to produce electrons that are used to reduce further methyl groups to methane. A few species can grow with acetate, effectively dissimilating acetate to CH 4 and CO 2 . However, acetate is not metabolized to CH 4 to any significant extent in the rumen (13). This is probably because the rate of passage of rumen contents through the rumen is greater than the growth rate of acetateutilizing methanogens (53).In a normally functioning rumen, proteins and polymeric carbohydrates, which usually make up the largest part of the incoming feed, are fermented by a mixed microbial community to volatile fatty acids (VFAs), NH 4 ϩ , CO 2 , and H 2 . The hydrogen is metabolized by the methanogens. The VFAs are taken up by the animal across the rumen wall and serve as major carbon and energy sources for the ruminant. A part of the VFAs, undigested feed components, and microbial cells leave the rumen and enter the rest of the animal's digestive tract. The central role of H 2 in the rumen fermentation (12) means that, although methanogenic archaea make up only a small part of the rumen microbial biomass, they play an important role in rumen function and animal nutrition. Efficient H 2 removal leads to a nutritionally more favorable pattern of VFA formation and to an increased rate of fermentation by eliminating the inhibitory effect of H 2 on the microbial fermentation (26, 53).The rumen can be simplistically described as an open system with discontinuous solid (feed) and liquid (saliva and drinking water) inputs and multiple fractions that have different turnover rates (53). The methanogens in the rumen are found free in the rumen fluid, attached to particulate material and rumen protozoa, associated as endosymbionts within rumen protozoa, and attached to the rumen epithelium. The methanogens associated with these different fractions can be expected to have different growth rates since they will be removed from the rumen at different rates. In addition, the animal itself and the feed also influence the rate of passage of digesta through the rumen system (25). These different habitats may allow niche division among the methanogens and may explain some of the observed phyloge...

Erratum: Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

“…Scaling these numbers according to average genome sizes using sequenced organisms from these groups actually increases this trend (Supplementary Table S3; Figure 5). However our estimates of the proportion of archaeal genes in the rumen metagenome from Methanobrevibacter (76.47%) and the relative proportions of genes from the major groups of bacteria are similar to those that were previously reported (Janssen and Kirs, 2008;Creevey et al, 2014), suggesting no sampling bias.…”

“…However if only those genera with a minimum four genes identified are considered, then 127 bacterial and 20 archaeal genera remain, which is similar to previous 16S-based estimates of both bacteria and archaea (Janssen and Kirs, 2008).…”

“…The differences observed between our current and previous estimates are likely due to differences in the technologies used (Janssen and Kirs, 2008;Steinberg and Regan, 2008). For instance, biases in the primers used for ribosomal RNA amplification in archaea can under-represent certain groups and because of differences in the primers used, the comparison of abundances of archaea and bacteria is nontrivial (Tymensen and McAllister, 2012).…”

Progress in the development of vaccines against rumen methanogens

“…Methanobrevibacter is nearly always the dominant genus in the rumen, and typically is the source of over half to nearly all of the 16S rRNA gene sequences detected in rumen samples. The rumen contains perhaps eight or more species of this genus (Janssen and Kirs, 2008;Jeyanathan et al, 2011). Members of the species Methanobrevibacter smithii, a human gut methanogen, seem to be almost completely absent.…”

“…Methanomicrobium mobile is a hydrogenotrophic methanogen (Paynter and Hungate, 1968) that should compete directly with Methanobrevibacter spp. Other members of the order Methanomicrobiales are detected or isolated occasionally, but are never abundant (Janssen and Kirs, 2008;Kim et al, 2011;Chaudhary et al, 2012).Members of a third order, Methanosarcinales, also occur in the rumen, but are reported in much lower numbers except under some special circumstances when rumen turnover rates are very low (Rowe et al, 1979). Members of the genus Methanosarcina are capable of growth with and methane formation from hydrogen, methyl compounds and acetate.…”