Methanogen

About: Methanogen is a research topic. Over the lifetime, 1146 publications have been published within this topic receiving 48254 citations.

Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol

Abstract: Dimethyl sulfide (DMS) has an impact on global warming and acid precipitation and on the global sulfur cycle because of its oxidation products (e.g., methanesulfonic acid and SO2), which are released into the atmosphere. For this reason transformations of volatile organic sulfur compounds have been intensively studied during the past few decades. Microbial formation and degradation of DMS and methanethiol (MT) have been shown to have a significant effect on the total flux of sulfur compounds in the atmosphere (13, 14, 21). In freshwater sediments, formation of MT and DMS is balanced by degradation of these compounds, which results in low steady-state concentrations (18–20). In contrast to marine and estuarine systems, in which DMS originates mainly from dimethylsulfoniumpropionate, volatile organic sulfur compounds in freshwater sediments are derived mainly from methylation of sulfide and MT (7, 15, 18). In systems with high salt contents, degradation of MT and DMS has been attributed to members of various groups of bacteria, including aerobes (e.g., thiobacilli and Methylophaga spp.) (4, 34–36) and anaerobes (anoxygenic phototrophs, sulfate reducers, and methanogens) (8, 16, 17, 23, 25, 26, 33, 39). The activity of members of these trophic groups depends on the light intensity and the availability of oxygen or alternative electron acceptors, such as sulfate and nitrate. Due to oxygen limitation in freshwater sediments, DMS and MT are degraded mainly anaerobically by means of methanogenic activity (19). Methanogenic conversion of MT and DMS in sediment slurries was first demonstrated by Zinder and Brock (40, 41). Since then, various methanogens have been isolated with DMS or MT from marine, estuarine, salt marsh, and salt lake sediments (8, 12, 16, 17, 23, 25). These methanogens belong to the genera Methanosarcina, Methanolobus, and Methanosalsus. Although methanogens have been identified as the dominant consumers of DMS and MT in sulfate-poor freshwater sediments (18–20, 40, 41), previous attempts to isolate methanogens which are able to grow on DMS or MT from such sediments were unsuccessful (33, 41). Moreover, production of methane or carbon dioxide (or [14C]methane and [14C]carbon dioxide) from MT or DMS (or [14C]MT and [14C]DMS) was not detected in pure cultures of methanogens isolated from nonsaline systems (e.g., Methanobacterium ruminantium, Methanobacterium thermautotrophicum, and Methanosarcina barkeri cultures) (28, 41). In this paper we describe the isolation of a nonhalophilic methylotrophic methanogen, strain DMS1T, from the sediment of a eutrophic freshwater pond on the campus of the Dekkerswald Institute, Nijmegen, The Netherlands. This strain has the salt tolerance characteristic of freshwater bacteria and is able to use DMS, MT, methanol, and methylamines for growth and methanogenesis. Characteristics of strain DMS1T are discussed in relation to its ecological niche. Phylogenetic analysis revealed that this strain represents a novel genus in the family Methanosarcinaceae.

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

Abstract: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep. Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY sheep, we show enrichment of lactate-producing Sharpea spp. in LMY sheep bacterial communities. Increased gene and transcript abundances for sugar import and utilisation and production of lactate, propionate and butyrate were also observed in LMY animals. Sharpea azabuensis and Megasphaera spp. act as important drivers of lactate production and utilisation according to phylogenetic analysis and read mappings. Our findings show that the rumen microbiome in LMY animals supports a rapid heterofermentative growth, leading to lactate production. We postulate that lactate is subsequently metabolised mainly to butyrate in LMY animals, producing 2 mol of hydrogen and 0.5 mol of methane per mol hexose, which represents 24 % less than the 0.66 mol of methane formed from the 2.66 mol of hydrogen produced if hexose fermentation was directly to acetate and butyrate. These findings are consistent with the theory that a smaller rumen size with a higher turnover rate, where rapid heterofermentative growth would be an advantage, results in lower hydrogen production and lower methane formation. Together with previous methanogen gene expression data, this builds a strong concept of how animal traits and microbial communities shape the methane phenotype in sheep.

Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata

Abstract: The class Thermoplasmata harbors huge uncultured archaeal lineages at the order level, so-called Groups E2 and E3. A novel archaeon Kjm51a affiliated with Group E2 was enriched from anaerobic sludge in the present study. Clone library analysis of the archaeal 16S rRNA and mcrA genes confirmed a unique archaeal population in the enrichment culture. The 16S rRNA gene-based phylogeny revealed that the enriched archaeon Kjm51a formed a distinct cluster within Group E2 in the class Thermoplasmata together with Methanomassiliicoccus luminyensis B10(T) and environmental clone sequences derived from anaerobic digesters, bovine rumen, and landfill leachate. Archaeon Kjm51a showed 87.7% 16S rRNA gene sequence identity to the closest cultured species, M. luminyensis B10(T), indicating that archaeon Kjm51a might be phylogenetically novel at least at the genus level. In fluorescence in situ hybridization analysis, archaeon Kjm51a was observed as coccoid cells completely corresponding to the archaeal cells detected, although bacterial rod cells still coexisted. The growth of archaeon Kjm51a was dependent on the presence of methanol and yeast extract, and hydrogen and methane were produced in the enrichment culture. The addition of 2-bromo ethanesulfonate to the enrichment culture completely inhibited methane production and increased hydrogen concentration, which suggested that archaeon Kjm51a is a methanol-reducing hydrogenotrophic methanogen. Taken together, we propose the provisional taxonomic assignment, named Candidatus Methanogranum caenicola, for the enriched archaeon Kjm51a belonging to Group E2. We also propose to place the methanogenic lineage of the class Thermoplasmata in a novel order, Methanomassiliicoccales ord. nov.

Vertical Profiles Of Methanogenesis And Methanogens In Two Contrasting Acidic Peatlands In Central New York State, USA

Abstract: Northern acidic peatlands are important sources of atmospheric methane, yet the methanogens in them are poorly characterized. We examined methanogenic activities and methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5-4.5) peat soils, but the pH of the deeper layers of CB is near-neutral, reflecting its previous existence as a neutral-pH fen. Acetotrophic and hydrogenotrophic methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T-RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales, called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at approximately 10(8) cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The methanogen populations detected by T-RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)-II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1-E1', as well as RC-I, RC-II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.