The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Stephen H. Zinder - One of the best experts on this subject based on the ideXlab platform.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources ofatmospheric methane, yet the Methanogens in themare poorly characterized. We examined Methanogenicactivities and Methanogen populations at differentdepths in two peatlands, McLean bog (MB) and Chicagobog (CB). Both have acidic (pH 3.5–4.5) peatsoils, but the pH of the deeper layers of CB is nearneutral,reflecting its previous existence as a neutralpHfen. Acetotrophic and hydrogenotrophic Methanogenesiscould be stimulated in upper samples fromboth bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone librariesand by terminal restriction fragment lengthpolymorphism (T-RFLP) analyses using a novelprimer/restriction enzyme set that we developed. Particularlydominant in the upper layers was a clade intheMethanomicrobiales, called E2 here and the R10or fen group elsewhere, estimated by quantitativepolymerase chain reaction to be present at~108cellsper gram of dry peat. Methanogenic activity was considerablylower in deeper samples from both bogs.The Methanogen populations detected by T-RFLP indeeper portions of MB were mainly E2 and the unculturedeuryarchaeal rice cluster (RC)-II group, whereaspopulations in the less acidic CB deep layers wereconsiderably different, and included aMethanomicrobialesclade we call E1-E1¢, as well as RC-I, RC-II,marine benthic group D, and a new cluster that we callthe subaqueous cluster. E2 was barely detectable inthe deeper samples from CB, further evidence for theassociations of most organisms in this group withacidic habitats
-
characterization of acid tolerant h2 co2 utilizing Methanogenic enrichment cultures from an acidic peat bog in new york state
FEMS Microbiology Ecology, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Joseph B Yavitt, Norikiyo Ueno, Stephen H. ZinderAbstract:Two Methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one Methanogen and two bacterial sequences. The Methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from Methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the Methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family Methanogens.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Christine L Sun, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources of atmospheric methane, yet the Methanogens in them are poorly characterized. We examined Methanogenic activities and Methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5-4.5) peat soils, but the pH of the deeper layers of CB is near-neutral, reflecting its previous existence as a neutral-pH fen. Acetotrophic and hydrogenotrophic Methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T-RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales, called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at approximately 10(8) cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The Methanogen populations detected by T-RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)-II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1-E1', as well as RC-I, RC-II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.
-
isolation of a novel acidiphilic Methanogen from an acidic peat bog
Nature, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Hinsby Cadilloquiroz, Joseph B Yavitt, Stephen H. ZinderAbstract:Microbiologists have succeeded in culturing the most acid-loving Methanogen ever discovered. The new species, a member of the Methanomicrobiales group, was found in McLean Bog in New York State. It grows at a preferred pH of around 5, beating the previous record-holder, Methanobacterium espanolae, which has an optimum pH of between 5.5 and 6.0. Although some other Methanogens can survive a pH as low as 4.5, the new species is the first to show growth and optimal Methanogenesis in such acidic conditions. Microbes living in acidic soils are important sources of atmospheric methane, which is linked to global warming. Acidic peatlands are among the largest natural sources of atmospheric methane and harbour a large diversity of Methanogenic Archaea1. Despite the ubiquity of Methanogens in these peatlands, indigenous Methanogens capable of growth at acidic pH values have resisted culture and isolation2,3,4; these recalcitrant Methanogens include members of an uncultured family-level clade in the Methanomicrobiales prevalent in many acidic peat bogs in the Northern Hemisphere1,5,6. However, we recently succeeded in obtaining a mixed enrichment culture of a member of this clade7. Here we describe its isolation and initial characterization. We demonstrate that the optimum pH for Methanogenesis by this organism is lower than that of any previously described Methanogen.
Quan Yuan - One of the best experts on this subject based on the ideXlab platform.
-
inhibitory effects of ammonia on Methanogen mcra transcripts in anaerobic digester sludge
FEMS Microbiology Ecology, 2014Co-Authors: Chen Zhang, Quan Yuan, Yahai LuAbstract:Methanogens in anaerobic ammonia-rich digesters show differential responses to ammonia stress. The mechanism for this is poorly understood. In the present study, we determined the rates of methane production, the composition of Methanogen mcrA (the gene coding for the alpha subunit of methyl-coenzyme M reductase) and their transcripts in response to ammonium addition in the anaerobic sludge retrieved from a full-scale digester treating swine manure. The rate of CH4 production substantially reduced with increased addition of ammonium. The analysis of natural 13C abundances of CH4 and CO2 indicated that the aceticlastic Methanogenesis was more sensitive than hydrogenotrophic Methanogenesis. Quantitative PCR analysis revealed that mcrA copy number decreased by one order of magnitude in the treatment with a large amount of ammonium (10 g ![Graphic][1] -N L−1) but did not change much with treatments of smaller amounts (3 and 7 g ![Graphic][2] -N L−1) compared with the control. T-RFLP analysis of mcrA compositions showed that the structure of the Methanogen community remained highly stable, with Methanosaetaceae dominating the Methanogen community in all incubations. The composition of mcrA transcripts, however, showed a substantial response to the addition of ammonium. The relative abundance of Methanosaetaceae transcripts declined with increasing amounts of ammonium, whereas the transcript level of Methanobacteriales mcrA was relatively resistant. The differential responses corresponded to the shift of Methanogenic pathway inferred from 13C isotope fractionation. Our study suggests that Methanogens in anaerobic sludge have a strong mcrA transcriptional response to ammonia stress without a change in the community structure. [1]: /embed/inline-graphic-1.gif [2]: /embed/inline-graphic-2.gif
-
inhibitory effects of ammonia on Methanogen mcra transcripts in anaerobic digester sludge
FEMS Microbiology Ecology, 2014Co-Authors: Chen Zhang, Quan YuanAbstract:Methanogens in anaerobic ammonia-rich digesters show differential responses to ammonia stress. The mechanism for this is poorly understood. In the present study, we determined the rates of methane production, the composition of Methanogen mcrA (the gene coding for the alpha subunit of methyl-coenzyme M reductase) and their transcripts in response to ammonium addition in the anaerobic sludge retrieved from a full-scale digester treating swine manure. The rate of CH4 production substantially reduced with increased addition of ammonium. The analysis of natural (13)C abundances of CH4 and CO2 indicated that the aceticlastic Methanogenesis was more sensitive than hydrogenotrophic Methanogenesis. Quantitative PCR analysis revealed that mcrA copy number decreased by one order of magnitude in the treatment with a large amount of ammonium (10 g NH4+-N L(-1)) but did not change much with treatments of smaller amounts (3 and 7 g NH4+-N L(-1)) compared with the control. T-RFLP analysis of mcrA compositions showed that the structure of the Methanogen community remained highly stable, with Methanosaetaceae dominating the Methanogen community in all incubations. The composition of mcrA transcripts, however, showed a substantial response to the addition of ammonium. The relative abundance of Methanosaetaceae transcripts declined with increasing amounts of ammonium, whereas the transcript level of Methanobacteriales mcrA was relatively resistant. The differential responses corresponded to the shift of Methanogenic pathway inferred from (13)C isotope fractionation. Our study suggests that Methanogens in anaerobic sludge have a strong mcrA transcriptional response to ammonia stress without a change in the community structure.
Suzanna L Brauer - One of the best experts on this subject based on the ideXlab platform.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources ofatmospheric methane, yet the Methanogens in themare poorly characterized. We examined Methanogenicactivities and Methanogen populations at differentdepths in two peatlands, McLean bog (MB) and Chicagobog (CB). Both have acidic (pH 3.5–4.5) peatsoils, but the pH of the deeper layers of CB is nearneutral,reflecting its previous existence as a neutralpHfen. Acetotrophic and hydrogenotrophic Methanogenesiscould be stimulated in upper samples fromboth bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone librariesand by terminal restriction fragment lengthpolymorphism (T-RFLP) analyses using a novelprimer/restriction enzyme set that we developed. Particularlydominant in the upper layers was a clade intheMethanomicrobiales, called E2 here and the R10or fen group elsewhere, estimated by quantitativepolymerase chain reaction to be present at~108cellsper gram of dry peat. Methanogenic activity was considerablylower in deeper samples from both bogs.The Methanogen populations detected by T-RFLP indeeper portions of MB were mainly E2 and the unculturedeuryarchaeal rice cluster (RC)-II group, whereaspopulations in the less acidic CB deep layers wereconsiderably different, and included aMethanomicrobialesclade we call E1-E1¢, as well as RC-I, RC-II,marine benthic group D, and a new cluster that we callthe subaqueous cluster. E2 was barely detectable inthe deeper samples from CB, further evidence for theassociations of most organisms in this group withacidic habitats
-
characterization of acid tolerant h2 co2 utilizing Methanogenic enrichment cultures from an acidic peat bog in new york state
FEMS Microbiology Ecology, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Joseph B Yavitt, Norikiyo Ueno, Stephen H. ZinderAbstract:Two Methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one Methanogen and two bacterial sequences. The Methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from Methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the Methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family Methanogens.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Christine L Sun, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources of atmospheric methane, yet the Methanogens in them are poorly characterized. We examined Methanogenic activities and Methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5-4.5) peat soils, but the pH of the deeper layers of CB is near-neutral, reflecting its previous existence as a neutral-pH fen. Acetotrophic and hydrogenotrophic Methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T-RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales, called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at approximately 10(8) cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The Methanogen populations detected by T-RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)-II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1-E1', as well as RC-I, RC-II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.
-
isolation of a novel acidiphilic Methanogen from an acidic peat bog
Nature, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Hinsby Cadilloquiroz, Joseph B Yavitt, Stephen H. ZinderAbstract:Microbiologists have succeeded in culturing the most acid-loving Methanogen ever discovered. The new species, a member of the Methanomicrobiales group, was found in McLean Bog in New York State. It grows at a preferred pH of around 5, beating the previous record-holder, Methanobacterium espanolae, which has an optimum pH of between 5.5 and 6.0. Although some other Methanogens can survive a pH as low as 4.5, the new species is the first to show growth and optimal Methanogenesis in such acidic conditions. Microbes living in acidic soils are important sources of atmospheric methane, which is linked to global warming. Acidic peatlands are among the largest natural sources of atmospheric methane and harbour a large diversity of Methanogenic Archaea1. Despite the ubiquity of Methanogens in these peatlands, indigenous Methanogens capable of growth at acidic pH values have resisted culture and isolation2,3,4; these recalcitrant Methanogens include members of an uncultured family-level clade in the Methanomicrobiales prevalent in many acidic peat bogs in the Northern Hemisphere1,5,6. However, we recently succeeded in obtaining a mixed enrichment culture of a member of this clade7. Here we describe its isolation and initial characterization. We demonstrate that the optimum pH for Methanogenesis by this organism is lower than that of any previously described Methanogen.
Andredenis G Wright - One of the best experts on this subject based on the ideXlab platform.
-
metagenomic analysis of Methanogen populations in three full scale mesophilic anaerobic manure digesters operated on dairy farms in vermont usa
Bioresource Technology, 2013Co-Authors: Benoit Stpierre, Andredenis G WrightAbstract:The microbial communities that produce biogas as a result of anaerobic digestion of manure remain poorly understood. Using next-generation sequencing, Methanogen populations were investigated in three full scale mesophilic anaerobic digesters operated on dairy farms. A combined 50 246 non-chimeric sequence reads covering the V1–V3 hypervariable regions of the Methanogen 16S rRNA gene were assigned to 307 species-level operational taxonomic units (OTUs). The Blue Spruce Farms (BSF) and Green Mountain Dairy (GMD) anaerobic digesters were found to have nearly identical Methanogen profiles, with the overwhelming predominance of OTU 1 (98.5% and 99.7%, respectively), which showed 99.2% sequence identity to Methanosarcina thermophila. In contrast, Methanogens from the Chaput Family Farms (CFF) anaerobic digester were more diverse, with five major OTUs belonging to four distinct phylogenetic groups (Methanomicrobiales, Methanosarcinales, Methanoplasmatales, and Methanobacteriales). Differences in management practices and years of operation were hypothesized as potential factors responsible for differences in the Methanogen profiles.
-
Methanogens methane producers of the rumen and mitigation strategies
Archaea, 2010Co-Authors: Sarah E Hook, Andredenis G Wright, B W McbrideAbstract:Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the Methanogen population in the rumen of cattle and sheep, as well as the relationship that Methanogens have with other microorganisms. The rumen Methanogen species differ depending on diet and geographical location of the host, as does Methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the Methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the Methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.
-
community composition and density of Methanogens in the foregut of the tammar wallaby macropus eugenii
Applied and Environmental Microbiology, 2009Co-Authors: Paul N. Evans, Chris Mcsweeney, Lyn A. Hinds, Mark Morrison, Andredenis G WrightAbstract:The composition of the Methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight.
-
a vaccine against rumen Methanogens can alter the composition of archaeal populations
Applied and Environmental Microbiology, 2009Co-Authors: Yvette J Williams, Sam Popovski, Andrew F Toovey, Korinne S Northwood, Lucy Skillman, Andredenis G WrightAbstract:The objectives of this study were to formulate a vaccine based upon the different species/strains of Methanogens present in sheep intended to be immunized and to determine if a targeted vaccine could be used to decrease the methane output of the sheep. Two 16S rRNA gene libraries were used to survey the Methanogenic archaea in sheep prior to vaccination, and Methanogens representing five phylotypes were found to account for >52% of the different species/strains of Methanogens detected. A vaccine based on a mixture of these five Methanogens was then formulated, and 32 sheep were vaccinated on days 0, 28, and 103 with either a control or the anti-Methanogen vaccine. Enzyme-linked immunosorbent assay analysis revealed that each vaccination with the anti-Methanogen formulation resulted in higher specific immunoglobulin G titers in plasma, saliva, and rumen fluid. Methane output levels corrected for dry-matter intake for the control and treatment groups were not significantly different, and real-time PCR data also indicated that Methanogen numbers were not significantly different for the two groups after the second vaccination. However, clone library data indicated that Methanogen diversity was significantly greater in sheep receiving the anti-Methanogen vaccine and that the vaccine may have altered the composition of the Methanogen population. A correlation between 16S rRNA gene sequence relatedness and cross-reactivity for the Methanogens (R2 = 0.90) also exists, which suggests that a highly specific vaccine can be made to target specific strains of Methanogens and that a more broad-spectrum approach is needed for success in the rumen. Our data also suggest that Methanogens take longer than 4 weeks to adapt to dietary changes and call into question the validity of experimental results based upon a 2- to 4-week acclimatization period normally observed for bacteria.
-
long term monensin supplementation does not significantly affect the quantity or diversity of Methanogens in the rumen of the lactating dairy cow
Applied and Environmental Microbiology, 2009Co-Authors: Sarah E Hook, Korinne S Northwood, Andredenis G Wright, B W McbrideAbstract:A long-term monensin supplementation trial involving lactating dairy cattle was conducted to determine the effect of monensin on the quantity and diversity of rumen Methanogens in vivo. Fourteen cows were paired on the basis of days in milk and parity and allocated to one of two treatment groups, receiving (i) a control total mixed ration (TMR) or (ii) a TMR with 24 mg of monensin premix/kg of diet dry matter. Rumen fluid was obtained using an ororuminal probe on day −15 (baseline) and days 20, 90, and 180 following treatment. Throughout the 6-month experiment, the quantity of rumen Methanogens was not significantly affected by monensin supplementation, as measured by quantitative real-time PCR. The diversity of the rumen Methanogen population was investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA clone gene libraries. DGGE analysis at each sampling point indicated that the molecular diversity of rumen Methanogens from monensin-treated cattle was not significantly different from that of rumen Methanogens from control cattle. 16S rRNA gene libraries were constructed from samples obtained from the rumen fluids of five cows, with a total of 166 clones examined. Eleven unique 16S rRNA sequences or phylotypes were identified, five of which have not been recognized previously. The majority of clones (98.2%) belonged to the genus Methanobrevibacter, with all libraries containing Methanobrevibacter strains M6 and SM9 and a novel phylotype, UG3322.2. Overall, long-term monensin supplementation was not found to significantly alter the quantity or diversity of Methanogens in the rumens of lactating dairy cattle in the present study.
Erika Yashiro - One of the best experts on this subject based on the ideXlab platform.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources ofatmospheric methane, yet the Methanogens in themare poorly characterized. We examined Methanogenicactivities and Methanogen populations at differentdepths in two peatlands, McLean bog (MB) and Chicagobog (CB). Both have acidic (pH 3.5–4.5) peatsoils, but the pH of the deeper layers of CB is nearneutral,reflecting its previous existence as a neutralpHfen. Acetotrophic and hydrogenotrophic Methanogenesiscould be stimulated in upper samples fromboth bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone librariesand by terminal restriction fragment lengthpolymorphism (T-RFLP) analyses using a novelprimer/restriction enzyme set that we developed. Particularlydominant in the upper layers was a clade intheMethanomicrobiales, called E2 here and the R10or fen group elsewhere, estimated by quantitativepolymerase chain reaction to be present at~108cellsper gram of dry peat. Methanogenic activity was considerablylower in deeper samples from both bogs.The Methanogen populations detected by T-RFLP indeeper portions of MB were mainly E2 and the unculturedeuryarchaeal rice cluster (RC)-II group, whereaspopulations in the less acidic CB deep layers wereconsiderably different, and included aMethanomicrobialesclade we call E1-E1¢, as well as RC-I, RC-II,marine benthic group D, and a new cluster that we callthe subaqueous cluster. E2 was barely detectable inthe deeper samples from CB, further evidence for theassociations of most organisms in this group withacidic habitats
-
characterization of acid tolerant h2 co2 utilizing Methanogenic enrichment cultures from an acidic peat bog in new york state
FEMS Microbiology Ecology, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Joseph B Yavitt, Norikiyo Ueno, Stephen H. ZinderAbstract:Two Methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one Methanogen and two bacterial sequences. The Methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from Methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the Methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family Methanogens.
-
vertical profiles of Methanogenesis and Methanogens in two contrasting acidic peatlands in central new york state usa
Environmental Microbiology, 2006Co-Authors: Hinsby Cadilloquiroz, Erika Yashiro, Suzanna L Brauer, Joseph B Yavitt, Christine L Sun, Stephen H. ZinderAbstract:Northern acidic peatlands are important sources of atmospheric methane, yet the Methanogens in them are poorly characterized. We examined Methanogenic activities and Methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5-4.5) peat soils, but the pH of the deeper layers of CB is near-neutral, reflecting its previous existence as a neutral-pH fen. Acetotrophic and hydrogenotrophic Methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of Methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T-RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales, called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at approximately 10(8) cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The Methanogen populations detected by T-RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)-II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1-E1', as well as RC-I, RC-II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.
-
isolation of a novel acidiphilic Methanogen from an acidic peat bog
Nature, 2006Co-Authors: Suzanna L Brauer, Erika Yashiro, Hinsby Cadilloquiroz, Joseph B Yavitt, Stephen H. ZinderAbstract:Microbiologists have succeeded in culturing the most acid-loving Methanogen ever discovered. The new species, a member of the Methanomicrobiales group, was found in McLean Bog in New York State. It grows at a preferred pH of around 5, beating the previous record-holder, Methanobacterium espanolae, which has an optimum pH of between 5.5 and 6.0. Although some other Methanogens can survive a pH as low as 4.5, the new species is the first to show growth and optimal Methanogenesis in such acidic conditions. Microbes living in acidic soils are important sources of atmospheric methane, which is linked to global warming. Acidic peatlands are among the largest natural sources of atmospheric methane and harbour a large diversity of Methanogenic Archaea1. Despite the ubiquity of Methanogens in these peatlands, indigenous Methanogens capable of growth at acidic pH values have resisted culture and isolation2,3,4; these recalcitrant Methanogens include members of an uncultured family-level clade in the Methanomicrobiales prevalent in many acidic peat bogs in the Northern Hemisphere1,5,6. However, we recently succeeded in obtaining a mixed enrichment culture of a member of this clade7. Here we describe its isolation and initial characterization. We demonstrate that the optimum pH for Methanogenesis by this organism is lower than that of any previously described Methanogen.