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At least 19 recordsLinked to original sources

PubMed1978

Acetic acid and hydrogen metabolism during coculture of an acetic acid producing bacterium with methanogenic bacteria.

Two microorganisms originally existing as a mixed culture obtained from an anaerobic digester fluid were separated for pure and coculture studies. One of these was motile, Gram-negative, and non-sporeforming, and it required yeast extract for growth and acetic acid production. This isolate produced H2 and did not need H2 and (or) CO2 for growth and acetate formation. The other isolate was a methanogen whick resembled Methanobacterium arbophilicum in morphology and substrate specificity. Coculture growth of the two isolates in yeast extract broth (80% N2--20% CO2 gas phase) indicated that the non-methanogen produced up to four to five times more H2 than when grown separately. Although the growth of the non-methanogen was not enhanced by the removal of H2 by the methanogen, the hydrogen produced was essential for the growth of methanogen. Similar results were obtained when the non-methanogen was cocultured with Methanospirillum hungatti GP1. Cultivation of the non-methanogen in the presence of M. hungatti GP1 (under abundance of 80% H2--20% CO2) indicated that the acetate produced was consumed by M. hungatii, without inhibiting the growth of the other culture.

Acetates↗

PubMed1977

Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria.

In the analysis of an ethanol-CO(2) enrichment of bacteria from an anaerobic sewage digestor, a strain tentatively identified as Desulfovibrio vulgaris and an H(2)-utilizing methanogen resembling Methanobacterium formicicum were isolated, and they were shown to represent a synergistic association of two bacterial species similar to that previously found between S organism and Methanobacterium strain MOH isolated from Methanobacillus omelianskii. In lowsulfate media, the desulfovibrio produced acetate and H(2) from ethanol and acetate, H(2), and, presumably, CO(2) from lactate; but growth was slight and little of the energy source was catabolized unless the organism was combined with an H(2)-utilizing methanogenic bacterium. The type strains of D. vulgaris and Desulfovibrio desulfuricans carried out the same type of synergistic growth with methanogens. In mixtures of desulfovibrio and strain MOH growing on ethanol, lactate, or pyruvate, diminution of methane produced was stoichiometric with the moles of sulfate added, and the desulfovibrios grew better with sulfate addition. The energetics of the synergistic associations and of the competition between the methanogenic system and sulfate-reducing system as sinks for electrons generated in the oxidation of organic materials such as ethanol, lactate, and acetate are discussed. It is suggested that lack of availability of H(2) for growth of methanogens is a major factor in suppression of methanogenesis by sulfate in natural ecosystems. The results with these known mixtures of bacteria suggest that hydrogenase-forming, sulfate-reducing bacteria could be active in some methanogenic ecosystems that are low in sulfate.

Acetates↗

PubMed1992

Molecular biology of methanogens.

Methanogens are a very diverse group of the Archaea (Archaebacteria). Their genomic DNAs range from 26 to 68 mol% G+C; they exhibit all known prokaryotic morphologies and inhabit anaerobic environments as varied as the human gut and deep-sea volcanic vents. They are, nevertheless, unified by their ability to gain energy by reducing CO, CO2, formate, methanol, methylamines, or acetate to methane. Methanogen genes are reviewed and analyzed in terms of their organization, structure, and expression and are compared with their bacterial (eubacterial) and eukaryal (eukaryotic) counterparts. Many methanogens are thermophiles, and some are hyperthermophiles. The influence of these extreme environments on their macromolecular structures is also addressed. Methanogens are oxygen-sensitive, fastidious anaerobes, and therefore their experimental manipulation in research laboratories has been very limited. The majority of the information currently available describing their molecular biology has been gained by gene cloning. With improvements in anaerobic handling procedures, this is beginning to change, and several experimentally tractable regulated systems of gene expression in methanogens are discussed. Anaerobic biodegradation terminating in methane biogenesis is an established, economically very important biotechnology used world-wide both to reduce waste and to generate fuel-grade biogas. The substantial progress made over the past decade, reviewed here, in understanding the molecular biology of methanogens should now provide a data base for considering genetic approaches to improving this process.

Euryarchaeota↗

PubMed2026

An integrated culturomic and genomic database and analysis platform for methanogenic archaea.

Methanogenic archaea research is challenged by limited strain resources, fragmented genomic data, inconsistent genome quality, substantial uncultured lineages, and difficulties in laboratory culturing, hindering advances in biogas production, climate mitigation, and microbial ecology. These archaea play crucial roles in global carbon cycling and anaerobic environments, yet scattered data and unculturable strains limit systematic studies and applications. To address this, we created MethArDB (Methanogenic Archaeal Genome Database), a specialized database for methanogenic archaea, compiling 3919 genomes, 87 host-associated plasmids, and 42 phages, with standardized quality classifications (complete, scaffold, draft), protein sequences, and metadata on geography, habitats, metabolism, and inheritable elements. Integrated MethArCT (Methanogenic Archaeal Culturomics Toolkit) employs a dual-threshold orthologous/paralogous protein analysis to evaluate metabolic pathway completeness, predicting cultivation parameters and suggesting candidate cultivation strategies, including potential medium formulations and conditions, to support strain isolation. Overall, MethArDB and MethArCT form an integrated platform combining genomics and culturomics to facilitate methanogenic archaea research. Database URL:  http://methardb.cn.

Genome, Archaeal↗

PubMed1978

Application of the fluorescent-antibody technique to the study of a methanogenic bacterium in lake sediments.

Fluorescent antibody (FA) was prepared for a methanogenic bacterium isolated from Wintergreen Lake pelagic sediment. The isolate resembles Methanobacterium formicicum. The FA did not cross-react with 9 other methanogens, including M. formicicum strains, or 24 heterotrophs, 18 of which had been isolated from Wintergreen Lake sediment. FA-reacting methanogens were detected in heat-fixed smears of several different lake sediments and anaerobic sewage sludge. Pretreatment of all samples with either rhodamine-conjugated geletin or bovine serum albumin adequately controlled nonspecific absorption of the FA. Autofluorescent particles were observed in the sediment samples but, with experience, they could easily be distinguished from FA-reacting bacteria. FA direct counts of the specific methanogen in Wintergreen Lake sediments were made on four different sampling dates and compared with five-tube most-probable-number estimates of the total methanogenic population that was present in the same samples. The FA counts ranged from 3.1 X 10(6) to 1.4 X 10(7)/g of dry sediment. The highest most-probable-number estimates were at least an order ofmagnitude lower.

Anaerobiosis↗

PubMed1992

Interrelations between populations of methanogenic archaea and sulfate-reducing bacteria in the human colon.

In humans, CH4 is produced in the colon by methanogenic archaea and is detected in breath samples from approximately 50% of healthy adults, identified as CH4-excretors. Methanogenesis and sulfate reduction have been described as two mutually exclusive processes, potentially regulated by sulfate availability. To determine whether microbial population balances reflected these apparently co-regulated activities, we compared sulfate-reducing bacteria, methanogenic archaea, sulfate and sulfide concentrations in faeces of 10 CH4-excretors (CH4+) and 9 non-CH4-excretors (CH4-). The mean +/- SE of the logarithm of methanogenic archaea per gram wet weight were 9.0 +/- 0.2 and 4.0 +/- 0.7 for CH4+ and CH4-, respectively (P < 0.001). Sulfate-reducing bacterial counts were 6.5 +/- 0.1 and 7.3 +/- 0.2, respectively (P < 0.001). Fecal sulfate and sulfide concentrations did not differ between groups. These results suggest that a competitive interrelation between methanogenic archaea and sulfate-reducing bacteria occurs in the human colon. However, it does not lead to a complete exclusion of the two populations.

Adolescent↗

PubMed1975

New method for the isolation and identification of methanogenic bacteria.

A new technique is reported for the rapid growth and detection of methanogenic bacteria by using petri plates. The method employs an anaerobic glove box containing an inner chamber with separate gas-flushing facilities. The numbers of methanogenic bacteria recovered from domestic sewage sludge are comparable to those recovered by other methods. The methanogenic organisms isolated from sludge include Methanosarcina, Methanospirillum, Methanobacterium strain M.o.H., and Methanobacterium formicicum. Identification of colonies containing methanogenic bacteria is facilitated by taking advantage of the unique fluorescence properties of these organisms. Colonies as small as 0.5 mm can be detected by exposing them to long-wave ultraviolet light.

Anaerobiosis↗

PubMed1992

Biotechnological potential of methanogens.

Methane produced microbiologically is currently used as an energy source, especially by cities and industries, albeit at a level far below its potential; the incentive is currently to save money on disposal costs for waste problems. Anaerobic digestion can be helpful in degrading several halogenated hydrocarbon wastes, and methanogens are partly responsible. Ethane instead of methane may be a future product of interest. Some pure cultures of methanogens may be suitable for production of B-12, or perhaps the speciality biochemical F420, a 5-deazaflavin of interest to both methanogen and streptomyces researchers. Methanogens can cause a variety of problems, including biocorrosion, increased atmospheric methane, and ruminant nutrition loss. Studies of tropical wetlands, including rice paddies and swamps, and the study of a variety of ruminants in the tropics are particularly interesting and appropriate at this time, with respect to methane produced in these ecosystems. In some cases, it may be possible to control methane production by the use of inhibitors or ecological control mechanisms.

Euryarchaeota↗

PubMed2026

Up-to-date, and taxonomy-curated mcrA reference databases for methanogen community profiling.

The methyl-coenzyme M reductase subunit alpha gene (mcrA) is an important phylogenetic marker for high throughput ecological profiling of methanogenic archaea, central to industrial biological methane production and greenhouse gas emissions. Yet, dedicated reference databases predate current relevant NCBI sequence accumulation and archaeal taxonomic revision. We present three updated mcrA reference databases: (i) one derived from NCBI-catalogued methanogen genomes (1572 sequences); (ii) a database built by expansion of a previously published reference dataset, leveraging the NCBI nucleotide collection (27,942 sequences); (iii) a curated-taxonomy version of the latter. The updated amplicon databases provide a ∼ 3.5-fold sequence richness expansion, extend genus-level richness from 31 to 83 taxa, more than 4-fold species-level richness, and incorporate novel lineages compared with the previous reference dataset (e.g. Thermoplasmatota-encompassed). All databases were formatted to support analysis with relevant contemporary software pipelines and packages. Overall, the generated databases facilitate a highly improved characterization of methanogen diversity and ecology.

Archaea↗

PubMed2025

ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans.

All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans , also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans , but other factor(s) are likely involved in directly sensing Mo.

Methanosarcina↗

PubMed2026

Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.

Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.

Manure↗

PubMed1979

Diphytanyl and dibiphytanyl glycerol ether lipids of methanogenic archaebacteria.

The lipids of nine different methanogenic bacterial strains are comprised of diphytanyl glycerol diethers, previously known only in extremely halophilic bacterial, as well as dibiphytanyl diglycerol tetraethers, known formerly only in the extremely thermoacidophilic bacteria Thermoplasma and Sulfolobus. Of the methanogens examined from four representative taxonomic groups, Methanobacterium and Methanospirillum contained both types of isopranyl ethers in nearly equal proportions, whereas the coccal forms, Methanosarcina and Methanococcus, possessed diphytanyl glycerol diethers, but with only a trace of or no dibiphytanyl diglycerol tetraethers. The occurrence of both types of isopranyl glycerol ethers in methanogenic bacteria supports the proposal that they have a close genealogical relationship to the extremely halophilic and thermoacidophilic bacteria.

Biological Evolution↗

PubMed1977

Effect of sodium chloride on growth and methane production of methanogens.

The effect of up to 263.7 mM sodium chloride on the growth and methane production by pure cultures of Methanospirillum hungatii GP1, Methanobacterium MOH, Methanobacterium thermoautotrophicum, and an unidentified methanogen was studied. Growth and methane production by M. hungatii GP1 were not affected up to 97.3 mM NaCl but there was some inhibition of growth at higher concentrations. Growth of Methanobacterium MOH was independent of sodium chloride concentration within the range investigated. For the unidentified methanogen, optimum growth and methane production occurred at 15.2 mM NaCl, while growth of M. thermoautotrophicum was not affected by sodium chloride concentrations up to 15.2 mM. Concentrations over 15.2 mM were inhibitory to these two organisms. The 15 mM sodium chloride concentration used by some investigators appears suitable for isolation and cultivation of methanogens since all the organisms tested in this study exhibited good growth and methane production at this salt concentration.

Anaerobiosis↗

PubMed1990

Early stages in biofilm development in methanogenic fluidized-bed reactors.

Biofilm development in methanogenic fluidized-bed reactors with sand as the carrier was studied on a laboratory scale. The microorganisms present in consecutive layers of the biofilm of mature sludge granules were preliminarily characterized on the basis of their morphology, element composition and adhesion capacity and were compared to bacteria which take part in the initial colonization of sand. The early phase of biofilm development was monitored with reactors receiving waste-waters containing different mixtures of volatile fatty acids and inoculated with fluidized-bed reactor effluent for different lengths of time. The results obtained indicate that facultative anaerobic bacteria abundantly present in the outermost biofilm layers of mature sludge granules are probably the main primary colonizers of the sand. Methanothrix spp. or other methanogens were rarely observed among the primary colonizers. The course of biofilm formation was comparable under the various start-up conditions employed including variations in waste-water composition, inoculation and anaerobicity. However, omission of waste-water and thus of substrate resulted in rapid wash-out of the attached biomass.

Bacterial Adhesion↗

PubMed1990

Thermodynamic evidence of trophic microniches in methanogenic granular sludge-bed reactors.

The Gibbs free energy changes in methanogenic granular biomass from sludge-bed reactors were evaluated using the in situ concentrations and partial pressures of metabolites during the metabolism of acetate, hydrogen, formate and propionate. Based on mass balance calculations it appeared that the degradation of propionate into acetate, hydrogen and bicarbonate was endergonic, even if propionate was effectively degraded. On the other hand, the methane-producing reactions, both from acetate and from hydrogen plus bicarbonate, were found to be exergonic and the free energy change was sufficient for the formation of ATP. Formate was detected in only one of the two reactors. When formate, instead of hydrogen, was considered as the electron carrier between propionate-degrading and methanogenic bacteria, similar thermodynamic results were obtained. The existence of trophic microniches in the granular biomass is suggested to explain propionate degradation even though the Gibbs free energy change in the liquid surrounding the granules was positive. Hence, to make propionate degradation exergonic the dissolved hydrogen concentration surrounding the propionate-degrading bacteria would have to be about 30 times lower than in the free liquid.

Anaerobiosis↗

PubMed1978

Chemical composition of the peptidoglycan-free cell walls of methanogenic bacteria.

Cell walls were prepared from freeze-dried samples of 7 strains of Methanobacterium by mechanical disintegration of the cells followed by incubation with trypsin. Electron microscopy revealed the presence of sacculi exhibiting the shape of the original cells, on which no surface structure could be detected. Ultrathin sections of the isolated sacculi showed a homogenously electron dense layer of about 10--15 nm in width. The ash content varied between 8 and 18% of dry weight. The sacculi of all the strains contained Lys: Ala:Glu:GlcNAc or GalNAc in a molar ratio of about 1:1.2:2:1. In one strain (M. ruminantium M1) alanine is replaced by threonine, however, Neutral sugars and--in some strains--additional amounts of the amino sugars were present in variable amounts, and could be removed by formamide extraction or HF treatment without destroying the sacculi. No muramic acid or D-amino acids typical of peptidoglycan were found. Therefore, the sacculi of the methanobacteria consist of a different polymer containing a set of three L-amino acids and one N-acetylated amino sugar. From cells of Methanospirillum hungatii no sacculi, but tube-like sheaths could be isolated, which tend to fracture perpendicularly to the long axis of the sheath along the fibrills seen on the surface. The sheaths consist of protein containing 18 amino acids and small amounts of neutral sugars. They are resistent to the proteinases tested and are not disintegrated by boiling in 2% sodium dodecylsulfate for 30 min. The three Gram-negative strains Black Sea isolate JR-1, Cariaco isolate JR-1 and Methanobacterium mobile do not contain a rigid sacculus, but merely a SDS-sensitive surface layer composed of regularly arranged protein subunits. This evidence indicates that, within the methanogens, different cell wall polymers characteristic of particular groups of organisms may have evolved during evolution, and supports the hypothesis that the evolution of the methanogens was separated from that of the peptidoglycan-containing procaryotic organisms at a very early stage.

Acetates↗

PubMed2026

Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture.

The anaerobic conversion of organic matter to methane and carbon dioxide typically relies on obligate syntrophic interactions between bacteria and methanogenic archaea, where interspecies electron transfer enables thermodynamically constrained reactions to proceed near equilibrium. Syntrophs often couple the oxidation of fermentation products such as fatty acids and alcohols to the reduction of protons to form hydrogen (H2). These reactions can only proceed if low H2 concentrations are maintained by H2-consuming syntrophic partners. Here, we describe "lithosyntrophy," a mode of syntrophic interaction in which electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (HPO32-, oxidation state +3) to phosphate coupled to hydrogenogenesis in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Physiology experiments, thermodynamic calculations, genomic annotation, and metaproteomics analysis collectively revealed a mechanism for syntrophic phosphite oxidation in Phox-21. In this pathway, electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase. Unlike previously characterized acetogenic phosphite oxidizers, Phox-21 is a mixotroph that assimilates acetate to form biomass. Lithosyntrophic phosphite oxidizers may play important roles both in transferring reducing equivalents as well as biologically available phosphorus to other members of their surrounding microbial communities, establishing a previously unrecognized metabolic and biogeochemical link between the phosphorus and carbon redox cycles in anoxic ecosystems.

Oxidation-Reduction↗

PubMed1976

New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressureized atmosphere.

The sensitivity of the requirement of Methanobacterium ruminantium strain M1 to a new coenzyme, 2-mercaptoethanesulfonic acid (HS-CoM) was examined by use of new techniques that were developed for rapid and efficient handling of large numbers of cultures of methanogenic bacteria. The system uses sealed tubes that contain a gas mixture of 80% hydrogen and 20% carbon dioxide under a pressure of 2 to 3 atm. This modification of the Hungate technique reduces variability among replicate cultures and simplifies the dispensing, sterilization, and storage of liquid media as well as the transfer and maintenance of methanogenic bacteria. Results indicate a limit of sensitivity of the assay at 5 nM HS-CoM, with half-maximal growth at 25 nM HS-CoM. Coenzyme activity could be replaced by 2,2'-dithiodiethanesulfonic acid at a half-molar equivalent of the HS-CoM concentration, or by 2-(methylthio)ethanesulfonic acid on an equimolar basis. These data reveal a very sensitive and precise requirement for HS-CoM in the nutrition of this fastidious anaerobe.

Anaerobiosis↗