The Experts below are selected from a list of 1173 Experts worldwide ranked by ideXlab platform
Guylaine Talbot - One of the best experts on this subject based on the ideXlab platform.
-
Phylogenetic identification of methanogens assimilating acetate-derived carbon in dairy and swine manures.
Systematic and Applied Microbiology, 2014Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Josh D. Neufeld, Guylaine TalbotAbstract:Abstract In order to develop approaches for reducing the carbon footprint of the swine and dairy industries, it is important first to identify the methanogenic communities that drive methane emissions from stored manure. In this study, the metabolically active methanogens in substrate-starved manure samples taken from two dairy and one swine manure storage tanks were identified using [ 13 C]-acetate and DNA stable-isotope probing (DNA-SIP). Molecular analysis of recovered genomic [ 13 C]-DNA revealed that two distinct clusters of unclassified methanogen populations affiliated with the Methanoculleus genus, and the populations affiliated with Methanoculleus chikugoensis assimilated acetate-derived carbon (acetate-C) in swine and dairy starved manure samples, respectively. Furthermore, carbon flow calculations indicated that these populations were the primary contributors to methane emissions during these anoxic SIP incubations. Comparative analysis of mcrA gene abundance (coding for a key enzyme of methanogenesis) for Methanoculleus spp. in fresh feces and a wider range of stored dairy or swine manure samples, by real-time quantitative PCR using newly designed specific primers, demonstrated that the abundance of this genus significantly increased during storage. The findings supported the involvement of these particular methanogen populations as methane emitters from swine and dairy manure storage tanks. The study revealed that the ability to assimilate acetate-C for growth in manure differed within the Methanoculleus genus.
-
Physico-chemical characteristics and methanogen communities in swine and dairy manure storage tanks: Spatio-temporal variations and impact on methanogenic activity
Water Research, 2013Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Lucie Masse, Daniel I. Massé, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major environmental problem associated with the management of manure from the livestock industry. Methane is the primary GHG emitted during manure outdoor storage. In this paper, the variability of two swine and two dairy manure storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy manure storage tanks.
-
identification of Methanoculleus spp as active methanogens during anoxic incubations of swine manure storage tank samples
Applied and Environmental Microbiology, 2013Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Josh D. Neufeld, Yris Verastegui, Guylaine TalbotAbstract:Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-¹³C] acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (~7g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.
-
Methanoculleus spp as a biomarker of methanogenic activity in swine manure storage tanks
FEMS Microbiology Ecology, 2012Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Lucie Masse, Daniel I. Massé, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Guylaine TalbotAbstract: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 each tank, as well as differences within each tank dependent on the depth of sampling. The dynamics of both the bacterial and archaeal communities within these samples were monitored over a 150-day period of anaerobic incubation to identify and track emerging microorganisms, which may be temporally important in the methanogenesis process. Analyses based on DNA fingerprinting of microbial communities identified trends common among all samples as well as trends specific to certain samples. All archaeal communities became enriched with Methanoculleus spp. over time, indicating that the hydrogenotrophic pathway of methanogenesis predominated. Although the emerging species differed in samples obtained from shallow depths compared to deep samples, the temporal enrichment of Methanoculleus suggests that this genus may represent a relevant indicator of methanogenic activity in swine manure storage tanks.
-
A novel fingerprint method to assess the diversity of methanogens in microbial systems
Fems Microbiology Letters, 2011Co-Authors: Nathalie Gagnon, Maialen Barret, Edward Topp, Lucie Masse, Daniel I. Massé, Martin Kalmokoff, Guylaine TalbotAbstract: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-subunit of the methyl-coenzyme M reductase, which is involved in the terminal step of methane production by methanogens. The methanogenic communities from stored swine and dairy manures were distinct from each other. To validate the method, methanogenic communities in a plug flow-type bioreactor (PFBR) treating swine manure were characterized using LH-mcrA method and correlated to mcrA gene clone libraries. The diversity and relative abundance of the methanogenic groups were assessed. Methanobrevibacter, Methanosarcinaceae, Methanoculleus, Methanogenium, Methanocorpusculum and one unidentified group were assigned to particular LH-mcrA amplicons. Particular phylotypes related to Methanoculleus were predominant in the last compartment of the PFBR where the bulk of methane was produced. LH-mcrA method was found to be a reliable, fast and cost-effective alternative for diversity assessment of methanogenic communities in microbial systems.
Rudolf K. Thauer - One of the best experts on this subject based on the ideXlab platform.
-
Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea
FEBS Journal, 2007Co-Authors: Jörg Kahnt, Bärbel Buchenau, Felix Mahlert, Martin Krüger, Seigo Shima, Rudolf K. ThauerAbstract: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 Methanocaldococcus jannaschii and Methanoculleus thermophilus, and MCR from Methanococcus voltae, Methanopyrus kandleri and Methanosarcina barkeri. Two MCRs isolated from Black Sea mats containing mainly methanotrophic archaea of the ANME-1 cluster were also analyzed.
-
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
FEBS Journal, 1996Co-Authors: Andreas R Klein, Holger Berk, Endang Purwantini, Lacy Daniels, Rudolf K. ThauerAbstract: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 tritium-labeled substrates. Our findings bring to eight the number of coenzyme-F420-dependent enzymes shown to be Si -face stereospecific. No F420-dependent enzyme with Re -face stereospecificity is known. This is noteworthy since coenzyme F420 is functionally similar to pyridine nucleotides for which both Si -face and Re -face specific enzymes have been found.
-
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
FEBS Journal, 1996Co-Authors: Andreas R Klein, Holger Berk, Endang Purwantini, Lacy Daniels, Rudolf K. ThauerAbstract: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 tritium-labeled substrates. Our findings bring to eight the number of coenzyme-F420-dependent enzymes shown to be Si -face stereospecific. No F420-dependent enzyme with Re -face stereospecificity is known. This is noteworthy since coenzyme F420 is functionally similar to pyridine nucleotides for which both Si -face and Re -face specific enzymes have been found.
Erko Stackebrandt - One of the best experts on this subject based on the ideXlab platform.
-
Methanoculleus palmolei sp nov an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north sumatra indonesia
International Journal of Systematic and Evolutionary Microbiology, 1998Co-Authors: G Zellner, Paul Messner, J Winter, Erko StackebrandtAbstract: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 INSLUZTwere highly irregularly coccoid, 1·25-2·0 in diameter, had a cell envelope consisting of the cytoplasmic membrane and an S-layer of hexagonally arranged glycoprotein subunits with an Mr of 120 000, and were flagellated (motility was not observed). Cells were mesophilic and grew most rapidly at 40 °C on H2/CO2, formate, 2-propanol/CO2′2-butanol/CO2and cyclopentanol/CO2to give methane. Tungstate promoted growth on H2/CO2 with acetate as the solely required organic medium supplement. The G+C content of DNA was 59 mol% (T m method) and 59·5 mol% (HPLC method). 16S rDNA analysis revealed a phylogenetic relationship to Methanoculleus species; the name Methanoculleus palmolei sp. nov. is therefore proposed for strain INSLUZT(= DSM 4273T).
-
Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia.
International journal of systematic bacteriology, 1998Co-Authors: G Zellner, Paul Messner, J Winter, Erko StackebrandtAbstract: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' formate, 2-propanol/CO2 2-butanol/CO2 and cyclopentanol/CO2 to give methane. Tungstate promoted growth on H2/CO2 with acetate as the solely required organic medium supplement. The G + C content of DNA was 59 mol% (Tm method) and 59.5 mol% (HPLC method). 16S rDNA analysis revealed a phylogenetic relationship to Methanoculleus species; the name Methanoculleus palmolei sp. nov. is therefore proposed for strain INSLUZT (= DSM 4273T).
Maialen Barret - One of the best experts on this subject based on the ideXlab platform.
-
Phylogenetic identification of methanogens assimilating acetate-derived carbon in dairy and swine manures.
Systematic and Applied Microbiology, 2014Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Josh D. Neufeld, Guylaine TalbotAbstract:Abstract In order to develop approaches for reducing the carbon footprint of the swine and dairy industries, it is important first to identify the methanogenic communities that drive methane emissions from stored manure. In this study, the metabolically active methanogens in substrate-starved manure samples taken from two dairy and one swine manure storage tanks were identified using [ 13 C]-acetate and DNA stable-isotope probing (DNA-SIP). Molecular analysis of recovered genomic [ 13 C]-DNA revealed that two distinct clusters of unclassified methanogen populations affiliated with the Methanoculleus genus, and the populations affiliated with Methanoculleus chikugoensis assimilated acetate-derived carbon (acetate-C) in swine and dairy starved manure samples, respectively. Furthermore, carbon flow calculations indicated that these populations were the primary contributors to methane emissions during these anoxic SIP incubations. Comparative analysis of mcrA gene abundance (coding for a key enzyme of methanogenesis) for Methanoculleus spp. in fresh feces and a wider range of stored dairy or swine manure samples, by real-time quantitative PCR using newly designed specific primers, demonstrated that the abundance of this genus significantly increased during storage. The findings supported the involvement of these particular methanogen populations as methane emitters from swine and dairy manure storage tanks. The study revealed that the ability to assimilate acetate-C for growth in manure differed within the Methanoculleus genus.
-
Physico-chemical characteristics and methanogen communities in swine and dairy manure storage tanks: Spatio-temporal variations and impact on methanogenic activity
Water Research, 2013Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Lucie Masse, Daniel I. Massé, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major environmental problem associated with the management of manure from the livestock industry. Methane is the primary GHG emitted during manure outdoor storage. In this paper, the variability of two swine and two dairy manure storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy manure storage tanks.
-
identification of Methanoculleus spp as active methanogens during anoxic incubations of swine manure storage tank samples
Applied and Environmental Microbiology, 2013Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Josh D. Neufeld, Yris Verastegui, Guylaine TalbotAbstract:Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-¹³C] acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (~7g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.
-
Methanoculleus spp as a biomarker of methanogenic activity in swine manure storage tanks
FEMS Microbiology Ecology, 2012Co-Authors: Maialen Barret, Nathalie Gagnon, Edward Topp, Lucie Masse, Daniel I. Massé, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Guylaine TalbotAbstract: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 each tank, as well as differences within each tank dependent on the depth of sampling. The dynamics of both the bacterial and archaeal communities within these samples were monitored over a 150-day period of anaerobic incubation to identify and track emerging microorganisms, which may be temporally important in the methanogenesis process. Analyses based on DNA fingerprinting of microbial communities identified trends common among all samples as well as trends specific to certain samples. All archaeal communities became enriched with Methanoculleus spp. over time, indicating that the hydrogenotrophic pathway of methanogenesis predominated. Although the emerging species differed in samples obtained from shallow depths compared to deep samples, the temporal enrichment of Methanoculleus suggests that this genus may represent a relevant indicator of methanogenic activity in swine manure storage tanks.
-
A novel fingerprint method to assess the diversity of methanogens in microbial systems
Fems Microbiology Letters, 2011Co-Authors: Nathalie Gagnon, Maialen Barret, Edward Topp, Lucie Masse, Daniel I. Massé, Martin Kalmokoff, Guylaine TalbotAbstract: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-subunit of the methyl-coenzyme M reductase, which is involved in the terminal step of methane production by methanogens. The methanogenic communities from stored swine and dairy manures were distinct from each other. To validate the method, methanogenic communities in a plug flow-type bioreactor (PFBR) treating swine manure were characterized using LH-mcrA method and correlated to mcrA gene clone libraries. The diversity and relative abundance of the methanogenic groups were assessed. Methanobrevibacter, Methanosarcinaceae, Methanoculleus, Methanogenium, Methanocorpusculum and one unidentified group were assigned to particular LH-mcrA amplicons. Particular phylotypes related to Methanoculleus were predominant in the last compartment of the PFBR where the bulk of methane was produced. LH-mcrA method was found to be a reliable, fast and cost-effective alternative for diversity assessment of methanogenic communities in microbial systems.
Kazunari Nagaoka - One of the best experts on this subject based on the ideXlab platform.
-
Methanoculleus bourgensis, Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Susumu Asakawa, Kazunari NagaokaAbstract: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:
-
Methanoculleus bourgensis Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: Susumu Asakawa, Kazunari NagaokaAbstract: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.
-
Methanoculleus chikugoensis sp nov a novel methanogenic archaeon isolated from paddy field soil in japan and dna dna hybridization among Methanoculleus species
International Journal of Systematic and Evolutionary Microbiology, 2001Co-Authors: Dayeri Dianou, Susumu Asakawa, Kazunari Nagaoka, Taro Miyaki, Hiroyuki Morii, Hiroshi Oyaizu, Satoshi MatsumotoAbstract: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, methanol or methylamines. The optimum temperature and pH were 25-30 degrees C and 6.7-7.2. Analysis of lipid component parts (core lipids, phospholipid polar head groups and glycolipid sugar moieties) showed the characteristic pattern of members of the family Methanomicrobiaceae except for the absence of glucose as a glycolipid sugar moiety. The G+C content of the DNA was 62.2 mol %. Sequence analysis of the 16S rDNA revealed that the strain belonged to the genus Methanoculleus. The strain had DNA-DNA hybridization values of less than 50% with type strains of Methanoculleus species. On the basis of phenotypic, genotypic and phylogenetic characteristics, the name Methanoculleus chikugoensis sp. nov. is proposed for strain MG62T (= JCM 10825T = DSM 13459T). The DNA hybridization study also revealed the close relationships of three species, Methanoculleus olentangyi, Methanoculleus bourgensis and Methanoculleus oldenburgensis, among Methanoculleus species.