BackgroundMethane (CH4) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO2). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.Methodology/Principal FindingsThe M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H2) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species.Conclusions/SignificanceThe M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment.

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Aim:  To screen rumen bacterial cultures and fresh ruminal isolates for indole and skatole production. Methods and Results:  Culture collection strains and fresh bacterial isolates from rumen contents of sheep and dairy cows were screened for the production of indolic compounds. Clostridium aminophilum FT, Peptostreptococcus ssp. S1, Fusobacterium necrophorum D4 produced indole and Clostridium sticklandii SR produced indoleacetic acid. Fresh isolates from sheep (TrE9262 and TrE7262) and dairy cows (152R‐1a, 152R‐1b, 152R‐3 and 152R‐4) produced indole, indolepropionic acid, tryptophol and skatole from the fermentation of tryptophan and indoleacetic acid. Glucose altered the indolic compounds produced in some, but not all, isolates. TrE7262 and 152R‐4 were identified as Clostridium sporogenes and 152R‐1b as a new Cl. aminophilum strain. Isolates TrE9262, 152R‐1a and 152R‐3 were not closely related to any described species but belong to Megasphaera, Prevotella and Actinomyces genera, respectively. Conclusions:  Rumen bacteria that produced a range of indolic compounds were identified. Some isolates are distinct from the previously described bacteria and may represent novel species. Significance and Impact of the Study:  These observations will contribute to understanding skatole and indole formation in the rumen and will lead to methods that control the formation of indolic compounds in pasture‐grazed ruminants.

A life cycle-based model, OSTUM (Oil Sands Technologies for Upgrading Model), which evaluates the energy intensity and greenhouse gas (GHG) emissions of current oil sands upgrading technologies, is developed. Upgrading converts oil sands bitumen into high quality synthetic crude oil (SCO), a refinery feedstock. OSTUM's novel attributes include the following: the breadth of technologies and upgrading operations options that can be analyzed, energy intensity and GHG emissions being estimated at the process unit level, it not being dependent on a proprietary process simulator, and use of publicly available data. OSTUM is applied to a hypothetical, but realistic, upgrading operation based on delayed coking, the most common upgrading technology, resulting in emissions of 328 kg COe/m SCO. The primary contributor to upgrading emissions (45%) is the use of natural gas for hydrogen production through steam methane reforming, followed by the use of natural gas as fuel in the rest of the process units' heaters (39%). OSTUM's results are in agreement with those of a process simulation model developed by CanmetENERGY, other literature, and confidential data of a commercial upgrading operation. For the application of the model, emissions are found to be most sensitive to the amount of natural gas utilized as feedstock by the steam methane reformer. OSTUM is capable of evaluating the impact of different technologies, feedstock qualities, operating conditions, and fuel mixes on upgrading emissions, and its life cycle perspective allows easy incorporation of results into well-to-wheel analyses.