Publications

characterization of two pterin derivatives isolated from methanoculleus thermophilicum.	methanoculleus thermophilicum was shown to contain two pterin derivatives. the structures of these pterin derivatives were established from amino acid analysis, 1h-nmr and fast-atom bombardment mass spectrometry data. one of the pterins was identified as tatiopterin-o, an aspartyl derivative of methanopterin with a proton at position 7 of the pterin moiety. the other pterin, which we named thermopterin, differed in the structure of the aniline group, containing two additional hydroxyl residues. ...	1991	1915350
in vitro inhibition of cell growth of molt-4 malignant human t-lymphoblasts by coenzyme f420.	the inhibitory effect of methanogenic coenzymes on the proliferation of molt-4 human malignant t-lymphoblasts was tested. furthermore the effects of methanogenic coenzymes on dihydrofolate reductase activity (dhfr) from chicken liver have been examined. the results showed that heat-stable extracts of the hydrogenotrophs methanobacterium thermoautotrophicum, methanoculleus thermophilicum and methanogenium tationis inhibit both proliferation of human t-lymphoblasts and dhfr activity. heat-stable e ...	1991	1997004
relatedness of the flagellins from methanogens.	purified flagellar filaments isolated from six methanogens were composed of multiple flagellins. two flagellins were present in methanococcus deltae (mr = 34,000 and 32,000), methanoculleus marisnigri (mr = 31,000 and 25,500) and methanococcus jannaschii (mr = 31,000 and 27,500), three in methanothermus fervidus (mr = 34,000, 25,000 and 24,000) and four or more in both methanococcus vannielii and methanococcus maripaludis (mr ranging from 27,500 to 32,000). the flagellins of m. fervidus and m. d ...	1992	1503530
correlation between glycosylation of flagellin proteins and sensitivity of flagellar filaments to triton x-100 in methanogens.	the flagellins of methanospirillum hungatei strains jf1 and gp1, methanococcus deltae, and methanothermus fervidus are glycosylated. isolated flagellar filaments from these organisms are dissociated by low concentrations (0.5% (v/v)) of triton x-100. flagellar filaments from other methanogens (methanococcus voltae, methanococcus vannielii and methanoculleus marisnigri) composed of non-glycosylated flagellins are resistant to triton x-100 treatment. consequently, the isolation techniques (employi ...	1992	1537540
cofactor contents of methanogenic bacteria reviewed.	the content of specific methanogenic cofactors was assessed for a range of hydrogenotrophic and methylotrophic methanogenic bacteria grown on different substrates using high performance liquid chromatography. in general, all methanogens were found to contain coenzyme f420 analogues, methanopterin (mpt) analogues and 5-hydroxybenzimidazolylcobamide (vitamin b12-hbi). in hydrogenotrophic methanogens of the genera methano-bacterium and methanobrevibacter, as a rule, coenzymes f420-2 and f420-3 as w ...	1994	7916957
si-face stereospecificity at c5 of coenzyme f420 for f420-dependent glucose-6-phosphate dehydrogenase from mycobacterium smegmatis and f420-dependent alcohol dehydrogenase from methanoculleus thermophilicus.	coenzyme f420 is a 5-deazaflavin. upon reduction, 1,5-dihydro-coenzyme f420 is formed with a prochiral center at c5. in this study we report that the f420-dependent glucose-6-phosphate dehydrogenase from mycobacterium smegmatis and the f420-dependent alcohol dehydrogenase from methanoculleus thermophilicus are si-face stereospecific with respect to c5 of the 5-deazaflavin. these results were obtained by following the stereochemical course of the reversible incorporation of 3h into f420 from trit ...	1996	8706724
phylogenetic diversity of archaea in sediment samples from a coastal salt marsh.	the archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16s rrna gene libraries created with archaea-specific primers. none of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. a wide range of euryarchaeota sequences w ...	1997	9406392
methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-sumatra, indonesia.	strain insluzt (= dsm 4273t) was isolated from a biogas-producing bioreactor treating wastewater of a palm oil mill on north-sumatra (indonesia). cells of strain insluzt were highly irregularly coccoid, 1.25-2.0 microns in diameter, had a cell envelope consisting of the cytoplasmic membrane and an s-layer of hexagonally arranged glycoprotein subunits with an m(r) of 120,000, and were flagellated (motility was not observed). cells were mesophilic and grew most rapidly at 40 degrees c on h2/co2' f ...	1998	9828413
phylogenetic diversity of methanogenic archaea in swine waste storage pits.	total dna was isolated from swine feces and a swine waste storage pit and used as templates for pcr amplification of archaeal 16 rdna using specific primers. only the sample from the center of the waste pit produced a pcr product. dna sequence analyses of random clones demonstrated a variety of methanogenic archaea. six groups of sequences were identified, including those similar to methanobrevibacter sp., methanocorpusculum sp., and methanoculleus sp. three groups of sequences represented unide ...	1999	10518719
culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.	recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. in this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in california. enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees c. heterotro ...	2000	10653739
methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in japan, and dna-dna hybridization among methanoculleus species.	a strictly anaerobic, irregularly coccoid, methanogenic archaeon, strain mg62t (= jcm 10825t = dsm 13459t), was isolated from paddy field soil in chikugo, fukuoka, japan. the cells stained gram-negative, were 1.0-2.0 microm in diameter, were lysed by sds and hypotonic solutions and were flagellated. motility was not observed. the strain was able to use h2/co2, 2-propanol/co2, formate, 2-butanol/co2 and cyclopentanol/co2 as substrates for methanogenesis, but did not utilize acetate, ethanol, meth ...	2001	11594593
comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a uk estuary.	abstract the 16s rrna sequence diversity of the euryarchaeal community in a predominately freshwater sediment at east hill bridge (ehb) on the river colne estuary, essex, uk was investigated and compared to that from marine sediments at the mouth of the river (colne point). the east hill bridge sediments appear to support the full range of methanogen phenotypes with some genotypes similar to those previously detected at colne point. however, no marine benthic group d or halophilic archaeal genot ...	2002	19709180
diversity and structure of the archaeal community in the leachate of a full-scale recirculating landfill as examined by direct 16s rrna gene sequence retrieval.	the diversity and structure of the archaeal community in the effluent leachate from a full-scale recirculating landfill was characterized by direct 16s rrna gene (16s rdna) retrieval. total-community dna was extracted from the microbial assemblages in the landfill leachate, and archaeal 16s rdnas were amplified with a universally conserved primer and an archaea-specific primer. the amplification product was then used to construct a 16s rdna clone library, and 70 randomly selected archaeal clones ...	2002	12351237
isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of methanoculleus submarinus sp. nov.	we isolated a methanogen from deep in the sediments of the nankai trough off the eastern coast of japan. at the sampling site, the water was 950 m deep and the sediment core was collected at 247 m below the sediment surface. the isolated methanogen was named nankai-1. cells of nankai-1 were nonmotile and highly irregular coccoids (average diameter, 0.8 to 2 micro m) and grew with hydrogen or formate as a catabolic substrate. cells required acetate as a carbon source. yeast extract and peptones w ...	2003	12788731
improved strategy for presumptive identification of methanogens using 16s riboprinting.	the predicted 16s riboprint patterns of 10 restriction endonucleases for 26 diverse methanogens were compared to actual patterns produced on agarose gels. the observed patterns corroborated the expected riboprints. our analyses confirmed that the endonuclease haeiii gave the best results generating 15 different riboprint sets. six of these 15 riboprints represented more than one strain. of these, three riboprint sets were further differentiated: methanomicrobium mobile, methanolacinia paynteri, ...	2003	14529955
molecular detection and direct enumeration of methanogenic archaea and methanotrophic bacteria in domestic solid waste landfill soils.	methane oxidizing and producing activities of cover soil (10, 30 cm depth) and burial waste (1, 3 m depth) were evaluated: top cover soil (10 cm) had the highest methane oxidizing activity, while 1 m depth buried waste showed the highest methane producing potential. all the sequences of the 1 m sample were found to be closely related to 16s rdnas of mainly hydrogenotrophic methanogens known, such as genera methanosarcina, methanoculleus, and methanobacterium. we developed a modified fluorescence ...	2003	14571983
characterization of methanogenic and methanotrophic assemblages in landfill samples.	a greater understanding of the tightly linked trophic groups of anaerobic and aerobic bacteria residing in municipal solid waste landfills will increase our ability to control methane emissions and pollutant fate in these environments. to this end, we characterized the composition of methanogenic and methanotrophic bacteria in samples taken from two regions of a municipal solid waste landfill that varied in age. a method combining polymerase chain reaction amplification, restriction fragment len ...	2003	14667383
effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation.	the community structures of two mesophilic acetate-degrading methanogenic consortia enriched at dilution rates of 0.025 and 0.6 d(-1) were analyzed by fluorescence in situ hybridization (fish) and phylogenetic analyses based on 16s rdna clonal sequences and quantitative real-time polymerase chain reaction (pcr). fish experiments with archaeal and bacterial domain-specific probes showed that archaeal cells were predominant and only a small number of bacterial cells were detected at both dilution ...	2003	16233572
methanoculleus bourgensis, methanoculleus olentangyi and methanoculleus oldenburgensis are subjective synonyms.	methanoculleus bourgensis, methanoculleus olentangyi and methanoculleus oldenburgensis are subjective synonyms on the basis of phenotypic, genotypic and phylogenetic characteristics. methanoculleus bourgensis must be the name of the united species because it is the type of the genus methanoculleus:	2003	13130046
coenzyme binding in f420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family.	f(420)-dependent secondary alcohol dehydrogenase (adf) from methanogenic archaea is a member of the growing bacterial luciferase family which are all tim barrel enzymes, most of which with an unusual nonprolyl cis peptide bond. we report here on the crystal structure of adf from methanoculleus thermophilicus at 1.8 a resolution in complex with a f(420)-acetone adduct. the knowledge of the f(420) binding mode in adf provides the molecular basis for modeling f(420) and fmn into the other enzymes o ...	2004	15016352
16s rdna characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure.	a laboratory-scale continuously stirred anaerobic thermophilic batch digester was inoculated with cattle manure. bacterial and archaeal communities, as well as digester performances, were analysed during reactor start-up for about 20 days. polymerase chain reaction-single strand conformation polymorphism (pcr-sscp) was used for overall detection and for study of the dynamics of microbial populations. dominant bacteria and archaea 16s rdnas were sequenced from the sample on day 12. ten bacteria a ...	2004	15062816
the effects of micro-aeration on the phylogenetic diversity of microorganisms in a thermophilic anaerobic municipal solid-waste digester.	we demonstrated previously that micro-aeration allows construction of an effective thermophilic methane-fermentation system for treatment of municipal solid waste (msw) without production of h(2)s. in the present study, we compared the microbial communities in a thermophilic msw digester without aeration and with micro-aeration by fluorescence in situ hybridization (fish), denaturing gradient gel electrophoresis (dgge), phylogenetic analysis of libraries of 16s rrna gene clones and quantitative ...	2004	15159157
effect of dilution rate on metabolic pathway shift between aceticlastic and nonaceticlastic methanogenesis in chemostat cultivation.	acetate conversion pathways of methanogenic consortia in acetate-fed chemostats at dilution rates of 0.025 and 0.6 day(-1) were investigated by using (13)c-labeled acetates, followed by gas chromatography-mass spectrometry (gc-ms) analysis of the ch(4) and co(2) produced. nonaceticlastic syntrophic oxidation by acetate-oxidizing syntrophs and hydrogenotrophic methanogens was suggested to occupy a primary pathway (approximately 62 to 90%) in total methanogenesis at the low dilution rate. in contr ...	2004	15240282
anaerobic 2-propanol degradation in anoxic paddy soil and the possible role of methanogens in its degradation.	the anaerobic degradation of 2-propanol in anoxic paddy soil was studied with soil cultures and a 2-propanol-utilizing methanogen. acetone was the first and the major intermediate involved in the methanogenic degradation of 2-propanol. analyses with a methanogenesis inhibitor, bacteria antibiotics, and the addition of h2 to the gas phase revealed that 2-propanol oxidation to acetone directly occurred using 2-propanol-utilizing methanogens, but not with h2-producing syntrophic bacteria, for which ...	2004	15297909
the molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by pcr-rflp.	to combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a pcr-restriction fragment length polymorphism (rflp) analysis.	2004	15479412
methanogenium frittonii harris et al. 1996 is a later synonym of methanoculleus thermophilus (rivard and smith 1982) maestrojuan et al. 1990.	the 16s rrna gene sequence of [methanogenium] frittonii dsm 2832(t) was determined and was found to be 99.9 % similar to the sequence of methanoculleus thermophilus dsm 2373(t). dna-dna hybridizations between both strains revealed 86 % dna-dna binding, indicating that both strains belong to the same species. the determination of the dna g + c content of both type strains, dsm 2832(t) and dsm 2373(t), revealed values of 56.1 and 59.1 mol%, respectively. based on the phenotypic and genotypic chara ...	2005	15879239
methanogen diversity evidenced by molecular characterization of methyl coenzyme m reductase a (mcra) genes in hydrothermal sediments of the guaymas basin.	the methanogenic community in hydrothermally active sediments of guaymas basin (gulf of california, mexico) was analyzed by pcr amplification, cloning, and sequencing of methyl coenzyme m reductase (mcra) and 16s rrna genes. members of the methanomicrobiales and methanosarcinales dominated the mcra and 16s rrna clone libraries from the upper 15 cm of the sediments. within the h2/co2- and formate-utilizing family methanomicrobiales, two mcra and 16s rrna lineages were closely affiliated with cult ...	2005	16085853
microbial community analysis of mesophilic anaerobic protein degradation process using bovine serum albumin (bsa)-fed continuous cultivation.	two mesophilic anaerobic chemostats, one without added ni2+ and co2+ (chemostat 1) and the other with added ni2+ and co2+ (chemostat 2), were supplied with synthetic wastewater containing bovine serum albumin (bsa) as the sole carbon and energy source in order to study the capacity of protein degradation, microbial community structure and the effects of the addition of trace metals. volatile fatty acids and ammonia were the main products of chemostat 1, while methane, co2 and ammonia were the ma ...	2005	16233772
population dynamics of anaerobic microbial consortia in thermophilic methanogenic sludge treating paper-containing solid waste.	to maintain a stable thermophilic (55 degrees c) anaerobic digestion treating toilet paper-containing garbage, it is necessary to operate the digester at long hydraulic retention time (hrt) and low organic loading rate (olr). critical conditions of the digestion were investigated by operating the digester at hrt 23 days and olr 3.4 gcod(cr)/l/d (r1) or hrt 14 days and olr 5.6 gcod/cr)/l/d (r2) separately. characteristics of methanogenesis of the two digesters were examined by measuring gas gener ...	2006	17163049
methanogenic diversity and activity in municipal solid waste landfill leachates.	archaeal microbial communities present in municipal solid waste landfill leachates were characterized using a 16s rdna approach. phylogenetic affiliations of 239 partial length 16s rdna sequences were determined. sequences belonging to the order methanosarcinales were dominant in the clone library and 65% of the clones belonged to the strictly acetoclastic methanogenic family methanosaetaceae. sequences affiliated to the metabolically versatile family methanosarcinaceae represented 18% of the re ...	2006	16779637
dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester.	in this study, the microbial community succession in a thermophilic methanogenic bioreactor under deteriorative and stable conditions that were induced by acidification and neutralization, respectively, was investigated using pcr-mediated single-strand conformation polymorphism (sscp) based on the 16s rrna gene, quantitative pcr, and fluorescence in situ hybridization (fish). the sscp analysis indicated that the archaeal community structure was closely correlated with the volatile fatty acid (vf ...	2006	16461718
microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16s rrna and acetate kinase genes.	we constructed a mesophilic anaerobic chemostat that was continuously fed with synthetic wastewater containing propionate as the sole source of carbon and energy. steady-state conditions were achieved below the critical dilution rate of 0.3 d (-1) with almost complete substrate degradation. the propionate-degrading methanogenic communities in the chemostat at dilution rates of 0.01, 0.08, and 0.3 d (-1) were analyzed using molecular biological techniques. fluorescence in situ hybridization with ...	2006	16496142
effect of dilution rate on the microbial structure of a mesophilic butyrate-degrading methanogenic community during continuous cultivation.	we constructed two mesophilic anaerobic chemostats that were continuously fed with synthetic wastewater containing butyrate as the sole source of carbon and energy. steady-state conditions were achieved at dilution rates between 0.025 and 0.7 day(-1). butyrate, fed into the chemostat, was almost completely mineralized to ch(4) and co(2) at dilution rates below 0.5 day(-1). the butyrate-degrading methanogenic communities in the chemostats at dilution rates between 0.025 and 0.7 day(-1) were monit ...	2007	17221191
anaerobic treatment performance and microbial population of thermophilic upflow anaerobic filter reactor treating awamori distillery wastewater.	distillery wastewater from awamori making was anaerobically treated for one year using thermophilic upflow anaerobic filter (uaf) reactors packed with pyridinium group-containing nonwoven fabric material. the microbial structure and spatial distribution of microorganisms on the support material were characterized using molecular biological methods. the reactor steadily achieved a high toc loading rate of 18 g/l/d with approximately 80% toc removal efficiency when non-diluted wastewater was fed. ...	2007	18023800
thermophilic methanogenic archaea in compost material: occurrence, persistence and possible mechanisms for their distribution to other environments.	since compost is widely used as soil amendment and the fact that during the processing of compost material high amounts of microorganisms are released into the air, we investigated whether compost may act as a carrier for thermophilic methanogens to temperate soils. all eight investigated compost materials showed a clear methane production potential between 0.01 and 0.98 micromol ch(4) g dw(-1)h(-1) at 50 degrees c. single strand conformation polymorphism (sscp) and cloning analysis indicated th ...	2007	17988815
post-translational modifications in the active site region of methyl-coenzyme m reductase from methanogenic and methanotrophic archaea.	methyl-coenzyme m reductase (mcr) catalyzes the methane-forming step in methanogenic archaea. isoenzyme i from methanothermobacter marburgensiswas shown to contain a thioxo peptide bond and four methylated amino acids in the active site region. we report here that mcrs from all methanogens investigated contain the thioxo peptide bond, but that the enzymes differ in their post-translational methylations. the ms analysis included mcr i and mcr ii from methanothermobacter marburgensis, mcr i from m ...	2007	17725644
phylogenetic analysis of methanogenic enrichment cultures obtained from lonar lake in india: isolation of methanocalculus sp. and methanoculleus sp.	the diversity of methanogenic archaea in enrichment cultures established from the sediments of lonar lake (india), a soda lake having ph approximately 10, was investigated using 16s rdna molecular phylogenetic approach. methanogenic enrichment cultures were developed in a medium that simulated conditions of soda lake with three different substrates viz., h(2):co(2), sodium acetate, and trimethylamine (tma), at alkaline ph. archaeal 16s rrna clone libraries were generated from enrichment cultures ...	2007	17483868
traditional cattle manure application determines abundance, diversity and activity of methanogenic archaea in arable european soil.	based on lipid analyses, 16s rrna/rrna gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in bad lauchstädt, germany. the investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. the archaeal phospholipid etherlip ...	2007	17298362
the metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.	composition and gene content of a biogas-producing microbial community from a production-scale biogas plant fed with renewable primary products was analysed by means of a metagenomic approach applying the ultrafast 454-pyrosequencing technology. sequencing of isolated total community dna on a genome sequencer flx system resulted in 616,072 reads with an average read length of 230 bases accounting for 141,664,289 bases sequence information. assignment of obtained single reads to cog (clusters of ...	2008	18597880
characterization of the methanogenic archaea within two-phase biogas reactor systems operated with plant biomass.	the two-phase leach-bed system is a biogas reactor system optimized for the utilization of energy crop silages at maximized loading rates under maintenance of an optimal microbial activity. in this study, a characterization of the methanogenic microbial community within this reactor system was conducted for the first time. accordingly, effluent samples from the anaerobic filter and the silage digesting leach-bed reactors of both a laboratory-scale two-phase biogas reactor system and a scaled-up ...	2008	18501543
analysis of microbial community structure and diversity in the thermophilic anaerobic digestion of waste activated sludge.	the microbial community structures in the thermophilic anaerobic digestion (tad) of waste activated sludge (was) and was were analyzed with molecular biological techniques including real-time polymerase chain reaction (pcr) and cloning. the microbial community of tad had less diversity than that of was, and the sequences obtained in was were not present in tad by the cloning analysis. in the tad bacterial clone library, 97.5% of total clones were affiliated with the phylum firmicutes and 73.1% w ...	2008	18469390
estimates of biogenic methane production rates in deep marine sediments at hydrate ridge, cascadia margin.	methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. we estimated the in situ methanogenesis rates in hydrate ridge (hr) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass ...	2008	18344348
taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.	a total community dna sample from an agricultural biogas reactor continuously fed with maize silage, green rye, and small proportions of chicken manure has recently been sequenced using massively parallel pyrosequencing. in this study, the sample was computationally characterized without a prior assembly step, providing quantitative insights into the taxonomic composition and gene content of the underlying microbial community. clostridiales from the phylum firmicutes is the most prevalent phylog ...	2008	18611419
diversity of the resident microbiota in a thermophilic municipal biogas plant.	biogas plants continuously convert biological wastes mainly into a mixture of methane, co2 and h2o-a conversion that is carried out by a consortium of bacteria and archaea. especially in the municipal plants dedicated towards waste treatment, the reactor feed may vary considerably, exposing the resident microbiota to a changing variety of substrates. to evaluate how and if such changes influence the microbiology, an established biogas plant (6,600 m3, up to 600 m3 biogas per h) was followed over ...	2008	18820906
evaluation of methanogenic strains and their ability to endure aeration and water stress.	during periods of drainage, both water stress and oxygen can cause damage to indigenous methanogens. in the present study, we evaluated the tolerance of seven methanogenic strains (methanobrevibacter arboriphilicus, methanobacterium formicicum, methanococcus vannielii, methanospirillum hungatei, methanoculleus olentangyi, methanoplanus limicola, and methanosarcina mazei) to long-term exposure to air/nitrogen and drying. we found that these methanogenic strains except for m. limicola and m. olent ...	2008	17990030
subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (odp leg204) in the cascadia margin.	the prokaryotic communities in deep subseafloor sediment collected during ocean drilling program (odp) leg 204 from the south hydrate ridge (shr) on the cascadia margin were analyzed by 16s rrna gene clone sequencing and a fluorescent quantitative pcr technique. the microbial communities came from sites with contrasting geological characteristics on the shr: sites 1244 and 1245 (located on the flank of the ridge, hydrate-rich sediment) and site 1251 (located on the slope basin of shr, hydrate-po ...	2008	21558725
isolation and characterization of methanoculleus receptaculi sp. nov. from shengli oil field, china.	three strictly anaerobic, thermophilic methanogens (zc-2t, zc-3 and zc-6) were isolated from shengli oil field, china. the 16s rrna gene sequences of the three strains were nearly identical, possessing > 99.8% sequence similarity. they also possessed high sequence similarity, 97.4%, to methanoculleus palmolei strain insluz(t) (97.4% and 97.5%, respectively), indicating that they represented a novel species within the genus methanoculleus. cells of strain zc-2t were nonmotile cocci, 0.8-1.7 micro ...	2008	18557787
phylogenetic characterization of a biogas plant microbial community integrating clone library 16s-rdna sequences and metagenome sequence data obtained by 454-pyrosequencing.	the phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. sequencing of 109 clones from a bacterial and an archaeal 16s-rdna amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16s-rdna database sequences d ...	2009	19480946
design and testing of real-time pcr primers for the quantification of methanoculleus, methanosarcina, methanothermobacter, and a group of uncultured methanogens.	in this study, 16s rrna gene primers were designed to complement the suite of already available pcr primers for the detection of different methanogens involved in biogas production through anaerobic digestion by sybr green real-time pcr. primers designed for use in taqman real-time pcr for the organisms methanosaeta, methanosarcina, and methanoculleus have been described previously; however, we found that (i) the methanoculleus primers were not specific to members of the genus and that (ii) the ...	2009	19483790
molecular identification and dynamics of microbial communities in reactor treating organic household waste.	the prokaryotic diversity associated with organic household waste (ohw), leachate (start-up inoculum), and mesophilic anaerobic digestion processes in the degradation of ohw for 44 and 90 days was investigated using a culture-independent approach. bacterial and archaeal 16s rrna and mcra gene clone libraries were constructed from community dna preparations. bacterial clones were affiliated with 13 phyla, of which firmicutes, proteobacteria, and bacteroidetes were represented in all libraries, wh ...	2009	19551378
design and development of the anaerochip microarray for investigation of methanogenic communities.	the aim of this study was to design a microarray targeting methanogens found in anaerobic digesters, and to apply this chip together with a cloning approach to investigate the methanogenic community present in an anaerobic digester. oligonucleotide probes were designed based on sequence differences in the 16s rrna genes in order to target microorganisms in situ. for microarray hybridisations, dna was subjected to pcr amplification of the 16s rrna gene and cy5-labeled. the microarray was tested w ...	2009	19799937
insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions.	dna-sip (stable isotope probing) was conducted on anaerobic municipal solid waste samples incubated with (13)c-cellulose, (13)c-glucose and (13)c-acetate under mesophilic conditions. a total of 567 full-length bacterial and 448 1100-bp-length archaeal 16s rrna gene sequences were analysed. in the clone libraries derived from 'heavy' dna fractions, the most abundant sequences were affiliated with the phyla firmicutes, bacteroidetes, the gamma-subclass of proteobacteria and methanogenic orders met ...	2009	19128320
thermophilic anaerobic co-digestion of garbage, screened swine and dairy cattle manure.	methane fermentation characteristics of garbage, swine manure (sm), dairy cattle manure (dcm) and mixtures of these wastes were studied. sm and dcm showed much lower volatile total solid (vts) digestion efficiencies and methane yield than those of garbage. vts digestion efficiency of sm was significantly increased when it was co-digested with garbage (garbage: sm=1:1). co-digestion of garbage, sm and dcm with respect to the relative quantity of each waste discharged in the kikuchi (1: 16: 27) an ...	2009	19147110
complete genome sequence of methanoculleus marisnigri romesser et al. 1981 type strain jr1.	methanoculleus marisnigri romesser et al. 1981 is a methanogen belonging to the order methanomicrobiales within the archaeal phylum euryarchaeota. the type strain, jr1, was isolated from anoxic sediments of the black sea. m. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order methanomicrobiales. we report here the complete genome sequence of m. marisnigri type strain jr1 and its annotation. this is p ...	2009	21304656
genomic characterization of methanomicrobiales reveals three classes of methanogens.	methanomicrobiales is the least studied order of methanogens. while these organisms appear to be more closely related to the methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to class i methanogens.	2009	19495416
the structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16s rdna sequencing analysis.	to identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16s rdna-based methods to investigate the microbial structure.	2009	19187154
effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor.	prokaryotic diversity was investigated near the inlet and outlet of a plug-flow reactor. after analyzing 800 clones, 50 bacterial and 3 archaeal phylogenetic groups were defined. clostridia (>92%) dominated among bacteria and methanoculleus (>90%) among archaea. significant changes in ph and volatile fatty acids did not invoke a major shift in the phylogenetic groups. we suggest that the environmental filter imposed by the saline conditions (20 g liter(-1)) selected a stable community of halotol ...	2009	19218417
investigation of factors influencing biogas production in a large-scale thermophilic municipal biogas plant.	a continuously operated, thermophilic, municipal biogas plant was observed over 26 months (sampling twice per month) in regard to a number of physicochemical parameters and the biogas production. biogas yields were put in correlation to parameters such as the volatile fatty acid concentration, the ph and the ammonium concentration. when the residing microbiota was classified via analysis of the 16s rrna genes, most bacterial sequences matched with unidentified or uncultured bacteria from similar ...	2009	19618178
focused-pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester.	the low yield of methane in anaerobic digestion systems represents a loss of energy that can be captured as renewable energy when the input sludge is pre-treated to make it more bioavailable. we investigated focused-pulsed (fp) pre-treatment, which make complex biological solids more bioavailable by exposing them to rapid pulses of a very strong electric field. we investigated how the microbial ecology in full-scale anaerobic digesters was altered when the digesters' methane production rate was ...	2009	19732933
identification of an archaeal presenilin-like intramembrane protease.	the gxgd-type diaspartyl intramembrane protease, presenilin, constitutes the catalytic core of the γ-secretase multi-protein complex responsible for activating critical signaling cascades during development and for the production of β-amyloid peptides (aβ) implicated in alzheimer's disease. the only other known gxgd-type diaspartyl intramembrane proteases are the eukaryotic signal peptide peptidases (spps). the presence of presenilin-like enzymes outside eukaryots has not been demonstrated. here ...	2010	20927381
effects of various fatty acid amendments on a microbial digester community in batch culture.	since biogas production is becoming increasingly important the understanding of anaerobic digestion processes is fundamental. however, large-scale digesters often lack online sensor equipment to monitor key parameters. furthermore the possibility to selectively change fermenting parameter settings in order to investigate methane output or microbial changes is limited. in the present study we examined the possibility to investigate the microbial community of a large scale (750,000 l) digester wit ...	2010	21071199
methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil.	an obligately anaerobic, methanogenic archaeon, strain hc(t), was isolated from soil of the zoige wetland on the tibetan plateau, china. the strain was isolated through construction of an artificial butyrate-degrading consortium in co-culture with a syntrophic bacterium, 'syntrophomonas erecta subsp. sporosyntropha' jcm 13344. cells of strain hc(t) were irregular coccoids, 0.8-2 mum in diameter, that occurred singly and utilized only h(2)/co(2) for growth and methane production. growth occurred ...	2010	19897615
polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants.	knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. to overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. fluorescence in situ hybridization (fish) was carried out to quantify the methanogenic archaea in the reactor samples. in addition, quantitative real ...	2010	20154117
microbial community dynamics in anaerobic bioreactors and algal tanks treating piggery wastewater.	integrated biosystem is becoming a major aspect of wastewater management practice. microbial communities in piggery wastewater sampled from anaerobic (thermophilic and mesophilic) and aerobic digesters (algal tanks) during waste remediation were analyzed by culture-independent techniques based on polymerase chain reaction-denaturing gradient gel electrophoresis (pcr-dgge). the use of muyzer's 314f-gc, 518r bacterial primers, and archaeal a934f, 1309r primers followed by partial 16s rdna sequence ...	2010	20349182
characterization of an anaerobic population digesting a model substrate for maize in the presence of trace metals.	the influence of a defined trace metal solution and additionally ni(2+) on anaerobic digestion of biomass was investigated. a novel synthetic model substrate was designed consisting of cellulose, starch and urea as carbon and nitrogen source in a ratio mimicking the basic composition of maize silage. two independent batch fermentations were carried out over 21 d with the synthetic model substrate in the presence of the trace metal solution. particularly an increase in nickel concentrations (17 a ...	2010	20615524
impact of trace element addition on biogas production from food industrial waste--linking process to microbial communities.	laboratory-scale reactors treating food industry waste were used to investigate the effects of additions of cobalt (co), nickel/molybdenum/boron (ni/mo/b) and selenium/tungsten (se/w) on the biogas process and the associated microbial community. the highest methane production (predicted value: 860 ml g(-1) vs) was linked to high se/w concentrations in combination with a low level of co. a combination of quantitative real-time pcr of 16s rrna genes, terminal restriction fragment length polymorphi ...	2010	20633047
adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37 degrees c and 55 degrees c.	the acclimatization of methanogens to two-phase olive mill wastes (tpomw) was investigated in pilot fermenters started up with cattle excreta (37°c) and after changing their feed to excreta plus tpomw (37°c or 55°c) or tpomw alone (37°c) until a steady state was reached (28 days). methanogenic diversity was screened using a phylogenetic microarray (anaerochip), and positive targets were quantified by real-time pcr. results revealed high phylogenetic richness, with representatives of three out of ...	2010	20675446
a comprehensive microbial insight into two-stage anaerobic digestion of food waste-recycling wastewater.	microbial community structures were assessed in a two-stage anaerobic digestion system treating food waste-recycling wastewater. the reactors were operated for 390 d at 10 different hydraulic retention times (hrts) ranging from 25 to 4 d. stable operation was achieved with the overall chemical oxygen demand (cod) removal efficiency of 73.0-85.9% at organic loading rate of up to 35.6 g cod/l·d. performance of the acidogenic reactors, however, changed significantly during operation. this change co ...	2010	20678786
methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste.	the methanogenic pathway and microbial community in a thermophilic anaerobic digestion process of organic solid waste were investigated in a continuous-flow stirred-tank reactor using artificial garbage slurry as a feedstock. the decomposition pathway of acetate, a significant precursor of ch(4) and a key intermediate metabolite in the anaerobic digestion process, was analyzed by using stable isotopes. a tracer experiment using (13)c-labeled acetate revealed that approximately 80% of the acetate ...	2011	20851673
comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.	biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. many countries are promoting the use of alternative energy sources for sustainable energy production. in this study, a metagenome from a production-scale biogas fermenter was analysed employing roche's gs flx titanium technology and compared to a previous dataset obtained from the same community dna sample that was sequenced on ...	2011	21297863
bacteria and archaea involved in anaerobic digestion of distillers grains with solubles.	cereal distillers grains, a by-product from bioethanol industry, proved to be a suitable feedstock for biogas production in laboratory scale anaerobic digesters. five continuously stirred tank reactors were run under constant conditions and monitored for biogas production and composition along with other process parameters. iron additives for sulfide precipitation significantly improved the process stability and efficiency, whereas aerobic pretreatment of the grains had no effect. the microbial ...	2011	21061007
kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash.	anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. treatment efficiency of the bioreactor was investigated at different hydraulic retention times (hrt) and organic loading rates (olr 5-20 kg cod môü+-¦ dôü+-¦). applying the modified stover-kincannon model to the reactor, the maximum removal rate constant (u(max)) and saturation value constant (k(b)) were fou ...	2011	21704352
a novel fingerprint method to assess the diversity of methanogens in microbial systems.	understanding the ecology of methanogens in natural and engineered environments is a prerequisite to predicting or managing methane emissions. in this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. the method described here, designated amplicon length heterogeneity pcr of the mcra gene (lh-mcra), is based on the natural length variation in the mcra gene. the mcra gene encodes the alpha-subu ...	2011	22093027
characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding.	thermophilic dry anaerobic digestion of sludge for cellulose methanization was acclimated at 53 °c for nearly 5 years using a waste paper-based medium. the stability of the microbial community structure and the microbial community responsible for the cellulose methanization were studied by 16s rrna gene-based clone library analysis. the microbial community structure remained stable during the long-term acclimation period. hydrogenotrophic methanogens dominated in methanogens and methanothermobac ...	2011	21789494
Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload.	Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable ...	2011	22192420
tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.	four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains re1(t), re2, t1 and t2, were isolated from two different mesophilic methanogenic systems. the strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. comparative 16s rrna gene sequence analysis confirmed that the strains belong to the firmicutes-clostridia class. the most closely related species to strains re1(t) ...	2011	21498020
performance and spatial community succession of an anaerobic baffled reactor treating acetone-butanol-ethanol fermentation wastewater.	an anaerobic baffled reactor with four compartments (c1-c4) was successfully used for treatment of acetone-butanol-ethanol fermentation wastewater and methane production. the chemical oxygen demand (cod) removal efficiency was 88.2% with a ch(4) yield of 0.25l/(g cod(removed)) when organic loading rate (olr) was 5.4kg codm(-3)d(-1). c1 played the most important role in solvents (acetone, butanol and ethanol) and cod removal. community structure of c2 was similar to that in c1 at stage 3 with hig ...	2011	21664129
methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks.	greenhouse gas emissions represent a major problem associated with manure management in the livestock industry. a prerequisite to mitigate methane emissions occurring during manure storage is a clearer understanding of how the microbial consortia involved in methanogenesis function. here, we have examined manure stored in outdoor tanks from two different farms, at different locations and depths. physico-chemical and microbiological characterization of these samples indicated differences between ...	2012	22268671