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Phylogenetic relationships of symbiotic methanogens in diverse termites.

Termites harbor symbiotic microorganisms in their gut which emit methane. The phylogeny of the termite methanogens was inferred without cultivation based on nucleotide sequences of PCR-amplified 16S ribosomal RNA genes. Seven methanogen sequences from four termite species were newly isolated, and together with those previously published, these sequences were phylogenetically compared. The termite methanogen sequences were divided into three clusters. Two clusters of sequences, derived from the gut DNA of so-called higher termites, were related to methanogens in the orders Methanosarcinales or Methanomicrobiales. All of the sequences in the case of lower termites were closely related to the genus Methanobrevibacter. However, most of the termite symbionts were found to be distinct from known methanogens. They are not dispersed among diverse methanogen species, but rather formed unique lineages in the phylogenetic trees.

Animals↗

A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea.

Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict demands to anaerobic culture conditions. These differences may, at least partly, be responsible for the delay in availability of genetic research tools for methanogens. At present, however, the research within genetics of methanogens and their gene regulation and expression is in rapid progress. Two complete methanogenic genomes have been sequenced and published and more are underway. Besides, sequences are known from a multitude of individual genes from methanogens. Standard methods for simple DNA and RNA work can normally be employed, but permeabilization of the cell wall may demand special procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology.

Euryarchaeota↗

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↗

Methanogenic bacteria from human dental plaque.

Samples of human dental plaque were examined for the presence of methanogenic bacteria. Of 54 samples from 36 patients, 20 yielded H2/CO2-using methanogenic enrichment cultures. All methanogen-positive samples were from patients with some degree of periodontal disease. The predominant populations in the enrichments had morphologies characteristic of Methanobrevibacter spp. In six enrichments derived from three patients, the common methanogen was antigenically similar to Methanobrevibacter smithii. The same was true for the three methanogenic isolates obtained in axenic culture from a fourth patient. The six enrichments and two of the three isolates were antigenically closer to strain ALI than to PS. Two of the enrichments also had subpopulations with weak antigenic similarity to Methanosphaera stadtmanae. The data indicate that methanogens in the oral cavity of humans are antigenically close to those found in the intestinal tract.

Antigens, Bacterial↗

Populations of methanogenic bacteria in a georgia salt marsh.

Methanogens represented about 0.5% of the total bacteria in sediments from a Georgia salt marsh in which Spartina alterniflora is the predominant vegetation. The population of methanogens was composed of at least two groups of nearly equal size. One group was represented by cocci which were able to utilize trimethylamine and were unable to use H(2) or acetate. The second group was composed of two subgroups which were able to utilize H(2) but were unable to use trimethylamine or acetate. The more common subgroup included rod- or plate-shaped methanogens which could utilize isopropanol in addition to H(2) and formate. The second subgroup included Methanococcus maripaludis, which utilized only H(2) and formate. Other groups of methanogens were also present, including Methanosarcina sp. which utilized acetate, H(2), and methylamines. In addition to the overall variability in the types of methanogens, the numbers of methanogens in sediments also exhibited significant spatial variability both within and between tall- and short-Spartina zones.

Journal Article↗

Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria.

When microorganisms eluted from upper Hudson River sediment were cultured without any substrate except polychlorobiphenyl (PCB)-free Hudson River sediment, methane formation was the terminal step of the anaerobic food chain. In sediments containing Aroclor 1242, addition of eubacterium-inhibiting antibiotics, which should have directly inhibited fermentative bacteria and thereby should have indirectly inhibited methanogens, resulted in no dechlorination activity or methane production. However, when substrates for methanogenic bacteria were provided along with the antibiotics (to free the methanogens from dependence on eubacteria), concomitant methane production and dechlorination of PCBs were observed. The dechlorination of Aroclor 1242 was from the para positions, a pattern distinctly different from, and more limited than, the pattern observed with untreated or pasteurized inocula. Both methane production and dechlorination in cultures amended with antibiotics plus methanogenic substrates were inhibited by 2-bromoethanesulfonic acid. These results suggest that the methanogenic bacteria are among the physiological groups capable of anaerobic dechlorination of PCBs, but that the dechlorination observed with methanogenic bacteria is less extensive than the dechlorination observed with more complex anaerobic consortia.

Journal Article↗

Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil.

Temperature is an important factor controlling CH(4) production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37 degrees C or in a temperature gradient block covering the same temperature range at intervals of 1 degrees C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH(4) production rates increased with temperature, with an apparent activation energy of 61 kJ mol(-1). Steady-state partial pressures of the methanogenic precursor H(2) also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H(2) plus CO(2)-dependent methanogenesis was kept at -20 to -25 kJ mol of CH(4)(-1) over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 microM. Simultaneously, the relative contribution of H(2) as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to (14)CH(4), so that the carbon and electron flow to CH(4) was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and Methanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

Agriculture↗

Methanogenic bacteria in human vaginal samples.

Twelve vaginal samples were collected from separate patients, processed anaerobically, and added to methanogenic enrichment medium. Methanogenic activity was detected in two samples, both of which were from patients with bacterial vaginosis. None of the samples from healthy patients yielded positive methanogen cultures. One sample from a patient with bacterial vaginosis did not show any detectable methanogenic activity. Two methanogen isolates were obtained from one of the methanogen-positive samples, and both were identified as Methanobrevibacter smithii on the basis of morphological, cultural, and immunological features.

Bacterial Infections↗

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↗

Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses.

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

Archaea↗

Ammonia inhibition on thermophilic aceticlastic methanogens.

The inhibition effects of total ammonia nitrogen (TAN) on aceticlastic methanogenic activity using biomass from thermophilic anaerobic reactors were investigated in this study. Anaerobic Toxicity Assays (ATA) were conducted after the biomass was acclimated to different levels of TAN. The TAN background concentrations in the reactors were 400, 1,200, and 3,050 mg/L. The results from ATA showed: 1) high TAN concentrations could cause inhibition of aceticlastic methanogens; 2) biomass acclimated to higher TAN concentrations could alleviate the inhibition effect due to the increase of TAN concentration; 3) the lethal TAN concentration for methanogens was approximately 10,000 mg/L regardless of the background TAN concentration; 4) ATA results also revealed the role played by pH. At a given TAN concentration, methanogenic activity varied with the pH values. The highest methanogenic activity was always observed at a pH of 7.0-7.5. 5) It was also observed that acclimation could increase the pH tolerance range, which made methanogens less sensitive to pH changes.

Adaptation, Physiological↗

Phosphate inhibition on thermophilic acetoclastic methanogens: a warning.

The inhibitory effect of phosphate on acetoclastic-methanogens was investigated for three different thermophilic (55 degrees C) anaerobic consortia. When 70 mM of phosphate was tested, acetoclastic methanogens was completely inhibited in "Eerbeek" sludge which is dominated by Methanosaeta-like methanogens. For the "Hoogezand" sludge the specific methanogenic activity dropped by 79%, indicating that any of the acetate-consuming methanogens present in the sludge was more resistant to the phosphate applied. The results demonstrated that the inhibitory effect of phosphate may affect both methane production rate and final methane concentration and might also be time dependent. This study indicates that the degree of inhibition is species-dependent, and even more resistant species may be affected during long-term experiments. Such inhibition is a matter of concern for researchers since misleading conclusions might be taken from growth and specific methanogenic activity tests when considerable concentrations of phosphate buffer are used and no interference is expected.

Acetates↗

Metabolic interactions in methanogenic and sulfate-reducing bioreactors.

In environments where the amount of electron acceptors is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic consortia of acetogenic bacteria and methanogenic archaea. Hydrogen consumption by methanogens is essential for acetogenic bacteria to convert organic acids to acetate and hydrogen. Several syntrophic cocultures growing on propionate and butyrate have been described. These syntrophic fatty acid-degrading consortia are affected by the presence of sulfate. When sulfate is present sulfate-reducing bacteria compete with methanogenic archaea for hydrogen and acetate, and with acetogenic bacteria for propionate and butyrate. Sulfate-reducing bacteria easily outcompete methanogens for hydrogen, but the presence of acetate as carbon source may influence the outcome of the competition. By contrast, acetoclastic methanogens can compete reasonably well with acetate-degrading sulfate reducers. Sulfate-reducing bacteria grow much faster on propionate and butyrate than syntrophic consortia.

Acetates↗

Methanogenic activity test as an aid in evaluating performance and stability of anaerobic bioreactors.

The correlation between methanogenic activity and anaerobic reactor performance is intuitive. In this paper, an attempt has been made to suggest a new parameter, defined on the basis of the relative activity of acetoclastic and hydrogen oxidising methanogens, to aid in evaluating the performance and stability of anaerobic reactors. Performance of three bench scale reactors was assessed at different relative populations of the trophic groups of methanogens as estimated through acetoclastic and total methanogenic activity tests. Results indicated that the acetoclastic to total methanogenic activity ratio 0.7 yielded stable and optimal reactor performance. The acetoclastic and total methanogenic activity tests provide a simple technique that may aid in evaluating the performance and stability of anaerobic bioreactors.

Anaerobiosis↗

Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids.

An aggressive start-up strategy was used to initiate codigestion in two anaerobic, continuously mixed bench-top reactors at mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions. The digesters were inoculated with mesophilic anaerobic sewage sludge and cattle manure and were fed a mixture of simulated municipal solid waste and biosolids in proportions that reflect U.S. production rates. The design organic loading rate was 3.1 kg volatile solids/m3/day and the retention time was 20 days. Ribosomal RNA-targeted oligonucleotide probes were used to determine the methanogenic community structure in the inocula and the digesters. Chemical analyses were performed to evaluate digester performance. The aggressive start-up strategy was successful for the thermophilic reactor, despite the use of a mesophilic inoculum. After a short start-up period (20 days), stable performance was observed with high gas production rates (1.52 m3/m3/day), high levels of methane in the biogas (59%), and substantial volatile solids (54%) and cellulose (58%) removals. In contrast, the mesophilic digester did not respond favorably to the start-up method. The concentrations of volatile fatty acids increased dramatically and pH control was difficult. After several weeks of operation, the mesophilic digester became more stable, but propionate levels remained very high. Methanogenic population dynamics correlated well with performance measures. Large fluctuations were observed in methanogenic population levels during the start-up period as volatile fatty acids accumulated and were subsequently consumed. Methanosaeta species were the most abundant methanogens in the inoculum, but their levels decreased rapidly as acetate built up. The increase in acetate levels was paralleled by an increase in Methanosarcina species abundance (up to 11.6 and 4.8% of total ribosomal RNA consisted of Methanosarcina species ribosomal RNA in mesophilic and thermophilic digesters, respectively). Methanobacteriaceae were the most abundant hydrogenotrophic methanogens in both digesters, but their levels were higher in the thermophilic digester.

Anaerobiosis↗

Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures.

The TaqMan quantitative PCR (QPCR) method was used to detect and quantify the 16S rRNA genes of aceticlastic methanogens at different taxonomic levels. Three different sets of primers coupled with a TaqMan probe for QPCR assays to detect the 16S rRNA genes of the order Methanosarcinales, as well as the families Methanosarcinaceae and Methanosaetaceae, were separately used. Using these primer and probe sets, the 16S rRNA genes of aceticlastic methanogens in samples from various anaerobic processes (i.e., nine pure cultures, batch experiment, and three different continuous processes including a full-scale digester), were monitored and quantified by QPCR assays. A batch experiment cultivating a mixture of aceticlastic methanogens, was conducted to monitor their population dynamics. Using this group-specific quantification method, the dynamics of a competition between two aceticlastic populations, as modulated by the acetate concentration, could well be described. The target 16S rRNA genes in environmental samples, collected from three different anaerobic processes treating sludge, cheese whey, and synthetic wastewaters, were additionally quantified. The quantified 16S rRNA gene concentrations for all samples successfully represented the community structures of the target methanogens, which were correlated accurately with the operational parameters of the anaerobic processes. It was also successful to demonstrate probe nesting of aceticlastic methanogens at the levels of order and family.

Acetates↗

Impact of long-term partial aeration on the removal of 2,4,6-trichlorophenol in an initially methanogenic fluidized bed bioreactor.

A fluidized bed bioreactor (FBBR) was operated for more than 1000 days under two regimes, Methanogenic (M) and Methanogenic-Aerobic (M-A), to remove 2,4,6-trichlorophenol (TCP) and phenol (Phe) from a synthetic wastewater, containing different amounts of TCP and Phe, using different aeration flow-rates (0, 2.13, and 1.06 NL O(2)/L.day). M conditions (80:20 mg/L of TCP:Phe, 0 NL O(2)/L.day) showed similar TCP and Phe removal (>95%). Nevertheless accumulation of 4-chlorophenol (4CP) up to 16 mg/L and Phe up to 4 mg/L was observed, while in M-A conditions (80:20 mg/L of TCP:Phe, 2.13 NL O(2)/L.day) TCP and Phe removal achieved 99.9(+)% and after 70 days no accumulation of intermediates were detected. The increase of TCP and Phe in the influent under M-A conditions from 80:20 to 120:30 mg/L of TCP:Phe did not negatively affect the removal of TCP, intermediates and Phe; in fact, they were similar to those in previous M-A conditions. The decrease in the oxygen flow rate from 2.13 to 1.06 NL O(2)/L.day had no negative effect on pollutant removals, which were as high as in previous two M-A conditions. The specific methanogenic activity of bioparticles of the fluidized bed decreased with long-term partial aeration, starting from 1.097 mmol CH(4)/h.g(TKN) in the M regime (day 60) to <0.02 mmolCH(4)/h.g(TKN) at day 1050, suggesting aerobic regime in the bioreactor rather than an M-A regime. In conclusion, complete removal of TCP and less chlorinated intermediates could be achieved in an initially methanogenic FBBR under conditions of partial aeration, although long-term operation seemed to negatively affect the methanogenic activity of biomass. It is also likely that after extended aeration the microbial community was finally enriched with strains with the ability to attack 2,4,6-TCP under aerobic conditions. This report represents the first evidence of a long exposure to oxygen of an anaerobic microbial consortium that efficiently remove TCP.

Air↗

Sodium, protons, and energy coupling in the methanogenic bacteria.

In this review, I focus on the bioenergetics of the methanogenic bacteria, with particular attention directed to the roles of transmembrane electrochemical gradients of sodium and proton. In addition, the mechanism of coupling ATP synthesis to methanogenic electron transfer is addressed. Evidence is reviewed which suggests that the methanogens possess great diversity in their bioenergetic machinery. In particular, in some methanogens the primary ion which is translocated coupled to metabolic energy is the proton, while others appear to utilize sodium. In addition, ATP synthesis driven by methanogenic electron transfer is accomplished in some organisms by a chemiosmotic mechanism and is coupled by a more direct mechanism in others. A possible explanation for this diversity (which is consistent with the relatedness of these organisms to each other and to other members of the Archaebacteria as determined by molecular biological techniques) is discussed.

Bacteria↗