Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

Abstract

Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ؎ standard deviation, 89.6% ؎ 9.8%) and Methanomassiliicoccales (10.4% ؎ 9.8%) were the two major orders and contributed 99.98% (؎0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (؎19.5% standard deviation) and 32.9% (؎18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ؎ 6.7%) and Methanosphaera sp. group5 (5.6% ؎ 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens.M ethane is the second most significant anthropogenic greenhouse gas, after carbon dioxide, and its concentration in the atmosphere is increasing (1). One major contributor to this is an intensification and expansion of global agricultural activities, in particular increased ruminant livestock numbers. Ruminants, such as cattle, sheep, and domesticated deer, produce large amounts of methane via enteric fermentation and are the most numerous farm animals in New Zealand. It is estimated that methane from these animals accounts for almost 30% of New Zealand's total anthropogenic greenhouse gas emissions (2).Methane is produced in the rumen by methanogenic archaea, here referred to as methanogens. Methanogens comprise a phylogenetically diverse group of microorganisms that are present in the rumen at up to ϳ10 10 cells/g rumen contents (3). Previous analyses have shown that members of the orders Methanobacteriales and Methanomassiliicoccales are dominant in the rumens of domesticated ruminants in New Zealand and many other geographic locations around the world (4). The order name Methanomassiliicoccales has only recently been proposed (5). These methanogens are closely related to the Thermoplasmatales (6) and were previously known as rice cluster III (RC-III) archaea (7), rumen cluster C (RCC) (4), or Methanoplasmatales (8). Within the order Methanobacteriales, hydrogenotrophic methanogens of the genus Methanobrevibacter appe...

Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation

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16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo

“…Unlike buffalo, many cattle studies have reported presence of Methanosphaera in moderate abundance [8,29]. In cattle, several studies have reported presence of Methanomassiliicoccales or RCC clade of Thermoplasmata [30,31]. In the rumen, methanol is a product of pectin hydrolysis by protozoa and esterase activity of bacteria.…”

Characterization of the Microbial Communities in Rumen Fluid Inoculated Reactors for the Biogas Digestion of Wheat Straw

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