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Sample records for moderately acid-tolerant methanogens

  1. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

    PubMed Central

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  2. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps.

    PubMed

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2-7.5 (optimal 5.5-6.0) and at a temperature range of 30-60°C (optimal 51-55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1-94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  3. Acid tolerance in amphibians

    SciTech Connect

    Pierce, B.A.

    1985-04-01

    Studies of amphibian acid tolerance provide information about the potential effects of acid deposition on amphibian communities. Amphibians as a group appear to be relatively acid tolerant, with many species suffering increased mortality only below pH 4. However, amphibians exhibit much intraspecific variation in acid tolerance, and some species are sensitive to even low levels of acidity. Furthermore, nonlethal effects, including depression of growth rates and increases in developmental abnormalities, can occur at higher pH.

  4. Methanol induces low temperature resilient methanogens and improves methane generation from domestic wastewater at low to moderate temperatures.

    PubMed

    Saha, Shaswati; Badhe, Neha; De Vrieze, Jo; Biswas, Rima; Nandy, Tapas

    2015-01-01

    Low temperature (<20 °C) limits bio-methanation of sewage. Literature shows that hydrogenotrophic methanogens can adapt themselves to low temperature and methanol is a preferred substrate by methanogens in cold habitats. The study hypothesizes that methanol can induce the growth of low-temperature resilient, methanol utilizing, hydrogenotrophs in UASB reactor. The hypothesis was tested in field conditions to evaluate the impact of seasonal temperature variations on methane yield in the presence and absence of methanol. Results show that 0.04% (v/v) methanol increased methane up to 15 times and its effect was more pronounced at lower temperatures. The qPCR analysis showed the presence of Methanobacteriales along with Methanosetaceae in large numbers. This indicates methanol induced the growth of both the hydrogenotrophic and acetoclastic groups through direct and indirect routes, respectively. This study thus demonstrated that methanol can impart resistance in methanogenic biomass to low temperature and can improve performance of UASB reactor. PMID:25913884

  5. Acid tolerance mechanisms utilized by Streptococcus mutans

    PubMed Central

    Matsui, Robert; Cvitkovitch, Dennis

    2010-01-01

    Since its discovery in 1924 by J Clarke, Streptococcus mutans has been the focus of rigorous research efforts due to its involvement in caries initiation and progression. Its ability to ferment a range of dietary carbohydrates can rapidly drop the external environmental pH, thereby making dental plaque inhabitable to many competing species and can ultimately lead to tooth decay. Acid production by this oral pathogen would prove suicidal if not for its remarkable ability to withstand the acid onslaught by utilizing a wide variety of highly evolved acid-tolerance mechanisms. The elucidation of these mechanisms will be discussed, serving as the focus of this review. PMID:20210551

  6. Genetic dissection of acetic acid tolerance in Saccharomyces cerevisiae.

    PubMed

    Geng, Peng; Xiao, Yin; Hu, Yun; Sun, Haiye; Xue, Wei; Zhang, Liang; Shi, Gui-Yang

    2016-09-01

    Dissection of the hereditary architecture underlying Saccharomyces cerevisiae tolerance to acetic acid is essential for ethanol fermentation. In this work, a genomics approach was used to dissect hereditary variations in acetic acid tolerance between two phenotypically different strains. A total of 160 segregants derived from these two strains were obtained. Phenotypic analysis indicated that the acetic acid tolerance displayed a normal distribution in these segregants, and suggested that the acetic acid tolerant traits were controlled by multiple quantitative trait loci (QTLs). Thus, 220 SSR markers covering the whole genome were used to detect QTLs of acetic acid tolerant traits. As a result, three QTLs were located on chromosomes 9, 12, and 16, respectively, which explained 38.8-65.9 % of the range of phenotypic variation. Furthermore, twelve genes of the candidates fell into the three QTL regions by integrating the QTL analysis with candidates of acetic acid tolerant genes. These results provided a novel avenue to obtain more robust strains. PMID:27430512

  7. Osmoregulation in methanogens

    SciTech Connect

    Roberts, M.F.

    1993-01-01

    Our major goal of our work has been to develop and use NMR techniques to study how methanogenic archaebacteria deal with osmotic stress with the hope of providing insights into increasing the salt tolerance of other cells. The project has three main sections: (i) in vivo studies of methanogens; (ii) use of [sup l3]C- and [sup l5]N- labeled potential precursors and in vitro analyses of specific label uptake for elucidation of osmolyte dynamics and biosynthetic pathways of osmolytes in these organisms, and isolation of key biosynthetic enzymes; and (iii) collaborative studies on identification of organic solutes in other methanogens.

  8. 40 CFR 180.180 - Orthoarsenic acid; tolerance for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... residues. 180.180 Section 180.180 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... § 180.180 Orthoarsenic acid; tolerance for residues. (a) General. A tolerance that expires on July 1... exemptions. (c) Tolerances with regional registrations. (d) Indirect or inadvertent residues....

  9. 40 CFR 180.180 - Orthoarsenic acid; tolerance for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... residues. 180.180 Section 180.180 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... § 180.180 Orthoarsenic acid; tolerance for residues. (a) General. A tolerance that expires on July 1... exemptions. (c) Tolerances with regional registrations. (d) Indirect or inadvertent residues....

  10. 40 CFR 180.180 - Orthoarsenic acid; tolerance for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... residues. 180.180 Section 180.180 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... § 180.180 Orthoarsenic acid; tolerance for residues. (a) General. A tolerance that expires on July 1... exemptions. (c) Tolerances with regional registrations. (d) Indirect or inadvertent residues....

  11. Differential soil acidity tolerance of dry bean genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil acidity is a major yield limiting factors for bean production in the tropical regions. Using soil acidity tolerant genotypes is an important strategy in improving bean yields and reducing cost of production. A greenhouse experiment was conducted with the objective of evaluating 20 dry bean geno...

  12. Response of Methanogens in Arctic Sediments to Temperature and Methanogenic Substrate Availability

    PubMed Central

    Blake, Lynsay I.; Tveit, Alexander; Øvreås, Lise; Head, Ian M.; Gray, Neil D.

    2015-01-01

    Although cold environments are major contributors to global biogeochemical cycles, comparatively little is known about their microbial community function, structure, and limits of activity. In this study a microcosm based approach was used to investigate the effects of temperature, and methanogenic substrate amendment, (acetate, methanol and H2/CO2) on methanogen activity and methanogen community structure in high Arctic wetlands (Solvatnet and Stuphallet, Svalbard). Methane production was not detected in Stuphallet sediment microcosms (over a 150 day period) and occurred within Solvatnet sediments microcosms (within 24 hours) at temperatures from 5 to 40°C, the maximum temperature being at far higher than in situ maximum temperatures (which range from air temperatures of -1.4 to 14.1°C during summer months). Distinct responses were observed in the Solvatnet methanogen community under different short term incubation conditions. Specifically, different communities were selected at higher and lower temperatures. At lower temperatures (5°C) addition of exogenous substrates (acetate, methanol or H2/CO2) had no stimulatory effect on the rate of methanogenesis or on methanogen community structure. The community in these incubations was dominated by members of the Methanoregulaceae/WCHA2-08 family-level group, which were most similar to the psychrotolerant hydrogenotrophic methanogen Methanosphaerula palustris strain E1-9c. In contrast, at higher temperatures, substrate amendment enhanced methane production in H2/CO2 amended microcosms, and played a clear role in structuring methanogen communities. Specifically, at 30°C members of the Methanoregulaceae/WCHA2-08 predominated following incubation with H2/CO2, and Methanosarcinaceaeand Methanosaetaceae were enriched in response to acetate addition. These results may indicate that in transiently cold environments, methanogen communities can rapidly respond to moderate short term increases in temperature, but not

  13. Nickel isotopes and methanogens

    NASA Astrophysics Data System (ADS)

    Neubeck, A.; Ivarsson, M.

    2013-12-01

    Methanogens require Ni for their growth and as a consequence the microbial fractionation of Ni isotopes can be used as a biomarker for activity of methanogenic communities1. Anaerobic laboratory experiments was performed using methanogens to investigate methanogenic growth in a modified nutrient media2 with olivine Fo91 (5g/l) added as an additional mineral nutrient source and as the only H2 provider. One of the investigated methanogens showed an increased growth in the experiments with added olivine. There were also a close relationship between the mobilized Ni and the growth of the methanogen. Ni is an element that previously has been neglected in the study of fossilized microorganisms and their interaction with mineral substrates and, thus, there are no records or published data of Ni in association with microfossils. However, we have detected enrichments of Ni in fossilized microorganisms and ichno-fossils, respectively, from three separate locations. Ni is not present in the host rock in any of the samples. Thus, Ni is present in association with fossilized microorganisms from environments and more extensive analysis is required to understand the magnitude, uptake, preservation and fractionation of Ni in microfossils. In order to analyze Ni isotope fractionation from microbe-mineral interaction, we plan to use a high-resolution Laser-Ablation Time-of-Flight Mass Spectrometer (LMS)3. In situ profile ablation will provide detailed and localized data on fractionation patterns between microfossils and their host rock. Also, this technique will allow us to identify the change in Ni isotopic fractionation in rock samples caused by abiotic and biogenic processes in a faster and easier way and with less risk for contamination compared to the wet chemistry analyses of Ni isotopes. 1. Cameron, V., Vance, D., Archer, C. & House, C. H. A biomarker based on the stable isotopes of nickel. Proceedings of the National Academy of Sciences 106, 10944-10948 (2009). 2. Schn

  14. Intracellular pH of acid-tolerant ruminal bacteria.

    PubMed Central

    Russell, J B

    1991-01-01

    Acid-tolerant ruminal bacteria (Bacteroides ruminicola B1(4), Selenomonas ruminantium HD4, Streptococcus bovis JB1, Megasphaera elsdenii B159, and strain F) allowed their intracellular pH to decline as a function of extracellular pH and did not generate a large pH gradient across the cell membrane until the extracellular pH was low (less than 5.2). This decline in intracellular pH prevented an accumulation of volatile fatty acid anions inside the cells. PMID:1781695

  15. Comparative acid tolerances and inhibitor sensitivities of isolated F-ATPases of oral lactic acid bacteria.

    PubMed Central

    Sturr, M G; Marquis, R E

    1992-01-01

    pH activity profiles and inhibitor sensitivities were compared for membrane ATPases isolated from three oral lactic acid bacteria, Lactobacillus casei ATCC 4646, Streptococcus mutans GS-5, and Streptococcus sanguis NCTC 10904, with, respectively, high, moderate, and low levels of acid tolerance. Membranes containing F1F0 ATPases were isolated by means of salt lysis of cells treated with muralytic enzymes. Membrane-free F1F0 complexes were then isolated from membranes by detergent extraction with Triton X-100 or octylglucoside. Finally, F1 complexes free of the proton-conducting F0 sector were obtained by washing membranes with buffers of low ionic strength. The pH activity profiles of the membrane-associated enzymes reflected the general acid tolerances of the organisms from which they were isolated; for example, pH optima were approximately 5.5, 6.0, and 7.0, respectively, for enzymes from L. casei, S. mutans, and S. sanguis. Roughly similar profiles were found for membrane-free F1F0 complexes, which were stabilized by phospholipids against loss of activity during storage. However, profiles for F1 enzymes were distinctly narrower, indicating that association with F0 and possibly other membrane components enhanced tolerance to both acid and alkaline media. All of the enzymes were found to have similar sensitivities to Al-F complexes, but only F1F0 enzymes were highly sensitive to dicyclohexylcarbodiimide. The procedures described for isolation of membrane-free F1F0 forms of the enzymes from oral lactic acid bacteria will be of use in future studies of the characteristics of the enzymes, especially in studies with liposomes. PMID:1386211

  16. Acid tolerance, proton permeabilities, and membrane ATPases of oral streptococci.

    PubMed Central

    Bender, G R; Sutton, S V; Marquis, R E

    1986-01-01

    Differences in acid tolerance among representative oral streptococci were found to be related more closely to the dynamic permeabilities of the bacteria to protons than to differences in the sensitivities of cell membranes to gross damage caused by environmental acidification. For Streptococcus mutans GS-5, Streptococcus sanguis NCTC 10904, and Streptococcus salivarius ATCC 13419, gross membrane damage, indicated by the release of magnesium from whole cells, occurred at pH values below about 4 and was rapid and extensive at pH values of about 3 or less. A more aciduric, lactic acid bacterium, Lactobacillus casei ATCC 4646, was more resistant to environmental acidification, and gross membrane damage was evident only at pH values below 3. Assessments of the movements of protons into S. mutans cells after an acid pulse at various pH values indicated that permeability to protons was minimal at a pH value of about 5, at which the average half time for pH equilibration across the cell membrane was about 12 min. The corresponding values for the less aciduric organism S. sanguis were pH 7 and 8.2 min, and the values for the intermediate organism S. salivarius were pH 6 and 6.6 min. The ATPase inhibitor dicyclohexylcarbodiimide acted to increase markedly the permeability of each organism to protons, and this action indicated that permeability involved not only the passive inflow of protons but also active outflow through the proton-translocating membrane ATPase. Membranes were isolated from each of the bacteria, and pH profiles for ATPase activities indicated pH optima of about 7.5, 7.0, 6.0, and 5.0 for S. sanguis, S. salivarius, S. mutans, and L. casei, respectively. Thus, the pH profiles for the enzymes reflected the acid tolerances of the bacteria and the permeabilities of whole cells to protons. PMID:3015800

  17. Distribution of compatible solutes in the halophilic methanogenic archaebacteria

    SciTech Connect

    Meichin Lai; Sowers, K.R.; Gunsalus, R.P. ); Robertson, D.E.; Roberts, M.F. )

    1991-09-01

    Accumulation of compatible solutes, by uptake or de novo synthesis, enables bacteria to reduce the difference between osmotic potentials of the cell cytoplasm and the extracellular environment. To examine this process in the halophilic and halotolerant methanogenic archaebacteria, 14 strains were tested for the accumulation of compatible solutes in response to growth in various extracellular concentrations of NaCl. In external NaCl concentrations of 0.7 to 3.4 M, the halophilic methanogens accumulated K{sup +} ion and low-molecular-weight organic compounds. {beta}-Glutamate was detected in two halotolerant strains that grew below 1.5 M NaCl. Two unusual {beta}-amino acids, N{sub {var epsilon}}-acetyl-{beta}-lysine and {beta}-glutamine (3-aminoglutaramic acid), as well as L-{alpha}-glutamate were compatible solutes among all of these strains. De novo synthesis of glycine betaine was also detected in several strains of moderately and extremely halophilic methanogens. The zwitterionic compounds ({beta}-glutamine, N{sub {var epsilon}}-acetyl-{beta}-lysine,a nd glycine betaine) and potassium were the predominant compatible solutes among the moderately and extremely halophilic methanogens. This is the first report of {beta}-glutamine as a compatible solute and de novo biosynthesis of glycine betaine in the methanogenic archaebacteria.

  18. Distribution of compatible solutes in the halophilic methanogenic archaebacteria.

    PubMed Central

    Lai, M C; Sowers, K R; Robertson, D E; Roberts, M F; Gunsalus, R P

    1991-01-01

    Accumulation of compatible solutes, by uptake or de novo synthesis, enables bacteria to reduce the difference between osmotic potentials of the cell cytoplasm and the extracellular environment. To examine this process in the halophilic and halotolerant methanogenic archaebacteria, 14 strains were tested for the accumulation of compatible solutes in response to growth in various extracellular concentrations of NaCl. In external NaCl concentrations of 0.7 to 3.4 M, the halophilic methanogens accumulated K+ ion and low-molecular-weight organic compounds. beta-Glutamate was detected in two halotolerant strains that grew below 1.5 M NaCl. Two unusual beta-amino acids, N epsilon-acetyl-beta-lysine and beta-glutamine (3-aminoglutaramic acid), as well as L-alpha-glutamate were compatible solutes among all of these strains. De novo synthesis of glycine betaine was also detected in several strains of moderately and extremely halophilic methanogens. The zwitterionic compounds (beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine) and potassium were the predominant compatible solutes among the moderately and extremely halophilic methanogens. This is the first report of beta-glutamine as a compatible solute and de novo biosynthesis of glycine betaine in the methanogenic archaebacteria. PMID:1909318

  19. 40 CFR 180.318 - 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...)butanoic acid, and its metabolite MCPA, (4-chloro-2-methylphenoxy)acetic acid, in or on the following food... acid; tolerance for residues. 180.318 Section 180.318 Protection of Environment ENVIRONMENTAL... FOOD Specific Tolerances § 180.318 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for...

  20. 40 CFR 180.325 - 2-(m-Chlorophenoxy) propionic acid; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false 2-(m-Chlorophenoxy) propionic acid... Tolerances § 180.325 2-(m-Chlorophenoxy) propionic acid; tolerances for residues. (a) General. A tolerance is established for negligible residues of the plant regulator 2-(m-chlorophenoxy) propionic acid from...

  1. 40 CFR 180.550 - Arsanilic acid [(4-aminophenyl) arsonic acid]; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Arsanilic acid ; tolerances for residues. 180.550 Section 180.550 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.550 Arsanilic acid ; tolerances...

  2. 40 CFR 180.202 - p-Chlorophenoxyacetic acid; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false p-Chlorophenoxyacetic acid; tolerances... Tolerances § 180.202 p-Chlorophenoxyacetic acid; tolerances for residues. (a) General. A tolerance is established for the combined residues of the plant regulator p-chlorophenoxyacetic acid and its metabolite...

  3. 40 CFR 180.202 - p-Chlorophenoxyacetic acid; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false p-Chlorophenoxyacetic acid; tolerances... Tolerances § 180.202 p-Chlorophenoxyacetic acid; tolerances for residues. (a) General. A tolerance is established for the combined residues of the plant regulator p-chlorophenoxyacetic acid and its metabolite...

  4. 40 CFR 180.202 - p-Chlorophenoxyacetic acid; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false p-Chlorophenoxyacetic acid; tolerances... Tolerances § 180.202 p-Chlorophenoxyacetic acid; tolerances for residues. (a) General. A tolerance is established for the combined residues of the plant regulator p-chlorophenoxyacetic acid and its metabolite...

  5. 40 CFR 180.202 - p-Chlorophenoxyacetic acid; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false p-Chlorophenoxyacetic acid; tolerances... Tolerances § 180.202 p-Chlorophenoxyacetic acid; tolerances for residues. (a) General. A tolerance is established for the combined residues of the plant regulator p-chlorophenoxyacetic acid and its metabolite...

  6. 40 CFR 180.202 - p-Chlorophenoxyacetic acid; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false p-Chlorophenoxyacetic acid; tolerances... Tolerances § 180.202 p-Chlorophenoxyacetic acid; tolerances for residues. (a) General. A tolerance is established for the combined residues of the plant regulator p-chlorophenoxyacetic acid and its metabolite...

  7. Iron transformations induced by an acid-tolerant Desulfosporosinus species.

    PubMed

    Bertel, Doug; Peck, John; Quick, Thomas J; Senko, John M

    2012-01-01

    The mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium, Desulfosporosinus sp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe₃S₄) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe₈O₈(OH)₆SO₄ · nH₂O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2. PMID:22038606

  8. Iron Transformations Induced by an Acid-Tolerant Desulfosporosinus Species

    PubMed Central

    Bertel, Doug; Peck, John; Quick, Thomas J.

    2012-01-01

    The mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium, Desulfosporosinus sp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe3S4) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe8O8(OH)6SO4 · nH2O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2. PMID:22038606

  9. Light sensitivity of methanogenic archaebacteria

    SciTech Connect

    Olson, K.D.; McMahon, C.W.; Wolfe, R.S. )

    1991-09-01

    Representatives of four families of methanogenic archaebacteria (archaea), Methanobacterium thermoautotrophicum {Delta}H, Methanobacterium thermoautotrophicum Marburg, Methanosarcina acetivorans, Methanococcus voltae, and Methanomicrobium mobile, were found to be light sensitive. The facultative anaerobic eubacteria Escherichia coli and Salmonella typhimurium, however, were tolerant of light when grown anaerobically under identical light conditions. Interference filters were used to show that the growth of the methanogens is inhibited by light in the blue end of the visible spectrum (370 to 430 nm).

  10. The Geobiochemistry of Methanogen Proteins

    NASA Astrophysics Data System (ADS)

    Prasad, A.; Shock, E.

    2013-12-01

    A principle of geobiochemistry is that adaptation over evolutionary time includes a thermodynamic drive to minimize costs of making biomolecules like proteins and lipids. If so, then biomolecule abundances will reflect, at least in part, their relative stabilities at the conditions imposed by external environments. We tested this hypothesis by comparing relative stabilities of 138 orthologous proteins between a representative lake-sediment methanogen (Methanoculleus marisnigri) and a representative rumen methanogen (Methanospirillum hungatei) at the compositional constraints of their respective environments. Chemical affinities of the proteins were calculated based on pH, temperature, and concentrations of dissolved hydrogen, bicarbonate, ammonia, and hydrogen sulfide, together with standard Gibbs energies of formation of proteins from the elements predicted with a group additivity algorithm for unfolded proteins [1]. Methanogens were chosen as they are chemoautotrophs and their metabolism proceeds at relatively small affinities. Also, they are found in a variety of compositionally varying habitats like rumen, sediments, hydrothermal systems and sewage. The methanogens selected belong to the same order of taxonomy and are closely related. Preliminary results show that a majority of the proteins belonging to the rumen methanogen (66%) are more stable in the rumen environment, while a majority of the proteins belonging to the lake-sediment methanogen (58%) are more stable at sediment conditions. In a separate observation, it was noted that while the complete protein ';proteasome subunit alpha' of another rumen methanogen (Methanobrevibacter smithii) was less stable in its more reducing habitat as compared to a sewage methanogen (Methanothermobacter thermoautotophicus), its first 26 amino acid residues (N terminal) were in fact more stable in its own environment. These 26 residues are reported to be unique as compared to other proteasome proteins and are suggested to

  11. Role for acetotrophic methanogens in methanogenic biodegradation of vinyl chloride

    SciTech Connect

    Bradley, P.M.; Chapelle, F.H.

    1999-10-01

    Under methanogenic conditions, stream-bed sediment microorganisms rapidly degraded [1,2-{sup 14}C]vinyl chloride to {sup 14}CH{sub 4} and {sup 14}CO{sub 2}. Amendment with 2-bromoethanesulfonic acid eliminated {sup 14}CH{sub 4} production and decreased {sup 14}CO{sub 2} recovery by an equal molar amount. Results obtained with [{sup 14}C]ethene, [{sup 14}C]acetate, or {sup 14}CO{sub 2} as substrates indicated that acetotrophic methanogens were responsible for the production of {sup 14}CH{sub 4} during biodegradation of [1,2-{sup 14}C]VC.

  12. Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance.

    PubMed

    Ma, Cui; Wei, Xiaowen; Sun, Cuihuan; Zhang, Fei; Xu, Jianren; Zhao, Xinqing; Bai, Fengwu

    2015-03-01

    Acetic acid is present in cellulosic hydrolysate as a potent inhibitor, and the superior acetic acid tolerance of Saccharomyces cerevisiae ensures good cell viability and efficient ethanol production when cellulosic raw materials are used as substrates. In this study, a mutant strain of S. cerevisiae ATCC4126 (Sc4126-M01) with improved acetic acid tolerance was obtained through screening strains transformed with an artificial zinc finger protein transcription factor (ZFP-TF) library. Further analysis indicated that improved acetic acid tolerance was associated with improved catalase (CAT) activity. The ZFP coding sequence associated with the improved phenotype was identified, and real-time RT-PCR analysis revealed that three of the possible genes involved in the enhanced acetic acid tolerance regulated by this ZFP-TF, namely YFL040W, QDR3, and IKS1, showed decreased transcription levels in Sc4126-M01 in the presence of acetic acid, compared to those in the control strain. Sc4126-M01 mutants having QDR3 and IKS1 deletion (ΔQDR3 and ΔIKS1) exhibited higher acetic acid tolerance than the wild-type strain under acetic acid treatment. Glucose consumption rate and ethanol productivity in the presence of 5 g/L acetic acid were improved in the ΔQDR3 mutant compared to the wild-type strain. Our studies demonstrated that the synthetic ZFP-TF library can be used to improve acetic acid tolerance of S. cerevisiae and that the employment of an artificial transcription factor can facilitate the exploration of novel functional genes involved in stress tolerance of S. cerevisiae. PMID:25698512

  13. Role for acetotrophic methanogens in methanogenic biodegradation of vinyl chloride

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.

    1999-01-01

    Under methanogenic conditions, stream-bed sediment microorganisms rapidly degraded [1,2-14C]vinyl chloride to 14CH4 and 14CO2. Amendment with 2-bromoethanesulfonic acid eliminated 14CH4 production and decreased 14CO2 recovery by an equal molar amount. Results obtained with [14C]ethene, [14C]acetate, or 14CO2 as substrates indicated that acetotrophic methanogens were responsible for the production of 14CH4 during biodegradation of [1,2-14C]VC.Under methanogenic conditions, stream-bed sediment microorganisms rapidly degraded [1,2-14C]vinyl chloride to 14CH4 and 14CO2. Amendment with 2-bromoethanesulfonic acid eliminated 14CH4 production and decreased 14CO2 recovery by an equal molar amount. Results obtained with [14C]-ethene, [14C]acetate, or 14CO2 as substrates indicated that acetotrophic methanogens were responsible for the production of 14CH4, during biodegradation of [1,2-14C]VC.

  14. Methanogens in the Solar System

    NASA Astrophysics Data System (ADS)

    Taubner, Ruth-Sophie; Schleper, Christa; Firneis, Maria G.; Rittmann, Simon

    2015-04-01

    The last decade of space science revealed that potential habitats in the Solar System may not be limited to the classical habitable zone supporting life as we know it. These microorganisms were shown to thrive under extremophilic growth conditions. Here, we outline the main eco-physiological characteristics of methanogens like their response on temperature, pressure, or pH changes or their resistance against radiation or desiccation. They can withstand extreme environmental conditions which makes them intriguing organisms for astrobiological studies. On Earth, they are found for example in wetlands, in arctic and antarctic subglacial environments, in ruminants, and even in the environment surrounding the Mars Desert Research Station in Utah. These obligate anaerobic chemolithoautotrophs or chemolithoheterotrophs are able to use e.g. hydrogen and C1 compounds like CO2, formate, or methanol as energy source and carbon source, respectively. We point out their capability to be able to habitat potential extraterrestrial biospheres all over the planetary system. We will give an overview about these possible environments on Mars, icy moons like Europa or Enceladus, and minor planets. We present an overview about studies of methanogens with an astrobiological relevance and we show our conclusions about the role of methanogens for the search for extraterrestrial life in the Solar System. We will present first results of our study about the possibility to cultivate methanogens under Enceladus-like conditions. For that, based on the observations obtained by the Cassini spacecraft concerning the plume compounds, we produce a medium with a composition similar to the ocean composition of this icy moon which is far more Enceladus-like than in any (published) experiment before. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies with these microbes. We point out the importance of future in-situ or even sample and return missions to

  15. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  16. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  17. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  18. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  19. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tolerances § 180.155 1-Naphthaleneacetic acid; tolerances for residues. (a) General. Tolerances are... Avocado 0.05 12/31/12 (c) Tolerances with regional registrations. (d) Indirect or inadvertent residues....

  20. STUDIES OF METHANOGENIC BACTERIA IN SLUDGE

    EPA Science Inventory

    Methanogenic bacteria were isolated from mesophilic anaerobic digesters. The isolates were able to utilize H2 and CO2 acetate, formate and methanol, but were not able to metabolize propionate and butyrate. It was shown the propionate and butyrate are not substrates for methanogen...

  1. Adaptive acid tolerance response of Vibrio parahaemolyticus as affected by acid adaptation conditions, growth phase, and bacterial strains.

    PubMed

    Chiang, Ming-Lun; Chou, Cheng-Chun; Chen, Hsi-Chia; Tseng, Yu-Ting; Chen, Ming-Ju

    2012-08-01

    Vibrio parahaemolyticus strain 690 was isolated from gastroenteritis patients. Its thermal and ethanol stress responses have been reported in our previous studies. In this study, we further investigated the effects of various acid adaptation conditions including pH (5.0-6.0) and time (30-90 min) on the acid tolerance in different growth phases of V. parahaemolyticus 690. Additionally, the adaptive acid tolerance among different V. parahaemolyticus strains was compared. Results indicated that the acid tolerance of V. parahaemolyticus 690 was significantly increased after acid adaptation at pH 5.5 and 6.0 for 30-90 min. Among the various acid adaptation conditions examined, V. parahaemolyticus 690 acid-adapted at pH 5.5 for 90 min exhibited the highest acid tolerance. The acid adaptation also influenced the acid tolerance of V. parahaemolyticus 690 in different growth phases with late-exponential phase demonstrating the greatest acid tolerance response (ATR) than other phases. Additionally, the results also showed that the induction of adaptive ATR varied with different strains of V. parahaemolyticus. An increase in acid tolerance of V. parahaemolyticus was observed after prior acid adaptation in five strains (556, 690, BCRC 13023, BCRC 13025, and BCRC 12864), but not in strains 405 and BCRC 12863. PMID:22827515

  2. Organic acid-tolerant microorganisms and uses thereof for producing organic acids

    DOEpatents

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-05-06

    Organic acid-tolerant microorganisms and methods of using same. The organic acid-tolerant microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid (3HP), acrylic acid, and propionic acid. Further modifications to the microorganisms such as increasing expression of malonyl-CoA reductase and/or acetyl-CoA carboxylase provide or increase the ability of the microorganisms to produce 3HP. Methods of generating an organic acid with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers include replacing acsA or homologs thereof in cells with genes of interest and selecting for the cells comprising the genes of interest with amounts of organic acids effective to inhibit growth of cells harboring acsA or the homologs.

  3. Koch–Haaf reaction of adamantanols in an acid-tolerant hastelloy-made microreactor

    PubMed Central

    Mukai, Yu

    2011-01-01

    Summary The Koch–Haaf reaction of adamantanols was successfully carried out in a microflow system at room temperature. By combining an acid-tolerant hastelloy-made micromixer, a PTFE tube, and a hastelloy-made microextraction unit, a packaged reaction-to-workup system was developed. By means of the present system, the multigram scale synthesis of 1-adamantanecarboxylic acid was achieved in ca. one hour operation. PMID:21977213

  4. Engineering Clostridium beijerinckii with the Cbei_4693 gene knockout for enhanced ferulic acid tolerance.

    PubMed

    Liu, Jun; Guo, Ting; Shen, Xiaoning; Xu, Jiahui; Wang, Junzhi; Wang, Yanyan; Liu, Dong; Niu, Huanqing; Liang, Lei; Ying, Hanjie

    2016-07-10

    A mutant strain of Clostridium beijerinckii NCIMB 8052, C. beijerinckii M11, which exhibited ferulic acid tolerance up to 0.9g/L, was generated using atmospheric pressure glow discharge and high-throughput screening. Comparative genomic analysis revealed that this strain harbored a mutation of the Cbei_4693 gene, which encodes a hypothetical protein suspected to be an NADPH-dependent FMN reductase. After disrupting the Cbei_4693 gene in C. beijerinckii NCIMB 8052 using the ClosTron group II intron-based gene inactivation system, we obtained the Cbei_4693 gene inactivated mutant strain, C. beijerinckii 4693::int. Compared with C. beijerinckii NCIMB 8052, 6.23g/L of butanol was produced in P2 medium containing 0.5g/L of ferulic acid by 4693::int, and the ferulic acid tolerance was also significantly increased up to 0.8g/L. These data showed, for the first time, that the Cbei_4693 gene plays an important role in regulating ferulic acid tolerance in ABE fermentation by C. beijerinckii. PMID:27164255

  5. The acid tolerance response of Salmonella typhimurium involves transient synthesis of key acid shock proteins.

    PubMed Central

    Foster, J W

    1993-01-01

    Although Salmonella typhimurium prefers neutral-pH environments, it can adapt to survive conditions of severe low-pH stress (pH 3.3). The process, termed the acid tolerance response (ATR), includes two distinct stages. The first stage, called pre-acid shock, is induced at pH 5.8 and involves the production of an inducible pH homeostasis system functional at external pH values below 4.0. The second stage occurs following an acid shock shift to pH 4.5 or below and is called the post-acid shock stage. During this stage of the ATR, 43 acid shock proteins (ASPs) are synthesized. The present data reveal that several ASPs important for pH 3.3 acid tolerance are only transiently produced. Their disappearance after 30 to 40 min of pH 4.4 acid shock coincides with an inability to survive subsequent pH 3.3 acid challenge. Clearly, an essential feature of inducible acid tolerance is an ability to synthesize these key ASPs. The pre-acid shock stage, with its inducible pH homeostasis system, offers the cell an enhanced ability to synthesize ASPs following rapid shifts to conditions below pH 4.0, an external pH that normally prevents ASP synthesis. The data also address possible signals for ASP synthesis. The inducing signal for 22 ASPs appears to be internal acidification, while external pH serves to induce 13 others. Of the 14 transient ASPs, 10 are induced in response to changes in internal pH. Mutations in the fur (ferric uptake regulator) locus that produce an Atr- acid-sensitive phenotype also eliminate induction of six transiently induced ASPs. Images PMID:8458840

  6. Molecular analysis of methanogens involved in methanogenic degradation of tetramethylammonium hydroxide in full-scale bioreactors.

    PubMed

    Whang, Liang-Ming; Hu, Tai-Ho; Liu, Pao-Wen Grace; Hung, Yu-Ching; Fukushima, Toshikazu; Wu, Yi-Ju; Chang, Shao-Hsiung

    2015-02-01

    This study investigated methanogenic communities involved in degradation of tetramethylammonium hydroxide (TMAH) in three full-scale bioreactors treating TMAH-containing wastewater. Based on the results of terminal-restriction fragment-length polymorphism (T-RFLP) and quantitative PCR analyses targeting the methyl-coenzyme M reductase alpha subunit (mcrA) genes retrieved from three bioreactors, Methanomethylovorans and Methanosarcina were the dominant methanogens involved in the methanogenic degradation of TMAH in the bioreactors. Furthermore, batch experiments were conducted to evaluate mcrA messenger RNA (mRNA) expression during methanogenic TMAH degradation, and the results indicated that a higher level of TMAH favored mcrA mRNA expression by Methansarcina, while Methanomethylovorans could only express considerable amount of mcrA mRNA at a lower level of TMAH. These results suggest that Methansarcina is responsible for methanogenic TMAH degradation at higher TMAH concentrations, while Methanomethylovorans may be important at a lower TMAH condition. PMID:25261128

  7. Enhance nisin yield via improving acid-tolerant capability of Lactococcus lactis F44.

    PubMed

    Zhang, Jian; Caiyin, Qinggele; Feng, Wenjing; Zhao, Xiuli; Qiao, Bin; Zhao, Guangrong; Qiao, Jianjun

    2016-01-01

    Traditionally, nisin was produced industrially by using Lactococcus lactis in the neutral fermentation process. However, nisin showed higher activity in the acidic environment. How to balance the pH value for bacterial normal growth and nisin activity might be the key problem. In this study, 17 acid-tolerant genes and 6 lactic acid synthetic genes were introduced in L. lactis F44, respectively. Comparing to the 2810 IU/mL nisin yield of the original strain F44, the nisin titer of the engineered strains over-expressing hdeAB, ldh and murG, increased to 3850, 3979 and 4377 IU/mL, respectively. These engineered strains showed more stable intracellular pH value during the fermentation process. Improvement of lactate production could partly provide the extra energy for the expression of acid tolerance genes during growth. Co-overexpression of hdeAB, murG, and ldh(Z) in strain F44 resulted in the nisin titer of 4913 IU/mL. The engineered strain (ABGL) could grow on plates with pH 4.2, comparing to the surviving pH 4.6 of strain F44. The fed-batch fermentation showed nisin titer of the co-expression L. lactis strain could reach 5563 IU/mL with lower pH condition and longer cultivation time. This work provides a novel strategy of constructing robust strains for use in industry process. PMID:27306587

  8. Enhance nisin yield via improving acid-tolerant capability of Lactococcus lactis F44

    PubMed Central

    Zhang, Jian; Caiyin, Qinggele; Feng, Wenjing; Zhao, Xiuli; Qiao, Bin; Zhao, Guangrong; Qiao, Jianjun

    2016-01-01

    Traditionally, nisin was produced industrially by using Lactococcus lactis in the neutral fermentation process. However, nisin showed higher activity in the acidic environment. How to balance the pH value for bacterial normal growth and nisin activity might be the key problem. In this study, 17 acid-tolerant genes and 6 lactic acid synthetic genes were introduced in L. lactis F44, respectively. Comparing to the 2810 IU/mL nisin yield of the original strain F44, the nisin titer of the engineered strains over-expressing hdeAB, ldh and murG, increased to 3850, 3979 and 4377 IU/mL, respectively. These engineered strains showed more stable intracellular pH value during the fermentation process. Improvement of lactate production could partly provide the extra energy for the expression of acid tolerance genes during growth. Co-overexpression of hdeAB, murG, and ldh(Z) in strain F44 resulted in the nisin titer of 4913 IU/mL. The engineered strain (ABGL) could grow on plates with pH 4.2, comparing to the surviving pH 4.6 of strain F44. The fed-batch fermentation showed nisin titer of the co-expression L. lactis strain could reach 5563 IU/mL with lower pH condition and longer cultivation time. This work provides a novel strategy of constructing robust strains for use in industry process. PMID:27306587

  9. Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea.

    PubMed

    Lazar, Cassandre Sara; Parkes, R John; Cragg, Barry A; L'Haridon, Stéphane; Toffin, Laurent

    2011-08-01

    Submarine mud volcanoes are a significant source of methane to the atmosphere. The Napoli mud volcano, situated in the brine-impacted Olimpi Area of the Eastern Mediterranean Sea, emits mainly biogenic methane particularly at the centre of the mud volcano. Temperature gradients support the suggestion that Napoli is a cold mud volcano with moderate fluid flow rates. Biogeochemical and molecular genetic analyses were carried out to assess the methanogenic activity rates, pathways and diversity in the hypersaline sediments of the centre of the Napoli mud volcano. Methylotrophic methanogenesis was the only significant methanogenic pathway in the shallow sediments (0-40 cm) but was also measured throughout the sediment core, confirming that methylotrophic methanogens could be well adapted to hypersaline environments. Hydrogenotrophic methanogenesis was the dominant pathway below 50 cm; however, low rates of acetoclastic methanogenesis were also present, even in sediment layers with the highest salinity, showing that these methanogens can thrive in this extreme environment. PCR-DGGE and methyl coenzyme M reductase gene libraries detected sequences affiliated with anaerobic methanotrophs (mainly ANME-1) as well as Methanococcoides methanogens. Results show that the hypersaline conditions in the centre of the Napoli mud volcano influence active biogenic methane fluxes and methanogenic/methylotrophic diversity. PMID:21382146

  10. Community and Proteomic Analysis of Methanogenic Consortia Degrading Terephthalate

    PubMed Central

    Wu, Feng-Yau; Chuang, Hui-Ping; Chen, Wei-Yu; Huang, Hung-Jen; Chen, Shu-Hui; Liu, Wen-Tso

    2013-01-01

    Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122–130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum, Methanosaeta, and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ. The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H2/CO2, and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems. PMID:23064332

  11. Identification and quantification of methanogenic archaea in adult chicken ceca

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methanogens, members of the domain Archaea, have been isolated from various animals but few reports exists regarding the isolation of methanogens from chicken, goose, and turkey feces. By using molecular methods for the identification and quantification of methanogenic archea in adult chicken ceca,...

  12. Seasonal Changes in Methanogenesis and Methanogenic Community in Three Peatlands, New York State

    PubMed Central

    Sun, Christine L.; Brauer, Suzanna L.; Cadillo-Quiroz, Hinsby; Zinder, Stephen H.; Yavitt, Joseph B.

    2012-01-01

    Fluctuating environmental conditions can promote diversity and control dominance in community composition. In addition to seasonal temperature and moisture changes, seasonal supply of metabolic substrates selects populations temporally. Here we demonstrate cascading effects in the supply of metabolic substrates on methanogenesis and community composition of anaerobic methanogenic archaea in three contrasting peatlands in upstate New York. Fresh samples of peat soils, collected about every 3 months for 20 months and incubated at 22 ± 2°C regardless of the in situ temperature, exhibited potential rates of methane (CH4) production of 0.02–0.2 mmol L−1 day−1 [380–3800 nmol g−1 (dry) day−1). The addition of acetate stimulated rates of CH4 production in a fen peatland soil, whereas addition of hydrogen (H2), and simultaneous inhibition of H2-consuming acetogenic bacteria with rifampicin, stimulated CH4 production in two acidic bog soils, especially, in autumn and winter. The methanogenic community structure was characterized using T-RFLP analyses of SSU rRNA genes. The E2 group of methanogens (Methanoregulaceae) dominated in the two acidic bog peatlands with relatively greater abundance in winter. In the fen peatland, the E1 group (Methanoregulaceae) and members of the Methanosaetaceae were co-dominant, with E1 having a high relative abundance in spring. Change in relative abundance profiles among methanogenic groups in response to added metabolic substrates was as predicted. The acetate-amendment increased abundance of Methanosarcinaceae, and H2-amendment enhanced abundance of E2 group in all peat soils studied, respectively. Additionally, addition of acetate increased abundance of Methanosaetaceae only in the bog soils. Variation in the supply of metabolic substrates helps explain the moderate diversity of methanogens in peatlands. PMID:22408638

  13. Mechanism of acid tolerance in a rhizobium strain isolated from Pueraria lobata (Willd.) Ohwi.

    PubMed

    Lei, Zhang; Jian-ping, Gu; Shi-qing, Wei; Ze-yang, Zhou; Chao, Zhang; Yongxiong, Yu

    2011-06-01

    The Rhizobium sp. strain PR389 was isolated from the root nodules of Pueraria lobata (Willd.) Ohwi, which grows in acidic (pH 4.6) yellow soil of the Jinyun Mountains of Beibei, Chongqing, China. While rhizobia generally have a pH range of 6.5-7.5 for optimum growth, strain PR389 grew in a liquid yeast extract - mannitol agar medium at pH 4.6, as well as in a pH 4.1 soil suspension, suggesting acid tolerance in this specific strain of rhizobium . However, at pH 4.6, the lag phase before vigorous growth was 40 h compared with 4 h under neutral conditions (pH 7.0). For PR389, the generation time after the lag phase remained the same at different pH levels despite the different durations of the lag phase. Except in the pH 4.4 treatment, the pH of the culturing media increased from 4.6, 4.8, 5.0, and 5.5 to neutral and slightly alkaline after 70 h of culture. Chloramphenicol was added to determine if protein production was involved in the increasing pH process. Chloramphenicol significantly inhibited PR389 growth under acid stress but had little effect under neutral conditions. Proton flux measured during a short acid shock (pH 3.8) revealed that this strain has an intrinsic ability to prevent H(+) from entering cells when compared with acid-sensitive rhizobia. We propose that the mechanism for acid tolerance in PR389 involves both intracellular and extracellular processes. When the extracellular pH is lower than pH 4.4, the cell membrane blocks hydrogen from entering the cell. When the pH exceeds 4.4, the rhizobium strain has the ability to raise the extracellular pH, thereby, potentially decreasing the toxicity of aluminum in acid soil. PMID:21635219

  14. Volatile hydrocarbons inhibit methanogenic crude oil degradation

    PubMed Central

    Sherry, Angela; Grant, Russell J.; Aitken, Carolyn M.; Jones, D. Martin; Head, Ian M.; Gray, Neil D.

    2014-01-01

    Methanogenic degradation of crude oil in subsurface sediments occurs slowly, but without the need for exogenous electron acceptors, is sustained for long periods and has enormous economic and environmental consequences. Here we show that volatile hydrocarbons are inhibitory to methanogenic oil biodegradation by comparing degradation of an artificially weathered crude oil with volatile hydrocarbons removed, with the same oil that was not weathered. Volatile hydrocarbons (nC5–nC10, methylcyclohexane, benzene, toluene, and xylenes) were quantified in the headspace of microcosms. Aliphatic (n-alkanes nC12–nC34) and aromatic hydrocarbons (4-methylbiphenyl, 3-methylbiphenyl, 2-methylnaphthalene, 1-methylnaphthalene) were quantified in the total hydrocarbon fraction extracted from the microcosms. 16S rRNA genes from key microorganisms known to play an important role in methanogenic alkane degradation (Smithella and Methanomicrobiales) were quantified by quantitative PCR. Methane production from degradation of weathered oil in microcosms was rapid (1.1 ± 0.1 μmol CH4/g sediment/day) with stoichiometric yields consistent with degradation of heavier n-alkanes (nC12–nC34). For non-weathered oil, degradation rates in microcosms were significantly lower (0.4 ± 0.3 μmol CH4/g sediment/day). This indicated that volatile hydrocarbons present in the non-weathered oil inhibit, but do not completely halt, methanogenic alkane biodegradation. These findings are significant with respect to rates of biodegradation of crude oils with abundant volatile hydrocarbons in anoxic, sulphate-depleted subsurface environments, such as contaminated marine sediments which have been entrained below the sulfate-reduction zone, as well as crude oil biodegradation in petroleum reservoirs and contaminated aquifers. PMID:24765087

  15. Microbiology and biochemistry of the methanogenic archaeobacteria

    NASA Astrophysics Data System (ADS)

    Abbanat, Darren R.; Aceti, David J.; Baron, Stephen F.; Terlesky, Katherine C.; Ferry, James C.

    The methane producing bacteria area diverse group of organisms that function in nature with other groups of strictly anaerobic bacteria to convert complex organic matter to methane and carbon dioxide. The methanogens belong to the archaeobacteria, a third primary kingdom distinct from all other procaryotes (eubacteria) and eucaryotes. The distinction is based on the unique structures of cell wall and membrane components present in archaeobacteria, as well as differences in the highly conserved 16s rRNA sequences among the three kingdoms. In addition, the methanogens contain several novel cofactors that function as one-carbon carriers during the reduction of carbon dioxide to methane with electrons derived from the oxidation of H2 or formate. Methanogens also convert acetate to methane by a pathway distinct from that for carbon dioxide reduction. The pathway involves activation of acetate to acetyl-SCoA followed by decarbonylation and reduction of the methyl group to methane coupled to the oxidation of the carbonyl group to carbon dioxide.

  16. Bioactive fractions from the pasture legume Biserrula pelecinus L. have an anti-methanogenic effect against key rumen methanogens.

    PubMed

    Banik, Bidhyut K; Durmic, Zoey; Erskine, William; Revell, Clinton K; Vadhanabhuti, Joy; McSweeney, Christopher S; Padmanabha, Jagadish; Flematti, Gavin R; Algreiby, Azizah A; Vercoe, Philip E

    2016-06-01

    Methanogenic archaea (methanogens) are common inhabitants of the mammalian intestinal tract. In ruminants, they are responsible for producing abundant amounts of methane during digestion of food, but selected bioactive plants and compounds may inhibit this activity. Recently, we have identified that, Biserrula pelecinus L. (biserrula) is one such plant and the current study investigated the specific anti-methanogenic activity of the plant. Bioassay-guided extraction and fractionation, coupled with in vitro fermentation batch culture were used to select the most bioactive fractions of biserrula. The four fractions were then tested against five species of methanogens grown in pure culture. Fraction bioactivity was assessed by measuring methane production and amplification of the methanogen mcrA gene. Treatments that showed bioactivity were subcultured in fresh broth without the bioactive fraction to distinguish between static and cidal effects. All four fractions were active against pure cultures, but the F2 fraction was the most consistent inhibitor of both methane production and cell growth, affecting four species of methanogens and also producing equivocal-cidal effects on the methanogens. Other fractions had selective activity affecting only some methanogens, or reducing either methane production or methanogenic cell growth. In conclusion, the anti-methanogenic activity of biserrula can be linked to compounds contained in selected bioactive fractions, with the F2 fraction strongly affecting key rumen methanogens. Further study is required to identify the specific plant compounds in biserrula that are responsible for the anti-methanogenic activity. These findings will help devise novel strategies to control methanogen populations and activity in the rumen, and consequently contribute in reducing greenhouse gas emissions from ruminants. PMID:27060275

  17. Global Transcriptome and Mutagenic Analyses of the Acid Tolerance Response of Salmonella enterica Serovar Typhimurium

    PubMed Central

    Ryan, Daniel; Pati, Niladri Bhusan; Ojha, Urmesh K.; Padhi, Chandrashekhar; Ray, Shilpa; Jaiswal, Sangeeta; Singh, Gajinder P.; Mannala, Gopala K.; Schultze, Tilman; Chakraborty, Trinad

    2015-01-01

    Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the leading causative agents of food-borne bacterial gastroenteritis. Swift invasion through the intestinal tract and successful establishment in systemic organs are associated with the adaptability of S. Typhimurium to different stress environments. Low-pH stress serves as one of the first lines of defense in mammalian hosts, which S. Typhimurium must efficiently overcome to establish an infection. Therefore, a better understanding of the molecular mechanisms underlying the adaptability of S. Typhimurium to acid stress is highly relevant. In this study, we have performed a transcriptome analysis of S. Typhimurium under the acid tolerance response (ATR) and found a large number of genes (∼47%) to be differentially expressed (more than 1.5-fold or less than −1.5-fold; P < 0.01). Functional annotation revealed differentially expressed genes to be associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Additionally, our knockout analysis of a subset of differentially regulated genes facilitated the identification of proteins that contribute to S. Typhimurium ATR and virulence. Mutants lacking genes encoding the K+ binding and transport protein KdpA, hypothetical protein YciG, the flagellar hook cap protein FlgD, and the nitrate reductase subunit NarZ were significantly deficient in their ATRs and displayed varied in vitro virulence characteristics. This study offers greater insight into the transcriptome changes of S. Typhimurium under the ATR and provides a framework for further research on the subject. PMID:26386064

  18. A low-pH-inducible, stationary-phase acid tolerance response in Salmonella typhimurium.

    PubMed Central

    Lee, I S; Slonczewski, J L; Foster, J W

    1994-01-01

    Acid is an important environmental condition encountered by Salmonella typhimurium during its pathogenesis. Our studies have shown that the organism can actively adapt to survive potentially lethal acid exposures by way of at least three possibly overlapping systems. The first is a two-stage system induced in response to low pH by logarithmic-phase cells called the log-phase acid tolerance response (ATR). It involves a major molecular realignment of the cell including the induction of over 40 proteins. The present data reveal that two additional systems of acid resistance occur in stationary-phase cells. One is a pH-dependent system distinct from log-phase ATR called stationary-phase ATR. It was shown to provide a higher level of acid resistance than log-phase ATR but involved the synthesis of fewer proteins. Maximum induction of stationary-phase ATR occurred at pH 4.3. A third system of acid resistance is not induced by low pH but appears to be part of a general stress resistance induced by stationary phase. This last system requires the alternative sigma factor, RpoS. Regulation of log-phase ATR and stationary-phase ATR remains RpoS independent. Although the three systems are for the most part distinct from each other, together they afford maximum acid resistance for S. typhimurium. Images PMID:8113183

  19. Heterotrophic Nitrification in an Acid Forest Soil and by an Acid-Tolerant Fungus

    PubMed Central

    Stroo, Hans F.; Klein, Theodore M.; Alexander, Martin

    1986-01-01

    Nitrate was formed from ammonium at pH 3.2 to 6.1 in suspensions of a naturally acid forest soil; the maximum rates of formation occurred at ca. pH 4 to 5. Nitrate was also formed from soil nitrogen in suspensions incubated at 50°C. Autotrophic nitrifying bacteria could not be isolated from this soil. Enrichment cultures produced nitrate in a medium with β-alanine if much soil was added to the medium, and nitrite but not nitrate was formed in the presence of small amounts of soil. Nitrification by these enrichments was abolished by eucaryotic but not procaryotic inhibitors. A strain of Absidia cylindrospora isolated from this soil was found to produce nitrate and nitrite in a medium with β-alanine at pH values ranging from 4.0 to 4.8. Nitrate production by A. cylindrospora required the presence of sterile soil. Free and bound hydroxylamine, hydroxamic acids, and primary aliphatic nitro compounds did not accumulate during the conversion of β-alanine to nitrite by the fungus. The organism also formed nitrite from ammonium in a medium containing acetate. We suggest that nitrification in this soil is a heterotrophic process catalyzed by acid-tolerant fungi and not by autotrophs or heterotrophs in nonacid microsites. PMID:16347210

  20. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations.

    PubMed

    Stopnisek, Nejc; Bodenhausen, Natacha; Frey, Beat; Fierer, Noah; Eberl, Leo; Weisskopf, Laure

    2014-06-01

    Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp. PMID:23945027

  1. Methanogens: Methane Producers of the Rumen and Mitigation Strategies

    PubMed Central

    Hook, Sarah E.; Wright, André-Denis G.; McBride, Brian W.

    2010-01-01

    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. PMID:21253540

  2. High tolerance of methanogens in granular sludge to oxygen

    SciTech Connect

    Kato, M.T.; Field, J.A.; Lettinga, G. . Dept. of Environmental Technology)

    1993-12-01

    This research assessed the effect of oxygen exposure on the methanogenic activity of anaerobic granular sludges. The toxicity of oxygen to acetoclastic methanogens in five different anaerobic granular sludges was determined in serum flasks with effective gas-to-liquid volumes of 4.65 to 1. The amount of oxygen that caused 50% inhibition of the methanogenic activity after 3 days of exposure ranged from 7% to 41% oxygen in the head space. These results indicate that methanogens located in granular sludge have a high tolerance for oxygen. The most important factor contributing to the tolerance was the oxygen consumption by facultative bacteria metabolizing biodegradable substrates. Uptake of oxygen by these bacteria creates anaerobic microenvironments where the methanogenic bacteria are protected. The results also indicate that methanogens in sludge consortia still have some tolerance to oxygen, even in the absence of facultative substrate for oxygen respiration.

  3. Levels of water-soluble vitamins in methanogenic and non-methanogenic bacteria

    SciTech Connect

    Leigh, J.A.

    1983-03-01

    The levels of seven water-soluble vitamins in Methanobacterium thermoautotropicum, Methanococcus voltae, Escherichia coli, Bacillus subtillis, Pseudomonas fluorescens, and Bacteroides thetaiotaomicron were compared by using a vitamin-requiring Leuconostoc strain. Both methanogens contained levels of folic acid and pantothenic acid which were approximately two orders of magnitude lower than levels in the nonmethanogens. Methanobacterium thermoautotrophicum contained levels of thiamine, biotin, nicotinic acid, and pyridoxine which were approximately one order of magnitude lower than levels in the nonmethanogens. The thiamine level in Methanococcus voltae was approximately one order of magnitude lower than levels in the nonmethanogens. Only the levels of riboflavin (and nicotinic acid and pyridoxine in Methanococcus voltae) were approximately equal in the methanogens and nonmethanogens. Folic acid may have been present in extracts of methanogens merely as a precursor, by-product, or hydrolysis product of methanopterin.

  4. Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens

    NASA Technical Reports Server (NTRS)

    Burggraf, S.; Stetter, K. O.; Rouviere, P.; Woese, C. R.

    1991-01-01

    Analysis of its 16S rRNA sequence shows that the newly discovered hyperthermophilic methanogen, Methanopryus kandleri, is phylogenetically unrelated to any other known methanogen. The organism represents a separate lineage originating near the root of the archaeal tree. Although the 16S rRNA sequence of Mp. kandleri resembles euryarchaeal 16S rRNAs more than it does crenarchaeal, it shows more crenarchaeal signature features than any known euryarchaeal rRNA. Attempts to place it in relation to the root of the archaeal tree show that the Mp. kandleri lineage likely arises from the euryarchaeal branch of the tree. While the existence of so deeply branching a methanogenic lineage brings into question the thesis that methanogenesis evolved from an earlier metabolism similar to that seen in Thermococcus, it at the same time reinforces the notion that the aboriginal [correction of aborginal] archaeon was a thermophile.

  5. Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes.

    PubMed

    Sorokin, Dimitry Y; Abbas, Ben; Merkel, Alexander Y; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Sukhacheva, Marina V; van Loosdrecht, Mark C M

    2015-10-01

    Two groups of haloalkaliphilic methanogenic archaea were dominating in enrichments from hypersaline soda lake sediments at pH 10. At moderate salt concentrations with formate or H2 as electron donor, methanogens belonging to the genus Methanocalculus were enriched, while at high salt concentrations with methylated substrates, a group related to Methanosalsum zhilinae was dominating. For both groups, several pure cultures were obtained including the type strains AMF2T for the Methanocalculus group and AME2T for the Methanosalsum group. The Methanocalculus group is characterized by lithoheterotrophic growth with either formate (preferable substrate) or H2 at moderate salinity up to 1.5-2 M total Na+ and obligate alkaliphilic growth with an optimum at pH 9.5. According to phylogenetic analysis, the group also includes closely related strains isolated previously from the low-salt alkaline Lonar Lake. The novel Methanosalsum group is characterized by high salt tolerance (up to 3.5 M total Na+) and obligate alkaliphilic growth with an optimum at pH 9.5. It has a typical methylotrophic substrate profile, utilizing methanol, methylamines and dimethyl sulfide (at low concentrations) as methanogenic substrates. On the basis of physiological and phylogenetic data, it is proposed that the two groups of soda lake methanogenic isolates are assigned into two novel species, Methanocalculus alkaliphilus sp. nov. (type strain AMF2T = DSM 24457T = UNIQEM U859T) and Methanosalsum natronophilum sp. nov. (type strain AME2T = DSM 24634T = NBRC 110091T). PMID:26228570

  6. Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

    PubMed Central

    Dziewit, Lukasz; Pyzik, Adam; Romaniuk, Krzysztof; Sobczak, Adam; Szczesny, Pawel; Lipinski, Leszek; Bartosik, Dariusz; Drewniak, Lukasz

    2015-01-01

    Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia. PMID:26217325

  7. Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities.

    PubMed

    Dziewit, Lukasz; Pyzik, Adam; Romaniuk, Krzysztof; Sobczak, Adam; Szczesny, Pawel; Lipinski, Leszek; Bartosik, Dariusz; Drewniak, Lukasz

    2015-01-01

    Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia. PMID:26217325

  8. Study of methanogen communities associated with different rumen protozoal populations

    PubMed Central

    Belanche, Alejandro; de la Fuente, Gabriel; Newbold, Charles J

    2014-01-01

    Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7–3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies. PMID:25195951

  9. System-level understanding of the potential acid-tolerance components of Acidithiobacillus thiooxidans ZJJN-3 under extreme acid stress.

    PubMed

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

    In previous study, two extremely acidophilic strains Acidithiobacillus thiooxidans ZJJN-3 (collection site: bioleaching leachate) and ZJJN-5 (collection site: bioleaching wastewater) were isolated from a typical industrial bio-heap in China. Here, we unraveled the potential acid-tolerance components of ZJJN-3 by comparing the physiological differences with ZJJN-5 under different acid stresses. The parameters used for comparison included intracellular pH (pHin), capsule morphology, fatty acid composition of cell membrane, transcription of key molecular chaperones, H(+)-ATPase activities and NAD(+)/NADH ratio. It was indicated that the acid-tolerance of A. thiooxidans ZJJN-3 was systematically regulated. Capsule first thickened and then shed off along with increased acid stress. Cell membrane maintained the intracellular stability by up-regulating the proportion of unsaturated fatty acid and cyclopropane fatty acids. Meanwhile, the transcription of key repair molecular chaperones (GrpE-DnaK-DnaJ) was up-regulated by 2.2-3.5 folds for ensuring the proper folding of peptide. Moreover, low pHin promoted ZJJN-3 to biosynthesize more H(+)-ATPase for pumping H(+) out of cells. Furthermore, the NAD(+)/NADH ratio increased due to the decreased H(+) concentration. Based on the above physiological analysis, the potential acid-tolerance components of A. thiooxidans ZJJN-3 were first proposed and it would be useful for better understanding how these extremophiles responded to the high acid stress. PMID:26264736

  10. Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

    SciTech Connect

    Anderson, Iain; Ulrich, Luke; Lupa, Boguslaw; Susanti, Dwi; Porat, I.; Hooper, Sean; Lykidis, A; Sieprawska-Lupa, Magdalena; Dharmarajan, Lakshmi; Goltsman, Eugene; Lapidus, Alla L.; Saunders, Elizabeth H; Han, Cliff; Land, Miriam L; Lucas, Susan; Mukhopadhyay, Biswarup; Whitman, William; Woese, Carl; Bristow, James; Kyrpides, Nikos C

    2009-01-01

    Background 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. Methodology/Principal Findings In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Conclusions/Significance Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

  11. Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

    SciTech Connect

    Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw; Susanti, Dwi; Porat, Iris; Hooper, Sean D.; Lykidis, Athanasios; Sieprawska-Lupa, Magdalena; Dharmarajan, Lakshmi; Goltsman, Eugene; Lapidus, Alla; Saunders, Elizabeth; Han, Cliff; Land, Miriam; Lucas, Susan; Mukhopadhyay, Biswarup; Whitman, William B.; Woese, Carl; Bristow, James; Kyrpides, Nikos

    2009-05-01

    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. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

  12. Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells.

    PubMed

    Wuchter, Cornelia; Banning, Erin; Mincer, Tracy J; Drenzek, Nicholas J; Coolen, Marco J L

    2013-01-01

    The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderate halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation (AMO) was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation. PMID:24367357

  13. Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells

    PubMed Central

    Wuchter, Cornelia; Banning, Erin; Mincer, Tracy J.; Drenzek, Nicholas J.; Coolen, Marco J. L.

    2013-01-01

    The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderate halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation (AMO) was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation. PMID:24367357

  14. Energetics of syntrophic cooperation in methanogenic degradation.

    PubMed Central

    Schink, B

    1997-01-01

    Fatty acids and alcohols are key intermediates in the methanogenic degradation of organic matter, e.g., in anaerobic sewage sludge digestors or freshwater lake sediments. They are produced by classical fermenting bacteria for disposal of electrons derived in simultaneous substrate oxidations. Methanogenic bacteria can degrade primarily only one-carbon compounds. Therefore, acetate, propionate, ethanol, and their higher homologs have to be fermented further to one-carbon compounds. These fermentations are called secondary or syntrophic fermentations. They are endergonic processes under standard conditions and depend on intimate coupling with methanogenesis. The energetic situation of the prokaryotes cooperating in these processes is problematic: the free energy available in the reactions for total conversion of substrate to methane attributes to each partner amounts of energy in the range of the minimum biochemically convertible energy, i.e., 20 to 25 kJ per mol per reaction. This amount corresponds to one-third of an ATP unit and is equivalent to the energy required for a monovalent ion to cross the charged cytoplasmic membrane. Recent studies have revealed that syntrophically fermenting bacteria synthesize ATP by substrate-level phosphorylation and reinvest part of the ATP-bound energy into reversed electron transport processes, to release the electrons at a redox level accessible by the partner bacteria and to balance their energy budget. These findings allow us to understand the energy economy of these bacteria on the basis of concepts derived from the bioenergetics of other microorganisms. PMID:9184013

  15. Slr2019, lipid A transporter homolog, is essential for acidic tolerance in Synechocystis sp. PCC6803.

    PubMed

    Matsuhashi, Ayumi; Tahara, Hiroko; Ito, Yutaro; Uchiyama, Junji; Ogawa, Satoru; Ohta, Hisataka

    2015-08-01

    Living organisms must defend themselves against various environmental stresses. Extracellular polysaccharide-producing cells exhibit enhanced tolerance toward adverse environmental stress. In Synechocystis sp. PCC6803 (Synechocystis), lipopolysaccharide (LPS) may play a role in this protection. To examine the relationship between stress tolerance of Synechocystis and LPS, we focused on Slr2019 because Slr2019 is homologous to MsbA in Escherichia coli, which is related to LPS synthesis. First, to obtain a defective mutant of LPS, we constructed the slr2019 insertion mutant (slr2019) strain. Sodium deoxycholate-polyacrylamide gel electrophoresis indicated that slr2019 strain did not synthesize normal LPS. Second, to clarify the participation of LPS in acid tolerance, wild type (WT) and slr2019 strain were grown under acid stress; slr2019 strain growth was significantly weaker than WT growth. Third, to examine influences on stress tolerance, slr2019 strain was grown under various stresses. Under salinity and temperature stress, slr2019 strain grew significantly slower than WT. To confirm cell morphology, cell shape and envelope of slr2019 strain were observed by transmission electron microscopy; slr2019 cells contained more electron-transparent bodies than WT cells. Finally, to confirm whether electron-transparent bodies are poly-3-hydroxybutyrate (PHB), slr2019 strain was stained with Nile Blue A, a PHB detector, and observed by fluorescence microscopy. The PHB granule content ratio of WT and slr2019 strain grown at BG-11 pH 8.0 was each 7.18 and 8.41 %. At pH 6.0, the PHB granule content ratio of WT and slr2019 strain was 2.99 and 2.60 %. However, the PHB granule content ratio of WT and slr2019 strain grown at BG-11N-reduced was 10.82 and 0.56 %. Because slr2019 strain significantly decreased PHB under BG-11N-reduced compared with WT, LPS synthesis may be related to PHB under particular conditions. These results indicated that Slr2019 is necessary for

  16. Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen.

    PubMed

    Lüdecke, Claudia; Reiche, Marco; Eusterhues, Karin; Nietzsche, Sandor; Küsel, Kirsten

    2010-10-01

    The ecological importance of Fe(II)-oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O(2) where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ∼ 5) located in northern Bavaria, Germany. Mean O(2) penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid-tolerant FeOB cultivated in gradient tubes were most abundant (10(6) cells g(-1) peat) at the 10-20 cm depth interval. A stable enrichment culture was active at up to 29% O(2) saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid-tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD-1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale-goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid-tolerant population of FeOB is thriving at redox interfaces formed by diffusion-limited O(2) transport in acidic peatlands. Furthermore, this well-adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle. PMID:20545739

  17. The Cytosolic pH of Individual Saccharomyces cerevisiae Cells Is a Key Factor in Acetic Acid Tolerance

    PubMed Central

    Fernández-Niño, Miguel; Marquina, Maribel; Swinnen, Steve; Rodríguez-Porrata, Boris

    2015-01-01

    It was shown recently that individual cells of an isogenic Saccharomyces cerevisiae population show variability in acetic acid tolerance, and this variability affects the quantitative manifestation of the trait at the population level. In the current study, we investigated whether cell-to-cell variability in acetic acid tolerance could be explained by the observed differences in the cytosolic pHs of individual cells immediately before exposure to the acid. Results obtained with cells of the strain CEN.PK113-7D in synthetic medium containing 96 mM acetic acid (pH 4.5) showed a direct correlation between the initial cytosolic pH and the cytosolic pH drop after exposure to the acid. Moreover, only cells with a low initial cytosolic pH, which experienced a less severe drop in cytosolic pH, were able to proliferate. A similar correlation between initial cytosolic pH and cytosolic pH drop was also observed in the more acid-tolerant strain MUCL 11987-9. Interestingly, a fraction of cells in the MUCL 11987-9 population showed initial cytosolic pH values below the minimal cytosolic pH detected in cells of the strain CEN.PK113-7D; consequently, these cells experienced less severe drops in cytosolic pH. Although this might explain in part the difference between the two strains with regard to the number of cells that resumed proliferation, it was observed that all cells from strain MUCL 11987-9 were able to proliferate, independently of their initial cytosolic pH. Therefore, other factors must also be involved in the greater ability of MUCL 11987-9 cells to endure strong drops in cytosolic pH. PMID:26341199

  18. Characterization of the sat Operon in Streptococcus mutans: Evidence for a Role of Ffh in Acid Tolerance

    PubMed Central

    Kremer, Bas H. A.; van der Kraan, Marieke; Crowley, Paula J.; Hamilton, Ian R.; Brady, L. Jeannine; Bleiweis, Arnold S.

    2001-01-01

    An essential protein translocation pathway in Escherichia coli and Bacillus subtilis involves the signal recognition particle (SRP), of which the 54-kDa homolog (Ffh) is an essential component. In a previous study, we found that a transposon insertion in the ylxM-ffh intergenic region of the designated secretion and acid tolerance (sat) operon of Streptococcus mutans resulted in an acid-sensitive phenotype. In the present study, we further characterized this genomic region in S. mutans after construction of bonafide sat operon mutants and confirmed the role of the SRP pathway in acid resistance. Northern blot and primer extension analyses identified an acid-inducible promoter upstream of ylxM that was responsible for upregulating the coordinate expression of all five genes of the sat operon when cells were grown at acid pH. Two constitutive promoters, one immediately upstream of satD and one just 3′ to the acid-inducible promoter, were also identified. Except for Ffh, the functions of the sat operon gene products are unknown. SatC, SatD, and SatE have no homology to proteins with known functions, although YlxM may function as a transcriptional regulator linked to genes encoding SRP pathway proteins. Nonpolar mutations created in each of the five genes of the sat locus resulted in viable mutants. Most striking, however, was the finding that a mutation in ffh did not result in loss of cell viability, as is the case in all other microbial species in which this pathway has been described. This mutant also lacked immunologically detectable Ffh and was severely affected in resistance to acid. Complementation of the mutation resulted in restoration of acid tolerance and reappearance of cytoplasmic Ffh. These data provide evidence that the SRP pathway plays an important role in acid tolerance in S. mutans. PMID:11274114

  19. [Community Structure and Succession of Methanogens in Beishenshu Landfill, Beijing].

    PubMed

    Song, Li-na; Wang, Lei; Xia, Meng-jing; Su, Yue; Li, Zhen-shan

    2015-09-01

    Methanogens are the key microorganisms for landfill stabilization. RT-PCR and qPCR detecting system were employed to determine the types and abundance of methanogens in 2-15 year-old solid wastes that sampled from Beishenshu Landfill, Beijing. The organic components were almost stable and the pH values were in alkaline range, which indicated that the landfill was in the methanogenic process. Methanobacterials, Methanosaeta, and Methanosarcina were detected, among which Methanosaeta and Methanosarcina are acetoclastic, and Methanobacterials are hydrogenotrophic. As landfill processing, within this time range, although the bacterial abundance was significantly decreased, the amount of methanogens was first increased and then decreased, and finally became stable after being landfilled for 9 years. Methanosarcina was the dominate taxa. Significant correlations were found between the methanogens and the volatile fatty acids, but the correlations between methanogens and larger molecular organic matters were relatively weak or even absent. Taken together, our study revealed that the amount of methanogens were affected by substrates, but hardly influenced by the conversion of large molecules in these wastes landfilled for more than 2 years. PMID:26717715

  20. Microbial precipitation of dolomite in methanogenic groundwater

    NASA Astrophysics Data System (ADS)

    Roberts, Jennifer A.; Bennett, Philip C.; González, Luis A.; MacPherson, G. L.; Milliken, Kitty L.

    2004-04-01

    We report low-temperature microbial precipitation of dolomite in dilute natural waters from both field and laboratory experiments. In a freshwater aquifer, microorganisms colonize basalt and nucleate nonstoichiometric dolomite on cell walls. In the laboratory, ordered dolomite formed at near-equilibrium conditions from groundwater with molar Mg:Ca ratios of <1; dolomite was absent in sterile experiments. Geochemical and microbiological data suggest that methanogens are the dominant metabolic guild in this system and are integral to dolomite precipitation. We hypothesize that the attached microbial consortium reacts with the basalt surface, releasing Mg and Ca into solution, which drives dolomite precipitation via nucleation on the cell wall. These findings provide insight into the long-standing dolomite problem and suggest a fundamental role for microbial processes in the formation of dolomite across a wide range of environmental conditions.

  1. The role of hydrogenotrophic methanogens in an acidogenic reactor.

    PubMed

    Huang, Wenhai; Wang, Zhenyu; Zhou, Yan; Ng, Wun Jern

    2015-12-01

    A laboratory-scale acidogenic anaerobic sequencing batch reactor was set up to test the effect of pH change on microbial community structure of the reactor biomass and process performance. No immediate performance change on acidogenesis was observed after the pH change. However, as the hydrogenotrophic methanogen population decreased, hydrogen content in biogas increased followed by a sharp decrease in volatile fatty acids (VFAs) with acetic acid (HAc) in particular. Recovery of reactor performance following pH correction was only apparent after recovery of hydrogenotrophic methanogen population. These suggested hydrogenotrophic methanogens played a very important role in performance of the acidogenic process. PMID:25466820

  2. Methanogenic Conversion of CO2 Into CH4

    SciTech Connect

    Stevens, S.H., Ferry, J.G., Schoell, M.

    2012-05-06

    This SBIR project evaluated the potential to remediate geologic CO2 sequestration sites into useful methane gas fields by application of methanogenic bacteria. Such methanogens are present in a wide variety of natural environments, converting CO2 into CH4 under natural conditions. We conclude that the process is generally feasible to apply within many of the proposed CO2 storage reservoir settings. However, extensive further basic R&D still is needed to define the precise species, environments, nutrient growth accelerants, and economics of the methanogenic process. Consequently, the study team does not recommend Phase III commercial application of the technology at this early phase.

  3. Methanogenic Community Dynamics during Anaerobic Utilization of Agricultural Wastes.

    PubMed

    Ziganshin, A M; Ziganshina, E E; Kleinsteuber, S; Pröter, J; Ilinskaya, O N

    2012-10-01

    This work is devoted to the investigation of the methanogenic archaea involved in anaerobic digestion of cattle manure and maize straw on the basis of terminal restriction fragment length polymorphism (T-RFLP) analysis of archaeal 16S rRNA genes. The biological diversity and dynamics of methanogenic communities leading to anaerobic degradation of agricultural organic wastes with biogas production were evaluated in laboratory-scale digesters. T-RFLP analysis, along with the establishment of archaeal 16S rRNA gene clone libraries, showed that the methanogenic consortium consisted mainly of members of the generaMethanosarcinaandMethanoculleus,with a predominance ofMethanosarcinaspp. throughout the experiment. PMID:23346384

  4. The potential of Methanogenic Life in the Solar System

    NASA Astrophysics Data System (ADS)

    Taubner, R.-S.; Firneis, M. G.; Leitner, J. J.; Schleper, C.; Rittmann, S. K.-M. R.

    2015-10-01

    Methanogens from the domain Archaea are obligate anaerobic chemolithoautotrophs or chemolithoheterotrophs producing methane (CH4). For the CH4-production they primarily use various C1 typecompounds (like carbon monoxide (CO), carbon dioxide (CO2), formate (HCO- 2)), but some strains are also able to utilize methanol (CH3OH), acetate, or even methylsulfides for energy production. The capability of methanogens thriving under various extreme environments on Earth is astonishing. Their enormous diversity and the similarity between their growth conditions and the environmental conditions on extraterrestrial bodies throughout the Solar System make methanogens to an ideal test object for astrobiological experiments.

  5. A hydrogen-based subsurface microbial community dominated by methanogens

    USGS Publications Warehouse

    Chapelle, F.H.; O'Neill, K.; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

    2002-01-01

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  6. A comment on methanogenic bacteria and the primitive ecology

    NASA Technical Reports Server (NTRS)

    Woese, C. R.

    1977-01-01

    As the phenotype of methanogenic bacteria is suggested to have been one of the major factors creating a dynamic balance between CO2 and CH4 in the primitive atmosphere, these organisms are thought to be very ancient. Their antiquity may be further postulated by comparative characterization of their ribosomal RNA. Accepting this antiquity, it is concluded that a carbon-dioxide-methane cycle, driven by photosynthesis, was the major carbon cycle in primitive ecology, and that photosynthesis and methanogens were thus contemporaneous.

  7. Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria

    SciTech Connect

    Ye, D.; Quensen, J.F.; Tiedje, J.M.

    1995-06-01

    When microorganisms eluted from upper Hudson River sediment were cultured without any substrate except polychlorobiphenyl (PCB)-free Hudson River sediment, methane formation was the terminal step of the anaerobic food chain. In sediments containing Aroclor 1242, addition of eubacterium-inhibiting antibiotics, which should have directly inhibited fermentative bacteria and thereby should have indirectly inhibited methanogens, resulted in no dechlorination activity or methane production. However, when substrates for methanogenic bacteria were provided along with the antibiotics (to free the methanogens from dependence on eubacteria), concomitant methane production and dechlorination of PCBs were observed. The dechlorination of Aroclor 1242 was from the para positions, a pattern distinctly different from, and more limited than, the pattern observed with untreated or pasteurized inocula. Both methane production and dechlorination in cultures amended with antibiotics plus methanogenic substrates were inhibited by 2-bromoethanesulfonic acid. These results suggest that the methanogenic bacteria are among the physiological groups capable of anaerobic dechlorination of PCBs, but that the dechlorination observed with methanogenic bacteria is less extensive than the dechlorination observed with more complex anaerobic consortia. 27 refs., 5 figs., 1 tab.

  8. Hydrogenotrophic methanogens dominate in biogas reactors fed with defined substrates.

    PubMed

    Kampmann, K; Ratering, S; Baumann, R; Schmidt, M; Zerr, W; Schnell, S

    2012-09-01

    Methanogenic communities in 200L biogas reactors containing liquid manure were investigated for 33 d. The reactors were consecutively fed with casein, starch and cream. Real-time PCR with primers targeting the gene for methyl coenzyme-M reductase (mcrA) resulted in copy numbers of up to 2.1×10(9) g dry mass(-1). Single strand conformation polymorphism (SSCP) analysis revealed a stable community consisting of few hydrogenotrophic methanogens. One of the two most abundant species was closely related to Methanospirillum hungatei, whereas the other one was only distantly related to other methanogens, with Methanopyrus kandleri being the closest cultivated relative. Most probable number (MPN) cultivations were accomplished with a sample from a 600 m(3) reactor from which all manures used in the experiments originated, and equal cell counts of ca. 10(9) g dry mass(-1) were found for cultivations with acetate, H(2) and methanol. SSCP analysis of these samples and sequencing of the DNA bands identified different hydrogenotrophic methanogens in all samples, and acetoclastic methanogens closely related to Methanosarcina mazei in the samples cultivated with acetate and methanol. As the acetoclastic species were not found in any other SSCP sample, it was supposed that the ammonia values in the manure of the laboratory biogas reactor, which ranged from 2.48 to 3.61 g NH(4)-NL(-1), inhibited the growth of the acetoclastic methanogens. PMID:22918024

  9. Methanogen communities in a municipal landfill complex in China.

    PubMed

    Tang, Wei; Wang, Yangqing; Lei, Yu; Song, Liyan

    2016-05-01

    Landfills are significant global sources of atmospheric methane, but little is known about the ecology and community structure of methanogens in these sites. Here, we investigated the methanogen community based on methyl coenzyme M reductase A gene amplicons in the vertical profiles of three different sites at a municipal landfill complex in China. Links between methanogen communities and refuse properties were explored using multivariate analysis. Clone library results showed that most clones (92%) were related to the hydrogenotrophic methanogens, Methanomicrobiales. Almost all of the Methanomicrobiales clones retrieved in this study are members of the genus Methanoculleus Eight clones were affiliated with the genus Methanofollis The remaining clones were clustered within the genus Methanosarcina Terminal restriction fragment length polymorphism profiles showed that the landfill was predominated by 22 taxa, making up 69%-96% of the community. Of these, a single taxon comprised 36%-65% of the communities across all sites and depths. Principal components analysis separated the methanogen community into three groups, irrespective of site or depth. Redundancy analysis suggested that total phosphorus and pH play roles in structuring methanogen communities in landfills. PMID:27036145

  10. Novel energetic coupling in the methanogenic bacteria

    SciTech Connect

    Carper, S.W.; Rogers, K.R.; Lancaster, J.R. Jr.

    1986-05-01

    The Archaebacteria are a diverse group of organisms which have been proposed to be a third major line of descent, separate and distinct from the prokaryotes and eukaryotes. Among the unique bioenergetic systems in this group are the light-driven ion pumps bacteriorhodopsin and halorhodopsin, present in the halobacteria. The methanogens are a major member of the Archaebacteria, and couple ATP synthesis to electron transfer to generate methane from several simple substrates. The authors report here studies on the basic overall scheme of energetics in these unique organisms, including the following observations: ATP synthesis coupled to electron transfer does not require the obligatory intermediacy of a transmembrane ion gradient, but appears to occur by a direct mechanism. Intracellular ion homeostasis is maintained by a sodium cycle, involving an electrogenic sodium-translocating ATPase. Based on EPR examinations of crude preparations in the presence of physiological electron donors or acceptors, a minimal electron transfer chain is proposed, involving nickel, flavin, and at least three iron-sulfur centers.

  11. Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

    NASA Astrophysics Data System (ADS)

    Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

    2015-12-01

    The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.

  12. Deficiency of PdxR in Streptococcus mutans affects vitamin B6 metabolism, acid tolerance response and biofilm formation

    PubMed Central

    Liao, S.; Bitoun, J.P.; Nguyen, A.H.; Bozner, D.; Yao, X.; Wen, Z.T.

    2015-01-01

    Summary Streptococcus mutans, a key etiological agent of the human dental caries, lives primarily on the tooth surface in tenacious biofilms. The SMU864 locus, designated pdxR, is predicted to encode a member of the novel MocR/GabR family proteins, which are featured with a winged helix DNA-binding N-terminal domain and a C-terminal domain highly homologous to the pyridoxal phosphate-dependent aspartate aminotransferases. A pdxR-deficient mutant, TW296, was constructed using allelic exchange. PdxR deficiency in S. mutans had little effect on cell morphology and growth when grown in brain heart infusion. However, when compared with its parent strain, UA159, the PdxR-deficient mutant displayed major defects in acid tolerance response and formed significantly fewer biofilms (P < 0.01). When analyzed by realtime polymerase chain reaction, PdxR deficiency was found to drastically reduce expression of an apparent operon encoding a pyridoxal kinase (SMU865) and a pyridoxal permease (SMU866) of the salvage pathway of vitamin B6 biosynthesis. In addition, PdxR deficiency also altered the expression of genes for ClpL protease, glucosyl-transferase B and adhesin SpaP, which are known to play important roles in stress tolerance and biofilm formation. Consistently, PdxR-deficiency affected the growth of the deficient mutant when grown in defined medium with and without vitamin B6. Further studies revealed that although S. mutans is known to require vitamin B6 to grow in defined medium, B6 vitamers, especially pyridoxal, were strongly inhibitory at millimolar concentrations, against S. mutans growth and biofilm formation. Our results suggest that PdxR in S. mutans plays an important role in regulation of vitamin B6 metabolism, acid tolerance response and biofilm formation. PMID:25421565

  13. Deficiency of PdxR in Streptococcus mutans affects vitamin B6 metabolism, acid tolerance response and biofilm formation.

    PubMed

    Liao, S; Bitoun, J P; Nguyen, A H; Bozner, D; Yao, X; Wen, Z T

    2015-08-01

    Streptococcus mutans, a key etiological agent of the human dental caries, lives primarily on the tooth surface in tenacious biofilms. The SMU864 locus, designated pdxR, is predicted to encode a member of the novel MocR/GabR family proteins, which are featured with a winged helix DNA-binding N-terminal domain and a C-terminal domain highly homologous to the pyridoxal phosphate-dependent aspartate aminotransferases. A pdxR-deficient mutant, TW296, was constructed using allelic exchange. PdxR deficiency in S. mutans had little effect on cell morphology and growth when grown in brain heart infusion. However, when compared with its parent strain, UA159, the PdxR-deficient mutant displayed major defects in acid tolerance response and formed significantly fewer biofilms (P < 0.01). When analyzed by real-time polymerase chain reaction, PdxR deficiency was found to drastically reduce expression of an apparent operon encoding a pyridoxal kinase (SMU865) and a pyridoxal permease (SMU866) of the salvage pathway of vitamin B6 biosynthesis. In addition, PdxR deficiency also altered the expression of genes for ClpL protease, glucosyltransferase B and adhesin SpaP, which are known to play important roles in stress tolerance and biofilm formation. Consistently, PdxR-deficiency affected the growth of the deficient mutant when grown in defined medium with and without vitamin B6 . Further studies revealed that although S. mutans is known to require vitamin B6 to grow in defined medium, B6 vitamers, especially pyridoxal, were strongly inhibitory at millimolar concentrations, against S. mutans growth and biofilm formation. Our results suggest that PdxR in S. mutans plays an important role in regulation of vitamin B6 metabolism, acid tolerance response and biofilm formation. PMID:25421565

  14. The Small RNA DsrA Influences the Acid Tolerance Response and Virulence of Salmonella enterica Serovar Typhimurium

    PubMed Central

    Ryan, Daniel; Ojha, Urmesh K.; Jaiswal, Sangeeta; Padhi, Chandrashekhar; Suar, Mrutyunjay

    2016-01-01

    The Gram-negative, enteropathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) is exposed to various stress conditions during pathogenesis, of which acid stress serves as a major defense mechanism in the host. Such environments are encountered in the stomach and Salmonella containing vacuole of phagocytic and non-phagocytic cells. It is only recently that small RNAs (sRNAs) have come to the forefront as major regulators of stress response networks. Consequently, the sRNA DsrA which regulates acid resistance in Escherichia coli, has not been characterized in the acid tolerance response (ATR) of Salmonella. In this study, we show dsrA to be induced two and threefold under adaptation and challenge phases of the ATR, respectively. Additionally, an isogenic mutant lacking dsrA (ΔDsrA) displayed lower viability under the ATR along with reduced motility, feeble adhesion and defective invasion efficacy in vitro. Expression analysis revealed down regulation of several Salmonella pathogenicity island-1 (SPI-1) effectors in ΔDsrA compared to the wild-type, under SPI-1 inducing conditions. Additionally, our in vivo data revealed ΔDsrA to be unable to cause gut inflammation in C57BL/6 mice at 72 h post infection, although intracellular survival and systemic dissemination remained unaffected. A possible explanation may be the significantly reduced expression of flagellin structural genes fliC and fljB in ΔDsrA, which have been implicated as major proinflammatory determinants. This study serves to highlight the role of sRNAs such as DsrA in both acid tolerance and virulence of S. Typhimurium. Additionally the robust phenotype of non-invasiveness could be exploited in developing SPI-I attenuated S. Typhimurium strains without disrupting SPI-I genes. PMID:27199929

  15. Methanogenic archaea isolated from Taiwan's Chelungpu fault.

    PubMed

    Wu, Sue-Yao; Lai, Mei-Chin

    2011-02-01

    Terrestrial rocks, petroleum reservoirs, faults, coal seams, and subseafloor gas hydrates contain an abundance of diverse methanoarchaea. However, reports on the isolation, purification, and characterization of methanoarchaea in the subsurface environment are rare. Currently, no studies investigating methanoarchaea within fault environments exist. In this report, we succeeded in obtaining two new methanogen isolates, St545Mb(T) of newly proposed species Methanolobus chelungpuianus and Methanobacterium palustre FG694aF, from the Chelungpu fault, which is the fault that caused a devastating earthquake in central Taiwan in 1999. Strain FG694aF was isolated from a fault gouge sample obtained at 694 m below land surface (mbls) and is an autotrophic, mesophilic, nonmotile, thin, filamentous-rod-shaped organism capable of using H(2)-CO(2) and formate as substrates for methanogenesis. The morphological, biochemical, and physiological characteristics and 16S rRNA gene sequence analysis revealed that this isolate belongs to Methanobacterium palustre. The mesophilic strain St545Mb(T), isolated from a sandstone sample at 545 mbls, is a nonmotile, irregular, coccoid organism that uses methanol and trimethylamine as substrates for methanogenesis. The 16S rRNA gene sequence of strain St545Mb(T) was 99.0% similar to that of Methanolobus psychrophilus strain R15 and was 96 to 97.5% similar to the those of other Methanolobus species. However, the optimal growth temperature and total cell protein profile of strain St545Mb(T) were different from those of M. psychrophilus strain R15, and whole-genome DNA-DNA hybridization revealed less than 20% relatedness between these two strains. On the basis of these observations, we propose that strain St545Mb(T) (DSM 19953(T); BCRC AR10030; JCM 15159) be named Methanolobus chelungpuianus sp. nov. Moreover, the environmental DNA database survey indicates that both Methanolobus chelungpuianus and Methanobacterium palustre are widespread in the

  16. Heavy-Machinery Traffic Impacts Methane Emissions as Well as Methanogen Abundance and Community Structure in Oxic Forest Soils▿†

    PubMed Central

    Frey, Beat; Niklaus, Pascal A.; Kremer, Johann; Lüscher, Peter; Zimmermann, Stephan

    2011-01-01

    Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH4 consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release. PMID:21742929

  17. Physiological and Transcriptomic Analyses of the Thermophilic, Aceticlastic Methanogen Methanosaeta thermophila Responding to Ammonia Stress

    PubMed Central

    Kato, Souichiro; Sasaki, Konomi; Watanabe, Kazuya; Yumoto, Isao; Kamagata, Yoichi

    2014-01-01

    The inhibitory effects of ammonia on two different degradation pathways of methanogenic acetate were evaluated using a pure culture (Methanosaeta thermophila strain PT) and defined co-culture (Methanothermobacter thermautotrophicus strain TM and Thermacetogenium phaeum strain PB), which represented aceticlastic and syntrophic methanogenesis, respectively. Growth experiments with high concentrations of ammonia clearly demonstrated that sensitivity to ammonia stress was markedly higher in M. thermophila PT than in the syntrophic co-culture. M. thermophila PT also exhibited higher sensitivity to high pH stress, which indicated that an inability to maintain pH homeostasis is an underlying cause of ammonia inhibition. Methanogenesis was inhibited in the resting cells of M. thermophila PT with moderate concentrations of ammonia, suggesting that the inhibition of enzymes involved in methanogenesis may be one of the major factors responsible for ammonia toxicity. Transcriptomic analysis revealed a broad range of disturbances in M. thermophila PT cells under ammonia stress conditions, including protein denaturation, oxidative stress, and intracellular cation imbalances. The results of the present study clearly demonstrated that syntrophic acetate degradation dominated over aceticlastic methanogenesis under ammonia stress conditions, which is consistent with the findings of previous studies on complex microbial community systems. Our results also imply that the co-existence of multiple metabolic pathways and their different sensitivities to stress factors confer resiliency on methanogenic processes. PMID:24920170

  18. Growth of Methanogens on a Mars Soil Simulant

    NASA Astrophysics Data System (ADS)

    Kral, Timothy A.; Bekkum, Curtis R.; McKay, Christopher P.

    2004-12-01

    Currently, the surface of Mars is probably too cold, too dry, and too oxidizing for life, as we know it, to exist. But the subsurface is another matter. Life forms that might exist below the surface could not obtain their energy from photosynthesis, but rather they would have to utilize chemical energy. Methanogens are one type of microorganism that might be able to survive below the surface of Mars. A potential habitat for existence of methanogens on Mars might be a geothermal source of hydrogen, possibly due to volcanic or hydrothermal activity, or the reaction of basalt and anaerobic water, carbon dioxide, which is abundant in the martian atmosphere, and of course, subsurface liquid water. We report here that certain methanogens can grow on a Mars soil simulant when supplied with carbon dioxide, molecular hydrogen, and varying amounts of water.

  19. Uranium Binding Mechanisms of the Acid-Tolerant Fungus Coniochaeta fodinicola.

    PubMed

    Vázquez-Campos, Xabier; Kinsela, Andrew S; Collins, Richard N; Neilan, Brett A; Aoyagi, Noboru; Waite, T David

    2015-07-21

    The uptake and binding of uranium [as (UO2)(2+)] by a moderately acidophilic fungus, Coniochaeta fodinicola, recently isolated from a uranium mine site, is examined in this work in order to better understand the potential impact of organisms such as this on uranium sequestration in hydrometallurgical systems. Our results show that the viability of the fungal biomass is critical to their capacity to remove uranium from solution. Indeed, live biomass (viable cells based on vital staining) were capable of removing ∼16 mg U/g dry weight in contrast with dead biomass (autoclaved) which removed ∼45 mg U/g dry weight after 2 h. Furthermore, the uranium binds with different strength, with a fraction ranging from ∼20-50% being easily leached from the exposed biomass by a 10 min acid wash. Results from X-ray absorption spectroscopy measurements show that the strength of uranium binding is strongly influenced by cell viability, with live cells showing a more well-ordered uranium bonding environment, while the distance to carbon or phosphorus second neighbors is similar in all samples. When coupled with time-resolved laser fluorescence and Fourier transformed infrared measurements, the importance of organic acids, phosphates, and polysaccharides, likely released with fungal cell death, appear to be the primary determinants of uranium binding in this system. These results provide an important progression to our understanding with regard to uranium sequestration in hydrometallurgical applications with implications to the unwanted retention of uranium in biofilms and/or its mobility in a remediation context. PMID:26106944

  20. Enzymatic lysis of the pseudomurein-containing methanogen Methanobacterium formicicum.

    PubMed Central

    Bush, J W

    1985-01-01

    A streptomycete isolated from cow manure produces an extracellular enzyme capable of lysing the pseudomurein-containing methanogen Methanobacterium formicicum. The lytic activity has been partially purified from culture fluid and appears to be a serine protease. Similar lytic activity has been fractionated from pronase. Optimal conditions have been developed for lysis of M. formicicum by commercial preparations of proteinase K. The three lytic enzymes have been partially characterized. The results with the three enzyme preparations tend to confirm that proteolytic enzymes are capable of lysing methanogen cells. Images PMID:3891731

  1. Molecular Signatures of Methanogens in Cultures and Environmental Samples

    NASA Astrophysics Data System (ADS)

    Summons, R. E.; Embaye, T.; Jahnke, L. L.; Baumgartner, M.

    2002-12-01

    The core lipids of methanogens comprise C20 and C40 isoprenoid chains, linked through ether bonds to glycerol. Additional structural diversity is encoded into the polar head groups that are attached to the glycerol ether cores. These compounds are potentially very useful as taxonomic markers in microbial mats and other environmental samples while the nature of the hydrocarbon chains provide a means to identify methanogenic inputs to ancient sediments. The structural diversity of methanogen polar lipids is most valuable when it can be directly correlated to 16S rRNA phylogeny. On the other hand, this diversity can also leads to analytical challenges because there is no single approach that works for all structural types. While some intact methanogen lipids have been identified using mass spectrometry and NMR spectroscopy, the most common means of analysing the lipid cores involves cleavage of the ether bonds using HI and subsequent reduction of the alkyl iodides to hydrocarbons with LiAlH4. One class of methanogenic lipids, the 3?-hydroxyarchaeols, escaped detection for some years because strong acid treatments in the analysis protocols destroyed hydroxyl-containing isoprenoid chains. We have been systematically re-examining the lipids of methanogens, using milder procedures involving weak acid hydrolysis of polar head groups, derivatisation to form trimethylsilyl ethers and analysis by GC-MS. As well as archaeol, sn-2- and sn-3-hydroxyarchaeol, we have tentatively identified a dihydroxyarchaeol in several Methanococcus sp. For Methanococcus thermolithotrophicus an analysis of the total lipid extracts using BBr3 as an ether cleavage reagent followed by LiBEt3H, reduction revealed a very complex mixture consisting of phytane, phytenes, biphytane, biphytenes and a suite of related alcohols. The latter compounds were analysed by GC-MS as their trimethylsilyl ethers and found to comprise a mixture tentatively identified as phytan-N-ol and biphytan-N-ol where N= 3 or 7

  2. Syntrophic Degradation of Lactate in Methanogenic Co-cultures

    SciTech Connect

    Meyer, Birte; Stahl, David

    2010-05-17

    In environments where the amount of the inorganic electron acceptors (oxygen, nitrate, sulfate, sulfur oroxidized metal ions (Fe3+;Mn4+) is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic associations of fermenting, acetogenic bacteria (e.g., sulfate-reducing bacteria (SRB) as"secondary fermenters") and methanogenic archaea. In these consortia, the conversion of lactate to acetate, CO2 and methane depends on the cooperating activities of both metabolically distinct microbial groups that are tightly linked by the need to maintain the exchanged metabolites (hydrogenandformate) at very low concentrations.

  3. An ancient divergence among the bacteria. [methanogenic phylogeny

    NASA Technical Reports Server (NTRS)

    Balch, W. E.; Magrum, L. J.; Fox, G. E.; Wolfe, R. S.; Woese, C. R.

    1977-01-01

    The 16S ribosomal RNZs from two species of met methanogenic bacteria, the mesophile Methanobacterium ruminantium and the thermophile Methanobacterium thermoautotrophicum, have been characterized in terms of the oligonucleotides produced by digestion with T1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to 'typical' Procaryotic genera; such as Escherichia, Bacillus and Anacystis. The divergence of the methanogenic bacteria from other bacteria may be the most ancient phylogenetic event yet detected - antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.

  4. Acid-Tolerant Sulfate-Reducing Bacteria Play a Major Role in Iron Cycling in Acidic Iron Rich Sediments

    NASA Astrophysics Data System (ADS)

    Enright, K. A.; Moreau, J. W.

    2008-12-01

    Climate change drives drying and acidification of many rivers and lakes. Abundant sedimentary iron in these systems oxidizes chemically and biologically to form iron-ox(yhydrox)ide crusts and "hardpans". Given generally high sulfate concentrations, the mobilization and cycling of iron in these environments can be strongly influenced by bacterial sulfate reduction. Sulfate-reducing bacteria (SRB) induce reductive dissolution of oxidized iron phases by producing the reductant bisulfide as a metabolic product. These environmentally ubiquitous microbes also recycle much of the fixed carbon in sediment-hosted microbial mat communities. With prevalent drying, the buffering capacity for protons liberated from iron oxidation is exceeded, and the activity of sulfate-reducers is restricted to those species capable of tolerating low pH (and generally highly saline, i.e. sulfate-rich) conditions. These species will sustain the recycling of iron from more crystalline phases to more bioavailable species, as well as act as the only source of bisulfide for photosynthesizing microbial communities. The phylogeny and physiology of acid-tolerant SRB is therefore important to Fe, S and C cycling in iron-rich sedimentary environments, particularly those on a geochemical trajectory towards acidification. Previous studies have shown that these SRB species tend to be highly novel. We studied two distinct environments along a geochemical continuum towards acidification. In both settings, iron redox transformations exert a major, if not controlling, influence on reduction potential. An acidified, iron- rich tidal marsh receiving acid-mine drainage (San Francisco Bay, CA, USA) contained abundant textural evidence for reductive dissolution of Fe(III) in sediments with pH values varying from 2.4 - 3.8. From these sediments, full-length novel dsrAB gene sequences from acid-tolerant SRB were recovered, and sulfur isotope profiles reflected biological fractionation of sulfur under even the most

  5. Snapshot of methanogen sensitivity to temperature in Zoige wetland from Tibetan plateau

    PubMed Central

    Fu, Li; Song, Tianze; Lu, Yahai

    2015-01-01

    Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH4 from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales, and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic methanogenesis to a mixture of hydrogenotrophic and aceticlastic methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this wetland sample. It appears that the aceticlastic methanogenesis dominating at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures. PMID:25745422

  6. Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia

    PubMed Central

    Walker, Robert; Watkin, Elizabeth; Tian, Rui; Bräu, Lambert; O’Hara, Graham; Goodwin, Lynne; Han, James; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2013-01-01

    Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod that was trapped in 2001 from acidic soil collected from Karijini National Park (Australia) using Gastrolobium capitatum as a host. WSM2232 was effective in nitrogen fixation with G. capitatum but subsequently lost symbiotic competence during long-term storage. Here we describe the features of Burkholderia sp. strain WSM2232, together with genome sequence information and its annotation. The 7,208,311 bp standard-draft genome is arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes and 61 RNA-only encoding genes. The loss of symbiotic capability can now be attributed to the loss of nodulation and nitrogen fixation genes from the genome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197442

  7. Absence of Rtt109p, a fungal-specific histone acetyltransferase, results in improved acetic acid tolerance of Saccharomyces cerevisiae.

    PubMed

    Cheng, Cheng; Zhao, Xinqing; Zhang, Mingming; Bai, Fengwu

    2016-03-01

    RTT109 is a histone acetyltransferase for the acetylation of histone H3. It is still not clear whether RTT109 plays a role in regulation of gene expression under environmental stresses. In this study, the involvement of RTT109 in acetic acid stress tolerance of Saccharomyces cerevisiae was investigated. It was revealed that the absence of RTT109 enhanced resistance to 5.5 g L(-1) acetic acid, which was indicated by improved growth of RTT109Δ mutant compared with that of the wild-type BY4741 strain. Meanwhile, the lag phase was shortened for 48 h and glucose consumption completed 36 h in advance for RTT109Δ mutant compared to the wild-type strain, with ethanol production rate increased from 0.39 to 0.60 g L(-1) h(-1). Significantly, elevated transcription levels of HSP12, CTT1 and GSH1, as well as increased activities of antioxidant enzymes were observed in RTT109Δ under acetic acid stress. Improved flocculation of RTT109Δ compared to that of the control strain BY4741 under the acetic acid stress was also observed. These results suggest that the absence of RTT109 not only activates transcription of stress responsive genes, but also improves resistance to oxidative stress, which ultimately contributes to improved acetic acid tolerance in S. cerevisiae. PMID:26851403

  8. Nuclear Localization of Haa1, Which Is Linked to Its Phosphorylation Status, Mediates Lactic Acid Tolerance in Saccharomyces cerevisiae

    PubMed Central

    Sugiyama, Minetaka; Akase, Shin-Pei; Nakanishi, Ryota; Horie, Hitoshi; Kaneko, Yoshinobu

    2014-01-01

    Improvement of the lactic acid resistance of the yeast Saccharomyces cerevisiae is important for the application of the yeast in industrial production of lactic acid from renewable resources. However, we still do not know the precise mechanisms of the lactic acid adaptation response in yeast and, consequently, lack effective approaches for improving its lactic acid tolerance. To enhance our understanding of the adaptation response, we screened for S. cerevisiae genes that confer enhanced lactic acid resistance when present in multiple copies and identified the transcriptional factor Haa1 as conferring resistance to toxic levels of lactic acid when overexpressed. The enhanced tolerance probably results from increased expression of its target genes. When cells that expressed Haa1 only from the endogenous promoter were exposed to lactic acid stress, the main subcellular localization of Haa1 changed from the cytoplasm to the nucleus within 5 min. This nuclear accumulation induced upregulation of the Haa1 target genes YGP1, GPG1, and SPI1, while the degree of Haa1 phosphorylation observed under lactic acid-free conditions decreased. Disruption of the exportin gene MSN5 led to accumulation of Haa1 in the nucleus even when no lactic acid was present. Since Msn5 was reported to interact with Haa1 and preferentially exports phosphorylated cargo proteins, our results suggest that regulation of the subcellular localization of Haa1, together with alteration of its phosphorylation status, mediates the adaptation to lactic acid stress in yeast. PMID:24682296

  9. The synergistic preservative effects of the essential oils of sweet basil (Ocimum basilicum L.) against acid-tolerant food microflora.

    PubMed

    Lachowicz, K J; Jones, G P; Briggs, D R; Bienvenu, F E; Wan, J; Wilcock, A; Coventry, M J

    1998-03-01

    Essential oils extracted by hydrodistillation from five different varieties of Ocimum basilicum L. plants (Anise, Bush, Cinnamon, Dark Opal and a commercial sample of dried basil) were examined for antimicrobial activity against a wide range of foodborne Gram-positive and -negative bacteria, yeasts and moulds by an agar well diffusion method. All five essential oils of basil showed antimicrobial activity against most of the organisms tested with the exception of Flavimonas oryzihabitans and Pseudomonas species. The inhibitory effect of Anise oil, in comparison with mixtures of the predominant components of pure linalool and methyl chavicol, against the acid-tolerant organisms, Lactobacillus curvatus and Saccharomyces cerevisiae, was examined in broth by an indirect impedance method. Synergistic effects between Anise oil, low pH (pH 4.2) and salt (5% NaCl) were determined. The antimicrobial effect of Anise oil was also assessed in a tomato juice medium by direct viable count, showing that the growth of Lact. curvatus and S. cerevisiae was completely inhibited by 0.1% and 1% Anise oil, respectively. The results of the current study indicate the need for further investigations to understand the antimicrobial effects of basil oils in the presence of other food ingredients and preservation parameters. PMID:9569711

  10. Open fermentative production of fuel ethanol from food waste by an acid-tolerant mutant strain of Zymomonas mobilis.

    PubMed

    Ma, Kedong; Ruan, Zhiyong; Shui, Zongxia; Wang, Yanwei; Hu, Guoquan; He, Mingxiong

    2016-03-01

    The aim of present study was to develop a process for open ethanol fermentation from food waste using an acid-tolerant mutant of Zymomonas mobilis (ZMA7-2). The mutant showed strong tolerance to acid condition of food waste hydrolysate and high ethanol production performance. By optimizing fermentation parameters, ethanol fermentation with initial glucose concentration of 200 g/L, pH value around 4.0, inoculum size of 10% and without nutrient addition was considered as best conditions. Moreover, the potential of bench scales fermentation and cell reusability was also examined. The fermentation in bench scales (44 h) was faster than flask scale (48 h), and the maximum ethanol concentration and ethanol yield (99.78 g/L, 0.50 g/g) higher than that of flask scale (98.31 g/L, 0.49 g/g). In addition, the stable cell growth and ethanol production profile in five cycles successive fermentation was observed, indicating the mutant was suitable for industrial ethanol production. PMID:26744803

  11. Comparative study of aluminum and copper transport and toxicity in an acid-tolerant freshwater green alga

    SciTech Connect

    Folsom, B.R.; Popescu, N.A.; Wood, J.M.

    1986-06-01

    A comparative study of the transport and toxicity of one nonessential metal (aluminum), and one essential metal (copper), has been performed with the acid-tolerant green alga Chlorella saccarophila. This organism was isolated from a naturally acidified lake and grows well in laboratory cultures at pH 3.0. Our results show that the fast-exchange ions Ca/sup 2 +/, Mg/sup 2 +/, and Na/sup +/ offer some protection against both Al/sup 3 +/ and Cu/sup 2 +/ toxicity whereas K/sup +/ protects against Al/sup 3 +/ toxicity but enhances Cu/sup 2 +/ toxicity. Plasma emission spectroscopy shows that complexation of Al/sup 3 +/ and Fe/sup 3 +/ to cell surfaces is important in preventing toxic cytoplasmic levels of these metals, both in culture media and in acid mine water. The aqueous ion chemistry for toxic metal uptake is simplified considerably in acidic conditions, where competing hydrolysis and precipitation reactions are eliminated. Therefore, simple competitive experiments can be performed quantitatively. 12 references, 7 figures, 1 table.

  12. Multiple-unit tablet of probiotic bacteria for improved storage stability, acid tolerability, and in vivo intestinal protective effect

    PubMed Central

    Park, Hee Jun; Lee, Ga Hyeon; Jun, Joonho; Son, Miwon; Kang, Myung Joo

    2016-01-01

    The aim of this study was to formulate probiotics-loaded pellets in a tablet form to improve storage stability, acid tolerability, and in vivo intestinal protective effect. Bacteria-loaded pellets primarily prepared with hydroxypropyl methylcellulose acetate succinate were compressed into tablets with highly compressible excipients and optimized for flow properties, hardness, and disintegration time. The optimized probiotic tablet consisted of enteric-coated pellets (335 mg), microcrystalline cellulose (Avicel PH102, 37.5 mg), and porous calcium silicate (25 mg) and allowed whole survival of living bacteria during the compaction process with sufficient tablet hardness (13 kp) and disintegration time (14 minutes). The multiple-unit tablet showed remarkably higher storage stability under ambient conditions (25°C/60% relative humidity) over 6 months and resistance to acidic medium compared to uncoated strains or pellets. Repeated intake of this multiple-unit tablet significantly lowered plasma level of endotoxin, a pathogenic material, compared to repeated intake of bare probiotics or marketed products in rats. These results, therefore, suggest that the multiple-unit tablet is advantageous to better bacterial viability and gain the beneficial effects on the gut flora, including the improvement of intestinal barrier function. PMID:27103789

  13. Multiple-unit tablet of probiotic bacteria for improved storage stability, acid tolerability, and in vivo intestinal protective effect.

    PubMed

    Park, Hee Jun; Lee, Ga Hyeon; Jun, Joonho; Son, Miwon; Kang, Myung Joo

    2016-01-01

    The aim of this study was to formulate probiotics-loaded pellets in a tablet form to improve storage stability, acid tolerability, and in vivo intestinal protective effect. Bacteria-loaded pellets primarily prepared with hydroxypropyl methylcellulose acetate succinate were compressed into tablets with highly compressible excipients and optimized for flow properties, hardness, and disintegration time. The optimized probiotic tablet consisted of enteric-coated pellets (335 mg), microcrystalline cellulose (Avicel PH102, 37.5 mg), and porous calcium silicate (25 mg) and allowed whole survival of living bacteria during the compaction process with sufficient tablet hardness (13 kp) and disintegration time (14 minutes). The multiple-unit tablet showed remarkably higher storage stability under ambient conditions (25°C/60% relative humidity) over 6 months and resistance to acidic medium compared to uncoated strains or pellets. Repeated intake of this multiple-unit tablet significantly lowered plasma level of endotoxin, a pathogenic material, compared to repeated intake of bare probiotics or marketed products in rats. These results, therefore, suggest that the multiple-unit tablet is advantageous to better bacterial viability and gain the beneficial effects on the gut flora, including the improvement of intestinal barrier function. PMID:27103789

  14. Solid and liquid media for isolating and cultivating acidophilic and acid-tolerant sulfate-reducing bacteria.

    PubMed

    Ňancucheo, Ivan; Rowe, Owen F; Hedrich, Sabrina; Johnson, D Barrie

    2016-05-01

    Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro The main features of the 'standard' solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors. PMID:27036143

  15. Survival of methanogens during desiccation: implications for life on Mars.

    PubMed

    Kendrick, Michael G; Kral, Timothy A

    2006-08-01

    The relatively recent discoveries that liquid water likely existed on the surface of past Mars and that methane currently exists in the martian atmosphere have fueled the possibility of extant or extinct life on Mars. One possible explanation for the existence of the methane would be the presence of methanogens in the subsurface. Methanogens are microorganisms in the domain Archaea that can metabolize molecular hydrogen as an energy source and carbon dioxide as a carbon source and produce methane. One factor of importance is the arid nature of Mars, at least at the surface. If one is to assume that life exists below the surface, then based on the only example of life that we know, liquid water must be present. Realistically, however, that liquid water may be seasonal just as it is at some locations on our home planet. Here we report on research designed to determine how long certain species of methanogens can survive desiccation on a Mars soil simulant, JSC Mars-1. Methanogenic cells were grown on JSC Mars-1, transferred to a desiccator within a Coy anaerobic environmental chamber, and maintained there for varying time periods. Following removal from the desiccator and rehydration, gas chromatographic measurements of methane indicated survival for varying time periods. Methanosarcina barkeri survived desiccation for 10 days, while Methanobacterium formicicum and Methanothermobacter wolfeii were able to survive for 25 days. PMID:16916281

  16. Survival of Methanogens During Desiccation: Implications for Life on Mars

    NASA Astrophysics Data System (ADS)

    Kendrick, Michael G.; Kral, Timothy A.

    2006-08-01

    The relatively recent discoveries that liquid water likely existed on the surface of past Mars and that methane currently exists in the martian atmosphere have fueled the possibility of extant or extinct life on Mars. One possible explanation for the existence of the methane would be the presence of methanogens in the subsurface. Methanogens are microorganisms in the domain Archaea that can metabolize molecular hydrogen as an energy source and carbon dioxide as a carbon source and produce methane. One factor of importance is the arid nature of Mars, at least at the surface. If one is to assume that life exists below the surface, then based on the only example of life that we know, liquid water must be present. Realistically, however, that liquid water may be seasonal just as it is at some locations on our home planet. Here we report on research designed to determine how long certain species of methanogens can survive desiccation on a Mars soil simulant, JSC Mars-1. Methanogenic cells were grown on JSC Mars-1, transferred to a desiccator within a Coy anaerobic environmental chamber, and maintained there for varying time periods. Following removal from the desiccator and rehydration, gas chromatographic measurements of methane indicated survival for varying time periods. Methanosarcina barkeri survived desiccation for 10 days, while Methanobacterium formicicum and Methanothermobacter wolfeii were able to survive for 25 days.

  17. NATURAL ATTENUATION OF MTBE IN THE SUBSURFACE UNDER METHANOGENIC CONDITIONS

    EPA Science Inventory

    This case study was conducted at the former Fuel Farm Site at the U.S.Coast Guard Support Center at Elizabeth City, North Carolina. The study is intended to answer the following questions. Can MTBE be biodegraded under methanogenic conditions in ground water that was contaminated...

  18. Dynamics of the Methanogenic Archaea in Tropical Estuarine Sediments

    PubMed Central

    Torres-Alvarado, María del Rocío; Fernández, Francisco José; Ramírez Vives, Florina; Varona-Cordero, Francisco

    2013-01-01

    Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g) compared with the dry season (104–106 cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA. PMID:23401664

  19. Methane as a product of chloroethene biodegradation under methanogenic conditions

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.

    1999-01-01

    Radiometric detection headspace analyses of microcosms containing bed sediments from two geographically distinct sites indicated that 10-39% of the radiolabeled carbon transformed during anaerobic biodegradation of [1,2- 14C]trichloroethene (TCE) or [1,2-14C]vinyl chloride (VC) under methanogenic conditions was ultimately incorporated into 14CH4. The results demonstrate that, in addition to ethene, ethane, and CO2, CH4 can be a significant product of chloroethene biodegradation in some methanogenic sediments.Radiometric detection headspace analyses of microcosms containing bed sediments from two geographically distinct sites indicated that 10-39% of the radiolabeled carbon transformed during anaerobic biodegradation of [1,2-14C]trichloroethene (TCE) or [1,2-14C]vinyl chloride (VC) under methanogenic conditions was ultimately incorporated into 14CH4. The results demonstrate that, in addition to ethene, ethane, and CO2, CH4 can be a significant product of chloroethene biodegradation in some methanogenic sediments.

  20. Relating methanogen community structure and anaerobic digester function.

    PubMed

    Bocher, B T W; Cherukuri, K; Maki, J S; Johnson, M; Zitomer, D H

    2015-03-01

    Much remains unknown about the relationships between microbial community structure and anaerobic digester function. However, knowledge of links between community structure and function, such as specific methanogenic activity (SMA) and COD removal rate, are valuable to improve anaerobic bioprocesses. In this work, quantitative structure-activity relationships (QSARs) were developed using multiple linear regression (MLR) to predict SMA using methanogen community structure descriptors for 49 cultures. Community descriptors were DGGE demeaned standardized band intensities for amplicons of a methanogen functional gene (mcrA). First, predictive accuracy of MLR QSARs was assessed using cross validation with training (n = 30) and test sets (n = 19) for glucose and propionate SMA data. MLR equations correlating band intensities and SMA demonstrated good predictability for glucose (q(2) = 0.54) and propionate (q(2) = 0.53). Subsequently, data from all 49 cultures were used to develop QSARs to predict SMA values. Higher intensities of two bands were correlated with higher SMA values; high abundance of methanogens associated with these two bands should be encouraged to attain high SMA values. QSARs are helpful tools to identify key microorganisms or to study and improve many bioprocesses. Development of new, more robust QSARs is encouraged for anaerobic digestion or other bioprocesses, including nitrification, nitritation, denitrification, anaerobic ammonium oxidation, and enhanced biological phosphorus removal. PMID:25562581

  1. Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

    SciTech Connect

    Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.; McHardy, Alice C.; Copeland, Alex 5; Kyrpides, Nikos C.; Hugenholtz, Philip; Liu, Wen-Tso

    2010-08-05

    Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium tinside a hyper-mesophilic (i.e., between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H{sub 2}/CO{sub 2} and acetate. These intermediates are converted to CH{sub 4}/CO{sub 2} by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to COsub 2}/H{sub 2} and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H{sub 2}-producing syntroph ? methanogen partnership that may serve to improve community stability.

  2. Adaptation of a methanogenic consortium to arsenite inhibition

    PubMed Central

    Rodriguez-Freire, Lucia; Moore, Sarah E.; Sierra-Alvarez, Reyes; Field, James A.

    2016-01-01

    Arsenic (As) is a ubiquitous metalloid known for its adverse effects to human health. Microorganisms are also impacted by As toxicity, including methanogenic archaea, which can affect the performance of process in which biological activity is required (i.e. stabilization of activated sludge in wastewater treatment plants). The novel ability of a mixed methanogenic granular sludge consortium to adapt to the inhibitory effect of arsenic (As) was investigated by exposing the culture to approximately 0.92 mM of AsIII for 160 d in an arsenate (AsV) reducing bioreactor using ethanol as the electron donor. The results of shaken batch bioassays indicated that the original, unexposed sludge was severely inhibited by arsenite (AsIII) as evidenced by the low 50% inhibition concentrations (IC50) determined, i.e., 19 and 90 μM for acetoclastic- and hydrogenotrophic methanogenesis, respectively. The tolerance of the acetoclastic and hydrogenotrophic methanogens in the sludge to AsIII increased 47-fold (IC50 = 910 μM) and 12-fold (IC50= 1100 μM), respectively, upon long-term exposure to As. In conclusion, the methanogenic community in the granular sludge demonstrated a considerable ability to adapt to the severe inhibitory effects of As after a prolonged exposure period. PMID:26823637

  3. Metabolism of 3-methylindole by a methanogenic consortium

    SciTech Connect

    Jidong Gu; Berry, D.F. )

    1992-08-01

    A methanogenic 3-methylindole (3-MI)-degrading consortium, enriched from wetland soil, completely mineralized 3-MI. Degradation proceeded through an initial hydroxylation reaction forming 3-methyloxindole. The consortium was unable to degrade oxindole or isatin, suggesting a new pathway for 3-MI fermentation. 3-Methylindole was identified by mass spectroscopy, ultraviolet spectroscopy, and proton nuclear magnetic resonance spectrometry.

  4. Impact of dewatering technologies on specific methanogenic activity.

    PubMed

    Batstone, Damien J; Lu, Yang; Jensen, Paul D

    2015-10-01

    Dewatering methods for recuperative thickening and final dewatering can potentially impact methanogenic activity and microbial community. This influences both the feasibility of recuperative thickening to increase solids residence time within a digester, and the utilisation of dewatered digestate as inoculum for new digesters. Thickening technology can reduce methanogenic activity through either air contact (rotary drum, DAF, or belt filter press), or by lysing cells through shear (centrifuge). To assess this, two plants with recuperative thickening (rotary drum) in their anaerobic digester, and five without recuperative thickening, had specific methanogenic activity tested in all related streams, including dewatering feed, thickened return, final cake, and centrate. All plants had high speed centrifuges for final dewatering. The digester microbial community was also assessed through 16s pyrotag sequencing and subsequent principal component analysis (PCA). The specific methanogenic activity of all samples was in the expected range of 0.2-0.4 gCOD gVS(-1)d(-1). Plants with recuperative thickening did not have lower digester activity. Centrifuge based dewatering had a significant and variable impact on methanogenic activity in all samples, ranging between 20% and 90% decrease but averaging 54%. Rotary drum based recuperative thickening had a far smaller impact on activity, with a 0% per-pass drop in activity in one plant, and a 20% drop in another. However, the presence of recuperative thickening was a major predictor of overall microbial community (PC1, p = 0.0024). Microbial community PC3 (mainly driven by a shift in methanogens) was a strong predictor for sensitivity in activity to shear (p = 0.0005, p = 0.00001 without outlier). The one outlier was related to a plant producing the wettest cake (17% solids). This indicates that high solids is a potential driver of sensitivity to shear, but that a resilient microbial community can also bestow resilience

  5. Methanogenic community shift in anaerobic batch digesters treating swine wastewater.

    PubMed

    Kim, Woong; Lee, Seungyong; Shin, Seung Gu; Lee, Changsoo; Hwang, Kwanghyun; Hwang, Seokhwan

    2010-09-01

    Qualitative and quantitative molecular analysis techniques were used to determine associations between differences in methanogenic microbial communities and the efficiency of batch anaerobic digesters. Two bioreactors were initially seeded with anaerobic sludge originating from a local municipal wastewater treatment plant and then supplemented with swine wastewater. Differences were observed in the total amount of methane produced in the two bioreactors (7.9L/L, and 4.5L/L, respectively). To explain these differences, efforts were taken to characterize the microbial populations present using a PCR-based DGGE analysis with methanogenic primer and probe sets. The groups Methanomicrobiales (MMB), Methanobacteriales (MBT), and Methanosarcinales (MSL) were detected, but Methanococcales (MCC) was not detected. Following this qualitative assay, real-time PCR was used to investigate quantitative differences in the populations of these methanogenic orders. MMB was found to be the dominant order present and its abundance patterns were different in the two digesters. The population profiles of the other methanogenic groups also differed. Through redundancy analysis, correlations between the concentrations of the different microbes and chemical properties such as volatile fatty acids were calculated. Correlations between MBT and MSL populations and chemical properties were found to be consistent in both digesters, however, differences were observed in the correlations between MMB and propionate. These results suggest that interactions between populations of MMB and other methanogens affected the final methane yield, despite MMB remaining the dominant group overall. The exact details of why changes in the MMB community caused different profiles of methane production could not be ascertained. However, this research provides evidence that microbial behavior is important for regulating the performance of anaerobic processes. PMID:20692007

  6. Anaerobic degradation of phthalate isomers by methanogenic consortia

    SciTech Connect

    Kleerebezem, R.; Pol, L.W.H.; Lettinga, G.

    1999-03-01

    Three methanogenic enrichment cultures, grown on ortho-phthalate, iso-phthalate, or terephthalate were obtained from digested sewage sludge or methanogenic granular sludge. Cultures grown on one of the phthalate isomers were not capable of degrading the other phthalate isomers. All three cultures had the ability to degrade benzoate. Maximum specific growth rates ({mu}{sub S}{sup max}) and biomass yields (Y{sub X{sub tot}S}) of the mixed cultures were determined by using both the phthalate isomers and benzoate as substrates. Comparable values for these parameters were found for all three cultures. Values for {mu}{sub X}{sup max} and Y{sub X{sub tot}S} were higher for growth on benzoate compared to the phthalate isomers. Based on measured and estimated values for the microbial yield of the methanogens in the mixed culture, specific yields for the phthalate and benzoate fermenting organisms were calculated. A kinetic model, involving three microbial species, was developed to predict intermediate acetate and hydrogen accumulation and the final production of methane. Values for the ratio of the concentrations of methanogenic organisms, versus the phthalate isomer and benzoate fermenting organisms, and apparent half-saturation constants (K{sub S}) for the methanogens were calculated. By using this combination of measured and estimated parameter values, a reasonable description of intermediate accumulation and methane formation was obtained, with the initial concentration of phthalate fermenting organisms being the only variable. The energetic efficiency for growth of the fermenting organisms on the phthalate isomers was calculated to be significantly smaller than for growth on benzoate.

  7. Ruminal Methanogen Community in Dairy Cows Fed Agricultural Residues of Corn Stover, Rapeseed, and Cottonseed Meals.

    PubMed

    Wang, Pengpeng; Zhao, Shengguo; Wang, Xingwen; Zhang, Yangdong; Zheng, Nan; Wang, Jiaqi

    2016-07-13

    The purpose was to reveal changes in the methanogen community in the rumen of dairy cows fed agricultural residues of corn stover, rapeseed, and cottonseed meals, compared with alfalfa hay or soybean meal. Analysis was based on cloning and sequencing the methyl coenzyme M reductase α-subunit gene of ruminal methanogens. Results revealed that predicted methane production was increased while population of ruminal methanogens was not significantly affected when cows were fed diets containing various amounts of agricultural residues. Richness and diversity of methanogen community were markedly increased by addition of agricultural residues. The dominant ruminal methanogens shared by all experimental groups belonged to rumen cluster C, accounting for 71% of total, followed by the order Methanobacteriales (29%). Alterations of ruminal methanogen community and prevalence of particular species occurred in response to fed agricultural residue rations, suggesting the possibility of regulating target methanogens to control methane production by dairy cows fed agricultural residues. PMID:27322573

  8. Complete genome sequence of Methanolinea tarda NOBI-1T, a hydrogenotrophic methanogen isolated from methanogenic digester sludge

    DOE PAGESBeta

    Yamamoto, Kyosuke; Tamaki, Hideyuki; Cadillo-Quiroz, Hinsby; Imachi, Hiroyuki; Kyrpides, Nikos; Woyke, Tanja; Goodwin, Lynne; Zinder, Stephen H.; Kamagata, Yoichi; Liu, Wen -Tso

    2014-09-04

    In this study, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1T, a methanogenic archaeon isolated from an anaerobic digested sludge. This is the first genome report of the genus Methanolinea isolate belonging to the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales.

  9. Association of Novel and Highly Diverse Acid-Tolerant Denitrifiers with N2O Fluxes of an Acidic Fen▿ †

    PubMed Central

    Palmer, Katharina; Drake, Harold L.; Horn, Marcus A.

    2010-01-01

    Wetlands are sources of denitrification-derived nitrous oxide (N2O). Thus, the denitrifier community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 1011 cells·gDW−1 (where DW is dry weight) and 108 cells·gDW−1, respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (vmax) values for denitrification in anoxic microcosms ranged from 1 to 24 and −19 to −105 nmol N2O h−1· gDW−1, with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitrification. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N2O at in situ pH. PMID:20023077

  10. Inflammation-Induced Acid Tolerance Genes gadAB in Luminal Commensal Escherichia coli Attenuate Experimental Colitis

    PubMed Central

    Tchaptchet, Sandrine; Fan, Ting-Jia; Goeser, Laura; Schoenborn, Alexi; Gulati, Ajay S.; Sartor, R. Balfour

    2013-01-01

    Dysregulated immune responses to commensal intestinal bacteria, including Escherichia coli, contribute to the development of inflammatory bowel diseases (IBDs) and experimental colitis. Reciprocally, E. coli responds to chronic intestinal inflammation by upregulating expression of stress response genes, including gadA and gadB. GadAB encode glutamate decarboxylase and protect E. coli from the toxic effects of low pH and fermentation acids, factors present in the intestinal lumen in patients with active IBDs. We hypothesized that E. coli upregulates gadAB during inflammation to enhance its survival and virulence. Using real-time PCR, we determined gadAB expression in luminal E. coli from ex-germfree wild-type (WT) and interleukin-10 (IL-10) knockout (KO) (IL-10−/−) mice selectively colonized with a commensal E. coli isolate (NC101) that causes colitis in KO mice in isolation or in combination with 7 other commensal intestinal bacterial strains. E. coli survival and host inflammatory responses were measured in WT and KO mice colonized with NC101 or a mutant lacking the gadAB genes (NC101ΔgadAB). The susceptibility of NC101 and NC101ΔgadAB to killing by host antimicrobial peptides and their translocation across intestinal epithelial cells were evaluated using bacterial killing assays and transwell experiments, respectively. We show that expression of gadAB in luminal E. coli increases proportionately with intestinal inflammation in KO mice and enhances the susceptibility of NC101 to killing by the host antimicrobial peptide cryptdin-4 but decreases bacterial transmigration across intestinal epithelial cells, colonic inflammation, and mucosal immune responses. Chronic intestinal inflammation upregulates acid tolerance pathways in commensal E. coli isolates, which, contrary to our original hypothesis, limits their survival and colitogenic potential. Further investigation of microbial adaptation to immune-mediated inflammation may provide novel insights into the

  11. Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate-oxidizing bacteria.

    PubMed

    Wang, Han; Fotidis, Ioannis A; Angelidaki, Irini

    2015-11-01

    Ammonia-rich substrates can cause inhibition on anaerobic digestion process. Syntrophic acetate-oxidizing bacteria (SAOB) and hydrogenotrophic methanogens are important for the ammonia inhibitory mechanism on anaerobic digestion. The roles and interactions of SAOB and hydrogenotrophic methanogens to ammonia inhibition effect are still unclear. The aim of the current study was to determine the ammonia toxicity levels of various pure strains of SAOB and hydrogenotrophic methanogens. Moreover, ammonia toxicity on the syntrophic-cultivated strains of SAOB and hydrogenotrophic methanogens was tested. Thus, four hydrogenotrophic methanogens (i.e. Methanoculleus bourgensis, Methanobacterium congolense, Methanoculleu thermophilus and Methanothermobacter thermautotrophicus), two SAOB (i.e. Tepidanaerobacter acetatoxydans and Thermacetogenium phaeum) and their syntrophic cultivation were assessed under 0.26, 3, 5 and 7 g NH4 (+)-N L(-1). The results showed that some hydrogenotrophic methanogens were equally, or in some cases, more tolerant to high ammonia levels compared to SAOB. Furthermore, a mesophilic hydrogenotrophic methanogen was more sensitive to ammonia toxicity compared to thermophilic methanogens tested in the study, which is contradicting to the general belief that thermophilic methanogens are more vulnerable to high ammonia loads compared to mesophilic. This unexpected finding underlines the fact that the complete knowledge of ammonia inhibition effect on hydrogenotrophic methanogens is still absent. PMID:26490748

  12. Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves

    PubMed Central

    Zhou, Mi; Chen, Yanhong; Griebel, Philip J; Guan, Le Luo

    2014-01-01

    The methanogenic community throughout the gastrointestinal tract (GIT) of pre-weaned calves has not been well studied. The current study firstly investigated the distribution and composition of the methanogenic community in the rumen, ileum, and colon of 3–4 week-old milk-fed dairy calves (n = 4) using 16S rRNA gene clone library analysis. The occurrence of methanogens in the GIT of pre-weaned calves was further validated by using PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and quantitative real-time PCR (qPCR) was applied to quantify the methanogenic community in the rumen, jejunum, ileum, cecum, colon and rectum of 8 3–4 week old animals. Both cloning libraries and PCR-DGGE revealed that phylotypes close to Methanobrevibacter were the main taxon along the GIT in pre-weaned sucking calves. The composition and abundance of methanogens varied significantly among individual animals, suggesting that host conditions may influence the composition of the symbiotic microbiota. Segregation of methanogenic communities throughout the GIT was also observed within individual animals, suggesting possible functional differences among methanogens residing in different GIT regions. This is the first study to analyze methanogenic communities throughout the GIT of milk-fed newborn dairy calves and reveal both their diversity and abundance. The identification of methanogens in the lower GIT of pre-weaned dairy calves warrants further investigation to better define methanogen roles in GIT function and their impact on host metabolism and health. PMID:25483332

  13. Vaccination of Sheep with a Methanogen Protein Provides Insight into Levels of Antibody in Saliva Needed to Target Ruminal Methanogens

    PubMed Central

    Subharat, Supatsak; Shu, Dairu; Zheng, Tao; Buddle, Bryce M.; Kaneko, Kan; Hook, Sarah; Janssen, Peter H.; Wedlock, D. Neil

    2016-01-01

    Methane is produced in the rumen of ruminant livestock by methanogens and is a major contributor to agricultural greenhouse gases. Vaccination against ruminal methanogens could reduce methane emissions by inducing antibodies in saliva which enter the rumen and impair ability of methanogens to produce methane. Presently, it is not known if vaccination can induce sufficient amounts of antibody in the saliva to target methanogen populations in the rumen and little is known about how long antibody in the rumen remains active. In the current study, sheep were vaccinated twice at a 3-week interval with a model methanogen antigen, recombinant glycosyl transferase protein (rGT2) formulated with one of four adjuvants: saponin, Montanide ISA61, a chitosan thermogel, or a lipid nanoparticle/cationic liposome adjuvant (n = 6/formulation). A control group of sheep (n = 6) was not vaccinated. The highest antigen-specific IgA and IgG responses in both saliva and serum were observed with Montanide ISA61, which promoted levels of salivary antibodies that were five-fold higher than the second most potent adjuvant, saponin. A rGT2-specific IgG standard was used to determine the level of rGT2-specific IgG in serum and saliva. Vaccination with GT2/Montanide ISA61 produced a peak antibody concentration of 7 × 1016 molecules of antigen-specific IgG per litre of saliva, and it was estimated that in the rumen there would be more than 104 molecules of antigen-specific IgG for each methanogen cell. Both IgG and IgA in saliva were shown to be relatively stable in the rumen. Salivary antibody exposed for 1–2 hours to an in vitro simulated rumen environment retained approximately 50% of antigen-binding activity. Collectively, the results from measuring antibody levels and stablility suggest a vaccination-based mitigation strategy for livestock generated methane is in theory feasible. PMID:27472482

  14. Vaccination of Sheep with a Methanogen Protein Provides Insight into Levels of Antibody in Saliva Needed to Target Ruminal Methanogens.

    PubMed

    Subharat, Supatsak; Shu, Dairu; Zheng, Tao; Buddle, Bryce M; Kaneko, Kan; Hook, Sarah; Janssen, Peter H; Wedlock, D Neil

    2016-01-01

    Methane is produced in the rumen of ruminant livestock by methanogens and is a major contributor to agricultural greenhouse gases. Vaccination against ruminal methanogens could reduce methane emissions by inducing antibodies in saliva which enter the rumen and impair ability of methanogens to produce methane. Presently, it is not known if vaccination can induce sufficient amounts of antibody in the saliva to target methanogen populations in the rumen and little is known about how long antibody in the rumen remains active. In the current study, sheep were vaccinated twice at a 3-week interval with a model methanogen antigen, recombinant glycosyl transferase protein (rGT2) formulated with one of four adjuvants: saponin, Montanide ISA61, a chitosan thermogel, or a lipid nanoparticle/cationic liposome adjuvant (n = 6/formulation). A control group of sheep (n = 6) was not vaccinated. The highest antigen-specific IgA and IgG responses in both saliva and serum were observed with Montanide ISA61, which promoted levels of salivary antibodies that were five-fold higher than the second most potent adjuvant, saponin. A rGT2-specific IgG standard was used to determine the level of rGT2-specific IgG in serum and saliva. Vaccination with GT2/Montanide ISA61 produced a peak antibody concentration of 7 × 1016 molecules of antigen-specific IgG per litre of saliva, and it was estimated that in the rumen there would be more than 104 molecules of antigen-specific IgG for each methanogen cell. Both IgG and IgA in saliva were shown to be relatively stable in the rumen. Salivary antibody exposed for 1-2 hours to an in vitro simulated rumen environment retained approximately 50% of antigen-binding activity. Collectively, the results from measuring antibody levels and stablility suggest a vaccination-based mitigation strategy for livestock generated methane is in theory feasible. PMID:27472482

  15. Composition and Role of Extracellular Polymers in Methanogenic Granules

    PubMed Central

    Veiga, M. C.; Jain, M. K.; Wu, W.; Hollingsworth, R. I.; Zeikus, J. G.

    1997-01-01

    Methanobacterium formicicum and Methanosarcina mazeii are two prevalent species isolated from an anaerobic granular consortium grown on a fatty acid mixture. The extracellular polysaccharides (EPS) were extracted from Methanobacterium formicicum and Methanosarcina mazeii and from the methanogenic granules to examine their role in granular development. The EPS made up approximately 20 to 14% of the extracellular polymer extracted from the granules, Methanobacterium formicicum, and Methanosarcina mazeii. The EPS produced by Methanobacterium formicicum was composed mainly of rhamnose, mannose, galactose, glucose, and amino sugars, while that produced by Methanosarcina mazeii contained ribose, galactose, glucose, and glucosamine. The same sugars were also present in the EPS produced by the granules. These results indicate that the two methanogens, especially Methanobacterium formicicum, contributed significantly to the production of the extracellular polymer of the anaerobic granules. Growth temperature, substrates (formate and H(inf2)-CO(inf2)), and the key nutrients (nitrogen and phosphate concentrations) affected polymer production by Methanobacterium formicicum. PMID:16535504

  16. Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen

    NASA Technical Reports Server (NTRS)

    Mathrani, I. M.; Boone, D. R.; Mah, R. A.; Fox, G. E.; Lau, P. P.

    1988-01-01

    Methanohalophilus zhilinae, a new alkaliphilic, halophilic, methylotrophic species of methanogenic bacteria, is described. Strain WeN5T (T = type strain) from Bosa Lake of the Wadi el Natrun in Egypt was designated the type strain and was further characterized. This strain was nonmotile, able to catabolize dimethylsulfide, and able to grow in medium with a methyl group-containing substrate (such as methanol or trimethylamine) as the sole organic compound added. Sulfide (21 mM) inhibited cultures growing on trimethylamine. The antibiotic susceptibility pattern of strain WeN5T was typical of the pattern for archaeobacteria, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 38 mol%. Characterization of the 16S ribosomal ribonucleic acid sequence indicated that strain WeN5T is phylogenetically distinct from members of previously described genera other than Methanohalophilus and supported the partition of halophilic methanogens into their own genus.

  17. Reducing methane emissions in sheep by immunization against rumen methanogens.

    PubMed

    Wright, A D G; Kennedy, P; O'Neill, C J; Toovey, A F; Popovski, S; Rea, S M; Pimm, C L; Klein, L

    2004-09-28

    This work was conducted to determine if methane emissions from sheep immunized with an anti-methanogen vaccine were significantly lower than methane emissions from non-immunized sheep, to test the effectiveness of two different vaccine formulations (VF) on methane abatement, and to compare methane emissions measured using a closed-circuit respiration chamber and the sulphur-hexafluoride (SF6) tracer technique. Thirty mature wether sheep were randomly allocated to three treatment groups (n = 10). One group received an immunization of adjuvant only on days 0 and 153 (control), a second group received an immunization with a 3-methanogen mix on days 0 and 153 (VF3 + 3), and a third group received an immunization of a 7-methanogen mix on day 0 followed by a 3-methanogen mix on day 153 (VF7 + 3). Four weeks post-secondary immunization, there was a significant 7.7% reduction in methane production per kg dry matter intake in the VF7 + 3 group compared to the controls (P = 0.051). However, methane emissions from sheep immunized with VF7 + 3 were not significantly different when compared to the sheep in the control group (P = 0.883). The average IgG and IgA antibody titres in both plasma and saliva of the VF3 + 3 immunized sheep were four to nine times higher than those immunized with VF7 + 3 (P< 0.001) at both 3 and 6 weeks post-secondary immunization. Data also revealed that SF6 methane estimates were consistently higher than the respiration chamber estimates and that there was no significant correlation between the SF6 methane estimates and the respiration chamber methane estimates (R2 = 0.11). PMID:15364447

  18. Transformation of phenol into phenylalanine by a methanogenic consortium

    SciTech Connect

    Lepine, F.; Milot, S.; Beaudet, R.; Villemur, R.

    1996-03-01

    Phenol is a widely used chemical found in many wastewaters of industrial origin. The degradation of phenol by methanogenic bacterial consortia has been reported by many investigators. To better characterise the metabolism of this consortium, a new metabolic pathway of benzoic acid, an intermediary in the degradation of phenol, is reported. This study describes the transformations of benzoic acid into 3-phenylpropionic acid and phenylalanine. 25 refs., 5 figs.

  19. An Intertwined Evolutionary History of Methanogenic Archaea and Sulfate Reduction

    PubMed Central

    Susanti, Dwi; Mukhopadhyay, Biswarup

    2012-01-01

    Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F420)-dependent sulfite reductase (Fsr) where N- and C-terminal halves (Fsr-N and Fsr-C) are homologs of F420H2 dehydrogenase and dissimilatory sulfite reductase (Dsr), respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP), both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest), carrying a coupled siroheme-[Fe4-S4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex), with group I features, a Dsr-type peripheral [Fe4-S4] cluster and an additional [Fe4-S4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe4-S4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F420H2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago) biologically produced sulfide deposit. PMID:23028926

  20. Pulp mill wastewater sediment reveals novel methanogenic and cellulolytic populations.

    PubMed

    Yang, Chunyu; Wang, Wei; Du, Miaofen; Li, Chunfang; Ma, Cuiqing; Xu, Ping

    2013-02-01

    Pulp mill wastewater generated from wheat straw is characterized as high alkalinity and very high COD pollution load. A naturally developed microbial community in a pulp mill wastewater storage pool that had been disused were investigated in this study. Owing to natural evaporation and a huge amount of lignocellulose's deposition, the wastewater sediment contains high concentrations of organic matters and sodium ions, but low concentrations of chloride and carbonate. The microbiota inhabiting especially anaerobic community, including methanogenic arhcaea and cellulolytic species, was studied. All archaeal sequences fall into 2 clusters of family Halobacteriaceae and methanogenic archaeon in the phylum Euryarchaeota. In the methanogenic community, phylogenetic analysis of methyl coenzyme M reductase A (mcrA) genes targeted to novel species in genus Methanoculleus or novel genus of order Methanomicrobiales. The predominance of Methanomicrobiales suggests that methanogenesis in this system might be driven by the hydrogenotrophic pathway. As the important primary fermenter for methane production, the cellulolytic community of enzyme GHF48 was found to be dominated by narrower breadth of novel clostridial cellulase genes. Novel anoxic functional members in such extreme sediment provide the possibility of enhancing the efficiency of anoxic treatment of saline and alkaline wastewaters, as well as benefiting to the biomass transformation and biofuel production processes. PMID:23228889

  1. Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies.

    PubMed

    Jiménez, Núria; Richnow, Hans H; Vogt, Carsten; Treude, Tina; Krüger, Martin

    2016-01-01

    Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed. PMID:26959375

  2. Kinetics of chlorinated ethylene dehalogenation under methanogenic conditions

    SciTech Connect

    Skeen, R.S.; Gao, J.; Hooker, B.S.

    1995-12-20

    Kinetics were determined for methanogenic activity and chlorinated ethylene dehalogenation by a methanol-enriched, anaerobic sediment consortium. The culture reductively dechlorinated perchloroethylene (PCE) to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), vinylchloride (VC), and ethylene and ethane. The absence of methanol or the addition of 2-bromoethanesulfonic acid in the presence of methanol suppressed both methanogenic activity and dechlorination. In contrast, acetate production continued in the presence of 2-bromoethanesulfonic acid. These results suggest that dechlorination was strongly linked to methane formation and not to acetate production. A kinetic model, developed to describe both methanogenesis and dechlorination, successfully predicted experimentally measured concentrations of biomass, methane, substrate, and chlorinated ethylenes. The average maximum specific dehalogenation rates for PCE, TCE, 1,1-DCE, and VC were 0.9 {+-} 0.6, 0.4 {+-} 0.1, 12 {+-} 0.1, and 2.5 {+-} 1.7 {micro}mol contaminant/g {center_dot} DW/day, respectively. This pattern for dechlorination rates is distinctly different than that reported for transition metal cofactors, where rates drop by approximately one order of magnitude as each successive chlorine is removed. The experimental results and kinetic analysis suggest that it will be impractical to targeting methanol consuming methanogenic organisms for in-situ groundwater restoration.

  3. Hydrogen consumption by methanogens on the early Earth

    NASA Technical Reports Server (NTRS)

    Kral, T. A.; Brink, K. M.; Miller, S. L.; McKay, C. P.; Bada, J. L. (Principal Investigator)

    1998-01-01

    It is possible that the first autotroph used chemical energy rather than light. This could have been the main source of primary production after the initial inventory of abiotic organic material had been depleted. The electron acceptor most readily available for use by this first chemoautotroph would have been CO2. The most abundant electron donor may have been H2 that would have been outgassing from volcanoes at a rate estimated to be as large as 10(12) moles yr-1, as well as from photo-oxidation of Fe+2. We report here that certain methanogens will consume H2 down to partial pressures as low as 4 Pa (4 x 10(-5) atm) with CO2 as the sole carbon source at a rate of 0.7 ng H2 min-1 microgram-1 cell protein. The lower limit of pH2 for growth of methanogens can be understood on the basis that the pH2 needs to be high enough for one ATP to be synthesized per CO2 reduced. The pH2 values needed for growth measured here are consistent with those measured by Stevens and McKinley for growth of methanogens in deep basalt aquifers. H2-consuming autotrophs are likely to have had a profound effect on the chemistry of the early atmosphere and to have been a dominant sink for H2 on the early Earth after life began rather than escape from the Earth's atmosphere to space.

  4. Environmental selection of planktonic methanogens in permafrost thaw ponds.

    PubMed

    Crevecoeur, Sophie; Vincent, Warwick F; Lovejoy, Connie

    2016-01-01

    The warming and thermal erosion of ice-containing permafrost results in thaw ponds that are strong emitters of methane to the atmosphere. Here we examined methanogens and other Archaea, in two types of thaw ponds that are formed by the collapse of either permafrost peat mounds (palsas) or mineral soil mounds (lithalsas) in subarctic Quebec, Canada. Using high-throughput sequencing of a hypervariable region of 16S rRNA, we determined the taxonomic structure and diversity of archaeal communities in near-bottom water samples, and analyzed the mcrA gene transcripts from two sites. The ponds at all sites were well stratified, with hypoxic or anoxic bottom waters. Their archaeal communities were dominated by Euryarchaeota, specifically taxa in the methanogenic orders Methanomicrobiales and Methanosarcinales, indicating a potentially active community of planktonic methanogens. The order Methanomicrobiales accounted for most of the mcrA transcripts in the two ponds. The Archaeal communities differed significantly between the lithalsa and palsa ponds, with higher alpha diversity in the organic-rich palsa ponds, and pronounced differences in community structure. These results indicate the widespread occurrence of planktonic, methane-producing Archaea in thaw ponds, with environmental selection of taxa according to permafrost landscape type. PMID:27501855

  5. Environmental selection of planktonic methanogens in permafrost thaw ponds

    NASA Astrophysics Data System (ADS)

    Crevecoeur, Sophie; Vincent, Warwick F.; Lovejoy, Connie

    2016-08-01

    The warming and thermal erosion of ice-containing permafrost results in thaw ponds that are strong emitters of methane to the atmosphere. Here we examined methanogens and other Archaea, in two types of thaw ponds that are formed by the collapse of either permafrost peat mounds (palsas) or mineral soil mounds (lithalsas) in subarctic Quebec, Canada. Using high-throughput sequencing of a hypervariable region of 16S rRNA, we determined the taxonomic structure and diversity of archaeal communities in near-bottom water samples, and analyzed the mcrA gene transcripts from two sites. The ponds at all sites were well stratified, with hypoxic or anoxic bottom waters. Their archaeal communities were dominated by Euryarchaeota, specifically taxa in the methanogenic orders Methanomicrobiales and Methanosarcinales, indicating a potentially active community of planktonic methanogens. The order Methanomicrobiales accounted for most of the mcrA transcripts in the two ponds. The Archaeal communities differed significantly between the lithalsa and palsa ponds, with higher alpha diversity in the organic-rich palsa ponds, and pronounced differences in community structure. These results indicate the widespread occurrence of planktonic, methane-producing Archaea in thaw ponds, with environmental selection of taxa according to permafrost landscape type.

  6. Environmental selection of planktonic methanogens in permafrost thaw ponds

    PubMed Central

    Crevecoeur, Sophie; Vincent, Warwick F.; Lovejoy, Connie

    2016-01-01

    The warming and thermal erosion of ice-containing permafrost results in thaw ponds that are strong emitters of methane to the atmosphere. Here we examined methanogens and other Archaea, in two types of thaw ponds that are formed by the collapse of either permafrost peat mounds (palsas) or mineral soil mounds (lithalsas) in subarctic Quebec, Canada. Using high-throughput sequencing of a hypervariable region of 16S rRNA, we determined the taxonomic structure and diversity of archaeal communities in near-bottom water samples, and analyzed the mcrA gene transcripts from two sites. The ponds at all sites were well stratified, with hypoxic or anoxic bottom waters. Their archaeal communities were dominated by Euryarchaeota, specifically taxa in the methanogenic orders Methanomicrobiales and Methanosarcinales, indicating a potentially active community of planktonic methanogens. The order Methanomicrobiales accounted for most of the mcrA transcripts in the two ponds. The Archaeal communities differed significantly between the lithalsa and palsa ponds, with higher alpha diversity in the organic-rich palsa ponds, and pronounced differences in community structure. These results indicate the widespread occurrence of planktonic, methane-producing Archaea in thaw ponds, with environmental selection of taxa according to permafrost landscape type. PMID:27501855

  7. Fast pyrolysis product distribution of biopretreated corn stalk by methanogen.

    PubMed

    Wang, Tipeng; Ye, Xiaoning; Yin, Jun; Jin, Zaixing; Lu, Qiang; Zheng, Zongming; Dong, Changqing

    2014-10-01

    After pretreated by methanogen for 5, 15 and 25 days, corn stalk (CS) were pyrolyzed at 250, 300, 350, 400, 450 and 500 °C by Py-GC/MS and product distribution in bio-oil was analyzed. Results indicated that methanogen pretreatment changed considerably the product distribution: the contents of sugar and phenols increased; the contents of linear carbonyls and furans decreased; the contents of linear ketones and linear acids changed slightly. Methanogen pretreatment improved significantly the pyrolysis selectivity of CS to phenols especially 4-VP. At 250 °C, the phenols content increased from 42.25% for untreated CS to 79.32% for biopretreated CS for 5 days; the 4-VP content increased from 28.6% to 60.9%. Increasing temperature was contributed to convert more lignin into 4-VP, but decreased its content in bio-oil due to more other chemicals formed. The effects of biopretreatment time on the chemicals contents were insignificant. PMID:25113883

  8. Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka

    PubMed Central

    Mach, Václav; Blaser, Martin B.; Claus, Peter; Chaudhary, Prem P.; Rulík, Martin

    2015-01-01

    Biological methanogenesis is linked to permanent water logged systems, e.g., rice field soils or lake sediments. In these systems the methanogenic community as well as the pathway of methane formation are well-described. By contrast, the methanogenic potential of river sediments is so far not well-investigated. Therefore, we analyzed (a) the methanogenic potential (incubation experiments), (b) the pathway of methane production (stable carbon isotopes and inhibitor studies), and (c) the methanogenic community composition (terminal restriction length polymorphism of mcrA) in depth profiles of sediment cores of River Sitka, Czech Republic. We found two depth-related distinct maxima for the methanogenic potentials (a) The pathway of methane production was dominated by hydrogenotrophic methanogenesis (b) The methanogenic community composition was similar in all depth layers (c) The main TRFs were representative for Methanosarcina, Methanosaeta, Methanobacterium, and Methanomicrobium species. The isotopic signals of acetate indicated a relative high contribution of chemolithotrophic acetogenesis to the acetate pool. PMID:26052322

  9. Energetic and hydrogen limitations of thermophilic and hyperthermophilic methanogens

    NASA Astrophysics Data System (ADS)

    Stewart, L. C.; Holden, J. F.

    2013-12-01

    Deep-sea hydrothermal vents are a unique ecosystem, based ultimately not on photosynthesis but chemosynthetic primary production. This makes them an excellent analog environment for the early Earth, and for potential extraterrestrial habitable environments, such as those on Mars and Europa. The habitability of given vent systems for chemoautotrophic prokaryotes can be modeled energetically by estimating the available Gibbs energy for specific modes of chemoautotrophy, using geochemical data and mixing models for hydrothermal fluids and seawater (McCollom and Shock, 1997). However, modeling to date has largely not taken into account variation in organisms' energy demands in these environments. Controls on maintenance energies are widely assumed to be temperature-dependent, rising with increasing temperature optima (Tijhuis et al., 1993), and species-independent. The impacts of other environmental stressors and particular energy-gathering strategies on maintenance energies have not been investigated. We have undertaken culture-based studies of growth and maintenance energies in thermophilic and hyperthermophilic methanogenic (hydrogenotrophic) archaea from deep-sea hydrothermal vents to investigate potential controls on energy demands in hydrothermal vent microbes, and to quantify their growth and maintenance energies for future bioenergetic modeling. We have investigated trends in their growth energies over their full temperature range and a range of nitrogen concentrations, and in their maintenance energies at different hydrogen concentrations. Growth energies in these organisms appear to rise with temperature, but do not vary between hyperthermophilic and thermophilic methanogens. Nitrogen availability at tested levels (40μM - 9.4 mM) does not appear to affect growth energies in all but one tested organism. In continuous chemostat culture, specific methane production varied with hydrogen availability but was similar between a thermophilic and a hyperthermophilic

  10. Estimation of Methanogen Biomass by Quantitation of Coenzyme M

    PubMed Central

    Elias, Dwayne A.; Krumholz, Lee R.; Tanner, Ralph S.; Suflita, Joseph M.

    1999-01-01

    Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363–370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 ± 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 ± 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass. PMID:10584015

  11. Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens.

    PubMed

    Wawrik, Boris; Marks, Christopher R; Davidova, Irene A; McInerney, Michael J; Pruitt, Shane; Duncan, Kathleen E; Suflita, Joseph M; Callaghan, Amy V

    2016-09-01

    Anaerobic microbial biodegradation of recalcitrant, water-insoluble substrates, such as paraffins, presents unique metabolic challenges. To elucidate this process, a methanogenic consortium capable of mineralizing long-chain n-paraffins (C28 -C50 ) was enriched from San Diego Bay sediment. Analysis of 16S rRNA genes indicated the dominance of Syntrophobacterales (43%) and Methanomicrobiales (26%). Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community members belonging to the bacterial genus Smithella and the archaeal genera Methanoculleus and Methanosaeta. Five contigs encoding homologs of the catalytic subunit of alkylsuccinate synthase (assA) were detected. Additionally, mRNA transcripts for these genes, including a homolog binned within the 'Smithella' sp. SDB genome scaffold, were detected via RT-PCR, implying that paraffins are activated via 'fumarate addition'. Metabolic reconstruction and comparison with genome scaffolds of uncultivated n-alkane degrading 'Smithella' spp. are consistent with the hypothesis that syntrophically growing 'Smithella' spp. may achieve reverse electron transfer by coupling the reoxidation of ETFred to a membrane-bound FeS oxidoreductase functioning as an ETF:menaquinone oxidoreductase. Subsequent electron transfer could proceed via a periplasmic formate dehydrogenase and/or hydrogenase, allowing energetic coupling to hydrogenotrophic methanogens such as Methanoculleus. Ultimately, these data provide fundamental insight into the energy conservation mechanisms that dictate interspecies interactions salient to methanogenic alkane mineralization. PMID:27198766

  12. Effects of triclosan, diclofenac, and nonylphenol on mesophilic and thermophilic methanogenic activity and on the methanogenic communities.

    PubMed

    Symsaris, Evangelos C; Fotidis, Ioannis A; Stasinakis, Athanasios S; Angelidaki, Irini

    2015-06-30

    In this study, a toxicity assay using a mesophilic wastewater treatment plant sludge-based (SI) and a thermophilic manure-based inoculum (MI), under different biomass concentrations was performed to define the effects of diclofenac (DCF), triclosan (TCS), and nonylphenol (NP) on anaerobic digestion (AD) process. Additionally, the influence of DCF, TCS, and NP on the relative abundance of the methanogenic populations was investigated. Results obtained demonstrated that, in terms of methane production, SI inoculum was more resistant to the toxicity effect of DCF, TCS, and NP, compared to the MI inoculum. The IC50 values were 546, 35, and 363 mg L(-1) for SI inoculum and 481, 32, and 74 mg L(-1) for MI inoculum for DCF, TCS, and NP, respectively. For both inocula, higher biomass concentrations reduced the toxic effect of TCS (higher methane production up to 64%), contrary to DCF, where higher biomass loads decreased methane yield up to 31%. Fluorescence in situ hybridization analysis showed that hydrogenotrophic methanogens were more resistant to the inhibitory effect of DCF, TCS, and NP compared to aceticlastic methanogens. PMID:25768988

  13. Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost

    PubMed Central

    Liebner, Susanne; Ganzert, Lars; Kiss, Andrea; Yang, Sizhong; Wagner, Dirk; Svenning, Mette M.

    2015-01-01

    The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs. PMID:26029170

  14. Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost.

    PubMed

    Liebner, Susanne; Ganzert, Lars; Kiss, Andrea; Yang, Sizhong; Wagner, Dirk; Svenning, Mette M

    2015-01-01

    The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs. PMID:26029170

  15. Osmoregulation in Methanogens (and Other Interesting Organisms)

    SciTech Connect

    Roberts, Mary Fedarko

    2014-12-03

    Our research has been aimed at (i) identifying, (ii) determining mode of regulation, and (iii) understanding how different classes of compatible solutes (also termed osmolytes) affect macromolecular stability in response to osmotic and thermal stress. For solutes we have identified (e.g., di-inositol-1,1’-phosphate (DIP)), we used NMR to elucidate biosynthetic pathways and then cloned suspected enzymes in the pathway to explore how they are regulated. Compatible solutes are thought to protect proteins from thermal and osmotic stresses by being excluded from the surface, allowing critical water molecules to interact with the protein. This implies there are no specific binding interactions between osmolytes and proteins. However, we and others have often observed very specific solute effects for proteins that suggest a more direct interaction between solute and protein is likely can occur. Measuring such a weak interaction is extremely difficult. We have developed a solution NMR method, high-resolution field cycling relaxometry, that can measure spin-lattice relaxation rates as a function of magnetic field from 11.7 (the field of a 500 MHz spectrometer) to 0.003 T. The methodology is ideal for nuclei in small molecules with moderately long relaxation times at high fields – phosphate groups (31P), enriched carbonyls (13C), or methyl groups (1H). The protein of interest is spin-labeled to introduce a large dipole on it that will dominate the relaxation of nuclei on any small molecules that bind transiently. The key is to measure relaxation below 1-2 T (and extract nuclei-spin label distances in the bound complex) where the small molecule relaxation will be dominated by dipolar mechanisms with a correlation time indicative of the large protein complex. Our explorations of an inositol monophosphatase (the last step in DIP generation) localized four discrete binding sides for the thermoprotectant α-glutamate. This is a novel approach, and while the work did not fully

  16. Draft genome sequence of the first acid-tolerant sulfate-reducing deltaproteobacterium Desulfovibrio sp. TomC having potential for minewater treatment.

    PubMed

    Karnachuk, Olga V; Mardanov, Andrey V; Avakyan, Marat R; Kadnikov, Vitaly V; Vlasova, Maria; Beletsky, Alexey V; Gerasimchuk, Anna L; Ravin, Nikolai V

    2015-02-01

    The sulfidogenic bacterium Desulfovibrio sp. TomC was isolated from acidic waste at the abandoned gold ore mining site in the Martaiga gold ore belt, Western Siberia. This bacterium, being the first reported acid-tolerant gram-negative sulfate-reducer of the order Deltaproteobacteria, is able to grow at pH as low as 2.5 and is resistant to high concentrations of metals. The draft 5.3 Mb genome sequence of Desulfovibrio sp. TomC has been established and provides the genetic basis for application of this microorganism in bioreactors and other bioremediation schemes for the treatment of metal-containing wastewater. PMID:25724779

  17. Kinetics of phenol biodegradation by an immobilized methanogenic consortium

    SciTech Connect

    Dwyer, D.F.; Krumme, M.L.; Boyd, S.A.; Tiedje, J.M.

    1986-08-01

    A phenol-degrading methanogenic enrichment was successfully immobilized in agar as shown by the stoichiometric conversion of phenol to CH/sub 4/ and CO/sub 2/. The enrichment contained members of three physiological groups necessary for the syntrophic mineralization of phenol: a phenol-oxidizing bacterium, a Methanothrix-like bacterium, and an H/sub 2/-utilizing methanogen. The immobilization technique resulted in the cells being embedded in a long, thin agar strans (1 mm in diameter by 2 to 50 cm in length) that resembled spaghetti. Immobilization had three effects as shown by a comparative kinetic analysis of phenol degradation by free versus immobilized cells. (1) The maximum rate of degradation was reduced from 14.8 to 10.0 ..mu..g of phenol per h; (2) the apparent K/sub m/ for the overall reaction was reduced from 90 to 46 ..mu..g of phenol per ml. probably because of the retention of acetate, H/sub 2/ and CO/sub 2/ in the proximity of immobilized methanogens; and (3) the cells were protected from substrate inhibition caused by high concentrations of phenol, which increased the apparent K/sub i/ value from 900 to 1725 ..mu..g of phenol per ml. Estimates for the kinetic parameters K/sub m/, K/sub i/, and V/sub max/ were used in a modified substrate inhibition model that simulated rates of phenol degradation for given phenol concentrations. The simulated rates were in close agreement with experimentally derived rates for both stimulatory and inhibitory concentrations of phenol.

  18. Hydrogen consumption by methanogens on the early Earth.

    PubMed

    Kral, T A; Brink, K M; Miller, S L; McKay, C P

    1998-06-01

    It is possible that the first autotroph used chemical energy rather than light. This could have been the main source of primary production after the initial inventory of abiotic organic material had been depleted. The electron acceptor most readily available for use by this first chemoautotroph would have been CO2. The most abundant electron donor may have been H2 that would have been outgassing from volcanoes at a rate estimated to be as large as 10(12) moles yr-1, as well as from photo-oxidation of Fe+2. We report here that certain methanogens will consume H2 down to partial pressures as low as 4 Pa (4 x 10(-5) atm) with CO2 as the sole carbon source at a rate of 0.7 ng H2 min-1 microgram-1 cell protein. The lower limit of pH2 for growth of methanogens can be understood on the basis that the pH2 needs to be high enough for one ATP to be synthesized per CO2 reduced. The pH2 values needed for growth measured here are consistent with those measured by Stevens and McKinley for growth of methanogens in deep basalt aquifers. H2-consuming autotrophs are likely to have had a profound effect on the chemistry of the early atmosphere and to have been a dominant sink for H2 on the early Earth after life began rather than escape from the Earth's atmosphere to space. PMID:9611769

  19. Degradation of hydrocarbons under methanogenic conditions in different geosystems

    NASA Astrophysics Data System (ADS)

    Straaten, Nontje; Jiménez García, Núria; Richnow, Hans-Hermann; Krueger, Martin

    2014-05-01

    With increasing energy demand the search for new resources is becoming increasingly important for the future energy supply. Therefore the knowledge about fossil fuels like oil or natural gas and their extraction should be expanded. Biodegraded oil is found in many reservoirs worldwide. Consequently, it is very important to get insight in the microbial communities and metabolic processes involved in hydrocarbon degradation. Due to the lack of alternative electron acceptors in hydrocarbon-rich geosystems, degradation often takes place under methanogenic conditions. The aim of the present study is to identify the microorganisms and mechanisms involved in the degradation of complex hydrocarbons, like BTEX and polycyclic aromatic hydrocarbons, using culture dependent and independent techniques. For this purpose enrichment cultures from marine sediments, shales, coal and oil reservoirs are monitored for their capability to degrade alkanes and aromatic compounds. Moreover the environmental samples of these different geosystems analysed for evidence for the in situ occurrence of methanogenic oil degradation. The gas geochemical data provided in several cases hints for a recent biological origin of the methane present. First results of the microbial community analysis showed in environmental samples and enrichment cultures the existence of Bacteria known to degrade hydrocarbons. Also a diverse community of methanogenic Archaea could be found in the clone libraries. Additionally, in oil and coal reservoir samples the degradation of model hydrocarbons, e.g. methylnaphthalene, hexadecane and BTEX, to CH4 was confirmed by 13C-labeling. To explore the mechanisms involved in biodegradation, the enrichments as well as the original environmental samples are further analysed for the presence of respective functional genes.

  20. Effect of temperature on perchloroethylene dechlorination by a methanogenic consortium

    SciTech Connect

    Gao, J.; Skeen, R.S.; Hooker, B.S.

    1995-04-01

    The effect of temperature on the kinetics of growth, substrate metabolism, and perchloroethylene (PCE) dechlorination by a methanogenic consortium is reported. In all cases, a simple kinetic model accurately reflected experimental data. Values for the substrate and methane yield coefficients, and the maximum specific growth rate are fairly consistent at each temperature. Also, the substrate and methane yield coefficients show little temperature sensitivity. In contrast, both the maximum specific growth rate and the PCE dechlorination yield coefficient (Y{sub PCE}) are temperature dependent.

  1. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics.

    PubMed

    Graham, David E; White, Robert H

    2002-04-01

    Methanogenesis, the anaerobic production of methane from CO2 or simple carbon compounds, requires seven organic coenzymes. This review describes pathways for the biosynthesis of methanofuran, 5,6,7,8-tetrahydromethanopterin, coenzyme F420, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoyl-L-threonine phosphate). Spectroscopic evidence for the pathways is reviewed and recent efforts are described to identify and characterize the biosynthetic enzymes from methanogenic archaea. The literature from 1971 to September 2001 is reviewed, and 169 references are cited. PMID:12013276

  2. Methane Production and Methanogenic Archaea in the Digestive Tracts of Millipedes (Diplopoda)

    PubMed Central

    Šustr, Vladimír; Chroňáková, Alica; Semanová, Stanislava; Tajovský, Karel; Šimek, Miloslav

    2014-01-01

    Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens’ diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia. PMID:25028969

  3. Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1

    PubMed Central

    Kelly, William J.; Li, Dong; Lambie, Suzanne C.; Cox, Faith; Attwood, Graeme T.; Altermann, Eric

    2016-01-01

    Methanobrevibacter olleyae YLM1 is a hydrogenotrophic methanogen, isolated from the rumen of a lamb. Its genome has been sequenced to provide information on the genomic diversity of rumen methanogens and support the development of approaches to reduce methane formation by ruminants. PMID:27056228

  4. Method for Indirect Quantification of CH4 Production via H2O Production Using Hydrogenotrophic Methanogens.

    PubMed

    Taubner, Ruth-Sophie; Rittmann, Simon K-M R

    2016-01-01

    Hydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. Methanogens exhibit extraordinary ecological, biochemical, and physiological characteristics and possess a huge biotechnological potential. Yet, the only possibility to assess the methane (CH4) production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH4. In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH4 production potential we developed a novel method for indirect quantification of the volumetric CH4 production rate by measuring the volumetric water production rate. This method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was estimated by determining the difference in mass increase in a quasi-isobaric setting. This novel CH4 quantification method is an accurate and precise analytical technique, which can be used to rapidly screen pure cultures of methanogens regarding their volumetric CH4 evolution rate. It is a cost effective alternative determining CH4 production of methanogens over CH4 quantification by using gas chromatography, especially if applied as a high throughput quantification method. Eventually, the method can be universally applied for quantification of CH4 production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens. PMID:27199898

  5. Method for Indirect Quantification of CH4 Production via H2O Production Using Hydrogenotrophic Methanogens

    PubMed Central

    Taubner, Ruth-Sophie; Rittmann, Simon K.-M. R.

    2016-01-01

    Hydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. Methanogens exhibit extraordinary ecological, biochemical, and physiological characteristics and possess a huge biotechnological potential. Yet, the only possibility to assess the methane (CH4) production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH4. In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH4 production potential we developed a novel method for indirect quantification of the volumetric CH4 production rate by measuring the volumetric water production rate. This method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was estimated by determining the difference in mass increase in a quasi-isobaric setting. This novel CH4 quantification method is an accurate and precise analytical technique, which can be used to rapidly screen pure cultures of methanogens regarding their volumetric CH4 evolution rate. It is a cost effective alternative determining CH4 production of methanogens over CH4 quantification by using gas chromatography, especially if applied as a high throughput quantification method. Eventually, the method can be universally applied for quantification of CH4 production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens. PMID:27199898

  6. Enhanced Acid Tolerance in Bifidobacterium longum by Adaptive Evolution: Comparison of the Genes between the Acid-Resistant Variant and Wild-Type Strain.

    PubMed

    Jiang, Yunyun; Ren, Fazheng; Liu, Songling; Zhao, Liang; Guo, Huiyuan; Hou, Caiyun

    2016-03-28

    Acid stress can affect the viability of probiotics, especially Bifidobacterium. This study aimed to improve the acid tolerance of Bifidobacterium longum BBMN68 using adaptive evolution. The stress response, and genomic differences of the parental strain and the variant strain were compared by acid stress. The highest acid-resistant mutant strain (BBMN68m) was isolated from more than 100 asexual lines, which were adaptive to the acid stress for 10(th), 20(th), 30(th), 40(th), and 50(th) repeats, respectively. The variant strain showed a significant increase in acid tolerance under conditions of pH 2.5 for 2 h (from 7.92 to 4.44 log CFU/ml) compared with the wildtype strain (WT, from 7.87 to 0 log CFU/ml). The surface of the variant strain was also smoother. Comparative whole-genome analysis showed that the galactosyl transferase D gene (cpsD, bbmn68_1012), a key gene involved in exopolysaccharide (EPS) synthesis, was altered by two nucleotides in the mutant, causing alteration in amino acids, pI (from 8.94 to 9.19), and predicted protein structure. Meanwhile, cpsD expression and EPS production were also reduced in the variant strain (p < 0.05) compared with WT, and the exogenous WT-EPS in the variant strain reduced its acid-resistant ability. These results suggested EPS was related to acid responses of BBMN68. PMID:26608165

  7. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

    PubMed Central

    Narihiro, Takashi; Sekiguchi, Yuji

    2011-01-01

    Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

  8. Chloramphenicol acetyltransferase should not provide methanogens with resistance to chloramphenicol. [Methanococcus voltae; Methanococcus vannielii; Methanococcus deltae; Methanobrevibacter smithii

    SciTech Connect

    Beckler, G.S.; Hook, L.A.; Reeve, J.N.

    1984-04-01

    Growth of the four methanogens investigated was inhibitied by chloramphenicol-3-acetate; therefore, introduction of chloramphenicol acetyltransferase-encoding genes should not confer chloramphenicol resistance on these methanogens. Reduction of the aryl nitro group of chloramphenicol produced a compound which did not inhibit the growth of these methanogens. 9 references.

  9. Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen

    PubMed Central

    Kelly, William J.; Li, Dong; Lambie, Suzanne C.; Jeyanathan, Jeyamalar; Cox, Faith; Li, Yang; Attwood, Graeme T.; Altermann, Eric

    2016-01-01

    Methanogenic archaeon ISO4-G1 is a methylotrophic methanogen belonging to the order Methanomassiliicoccales that was isolated from a sheep rumen. Its genome has been sequenced to provide information on the genetic diversity of rumen methanogens in order to develop technologies for ruminant methane mitigation. PMID:27056226

  10. Glycine betaine as a direct substrate for methanogens (Methanococcoides spp.).

    PubMed

    Watkins, Andrew J; Roussel, Erwan G; Parkes, R John; Sass, Henrik

    2014-01-01

    Nine marine methanogenic Methanococcoides strains, including the type strains of Methanococcoides methylutens, M. burtonii, and M. alaskense, were tested for the utilization of N-methylated glycines. Three strains (NM1, PM2, and MKM1) used glycine betaine (N,N,N-trimethylglycine) as a substrate for methanogenesis, partially demethylating it to N,N-dimethylglycine, whereas none of the strains used N,N-dimethylglycine or sarcosine (N-methylglycine). Growth rates and growth yields per mole of substrate with glycine betaine (3.96 g [dry weight] per mol) were similar to those with trimethylamine (4.11 g [dry weight] per mol). However, as glycine betaine is only partially demethylated, the yield per methyl group was significantly higher than with trimethylamine. If glycine betaine and trimethylamine are provided together, trimethylamine is demethylated to dimethyl- and methylamine with limited glycine betaine utilization. After trimethylamine is depleted, dimethylamine and glycine betaine are consumed rapidly, before methylamine. Glycine betaine extends the range of substrates that can be directly utilized by some methanogens, allowing them to gain energy from the substrate without the need for syntrophic partners. PMID:24162571

  11. Diffusional Properties of Methanogenic Granular Sludge: 1H NMR Characterization

    PubMed Central

    Lens, Piet N. L.; Gastesi, Rakel; Vergeldt, Frank; van Aelst, Adriaan C.; Pisabarro, Antonio G.; Van As, Henk

    2003-01-01

    The diffusive properties of anaerobic methanogenic and sulfidogenic aggregates present in wastewater treatment bioreactors were studied using diffusion analysis by relaxation time-separated pulsed-field gradient nuclear magnetic resonance (NMR) spectroscopy and NMR imaging. NMR spectroscopy measurements were performed at 22°C with 10 ml of granular sludge at a magnetic field strength of 0.5 T (20 MHz resonance frequency for protons). Self-diffusion coefficients of H2O in the investigated series of mesophilic aggregates were found to be 51 to 78% lower than the self-diffusion coefficient of free water. Interestingly, self-diffusion coefficients of H2O were independent of the aggregate size for the size fractions investigated. Diffusional transport occurred faster in aggregates growing under nutrient-rich conditions (e.g., the bottom of a reactor) or at high (55°C) temperatures than in aggregates cultivated in nutrient-poor conditions or at low (10°C) temperatures. Exposure of aggregates to 2.5% glutaraldehyde or heat (70 or 90°C for 30 min) modified the diffusional transport up to 20%. In contrast, deactivation of aggregates by HgCl2 did not affect the H2O self-diffusion coefficient in aggregates. Analysis of NMR images of a single aggregate shows that methanogenic aggregates possess a spin-spin relaxation time and self-diffusion coefficient distribution, which are due to both physical (porosity) and chemical (metal sulfide precipitates) factors. PMID:14602624

  12. Genome Copy Numbers and Gene Conversion in Methanogenic Archaea▿

    PubMed Central

    Hildenbrand, Catherina; Stock, Tilmann; Lange, Christian; Rother, Michael; Soppa, Jörg

    2011-01-01

    Previous studies revealed that one species of methanogenic archaea, Methanocaldococcus jannaschii, is polyploid, while a second species, Methanothermobacter thermoautotrophicus, is diploid. To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera—Methanosarcina acetivorans and Methanococcus maripaludis—were investigated. M. acetivorans was found to be polyploid during fast growth (tD = 6 h; 17 genome copies) and oligoploid during slow growth (doubling time = 49 h; 3 genome copies). M. maripaludis has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca. 30 in stationary phase. A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid (haploid), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms. Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero (called “Muller's ratchet”). A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon. Making use of a previously constructed heterozygous mutant strain of the polyploid M. maripaludis we could show that in the absence of selection very fast equalization of genomes in M. maripaludis took place probably via a gene conversion mechanism. In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection. PMID:21097629

  13. Restricted diversity of dental calculus methanogens over five centuries, France

    PubMed Central

    Huynh, Hong T. T.; Nkamga, Vanessa D.; Signoli, Michel; Tzortzis, Stéfan; Pinguet, Romuald; Audoly, Gilles; Aboudharam, Gérard; Drancourt, Michel

    2016-01-01

    Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14th to 19th centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus. PMID:27166431

  14. Methane formation and methane oxidation by methanogenic bacteria.

    PubMed Central

    Zehnder, A J; Brock, T D

    1979-01-01

    Methanogenic bacteria were found to form and oxidize methane at the same time. As compared to the quantity of methane formed, the amount of methane simultaneously oxidized varied between 0.3 and 0.001%, depending on the strain used. All the nine tested strains of methane producers (Methanobacterium ruminantium, Methanobacterium strain M.o.H., M. formicicum, M. thermoautotrophicum, M. arbophilicum, Methanobacterium strain AZ, Methanosarcina barkeri, Methanospirillum hungatii, and the "acetate organism") reoxidized methane to carbon dioxide. In addition, they assimilated a small part of the methane supplied into cell material. Methanol and acetate also occurred as oxidation products in M. barkeri cultures. Acetate was also formed by the "acetate organism," a methane bacterium unable to use methanogenic substrates other than acetate. Methane was the precursor of the methyl group of the acetate synthesized in the course of methane oxidation. Methane formation and its oxidation were inhibited equally by 2-bromoethanesulfonic acid. Short-term labeling experiments with M. thermoautotrophicum and M. hungatii clearly suggest that the pathway of methane oxidation is not identical with a simple back reaction of the methane formation process. Images PMID:762019

  15. Methanogens rapidly transition from methane production to iron reduction.

    PubMed

    Sivan, O; Shusta, S S; Valentine, D L

    2016-03-01

    Methanogenesis, the microbial methane (CH4 ) production, is traditionally thought to anchor the mineralization of organic matter as the ultimate respiratory process in deep sediments, despite the presence of oxidized mineral phases, such as iron oxides. This process is carried out by archaea that have also been shown to be capable of reducing iron in high levels of electron donors such as hydrogen. The current pure culture study demonstrates that methanogenic archaea (Methanosarcina barkeri) rapidly switch from methanogenesis to iron-oxide reduction close to natural conditions, with nitrogen atmosphere, even when faced with substrate limitations. Intensive, biotic iron reduction was observed following the addition of poorly crystalline ferrihydrite and complex organic matter and was accompanied by inhibition of methane production. The reaction rate of this process was of the first order and was dependent only on the initial iron concentrations. Ferrous iron production did not accelerate significantly with the addition of 9,10-anthraquinone-2,6-disulfonate (AQDS) but increased by 11-28% with the addition of phenazine-1-carboxylate (PCA), suggesting the possible role of methanophenazines in the electron transport. The coupling between ferrous iron and methane production has important global implications. The rapid transition from methanogenesis to reduction of iron-oxides close to the natural conditions in sediments may help to explain the globally-distributed phenomena of increasing ferrous concentrations below the traditional iron reduction zone in the deep 'methanogenic' sediment horizon, with implications for metabolic networking in these subsurface ecosystems and in past geological settings. PMID:26762691

  16. Restricted diversity of dental calculus methanogens over five centuries, France.

    PubMed

    Huynh, Hong T T; Nkamga, Vanessa D; Signoli, Michel; Tzortzis, Stéfan; Pinguet, Romuald; Audoly, Gilles; Aboudharam, Gérard; Drancourt, Michel

    2016-01-01

    Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus. PMID:27166431

  17. Study of methanogens by genetic techniques. A subcontract progress report

    SciTech Connect

    Baresi, L.; Bertani, G.

    1984-06-01

    Genetic studies of methanogenic bacteria could lead to better exploitation of these organisms in the production of methane from biomass. The objective of this study is to develop a workable genetic system for these bacteria. We have tried to apply standard genetic techniques to these slow growing, strictly anaerobic bacteria. We have been able to isolate several types of mutants both spontaneous and induced. For Methanococcus voltae we have (a) established survival curves to ultraviolet light and gamma ray irradiation, (b) isolated by direct selection mutants resistant to bromo-ethane-sulfonate and to 5-methyl-tryptophan, and a double mutant exhibiting both resistances, (c) isolated after mutagenesis two nutritional mutants (one requiring histidine and the other requiring adenine and possibly another factor). For Methanobacterium thermoautotrophicum we have (a) established an ultraviolet light survival curve, (b) isolated by direct selection mutants resistant to bromo-ethane-sulfonate and to gentamicin. We have developed a routine technique for the purpose of isolating phages capable of infecting methanogenic bacteria. 10 figures, 1 table.

  18. Glycine Betaine as a Direct Substrate for Methanogens (Methanococcoides spp.)

    PubMed Central

    Watkins, Andrew J.; Roussel, Erwan G.; Parkes, R. John

    2014-01-01

    Nine marine methanogenic Methanococcoides strains, including the type strains of Methanococcoides methylutens, M. burtonii, and M. alaskense, were tested for the utilization of N-methylated glycines. Three strains (NM1, PM2, and MKM1) used glycine betaine (N,N,N-trimethylglycine) as a substrate for methanogenesis, partially demethylating it to N,N-dimethylglycine, whereas none of the strains used N,N-dimethylglycine or sarcosine (N-methylglycine). Growth rates and growth yields per mole of substrate with glycine betaine (3.96 g [dry weight] per mol) were similar to those with trimethylamine (4.11 g [dry weight] per mol). However, as glycine betaine is only partially demethylated, the yield per methyl group was significantly higher than with trimethylamine. If glycine betaine and trimethylamine are provided together, trimethylamine is demethylated to dimethyl- and methylamine with limited glycine betaine utilization. After trimethylamine is depleted, dimethylamine and glycine betaine are consumed rapidly, before methylamine. Glycine betaine extends the range of substrates that can be directly utilized by some methanogens, allowing them to gain energy from the substrate without the need for syntrophic partners. PMID:24162571

  19. Recovery of palladium(II) by methanogenic granular sludge.

    PubMed

    Pat-Espadas, Aurora M; Field, James A; Otero-Gonzalez, Lila; Razo-Flores, Elías; Cervantes, Francisco J; Sierra-Alvarez, Reyes

    2016-02-01

    This is the first report that demonstrates the ability of anaerobic methanogenic granular sludge to reduce Pd(II) to Pd(0). Different electron donors were evaluated for their effectiveness in promoting Pd reduction. Formate and H2 fostered both chemically and biologically mediated Pd reduction. Ethanol only promoted the reduction of Pd(II) under biotic conditions and the reduction was likely mediated by H2 released from ethanol fermentation. No reduction was observed in biotic or abiotic assays with all other substrates tested (acetate, lactate and pyruvate) although a large fraction of the total Pd was removed from the liquid medium likely due to biosorption. Pd(II) displayed severe inhibition towards acetoclastic and hydrogenotrophic methanogens, as indicated by 50% inhibiting concentrations as low as 0.96 and 2.7 mg/L, respectively. The results obtained indicate the potential of utilizing anaerobic granular sludge bioreactor technology as a practical and promising option for Pd(II) reduction and recovery offering advantages over pure cultures. PMID:26408982

  20. Absolute Quantification of Individual Biomass Concentrations in a Methanogenic Coculture

    PubMed Central

    2014-01-01

    Identification of individual biomass concentrations is a crucial step towards an improved understanding of anaerobic digestion processes and mixed microbial conversions in general. The knowledge of individual biomass concentrations allows for the calculation of biomass specific conversion rates which form the basis of anaerobic digestion models. Only few attempts addressed the absolute quantification of individual biomass concentrations in methanogenic microbial ecosystems which has so far impaired the calculation of biomass specific conversion rates and thus model validation. This study proposes a quantitative PCR (qPCR) approach for the direct determination of individual biomass concentrations in methanogenic microbial associations by correlating the native qPCR signal (cycle threshold, Ct) to individual biomass concentrations (mg dry matter/L). Unlike existing methods, the proposed approach circumvents error-prone conversion factors that are typically used to convert gene copy numbers or cell concentrations into actual biomass concentrations. The newly developed method was assessed and deemed suitable for the determination of individual biomass concentrations in a defined coculture of Desulfovibrio sp. G11 and Methanospirillum hungatei JF1. The obtained calibration curves showed high accuracy, indicating that the new approach is well suited for any engineering applications where the knowledge of individual biomass concentrations is required. PMID:24949269

  1. Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil.

    PubMed

    Schmidt, Oliver; Horn, Marcus A; Kolb, Steffen; Drake, Harold L

    2015-03-01

    The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat. PMID:24813682

  2. Pressure-Enhanced Activity and Stability of a Hyperthermophilic Protease from a Deep-Sea Methanogen

    PubMed Central

    Michels, P. C.; Clark, D. S.

    1997-01-01

    We describe the properties of a hyperthermophilic, barophilic protease from Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen. This enzyme is the first protease to be isolated from an organism adapted to a high-pressure-high-temperature environment. The partially purified enzyme has a molecular mass of 29 kDa and a narrow substrate specificity with strong preference for leucine at the P1 site of polypeptide substrates. Enzyme activity increased up to 116(deg)C and was measured up to 130(deg)C, one of the highest temperatures reported for the function of any enzyme. In addition, enzyme activity and thermostability increased with pressure: raising the pressure to 500 atm increased the reaction rate at 125(deg)C 3.4-fold and the thermostability 2.7-fold. Spin labeling of the active-site serine revealed that the active-site geometry of the M. jannaschii protease is not grossly different from that of several mesophilic proteases; however, the active-site structure may be relatively rigid at moderate temperatures. The barophilic and thermophilic behavior of the enzyme is consistent with the barophilic growth of M. jannaschii observed previously (J. F. Miller et al., Appl. Environ. Microbiol. 54:3039-3042, 1988). PMID:16535711

  3. Taxonomic status and ecologic function of methanogenic bacteria isolated from the oral cavity of humans

    SciTech Connect

    Kemp, C.W.

    1985-01-01

    The detection of methane gas in samples of dental plaque and media inoculated with dental plaque was attributed to the presence of methane-producing bacteria in the plaque microbiota. The results of a taxonomic analysis of the 12 methanogenic isolates obtained from human dental plaque, (ABK1-ABK12), placed the organisms in the genus Methanobrevibacter. A DNA-DNA hybridization survey established three distinct genetic groups of oral methanogens based on percent homology values. The groups exhibited less than 32% homology between themselves and less than 17% homology with the three known members of the genus methanobrevibacter. The ecological role of the oral methanogens was established using mixed cultures of selected methanogenic isolates (ABK1, ABK4, ABK6, or ABK7) with oral heterotrophic bacteria. Binary cultures of either Streptococcus mutans, Streptococcus sanguis, Veillonella rodentium, Lactobacillus casei, or Peptostreptococcus anaerobius together with either methanogenic isolates ABK6 or ABK7 were grown to determine the effect of the methanogens on the distribution of carbon end products produced by the heterotrophs. Binary cultures of S. mutans and ABK7 exhibited a 27% decrease in lactic acid formation when compared to pure culture of S. mutans. The decrease in lactic acid production was attributed to the removal of formate by the methanogen, (ABK7), which caused an alteration in the distribution of carbon end products by S. mutans.

  4. Acceleration of cellulose degradation and shift of product via methanogenic co-culture of a cellulolytic bacterium with a hydrogenotrophic methanogen.

    PubMed

    Sasaki, Daisuke; Morita, Masahiko; Sasaki, Kengo; Watanabe, Atsushi; Ohmura, Naoya

    2012-10-01

    Although the effects of syntrophic relationships between bacteria and methanogens have been reported in some environments, those on cellulose decomposition using cellulolytic bacteria from methanogenic reactors have not yet been examined. The effects of syntrophic co-culture on the decomposition of a cellulosic material were investigated in a co-culture of Clostridium clariflavum strain CL-1 and the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus strain ΔH and a single-culture of strain CL-1 under thermophilic conditions. In this study, strain CL-1 was newly isolated as a cellulolytic bacterium from a thermophilic methanogenic reactor used for degrading garbage slurry. The degradation efficiency and cell density of strain CL-1 were 2.9- and 2.7-fold higher in the co-culture than in the single-culture after 60 h of incubation, respectively. Acetate, lactate and ethanol were the primary products in both cultures, and the concentration of propionate was low. The content of acetate to total organic acids plus ethanol was 59.3% in the co-culture. However, the ratio decreased to 24.9% in the single-culture, although acetate was the primary product. Therefore, hydrogen scavenging by the hydrogenotrophic methanogen strain ΔH could shift the metabolic pathway to the acetate production pathway in the co-culture. Increases in the cell density and the consequent acceleration of cellulose degradation in the co-culture would be caused by increases in adenosine 5'-triphosphate (ATP) levels, as the acetate production pathway includes ATP generation. Syntrophic cellulose decomposition by the cellulolytic bacteria and hydrogenotrophic methanogens would be the dominant reaction in the thermophilic methanogenic reactor degrading cellulosic materials. PMID:22652087

  5. Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea

    DOE PAGESBeta

    Rother, Michael; Krzycki, Joseph A.

    2010-01-01

    Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to putmore » this knowledge into the context of their unique energy metabolism.« less

  6. Conversion of indole to oxindole under methanogenic conditions

    SciTech Connect

    Berry, D.F.; Madsen, E.L.; Bollag, J.M.

    1987-01-01

    Aromatic N-heterocyclic compounds are often present in aqueous effluents associated with coal mining and processing operations. The environmental fate of these chemicals is of great concern because they are toxic and may contaminate both surface water and groundwater. Previous investigations of microbial metabolism of aromatic chemicals under aerobic and anaerobic conditions suggest that microorganisms may play a key role in determining the fate of this class of compounds. When indole was incubated under methanogenic conditions with an inoculum of sewage sludge, the chemical was metabolized within 10 days and temporary formation of an intermediate was observed. The metabolite was isolated by thin-layer chromatography and determined to be 1,3-dihydro-2H-indol-2-one (oxindole) by UV spectroscopy (lambda/sub max/, 247 nm) and mass spectrometry (m/z, 133). The methane produced (net amount) indicated nearly complete mineralization of indole.

  7. Methanogenic burst in the end-Permian carbon cycle

    PubMed Central

    Rothman, Daniel H.; Fournier, Gregory P.; French, Katherine L.; Alm, Eric J.; Boyle, Edward A.; Cao, Changqun; Summons, Roger E.

    2014-01-01

    The end-Permian extinction is associated with a mysterious disruption to Earth’s carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth’s greatest mass extinction by a specific microbial innovation. PMID:24706773

  8. A mechanistic model of hydrogen-methanogen dynamics in the rumen.

    PubMed

    Wang, Yuancheng; Janssen, Peter H; Lynch, Tammy A; Brunt, Bruce van; Pacheco, David

    2016-03-21

    Existing mathematical models to estimate methane production in the rumen are based on calculation of hydrogen balances without considering the presence of methanogens. In this study, a mechanistic model of methane production is proposed that depicts the interaction between hydrogen concentration and methanogens in the rumen. Analytical results show that it meets biological expectations, namely increased fractional passage rate leads to a greater growth rate of methanogens, and a greater steady state hydrogen concentration. This model provides a basis on which to develop a more comprehensive model of methane production in the rumen that includes thermodynamics and feed fermentation pathways. PMID:26780651

  9. Osmoregulation in methanogens. Progress report, May 15, 1991--January 15, 1993

    SciTech Connect

    Roberts, M.F.

    1993-01-01

    Our major goal of our work has been to develop and use NMR techniques to study how methanogenic archaebacteria deal with osmotic stress with the hope of providing insights into increasing the salt tolerance of other cells. The project has three main sections: (i) in vivo studies of methanogens; (ii) use of {sup l3}C- and {sup l5}N- labeled potential precursors and in vitro analyses of specific label uptake for elucidation of osmolyte dynamics and biosynthetic pathways of osmolytes in these organisms, and isolation of key biosynthetic enzymes; and (iii) collaborative studies on identification of organic solutes in other methanogens.

  10. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization.

    PubMed Central

    Raskin, L; Poulsen, L K; Noguera, D R; Rittmann, B E; Stahl, D A

    1994-01-01

    The microbial community structure of anaerobic biological reactors was evaluated by using oligonucleotide probes complementary to conserved tracts of the 16S rRNAs of phylogenetically defined groups of methanogens. Phylogenetically defined groups of methanogens were quantified and visualized, respectively, by hybridization of 32P- and fluorescent-dye-labeled probes to the 16S rRNAs from samples taken from laboratory acetate-fed chemostats, laboratory municipal solid waste digestors, and full-scale sewage sludge digestors. Methanosarcina species, members of the order Methanobacteriales, and Methanosaeta species were the most abundant methanogens present in the chemostats, the solid-waste digestors, and the sewage sludge digestors, respectively. PMID:7517129

  11. Progression of methanogenic degradation of crude oil in the subsurface

    USGS Publications Warehouse

    Bekins, B.A.; Hostettler, F.D.; Herkelrath, W.N.; Delin, G.N.; Warren, E.; Essaid, H.I.

    2005-01-01

    Our results show that subsurface crude-oil degradation rates at a long-term research site were strongly influenced by small-scale variations in hydrologic conditions. The site is a shallow glacial outwash aquifer located near Bemidji in northern Minnesota that became contaminated when oil spilled from a broken pipeline in August 1979. In the study area, separate-phase oil forms a subsurface oil body extending from land surface to about 1 m (3.3 ft) below the 6-8-m (20-26 ft)-deep water table. Oil saturation in the sediments ranges from 10-20% in the vadose zone to 30-70% near the water table. At depths below 2 m (6.6 ft), degradation of the separate-phase crude oil occurs under methanogenic conditions. The sequence of methanogenic alkane degradation depletes the longer chain n-alkanes before the shorter chain n-alkanes, which is opposite to the better known aerobic sequence. The rates of degradation vary significantly with location in the subsurface. Oil-coated soils within 1.5 m (5 ft) of land surface have experienced little degradation where soil water saturation is less than 20%. Oil located 2-8 m (6.6-26 ft) below land surface in areas of higher recharge has been substantially degraded. The best explanation for the association between recharge and enhanced degradation seems to be increased downward transport of microbial growth nutrients to the oil body. This is supported by observations of greater microbial numbers at higher elevations in the oil body and significant decreases with depth in nutrient concentrations, especially phosphorus. Our results suggest that environmental effects may cause widely diverging degradation rates in the same spill, calling into question dating methods based on degradation state. Copyright ?? 2005. The American Association of Petroleum Geologists/Division of Environmental Geosciences. All rights reserved.

  12. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies.

    PubMed

    Taubner, Ruth-Sophie; Schleper, Christa; Firneis, Maria G; Rittmann, Simon K-M R

    2015-01-01

    Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens. PMID:26703739

  13. SEQUENTIAL REDUCTIVE DEHALOGATION OF CHLOROANILINES BY MICROORGANISMS FROM A METHANOGENIC AQUIFER

    EPA Science Inventory

    Chloroaniline-based compounds are widely used chem- icals and important contaminants of aquatic and terrestrial environments. We have found that chloroanilines can be biologically dehalogenated in polluted aquifers when methanogenic, but not sulfate-reducing conditions prevail. T...

  14. BIOTRANSFORMATIONS OF SELECTED ALKYLBENZENES AND HALOGENATED ALIPHATIC HYDROCARBONS IN METHANOGENIC AQUIFER MATERIAL: A MICROCOSM STUDY

    EPA Science Inventory

    Leachates from municipal landfills commonly contain a variety of organic contaminants of industrial origin. The behavior of these compounds in anaerobic, and particularly in methanogenic, subsurface materials is poorly understood. The behavior of benzene, toluene, ethylbenzene, o...

  15. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

    NASA Astrophysics Data System (ADS)

    Taubner, Ruth-Sophie; Schleper, Christa; Firneis, Maria G.; Rittman, Simon K.-M. R.

    2015-12-01

    Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.

  16. Transformations of 1- and 2-carbon halogenated aliphatic organic compounds under methanogenic conditions.

    PubMed Central

    Bouwer, E J; McCarty, P L

    1983-01-01

    Several 1- and 2-carbon halogenated aliphatic organic compounds present at low concentrations (less than 100 micrograms/liter) were degraded under methanogenic conditions in batch bacterial cultures and in a continuous-flow methanogenic fixed-film laboratory-scale column. Greater than 90% degradation was observed within a 2-day detention time under continuous-flow methanogenic conditions with acetate as a primary substrate. Carbon-14 measurements indicated that chloroform, carbon tetrachloride, and 1,2-dichloroethane were almost completely oxidized to carbon dioxide, confirming removal by biooxidation. The initial step in the transformations of tetrachloroethylene and 1,1,2,2-tetrachloroethane to nonchlorinated end products appeared to be reductive dechlorination to trichloroethylene and 1,1,2-trichloroethane, respectively. Transformations of the brominated aliphatic compounds appear to be the result of both biological and chemical processes. The data suggest that transformations of halogenated aliphatic compounds can occur under methanogenic conditions in the environment. PMID:6859849

  17. Enumeration of methanogens with a focus on fluorescence in situ hybridization

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjay; Dagar, Sumit Singh; Mohanty, Ashok Kumar; Sirohi, Sunil Kumar; Puniya, Monica; Kuhad, Ramesh C.; Sangu, K. P. S.; Griffith, Gareth Wyn; Puniya, Anil Kumar

    2011-06-01

    Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

  18. SEQUENTIAL REDUCTIVE DEHALOGENATION OF CHLORANILINES BY MICROORGANISMS FROM A METHANOGENIC AQUIFER

    EPA Science Inventory

    Chloroaniline-based compounds are widely used chemicals and important contaminants of aquatic and terrestrial environments. We have found that chloroanilines can be bio-logically dehalogenated in polluted aquifers when methanogenic, but not sulfate-reducing conditions prevail. Th...

  19. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

    PubMed Central

    Taubner, Ruth-Sophie; Schleper, Christa; Firneis, Maria G.; Rittmann, Simon K.-M. R.

    2015-01-01

    Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens. PMID:26703739

  20. Higher Temperature and Hydrogen Availability Stimulated the Methanogenic Activity in East Antarctic Subglacial Sediment

    NASA Astrophysics Data System (ADS)

    Ma, H.

    2014-12-01

    Subglacial ecosystem has been recognized as an environment with considerable methanogenic activity, and therefore is of significant impact on global methane budget and climate change. Although the methanogens have been discovered at a few subglacial environments, the methanogenic activity there is yet insufficiently studied, especially on the effects of environmental parameters, due to technical difficulties on sampling and cultivation. Here, in this study, we attempt to access the methanogenic activity and community structure in response to temperature and substrate availability. An integrated approach including in vitro cultivation and molecular techniques were employed. A subglacial sediment from Larsemann Hills, East Antarctica was incubated at different temperatures (1, 4, 12 oC) supplied with H2+CO2 or sodium acetate to estimate the methanogenic activity. The McrA gene which is a specific marker for methanogens was amplified with primer ME and ML to construct phylogenetic trees. This functional gene was also quantified by Q-PCR before and after the incubation to estimate the increase of methanogens. After 8 months a highest methanogenesis rate of 226 pmol/ day/ gram sediment was observed at 12 oC with H2 supplying, which was 2 times higher than that with acetate supplying, clearly suggesting that H2 is a preferable substrate than acetate. The methanogenesis rate without supplying extra substrate showed positive temperature dependence with rate of 23.3, 24.8, 131 pmol/day/gram sediment at 1 oC, 4 oC, and 12 oC, respectively. The McrA copy number was increased more than 300 times and 50 times with H2 and acetate supplying respectively after the incubation. 94% and 67% of the mcrA gene sequences were classed into methanomicrobiales which were hydrogen-trophic methanogens in the two clone libraries with primer ML and ME respectively. This finding suggests the potential effect of methanogenesis under glacier on the climate change.

  1. Environmental controls on methanogen viability in the hydrothermal waters of the El Tatio geyser field, Chile.

    NASA Astrophysics Data System (ADS)

    Franks, M. A.; Bennett, P. C.; Omelon, C.; Engel, A. S.

    2007-12-01

    At the El Tatio geyser field, a unique hydrothermal site located in the Andes Mountains in Chile, methanogenic archaea were found in only two of the hundreds of hydrothermal features. Reported here is an investigation into the environmental and geochemical controls on the distribution of methanogenic archaea. Located in the hyper- arid Atacama Desert, El Tatio waters are characterized by high salinity (95-175mM), Na-Cl type waters and circum-neutral pH (6.5-7), with very low inorganic carbon (0.1-0.5 mM TIC), but very high concentrations of As and Sb (300-700 uM As, 10-30uM Sb). Extensive bacterial mats thrive in most of the shallow run-off streams originating from hydrothermal features. In order to determine geochemical controls on methanogen populations, major and trace elements, including As and Sb speciation and concentrations, were determined using IC and HPLC-ICP-MS methods. The structure of microbial communities was analyzed using MPN enumeration of methanogens, culturing, and phylogenetic analysis using molecular techniques. Here, as in many hydrothermal regions, temperature and geochemical gradients influence the microbial ecology. Results from MPN enumeration indicate methanogen populations are dominated by H2-utilizing (carbonate reducing) archaea at both of the sites, with some acetate-oxidizing archaea present. These sites contain comparatively high DIC concentrations; however, it is unclear whether this is a control or a product of methanogenic archaea. Water quality analyses also show a strong correlation between antimony concentrations and the presence of methanogens; methanogenic archaea being present only at sites with 17 uM Sb concentrations or less.

  2. Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil.

    PubMed

    Schulz, Kristin; Hunger, Sindy; Brown, George G; Tsai, Siu M; Cerri, Carlos C; Conrad, Ralf; Drake, Harold L

    2015-08-01

    The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH4) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [(13)C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H2), carbon dioxide (CO2), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceae-affiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and (13)C-labeling of CH4 verified that supplemental [(13)C]-glucose derived carbon was dissimilated to CH4. Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae. PMID:25615437

  3. Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments

    PubMed Central

    Fowler, S. Jane; Toth, Courtney R. A.; Gieg, Lisa M.

    2016-01-01

    The methanogenic biodegradation of crude oil involves the conversion of hydrocarbons to methanogenic substrates by syntrophic bacteria and subsequent methane production by methanogens. Assessing the metabolic roles played by various microbial species in syntrophic communities remains a challenge, but such information has important implications for bioremediation and microbial enhanced energy recovery technologies. Many factors such as changing environmental conditions or substrate variations can influence the composition and biodegradation capabilities of syntrophic microbial communities in hydrocarbon-impacted environments. In this study, a methanogenic crude oil-degrading enrichment culture was successively transferred onto the single long chain fatty acids palmitate or stearate followed by their parent alkanes, hexadecane or octadecane, respectively, in order to assess the impact of different substrates on microbial community composition and retention of hydrocarbon biodegradation genes. 16S rRNA gene sequencing showed that a reduction in substrate diversity resulted in a corresponding loss of microbial diversity, but that hydrocarbon biodegradation genes (such as assA/masD encoding alkylsuccinate synthase) could be retained within a community even in the absence of hydrocarbon substrates. Despite substrate-related diversity changes, all communities were dominated by hydrogenotrophic and acetotrophic methanogens along with bacteria including Clostridium sp., members of the Deltaproteobacteria, and a number of other phyla. Microbial co-occurrence network analysis revealed a dense network of interactions amongst syntrophic bacteria and methanogens that were maintained despite changes in the substrates for methanogenesis. Our results reveal the effect of substrate diversity loss on microbial community diversity, indicate that many syntrophic interactions are stable over time despite changes in substrate pressure, and show that syntrophic interactions amongst

  4. Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil

    PubMed Central

    Schulz, Kristin; Hunger, Sindy; Brown, George G; Tsai, Siu M; Cerri, Carlos C; Conrad, Ralf; Drake, Harold L

    2015-01-01

    The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH4) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [13C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H2), carbon dioxide (CO2), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceae-affiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and 13C-labeling of CH4 verified that supplemental [13C]-glucose derived carbon was dissimilated to CH4. Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae. PMID:25615437

  5. Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission.

    PubMed

    Pump, Judith; Pratscher, Jennifer; Conrad, Ralf

    2015-07-01

    The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4 ) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4 ), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots. PMID:25367104

  6. Mesophilic fermentation of renewable biomass: does hydraulic retention time regulate methanogen diversity?

    PubMed

    Krakat, Niclas; Schmidt, Stefan; Scherer, Paul

    2010-09-01

    The present long-term study (about 1,100 days) monitored the diversity of methanogens during the mesophilic, anaerobic digestion of beet silage. Six fermentor samples were analyzed by ribosomal RNA gene restriction analysis, fluorescence in situ hybridization, and fluorescence microscopy. Hydrogenotrophic methanogens dominated within the population in all samples analyzed. Multidimensional scaling revealed that a rapid decrease in hydraulic retention time resulted in increased species richness, which in turn led to slightly higher CH(4) yields. PMID:20675458

  7. Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments.

    PubMed

    Fowler, S Jane; Toth, Courtney R A; Gieg, Lisa M

    2016-01-01

    The methanogenic biodegradation of crude oil involves the conversion of hydrocarbons to methanogenic substrates by syntrophic bacteria and subsequent methane production by methanogens. Assessing the metabolic roles played by various microbial species in syntrophic communities remains a challenge, but such information has important implications for bioremediation and microbial enhanced energy recovery technologies. Many factors such as changing environmental conditions or substrate variations can influence the composition and biodegradation capabilities of syntrophic microbial communities in hydrocarbon-impacted environments. In this study, a methanogenic crude oil-degrading enrichment culture was successively transferred onto the single long chain fatty acids palmitate or stearate followed by their parent alkanes, hexadecane or octadecane, respectively, in order to assess the impact of different substrates on microbial community composition and retention of hydrocarbon biodegradation genes. 16S rRNA gene sequencing showed that a reduction in substrate diversity resulted in a corresponding loss of microbial diversity, but that hydrocarbon biodegradation genes (such as assA/masD encoding alkylsuccinate synthase) could be retained within a community even in the absence of hydrocarbon substrates. Despite substrate-related diversity changes, all communities were dominated by hydrogenotrophic and acetotrophic methanogens along with bacteria including Clostridium sp., members of the Deltaproteobacteria, and a number of other phyla. Microbial co-occurrence network analysis revealed a dense network of interactions amongst syntrophic bacteria and methanogens that were maintained despite changes in the substrates for methanogenesis. Our results reveal the effect of substrate diversity loss on microbial community diversity, indicate that many syntrophic interactions are stable over time despite changes in substrate pressure, and show that syntrophic interactions amongst

  8. Sensitivity and adaptability of methanogens to perchlorates: Implications for life on Mars

    NASA Astrophysics Data System (ADS)

    Kral, Timothy A.; Goodhart, Timothy H.; Harpool, Joshua D.; Hearnsberger, Christopher E.; McCracken, Graham L.; McSpadden, Stanley W.

    2016-01-01

    In 2008, the Mars Phoenix Lander discovered perchlorate at its landing site, and in 2012, the Curiosity rover confirmed the presence of perchlorate on Mars. The research reported here was designed to determine if certain methanogens could grow in the presence of three different perchlorate salt solutions. The methanogens tested were Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum and Methanococcus maripaludis. Media were prepared containing 0%, 0.5%, 1.0%, 2%, 5% and 10% wt/vol magnesium perchlorate, sodium perchlorate, or calcium perchlorate. Organisms were inoculated into their respective media followed by incubation at each organism's growth temperature. Methane production, commonly used to measure methanogen growth, was measured by gas chromatography of headspace gas samples. Methane concentrations varied with species and perchlorate salt tested. However, all four methanogens produced substantial levels of methane in the presence of up to 1.0% perchlorate, but not higher. The standard procedure for growing methanogens typically includes sodium sulfide, a reducing agent, to reduce residual molecular oxygen. However, the sodium sulfide may have been reducing the perchlorate, thus allowing for growth of the methanogens. To investigate this possibility, experiments were conducted where stainless steel nails were used instead of sodium sulfide as the reducing agent. Prior to the addition of perchlorate and inoculation, the nails were removed from the liquid medium. Just as in the prior experiments, the methanogens produced methane at comparable levels to those seen with sodium sulfide as the reductant, indicating that sodium sulfide did not reduce the perchlorate to any significant extent. Additionally, cells metabolizing in 1% perchlorate were transferred to 2%, cells metabolizing in 2% were transferred to 5%, and finally cells metabolizing in 5% were transferred to 10%. All four species produced methane at 2% and 5%, but not 10

  9. A T-RFLP database for the rapid profiling of methanogenic communities in anaerobic digesters.

    PubMed

    Bühligen, Franziska; Lucas, Rico; Nikolausz, Marcell; Kleinsteuber, Sabine

    2016-06-01

    We present a simple protocol for the cost- and time-efficient profiling of methanogens based on T-RFLP fingerprinting of mcrA amplicons. Sequence data were compiled from mesophilic lab-scale and full-scale biogas reactors operated under various conditions and fed with various substrates. The database facilitates the rapid identification of methanogens, thus reducing the need of cloning and sequencing. PMID:27046270

  10. Phylogenetic Characterization of Methanogenic Assemblages in Eutrophic and Oligotrophic Areas of the Florida Everglades†

    PubMed Central

    Castro, Hector; Ogram, Andrew; Reddy, K. R.

    2004-01-01

    Agricultural activities have produced well-documented changes in the Florida Everglades, including establishment of a gradient in phosphorus concentrations in Water Conservation Area 2A (WCA-2A) of the northern Everglades. An effect of increased phosphorus concentrations is increased methanogenesis in the eutrophic regions compared to the oligotrophic regions of WCA-2A. The goal of this study was to identify relationships between eutrophication and composition and activity of methanogenic assemblages in WCA-2A soils. Distributions of two genes associated with methanogens were characterized in soils taken from WCA-2A: the archaeal 16S rRNA gene and the methyl coenzyme M reductase gene. The richness of methanogen phylotypes was greater in eutrophic than in oligotrophic sites, and sequences related to previously cultivated and uncultivated methanogens were found. A preferential selection for the order Methanomicrobiales was observed in mcrA clone libraries, suggesting primer bias for this group. A greater diversity within the Methanomicrobiales was observed in mcrA clone libraries than in 16S rRNA gene libraries. 16S rRNA phylogenetic analyses revealed a dominance of clones related to Methanosaeta spp., an acetoclastic methanogen dominant in environments with low acetate concentrations. A significant number of clones were related to Methanomicrobiales, an order characterized by species utilizing hydrogen and formate as methanogenic substrates. No representatives of the orders Methanobacteriales and Methanococcales were found in any 16S rRNA clone library, although some Methanobacteriales were found in mcrA libraries. Hydrogenotrophs are the dominant methanogens in WCA-2A, and acetoclastic methanogen genotypes that proliferate in low acetate concentrations outnumber those that typically dominate in higher acetate concentrations. PMID:15528519

  11. Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas

    PubMed Central

    Aschenbach, Katrin; Conrad, Ralf; Řeháková, Klára; Doležal, Jiří; Janatková, Kateřina; Angel, Roey

    2013-01-01

    Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high-altitude cold deserts in the western Himalayas (Ladakh, India) produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival) were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust) were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, ~103 gdw−1 soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonizers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts. PMID:24348469

  12. Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas.

    PubMed

    Aschenbach, Katrin; Conrad, Ralf; Reháková, Klára; Doležal, Jiří; Janatková, Kateřina; Angel, Roey

    2013-01-01

    Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high-altitude cold deserts in the western Himalayas (Ladakh, India) produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival) were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust) were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, ~10(3) gdw(-1) soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonizers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts. PMID:24348469

  13. Performance of methanogenic reactors in temperature phased two-stage anaerobic digestion of swine wastewater.

    PubMed

    Kim, Woong; Shin, Seung Gu; Cho, Kyungjin; Lee, Changsoo; Hwang, Seokhwan

    2012-12-01

    The present study investigated the shifts in the chemical profiles of a two-phase anaerobic digestion system in methanogenic and acidogenic reactors for the treatment of swine wastewater. Acidogenic and methanogenic digesters were used with overall HRTs ranging from 27 to 6 d. In the optimized thermophilic/acidogenic phase throughout the entire experimental period, VS was reduced by 13.8% (1.6%); however, COD hardly decreased because of the thermophilic hydrolysis of organic materials, such as carbohydrates, proteins, and lipids, without any significant consumption of volatile fatty acids. In the methanogenic/mesophilic phase, COD was reduced by 65.8 (1.1)% compared to a 47.4 (2.9)% reduction in VS reduction efficiency with the gradual increase in methane production during a methanogenic HRT between 25 and 10 d. A high protein degradation rate was observed in the optimized acidogenic phase, which is assumed to be due to the low content of carbohydrates in raw swine wastewater as well as the readily thermophilic hydrolysis of proteins. Two-phase systems of anaerobic digestion consisting of optimized thermophilic and mesophilic methanogenic digesters showed a stable performance with respect to VS reduction efficiency with OLRs less than 3 g VS/L·d, in other words, more than 10 days of methanogenic HRT in this study. PMID:23041140

  14. Methanogenic archaea in marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources.

    PubMed

    Tucker, Yael Tarlovsky; Kotcon, James; Mroz, Thomas

    2015-06-01

    Marcellus Shale occurs at depths of 1.5-2.5 km (5000 to 8000 feet) where most geologists generally assume that thermogenic processes are the only source of natural gas. However, methanogens in produced fluids and isotopic signatures of biogenic methane in this deep shale have recently been discovered. This study explores whether those methanogens are indigenous to the shale or are introduced during drilling and hydraulic fracturing. DNA was extracted from Marcellus Shale core samples, preinjected fluids, and produced fluids and was analyzed using Miseq sequencing of 16s rRNA genes. Methanogens present in shale cores were similar to methanogens in produced fluids. No methanogens were detected in injected fluids, suggesting that this is an unlikely source and that they may be native to the shale itself. Bench-top methane production tests of shale core and produced fluids suggest that these organisms are alive and active under simulated reservoir conditions. Growth conditions designed to simulate the hydrofracture processes indicated somewhat increased methane production; however, fluids alone produced relatively little methane. Together, these results suggest that some biogenic methane may be produced in these wells and that hydrofracture fluids currently used to stimulate gas recovery could stimulate methanogens and their rate of producing methane. PMID:25924080

  15. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

    PubMed Central

    Angel, Roey; Claus, Peter; Conrad, Ralf

    2012-01-01

    The prototypical representatives of the Euryarchaeota—the methanogens—are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ13C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment. PMID:22071343

  16. Stereochemical studies of acyclic isoprenoids-XII. Lipids of methanogenic bacteria and possible contributions to sediments

    USGS Publications Warehouse

    Risatti, J.B.; Rowland, S.J.; Yon, D.A.; Maxwell, J.R.

    1984-01-01

    Abundant volatile lipids of Methanobacterium thermoautotrophicum and Methanosarcina barkeri include isoprenoid hydrocarbons (??? C30), and C15, C20 and C25 isoprenoid alcohols. M. barkeri contains 2,6,10,15,19-pentamethyleicosane, whose relative stereochemistry is the same as found in marine sediments, indicating that it is a marker of methanogenic activity. The C20, C30 and C25 alkenes in M. thermoautotrophicum also have a preferred sterochemistry; the latter have the 2,6,10,14,18-pentamethyleicosanyl skeleton, suggesting that the alkane in marine sediments may derive from methanogens. The stereochemistry of squalane in a marine sediment is also compatible with an origin in methanogens; in contrast, the stereochemistry of pristane in M. thermoautotrophicum indicates a fossil fuel contaminant origin, suggesting that this and certain other alkanes reported in archaebacteria might also be of contaminant origin. There is, therefore, little evidence at present that the pristane in immature marine sediments originates in methanogens. The C15 and C20 saturated alcohols in M. thermoautotrophicum have mainly the all-R configuration. If this is generally true for methanogens, the C20 alcohol in the Messel shale may originate mainly from methanogens, whereas that in the Green River shale may originate mainly from photosynthetic organisms. ?? 1984.

  17. Methanogenic archaea diversity in hyporheic sediments of a small lowland stream.

    PubMed

    Brablcová, Lenka; Buriánková, Iva; Badurová, Pavlína; Chaudhary, Prem Prashant; Rulík, Martin

    2015-04-01

    Abundance and diversity of methanogenic archaea were studied at five localities along a longitudinal profile of a Sitka stream (Czech Republic). Samples of hyporheic sediments were collected from two sediment depths (0-25 cm and 25-50 cm) by freeze-core method. Methanogen community was analyzed by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequencing method. The proportion of methanogens to the DAPI-stained cells varied among all localities and depths with an average value 2.08 × 10(5) per g of dry sediment with the range from 0.37 to 4.96 × 10(5) cells per g of dry sediment. A total of 73 bands were detected at 19 different positions on the DGGE gel and the highest methanogen diversity was found at the downstream located sites. There was no relationship between methanogen diversity and sediment depth. Cluster analysis of DGGE image showed three main clusters consisting of localities that differed in the number and similarity of the DGGE bands. Sequencing analysis of representative DGGE bands revealed phylotypes affiliated with members belonging to the orders Methanosarcinales, Methanomicrobiales and Methanocellales. The knowledge about occurrence and diversity of methanogenic archaea in freshwater ecosystems are essential for methane dynamics in river sediments and can contribute to the understanding of global warming process. PMID:25460192

  18. Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

    PubMed Central

    Singh, Rajesh; Dong, Hailiang; Liu, Deng; Zhao, Linduo; Marts, Amy R.; Farquhar, Erik; Tierney, David L.; Almquist, Catherine B.; Briggs, Brandon R.

    2015-01-01

    Despite the significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70°C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations with the 1, 5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to1.9 µM h−1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by X-ray diffraction and selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr6+ to less toxic Cr3+ and its potential application in metal bioremediation, especially at high temperature

  19. Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

    NASA Astrophysics Data System (ADS)

    Singh, Rajesh; Dong, Hailiang; Liu, Deng; Zhao, Linduo; Marts, Amy R.; Farquhar, Erik; Tierney, David L.; Almquist, Catherine B.; Briggs, Brandon R.

    2015-01-01

    Despite significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70 °C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations using 1,5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to 1.9 μM h-1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr6+ to less toxic Cr3+ and its potential application in metal bioremediation, especially at high temperature subsurface radioactive waste disposal

  20. Methanogenic Oil Degradation in the Dagang Oil Field

    NASA Astrophysics Data System (ADS)

    Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans Hermann; Krüger, Martin

    2014-05-01

    Anaerobic biodegradation is one of the main in situ oil transformation processes in subsurface oil reservoirs. Recent studies have provided evidence of biodegradation of residual oil constituents under methanogenic conditions. Methane, like other biogenic gases, may contribute to reduce the viscosity of oil and enhance its flow characteristics (making it more available) but it can also be used as a energy source. So the aim of the present study was to provide reliable information on in situ biotransformation of oil under methanogenic conditions, and to assess the feasibility of implementing a MEOR strategy at this site. For this reason, chemical and isotopic analyses of injection and production fluids of the Dagang oil field (Hebei province, China) were performed. Microbial abundances were assessed by qPCR, and clone libraries were performed to study the diversity. In addition, microcosms with either oil or 13C-labelled hydrocarbons were inoculated with injection or production waters to characterize microbial processes in vitro. Geochemical and isotopic data were consistent with in situ biogenic methane production linked to aliphatic and aromatic hydrocarbon degradation: GC-MS profiles of petroleum samples were nearly devoid of n-alkanes, linear alkylbenzenes, and alkyltoluenes, and light PAH, confirming that Dagang oil is mostly highly weathered. In addition, carbon and hydrogen isotopic signatures of methane (δ13CCH4 and δDCH4, respectively), and the bulk isotopic discrimination (Δδ13C) between methane and CO2 (between 32 and 65 ) were in accordance with previously reported values for methane formation during hydrocarbon degradation. Furthermore, methane-producing Archaea and hydrocarbon-degrading Bacteria were abundant in produced oil-water samples. On the other hand, our laboratory degradation experiments revealed that autochthonous microbiota are capable of significantly degrade oil within several months, with biodegradation patterns resembling those

  1. Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

    DOE PAGESBeta

    Singh, Rajesh; Dong, Hailiang; Liu, Deng; Zhao, Linduo; Marts, Amy R.; Farquhar, Erik; Tierney, David L.; Almquist, Catherine B.; Briggs, Brandon R.

    2014-10-22

    Despite the significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70°C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations with the 1, 5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions bymore » this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to1.9 μM h₋1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by X-ray diffraction and selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr6+ to less toxic Cr3+ and its potential application in metal bioremediation, especially at high temperature

  2. Relationship between Trophic Status and Methanogenic Pathways in Alaskan Peatlands

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Liu, X.; Sidelinger, W.; Wang, Y.; Hines, M. E.; Langford, L.; Chanton, J.

    2015-12-01

    To improve predictions of naturally emitted CH4 from northern wetlands, it is necessary to further examine the methanogenic pathways in these wetlands. Stable isotope C ratios (δ13C) have been used as a robust tool to distinguish different pathways, but different sources of parent compounds (acetate and CO2) with unique δ13C may add complexity to previously established criteria. Large portions of peatlands accommodate a mixture of different sphagna and sedges. Plant species may look very similar and belong to the same genus but are different morphologically and physiologically. To better understand the relationships between surface vegetation patterns and methanogenic pathways, 26 peatland sites were studied in Fairbanks and Anchorage, Alaska in summers of 2014 and 2015. These sites were ordinated using multiple factor analysis into 3 clusters based on pH, temp, CH4 and volatile fatty acids production rates, δ13C values, and surface vegetation species/pattern. In the low-pH trophic cluster (pH~3.5), non-vascular/vascular plant ratios (NV/V) were ~ 0.87 and dominated by diverse Sphagnum species and specific sedges (Eriophorum vaginatum), and fermentation was the dominant end-point in decomposition with no CH4 detected. Although NV/V is about the same in the intermediate cluster (0.74) (pH~4.5), and Sphagnum squarrosum was largely present, both hydrogenotrophic (HM) and acetoclastic methanogenesis (AM) were very active. Syntrophy was present at certain sites, which may provide CO2 with unique δ13C for CH4 production. At the highest pH trophic cluster examined in this study (pH~5), non-vascular plants were almost not existent and Carex aquatilis dominated. CH4 production rates (mainly HM) were slower than those in the intermediate cluster and the apparent fractionation factor a was lower than in the sites with syntrophy, which warrants further investigation of the position and compound specific δ13C analysis of volatile fatty acids.

  3. Reduction of hexavalent chromium by the thermophilic methanogen Methanothermobacter thermautotrophicus

    SciTech Connect

    Singh, Rajesh; Dong, Hailiang; Liu, Deng; Zhao, Linduo; Marts, Amy R.; Farquhar, Erik; Tierney, David L.; Almquist, Catherine B.; Briggs, Brandon R.

    2014-10-22

    Despite the significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70°C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations with the 1, 5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to1.9 μM h₋1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by X-ray diffraction and selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of

  4. Study on two methylotrophic and halophilic methanogens, Methanosarcina siciliae HI350 and Methanolobus taylorii GS-16

    SciTech Connect

    Ni, S.

    1994-01-01

    Strain HI350, similar to Methanolobus siciliae T4/M[sup T] (T = type strain) morphologically and physiologically, was isolated from an oil well in the Gulf of Mexico. Catabolic substrates included methanol, trimethylamine, dimethyl sulfide, and methane thiol, but not H[sub 2]-CO[sub 2], formate, or acetate. Growth was fastest in the presence of 0.4 to 0.6 M Na[sup +], in the presence of 60 to 200 mM Mg[sup 2+], at pH 6.5 to 6.8, and at 40[degrees]C. Methanolobus siciliae T4/M[sup T] was closely related to Methanosarcina. Transfer of Methanolobus siciliae T4/M[sup T] to the genus Methanosarcina as Methanosarcina siciliae is proposed with strain HI350 as its reference strain. Degradation of dimethyl sulfide or methane thiol by strain HI350 was complete, and stoichiometric quantities of methane and hydrogen sulfide were formed. Studies of cell-free extracts suggested that enzymes for degradation of dimethyl sulfide and methane thiol were inducible, whereas those for the degradation of methanol or trimethylamine were constitutive. Methanolobus taylorii GS-16, a moderately halophilic and alkcaliphilic methanogen, grows over a wide pH range. The key observation indicative of the involvement of K[sup +] transport in cytosolic acidification was that valinomycin (0.8 [mu]M), a K[sup +] uniporter, inhibited the growth of strain GS-16 only at alkaline pH. Experiments with resting cells indicated that, at alkaline pH, valinomycin uncoupled catabolic reactions from ATP synthesis. Thus, a K[sup +]/H[sup +] antiporter was proposed to account for the K[sup +] extrusion and the uncoupling effect of valinomycin at alkaline pH.

  5. Methane production improvement by modulation of solid phase immersion in dry batch anaerobic digestion process: Dynamic of methanogen populations.

    PubMed

    André, L; Ndiaye, M; Pernier, M; Lespinard, O; Pauss, A; Lamy, E; Ribeiro, T

    2016-05-01

    Several 60L dry batch anaerobic digestion (AD) reactors were implemented with or without liquid reserve on cattle manure. The immersed part modulation of cattle manure increased the methane flow of about 13%. The quantitative real time PCR and the optimized DNA extraction were implemented and validated to characterize and quantify the methanogen dynamic in dry batch AD process. Final quantities of methanogens converged toward the same level in several inocula at the end of AD. Methanogen dynamic was shown by dominance of Methanosarcinaceae for acetotrophic methanogens and Methanobacteriales for the hydrogenotrophic methanogens. Overall, methanogens populations were stabilized in liquid phase, except Methanosaetaceae. Solid phase was colonized by Methanomicrobiales and Methanosarcinaceae populations giving a support to biofilm development. The methane increase could be explained by a raise of Methanosarcinaceae population in presence of a total contact between solid and liquid phases. Methanosarcinaceae was a bio-indicator of the methane production. PMID:26897414

  6. Bacterial surface antigens defined by monoclonal antibodies: the methanogens

    SciTech Connect

    Conway de Macario, E.; Macario, A.J.L.; Magarinos, M.C.; Jovell, R.J.; Kandler, O.

    1982-01-01

    The methanogens (MB) are unique microbes of great evolutionary interest with applications in biotechnology-bioengineerings and are important in digestive processes. Their cell-wall composition is distinctively different from that of Eubacteria, e.g. the Methanobacteriaceae possess the peptidoglycan pseudomurein rather than murein. The range of cell-wall compositions among MB and their evolutionary and functional significance is not well known. The authors undertook a systematic study of the MB's surface structure using monoclonal antibodies through the following steps: (1) generation of hybridomas that produce antibody to several MB from 3 of their 4 families; (2) development of immunoenzymatic assays for MB's antigens and antibodies; (3) determination of the fine specificity of monoclonal antibodies by inhibition-blocking tests using cell-wall extracts and compounds of known structure; thus a set of monoclonal probes of predetermined specificity was assembled; and (4) resolution of surface determinants of MB representative of the Methanobacteriaceae using the monoclonal probes. Specific markers of MB strains were characterized. Two epitopes were identified within the pseudomurein molecule.

  7. Reductive dechlorination of chlorophenols by a pentachlorophenol- acclimated methanogenic consortium.

    PubMed Central

    Nicholson, D K; Woods, S L; Istok, J D; Peek, D C

    1992-01-01

    Anaerobic digester sludge fed 5,300 mg of acetate per liter, 3.4 microM pentachlorophenol, and nutrients for 10 days biotransformed pentachlorophenol by sequential ortho dechlorinations to produce 2,3,4,5-tetrachlorophenol and 3,4,5-trichlorophenol. Upon acclimation to 3.4 microM pentachlorophenol for 6 months, the methanogenic consortium removed chlorines from the ortho, meta, and para positions of pentachlorophenol and its reductive dechlorination products. Pentachlorophenol was degraded to produce 2,3,4,5-tetrachlorophenol, 2,3,4,6-tetrachlorophenol, and 2,3,5,6-tetrachlorophenol. Dechlorination of 2,3,4,5-tetrachlorophenol produced 3,4,5-trichlorophenol, which was subsequently degraded to produce 3,4-dichlorophenol and 3,5-dichlorophenol. 2,3,4,6-Tetrachlorophenol was dechlorinated at the ortho and meta positions to produce 2,4,6-trichlorophenol and 2,4,5-trichlorophenol. 2,3,5,6-Tetrachlorophenol yielded 2,3,5-trichlorophenol, followed by production of 3,5-dichlorophenol. 2,4,6-Trichlorophenol was degraded to form 2,4-dichlorophenol, and 2,4,5-trichlorophenol was dechlorinated at two positions to form 2,4-dichlorophenol and 3,4-dichlorophenol. Of the three dichlorophenols produced (2,4-dichlorophenol, 3,4-dichlorophenol, and 3,5-dichlorophenol), only 2,4-dichlorophenol was degraded significantly within 3 weeks, to produce 4-chlorophenol. PMID:1637165

  8. Fate of neptunium in an anaerobic, methanogenic microcosm.

    SciTech Connect

    Banaszak, J. E.

    1998-12-21

    Neptunium is found predominantly as Np(IV) in reducing environments, but Np(V) in aerobic environments. However, currently it is not known how the interplay between biotic and abiotic processes affects Np redox speciation in the environment. In order to evaluate the effect of anaerobic microbial activity on the fate of Np in natural systems, Np(V) was added to a microcosminoculated with anaerobic sediments from a metal-contaminated fresh water lake. The consortium included metal-reducing, sulfate-reducing, and methanogenic microorganisms, and acetate was supplied as the only exogenous substrate. Addition of more than 10{sup {minus}5} M Np did not inhibit methane production. Total Np volubility in the active microcosm, as well as in sterilized control samples, decreased by nearly two orders of magnitude. A combination of analytical techniques, including VIS-NIR absorption spectroscopy and XANES, identified Np(IV) as the oxidation state associated with the sediments. The similar results from the active microcosm and the abiotic controls suggest that microbian y produced Mn(II/HI) and Fe(II) may serve as electron donors for Np reduction.

  9. Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

    PubMed Central

    Hamilton, Joshua J.; Calixto Contreras, Montserrat; Reed, Jennifer L.

    2015-01-01

    Microorganisms in nature do not exist in isolation but rather interact with other species in their environment. Some microbes interact via syntrophic associations, in which the metabolic by-products of one species serve as nutrients for another. These associations sustain a variety of natural communities, including those involved in methanogenesis. In anaerobic syntrophic communities, energy is transferred from one species to another, either through direct contact and exchange of electrons, or through small molecule diffusion. Thermodynamics plays an important role in governing these interactions, as the oxidation reactions carried out by the first community member are only possible because degradation products are consumed by the second community member. This work presents the development and analysis of genome-scale network reconstructions of the bacterium Syntrophobacter fumaroxidans and the methanogenic archaeon Methanospirillum hungatei. The models were used to verify proposed mechanisms of ATP production within each species. We then identified additional constraints and the cellular objective function required to match experimental observations. The thermodynamic S. fumaroxidans model could not explain why S. fumaroxidans does not produce H2 in monoculture, indicating that current methods might not adequately estimate the thermodynamics, or that other cellular processes (e.g., regulation) play a role. We also developed a thermodynamic coculture model of the association between the organisms. The coculture model correctly predicted the exchange of both H2 and formate between the two species and suggested conditions under which H2 and formate produced by S. fumaroxidans would be fully consumed by M. hungatei. PMID:26147299

  10. Continuous culture of Methanococcus jannaschii, an extremely thermophilic methanogen

    SciTech Connect

    Jiahuey Tsao; Kaneshiro, S.M.; Shusan Yu; Clark, D.S. . Dept. of Chemical Engineering)

    1994-02-05

    Methanococcus jannaschii, an extremely thermophilic methanogen isolated from a deep-sea hydrothermal vent was grown at 80 C in continuous culture on a mineral salts medium gassed with H[sub 2] and CO[sub 2] at three different flow rates. The maximum specific growth rate was 0.56 h[sup [minus]1], and the maximum specific methane productivity was 0.32 (mol g[sup [minus]1] h[sup [minus]1]). Uncoupling of growth and methane production was evidenced by an increase in the non-growth-associated rate of methane formation, [Beta], with increasing gaseous input. The specific hydrogenase activity exhibited growth-associated behavior at low growth rates, but showed no dependence on growth at higher growth rates. The growth dependence of hydrogenase activity is consistent with the pressure dependence of hydrogenase activity measured in previous experiments. In contrast, the specific protease activity was independent of the growth rate over the entire range of dilution rates studied.

  11. Interaction of acetogens and methanogens in anaerobic freshwater sediments.

    PubMed

    Jones, J G; Simon, B M

    1985-04-01

    Anaerobic decomposition processes in the profundal sediments of Blelham Tarn (English Lake District) are often limited during late summer by the input of organic carbon. The concentration of acetate in the interstitial water fell from about 100 microM (immediately after sedimentation of the spring diatom bloom) to a relatively constant value of about 20 microM in late summer, during which acetate utilization appeared to be balanced by production. Addition of chloroform and molybdate caused an accumulation of cold acetate in large sediment cores and of [14C]acetate in small cores to which [14C]bicarbonate had been added. In both cases chloroform caused the greater accumulation, implying that acetoclastic methanogens were the more active consumers. The conversion of 14CO2 to [14C]acetate was inversely related, with depth, to its conversion to 14CH4. Methanogenesis from CO2 decreased during late summer, whereas acetogenesis and acetoclastic methanogenesis increased over the same time period. The production of acetate from CO2 was generally equivalent to less than 10% of the acetate carbon utilized but could be as high as 25% of that value. Hydrogen consumption by acetogens could be as high as 50% of that utilized in methanogenesis. The role of acetogenic bacteria in anaerobic processes may therefore be of greater significance in lakes such as Blelham Tarn than in more eutrophic systems. PMID:4004224

  12. Substrate sources regulate spatial variation of metabolically active methanogens from two contrasting freshwater wetlands.

    PubMed

    Lin, Yongxin; Liu, Deyan; Ding, Weixin; Kang, Hojeong; Freeman, Chris; Yuan, Junji; Xiang, Jian

    2015-12-01

    There is ample evidence that methane (CH4) emissions from natural wetlands exhibit large spatial variations at a field scale. However, little is known about the metabolically active methanogens mediating these differences. We explored the spatial patterns in active methanogens of summer inundated Calamagrostis angustifolia marsh with low CH4 emissions and permanently inundated Carex lasiocarpa marsh with high CH4 emissions in Sanjiang Plain, China. In C. angustifolia marsh, the addition of (13)C-acetate significantly increased the CH4 production rate, and Methanosarcinaceae methanogens were found to participate in the consumption of acetate. In C. lasiocarpa marsh, there was no apparent increase in the CH4 production rate and no methanogen species were labeled with (13)C. When (13)CO2-H2 was added, however, CH4 production was found to be due to Fen Cluster (Methanomicrobiales) in C. angustifolia marsh and Methanobacterium Cluster B (Methanobacteriaceae) together with Fen Cluster in C. lasiocarpa marsh. These results suggested that CH4 was produced primarily by hydrogenotrophic methanogens using substrates mainly derived from plant litter in C. lasiocarpa marsh and by both hydrogenotrophic and acetoclastic methanogens using substrates mainly derived from root exudate in C. angustifolia marsh. The significantly lower CH4 emissions measured in situ in C. angustifolia marsh was primarily due to a deficiency of substrates compared to C. lasiocarpa marsh. Therefore, we speculate that the substrate source regulates both the type of active methanogens and the CH4 production pathway and consequently contributes to the spatial variations in CH4 productions observed in these freshwater marshes. PMID:26286511

  13. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    PubMed Central

    Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A.; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Plugge, Caroline M.

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria. PMID:26074892

  14. The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes

    PubMed Central

    Gray, N D; Sherry, A; Grant, R J; Rowan, A K; Hubert, C R J; Callbeck, C M; Aitken, C M; Jones, D M; Adams, J J; Larter, S R; Head, I M

    2011-01-01

    Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell-C)/g(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell-C)/g(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella. PMID:21914097

  15. Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses.

    PubMed

    Koga, Y; Nishihara, M; Morii, H; Akagawa-Matsushita, M

    1993-03-01

    Complete structures of nearly 40 ether polar lipids from seven species of methanogens have been elucidated during the past 10 years. Three kinds of variations of core lipids, macrocyclic archaeol and two hydroxyarchaeols, were identified, in addition to the usual archaeol and caldarchaeol (for the nomenclature of archaeal [archaebacterial] ether lipids, see the text). Polar head groups of methanogen phospholipids include ethanolamine, serine, inositol, N-acetylglucosamine, dimethyl- and trimethylaminopentanetetrol, and glucosaminylinositol. Glucose is the sole hexose moiety of glycolipids in most methanogens, and galactose and mannose have been found in a few species. Methanogen lipids are characterized by their diversity in phosphate-containing polar head groups and core lipids, which in turn can be used for chemotaxonomy of methanogens. This was shown by preliminary simplified analyses of lipid component residues. Core lipid analysis by high-pressure liquid chromatography provides a method of determining the methanogenic biomass in natural samples. There has been significant progress in the biosynthetic studies of methanogen lipids in recent years. In vivo incorporation experiments have led to delineation of the outline of the synthetic route of the diphytanylglycerol ether core. The mechanisms of biosynthesis of tetraether lipids and various polar lipids, and cell-free systems of either lipid synthesis, however, remain to be elucidated. The significance and the origin of archaeal ether lipids is discussed in terms of the lipid composition of bacteria living in a wide variety of environments, the oxygen requirement for biosynthesis of hydrocarbon chains, and the physicochemical properties and functions of lipids as membrane constituents. PMID:8464404

  16. Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses.

    PubMed Central

    Koga, Y; Nishihara, M; Morii, H; Akagawa-Matsushita, M

    1993-01-01

    Complete structures of nearly 40 ether polar lipids from seven species of methanogens have been elucidated during the past 10 years. Three kinds of variations of core lipids, macrocyclic archaeol and two hydroxyarchaeols, were identified, in addition to the usual archaeol and caldarchaeol (for the nomenclature of archaeal [archaebacterial] ether lipids, see the text). Polar head groups of methanogen phospholipids include ethanolamine, serine, inositol, N-acetylglucosamine, dimethyl- and trimethylaminopentanetetrol, and glucosaminylinositol. Glucose is the sole hexose moiety of glycolipids in most methanogens, and galactose and mannose have been found in a few species. Methanogen lipids are characterized by their diversity in phosphate-containing polar head groups and core lipids, which in turn can be used for chemotaxonomy of methanogens. This was shown by preliminary simplified analyses of lipid component residues. Core lipid analysis by high-pressure liquid chromatography provides a method of determining the methanogenic biomass in natural samples. There has been significant progress in the biosynthetic studies of methanogen lipids in recent years. In vivo incorporation experiments have led to delineation of the outline of the synthetic route of the diphytanylglycerol ether core. The mechanisms of biosynthesis of tetraether lipids and various polar lipids, and cell-free systems of either lipid synthesis, however, remain to be elucidated. The significance and the origin of archaeal ether lipids is discussed in terms of the lipid composition of bacteria living in a wide variety of environments, the oxygen requirement for biosynthesis of hydrocarbon chains, and the physicochemical properties and functions of lipids as membrane constituents. PMID:8464404

  17. Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid

    PubMed Central

    Zhai, Zhengyuan; An, Haoran; Wang, Guohong; Luo, Yunbo; Hao, Yanling

    2015-01-01

    Lactobacillus delbrueckii subsp. bulgaricus develops acid tolerance response when subjected to acid stress conditions, such as the induction of enzymes associated with carbohydrate metabolism. In this study, pyk gene encoding pyruvate kinase was over-expressed in heterologous host Lactococcus lactis NZ9000, and SDS-PAGE analysis revealed the successful expression of this gene in NZ9000. The survival rate of Pyk-overproducing strain was 45-fold higher than the control under acid stress condition (pH 4.0). In order to determine the transcription factor (TF) which regulates the expression of pyk by bacterial one-hybrid, we constructed a TF library including 65 TFs of L. bulgaricus. Western blotting indicated that TFs in this library could be successfully expressed in host strains. Subsequently, the promoter of pfk-pyk operon in L. bulgaricus was identified by 5′-RACE PCR. The bait plasmid pH3U3-p01 carrying the deletion fragment of pfk-pyk promoter captured catabolite control protein A (CcpA) which could regulate the expression of pyk by binding to a putative catabolite-responsive element (5′-TGTAAGCCCTAACA-3′) upstream the -35 region. Real-time qPCR analysis revealed the transcription of pyk was positively regulated by CcpA. This is the first report about identifying the TF of pyk in L. bulgaricus, which will provide new insight into the regulatory network. PMID:26581248

  18. Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

    PubMed Central

    Yadav, Shailendra; Kundu, Sharbadeb; Ghosh, Sankar K.; Maitra, S. S.

    2015-01-01

    Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process. PMID:26568700

  19. Windrow composting mitigated CH4 emissions: characterization of methanogenic and methanotrophic communities in manure management.

    PubMed

    Chen, Ruirui; Wang, Yiming; Wei, Shiping; Wang, Wei; Lin, Xiangui

    2014-12-01

    With increasing livestock breeding, methane (CH4 ) emissions from manure management will increasingly contribute more to atmospheric CH4 concentration. The dynamics of methanogens and methanotrophs have not yet been studied in the manure environment. The current study combines surface CH4 emissions with methanogenic and methanotrophic community analyses from two management practices, windrow composting (WCOM) and solid storage (SSTO). Our results showed that there was an c. 50% reduction of CH4 emissions with WCOM compared with SSTO over a 50-day period. A sharp decrease in the quantities of both methanogens and methanotrophs in WCOM suggested that CH4 mitigation was mainly due to decreased CH4 production rather than increased CH4 oxidation. Pyrosequencing analysis demonstrated that aeration caused a clear shift of dominant methanogens in the manure, with specifically a significant decrease in Methanosarcina and increase in Methanobrevibacter. The composition of methanogenic community was influenced by manure management and regulated CH4 production. A sharp increase in the quantity of methanotrophs in SSTO suggested that microbial CH4 oxidation is an important sink for the CH4 produced. The increased abundance of Methylococcaceae in SSTO suggested that Type I methanotrophs have an advantage in CH4 oxidation in occupying niches under low CH4 and high O2 conditions. PMID:25135448

  20. Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea.

    PubMed

    Lazar, Cassandre Sara; John Parkes, R; Cragg, Barry A; L'Haridon, Stephane; Toffin, Laurent

    2012-07-01

    Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano (AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. (14)C-radiotracer measurements showed that methylamines/methanol, H(2)/CO(2) and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16S PCR-DGGE and mcrA gene libraries, and enrichments of methanogens showed the presence of Methanococcoides in the shallow sediment layers. Overall acetoclastic methanogenesis was higher than hydrogenotrophic methanogenesis, which is unusual for cold seep sediments. Interestingly, acetate porewater concentrations were extremely high in the AMV sediments. This might be the result of organic matter cracking in deeper hotter sediment layers. Methane was also produced from hexadecanes. For the most part, the methanogenic community diversity was in accordance with the depth distribution of the H(2)/CO(2) and acetate methanogenesis. These results demonstrate the importance of methanogenic communities in the centres of marine mud volcanoes. PMID:22458514

  1. Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil

    PubMed Central

    Kato, Souichiro; Chino, Kanako; Kamimura, Naofumi; Masai, Eiji; Yumoto, Isao; Kamagata, Yoichi

    2015-01-01

    Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions. PMID:26399549

  2. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    PubMed

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research. PMID:23877581

  3. Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments.

    PubMed

    Mathai, Prince P; Zitomer, Daniel H; Maki, James S

    2015-06-01

    In methanogenic habitats, volatile fatty acids (VFA), such as propionate and butyrate, are major intermediates in organic matter degradation. VFA are further metabolized to H(2), acetate and CO(2) by syntrophic fatty acid-degrading bacteria (SFAB) in association with methanogenic archaea. Despite their indispensable role in VFA degradation, little is known about SFAB abundance and their environmental distribution. To facilitate ecological studies, we developed four novel genus-specific quantitative PCR (qPCR) assays, with primer sets targeting known SFAB: Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas. Primer set specificity was confirmed using in silico and experimental (target controls, clone libraries and melt-curve analysis) approaches. These qPCR assays were applied to quantify SFAB in a variety of mesophilic methanogenic habitats, including a laboratory propionate enrichment culture, pilot- and full-scale anaerobic reactors, cow rumen, horse faeces, an experimental rice paddy soil, a bog stream and swamp sediments. The highest SFAB 16S rRNA gene copy numbers were found in the propionate enrichment culture and anaerobic reactors, followed by the bog stream and swamp sediment samples. In addition, it was observed that SFAB and methanogen abundance varied with reactor configuration and substrate identity. To our knowledge, this research represents the first comprehensive study to quantify SFAB in methanogenic habitats using qPCR-based methods. These molecular tools will help investigators better understand syntrophic microbial communities in engineered and natural environments. PMID:25814038

  4. Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil.

    PubMed

    Kato, Souichiro; Chino, Kanako; Kamimura, Naofumi; Masai, Eiji; Yumoto, Isao; Kamagata, Yoichi

    2015-01-01

    Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions. PMID:26399549

  5. Effect of adding carbon fiber textiles to methanogenic bioreactors used to treat an artificial garbage slurry.

    PubMed

    Sasaki, Kengo; Morita, Masahiko; Hirano, Shin-Ichi; Ohmura, Naoya; Igarashi, Yasuo

    2009-08-01

    To compare the performances and microbial populations of methanogenic reactors with and without carbon fiber textiles (CFT), we operated small-scale (200 ml) reactors using a slurry of artificial garbage. For both types of reactors, the organic loading rate (OLR) was stepwisely and rapidly increased in the same manner. Start-up period was shortened by adding CFT. Reactors with CFT showed greater efficiency for removal of suspended solid and volatile suspended solid than reactors without CFT at a long hydraulic retention time (HRT) between 8 and 13 days. The reactors with CFT maintained stable methane production at an OLR of 15.3 g dichromate chemical oxygen demand (CODcr)/l/day and DNAs from microorganisms were highly concentrated in adhering fractions on CFT. As shown by quantitative PCR analysis, the proportions of methanogenic archaea were conserved more than 25% in adhering fractions on CFT in reactors with CFT. By contrast, reactors without CFT showed accumulation of volatile fatty acid and deteriorated at an OLR of 2.4 gCODcr/l/day. Methanogenic proportions dropped to 17.1% in suspended fractions of reactors without CFT. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that all archaeal DGGE bands in both types of reactors were related to methanogens, but more bands were observed in reactors with CFT. Thus the higher performance of reactors with CFT likely reflects the greater abundance of microorganisms and methanogenic diversity. PMID:19619860

  6. Enrichment of hydrogenotrophic methanogens in coupling with methane production using an electrochemical bioreactor.

    PubMed

    Jeon, Bo Young; Kim, Sung Yong; Park, Yong Keun; Park, Doo Hyun

    2009-12-01

    Anaerobic digestion sludge was cultivated in an electrochemical bioreactor (ECB) to enrich the hydrogenotrophic methanogens. A modified graphite felt cathode with neutral red (NR-cathode) was charged with electrochemical reducing power generated from a solar cell. The methane and carbon dioxide collected in a Teflon bag from the ECB were more than 80 ml/l of reactant/day and less than 20 ml/l of reactant/day, respectively, whereas the methane and carbon dioxide collected from a conventional bioreactor (CB) was around 40 ml/l of reactant/day, respectively. Moreover, the maximal volume ratios of methane to carbon dioxide (M/C ratio) collected in the Teflon bag from the ECB and CB were 7 and 1, respectively. The most predominant methanogens isolated from the CB on the 20th, 80th, and 150th days of incubation were hydrogenotrophs. The methanogenic diversity analyzed by temperature gradient gel electrophoresis (TGGE) of the 16S rDNA variable region was higher in the ECB than in the CB. The DNA extracted from the TGGE bands was more than 95% homologous with hydrogenotrophic methanogens in the CB. In conclusion, the ECB was demonstrated as a useful system for enriching hydrogenotrophic methanogens and increasing the M/C ratio of the gas product. PMID:20075635

  7. Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery.

    PubMed

    Gray, N D; Sherry, A; Hubert, C; Dolfing, J; Head, I M

    2010-01-01

    Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems. PMID:20602990

  8. Structure and Function of Methanogens along a Short-Term Restoration Chronosequence in the Florida Everglades▿

    PubMed Central

    Smith, Jason M.; Castro, Hector; Ogram, Andrew

    2007-01-01

    The removal of plants and soil to bedrock to eradicate exotic invasive plants within the Hole-in-the-Donut (HID) region, part of the Everglades National Park (Florida), presented a unique opportunity to study the redevelopment of soil and the associated microbial communities in the context of short-term primary succession and ecosystem restoration. The goal of this study was to identify relationships between soil redevelopment and activity and composition of methanogenic assemblages in HID soils. Methane production potentials indicated a general decline in methanogenic activity with restoration age. Microcosm incubations strongly suggested hydrogenotrophic methanogenesis as the most favorable pathway for methane formation in HID soils from all sites. Culture-independent techniques targeting methyl coenzyme M reductase genes (mcrA) were used to assess the dynamics of methanogenic assemblages. Clone libraries were dominated by sequences related to hydrogenotrophic methanogens of the orders Methanobacteriales and Methanococcales and suggested a general decline in the relative abundance of Methanobacteriales mcrA with time since restoration. Terminal restriction fragment length polymorphism analysis indicated methanogenic assemblages remain relatively stable between wet and dry seasons. Interestingly, analysis of soils across the restoration chronosequence indicated a shift in Methanobacteriales populations with restoration age, suggesting genotypic shifts due to site-specific factors. PMID:17449688

  9. Transduction-Like Gene Transfer in the Methanogen Methanococcus voltae

    PubMed Central

    Bertani, Giuseppe

    1999-01-01

    Strain PS of Methanococcus voltae (a methanogenic, anaerobic archaebacterium) was shown to generate spontaneously 4.4-kbp chromosomal DNA fragments that are fully protected from DNase and that, upon contact with a cell, transform it genetically. This activity, here called VTA (voltae transfer agent), affects all markers tested: three different auxotrophies (histidine, purine, and cobalamin) and resistance to BES (2-bromoethanesulfonate, an inhibitor of methanogenesis). VTA was most effectively prepared by culture filtration. This process disrupted a fraction of the M. voltae cells (which have only an S-layer covering their cytoplasmic membrane). VTA was rapidly inactivated upon storage. VTA particles were present in cultures at concentrations of approximately two per cell. Gene transfer activity varied from a minimum of 2 × 10−5 (BES resistance) to a maximum of 10−3 (histidine independence) per donor cell. Very little VTA was found free in culture supernatants. The phenomenon is functionally similar to generalized transduction, but there is no evidence, for the time being, of intrinsically viral (i.e., containing a complete viral genome) particles. Consideration of VTA DNA size makes the existence of such viral particles unlikely. If they exist, they must be relatively few in number;perhaps they differ from VTA particles in size and other properties and thus escaped detection. Digestion of VTA DNA with the AluI restriction enzyme suggests that it is a random sample of the bacterial DNA, except for a 0.9-kbp sequence which is amplified relative to the rest of the bacterial chromosome. A VTA-sized DNA fraction was demonstrated in a few other isolates of M. voltae. PMID:10321998

  10. Transformation of toluene and benzene by mixed methanogenic cultures.

    PubMed Central

    Grbić-Galić, D; Vogel, T M

    1987-01-01

    The aromatic hydrocarbons toluene and benzene were anaerobically transformed by mixed methanogenic cultures derived from ferulic acid-degrading sewage sludge enrichments. In most experiments, toluene or benzene was the only semicontinuously supplied carbon and energy source in the defined mineral medium. No exogenous electron acceptors other than CO2 were present. The cultures were fed 1.5 to 30 mM unlabeled or 14C-labeled aromatic substrates (ring-labeled toluene and benzene or methyl-labeled toluene). Gas production from unlabeled substrates and 14C activity distribution in products from the labeled substrates were monitored over a period of 60 days. At least 50% of the substrates were converted to CO2 and methane (greater than 60%). A high percentage of 14CO2 was recovered from the methyl group-labeled toluene, suggesting nearly complete conversion of the methyl group to CO2 and not to methane. However, a low percentage of 14CO2 was produced from ring-labeled toluene or from benzene, indicating incomplete conversion of the ring carbon to CO2. Anaerobic transformation pathways for unlabeled toluene and benzene were studied with the help of gas chromatography-mass spectrometry. The intermediates detected are consistent with both toluene and benzene degradation via initial oxidation by ring hydroxylation or methyl oxidation (toluene), which would result in the production of phenol, cresols, or aromatic alcohol. Additional reactions, such as demethylation and ring reduction, are also possible. Tentative transformation sequences based upon the intermediates detected are discussed. PMID:3105454