Rice Cluster I, an Important Group of Archaea Producing Methane in Rice Fields

NASA Astrophysics Data System (ADS)

Conrad, R.

2006-12-01

Rice fields are an important source for the greenhouse gas methane. Methane is a major degradation product of organic matter in the anoxic soil, is partially oxidized in the rhizosphere and is emitted into the atmosphere through the aerenchyma system of the plants. Anaerobic degradation of organic matter by fermenting bacteria eventually results in the production of acetate and hydrogen, the two major substrates for microbial methanogenesis. The community of methanogenic archaea consists of several major orders or families including hydrogen-utilizing Rice Cluster-I (RC-I). Environmental conditions affect the methanogenic degradation process and the community structure of the methanogenic archaea in soil and rhizosphere. For example, populations of acetoclastic Methanosaetaceae and Methanosarcinaceae are enhanced by low and high acetate concentrations, respectively. Stable isotope probing of 16S rRNA showed that RC-I methanogens are mainly active on rice roots and at low H2 concentrations. Growth and population size is largely consistent with energetic conditions. RC-I methanogens on roots seem to be responsible for methane production from plant photosynthates that account for a major part of the emitted methane. Populations of RC-I methanogens in rice field soil are also enhanced at elevated temperatures (40-50°C). Moderately thermophilic members of RC-I methanogens or other methanogenic families were found to be ubiquitously present in soils from rice fields and river marshes. The genome of a RC-I methanogen was completely sequenced out of an enrichment culture using a metagenome approach. Genes found are consistent with life in the rhizosphere and in temporarily drained, oxic soil. We found that the methanogenic community structure on the rice roots is mainly determined by the respective community structure of the soil, but is in addition affected by the rice cultivar. Rice microcosms in which soil and rice roots are mainly colonized by RC-I methanogens produce and emit more methane than when inhabited by Methanomicrobiales, indicating that the methanogenic archaeal community is an important factor for methane emission from rice fields.

Changes in methanogenic substrate utilization and communities with depth in a salt-marsh, creek sediment in southern England

NASA Astrophysics Data System (ADS)

John Parkes, R.; Brock, Fiona; Banning, Natasha; Hornibrook, Edward R. C.; Roussel, Erwan G.; Weightman, Andrew J.; Fry, John C.

2012-01-01

A combined biogeochemical and molecular genetic study of creek sediments (down to 65 cm depth) from Arne Peninsula salt-marsh (Dorset, UK) determined the substrates used for methanogenesis and the distribution of the common methanogens, Methanosarcinales and Methanomicrobiales capable of metabolising these substrates. Methane concentrations increased by 11 cm, despite pore water sulphate not being removed until 45 cm. Neither upward methane diffusion or anaerobic oxidation of methane seemed to be important in this zone. In the near-surface sulphate-reduction zone (5-25 cm) turnover time to methane for the non-competitive methanogenic substrate trimethylamine was most rapid (80 days), and were much longer for acetate (7900 days), methanol (40,500 days) and bicarbonate (361,600 days). Methylamine-utilizing Methanosarcinales were the dominant (60-95%) methanogens in this zone. In deeper sediments rates of methanogenesis from competitive substrates increased substantially, with acetate methanogenic rates becoming ˜100 times greater than H 2/CO 2 methanogenesis below 50 cm. In addition, there was a dramatic change in methanogen diversity with obligate acetate-utilizing, Methanosaeta related sequences being dominant. At a similar depth methanol turnover to methane increased to its most rapid (1700 days). This activity pattern is consistent with deeper methanogen populations (55 cm) being dominated by acetate-utilizing Methanosaeta with H 2/CO 2 and alcohol-utilizing Methanomicrobiales also present. Hence, there is close relationship between the depth distribution of methanogenic substrate utilization and specific methanogens that can utilize these compounds. It is unusual for acetate to be the dominant methanogenic substrate in coastal sediments and δ13C-CH 4 values (-74 to -71‰) were atypical for acetate methanogenesis, suggesting that common stable isotope proxy models may not apply well in this type of dynamic anoxic sediment, with multiple methanogenic substrates.

Use of a Hierarchical Oligonucleotide Primer Extension Approach for Multiplexed Relative Abundance Analysis of Methanogens in Anaerobic Digestion Systems

PubMed Central

Chuang, Hui-Ping; Hsu, Mao-Hsuan; Chen, Wei-Yu

2013-01-01

In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products. PMID:24077716

Microbial diversity and dynamics during methane production from municipal solid waste

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bareither, Christopher A., E-mail: christopher.bareither@colostate.edu; Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706; Wolfe, Georgia L., E-mail: gwolfe@wisc.edu

2013-10-15

Highlights: ► Similar bacterial communities developed following different start-up operation. ► Total methanogens in leachate during the decelerated methane phase reflected overall methane yield. ► Created correlations between methanogens, methane yield, and available substrate. ► Predominant bacteria identified with syntrophic polysaccharide degraders. ► Hydrogenotrophic methanogens were dominant in the methane generation process. - Abstract: The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing ofmore » 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and hemicellulose contents supported growth of larger methanogen populations that resulted in higher methane yield.« less

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Iain; Ulrich, Luke; Lupa, Boguslaw

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. Inmore » 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).« less

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

PubMed Central

Sorokin, Dimitry Y.; Makarova, Kira S.; Abbas, Ben; Ferrer, Manuel; Golyshin, Peter N.; Galinski, Erwin A.; Ciordia, Sergio; Mena, María Carmen; Merkel, Alexander Y.; Wolf, Yuri I.; van Loosdrecht, Mark C.M.; Koonin, Eugene V.

2017-01-01

Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes, and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage “Methanonatronarchaeia” that is most closely related to the class Halobacteria. Similar to the Halobacteria, “Methanonatronarchaeia” are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that “Methanonatronarchaeia” employ the “salt-in” osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that utilize C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterosulfide reductase and cytochromes. These features differentiates “Methanonatronarchaeia” from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway. PMID:28555626

Shifts in methanogen community structure and function across a coastal marsh transect: effects of exotic Spartina alterniflora invasion

PubMed Central

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

2016-01-01

Invasion of Spartina alterniflora in coastal areas of China increased methane (CH4) emissions. To elucidate the underlying mechanisms, we measured CH4 production potential, methanogen community structure and biogeochemical factors along a coastal wetland transect comprised of five habitat regions: open water, bare tidal flat, invasive S. alterniflora marsh and native Suaeda salsa and Phragmites australis marshes. CH4 production potential in S. alterniflora marsh was 10 times higher than that in other regions, and it was significantly correlated with soil organic carbon, dissolved organic carbon and trimethylamine concentrations, but was not correlated with acetate or formate concentrations. Although the diversity of methanogens was lowest in S. alterniflora marsh, invasion increased methanogen abundance by 3.48-fold, compared with native S. salsa and P. australis marshes due to increase of facultative Methanosarcinaceae rather than acetotrophic and hydrogenotrophic methanogens. Ordination analyses suggested that trimethylamine was the primary factor regulating shift in methanogen community structure. Addition of trimethylamine increased CH4 production rates by 1255-fold but only by 5.61- and 11.4-fold for acetate and H2/CO2, respectively. S. alterniflora invasion elevated concentration of non-competitive trimethylamine, and shifted methanogen community from acetotrophic to facultative methanogens, which together facilitated increased CH4 production potential. PMID:26728134

[Effects of selective methanogenic inhibitors on methanogenesis and methanogenic communities in acetate degrading cultures].

PubMed

Ma, Tingting; Cheng, Lei; Liu, Laiyan; Dai, Lirong; Zhou, Zheng; Zhang, Hui

2015-05-04

We evaluated the role of syntrophic acetate oxidation coupled with hydrogenotrophic methanogens in three different methanogenic consortia. Three methanogenic hexadecane degrading consortia named Y15, M82 and SK were taken from the same oily sludge of Shengli oil-field and enriched. They were incubated at 15, 35 and 55 °C, respectively. The consortia amended with acetate and inhibitors of NH4Cl or CH3F were further transferred and incubated at corresponding temperatures. The cultures atlate logarithmic phase were collected for terminal restriction fragment length polymorphism (T-RFLP) combined with cloning and phylogenetic analysis of 16S rRNA gene fragments. Gas chromatograph analysis showed that all of the consortia could grow and produce methane, but the lag phase was delayed and the growth rate was retarded in the cultures amended with inhibitor. Combination analysis of T-RFLP and clone library revealed the predominance of obligate aceticlastic Methanosaeta in the acetate cultures of Y15, M82 and SK. Under the mesophilic and thermophilic conditions, after add inginhibitor the relative abundance of aceticlastic methanogen decreased but hydrogenotrophic methanogen increased. Syntrophic acetate oxidation during methanogenic degradation of petroleum hydrocarbons occurs under mesophilic and thermophilic conditions, although the situation at low temperature seems uncertain.

Evaluation of methanogenic treatment of TMAH (tetra-methyl ammonium hydroxide) in a full-scale TFT-LCD wastewater treatment process.

PubMed

Hu, T H; Whang, L M; Lei, C N; Chen, C F; Chiang, T Y; Lin, L B; Chen, H W; Liu, P W G; Cheng, S S

2010-01-01

This study evaluated TMAH biodegradation under methanogenic conditions. Under methanogenic conditions, a sludge from a full-scale UASB treating TFT-LCD wastewater was able to degrade 2,000 mg/L of TMAH within 10 h and attained a specific degradation rate of 19.2 mgTMAH/gVSS-h. Furthermore, several chemicals including some surfactants, DMSO, and sulfate were examined for their potential inhibitory effects on TMAH biodegradation under methanogenic conditions. The results indicated that surfactant S1 (up to 2%) and DMSO (up to 1,000 mg/L) presented negligible inhibitory effects on TMAH degradation, while surfactant S2 (0.2-1%) might inhibit methanogenic reaction without any TMAH degradation for 3-5 h. At sulfate concentrations higher than 300 mg/L, a complete inhibition of methanogenic reaction and TMAH biodegradation was observed. Results from cloning and sequencing of archaeal 16S rRNA gene fragments showed that Methanosarcina barkeri and Methanosarcina mazei were the dominant methanogens in the UASB treating TMAH-containing TFT-LCD wastewater.

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

Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals.

PubMed

Morvan, B; Bonnemoy, F; Fonty, G; Gouet, P

1996-03-01

Total number of bacteria, cellulolytic bacteria, and H2-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogenes were not detected in some samples of each animal. Archaea methanogens were the largest H2-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 x 10(4) and 4 x 10(4) cells ml-1 respectively).

Carbon nanotubes accelerate methane production in pure cultures of methanogens and in a syntrophic coculture.

PubMed

Salvador, Andreia F; Martins, Gilberto; Melle-Franco, Manuel; Serpa, Ricardo; Stams, Alfons J M; Cavaleiro, Ana J; Pereira, M Alcina; Alves, M Madalena

2017-07-01

Carbon materials have been reported to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens improving methane production in anaerobic processes. In this work, the effect of increasing concentrations of carbon nanotubes (CNT) on the activity of pure cultures of methanogens and on typical fatty acid-degrading syntrophic methanogenic coculture was evaluated. CNT affected methane production by methanogenic cultures, although acceleration was higher for hydrogenotrophic methanogens than for acetoclastic methanogens or syntrophic coculture. Interestingly, the initial methane production rate (IMPR) by Methanobacterium formicicum cultures increased 17 times with 5 g·L -1 CNT. Butyrate conversion to methane by Syntrophomonas wolfei and Methanospirillum hungatei was enhanced (∼1.5 times) in the presence of CNT (5 g·L -1 ), but indications of DIET were not obtained. Increasing CNT concentrations resulted in more negative redox potentials in the anaerobic microcosms. Remarkably, without a reducing agent but in the presence of CNT, the IMPR was higher than in incubations with reducing agent. No growth was observed without reducing agent and without CNT. This finding is important to re-frame discussions and re-interpret data on the role of conductive materials as mediators of DIET in anaerobic communities. It also opens new challenges to improve methane production in engineered methanogenic processes. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.

PubMed

Laskar, Folguni; Das Purkayastha, Sumi; Sen, Aniruddha; Bhattacharya, Mrinal K; Misra, Biswapriya B

2018-02-01

About half of the global methane (CH 4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH 4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions.

PubMed

Weimar, M R; Cheung, J; Dey, D; McSweeney, C; Morrison, M; Kobayashi, Y; Whitman, W B; Carbone, V; Schofield, L R; Ronimus, R S; Cook, G M

2017-08-01

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H 2 and CO 2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions. IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions. Copyright © 2017 American Society for Microbiology.

Development of a vaccine to mitigate greenhouse gas emissions in agriculture: vaccination of sheep with methanogen fractions induces antibodies that block methane production in vitro.

PubMed

Wedlock, D N; Pedersen, G; Denis, M; Dey, D; Janssen, P H; Buddle, B M

2010-02-01

To develop an understanding of the immune responses of ruminants to methanogens, and to provide proof of a concept that harnessing the immune system of ruminants is a potentially viable approach to mitigate greenhouse gas emissions from agriculture. Four subcellular fractions, namely cytoplasmic, two cell-wall preparations, and cell wall-derived proteins were prepared from Methanobrevibacter ruminantium M1. Twenty sheep (10 months of age) were vaccinated with these fractions or with whole cells (n=4 per group). Sheep were re-vaccinated once after 3 weeks, and antibody responses to M. ruminantium M1 antigens in sera and saliva measured using ELISA at 2 weeks after the second vaccination. Antigens recognised by the antisera were visualised using Western blotting. The antisera were tested in vitro for their impact on M. ruminantium M1, measuring the effect on cell growth, methane production, and ability to induce agglutination. Basal levels (pre-vaccination) of antibodies against M. ruminantium M1 antigens were low. Vaccination with the antigenic fractions induced strong antibody responses in serum. Both IgG and IgA responses to methanogen antigens were detected in saliva following vaccination. Western blot analysis of the antisera indicated reactivity of antibodies, and a wide range of proteins was present in the different methanogen fractions. Antisera against the various fractions agglutinated methanogens in an in-vitro assay. In addition, these antisera decreased the growth of a pure culture of a methanogen and production of methane in vitro. Antigens from methanogens are immunogenic in ruminants, and antisera from sheep vaccinated with fractions of methanogens have a significant impact on these organisms, inducing cell agglutination, and decreasing growth of methanogens and production of methane. Only antisera to selected methanogen fractions were able to achieve these effects. The results demonstrate the feasibility of a vaccination strategy to mitigate emission of methane.

Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)▿

PubMed Central

Evans, Paul N.; Hinds, Lyn A.; Sly, Lindsay I.; McSweeney, Christopher S.; Morrison, Mark; Wright, André-Denis G.

2009-01-01

The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight. PMID:19218421

Methanogens and Martian natural resources: Investigations regarding the possibility of biogenic methane on Mars

NASA Astrophysics Data System (ADS)

Chastain, Brendon Kelly

Archaeal methanogens were suggested as terrestrial models of possible subsurface martian microbial life prior to the actual detection of methane in Mars' atmosphere. This idea gained even more interest after the methane on Mars was observed. However, the amount of methane detected was very small, and release of methane was localized and episodic. This led some scientists to doubt that an active or ancient biosphere could be the source of the methane. Moreover, even extremophilic methanogens have not been shown to metabolize in conditions exactly analogous to those known to be available on Mars. The following chapters present a realistic and viable mechanism that allows a large or ancient biosphere to be the original source of the observed methane, and they detail experimental work that was done in order to systematically investigate nutritional and conditional variables related to those that might be available in the martian subsurface. The results of the experimental work indicate that some components of Mars' regolith can support methanogenic metabolism without being detrimental to the organisms, and that certain known components of Mars' regolith can promote periods of methanogenic dormancy without being lethal to the methanogens. The results of the experimental studies also show that material known to exist at and near Mars' surface has the potential to supply electrons for biological methanogenesis and that methanogenic metabolism can occur even when artificial media, buffers, and reductants are omitted in order to create more Mars-relevant conditions. These findings may have implications regarding the viability of methanogenic organisms as a source of the observed methane and should assist future efforts to study methanogenic metabolism in conditions exactly analogous to those available in niches on Mars.

mcrA-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities▿

PubMed Central

Steinberg, Lisa M.; Regan, John M.

2009-01-01

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members. PMID:19447957

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

Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge.

PubMed

Steinberg, Lisa M; Regan, John M

2008-11-01

Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.

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. Copyright 2010 Elsevier Inc. All rights reserved.

Conductive properties of methanogenic biofilms.

PubMed

Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

2018-02-01

Extracellular electron transfer between syntrophic partners needs to be efficiently maintained in methanogenic environments. Direct extracellular electron transfer via electrical current is an alternative to indirect hydrogen transfer but requires construction of conductive extracellular structures. Conductive mechanisms and relationship between conductivity and the community composition in mixed-species methanogenic biofilms are not well understood. The present study investigated conductive behaviors of methanogenic biofilms and examined the correlation between biofilm conductivity and community composition between different anaerobic biofilms enriched from the same inoculum. Highest conductivity observed in methanogenic biofilms was 71.8±4.0μS/cm. Peak-manner response of conductivity upon changes over a range of electrochemical potentials suggests that electron transfer in methanogenic biofilms occurs through redox driven super-exchange. The strong correlation observed between biofilm conductivity and Geobacter spp. in the metabolically diverse anaerobic communities suggests that the efficiency of DEET may provide pressure for microbial communities to select for species that can produce electrical conduits. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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

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.

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

PubMed

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

2015-06-02

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.

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

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments.

PubMed

Ozbayram, Emine Gozde; Kleinsteuber, Sabine; Nikolausz, Marcell; Ince, Bahar; Ince, Orhan

2018-01-01

The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.

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. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Characterization of acid-tolerant H/CO-utilizing methanogenic enrichment cultures from an acidic peat bog in New York State.

PubMed

Bräuer, Suzanna L; Yashiro, Erika; Ueno, Norikiyo G; Yavitt, Joseph B; Zinder, Stephen H

2006-08-01

Two methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one methanogen and two bacterial sequences. The methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family methanogens.

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen.

PubMed

McGovern, Emily; McCabe, Matthew S; Cormican, Paul; Popova, Milka; Keogh, Kate; Kelly, Alan K; Kenny, David A; Waters, Sinead M

2017-10-12

Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal's compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH 4 mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing.

PubMed

Han, Cheng; Liu, Biao; Zhong, Wenhui

2018-05-30

This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities. The non-transgenic parental line was used as the control (Ck rice). DNA-based stable isotope probing (DNA-SIP) technology traced the rhizospheric active methanogens at the tillering stage. The results revealed significantly lower CH 4 emission flux from Bt soil than that from Ck soil during the whole growth period. The active methanogenic community composition remained stable. The RC-I lineage (77.9-79.8%) and Methanosaetaceae (13.9-15.1%) were the predominant active methanogens in Bt and Ck rice rhizospheres. However, the abundance of functionally active methanogens in the Bt rice rhizosphere was significantly reduced. Lower levels of root exudates (that included carbohydrate and organic acids) from Bt rice were also detected at the tillering stage. This study found that the genetic modification of rice reduced the potential methanogenic substrates came from plant-derived root exudates, which represented an important factor in reducing CH 4 generation and active methanogenic archaeal abundance in Bt rhizosphere soil. The effect of genetically modified (GM) insect-resistant crops on soil microorganisms has become an issue of public concern, especially the indirect effect of plant metabolisms caused by the insertion of foreign genes. Methanogenesis, which is regarded as a critical ecological process in paddy soil, is influenced by plant root exudates; these are mainly derived from photosynthesis. The variations in root exudates across the Bt and Ck rice suggested the indirect influence of foreign gene insertion. DNA-SIP successfully traced the active methanogenic archaeal populations assimilating 13 C-labeled photosynthetic carbon and found a strong influence of planting Bt rice on active methanogens. As a consequence, we proposed that analysis of functionally active microorganisms is more suitable for monitoring and predicting the environmental influence of GM plants. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Long-term effects of operating temperature and sulphate addition on the methanogenic community structure of anaerobic hybrid reactors.

PubMed

Pender, Seán; Toomey, Margaret; Carton, Micheál; Eardly, Dónal; Patching, John W; Colleran, Emer; O'Flaherty, Vincent

2004-02-01

The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sludges from two anaerobic hybrid reactors treating a molasses wastewater both mesophilically (37 degrees C) and thermophilically (55 degrees C) during a 1081 day trial were determined. The influent to one of the reactors was supplemented with sulphate, after an acclimation period of 112 days, to determine the effect of competition with sulphate-reducing bacteria on the methanogenic community structure. Sludge samples were removed from the reactors at intervals throughout the operational period and examined by amplified ribosomal DNA (rDNA) restriction analysis (ARDRA) and partial sequencing of 16S rRNA genes. In total, 18 operational taxonomic units (OTUs) were identified, 12 of which were sequenced. The methanogenic communities in both reactors changed during the operational period. The seed sludge and the reactor biomass sampled during mesophilic operation, both in the presence and absence of sulphate, was characterised by a predominance of Methanosaeta spp. Following temperature elevation, the dominant methanogenic sequences detected in the non-sulphate supplemented reactor were closely related to Methanocorpusculum parvum. By contrast, the dominant OTUs detected in the sulphate-supplemented reactor upon temperature increase were related to the hydrogen-utilising methanogen, Methanobacterium thermoautotrophicum. The observed methanogenic community structure in the reactors correlated with the operational performance of the reactors during the trial and with physiological measurements of the reactor biomass. Both reactors achieved chemical oxygen demand (COD) removal efficiencies of over 90% during mesophilic operation, with or without sulphate supplementation. During thermophilic operation, the presence of sulphate resulted in decreased reactor performance (effluent acetate concentrations of >3000 mg/l and biogas methane content of <25%). It was demonstrated that methanogenic conversion of acetate at 55 degrees C was extremely sensitive to inhibition by sulphide (50% inhibition at 8-17 mg/l unionised sulphide at pH 7.6-8.0), while the conversion of H(2)/CO(2) methanogenically was favoured. The combination of experiments carried out demonstrated the presence of specific methanogenic populations during periods of successful operational performance.

Higher-level classification of the Archaea: evolution of methanogenesis and methanogens

PubMed Central

Bapteste, Éric; Brochier, Céline; Boucher, Yan

2005-01-01

We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO2) are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO2, formate, acetate, methylated C-1 compounds), these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole) from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon. PMID:15876569

Approaching Mars-like geochemical conditions in the laboratory: omission of artificial buffers and reductants in a study of biogenic methane production on a smectite clay.

PubMed

Chastain, Brendon K; Kral, Timothy A

2010-11-01

Methanogens have not been shown to metabolize in conditions exactly analogous to those present in Mars' subsurface. In typical studies of methanogenic metabolism, nutrient-rich buffered media and reducing agents are added to the cultures in an attempt to optimize the environment for methanogen survival and growth. To study methanogens in more Mars-relevant laboratory conditions, efforts should be made to eliminate artificial media, buffers, and reducing agents from investigations of methanogenic metabolism. After preliminary work to compare methanogen viability on montmorillonite clay and JSC Mars-1 regolith simulant, a study was conducted to determine whether biological methanogenesis could occur in non-reduced, non-buffered environments containing only H(2), CO(2), montmorillonite, and the liquid fraction extracted from a montmorillonite/deionized water suspension. Biogenic methane was observed in the microenvironments despite the omission of traditional media, buffers, and reducing agents. Mean headspace methane concentration after 96 days of observation was 10.23% ± 0.64% (% vol ± SEM, n = 4). However, methane production was severely decreased with respect to reduced, buffered microenvironments (Day 28: 31.98% ± 0.19%, n = 3). Analysis of results and comparison to previous work indicate that montmorillonite clay has a strong ability to supply micronutrients necessary for methanogenic metabolism, and the liquid fraction from a montmorillonite/deionized water slurry can successfully be used as an alternative to reduced and buffered nutritive media in Mars-relevant studies of methanogenic metabolism.

The Effects of Perchlorates on the Permafrost Methanogens: Implication for Autotrophic Life on Mars.

PubMed

Shcherbakova, Viktoria; Oshurkova, Viktoria; Yoshimura, Yoshitaka

2015-09-09

The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2(T) M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth's subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars.

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

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

PubMed

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

2011-11-01

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. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor

NASA Astrophysics Data System (ADS)

Gryta, Agata; Oszust, Karolina; Brzezińska, Małgorzata; Ziemiński, Krzysztof; Bilińska-Wielgus, Nina; Frąc, Magdalena

2017-07-01

The aim of the study was to elucidate the substantial relationship between the compositions of methanogen community that assembles in the anaerobic digester mass and link it to methane production activity. The results of the metagenomic studies were used to evaluate how the methanogen structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 days). Phylogenetically coherent populations of methanogens were assessed by 16S rRNA gene next-generation sequencing and terminal restriction fragment length polymorphism fingerprinting of a specific molecular marker, the mcrA gene. The results indicated multiple phylogenetically diverse methanogen populations associated with the various steps of anaerobic digestion. The stages of the anaerobic digestion process and waste retention times determine the microbial composition. The most dominant and acclimated microbial communities in all samples belonged to the genera Methanosaeta and Methanobacterium. The methane yield was consistent with the results of the microbial community structure, which indicated that acetotrophic Methanosaeta was the most active and most important during the methanogenic stage.

Evidence of syntrophic acetate oxidation by Spirochaetes during anaerobic methane production.

PubMed

Lee, Sang-Hoon; Park, Jeong-Hoon; Kim, Sang-Hyoun; Yu, Byung Jo; Yoon, Jeong-Jun; Park, Hee-Deung

2015-08-01

To search for evidence of syntrophic acetate oxidation by cluster II Spirochaetes with hydrogenotrophic methanogens, batch reactors seeded with five different anaerobic sludge samples supplemented with acetate as the sole carbon source were operated anaerobically. The changes in abundance of the cluster II Spirochaetes, two groups of acetoclastic methanogens (Methanosaetaceae and Methanosarcinaceae), and two groups of hydrogenotrophic methanogens (Methanomicrobiales and Methanobacteriales) in the reactors were assessed using qPCR targeting the 16S rRNA genes of each group. Increase in the cluster II Spirochaetes (9.0±0.4-fold) was positively correlated with increase in hydrogenotrophic methanogens, especially Methanomicrobiales (5.6±1.0-fold), but not with acetoclastic methanogens. In addition, the activity of the cluster II Spirochaetes decreased (4.6±0.1-fold) in response to high hydrogen partial pressure, but their activity was restored after consumption of hydrogen by the hydrogenotrophic methanogens. These results strongly suggest that the cluster II Spirochaetes are involved in syntrophic acetate oxidation in anaerobic digesters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Methanosarcina as the dominant aceticlastic methanogens during mesophilic anaerobic digestion of putrescible waste.

PubMed

Vavilin, Vasily A; Qu, Xian; Mazéas, Laurent; Lemunier, Melanie; Duquennoi, Christian; He, Pinjing; Bouchez, Theodore

2008-11-01

Taking into account isotope (13)C value a mathematical model was developed to describe the dynamics of methanogenic population during mesophilic anaerobic digestion of putrescible solid waste and waste imitating Chinese municipal solid waste. Three groups of methanogens were considered in the model including unified hydrogenotrophic methanogens and two aceticlastic methanogens Methanosaeta sp. and Methanosarcina sp. It was assumed that Methanosaeta sp. and Methanosarcina sp. are inhibited by high volatile fatty acids concentration. The total organic and inorganic carbon concentrations, methane production, methane and carbon dioxide partial pressures as well as the isotope (13)C incorporation in PSW and CMSW were used for the model calibration and validation. The model showed that in spite of the high initial biomass concentration of Methanosaeta sp. Methanosarcina sp. became the dominant aceticlastic methanogens in the system. This prediction was confirmed by FISH. It is concluded that Methanosarcina sp. forming multicellular aggregates may resist to inhibition by volatile fatty acids (VFAs) because a slow diffusion rate of the acids limits the VFA concentrations inside the Methanosarcina sp. aggregates.

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste.

PubMed

Zahedi, S; Solera, R; Micolucci, F; Cavinato, C; Bolzonella, D

2016-03-01

In this paper, the microbial community in a two-phase thermophilic anaerobic co-digestion process was investigated for its role in hydrogen and methane production, treating waste activated sludge and treating the organic fraction of municipal solid waste. In the acidogenic phase, in which hydrogen is produced, Clostridium sp. clusters represented 76% of total Firmicutes. When feeding the acidogenic effluent into the methanogenic reactors, these acidic conditions negatively influenced methanogenic microorganisms: Methanosaeta sp., (Methanobacteriales, Methanomicrobiales, Methanococcales) decreased by 75%, 50%, 38% and 52%, respectively. At the same time, methanogenic digestion lowered the numbers of Clostridium sp. clusters due to both pH increasing and substrate reduction, and an increase in both Firmicutes genera (non Clostridium) and methanogenic microorganisms, especially Methanosaeta sp. (208%). This was in accordance with the observed decrease in acetic (98%) and butyric (100%) acid contents. To ensure the activity of the acetate-utilizing methanogens (AUM) and the acetogens, high ratios of H2-utilizing methanogens (HUM)/AUM (3.6) were required. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

PubMed Central

Leahy, Sinead C.; Kelly, William J.; Altermann, Eric; Ronimus, Ron S.; Yeoman, Carl J.; Pacheco, Diana M.; Li, Dong; Kong, Zhanhao; McTavish, Sharla; Sang, Carrie; Lambie, Suzanne C.; Janssen, Peter H.; Dey, Debjit; Attwood, Graeme T.

2010-01-01

Background Methane (CH4) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO2). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. Methodology/Principal Findings The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H2) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. Conclusions/Significance The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases. PMID:20126622

Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen

PubMed Central

Jennings, Matthew E.; Schaff, Cody W.; Horne, Alexandra J.; Lessner, Faith H.

2014-01-01

Haem-dependent catalase is an antioxidant enzyme that degrades H2O2, producing H2O and O2, and is common in aerobes. Catalase is present in some strictly anaerobic methane-producing archaea (methanogens), but the importance of catalase to the antioxidant system of methanogens is poorly understood. We report here that a survey of the sequenced genomes of methanogens revealed that the majority of species lack genes encoding catalase. Moreover, Methanosarcina acetivorans is a methanogen capable of synthesizing haem and encodes haem-dependent catalase in its genome; yet, Methanosarcina acetivorans cells lack detectable catalase activity. However, inducible expression of the haem-dependent catalase from Escherichia coli (EcKatG) in the chromosome of Methanosarcina acetivorans resulted in a 100-fold increase in the endogenous catalase activity compared with uninduced cells. The increased catalase activity conferred a 10-fold increase in the resistance of EcKatG-induced cells to H2O2 compared with uninduced cells. The EcKatG-induced cells were also able to grow when exposed to levels of H2O2 that inhibited or killed uninduced cells. However, despite the significant increase in catalase activity, growth studies revealed that EcKatG-induced cells did not exhibit increased tolerance to O2 compared with uninduced cells. These results support the lack of catalase in the majority of methanogens, since methanogens are more likely to encounter O2 rather than high concentrations of H2O2 in the natural environment. Catalase appears to be a minor component of the antioxidant system in methanogens, even those that are aerotolerant, including Methanosarcina acetivorans. Importantly, the experimental approach used here demonstrated the feasibility of engineering beneficial traits, such as H2O2 tolerance, in methanogens. PMID:24222618

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% indicating some success in adapting cells to concentrations higher than 1%. The results reported here indicate that the presence of perchlorate on Mars does not rule out the possible existence of methanogens.

Growth of methylaminotrophic, acetotrophic and hydrogenotrophic methanogenic bacteria on artificial supports.

PubMed

Urrutia, H; Vidal, R; Baeza, M; Reyes, J E; Aspe, E

1997-06-01

The efficiency of organic matter degradation in attached biomass reactors depends on the suitable selection of artificial support for the retention of bacterial communities. We have studied the growth on glass and clay beads of methylaminotrophic, acetotrophic and hydrogenotrophic methanogenic bacterial communities isolated from anaerobic reactors. Bacterial counts were performed by the standard MPN technique. Experiments were performed in 50 ml vials for 12 days at 35 degrees C. Increase in the counts of methylaminotrophic and hydrogenotrophic methanogens occurred on both glass and clay beads. The latter support material also stimulated the growth rate of methylaminotrophic methanogens.

Surpassing the current limitations of high purity H2 production in microbial electrolysis cell (MECs): Strategies for inhibiting growth of methanogens.

PubMed

Kadier, Abudukeremu; Kalil, Mohd Sahaid; Chandrasekhar, Kuppam; Mohanakrishna, Gunda; Saratale, Ganesh Dattatraya; Saratale, Rijuta Ganesh; Kumar, Gopalakrishnan; Pugazhendhi, Arivalagan; Sivagurunathan, Periyasamy

2018-02-01

Microbial electrolysis cells (MECs) are perceived as a potential and promising innovative biotechnological tool that can convert carbon-rich waste biomass or wastewater into hydrogen (H 2 ) or other value-added chemicals. Undesired methane (CH 4 ) producing H 2 sinks, including methanogens, is a serious challenge faced by MECs to achieve high-rate H 2 production. Methanogens can consume H 2 to produce CH 4 in MECs, which has led to a drop of H 2 production efficiency, H 2 production rate (HPR) and also a low percentage of H 2 in the produced biogas. Organized inference related to the interactions of microbes and potential processes has assisted in understanding approaches and concepts for inhibiting the growth of methanogens and profitable scale up design. Thus, here in we review the current developments and also the improvements constituted for the reduction of microbial H 2 losses to methanogens. Firstly, the greatest challenge in achieving practical applications of MECs; undesirable microorganisms (methanogens) growth and various studied techniques for eliminating and reducing methanogens activities in MECs were discussed. Additionally, this extensive review also considers prospects for stimulating future research that could help to achieve more information and would provide the focus and path towards MECs as well as their possibilities for simultaneously generating H 2 and waste remediation. Copyright © 2017 Elsevier B.V. All rights reserved.

Archaeal Diversity Associated with Deep Sea Whalefalls

NASA Astrophysics Data System (ADS)

Wilpiszeski, R.; Goffredi, S.; Turk, K.; Vrijenhoek, R.; House, C. H.; Orphan, V.

2005-12-01

Deep sea whale fall sites support a diverse population of organisms in an otherwise sparsely populated environment. While the macro- and megafauna of these ecosystems have been investigated in some detail, less is known about the nature of associated microbial populations. 16S rRNA gene surveys were used to evaluate the diversity of Archaea in the sediment below one such whale fall at 2800 m water depth and at a nearby control site. A variety of Archaea were identified, including diverse uncultured marine crenarchaeota, phylotypes related to hydrogenotrophic methanogens (Methanogenium spp.), and methylotrophic methanogens associated with the Methanococcoides. No methanogens were discovered at the control site, while hydrogenotrophic methanogens accounted for approximately 20% of the samples from surface sediments below the whale and 35% of the Archaea identified from 12.5 to 15 cm below the whale; the single methylotrophic methanogen was identified within the 12.5 to 15 cm depth sample. The presence of methanogenic phylotypes associated with the whale fall corroborates geochemical observations of elevated methane concentrations observed in the shallow sediments directly beneath the whale fall. This combined geochemical and microbiological evidence suggests that near surface organic matter remineralization is occurring via a methanogenic pathway within this deep sea whale fall habitat rather than the typical sulfidogenic dominated diagenesis commonly observed at other whale fall locations and within shallow marine sediments worldwide.

Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

PubMed

Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

2015-12-01

Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis.

PubMed

Horz, H P; Robertz, N; Vianna, M E; Henne, K; Conrads, G

2015-10-01

We compared the amounts of methanogenic archaea with ten of the most important periodontal pathogens in 125 clinical samples. Correlation analysis suggests that the support of the periodontitis-associated bacterial consortium by methanogenic archaea may be driven through direct or indirect interactions with Prevotella intermedia. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

DOE PAGES

Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.; ...

2017-08-21

The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis ofmore » the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO 2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO 2 and formate are common electron carriers in microbial communities.« less

Immobilization patterns and dynamics of acetate-utilizing methanogens immobilized in sterile granular sludge in upflow anaerobic sludge blanket reactors.

PubMed

Schmidt, J E; Ahring, B K

1999-03-01

Sterile granular sludge was inoculated with either Methanosarcina mazeii S-6, Methanosaeta concilii GP-6, or both species in acetate-fed upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After several months of reactor operation, the methanogens were immobilized, either separately or together. The fastest immobilization was observed in the reactor containing M. mazeii S-6. The highest effluent concentration of acetate was observed in the reactor with only M. mazeii S-6 immobilized, while the lowest effluent concentration of acetate was observed in the reactor where both types of methanogens were immobilized together. No changes were observed in the kinetic parameters (Ks and mumax) of immobilized M. concilii GP-6 or M. mazeii S-6 compared with suspended cultures, indicating that immobilization does not affect the growth kinetics of these methanogens. An enzyme-linked immunosorbent assay using polyclonal antibodies against either M. concilii GP-6 or M. mazeii S-6 showed significant variations in the two methanogenic populations in the different reactors. Polyclonal antibodies were further used to study the spatial distribution of the two methanogens. M. concilii GP-6 was immobilized only on existing support material without any specific pattern. M. mazeii S-6, however, showed a different immobilization pattern: large clumps were formed when the concentration of acetate was high, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps. The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor.

[Detection and diversity analysis of rumen methanogens in the co-cultures with anaerobic fungi].

PubMed

Cheng, Yan-fen; Mao, Sheng-yong; Pei, Cai-xia; Liu, Jian-xin; Zhu, Wei-yun

2006-12-01

Rumen methanogen diversity in the co-cultures with anaerobic fungi from goat rumen was analyzed. Mix-cultures of anaerobic fungi and methanogens were obtained from goat rumen using anaerobic fungal medium and the addition of penicillin and streptomycin and then subcultured 62 times by transferring cultures every 3 - 4d. Total DNA from the original rumen fluid and subcultured fungal cultures was used for PCR/DGGE and RFLP analysis. 16S rDNA of clones corresponding to representative OTUs were sequenced. Results showed that the diversity index (Shannon index) of the methanogens generated from DGGE profiles reduced from 1.32 to 0.99 from rumen fluid to fungal culture after 45 subculturing, with the lowest similarity of DGGE profiles at 34.7%. The Shannon index increased from 0.99 to 1.15 from the fungal culture after 45 subculturing to that after 62 subculturing, with the lowest similarity at 89.2% . A total of 5 OTUs were obtained from 69. clones using RFLP analysis and six clones representing the 5 OTUs respectively were sequenced. Of the 5 OTUs, three had their cloned 16S rDNA sequences most closely related to uncultured archaeal symbiont PA202 with the same similarity of 95 %, but had not closely related to any identified culturable methanogen. The rest two OTUs had their cloned 16S rDNA sequences sharing the same closest relative, uncultured rumen methanogen 956, with the same similarity of 97% .Their 16S rDNA sequences of these two OTUs also showed 97% similar to the closest identified culturable methanogen Methanobrevibacter sp. NT7. In conclusion, diverse yet unidentified rumen methanogen species exist in the co-cultures with anaerobic fungi isolated from the goat rumen.

Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil.

PubMed

Singh, Alpana; Singh, Ram S; Upadhyay, Siddh N; Joshi, Chaitanya G; Tripathi, Ajay K; Dubey, Suresh K

2012-10-01

The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stages of rice plant cultivated in compost-treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.40 × 10(6) to 1.11 × 10(7)  copies g(-1)  dws, in the year 2009 and 4.37 × 10(6) to 1.36 × 10(7)  copies g(-1)  dws in the year 2010. Apart from methanogens, a large number of bacterial (9.60 × 10(9) -1.44 × 10(10)  copies g(-1)  dws) and archaeal (7.13 × 10(7) -3.02 × 10(8)  copies g(-1)  dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > postharvest > preplantation stage. The RFLP-based 16S rRNA gene-targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH(4) at the flowering stage. The integration of methanogenic community structure and CH(4) production potential of soil resulted in a better understanding of the dynamics of CH(4) production in organically treated rice-field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH(4) production has been successfully tested. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

PubMed

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.

Immobilization Patterns and Dynamics of Acetate-Utilizing Methanogens Immobilized in Sterile Granular Sludge in Upflow Anaerobic Sludge Blanket Reactors

PubMed Central

Schmidt, Jens Ejbye; Ahring, Birgitte Kjær

1999-01-01

Sterile granular sludge was inoculated with either Methanosarcina mazeii S-6, Methanosaeta concilii GP-6, or both species in acetate-fed upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After several months of reactor operation, the methanogens were immobilized, either separately or together. The fastest immobilization was observed in the reactor containing M. mazeii S-6. The highest effluent concentration of acetate was observed in the reactor with only M. mazeii S-6 immobilized, while the lowest effluent concentration of acetate was observed in the reactor where both types of methanogens were immobilized together. No changes were observed in the kinetic parameters (Ks and μmax) of immobilized M. concilii GP-6 or M. mazeii S-6 compared with suspended cultures, indicating that immobilization does not affect the growth kinetics of these methanogens. An enzyme-linked immunosorbent assay using polyclonal antibodies against either M. concilii GP-6 or M. mazeii S-6 showed significant variations in the two methanogenic populations in the different reactors. Polyclonal antibodies were further used to study the spatial distribution of the two methanogens. M. concilii GP-6 was immobilized only on existing support material without any specific pattern. M. mazeii S-6, however, showed a different immobilization pattern: large clumps were formed when the concentration of acetate was high, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps. The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor. PMID:10049862

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

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.

The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis ofmore » the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO 2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO 2 and formate are common electron carriers in microbial communities.« less

The Effects of Perchlorates on the Permafrost Methanogens: Implication for Autotrophic Life on Mars

PubMed Central

Shcherbakova, Viktoria; Oshurkova, Viktoria; Yoshimura, Yoshitaka

2015-01-01

The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2T M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth’s subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars. PMID:27682103

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hackstein, J.H.P.; Stumm, C.K.

The authors have screened more than 110 representatives of the different taxa of terrestrial arthropods for methane production in order to obtain additional information about the origins of biogenic methane. Methanogenic bacteria occur in the hindguts of nearly all tropical representatives of millipedes (Diplopoda), cockroaches (Blattaria), termites (Isoptera), and scarab beetles (Scarabaeidae), while such methanogens are absent from 66 other arthropod species investigated. Three types of symbiosis were found: in the first type, the arthropod's hindgut is colonized by free methanogenic bacteria; in the second type, methanogens are closely associated with chitinous structures formed by the host's hindgut; the thirdmore » type is mediated by intestinal anaerobic protists with intracellular methanogens. Such symbiotic associations are likely to be a characteristic property of the particular taxon. Since these taxa represent many families with thousands of species, the world populations of methane-producing arthropods constitute an enormous biomass. The authors show that arthropod symbionts can contribute substantially to atmospheric methane.« less

Microbial ecology of a crude oil contaminated aquifer

USGS Publications Warehouse

Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

2002-01-01

Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

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.

A hydrogen-based subsurface microbial community dominated by methanogens

USGS Publications Warehouse

Chapelle, F.H.; O'Neil, Kyle; 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.

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

DOE PAGES

Yamamoto, Kyosuke; Tamaki, Hideyuki; Cadillo-Quiroz, Hinsby; ...

2014-09-04

In this study, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1 T, 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.

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.

Molecular Characterization of Methanogenic Communities in Core Sediments of the Dajiuhu Peatland, Central China

NASA Astrophysics Data System (ADS)

Wang, R.; Wang, H.

2017-12-01

Methane (CH4) is an important greenhouse gas with a global warming potential 22 times greater than carbon dioxide. Large amounts of CH4 can be produced and released by methanogenesis in peatland ecosystems, which make peatland ecosystems play an important role in mediating global climate change. Here we report the abundance and distribution of methanogenic communities and their correlation with physicochemical parameters along two sediment cores in the Dajiuhu Peatland via quantitative PCR, clone library construction of functional genes and statistical analysis. Uncultured Group and Fen Cluster were found to be the dominant methanogens at the upper part of the cores, and Rice and Related Rice Cluster became dominant in the bottom of the cores. Quantitative PCR showed that abundances of methanogenic communities ranged from 104 to 106 copies/ng DNA throughout the cores. Canonical Correlation Analysis (CCA) indicated that dissolved oxygen (DO) (P=0.046, F=1.4) was the main factor significantly controlling methanogenic communities. Our results enhance the understanding of the compositions and variations of methanogenic communities vertically and greatly help us to further investigate process of microbial methanogenesis in Dajiuhu Peatland.

Temperature limitation of methanogenesis in aquatic sediments.

PubMed Central

Zeikus, J G; Winfrey, M R

1976-01-01

Microbial methanogenesis was examined in sediments collected from Lake Mendota, Wisconsin, at water depths of 5, 10, and 18 m. The rate of sediment methanogenesis was shown to vary with respect to sediment site and depth, sampling date, in situ temperature, and number of methanogens. Increased numbers of methanogenic bacteria and rates of methanogenesis correlated with increased sediment temperature during seasonal change. The greatest methanogenic activity was observed for 18-m sediments throughout the sampling year. As compared with shallower sediments, 18-m sediment was removed from oxygenation effects and contained higher amounts of ammonia, carbonate, and methanogenic bacteria, and the population density of methanogens fluctuated less during seasonal change. Rates of methanogenesis in 18-m sediment cores decreased with increasing sediment depth. The optimum temperature, 35 to 42 C, for sediment methanogenesis was considerably higher than the maximum observed in situ temperature of 23 C. The conversion of H2 and [14C]carbonate to [14C]methane displayed the same temperature optimum when these substrates were added to sediments. The predominant methanogenic population had simple nutritional requirements and were metabolically active at 4 to 45 C. Hydrogen oxidizers were the major nutritional type of sediment methanogens; formate and methanol fermentors were present, but acetate fermentors were not observed. Methanobacterium species were most abundant in sediments although Methanosarcina, Methanococcus, and Methanospirillum species were observed in enrichment cultures. A chemolithotropic species of Methanosarcina and Methanobacterium was isolated in pure culture that displayed temperature optima above 30 C and had simple nutritional requirements. PMID:821396

Microbial Ecology of Thermophilic Anaerobic Digestion. Final Report

DOE R&D Accomplishments Database

Zinder, Stephen H.

2000-04-15

This grant supported research on methanogenic archaea. The two major areas that were supported were conversion of acetic acid to methane and nitrogen fixation by Methanosarcina. Among the achievements of this research were the isolation of novel methanogenic cultures, elucidation of the pathways from acetate to methane, description of a specific DNA-binding complex in nitrogen fixing methanogens, and demonstration of an alternative nitrogenase in Methanosarcina.

The ribosomal gene spacer region in archaebacteria

NASA Technical Reports Server (NTRS)

Achenbach-Richter, L.; Woese, C. R.

1988-01-01

Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass.

PubMed

Hardegen, Justus; Latorre-Pérez, Adriel; Vilanova, Cristina; Günther, Thomas; Porcar, Manuel; Luschnig, Olaf; Simeonov, Claudia; Abendroth, Christian

2018-06-06

In this work, liquid and solid fractions of grass biomass were used as co-substrates for anaerobic co-digestion of sewage sludge. The input of grass biomass was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based cell counting and full-length 16S rRNA gene high-throughput sequencing, proving for the first time the suitability of nanopore-based portable sequencers as a monitoring tool for anaerobic digestion systems. In both cases co-fermentation resulted in an increased number of bacteria and methanogenic archaea. Interestingly, the microbial communities were highly different between solid and liquid-fed batches. Liquid-fed batches developed a more stable microbiome, enriched in Methanosarcina spp., and resulted in higher methanogenic yield. In contrast, solid-fed batches were highly unstable at higher substrate concentrations, and kept Methanosaeta spp. - typically associated to sewage sludge - as the majoritary methanogenic archaea. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

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

2015-09-24

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.

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

Zero-valent iron enhanced methanogenic activity in anaerobic digestion of waste activated sludge after heat and alkali pretreatment.

PubMed

Zhang, Yaobin; Feng, Yinghong; Quan, Xie

2015-04-01

Heat or alkali pretreatment is the effective method to improve hydrolysis of waste sludge and then enhance anaerobic sludge digestion. However the pretreatment may inactivate the methanogens in the sludge. In the present work, zero-valent iron (ZVI) was used to enhance the methanogenic activity in anaerobic sludge digester under two methanogens-suppressing conditions, i.e. heat-pretreatment and alkali condition respectively. With the addition of ZVI, the lag time of methane production was shortened, and the methane yield increased by 91.5% compared to the control group. The consumption of VFA was accelerated by ZVI, especially for acetate, indicating that the acetoclastic methanogenesis was enhanced. In the alkali-condition experiment, the hydrogen produced decreased from 27.6 to 18.8 mL when increasing the ZVI dosage from 0 to 10 g/L. Correspondingly, the methane yield increased from 1.9 to 32.2 mL, which meant that the H2-utilizing methanogenes was enriched. These results suggested that the addition of ZVI into anaerobic digestion of sludge after pretreated by the heat or alkali process could efficiently recover the methanogenic activity and increase the methane production and sludge reduction. Copyright © 2015 Elsevier Ltd. All rights reserved.

Community structure of rare methanogenic archaea: insight from a single functional group

PubMed Central

Winkel, Matthias; Wagner, Dirk

2017-01-01

Abstract The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups. PMID:29029047

Methanogenesis at low temperatures by microflora of tundra wetland soil.

PubMed

Kotsyurbenko, O R; Nozhevnikova, A N; Soloviova, T I; Zavarzin, G A

1996-01-01

Active methanogenesis from organic matter contained in soil samples from tundra wetland occurred even at 6 degrees C. Methane was the only end product in balanced microbial community with H2/CO2 as a substrate, besides acetate was produced as an intermediate at temperatures below 10 degrees C. The activity of different microbial groups of methanogenic community in the temperature range of 6-28 degrees C was investigated using 5% of tundra soil as inoculum. Anaerobic microflora of tundra wetland fermented different organic compounds with formation of hydrogen, volatile fatty acids (VFA) and alcohols. Methane was produced at the second step. Homoacetogenic and methanogenic bacteria competed for such substrates as hydrogen, formate, carbon monoxide and methanol. Acetogens out competed methanogens in an excess of substrate and low density of microbial population. Kinetic analysis of the results confirmed the prevalence of hydrogen acetogenesis on methanogenesis. Pure culture of acetogenic bacteria was isolated at 6 degrees C. Dilution of tundra soil and supply with the excess of substrate disbalanced the methanoigenic microbial community. It resulted in accumulation of acetate and other VFA. In balanced microbial community obviously autotrophic methanogens keep hydrogen concentration below a threshold for syntrophic degradation of VFA. Accumulation of acetate- and H2/CO2-utilising methanogens should be very important in methanogenic microbial community operating at low temperatures.

Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers.

PubMed

Katayama, Taiki; Yoshioka, Hideyoshi; Muramoto, Yoshiyuki; Usami, Jun; Fujiwara, Kazuhiro; Yoshida, Satoshi; Kamagata, Yoichi; Sakata, Susumu

2015-02-01

The Minami-Kanto gas field, where gases are dissolved in formation water, is a potential analogue for a marine gas hydrate area because both areas are characterized by the accumulation of microbial methane in marine turbidite sand layers interbedded with mud layers. This study examined the physicochemical impacts associated with natural gas production and well drilling on the methanogenic activity and composition in this gas field. Twenty-four gas-associated formation water samples were collected from confined sand aquifers through production wells. The stable isotopic compositions of methane in the gases indicated their origin to be biogenic via the carbonate reduction pathway. Consistent with this classification, methanogenic activity measurements using radiotracers, culturing experiments and molecular analysis of formation water samples indicated the predominance of hydrogenotrophic methanogenesis. The cultivation of water samples amended only with methanogenic substrates resulted in significant increases in microbial cells along with high-yield methane production, indicating the restricted availability of substrates in the aquifers. Hydrogenotrophic methanogenic activity increased with increasing natural gas production from the corresponding wells, suggesting that the flux of substrates from organic-rich mudstones to adjacent sand aquifers is enhanced by the decrease in fluid pressure in sand layers associated with natural gas/water production. The transient predominance of methylotrophic methanogens, observed for a few years after well drilling, also suggested the stimulation of the methanogens by the exposure of unutilized organic matter through well drilling. These results provide an insight into the physicochemical impacts on the methanogenic activity in biogenic gas deposits including marine gas hydrates.

Microbial community structures in an integrated two-phase anaerobic bioreactor fed by fruit vegetable wastes and wheat straw.

PubMed

Wang, Chong; Zuo, Jiane; Chen, Xiaojie; Xing, Wei; Xing, Linan; Li, Peng; Lu, Xiangyang; Li, Chao

2014-12-01

The microbial community structures in an integrated two-phase anaerobic reactor (ITPAR) were investigated by 16S rDNA clone library technology. The 75L reactor was designed with a 25L rotating acidogenic unit at the top and a 50L conventional upflow methanogenic unit at the bottom, with a recirculation connected to the two units. The reactor had been operated for 21 stages to co-digest fruit/vegetable wastes and wheat straw, which showed a very good biogas production and decomposition of cellulosic materials. The results showed that many kinds of cellulose and glycan decomposition bacteria related with Bacteroidales, Clostridiales and Syntrophobacterales were dominated in the reactor, with more bacteria community diversities in the acidogenic unit. The methanogens were mostly related with Methanosaeta, Methanosarcina, Methanoculleus, Methanospirillum and Methanobacterium; the predominating genus Methanosaeta, accounting for 40.5%, 54.2%, 73.6% and 78.7% in four samples from top to bottom, indicated a major methanogenesis pathway by acetoclastic methanogenesis in the methanogenic unit. The beta diversity indexes illustrated a more similar distribution of bacterial communities than that of methanogens between acidogenic unit and methanogenic unit. The differentiation of methanogenic community composition in two phases, as well as pH values and volatile fatty acid (VFA) concentrations confirmed the phase separation of the ITPAR. Overall, the results of this study demonstrated that the special designing of ITPAR maintained a sufficient number of methanogens, more diverse communities and stronger syntrophic associations among microorganisms, which made two phase anaerobic digestion of cellulosic materials more efficient. Copyright © 2014. Published by Elsevier B.V.

Anaerobic biodegradation of cellulosic material: Batch experiments and modelling based on isotopic data and focusing on aceticlastic and non-aceticlastic methanogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qu, X.; Cemagref, UR-HBAN, Parc de Tourvoie, Antony cedex F-92163; Vavilin, V.A.

Utilizing stable carbon isotope data to account for aceticlastic and non-aceticlastic pathways of methane generation, a model was created to describe laboratory batch anaerobic decomposition of cellulosic materials (office paper and cardboard). The total organic and inorganic carbon concentrations, methane production volume, and methane and CO{sub 2} partial pressure values were used for the model calibration and validation. According to the fluorescent in situ hybridization observations, three groups of methanogens including strictly hydrogenotrophic methanogens, strictly aceticlastic methanogens (Methanosaeta sp.) and Methanosarcina sp., consuming both acetate and H{sub 2}/H{sub 2}CO{sub 3} as well as acetate-oxidizing syntrophs, were considered. It was shownmore » that temporary inhibition of aceticlastic methanogens by non-ionized volatile fatty acids or acidic pH was responsible for two-step methane production from office paper at 35 {sup o}C where during the first and second steps methane was generated mostly from H{sub 2}/H{sub 2}CO{sub 3} and acetate, respectively. Water saturated and unsaturated cases were tested. According to the model, at the intermediate moisture (150%), much lower methane production occurred because of full-time inhibition of aceticlastic methanogens. At the lowest moisture, methane production was very low because most likely hydrolysis was seriously inhibited. Simulations showed that during cardboard and office paper biodegradation at 55 {sup o}C, non-aceticlastic syntrophic oxidation by acetate-oxidizing syntrophs and hydrogenotrophic methanogens were the dominant methanogenic pathways.« less

Growth of Desulfovibrio in Lactate or Ethanol Media Low in Sulfate in Association with H2-Utilizing Methanogenic Bacteria

PubMed Central

Bryant, M. P.; Campbell, L. Leon; Reddy, C. A.; Crabill, M. R.

1977-01-01

In the analysis of an ethanol-CO2 enrichment of bacteria from an anaerobic sewage digestor, a strain tentatively identified as Desulfovibrio vulgaris and an H2-utilizing methanogen resembling Methanobacterium formicicum were isolated, and they were shown to represent a synergistic association of two bacterial species similar to that previously found between S organism and Methanobacterium strain MOH isolated from Methanobacillus omelianskii. In lowsulfate media, the desulfovibrio produced acetate and H2 from ethanol and acetate, H2, and, presumably, CO2 from lactate; but growth was slight and little of the energy source was catabolized unless the organism was combined with an H2-utilizing methanogenic bacterium. The type strains of D. vulgaris and Desulfovibrio desulfuricans carried out the same type of synergistic growth with methanogens. In mixtures of desulfovibrio and strain MOH growing on ethanol, lactate, or pyruvate, diminution of methane produced was stoichiometric with the moles of sulfate added, and the desulfovibrios grew better with sulfate addition. The energetics of the synergistic associations and of the competition between the methanogenic system and sulfate-reducing system as sinks for electrons generated in the oxidation of organic materials such as ethanol, lactate, and acetate are discussed. It is suggested that lack of availability of H2 for growth of methanogens is a major factor in suppression of methanogenesis by sulfate in natural ecosystems. The results with these known mixtures of bacteria suggest that hydrogenase-forming, sulfate-reducing bacteria could be active in some methanogenic ecosystems that are low in sulfate. PMID:879775

Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria.

PubMed

Bryant, M P; Campbell, L L; Reddy, C A; Crabill, M R

1977-05-01

In the analysis of an ethanol-CO(2) enrichment of bacteria from an anaerobic sewage digestor, a strain tentatively identified as Desulfovibrio vulgaris and an H(2)-utilizing methanogen resembling Methanobacterium formicicum were isolated, and they were shown to represent a synergistic association of two bacterial species similar to that previously found between S organism and Methanobacterium strain MOH isolated from Methanobacillus omelianskii. In lowsulfate media, the desulfovibrio produced acetate and H(2) from ethanol and acetate, H(2), and, presumably, CO(2) from lactate; but growth was slight and little of the energy source was catabolized unless the organism was combined with an H(2)-utilizing methanogenic bacterium. The type strains of D. vulgaris and Desulfovibrio desulfuricans carried out the same type of synergistic growth with methanogens. In mixtures of desulfovibrio and strain MOH growing on ethanol, lactate, or pyruvate, diminution of methane produced was stoichiometric with the moles of sulfate added, and the desulfovibrios grew better with sulfate addition. The energetics of the synergistic associations and of the competition between the methanogenic system and sulfate-reducing system as sinks for electrons generated in the oxidation of organic materials such as ethanol, lactate, and acetate are discussed. It is suggested that lack of availability of H(2) for growth of methanogens is a major factor in suppression of methanogenesis by sulfate in natural ecosystems. The results with these known mixtures of bacteria suggest that hydrogenase-forming, sulfate-reducing bacteria could be active in some methanogenic ecosystems that are low in sulfate.

Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers

PubMed Central

Katayama, Taiki; Yoshioka, Hideyoshi; Muramoto, Yoshiyuki; Usami, Jun; Fujiwara, Kazuhiro; Yoshida, Satoshi; Kamagata, Yoichi; Sakata, Susumu

2015-01-01

The Minami-Kanto gas field, where gases are dissolved in formation water, is a potential analogue for a marine gas hydrate area because both areas are characterized by the accumulation of microbial methane in marine turbidite sand layers interbedded with mud layers. This study examined the physicochemical impacts associated with natural gas production and well drilling on the methanogenic activity and composition in this gas field. Twenty-four gas-associated formation water samples were collected from confined sand aquifers through production wells. The stable isotopic compositions of methane in the gases indicated their origin to be biogenic via the carbonate reduction pathway. Consistent with this classification, methanogenic activity measurements using radiotracers, culturing experiments and molecular analysis of formation water samples indicated the predominance of hydrogenotrophic methanogenesis. The cultivation of water samples amended only with methanogenic substrates resulted in significant increases in microbial cells along with high-yield methane production, indicating the restricted availability of substrates in the aquifers. Hydrogenotrophic methanogenic activity increased with increasing natural gas production from the corresponding wells, suggesting that the flux of substrates from organic-rich mudstones to adjacent sand aquifers is enhanced by the decrease in fluid pressure in sand layers associated with natural gas/water production. The transient predominance of methylotrophic methanogens, observed for a few years after well drilling, also suggested the stimulation of the methanogens by the exposure of unutilized organic matter through well drilling. These results provide an insight into the physicochemical impacts on the methanogenic activity in biogenic gas deposits including marine gas hydrates. PMID:25105906

Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils.

PubMed

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

2011-09-01

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 CH(4) 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.

Methane production correlates positively with methanogens, sulfate-reducing bacteria and pore water acetate at an estuarine brackish-marsh landscape scale

NASA Astrophysics Data System (ADS)

Tong, C.; She, C. X.; Jin, Y. F.; Yang, P.; Huang, J. F.

2013-11-01

Methane production is influenced by the abundance of methanogens and the availability of terminal substrates. Sulfate-reducing bacteria (SRB) also play an important role in the anaerobic decomposition of organic matter. However, the relationships between methane production and methanogen populations, pore water terminal substrates in estuarine brackish marshes are poorly characterized, and even to our knowledge, no published research has explored the relationship between methane production rate and abundance of SRB and pore water dimethyl sulfide (DMS) concentration. We investigated methane production rate, abundances of methanogens and SRB, concentrations of pore water terminal substrates and electron acceptors at a brackish marsh landscape dominated by Phragmites australis, Cyperus malaccensis and Spatina alterniflora marshes zones in the Min River estuary. The average rates of methane production at a soil depth of 30 cm in the three marsh zones were 0.142, 0.058 and 0.067 μg g-1 d-1, respectively. The abundance of both methanogens and SRB in the soil of the P. australis marsh with highest soil organic carbon content was higher than in the C. malaccensis and S. alterniflora marshes. The abundance of methanogens and SRB in the three soil layers was statistically indistinguishable. Mean pore water DMS concentrations at a soil depth of 30 cm under the S. alterniflora marsh were higher than those in the C. malaccensis and P. australis marshes. Methane production rate increased with the abundance of both methanogens and SRB across three marsh zones together at the landscape scale, and also increased with the concentration of pore water acetate, but did not correlate with concentrations of pore water DMS and dissolved CO2. Our results suggest that, provided that substrates are available in ample supply, methanogens can continue to produce methane regardless of whether SRB are prevalent in estuarine brackish marshes.

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

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lerm, S.; Kleyboecker, A.; Miethling-Graff, R.

2012-03-15

Highlights: Black-Right-Pointing-Pointer Two types of methanogens are necessary to respond successfully to perturbation. Black-Right-Pointing-Pointer Diversity of methanogens correlates with the VFA concentration and methane yield. Black-Right-Pointing-Pointer Aggregates indicate tight spatial relationship between minerals and microorganisms. - Abstract: Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit themore » gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge. Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.« less

Comparative community structure of archaea in rumen of buffaloes and cattle.

PubMed

Paul, Shyam S; Dey, Avijit; Baro, Daoharu; Punia, Balbir S

2017-08-01

Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank. Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes. This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Robust Mercury Methylation across Diverse Methanogenic Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilmour, Cynthia C.; Bullock, Allyson L.; McBurney, Alyssa

ABSTRACT. Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that containhgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were capable of MeHg production greater than that of spent- and uninoculated-medium controls during batch culture growth.Methanococcoides methylutens, anhgcAB +strain with a fused gene pair, was unable to produce more MeHg than controls. Maximal conversion of Hg to MeHg through a full batch culture growth cycle for each species (exceptM. methylutens) ranged from 2 to >50%more » of the added Hg(II) or between 0.2 and 17 pmol of MeHg/mg of protein. Three of the species produced >10% MeHg. The ability to produce MeHg was confirmed in severalhgcAB +methanogens that had not previously been tested (Methanocella paludicolaSANAE,Methanocorpusculum bavaricum,Methanofollis liminatansGKZPZ, andMethanosphaerula palustrisE1-9c). Maximal methylation was observed at low sulfide concentrations (<100 μM) and in the presence of 0.5 to 5 mM cysteine. ForM. hollandica, the addition of up to 5 mM cysteine enhanced MeHg production and cell growth in a concentration-dependent manner. As observed for bacterial Hg methylators, sulfide inhibited MeHg production. An initial evaluation of sulfide and thiol impacts on bioavailability showed methanogens responding to Hg complexation in the same way as doDeltaproteobacteria. The mercury methylation rates of several methanogens rival those of the better-studied Hg-methylating sulfate- and iron-reducing Deltaproteobacteria. IMPORTANCE. Archaea, specifically methanogenic organisms, play a role in mercury methylation in nature, but their global importance to MeHg production and the subsequent risk to ecosystems are not known. Methanogenesis has been linked to Hg methylation in several natural habitats where methylmercury production incurs risk to people and ecosystems, including rice paddies and permafrost. In this study, we confirm that most methanogens carrying thehgcABgene pair are capable of Hg methylation. Finally, we found that methylation rates vary inherently amonghgcAB +methanogens but that several species are capable of MeHg production at rates that rival those of the better-know Hg-methylating sulfate- and iron-reducing bacteria. Methanogens may need to be considered equally with sulfate and iron reducers in evaluations of MeHg production in nature.« less

Robust Mercury Methylation across Diverse Methanogenic Archaea

DOE PAGES

Gilmour, Cynthia C.; Bullock, Allyson L.; McBurney, Alyssa; ...

2018-04-10

ABSTRACT. Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that containhgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were capable of MeHg production greater than that of spent- and uninoculated-medium controls during batch culture growth.Methanococcoides methylutens, anhgcAB +strain with a fused gene pair, was unable to produce more MeHg than controls. Maximal conversion of Hg to MeHg through a full batch culture growth cycle for each species (exceptM. methylutens) ranged from 2 to >50%more » of the added Hg(II) or between 0.2 and 17 pmol of MeHg/mg of protein. Three of the species produced >10% MeHg. The ability to produce MeHg was confirmed in severalhgcAB +methanogens that had not previously been tested (Methanocella paludicolaSANAE,Methanocorpusculum bavaricum,Methanofollis liminatansGKZPZ, andMethanosphaerula palustrisE1-9c). Maximal methylation was observed at low sulfide concentrations (<100 μM) and in the presence of 0.5 to 5 mM cysteine. ForM. hollandica, the addition of up to 5 mM cysteine enhanced MeHg production and cell growth in a concentration-dependent manner. As observed for bacterial Hg methylators, sulfide inhibited MeHg production. An initial evaluation of sulfide and thiol impacts on bioavailability showed methanogens responding to Hg complexation in the same way as doDeltaproteobacteria. The mercury methylation rates of several methanogens rival those of the better-studied Hg-methylating sulfate- and iron-reducing Deltaproteobacteria. IMPORTANCE. Archaea, specifically methanogenic organisms, play a role in mercury methylation in nature, but their global importance to MeHg production and the subsequent risk to ecosystems are not known. Methanogenesis has been linked to Hg methylation in several natural habitats where methylmercury production incurs risk to people and ecosystems, including rice paddies and permafrost. In this study, we confirm that most methanogens carrying thehgcABgene pair are capable of Hg methylation. Finally, we found that methylation rates vary inherently amonghgcAB +methanogens but that several species are capable of MeHg production at rates that rival those of the better-know Hg-methylating sulfate- and iron-reducing bacteria. Methanogens may need to be considered equally with sulfate and iron reducers in evaluations of MeHg production in nature.« less

Effects of Mars Regolith Analogs, UVC radiation, Temperature, Pressure, and pH on the Growth and Survivability of Methanogenic Archaea and Stable Carbon Isotope Fractionation: Implications for Surface and Subsurface Life on Mars

NASA Astrophysics Data System (ADS)

Sinha, Navita

Mars is one of the suitable bodies in our solar system that can accommodate extraterrestrial life. The detection of plumes of methane in the Martian atmosphere, geochemical evidence, indication of flow of intermittent liquid water on the Martian surface, and geomorphologies of Mars have bolstered the plausibility of finding extant or evidence of extinct life on its surface and/or subsurface. However, contemporary Mars has been considered as an inhospitable planet for several reasons, such as low atmospheric surface pressure, low surface temperature, and intense DNA damaging radiation. Despite the hostile conditions of Mars, a few strains of methanogenic archaea have shown survivability in limited surface and subsurface conditions of Mars. Methanogens, which are chemolithoautotrophic non-photosynthetic anaerobic archaea, have been considered ideal models for possible Martian life forms for a long time. The search for biosignatures in the Martian atmosphere and possibility of life on the Martian surface under UVC radiation and deep subsurface under high pressure, temperature, and various pHs are the motivations of this research. Analogous to Earth, Martian atmospheric methane could be biological in origin. Chapter 1 provides relevant information about Mars' habitability, methane on Mars, and different strains of methanogens used in this study. Chapter 2 describes the interpretation of the carbon isotopic data of biogenic methane produced by methanogens grown on various Mars analogs and the results provide clues to determine ambiguous sources of methane on Mars. Chapter 3 illustrates the sensitivity of hydrated and desiccated cultures of halophilic and non-halophilic methanogens to DNA-damaging ultraviolet radiations, and the results imply that UVC radiation may not be an enormous constraint for methanogenic life forms on the surface of Mars. Chapters 4, 5, and 6 discuss the data for the survivability, growth, and morphology of methanogens in presumed deep subsurface physicochemical conditions such as temperature, pressure, hydrogen concentration, and pH of Mars. Finally, chapter 7 provides conclusions, limitations of the experiments, and future perspective of the work. Overall, the quantitative measurements obtained in the various sections of this novel work provide insights to atmospheric biosignatures and survivability of methanogenic organisms on the surface and subsurface of Mars.

Effect of dietary fiber on the methanogen community in the hindgut of Lantang gilts.

PubMed

Cao, Z; Liang, J B; Liao, X D; Wright, A D G; Wu, Y B; Yu, B

2016-10-01

The primary objective of this study was to investigate the effect of dietary fiber on methanogenic diversity and community composition in the hindgut of indigenous Chinese Lantang gilts to explain the unexpected findings reported earlier that Lantang gilts fed low-fiber diet (LFD) produced more methane than those fed high-fiber diet (HFD). In total, 12 Lantang gilts (58.7±0.37 kg) were randomly divided into two dietary groups (six replicates (pigs) per group) and fed either LFD (NDF=201.46 g/kg) or HFD (NDF=329.70 g/kg). Wheat bran was the main source of fiber for the LFD, whereas ground rice hull (mixture of rice hull and rice bran) was used for the HFD. Results showed that the methanogens in the hindgut of Lantang gilts belonged to four known species (Methanobrevibacter ruminantium, Methanobrevibacter wolinii, Methanosphaera stadtmanae and Methanobrevibacter smithii), with about 89% of the methanogens belonging to the genus Methanobrevibacter. The 16S ribosomal RNA (rRNA) gene copies of Methanobrevibacter were more than three times higher (P0.05) was observed in 16S rRNA gene copies of Fibrobacter succinogenes between the two dietary groups, and 18S rRNA gene copies of anaerobic fungi in gilts fed LFD were lower than (P<0.05) those fed HFD. To better explain the effect of different fiber source on the methanogen community, a follow-up in vitro fermentation using a factorial design comprised of two inocula (prepared from hindgut content of gilts fed two diets differing in their dietary fiber)×four substrates (LFD, HFD, wheat bran, ground rice hull) was conducted. Results of the in vitro fermentation confirmed that the predominant methanogens belonged to the genus of Methanobrevibacter, and about 23% methanogens was found to be distantly related (90%) to Thermogymnomonas acidicola. In vitro fermentation also seems to suggest that fiber source did change the methanogens community. Although the density of Methanobrevibacter species was positively correlated with CH4 production in both in vivo (P<0.01, r=0.737) and in vitro trials (P<0.05, r=0.854), which could partly explain the higher methane production from gilts fed LFD compared with those in the HFD group. Further investigation is needed to explain how the rice hull affected the methanogens and inhibited CH4 emission from gilts fed HFD.

Biomethanation of Syngas Using Anaerobic Sludge: Shift in the Catabolic Routes with the CO Partial Pressure Increase.

PubMed

Sancho Navarro, Silvia; Cimpoia, Ruxandra; Bruant, Guillaume; Guiot, Serge R

2016-01-01

Syngas generated by thermal gasification of biomass or coal can be steam reformed and purified into methane, which could be used locally for energy needs, or re-injected in the natural gas grid. As an alternative to chemical catalysis, the main components of the syngas (CO, CO2, and H2) can be used as substrates by a wide range of microorganisms, to be converted into gas biofuels, including methane. This study evaluates the carboxydotrophic (CO-consuming) methanogenic potential present in an anaerobic sludge from an upflow anaerobic sludge bed (UASB) reactor treating waste water, and elucidates the CO conversion routes to methane at 35 ± 3°C. Kinetic activity tests under CO at partial pressures (pCO) varying from 0.1 to 1.5 atm (0.09-1.31 mmol/L in the liquid phase) showed a significant carboxydotrophic activity potential for growing conditions on CO alone. A maximum methanogenic activity of 1 mmol CH4 per g of volatile suspended solid and per day was achieved at 0.2 atm of CO (0.17 mmol/L), and then the rate decreased with the amount of CO supplied. The intermediary metabolites such as acetate, H2, and propionate started to accumulate at higher CO concentrations. Inhibition experiments with 2-bromoethanesulfonic acid (BES), fluoroacetate, and vancomycin showed that in a mixed culture CO was converted mainly to acetate by acetogenic bacteria, which was further transformed to methane by acetoclastic methanogens, while direct methanogenic CO conversion was negligible. Methanogenesis was totally blocked at high pCO in the bottles (≥1 atm). However it was possible to achieve higher methanogenic potential under a 100% CO atmosphere after acclimation of the sludge to CO. This adaptation to high CO concentrations led to a shift in the archaeal population, then dominated by hydrogen-utilizing methanogens, which were able to take over acetoclastic methanogens, while syntrophic acetate oxidizing (SAO) bacteria oxidized acetate into CO2 and H2. The disaggregation of the granular sludge showed a negative impact on their methanogenic activity, confirming that the acetoclastic methanogens were the most sensitive to CO, and a contrario, the advantage of using granular sludge for further development toward large-scale methane production from CO-rich syngas.

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 or 11 or 15. Apart from phytan-3-ol, these compounds appear to have been overlooked in previous analyses of methanogen lipids. Methanopyrus kandleri, a hyperthermophile that is distinguished from other methanogens by some unusual biochemical features, is also differentiated by having biphytanyl chains with cyclopentane rings. This is a structural feature more commonly found in the Crenarchaeota. We are applying this biomarker methodology to environmental samples in studies of the spatial distribution of methanogenesis relative to other physiologies.

Biomethanation of Syngas Using Anaerobic Sludge: Shift in the Catabolic Routes with the CO Partial Pressure Increase

PubMed Central

Sancho Navarro, Silvia; Cimpoia, Ruxandra; Bruant, Guillaume; Guiot, Serge R.

2016-01-01

Syngas generated by thermal gasification of biomass or coal can be steam reformed and purified into methane, which could be used locally for energy needs, or re-injected in the natural gas grid. As an alternative to chemical catalysis, the main components of the syngas (CO, CO2, and H2) can be used as substrates by a wide range of microorganisms, to be converted into gas biofuels, including methane. This study evaluates the carboxydotrophic (CO-consuming) methanogenic potential present in an anaerobic sludge from an upflow anaerobic sludge bed (UASB) reactor treating waste water, and elucidates the CO conversion routes to methane at 35 ± 3°C. Kinetic activity tests under CO at partial pressures (pCO) varying from 0.1 to 1.5 atm (0.09–1.31 mmol/L in the liquid phase) showed a significant carboxydotrophic activity potential for growing conditions on CO alone. A maximum methanogenic activity of 1 mmol CH4 per g of volatile suspended solid and per day was achieved at 0.2 atm of CO (0.17 mmol/L), and then the rate decreased with the amount of CO supplied. The intermediary metabolites such as acetate, H2, and propionate started to accumulate at higher CO concentrations. Inhibition experiments with 2-bromoethanesulfonic acid (BES), fluoroacetate, and vancomycin showed that in a mixed culture CO was converted mainly to acetate by acetogenic bacteria, which was further transformed to methane by acetoclastic methanogens, while direct methanogenic CO conversion was negligible. Methanogenesis was totally blocked at high pCO in the bottles (≥1 atm). However it was possible to achieve higher methanogenic potential under a 100% CO atmosphere after acclimation of the sludge to CO. This adaptation to high CO concentrations led to a shift in the archaeal population, then dominated by hydrogen-utilizing methanogens, which were able to take over acetoclastic methanogens, while syntrophic acetate oxidizing (SAO) bacteria oxidized acetate into CO2 and H2. The disaggregation of the granular sludge showed a negative impact on their methanogenic activity, confirming that the acetoclastic methanogens were the most sensitive to CO, and a contrario, the advantage of using granular sludge for further development toward large-scale methane production from CO-rich syngas. PMID:27536280

Evidence of Archaeal Methanogens in Brain Abscess.

PubMed

Drancourt, Michel; Nkamga, Vanessa Demonfort; Lakhe, Ndèye Aïssatou; Régis, Jean-Marie; Dufour, Henry; Fournier, Pierre-Edouard; Bechah, Yassina; Scheld, W Michael; Raoult, Didier

2017-07-01

Methanogens are antibiotic-resistant anaerobic archaea that escape routine detection in clinical microbiology. We hypothesized that methanogens are part of the anaerobic community that cause brain abscess. Methanogens were investigated in 1 index sample using specific polymerase chain reaction (PCR) sequencing and culture. The pathogenesis of a methanogen isolate was assessed in a mouse model. Archaea-specific quantitative (q) PCR and metagenomics were used to detect specific archaeal sequences in brain abscess samples and controls. In 1 index sample, routine culture found Porphyromonas endodontalis and Streptococcus intermedius, and specific culture found Methanobrevibacter oralis susceptible to metronidazole and fusidic acid. Archaea-targeted PCR sequencing and metagenomics confirmed M. oralis along with 14 bacteria, including S. intermedius. Archaea-specific qPCR yielded archaea in 8/18 brain abscess specimens and 1/27 controls (P < .003), and metagenomics yielded archaea, mostly methanogens, in 28/32 brain abscess samples, and no archaea in 71 negative controls (P < 10-6). Infection of mice brains yielded no mortality in 14 controls and death in 17/22 M. oralis-inoculated mice (P < 10-6), 32/95 S. intermedius-inoculated mice (P < 10-6), and 75/104 mice inoculated with M. oralis mixed with S. intermedius (P < 10-6) 7 days post-inoculation. Methanogens belong to the anaerobic community responsible for brain abscess, and M. oralis may participate in the pathogenicity of this deadly infection. In mice, a synergy of M. oralis and S. intermedius was observed. Antibiotic treatment of brain abscess should contain anti-archaeal compounds such as imidazole derivatives in most cases. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Reactive transport model of growth and methane production by high-temperature methanogens in hydrothermal regions of the subseafloor

NASA Astrophysics Data System (ADS)

Stewart, L. C.; Algar, C. K.; Topçuoğlu, B. D.; Fortunato, C. S.; Larson, B. I.; Proskurowski, G. K.; Butterfield, D. A.; Vallino, J. J.; Huber, J. A.; Holden, J. F.

2014-12-01

Hydrogenotrophic methanogens are keystone high-temperature autotrophs in deep-sea hydrothermal vents and tracers of habitability and biogeochemical activity in the hydrothermally active subseafloor. At Axial Seamount, nearly all thermophilic methanogens are Methanothermococcus and Methanocaldococcus species, making this site amenable to modeling through pure culture laboratory experiments coupled with field studies. Based on field microcosm incubations with 1.2 mM, 20 μM, or no hydrogen, the growth of methanogens at 55°C and 80°C is limited primarily by temperature and hydrogen availability, with ammonium amendment showing no consistent effect on total methane output. The Arrhenius constants for methane production by Methanocaldococcus jannaschii (optimum 82°C) and Methanothermococcus thermolithotrophicus (optimum 65°C) were determined in pure culture bottle experiments. The Monod constants for hydrogen concentration were measured by growing both organisms in a 2-liter chemostat at two dilution rates; 55°C, 65°C and 82°C; and variable hydrogen concentrations. M. jannaschii showed higher ks and Vmax constants than M. thermolithotrophicus. In the field, hydrogen and methane concentrations in hydrothermal end-member and low-temperature diffuse fluids were measured, and the concentrations of methanogens that grow at 55°C and 80°C in diffuse fluids were determined using most-probable-number estimates. Methane concentration anomalies in diffuse fluids relative to end-member hydrothermal concentrations and methanogen cell concentrations are being used to constrain a 1-D reactive transport model using the laboratory-determined Arrhenius and Monod constants for methane production by these organisms. By varying flow path length and subseafloor cell concentrations in the model, our goal is to determine solutions for the potential depth of the subseafloor biosphere coupled with the amount of methanogenic biomass it contains.

Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens

PubMed Central

2016-01-01

Hydrogen (H2) consumption and methane (CH4) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH4 production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH4 formation rate in the cytochrome-containing Methanosarcina barkeri grown on H2 and CO2. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H2 partial pressure (pH2) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH2 values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH2 threshold recorded to date in pure methanogen culture, which suggests that M.bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H2 concentrations. Our study has implications for research on the H2-driven deep subsurface biosphere and biogas reactor performance. PMID:27992585

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. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea.

PubMed

Sundset, Monica A; Edwards, Joan E; Cheng, Yan Fen; Senosiain, Roberto S; Fraile, Maria N; Northwood, Korinne S; Praesteng, Kirsti E; Glad, Trine; Mathiesen, Svein D; Wright, André-Denis G

2009-12-01

Ruminal methanogens, bacteria and ciliate protozoa of Svalbard reindeer grazing natural pastures in October (late fall) and April (late winter) were investigated using molecular-based approaches. The appetite of the Svalbard reindeer peaks in August (summer) and is at its lowest in March (winter). Microbial numbers, quantified by real-time PCR, did not change significantly between October and April, when food intakes are at similar levels, although the numbers of methanogens tended to be higher in October (P=0.074), and ciliate numbers tended to be higher in April (P=0.055). Similarly, no change was detected in the bacterial and protozoal population composition by rRNA gene-based denaturing gradient gel electrophoresis analysis. Dominant methanogens were identified using a 16S rRNA gene library (97 clones) prepared from pooled PCR products from reindeer on October pasture (n=5). Eleven of the 22 distinct operational taxonomic units (OTUs) generated exhibited a high degree of sequence similarity to methanogens affiliated with Methanobacteriales (eight OTUs), Methanomicrobiales (one OTU) and Methanosarcinales (two OTUs). The remaining 11 OTUs (53% of the clones) were associated with a cluster of uncultivated ruminal archaea. This study has provided important insights into the rumen microbiome of a high-arctic herbivorous animal living under harsh nutritional conditions, and evidence suggesting that host type affects the population size of ruminal methanogens.

Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens.

PubMed

Neubeck, Anna; Sjöberg, Susanne; Price, Alex; Callac, Nolwenn; Schnürer, Anna

2016-01-01

Hydrogen (H2) consumption and methane (CH4) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH4 production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH4 formation rate in the cytochrome-containing Methanosarcina barkeri grown on H2 and CO2. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H2 partial pressure (pH2) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH2 values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH2 threshold recorded to date in pure methanogen culture, which suggests that M.bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H2 concentrations. Our study has implications for research on the H2-driven deep subsurface biosphere and biogas reactor performance.

Changes in methane emission, rumen fermentation, and methanogenic community in response to silage and dry cornstalk diets.

PubMed

Chong, Liu; Zhuping, Zhu; Tongjun, Guo; Yongming, Luo; Hongmin, Dong

2014-06-01

This study aimed to investigate the effect of silage or dry cornstalk diets on methane emission, rumen fermentation, and methanogenic community, and reveal whether the change of methanogenic compositions was related to the methane production. A total of 39 sheep were divided into four groups, fed diets of different concentrate level based on silage or dry cornstalk roughage for 40 days. It was found that, at 20% concentrate level, the sheep fed silage could suppress methanogenesis significantly in contrast with the silage diet (p < 0.05). The ruminal acetate:propionate ratio was 3.17 in the silage-fed sheep significantly lower than 3.78 in the dry cornstalk-fed sheep (p < 0.05), reflecting the effect of fermentation on methane output was related to roughage types. Furthermore, the methanogens was found to be significantly lower abundance (p < 0.05), and showed a different pattern using multivariate statistical analysis in silage-fed sheep. Compared with dry cornstalk diet, silage diet of 20% concentrate reduced methane production, decreased methanogenic abundance, and induced change of Methanobrevibacter composition at strain levels. This study showed variation of methanogenic compositions at strain level and its probable relationship with methane production, and provided microbial information to explain the low methane output when the animals were fed silage. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.

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 WWE1more » 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.« less

Is aceticlastic methanogen composition in full-scale anaerobic processes related to acetate utilization capacity?

PubMed

Yilmaz, Vedat; Ince-Yilmaz, Ebru; Yilmazel, Yasemin Dilsad; Duran, Metin

2014-06-01

In this study, biomass samples were obtained from six municipal and nine industrial full-scale anaerobic processes to investigate whether the aceticlastic methanogen population composition is related to acetate utilization capacity and the nature of the wastewater treated, i.e. municipal sludge or industrial wastewater. Batch serum bottle tests were used to determine the specific acetate utilization rate (AUR), and a quantitative real-time polymerase chain reaction protocol was used to enumerate the acetate-utilizing Methanosaeta and Methanosarcina populations in the biomass samples. Methanosaeta was the dominant aceticlastic methanogen in all samples, except for one industrial wastewater-treating anaerobic process. However, Methanosarcina density in industrial biomass samples was higher than the Methanosarcina density in the municipal samples. The average AUR values of municipal and industrial wastewater treatment plant biomass samples were 10.49 and 10.65 mg CH3COO(-)/log(aceticlastic methanogen gene copy).d, respectively. One-way ANOVA test and principle component analysis showed that the acetate utilization capacities and aceticlastic methanogen community composition did not show statistically significant correlation among the municipal digesters and industrial wastewater-treating processes investigated.

Evolution of microorganisms in thermophilic-dry anaerobic digestion.

PubMed

Montero, B; Garcia-Morales, J L; Sales, D; Solera, R

2008-05-01

Microbial population dynamics were studied during the start-up and stabilization periods in thermophilic-dry anaerobic digestion at lab-scale. The experimental protocol was defined to quantify Eubacteria and Archaea using Fluorescent in situ hybridization (FISH) in a continuously stirred tank reactor (CSTR), without recycling solids. The reactor was subjected to a programme of steady-state operation over a range of the retention times from 40 to 25 days, with an organic loading rate between 4.42 and 7.50 kg volatile solid/m3/day. Changes in microbial concentrations were linked to traditional performance parameters such as biogas production and VS removal. The relations of Eubacteria:Archaea and H2-utilising methanogens:acetate-utilising methanogens were 88:12 and 11:1, respectively, during start-up stage. Hydrogenotrophic methanogens, although important in the initial phase of the reactor start-up, were displaced by acetoclastic methanogens at steady-state, thus their relation were 7:32, respectively. The methane yield coefficient, the methane content in the biogas and VS removal were stabilized around 0.30 LCH4/gCOD, 50% and 80%, respectively. Methanogenic population correlated well with performance measurements.

Rapid degradation of 2,4-dichlorophenoxyacetic acid facilitated by acetate under methanogenic condition.

PubMed

Yang, Zhiman; Xu, Xiaohui; Dai, Meng; Wang, Lin; Shi, Xiaoshuang; Guo, Rongbo

2017-05-01

Acetate can be used as an electron donor to stimulate 2,4-dichlorophenoxyacetic acid (2,4-D), which has not been determined under methanogenic condition. This study applied high-throughput sequencing and methanogenic inhibition approaches to investigate the 2,4-D degradation process using the enrichments obtained from paddy soil. Acetate addition significantly promoted 2,4-D degradation, which was 5-fold higher than in the acetate-unsupplemented enrichments in terms of the 2,4-D degradation rate constant. Dechloromonas and Pseudomonas were the dominant 2,4-D degraders. Methanogenic inhibition experiments indicated that the 2,4-D degradation was independent of methanogenesis. It was proposed that the accelerated 2,4-D degradation in the acetate-supplemented enrichment involved an unusual interaction, where members of the acetate oxidizers primarily oxidized acetate and produced H 2 . H 2 was utilized by the 2,4-D degraders to degrade 2,4-D, but also partially consumed by the hydrogenotrophic methanogens to produce methane. The findings presented here provide a new strategy for the remediation of 2,4-D-polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution of butyric acid and the methanogenic microbial population in a thermophilic dry anaerobic reactor.

PubMed

Montero, B; Garcia-Morales, J L; Sales, D; Solera, R

2010-10-01

Knowledge of the relationship between the evolution of butyric acid, the main precursor of methane, and the methanogenic microbial population, quantified by fluorescent in situ hybridization (FISH), is important for understating and controlling the anaerobic digestion of solid waste. In this study, a statistical analysis has been made of this relationship in a laboratory-scale continuously stirred tank reactor (CSTR) without recycling of biomass. The CSTR has been operated at four organic loading rates (OLR) between 4.42 and 7.50 kg VS m(-3)day(-1), using the Organic Fraction of Municipal Solid Waste (OFMSW) as the substrate. During the start-up stage, the consumption of butyric acid is related to the population of H(2)-utilising methanogens (R(2)=0.774), whereas in the stabilization stage, it is related to that of acetoclastic methanogens (R(2)=0.716). Therefore, it can be concluded that the methanogenic population dynamics are closely correlated with the concentration of volatile fatty acids, and in particular, with that of butyric acid. (c) 2010 Elsevier Ltd. All rights reserved.

High-Performance Biogas Upgrading Using a Biotrickling Filter and Hydrogenotrophic Methanogens.

PubMed

Dupnock, Trisha L; Deshusses, Marc A

2017-10-01

This research reports the development of a biotrickling filter (BTF) to upgrade biogas, which is achieved by adding H 2 to reduce CO 2 . H 2 and CO 2 (80:20% vol.) were fed to a bench-scale BTF packed with polyurethane foam (PUF) and inoculated with hydrogenotrophic methanogens. Maximum CH 4 production rates recorded were as high as 38 m 3 CH4  m -3 reactor  day -1 , which is 5-30 times faster than earlier reports with other kinds of bioreactors. The high rates were attributed to the efficient mass transfer and high density of methanogens in the BTF. The removal efficiencies for H 2 and CO 2 were 83 and 96%, respectively. 5-Cyano-2,3-ditolyl tetrazolium chloride/DAPI staining revealed that 67% of cells were alive near the gas entrance port, while only 8.3% were alive at the exit. Furthermore, DNA sequencing showed that only 27% of the biomass was composed of Euryarchaeota, the phylum which includes methanogens. These two observations suggest that optimizing the methanogen density and activity could possibly reach even higher biogas upgrading rates.

In-situ biogas upgrading with pulse H2 additions: The relevance of methanogen adaption and inorganic carbon level.

PubMed

Agneessens, Laura Mia; Ottosen, Lars Ditlev Mørck; Voigt, Niels Vinther; Nielsen, Jeppe Lund; de Jonge, Nadieh; Fischer, Christian Holst; Kofoed, Michael Vedel Wegener

2017-06-01

Surplus electricity from fluctuating renewable power sources may be converted to CH 4 via biomethanisation in anaerobic digesters. The reactor performance and response of methanogen population of mixed-culture reactors was assessed during pulsed H 2 injections. Initial H 2 uptake rates increased immediately and linearly during consecutive pulse H 2 injections for all tested injection rates (0.3 to 1.7L H2 /L sludge /d), while novel high throughput mcrA sequencing revealed an increased abundance of specific hydrogenotrophic methanogens. These findings illustrate the adaptability of the methanogen population to H 2 injections and positively affects the implementation of biomethanisation. Acetate accumulated by a 10-fold following injections exceeding a 4:1 H 2 :CO 2 ratio and may act as temporary storage prior to biomethanisation. Daily methane production decreased for headspace CO 2 concentrations below 12% and may indicate a high sensitivity of hydrogenotrophic methanogens to CO 2 limitation. This may ultimately decide the biogas upgrading potential which can be achieved by biomethanisation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Formation of methane and carbon dioxide from dimethylselenide in anoxic sediments and by a methanogenic bacterium

USGS Publications Warehouse

Oremland, Ronald S.; Zehr, Jon P.

1986-01-01

Anaerobic San Francisco Bay salt marsh sediments rapidly metabolized [14C]dimethylselenide (DMSe) to 14CH4 and 14CO2. Addition of selective inhibitors (2-bromoethanesulfonic acid or molybdate) to these sediments indicated that both methanogenic and sulfate-respiring bacteria could degrade DMSe to gaseous products. However, sediments taken from the selenium-contaminated Kesterson Wildlife Refuge produced only 14CO2 from [14C]DMSe, implying that methanogens were not important in the Kesterson samples. A pure culture of a dimethylsulfide (DMS)-grown methylotrophic methanogen converted [14C]DMSe to 14CH4 and14CO2. However, the organism could not grow on DMSe. Addition of DMS to either sediments or the pure culture retarded the metabolism of DMSe. This effect appeared to be caused by competitive inhibition, thereby indicating a common enzyme system for DMS and DMSe metabolism. DMSe appears to be degraded as part of the DMS pool present in anoxic environments. These results suggest that methylotrophic methanogens may demethylate methylated forms of other metals and metalloids found in nature.

Fermentation Enhancement of Methanogenic Archaea Consortia from an Illinois Basin Coalbed via DOL Emulsion Nutrition

PubMed Central

Xiao, Dong; Peng, Su-Ping; Wang, En-Yuan

2015-01-01

Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate. PMID:25884952

Methanogenic activity in plankton samples and fish intestines A mechanism for in situ methanogenesis in oceanic surface waters

USGS Publications Warehouse

Oremland, Ronald S.

1979-01-01

When plankton samples were incubated anaerobically with a cysteine-sulfide reducing agent, pronounced methane evolution occurred. This activity was inhibited by air, CHCl3, C2H2, and 2-bromoethanesulfonic acid. Adding [14C]CO32− resulted in accumulation of [14C]CH4. Portions of the digestive tracts of three fishes were incubated in methanogenic media, and two of the samples showed the presence of methanogenic bacteria.

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.

Methane production from coal by a single methanogen

NASA Astrophysics Data System (ADS)

Sakata, S.; Mayumi, D.; Mochimaru, H.; Tamaki, H.; Yamamoto, K.; Yoshioka, H.; Suzuki, Y.; Kamagata, Y.

2017-12-01

Previous geochemical studies indicate that biogenic methane greatly contributes to the formation of coalbed methane (CBM). It is unclear, however, what part of coal is used for the methane production and what types of microbes mediate the process. Here we hypothesized that methylotrophic methanogens use methoxylated aromatic compounds (MACs) derived from lignin. We incubated 11 species of methanogens belonging to order Methanosarcinales with 7 types of MACs. Two strains of methanogens, i.e., Methermicoccus shengliensis AmaM and ZC-1, produced methane from the MACs. In fact, these methanogens used over 30 types of commercially available MACs in addition to methanol and methylamines. To date, it is widely believed that methanogens use very limited number of small compounds such as hydrogen plus carbon dioxide, acetate, and methanol, and only three methanogenic pathways are recognized accordingly. Here, in contrast, two Methermicoccus strains used many types of MACs. We therefore propose this "methoxydotrophic" process as the fourth methanogenic pathway. Incubation of AmaM with 2-methoxybenzoate resulted in methanogenesis associated with the stoichiometric production of 2-hydroxybenzoate. Incubation with 2-methoxy-[7-13C] benzoate and with [13C] bicarbonate indicated that two thirds of methane carbon derived from the methoxy group and one third from CO2. Furthermore, incubation with [2-13C] acetate resulted in significant increases of 13C in both methane and CO2. These results suggest the occurrence of O-demethylation, CO2 reduction and acetyl-CoA metabolism in the methoxydotrophic methanogenesis. Furthermore, incubation of AmaM with lignite, subbituminous or bituminous coals in the bicarbonate-buffered media revealed that AmaM produced methane directly from coals via the methoxydotrophic pathway. Although 4 types of MACs were detected in the coal media in addition to methanol and methylamines, their total concentrations were too low to account for the methane production, suggesting that AmaM produced methane from MACs in the media not analyzed this time and/or MACs bound to the coal surface. In conclusion, the contribution of methoxydotrophic methanogenesis may be important not only to the formation of CBM but also to the global carbon cycle.

Hydrocarbon activation under sulfate-reducing and methanogenic conditions proceeds by different mechanisms.

NASA Astrophysics Data System (ADS)

Head, Ian; Gray, Neil; Aitken, Caroline; Sherry, Angela; Jones, Martin; Larter, Stephen

2010-05-01

Microbial degradation of alkanes typically involves their conversion to fatty acids which are then catabolised by beta-oxidation. The critical step in this process is activation of the hydrocarbon. Under oxic conditions this is catalyzed by monooxygenase enzymes with the formation of long chain alcohols. In the absence of oxygen alternative alkane activation mechanisms have been observed or proposed. Fumarate addition to alkanes to form alkyl succinates is considered a central process in anaerobic hydrocarbon degradation. Comparative studies of crude oil degradation under sulphate-reducing and methanogenic conditions revealed distinctive patterns of compound class removal and metabolite formation. Alkyl succinates derived from C7 to C26 n-alkanes and branched chain alkanes were found in abundance in sulfate-reducing systems but these were not detected during methanogenic crude oil degradation. Only one other mechanism of alkane activation has been elucidated to date. This involves addition of carbon derived from bicarbonate/CO2 to C-3 of an alkane chain to form a 2-ethylalkane with subsequent removal of the ethyl group leading to the formation of a fatty acid 1 carbon shorter than the original alkane. 2-ethylalkanes have never been detected as metabolites of anaerobic alkane degradation and were not detected in crude oil-degrading methanogenic systems. Due to the range of alkanes present in crude oil it was not possible to infer the generation of C-odd acids from C-even alkanes which is characteristic of the C-3 carboxylation mechanism. Furthermore genes homologous to alkysuccinate synthetases were not detected in the methanogenic hydrocarbon degrading community by pyrosequencing of total DNA extracted from methanogenic enrichments cultures. beta-oxidation genes were detected and intriguingly, alcohol and aldehyde dehydrogenase genes were present. This offers the possibility that alkane activation in the methanogenic system does not proceed via acid metabolites, but may be initiated by an anaerobic hydroxylation reaction. This is not unprecedented and hydroxylation of ethylbenzene has been demonstrated. However the C-H bond dissociation energy of alkanes is typically considered too high to readily permit alkane hydroxylation. It is however clear that alkane activation in these methanogenic crude oil-degrading systems involves mechanisms other than the well-known fumarate-addition reactions.

Growth of methanogens on a Mars soil simulant.

PubMed

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.

Growth and analysis of anaerobic wastewater methanogens using microfluidics

NASA Astrophysics Data System (ADS)

Steinhaus, Ben

2005-11-01

A micro-bioreactor (μBR) with a total system volume of 5 μl was developed using microfluidics and used to study the anaerobic waste-water methanogen methanosaeta concilli. The μBR was contained inside of an anaerobic chamber designed to be placed directly under an inverted light microscope while maintaining the reactor under a N2/CO2 gas mixture. Methanogens were cultured for periods of up to 3 months inside channels of varying width. The varying channel widths created varying fluid velocities and hence varying shear-rates inside the μBR. This allowed for direct study of the behavior and response of the anaerobe to varying shear-rates. After completion of the study, fluorescent in situ hybridization (FISH) was performed directly inside the microchannels to allow for further analysis and identification of the methanogens.

Inhibition of acetoclastic methanogenesis in crude oil- and creosote-contaminated groundwater

USGS Publications Warehouse

Warren, E.; Bekins, B.A.; Godsy, E.M.; Smith, V.K.

2004-01-01

Results from a series of studies of methanogenic processes in crude oil- and creosote-contaminated aquifers indicated that acetoctastic methanogenesis is inhibited near non-aqueous sources. Acetoclastic methanogenesis was more susceptible to the toxic inhibition of crude oil and creosote than either hydrogen- or formate-utilizing methanogenesis. The effect of this toxic inhibition was apparent in the population of the methanogenic trophic groups near nonaqueous crude oil at the Bemidji, MN, site. At that site, acetoclastic methanogens were < 2/g within or near the oil where hydrogen- and formate-utilizing methanogens were 10-100/g. The geochemical effect of this toxic inhibition was the buildup of low molecular weight volatile acids, particularly acetate. Wastewater reactor studies indicated that this toxicity will result in a decrease in the biodegradation rate of contaminants at sites where toxic compounds are present.

The role of different methanogen groups evaluated by Real-Time qPCR as high-efficiency bioindicators of wet anaerobic co-digestion of organic waste

PubMed Central

2011-01-01

Methanogen populations and their domains are poorly understood; however, in recent years, research on this topic has emerged. The relevance of this field has also been enhanced by the growing economic interest in methanogen skills, particularly the production of methane from organic substrates. Management attention turned to anaerobic wastes digestion because the volume and environmental impact reductions. Methanogenesis is the biochemically limiting step of the process and the industrially interesting phase because it connects to the amount of biogas production. For this reason, several studies have evaluated the structure of methanogen communities during this process. Currently, it is clear that the methanogen load and diversity depend on the feeding characteristics and the process conditions, but not much data is available. In this study, we apply a Real-Time Polymerase Chain Reaction (RT-PCR) method based on mcrA target to evaluate, by specific probes, some subgroups of methanogens during the mesophilic anaerobic digestion process fed wastewater sludge and organic fraction of the municipal solid waste with two different pre-treatments. The obtained data showed the prevalence of Methanomicrobiales and significantly positive correlation between Methanosarcina and Methanosaetae and the biogas production rate (0.744 p < 0.01 and 0.641 p < 0.05). Methanosarcina detected levels are different during the process after the two pre-treatment of the input materials (T-test p < 0.05). Moreover, a role as diagnostic tool could be suggested in digestion optimisation. PMID:21982396

Crude oil degradation by bacterial consortia under four different redox and temperature conditions.

PubMed

Xiong, Shunzi; Li, Xia; Chen, Jianfa; Zhao, Liping; Zhang, Hui; Zhang, Xiaojun

2015-02-01

There is emerging interest in the anaerobic degradation of crude oil. However, there is limited knowledge about the geochemical effects and microbiological activities for it. A mixture of anaerobic sludge and the production water from an oil well was used as an inoculum to construct four consortia, which were incubated under sulfate-reducing or methanogenic conditions at either mesophilic or thermophilic temperatures. Significant degradation of saturated and aromatic hydrocarbons and the changing quantities of some marker compounds, such as pristane, phytane, hopane and norhopane, and their relative quantities, suggested the activity of microorganisms in the consortia. Notably, the redox conditions and temperature strongly affected the diversity and structure of the enriched microbial communities and the oil degradation. Although some specific biomarker showed larger change under methanogenic condition, the degradation efficiencies for total aromatic and saturated hydrocarbon were higher under sulfate-reducing condition. After the 540-day incubation, bacteria of unknown classifications were dominant in the thermophilic methanogenic consortia, whereas Clostridium dominated the mesophilic methanogenic consortia. With the exception of the dominant phylotypes that were shared with the methanogenic consortia, the sulfate-reducing consortia were predominantly composed of Thermotogae, Deltaproteobacteria, Spirochaeta, and Synergistetes phyla. In conclusion, results in this study demonstrated that the different groups of degraders were responsible for degradation in the four constructed crude oil degrading consortia and consequently led to the existence of different amount of marker compounds under these distinct conditions. There might be distinct metabolic mechanism for degrading crude oil under sulfate-reducing and methanogenic conditions.

Kinetics of DCE and VC mineralization under methanogenic and Fe(III)- reducing conditions

USGS Publications Warehouse

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

1997-01-01

The kinetics of anaerobic mineralization of DCE and VC under mathanogenic and Fe(III)-reducing conditions as a function of dissolved contaminant concentration were evaluated. Microorganisms indigenous to creek bed sediments, where groundwater contaminated with chlorinated ethenes continuously discharges, demonstrated significant mineralization of DCE and VC under methanogenic and Fe(III)- reducing conditions. Over 37 days, the recovery of [1,214C]VC radioactivity as 14CO2 ranged from 5% to 44% and from 8% to 100% under methanogenic and Fe(III)-reducing conditions, respectively. The recovery of [1,2-14C]DCE radioactivity as 14CO2 ranged from 4% to 14% and did not vary significantly between methanogenic and Fe(III)reducing conditions. VC mineralization was described by Michaelis- Menten kinetics. Under methanogenic conditions, V(max) was 0.19 ?? 0.01 ??mol L-1 d-1 and the half-saturation constant, k(m), was 7.6 ?? 1.7 ??M. Under Fe(III)-reducing conditions, V(max) was 0.76 ?? 0.07 ??mol L-1 d-1 and k(m) was 1.3 ?? 0.5 ??M. In contrast, DCE mineralization could be described by first-order kinetics. The first-order degradation rate constant for DCE mineralization was 0.6 ?? 0.2% d-1 under methanogenic and Fe(III)-reducing conditions. The results indicate that the kinetics of chlorinated ethane mineralization can vary significantly with the specific contaminant and the predominant redox conditions under which mineralization occurs.

Anaerobic Degradation of Phthalate Isomers by Methanogenic Consortia

PubMed Central

Kleerebezem, Robbert; Pol, Look W. Hulshoff; Lettinga, Gatze

1999-01-01

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 (μSmax) and biomass yields (YXtotS) 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 μSmax and YXtotS 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 (KS) 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. PMID:10049876

Toxicity assessment of inorganic nanoparticles to acetoclastic and hydrogenotrophic methanogenic activity in anaerobic granular sludge.

PubMed

Gonzalez-Estrella, Jorge; Sierra-Alvarez, Reyes; Field, James A

2013-09-15

Release of engineered nanoparticles (NPs) to municipal wastewater from industrial and residential sources could impact biological systems in wastewater treatment plants. Methanogenic inhibition can cause failure of anaerobic waste(water) treatment. This study investigated the inhibitory effect of a wide array of inorganic NPs (Ag(0), Al₂O₃, CeO₂, Cu(0), CuO, Fe(0), Fe₂O₃, Mn₂O₃, SiO₂, TiO₂, and ZnO supplied up to 1500 mgL(-1)) to acetoclastic and hydrogenotrophic methanogenic activity of anaerobic granular sludge. Of all the NPs tested, only Cu(0) and ZnO caused severe methanogenic inhibition. The 50% inhibiting concentrations determined towards acetoclastic and hydrogenotrophic methanogens were 62 and 68 mgL(-1) for Cu(0) NP; and 87 and 250 mgL(-1) for ZnO NP, respectively. CuO NPs also caused inhibition of acetoclastic methanogens. Cu(2+) and Zn(2+) salts caused similar levels of inhibition as Cu(0) and ZnO NPs based on equilibrium soluble metal concentrations measured during the assays, suggesting that the toxicity was due to the release of metal ions by NP-corrosion. A commercial dispersant, Dispex, intended to increase NP stability did not affect the inhibitory impact of the NPs. The results taken as a whole suggest that Zn- and Cu-containing NPs can release metal ions that are inhibitory for methanogenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of soil structure destruction on methane production and carbon partitioning between methanogenic pathways in tropical rain forest soils

NASA Astrophysics Data System (ADS)

Teh, Yit Arn; Silver, Whendee L.

2006-03-01

Controls on methanogenesis are often determined from laboratory incubations of soils converted to slurries. Destruction of soil structure during slurry conversion may disrupt syntrophic associations, kill methanogens, and/or alter the microsite distribution of methanogenic activity, suppressing CH4 production. The effects of slurry conversion on methanogenesis were investigated to determine if disruption of aggregate structure impacted methanogenesis, substrate utilization, and C partitioning between methanogenic pathways. Soils were collected from the tropical rain forest life zone of the Luquillo Experimental Forest, Puerto Rico, and exposed to different physical disturbances, including flooding and physical homogenization. Slurry conversion negatively impacted methanogenesis. Rates of CH4 production declined by a factor of 17 after well-aggregated soils were converted to slurries. Significantly more 13C-acetate was recovered in CO2 compared to CH4 after slurry conversion, suggesting that methanogens consumed less acetate after slurry conversion and may have competed less effectively with other anaerobes for acetate. Isotopic data indicate that the relative partitioning of C between aceticlastic and hydrogenotrophic pathways was unchanged after slurry conversion. These data suggest that experiments which destroy soil structure may significantly underestimate methanogenesis and overestimate the potential for other microorganisms to compete with methanogens for organic substrates. Current knowledge of the factors that regulate methanogenesis in soil may be biased by the findings of slurry-based experiments, that do not accurately represent the complex, spatially heterogeneous conditions found in well-aggregated soils.

Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers.

PubMed

Zhao, Liping; Meng, Qingxiang; Li, Yan; Wu, Hao; Huo, Yunlong; Zhang, Xinzhuang; Zhou, Zhenming

2018-03-20

This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (P L  = 0.0033) and Methanimicrococcus (P L  = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (P L  = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (P Q  = 0.0140). Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.

Physico-chemical characteristics and methanogen communities in swine and dairy manure storage tanks: spatio-temporal variations and impact on methanogenic activity.

PubMed

Barret, Maialen; Gagnon, Nathalie; Topp, Edward; Masse, Lucie; Massé, Daniel I; Talbot, Guylaine

2013-02-01

Greenhouse gas emissions represent a major environmental problem associated with the management of manure from the livestock industry. Methane is the primary GHG emitted during manure outdoor storage. In this paper, the variability of two swine and two dairy manure storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy manure storage tanks. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Identification of novel potential acetate-oxidizing bacteria in an acetate-fed methanogenic chemostat based on DNA stable isotope probing.

PubMed

Wang, Hui-Zhong; Gou, Min; Yi, Yue; Xia, Zi-Yuan; Tang, Yue-Qin

2018-05-11

Acetate is a significant intermediate of anaerobic fermentation. There are two pathways for converting acetate to CH 4 and CO 2 : acetoclastic methanogenesis by acetoclastic methanogens, and syntrophic acetate oxidation by acetate-oxidizing bacteria (AOB) and hydrogenotrophic methanogens. Detailed investigations of syntrophic acetate-oxidizing bacteria (SAOB) should contribute to the elucidation of the microbial mechanisms of methanogenesis. In this study, we investigated the major phylogenetic groups of acetate-utilizing bacteria (AUB) in a mesophilic methanogenic chemostat fed with acetate as the sole carbon source by using DNA stable isotope probing (SIP) technology. The results indicated that acetoclastic methanogenesis and acetate oxidization/hydrogenotrophic methanogenesis coexisted in the mesophilic chemostat fed with acetate, operated at a dilution rate of 0.1 d -1 . OTU Ace13(9-17) (KU869530), Ace13(9-4) (KU667241), and Ace13(9-23) (KU667236), assigned to the phyla Firmicutes and Bacteroidetes, were probably potential SAOB in the chemostat, which needs further investigation. Species in the phyla Proteobacteria, Deferribacteres, Acidobacteria, Spirochaetes and Actinobacteria were probably capable of utilizing acetate for their growth. Methanoculleus was likely to be the preferred hydrogenotrophic methanogen for syntrophy with AOB in the chemostat.

An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms.

PubMed

Ng, Filomena; Kittelmann, Sandra; Patchett, Mark L; Attwood, Graeme T; Janssen, Peter H; Rakonjac, Jasna; Gagic, Dragana

2016-09-01

Symbiotic associations are ubiquitous in the microbial world and have a major role in shaping the evolution of both partners. One of the most interesting mutualistic relationships exists between protozoa and methanogenic archaea in the fermentative forestomach (rumen) of ruminant animals. Methanogens reside within and on the surface of protozoa as symbionts, and interspecies hydrogen transfer is speculated to be the main driver for physical associations observed between the two groups. In silico analyses of several rumen methanogen genomes have previously shown that up to 5% of genes encode adhesin-like proteins, which may be central to rumen interspecies attachment. We hypothesized that adhesin-like proteins on methanogen cell surfaces facilitate attachment to protozoal hosts. Using phage display technology, we have identified a protein (Mru_1499) from Methanobrevibacter ruminantium M1 as an adhesin that binds to a broad range of rumen protozoa (including the genera Epidinium and Entodinium). This unique adhesin also binds the cell surface of the bacterium Butyrivibrio proteoclasticus, suggesting a broad adhesion spectrum for this protein. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Spatial Variation in Anaerobic Microbial Communities in Wetland Margin Soils

NASA Astrophysics Data System (ADS)

Rich, H.; Kannenberg, S.; Ludwig, S.; Nelson, L. C.; Spawn, S.; Porterfield, J.; Schade, J. D.

2012-12-01

Climate change is predicted to increase the severity and frequency of precipitation and drought events, which may result in substantial temporal variation in the size of wetlands. Wetlands are the world's largest natural emitter of methane, a greenhouse gas that is 20 times more effective at trapping heat than carbon dioxide. Changes in the dynamics of wetland size may lead to changes in the extent and timing of inundation of soils in ephemeral margins, which is likely to influence microbes that rely on anoxic conditions. The impact on process rates may depend on the structure of the community of microbes present in the soil, however, the link between microbial structure and patterns in process rates in soils is not well understood. Our goal was to use molecular techniques to compare microorganism communities in two wetlands that differ in the extent and duration of inundation of marginal soils to assess how these communities may change with changes in climate, and the potential consequences for methane production. This will allow us to examine how community composition changes with soil conditions such as moisture content, frequency of drought and abundance of available carbon. The main focus of this project was to determine the presence or absence of acetoclastic (AC) and hydrogenotrophic (HT) methanogens. AC methanogens use acetate as their main substrate, while HT methanogens use Hydrogen and Carbon dioxide. The relative proportion of these pathways depends on soil conditions, such as competition with other anaerobic microbes and the amount of labile carbon, and spatial patterns in the presence of each can give insight into the soil conditions of a wetland site. We sampled soil from three different wetland ponds of varying permanence in the St Olaf Natural Lands in Northfield, Minnesota, and extracted DNA from these soil samples with a MoBio PowerSoil DNA Isolation Kit. With PCR and seven different primer sets, we tested the extracted DNA for the presence of four different methanogen taxa as well as denitrifying, iron reducing and sulfate reducing bacteria. We used the percentage of soil replicates that tested positive for a primer as an indicator of the population size of each microorganism at each site. The results of the presence/absence test suggested a relationship between soil moisture and abundance of methanogens. The sites with over 25% moisture content showed a higher percent presence than the soil sites with under 25% moisture content for all taxa except for sulfate reducing bacteria. The impact of soil moisture is likely due to negative effects of oxygen on methanogens. However, the presence of methanogens in drier soils shows that methanogens can still exist in a dormant state in aerobic environments. Methanogens may be ubiquitous but vary in population size and activity depending on soil conditions. With changes in wetland soil moisture in response to changes in precipitation patterns, the populations of methanogens may change, affecting the amount of methane production and ultimately the amount of heat trapped by the atmosphere.

Methanogenic pathways in Alaskan peatlands at different trophic levels with evidence from stable isotope ratios and metagenomics

NASA Astrophysics Data System (ADS)

Zhang, L.; Liu, X.; Langford, L.; Chanton, J.; Roth, S.; Schaefer, J.; Barkay, T.; Hines, M. E.

2017-12-01

To better constrain the large uncertainties in emission fluxes, it is necessary to improve the understanding of methanogenic pathways in northern peatlands with heterogeneous surface vegetation and pH. Surface vegetation is an excellent indicator of porewater pH, which heavily influences the microbial communities in peatlands. Stable C isotope ratios (d13C) have been used as a robust tool to distinguish methanogenic pathways, especially in conjunction with metagenomic analysis of the microbial communities. To link surface vegetation species compositions, pH, microbial communities, and methanogenic pathways, 15 peatland sites were studied in Fairbanks and Anchorage, Alaska in the summer of 2014. These sites were ordinated using multiple factor analysis into 3 clusters based on pH, temp, CH4 and volatile fatty acid production rates, d13C values, and surface vegetation composition. In the ombrotrophic group (pH 3.3), various Sphagna species dominanted, but included shrubs Ledum decumbens and Eriophorum vaginatum. Primary fermentation rates were slow with no CH4 detected. The fen cluster (pH 5.3) was dominated by various Carex species, and CH4 production rates were lower than those in the intermediate cluster but more enriched in 13C (-49‰). Methanosaeta and Methanosarcina were the dominant methanogens. In the intermediate trophic level (pH 4.7), Sphagnum squarrosum and Carex aquatilis were abundant. The same methanogens as in fen cluster also dominated this group, but with higher abundances, which, in part, lead to the higher CH4 production rates in this cluster. The syntrophs Syntrophobacter and Pelobacter were also more abundant than the fen sites, which may explain the d13CH4 values that were the lighetest among the three clusters (-54‰). The high methanogenic potential in the intermediate trophic sites warrant further study since they are not only present in large areas currently, but also represent the transient stage during the evolution from bog to fen in projected climate change scenarios.

Application of stable isotope measurements and microbiological analysis for detecting methanogenic activity in a temperate forest wetland

NASA Astrophysics Data System (ADS)

Itoh, M.; Katsuyama, C.; Kondo, N.; Ohte, N.; Kato, K.

2009-12-01

Generally, forest soils act as a sink for methane (CH4). However, wetlands in riparian zones are recently reported to be “hot spots” of CH4 emissions, especially in forests under a humid climate. To understand how environmental conditions (i.e. hydrological and/or geomorphic condition) control on CH4 production, we investigated both methanogenic pathways (CO2/H2 reduction and acetate fermentation) and metahanogenic microbial communities in a wetland in a temperate forest catchment, central Japan. We used stable carbon isotopic analysis for detecting change in methanogenic pathways, and applied microbiological analysis for understanding the structure of methanogenic community. CH4 emission rates in wetland were strongly dependent on soil temperatures, and were highest in summer and lowest in winter. δ13CO2 increased with CH4 production in every summer, suggesting preferential use of 12CO2 as substrate for CO2/H2 reduction methanogenesis during high CH4 production period. δ13CH4 also increased in summer with δ13CO2. δ13CH4 changed more wildly than δ13CO2 did in summer with normal precipitation when CH4 production was strongly activated under high temperature and high groundwater table condition. This indicates increase in acetoclastic methanogenesis under hot and wet condition, considering that acetclastic methnogens produce heavier CH4 than that from CO2/H2 reducing pathway. Methanogen community composition estimated by cloning and sequence analyses implied that both acetoclastic and CO2/H2 reducing methanogens prevailed in wetland soil sampled in summer. This was consistent with the results of isotope measuremaents. Our results contribute to understand fully how the CH4 production changes with environmental conditions, with considering the activities of both main methanogenic pathway (from CO2 and acetate).

Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China.

PubMed

Huang, Xiao Dan; Tan, Hui Yin; Long, Ruijun; Liang, Juan Boo; Wright, André-Denis G

2012-10-19

Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from "energy-saving" animal (yak) and normal animal (cattle) in order to investigate the link between methanogen structure and low methane production. Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones) and four cattle (205 clones) from the Qinghai-Tibetan Plateau area (QTP). Overall, a total of 414 clones (i.e. sequences) were examined and assigned to 95 operational taxonomic units (OTUs) using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC) were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110) was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle. This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different from that of cattle, this may also help to explain why yak produce less methane than cattle.

Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China

PubMed Central

2012-01-01

Background Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from “energy-saving” animal (yak) and normal animal (cattle) in order to investigate the link between methanogen structure and low methane production. Results Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones) and four cattle (205 clones) from the Qinghai-Tibetan Plateau area (QTP). Overall, a total of 414 clones (i.e. sequences) were examined and assigned to 95 operational taxonomic units (OTUs) using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC) were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110) was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle. Conclusion This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different from that of cattle, this may also help to explain why yak produce less methane than cattle. PMID:23078429

Methanogenic H2 syntrophy among thermophiles: a model of metabolism, adaptation and survival in the subsurface

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Stewart, L. C.; Butterfield, D. A.; Huber, J. A.; Holden, J. F.

2016-12-01

Approximately 1 giga ton (Gt, 1015 g) of CH4 is formed globally per year from H2, CO2 and acetate through methanogenesis, largely by methanogens growing in syntrophic association with anaerobic microbes that hydrolyze and ferment biopolymers. However, our understanding of methanogenesis in hydrothermal regions of the subseafloor and potential syntrophic methanogenesis at thermophilic temperatures (i.e., >50°C) is nascent. In this study, the growth of natural assemblages of thermophilic methanogens from Axial Seamount was primarily limited by H2 availability. Heterotrophs supported thermophilic methanogenesis by H2 syntrophy in microcosm incubations of hydrothermal fluids at 55°C and 80°C supplemented with tryptone only. Based on 16S rRNA gene sequencing, only heterotrophic archaea that produce H2, H2-consuming methanogens, and sulfate reducing archaea were found in 80°C tryptone microcosms from Marker 113 vent. No bacteria were found. In 55°C tryptone microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. In order to model the impact of H2 syntrophy at hyperthemophilic temperatures, a co-culture was established consisting of the H2-producing hyperthermophilic heterotroph Thermococcus paralvinellae and a H2-consuming hyperthermophilic methanogen Methanocaldococcus bathoardescens. When grown alone in a chemostat, the growth rates and steady-state cell concentrations of T. paralvinellae decreased significantly when a high H2 (70 µM) background was present. H2 inhibition was ameliorated by the production of formate, but in silico modeling suggests less energetic yield for the cells. H2 syntrophy relieved H2 inhibition for both the heterotroph and the methanogenic partners. The results demonstrate that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important alternative energy source for thermophilic autotrophs in marine geothermal environments.

Establishment of a Methanogenic Benzene-Degrading Culture and its Implication in Bioremediation

NASA Astrophysics Data System (ADS)

Qiao, W.; Luo, F.; Bawa, N.; Guo, S.; Ye, S.; Edwards, E.

2017-12-01

Benzene is a known human carcinogen and it is a common pollutant in groundwater, mainly resulting from petrochemical industry. Anaerobic degradation of benzene has significant advantages over aerobic processes for in situ bioremediation. In this study, new methanogenic and sulfate-reducing benzene degrading cultures have been enriched. Microbial community composition was characterized with two other previously established benzene-degrading cultures, and their potential use in bioaugmentation is investigated. In this study, a lab microcosm study was conducted anaerobically with contaminated soil and groundwater from a former chemical plant. Benzene degradation was observed in the presence of co-contaminants and electron donor. Through repetitive amendment of benzene, two enrichment cultures have been developed under sulfate and methanogenic conditions. Results from DNA amplicon sequencing and qPCR analysis revealed that an organism similar to previously described benzene-degrading Deltaproteobacterium has been enriched. The microbial community of this culture was compared with other two methanogenic benzene-degrading enrichment cultures that were derived from an oil refinery and a decommissioned gasoline station, and have been maintained for decades. Deltaproteobacterium ORM2-like microbes were dominate in all enrichment cultures, which brought to light benzene-degrading microbes, ORM2 were enriched under different geological conditions distributed around the world. The relative abundance of methanogens was much lower compared to previously established cultures, although substantial amount of methane was produced. The peripheral organisms also vary. To investigate effectiveness of using ORM2-dominant enrichment cultures in bioremediation, microcosm studies were set up using contaminated materials, and a ORM2-dominating methanogenic benzene-degrading culture was used for bioaugmentation. Results revealed that benzene degradation was speeded up under methanogenic or sulfate-reducing condition, and the growth of ORM2 was observed via qPCR analysis. The treatability test is on-going to establish more reliable correspondence between the benzene degraders and natural attenuation potential, to provide more insights into contaminated site management.

The Effects of Perchlorate on Methane Production of Methanogens

NASA Astrophysics Data System (ADS)

Goodhart, T.; Kral, T. A.

2010-04-01

In May 2008, the Phoenix space craft analyzed the martian soil, detecting perchlorate, which is a highly oxidizing compound and potentially harmful to organic matter. This presentation discusses the effects that perchlorate has on methanogen growth.

Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animalsr

PubMed Central

St-Pierre, Benoit; Cersosimo, Laura M.; Ishaq, Suzanne L.; Wright, André-Denis G.

2015-01-01

In herbivores, enteric methane is a by-product from the digestion of plant biomass by mutualistic gastrointestinal tract (GIT) microbial communities. Methane is a potent greenhouse gas that is not assimilated by the host and is released into the environment where it contributes to climate change. Since enteric methane is exclusively produced by methanogenic archaea, the investigation of mutualistic methanogen communities in the GIT of herbivores has been the subject of ongoing research by a number of research groups. In an effort to uncover trends that would facilitate the development of efficient methane mitigation strategies for livestock species, we have in this review summarized and compared currently available results from published studies on this subject. We also offer our perspectives on the importance of pursuing current research efforts on the sequencing of gut methanogen genomes, as well as investigating their cellular physiology and interactions with other GIT microorganisms. PMID:26284054

Factors influencing the degradation of garbage in methanogenic bioreactors and impacts on biogas formation.

PubMed

Morita, Masahiko; Sasaki, Kengo

2012-05-01

Anaerobic digestion of garbage is attracting much attention because of its application in waste volume reduction and the recovery of biogas for use as an energy source. In this review, various factors influencing the degradation of garbage and the production of biogas are discussed. The surface hydrophobicity and porosity of supporting materials are important factors in retaining microorganisms such as aceticlastic methanogens and in attaining a higher degradation of garbage and a higher production of biogas. Ammonia concentration, changes in environmental parameters such as temperature and pH, and adaptation of microbial community to ammonia have been related to ammonia inhibition. The effects of drawing electrons from the methanogenic community and donating electrons into the methanogenic community on methane production have been shown in microbial fuel cells and bioelectrochemical reactors. The influences of trace elements, phase separation, and co-digestion are also summarized in this review.

Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China.

PubMed

Dong, Minghua; Wu, Yan; Li, Qiumin; Tian, Guangliang; Yang, Bin; Li, Yingjuan; Zhang, Lijuan; Wang, Yongxia; Xiao, Wei; Yin, Fang; Zhao, Xingling; Zhang, Wudi; Cui, Xiaolong

2015-05-01

Understanding of the microbial community structures of the biogas digesters in different climatic regions can help improve the methane production in the fermentation process. The methanogenic archaeal diversity in four rural biogas digesters (BNA, JSA, LJA, and XGA) was investigated by a culture-independent rRNA approach in different climatic regions in Yunnan. Community structure composed of 711 clones in the all libraries. A total of 33 operational taxonomic units (OTUs) were detected, and major groups of methanogens were the orders Methanosarcinales and Methanomicrobiales. 63.2 % of all archaeal OTUs belong to the order Methanosarcinales which mostly contain acetotrophic methanogens. Methanomicrobiales (19.5 % in all OTUs) were detected in considerable number. Additionally, there were minor rates of uncultured archaea. The principal component analysis indicated that the genus Methanosaeta was mainly affected by the fermentation temperatures.

New approach to control the methanogenic reactor of a two-phase anaerobic digestion system.

PubMed

von Sachs, Jürgen; Meyer, Ulrich; Rys, Paul; Feitkenhauer, Heiko

2003-03-01

A new control strategy for the methanogenic reactor of a two-phase anaerobic digestion system has been developed and successfully tested on the laboratory scale. The control strategy serves the purpose to detect inhibitory effects and to achieve good conversion. The concept is based on the idea that volatile fatty acids (VFA) can be measured in the influent of the methanogenic reactor by means of titration. Thus, information on the output (methane production) and input of the methanogenic reactor is available, and a (carbon) mass balance can be obtained. The control algorithm comprises a proportional/integral structure with the ratio of (a) the methane production rate measured online and (b) a maximum methane production rate expected (derived from the stoichiometry) as a control variable. The manipulated variable is the volumetric feed rate. Results are shown for an experiment with VFA (feed) concentration ramps and for experiments with sodium chloride as inhibitor.

A mathematical model for the interactive behavior of sulfate-reducing bacteria and methanogens during anaerobic digestion.

PubMed

Ahammad, S Ziauddin; Gomes, James; Sreekrishnan, T R

2011-09-01

Anaerobic degradation of waste involves different classes of microorganisms, and there are different types of interactions among them for substrates, terminal electron acceptors, and so on. A mathematical model is developed based on the mass balance of different substrates, products, and microbes present in the system to study the interaction between methanogens and sulfate-reducing bacteria (SRB). The performance of major microbial consortia present in the system, such as propionate-utilizing acetogens, butyrate-utilizing acetogens, acetoclastic methanogens, hydrogen-utilizing methanogens, and SRB were considered and analyzed in the model. Different substrates consumed and products formed during the process also were considered in the model. The experimental observations and model predictions showed very good prediction capabilities of the model. Model prediction was validated statistically. It was observed that the model-predicted values matched the experimental data very closely, with an average error of 3.9%.

Greenhouse gas emissions from rice microcosms amended with a plant microbial fuel cell.

PubMed

Arends, Jan B A; Speeckaert, Jonas; Blondeel, Evelyne; De Vrieze, Jo; Boeckx, Pascal; Verstraete, Willy; Rabaey, Korneel; Boon, Nico

2014-04-01

Methane (CH4) release from wetlands is an important source of greenhouse gas emissions. Gas exchange occurs mainly through the aerenchyma of plants, and production of greenhouse gases is heavily dependent on rhizosphere biogeochemical conditions (i.e. substrate availability and redox potential). It is hypothesized that by introducing a biocatalyzed anode electrode in the rhizosphere of wetland plants, a competition for carbon and electrons can be invoked between electrical current-generating bacteria and methanogenic Archaea. The anode electrode is part of a bioelectrochemical system (BES) capable of harvesting electrical current from microbial metabolism. In this work, the anode of a BES was introduced in the rhizosphere of rice plants (Oryza sativa), and the impact on methane emissions was monitored. Microbial current generation was able to outcompete methanogenic processes when the bulk matrix contained low concentrations of organic carbon, provided that the electrical circuit with the effective electroactive microorganisms was in place. When interrupting the electrical circuit or supplying an excess of organic carbon, methanogenic metabolism was able to outcompete current generating metabolism. The qPCR results showed hydrogenotrophic methanogens were the most abundant methanogenic group present, while mixotrophic or acetoclastic methanogens were hardly detected in the bulk rhizosphere or on the electrodes. Competition for electron donor and acceptor were likely the main drivers to lower methane emissions. Overall, electrical current generation with BESs is an interesting option to control CH4 emissions from wetlands but needs to be applied in combination with other mitigation strategies to be successful and feasible in practice.

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil.

PubMed

Bao, Qiongli; Huang, Yizong; Wang, Fenghua; Nie, Sanan; Nicol, Graeme W; Yao, Huaiying; Ding, Longjun

2016-07-01

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste.

PubMed

Angenent, Largus T; Sung, Shihwu; Raskin, Lutgarde

2002-11-01

Changes in methanogenic population levels were followed during startup of a full-scale, farm-based anaerobic sequencing batch reactor (ASBR) and these changes were linked to operational and performance data. The ASBR was inoculated with anaerobic digester sludge from a municipal wastewater treatment facility. During an acclimation period of approximately 3 months, the ASBR content was diluted to maintain a total ammonia-N level of approximately 2000mg l(-1). After this acclimation period, the volatile solids loading rate was increased to its design value of 1.7g l(-1) day(-1) with a 15-day hydraulic retention time, which increased the total ammonia-N level in the ASBR to approximately 3,600 mg l(-1). The 16S ribosomal RNA (rRNA) levels of the acetate-utilizing methanogens of the genus Methanosarcina decreased from 3.8% to 1.2% (expressed as a percentage of the total 16S rRNA levels) during this period, while the 16S rRNA levels of Methanosaeta concilii remained low (below 2.2%). Methane production and reactor performance were not affected as the 16S rRNA levels of the hydrogen-utilizing methanogens of the order Methanomicrobiales increased from 2.3% to 7.0%. Hence, it is likely that during operation with high ammonia levels, the major route of methane production is through a syntrophic relationship between acetate-oxidizing bacteria and hydrogen-utilizing methanogens. Anaerobic digestion at total ammonia-N levels exceeding 3500mg l(-1) was sustainable apparently due to the acclimation of hydrogen-utilizing methanogens to high ammonia levels.

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines

PubMed Central

Liang, Renxing; Grizzle, Robert S.; Duncan, Kathleen E.; McInerney, Michael J.; Suflita, Joseph M.

2014-01-01

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm2, while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens. PMID:24639674

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines.

PubMed

Liang, Renxing; Grizzle, Robert S; Duncan, Kathleen E; McInerney, Michael J; Suflita, Joseph M

2014-01-01

Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics.

PubMed

Ju, Feng; Wang, Yubo; Zhang, Tong

2018-01-01

Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured ε - Proteobacterium G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a Sulfurovum -like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a Chloroflexi T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a Cryptanaerobacter bacterium. Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.

Microbial Methane Production Associated with Carbon Steel Corrosion in a Nigerian Oil Field

PubMed Central

Mand, Jaspreet; Park, Hyung S.; Okoro, Chuma; Lomans, Bart P.; Smith, Seun; Chiejina, Leo; Voordouw, Gerrit

2016-01-01

Microbially influenced corrosion (MIC) in oil field pipeline systems can be attributed to many different types of hydrogenotrophic microorganisms including sulfate reducers, methanogens and acetogens. Samples from a low temperature oil reservoir in Nigeria were analyzed using DNA pyrotag sequencing. The microbial community compositions of these samples revealed an abundance of anaerobic methanogenic archaea. Activity of methanogens was demonstrated by incubating samples anaerobically in a basal salts medium, in the presence of carbon steel and carbon dioxide. Methane formation was measured in all enrichments and correlated with metal weight loss. Methanogens were prominently represented in pipeline solids samples, scraped from the inside of a pipeline, comprising over 85% of all pyrosequencing reads. Methane production was only witnessed when carbon steel beads were added to these pipeline solids samples, indicating that no methane was formed as a result of degradation of the oil organics present in these samples. These results were compared to those obtained for samples taken from a low temperature oil field in Canada, which had been incubated with oil, either in the presence or in the absence of carbon steel. Again, methanogens present in these samples catalyzed methane production only when carbon steel was present. Moreover, acetate production was also found in these enrichments only in the presence of carbon steel. From these studies it appears that carbon steel, not oil organics, was the predominant electron donor for acetate production and methane formation in these low temperature oil fields, indicating that the methanogens and acetogens found may contribute significantly to MIC. PMID:26793176

Cysteine-Accelerated Methanogenic Propionate Degradation in Paddy Soil Enrichment.

PubMed

Zhuang, Li; Ma, Jinlian; Tang, Jia; Tang, Ziyang; Zhou, Shungui

2017-05-01

Propionate degradation is a critical step during the conversion of complex organic matter under methanogenic conditions, and it requires a syntrophic cooperation between propionate-oxidizing bacteria and methanogenic archaea. Increasing evidences suggest that interspecies electron transfer for syntrophic metabolism is not limited to the reducing equivalents of hydrogen and formate. This study tested the ability of an electron shuttle to mediate interspecies electron transfer in syntrophic methanogenesis. We found that cysteine supplementation (100, 400, and 800 μM) accelerated CH 4 production from propionate in paddy soil enrichments. Of the concentrations tested, 100 μM cysteine was the most effective at enhancing propionate degradation to CH 4 , and the rates of CH 4 production and propionate degradation were increased by 109 and 79%, respectively, compared with the cysteine-free control incubations. We eliminated the possibility that the stimulatory effect of cysteine on methanogenesis was attributable to the function of cysteine as a methanogenic substrate in the presence of propionate. The potential catalytic effect involved cysteine serving as an electron carrier to mediate interspecies electron transfer in syntrophic propionate oxidization. The redox potential of cystine/cysteine, which is dependent on the concentration, might be more suitable to facilitate interspecies electron transfer between syntrophic partners at a concentration of 100 μM. Pelotomaculum, obligately syntrophic, propionate-oxidizing bacteria, and hydrogenotrophic methanogens of the family Methanobacteriaceae are predominant in cysteine-mediated methanogenic propionate degradation. The stimulatory effect of cysteine on syntrophic methanogenesis offers remarkable potential for improving the performance of anaerobic digestion and conceptually broaden strategies for interspecies electron transfer in syntrophic metabolism.

Progression of natural attenuation processes at a crude oil spill site: II. Controls on spatial distribution of microbial populations

NASA Astrophysics Data System (ADS)

Bekins, Barbara A.; Cozzarelli, Isabelle M.; Godsy, E. Michael; Warren, Ean; Essaid, Hedeff I.; Tuccillo, Mary Ellen

2001-12-01

A multidisciplinary study of a crude-oil contaminated aquifer shows that the distribution of microbial physiologic types is strongly controlled by the aquifer properties and crude oil location. The microbial populations of four physiologic types were analyzed together with permeability, pore-water chemistry, nonaqueous oil content, and extractable sediment iron. Microbial data from three vertical profiles through the anaerobic portion of the contaminated aquifer clearly show areas that have progressed from iron-reduction to methanogenesis. These locations contain lower numbers of iron reducers, and increased numbers of fermenters with detectable methanogens. Methanogenic conditions exist both in the area contaminated by nonaqueous oil and also below the oil where high hydrocarbon concentrations correspond to local increases in aquifer permeability. The results indicate that high contaminant flux either from local dissolution or by advective transport plays a key role in determining which areas first become methanogenic. Other factors besides flux that are important include the sediment Fe(II) content and proximity to the water table. In locations near a seasonally oscillating water table, methanogenic conditions exist only below the lowest typical water table elevation. During 20 years since the oil spill occurred, a laterally continuous methanogenic zone has developed along a narrow horizon extending from the source area to 50-60 m downgradient. A companion paper [J. Contam. Hydrol. 53, 369-386] documents how the growth of the methanogenic zone results in expansion of the aquifer volume contaminated with the highest concentrations of benzene, toluene, ethylbenzene, and xylenes.

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples.

PubMed

Tan, Boonfei; Fowler, S Jane; Abu Laban, Nidal; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

2015-09-01

Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.

Rumen protozoa and methanogenesis: not a simple cause-effect relationship.

PubMed

Morgavi, Diego P; Martin, Cécile; Jouany, Jean-Pierre; Ranilla, Maria José

2012-02-01

Understanding the interactions between hydrogen producers and consumers in the rumen ecosystem is important for ruminant production and methane mitigation. The present study explored the relationships between rumen protozoa, methanogens and fermentation characteristics. A total of six donor sheep harbouring (F, faunated) or not (D, defaunated) protozoa in their rumens (D animals were kept without protozoa for a period of a few months (D - ) or for more than 2 years (D+)) were used in in vitro and in vivo experiments. In vitro the absence of protozoa decreased NH3 and butyrate production and had no effect on methane. In contrast, the liquid-associated bacterial and methanogens fraction of D+ inocula produced more methane than D -  and F inoculum (P < 0·05). In vivo fermentation parameters of donor animals showed the same trend on NH3 and butyrate and showed that D+ animals were high methane emitters, while D -  were the lowest ( - 35 %). The concentration of dissolved dihydrogen measured after feeding followed the opposite trend. Methane emissions did not correlate with the relative abundance of methanogens in the rumen measured by quantitative PCR, but there was a trend for higher methanogens concentration in the solid-associated population of D+ animals compared with D -  animals. In contrast, PCR-denaturing gradient gel electrophoresis profiles of methanogens' methyl coenzyme-M reductase A gene showed a clear clustering in liquid-associated fractions for all three groups of donors but fewer differences in solid-associated fractions. These results show that the absence of protozoa may affect differently the methanogen community and methane emissions in wethers.

Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows.

PubMed

Hook, Sarah E; Steele, Michael A; Northwood, Korinne S; Wright, André-Denis G; McBride, Brian W

2011-07-01

Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P=0.049) and rumen solids (P=0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P=0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.

Methanogenesis limitations in degraded peatlands after their hydrological restoration

NASA Astrophysics Data System (ADS)

Urbanová, Zuzana

2017-04-01

Peatlands are ecosystems that can have a high degree of carbon sequestration due to CO2 fixation and low decomposition rates, but on the other hand, they are a source of CH4. Past drainage or mining can disturb these natural functions with rewetting being the main method used to bring back their original ecosystem properties. Methanogenic community composition and its activity seems to be very sensitive to environmental changes and therefore its limited activity after restoration can reflect the not fully restored functioning of the microbial community and its processes in the rewetted peatlands. To find the cause for this methanogenesis limitation we determined the abundance and composition of the methanogenic community and methane potential production in pristine, long-term drained and rewetted bogs and spruce swamp forests (SSF) in the Šumava Mountains (Czech Republic), using high-throughput barcoded sequencing, qPCR and anaerobic incubation of peat samples in relation to peat biochemical properties. Long-term drainage led to a strongly reduced diversity, abundance and activity of the methanogenic community in both peatland types. In restored sites, methanogenic abundance and community composition reached a pristine like state, however their activity measured as CH4 production remained as low as in drained sites. Substrate limitation was expected; therefore we further added different substrates during anaerobic incubation of the peat samples. In addition to glucose and ethanol, we added natural complex substrates from peatland plants (sedges, Sphagnum) to simulate the effect of the spreading of peatland species and their litter on methanogenic activity. The results unambiguously confirmed the limitation of methanogens by substrate availability due to the previous long-term drainage and strongly decomposed peat. The addition of natural substrates led to an increase in CH4 production, which was close to values in pristine sites. The limited CH4 production reflected a not fully restored vegetation structure with sufficient litter production. Thus, the re-establishment of peatland vegetation structure should lead to regeneration of methanogenic activity and microbial processes in restored peatlands. Moreover, the results showed that there is no risk of increased CH4 emissions in the case of nutrient poor bogs and SSF after re-wetting. For management, the methanogenic community composition, abundance and activity could be used as indicators of restoration success.

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...

REDUCTIVE DEHALOGENATION OF A NITROGEN HETEROCYCLIC HERBICIDE IN ANOXIC AQUIFER SLURRIES

EPA Science Inventory

We studied the metabolic fate of bromacil in anaerobic aquifer slurries held under denitrifying, sulfate-reducing, or methanogenic conditions. Liquid chromatograhy-mass spectrometry of the slurries confirmed that bromacil was debrominated under methanogenic conditions but was not...

Biotreatment of Gaseous-Phase Volatile Organic Compounds

DTIC Science & Technology

1990-07-31

determined benzene to be degradable by methanogenic cultures acclimated to lignin-derived aromatic acids under strict anaerobic conditions. 5.3 CARBON...1986. Toluene and benzene transformation by ferulate - acclimated methanogenic consortia. Abstracts of the 86th Annual Meeting of the American Society

Response of Syntrophic Propionate Degradation to pH Decrease and Microbial Community Shifts in an UASB Reactor.

PubMed

Zhang, Liguo; Ban, Qiaoying; Li, Jianzheng; Jha, Ajay Kumar

2016-08-28

The effect of pH on propionate degradation in an upflow anaerobic sludge blanket (UASB) reactor containing propionate as a sole carbon source was studied. Under influent propionate of 2,000 mg/l and 35ºC, propionate removal at pH 7.5-6.8 was above 93.6%. Propionate conversion was significantly inhibited with stepwise pH decrease from pH 6.8 to 6.5, 6.0, 5.5, 5.0, 4.5, and then to 4.0. After long-term operation, the propionate removal at pH 6.5-4.5 maintained an efficiency of 88.5%-70.1%, whereas propionate was hardly decomposed at pH 4.0. Microbial composition analysis showed that propionate-oxidizing bacteria from the genera Pelotomaculum and Smithella likely existed in this system. They were significantly reduced at pH ≤5.5. The methanogens in this UASB reactor belonged to four genera: Methanobacterium, Methanospirillum, Methanofollis, and Methanosaeta. Most detectable hydrogenotrophic methanogens were able to grow at low pH conditions (pH 6.0-4.0), but the acetotrophic methanogens were reduced as pH decreased. These results indicated that propionate-oxidizing bacteria and acetotrophic methanogens were more sensitive to low pH (5.5-4.0) than hydrogenotrophic methanogens.

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

PubMed Central

2012-01-01

Background Methanogens that populate the gastrointestinal tract of livestock ruminants contribute significantly to methane emissions from the agriculture industry. There is a great need to analyze archaeal microbiomes from a broad range of host species in order to establish causal relationships between the structure of methanogen communities and their potential for methane emission. In this report, we present an investigation of methanogenic archaeal populations in the foregut of alpacas. Results We constructed individual 16S rRNA gene clone libraries from five sampled animals and recovered a total of 947 sequences which were assigned to 51 species-level OTUs. Individuals were found to each have between 21 and 27 OTUs, of which two to six OTUs were unique. As reported in other host species, Methanobrevibacter was the dominant genus in the alpaca, representing 88.3% of clones. However, the alpaca archaeal microbiome was different from other reported host species, as clones showing species-level identity to Methanobrevibacter millerae were the most abundant. Conclusion From our analysis, we propose a model to describe the population structure of Methanobrevibacter-related methanogens in the alpaca and in previously reported host species, which may contribute in unraveling the complexity of symbiotic archaeal communities in herbivores. PMID:22221383

Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours

PubMed Central

Guzman, Cesar E.; Bereza-Malcolm, Lara T.; De Groef, Bert; Franks, Ashley E.

2015-01-01

The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0–20 mins after birth), day 1 (24 ± 1 h after birth), day 2 (48 ± 1 h after birth), and day 3 (72 ± 1 h after birth). Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose. PMID:26186002

Effect of UVC Radiation on Hydrated and Desiccated Cultures of Slightly Halophilic and Non-Halophilic Methanogenic Archaea: Implications for Life on Mars.

PubMed

Sinha, Navita; Kral, Timothy A

2018-05-12

Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation. Hydrated M. maripaludis survived 24 h of UVC exposure, while in a desiccated condition they endured for 16 h. M. formicicum also survived UVC radiation for 24 h in a liquid state; however, in a desiccated condition, the survivability of M. formicicum was only 12 h. Some of the components of the growth media could have served as shielding agents that protected cells from damage caused by exposure to ultraviolet radiation. Overall, these results suggest that limited exposure (12⁻24 h) to UVC radiation on the surface of Mars would not necessarily be a limiting factor for the survivability of M. maripaludis and M. formicicum .

A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii.

PubMed

Steinhaus, Benjamin; Garcia, Marcelo L; Shen, Amy Q; Angenent, Largus T

2007-03-01

Conventional studies of the optimum growth conditions for methanogens (methane-producing, obligate anaerobic archaea) are typically conducted with serum bottles or bioreactors. The use of microfluidics to culture methanogens allows direct microscopic observations of the time-integrated response of growth. Here, we developed a microbioreactor (microBR) with approximately 1-microl microchannels to study some optimum growth conditions for the methanogen Methanosaeta concilii. The microBR is contained in an anaerobic chamber specifically designed to place it directly onto an inverted light microscope stage while maintaining a N2-CO2 environment. The methanogen was cultured for months inside microchannels of different widths. Channel width was manipulated to create various fluid velocities, allowing the direct study of the behavior and responses of M. concilii to various shear stresses and revealing an optimum shear level of approximately 20 to 35 microPa. Gradients in a single microchannel were then used to find an optimum pH level of 7.6 and an optimum total NH4-N concentration of less than 1,100 mg/liter (<47 mg/liter as free NH3-N) for M. concilii under conditions of the previously determined ideal shear stress and pH and at a temperature of 35 degrees C.

Biogeochemical metabolic modeling of methanogenesis by Methanosarcina barkeri

NASA Astrophysics Data System (ADS)

Jensvold, Z. D.; Jin, Q.

2015-12-01

Methanogenesis, the biological process of methane production, is the final step of natural organic matter degradation. In studying natural methanogenesis, important questions include how fast methanogenesis proceeds and how methanogens adapt to the environment. To address these questions, we propose a new approach - biogeochemical reaction modeling - by simulating the metabolic networks of methanogens. Biogeochemical reaction modeling combines geochemical reaction modeling and genome-scale metabolic modeling. Geochemical reaction modeling focuses on the speciation of electron donors and acceptors in the environment, and therefore the energy available to methanogens. Genome-scale metabolic modeling predicts microbial rates and metabolic strategies. Specifically, this approach describes methanogenesis using an enzyme network model, and computes enzyme rates by accounting for both the kinetics and thermodynamics. The network model is simulated numerically to predict enzyme abundances and rates of methanogen metabolism. We applied this new approach to Methanosarcina barkeri strain fusaro, a model methanogen that makes methane by reducing carbon dioxide and oxidizing dihydrogen. The simulation results match well with the results of previous laboratory experiments, including the magnitude of proton motive force and the kinetic parameters of Methanosarcina barkeri. The results also predict that in natural environments, the configuration of methanogenesis network, including the concentrations of enzymes and metabolites, differs significantly from that under laboratory settings.

Activation of CO2-reducing methanogens in oil reservoir after addition of nutrient.

PubMed

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge Maurice; You, Jing; Yang, Hua-Zhen; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-12-01

Nutrient addition as part of microbial enhanced oil recovery (MEOR) operations have important implications for more energy recovery from oil reservoirs, but very little is known about the in situ response of microorganisms after intervention. An analysis of two genes as biomarkers, mcrA encoding the key enzyme in methanogenesis and fthfs encoding the key enzyme in acetogenesis, was conducted during nutrient addition in oil reservoir. Clone library data showed that dominant mcrA sequences changed from acetoclastic (Methanosaetaceae) to CO 2 -reducing methanogens (Methanomicrobiales and Methanobacteriales), and the authentic acetogens affiliated to Firmicutes decreased after the intervention. Principal coordinates analysis (PCoA) and Jackknife environment clusters revealed evidence on the shift of the microbial community structure among the samples. Quantitative analysis of methanogens via qPCR showed that Methanobacteriales and Methanomicrobiales increased after nutrient addition, while acetoclastic methanogens (Methanosaetaceae) changed slightly. Nutrient treatment activated native CO 2 -reducing methanogens in oil reservoir. The high frequency of Methanobacteriales and Methanomicrobiales (CO 2 -reducers) after nutrient addition in this petroleum system suggested that CO 2 -reducing methanogenesis was involved in methane production. The nutrient addition could promote the methane production. The results will likely improve strategies of utilizing microorganisms in subsurface environments. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.

PubMed

Nobu, Masaru K; Narihiro, Takashi; Rinke, Christian; Kamagata, Yoichi; Tringe, Susannah G; Woyke, Tanja; Liu, Wen-Tso

2015-08-01

Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.

Progressive Degradation of Crude Oil n-Alkanes Coupled to Methane Production under Mesophilic and Thermophilic Conditions

PubMed Central

Cheng, Lei; Shi, Shengbao; Li, Qiang; Chen, Jianfa; Zhang, Hui; Lu, Yahai

2014-01-01

Although methanogenic degradation of hydrocarbons has become a well-known process, little is known about which crude oil tend to be degraded at different temperatures and how the microbial community is responded. In this study, we assessed the methanogenic crude oil degradation capacity of oily sludge microbes enriched from the Shengli oilfield under mesophilic and thermophilic conditions. The microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes combined with cloning and sequencing. Enrichment incubation demonstrated the microbial oxidation of crude oil coupled to methane production at 35 and 55°C, which generated 3.7±0.3 and 2.8±0.3 mmol of methane per gram oil, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that crude oil n-alkanes were obviously degraded, and high molecular weight n-alkanes were preferentially removed over relatively shorter-chain n-alkanes. Phylogenetic analysis revealed the concurrence of acetoclastic Methanosaeta and hydrogenotrophic methanogens but different methanogenic community structures under the two temperature conditions. Candidate divisions of JS1 and WWE 1, Proteobacteria (mainly consisting of Syntrophaceae, Desulfobacteraceae and Syntrophorhabdus) and Firmicutes (mainly consisting of Desulfotomaculum) were supposed to be involved with n-alkane degradation in the mesophilic conditions. By contrast, the different bacterial phylotypes affiliated with Caldisericales, “Shengli Cluster” and Synergistetes dominated the thermophilic consortium, which was most likely to be associated with thermophilic crude oil degradation. This study revealed that the oily sludge in Shengli oilfield harbors diverse uncultured microbes with great potential in methanogenic crude oil degradation over a wide temperature range, which extend our previous understanding of methanogenic degradation of crude oil alkanes. PMID:25409013

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

PubMed Central

Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng

2014-01-01

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield. PMID:25381241

Trace Elements Affect Methanogenic Activity and Diversity in Enrichments from Subsurface Coal Bed Produced Water

PubMed Central

Ünal, Burcu; Perry, Verlin Ryan; Sheth, Mili; Gomez-Alvarez, Vicente; Chin, Kuk-Jeong; Nüsslein, Klaus

2012-01-01

Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community. PMID:22590465

Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils.

PubMed

Allan, J; Ronholm, J; Mykytczuk, N C S; Greer, C W; Onstott, T C; Whyte, L G

2014-04-01

Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. In situ CO2 and CH4 flux, measured in 2010 and 2011 from ice-wedge polygons, indicate that these soil formations are a net source of CO2 emissions, but a CH4 sink. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Gas flux was measured regularly and indicated an increase in CH4 flux after extended incubation. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw. This study provides evidence that although High Arctic ice-wedge polygons are currently a sink for CH4, higher arctic temperatures and anaerobic conditions, a possible result of climate change, could result in this soil becoming a source for CH4 gas flux. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Role of dietary sulphate in the regulation of methanogenesis in the human large intestine.

PubMed Central

Christl, S U; Gibson, G R; Cummings, J H

1992-01-01

Hydrogen produced during colonic fermentation may be excreted, or removed by H2 consuming bacteria such as methanogenic and sulphate reducing bacteria. In vitro, sulphate reducing bacteria compete with methanogenic bacteria for hydrogen when sulphate is present. In this study the hypothesis that sulphate in the diet could alter CH4 production in vivo has been tested. Six methane excreting volunteers were fed a low sulphate diet (1.6 mmol/d) for 34 days with the addition of 15 mmol sodium sulphate from days 11-20. Breath methane was measured and viable counts and metabolic activities of methanogenic bacteria and sulphate reducing bacteria determined in faeces. Whole gut transit time and daily stool weight were also measured. When sulphate was added to the diet, breath methane excretion decreased in three of the subjects while faecal sulphate reduction rates rose from 7.5 (0.5) to 20.3 (4.3) nmol SO4 reduced/h/g faeces. Sulphate reducing bacteria, which were not detected during the control diet, were found and viable counts of methanogenic bacteria fell from 10(7)-10(9)/g faeces to 10(6)/g. Methanogenic counts and breath CH4 recovered after sulphate addition was stopped. No change was found in the other three subjects. Faecal weights and transit times were not different between study periods. It is concluded that methanogenesis is regulated by dietary sulphate if sulphate reducing bacteria are present. Dietary sulphate may allow growth of sulphate reducing bacteria which inhibit the growth of methanogenic bacteria. This may explain the absence of CH4 in the breath of many people in western populations. PMID:1427377

Anaerobic Biodegradation of Soybean Biodiesel and Diesel Blends under Methanogenic Conditions

EPA Science Inventory

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic...

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

PubMed Central

Gründger, Friederike; Jiménez, Núria; Thielemann, Thomas; Straaten, Nontje; Lüders, Tillmann; Richnow, Hans-Hermann; Krüger, Martin

2015-01-01

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport. PMID:25852663

Studying gene regulation in methanogenic archaea.

PubMed

Rother, Michael; Sattler, Christian; Stock, Tilmann

2011-01-01

Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well. Copyright © 2011 Elsevier Inc. All rights reserved.

Impact of temperature, microwave radiation and organic loading rate on methanogenic community and biogas production during fermentation of dairy wastewater.

PubMed

Zielińska, Magdalena; Cydzik-Kwiatkowska, Agnieszka; Zieliński, Marcin; Dębowski, Marcin

2013-02-01

This study analyzed dairy wastewater fermentation in convection- and microwave-heated hybrid reactors at loadings of 1 and 2 kg COD/(m3 d) and temperatures of 35 and 55 °C. The biomass was investigated at a molecular level to determine the links between the operational parameters of anaerobic digestion and methanogenic Archaea structure. The highest production of biogas with methane content of ca. 67% was noted in the mesophilic microwave-heated reactors. The production of methane-rich biogas and the overall diversity of Archaea was determined by Methanosarcinaceae presence. The temperature and the application of microwaves were the main factors explaining the variations in the methanogen community. At 35 °C, the microwave heating stimulated the growth of highly diverse methanogen assemblages, promoting Methanosarcina barkeri presence and excluding Methanosarcina harudinacea from the biomass. A temperature increase to 55 °C lowered Methanosarcinaceae abundance and induced a replacement of Methanoculleus palmolei by Methanosarcina thermophila. Copyright © 2012 Elsevier Ltd. All rights reserved.

Molecular diversity of methanogens in fecal samples from Bactrian camels (Camelus bactrianus) at two zoos.

PubMed

Turnbull, Kathryn L; Smith, Rachel P; St-Pierre, Benoit; Wright, André-Denis G

2012-08-01

Animals are dependent on mutualistic microbial communities that reside in their gastrointestinal track for essential physiological functions such as nutrition and pathogen resistance. The composition of microbial communities in an animal is influenced by various factors, including species, diet and geographical location. In this preliminary study, the population structure of fecal methanogens in Bactrian camels (Camelus bactrianus) from two zoos was studied using separate 16S rRNA gene libraries for each zoo. While methanogen sequences belonging to the genus Methanobrevibacter were dominant in both libraries, they showed significant differences in diversity (p=0.05) and structure (p<0.0001). Population structure analysis revealed that only two operational taxonomic units (OTUs) were shared between libraries, while two OTUs were unique to the Southwick Zoo library and seven OTUs were unique to the Potter Park Zoo library. These preliminary results highlight how methanogen population structures can vary greatly between animals of the same species maintained in captivity at different locations. Copyright © 2011 Elsevier Ltd. All rights reserved.

Biological treatment of TMAH (tetra-methyl ammonium hydroxide) in a full-scale TFT-LCD wastewater treatment plant.

PubMed

Hu, Tai-Ho; Whang, Liang-Ming; Liu, Pao-Wen Grace; Hung, Yu-Ching; Chen, Hung-Wei; Lin, Li-Bin; Chen, Chia-Fu; Chen, Sheng-Kun; Hsu, Shu Fu; Shen, Wason; Fu, Ryan; Hsu, Romel

2012-06-01

This study evaluated biological treatment of TMAH in a full-scale methanogenic up-flow anaerobic sludge blanket (UASB) followed by an aerobic bioreactor. In general, the UASB was able to perform a satisfactory TMAH degradation efficiency, but the effluent COD of the aerobic bioreactor seemed to increase with an increased TMAH in the influent wastewater. The batch test results confirmed that the UASB sludge under methanogenic conditions would be favored over the aerobic ones for TMAH treatment due to its superb ability of handling high strength of TMAH-containing wastewaters. Based on batch experiments, inhibitory chemicals present in TFT-LCD wastewater like surfactants and sulfate should be avoided to secure a stable methanogenic TMAH degradation. Finally, molecular monitoring of Methanomethylovorans hollandica and Methanosarcina mazei in the full-scale plant, the dominant methanogens in the UASB responsible for TMAH degradation, may be beneficial for a stable TMAH treatment performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

An explanation of the methanogenic pathway for methane production in anaerobic digestion of nitrogen-rich materials under mesophilic and thermophilic conditions.

PubMed

Yin, Dong-Min; Westerholm, Maria; Qiao, Wei; Bi, Shao-Jie; Wandera, Simon M; Fan, Run; Jiang, Meng-Meng; Dong, Ren-Jie

2018-05-18

The impact of temperature on the anaerobic digestion of chicken manure was investigated by studying the process performance and pathway for continuously-fed digesters under mesophilic and thermophilic conditions. The mesophilic digester obtained a 15% higher methane yield compared with the thermophilic digester. Mesophilic and thermophilic digester had free ammonia of 31 and 145 mg/L, respectively. The stable carbon isotope analysis indicated that 41% and 50% of acetate was converted to methane through the syntrophic acetate oxidation and hydrogenotrophic methanogenesis (SAO-HM) pathway under mesophilic and thermophilic conditions, respectively. The genus Pseudomonas represented 10% and 16% under mesophilic and thermophilic conditions, respectively. A high abundance of the methanogens genus Methanoculleus (94% of total methanogens) in mesophilic and the genus Methanothermobacter (96%) in thermophilic digesters indicated they were the main hydrogenotrophic partners in SAO. The present study therefore illustrated that methanogenic pathway shifting, induced by free ammonia, closely correlated to the process performance. Copyright © 2018. Published by Elsevier Ltd.

Methanogenesis control by employing various environmental stress conditions in two-chambered microbial fuel cells.

PubMed

Chae, Kyu-Jung; Choi, Mi-Jin; Kim, Kyoung-Yeol; Ajayi, F F; Park, Woosin; Kim, Chang-Won; Kim, In S

2010-07-01

This study examines methanogen activity in microbial fuel cells when exposed to various environmental stresses, such as oxygen, low pH, low temperature, inhibitor (2-bromoethanesulfonate (BES)), and variations in external resistance. Controlling methanogenesis resulted in an increase in Coulombic efficiency (CE) because it was a major cause of electron loss. Methane was mainly produced from aceticlastic methanogenesis, rather than by syntrophic acetate oxidation, with Methanosarcinaceae being the primary contributor. Lowering the resistance from 600 to 50 Omega reduced the methanogenic electron loss by 24%; however, changing the temperature or pH level had little effect. A BES injection was the most potent strategy for the selective inhibition of methanogens without damaging exoelectrogens. The addition of 0.1-0.27 mM BES increased the CE from 35% to 70%. Oxygen stress successfully inhibited methanogens, while slightly suppressing the exoelectrogens, and is believed to be a practical option due to its low operating cost. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Iron Sulfide Attenuates the Methanogenic Toxicity of Elemental Copper and Zinc Oxide Nanoparticles and their Soluble Metal Ion Analogs

PubMed Central

Gonzalez-Estrella, Jorge; Gallagher, Sara; Sierra-Alvarez, Reyes; Field, Jim A.

2016-01-01

Elemental copper (Cu0) and zinc oxide (ZnO) nanoparticle (NP) toxicity to methanogens has been attributed to the release of soluble metal ions. Iron sulfide (FeS) partially controls the soluble concentration of heavy metals and their toxicity in aquatic environments. Heavy metals displace the Fe from FeS forming poorly soluble metal sulfides in the FeS matrix. Therefore, FeS may be expected to attenuate the NP toxicity. This work assessed FeS as an attenuator of the methanogenic toxicity of Cu0 and ZnO NPs and their soluble salt analogs. The toxicity attenuation capacity of fine (25–75 µm) and coarse (500 to 1200 µm) preparations of FeS (FeS-f and FeS-c respectively) was tested in the presence of highly inhibitory concentrations of CuCl2, ZnCl2 Cu0 and ZnO NPs. FeS-f attenuated methanogenic toxicity better than FeS-c. The results revealed that 2.5× less FeS-f than FeS-c was required to recover the methanogenic activity to 50% (activity normalized to uninhibited controls). The results also indicated that a molar FeS-f/Cu0 NP, FeS-f/ZnO NP, FeS-f/ZnCl2, and FeS-f/CuCl2 ratio of 2.14, 2.14, 4.28, and 8.56 respectively, was necessary to recover the methanogenic activity to >75%. Displacement experiments demonstrated that CuCl2 and ZnCl2 partially displaced Fe from FeS. As a whole, the results indicate that not all the sulfide in FeS was readily available to react with the soluble Cu and Zn ions which may explain the need for a large stoichiometric excesses of FeS to highly attenuate Cu and Zn toxicity. Overall, this study provides evidence that FeS attenuates the toxicity caused by Cu0 and ZnO NPs and their soluble ion analogs to methanogens. PMID:26803736

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.

Characterization of feedback-resistant mevalonate kinases from the methanogenic archaeons Methanosaeta concilii and Methanocella paludicola.

PubMed

Kazieva, Ekaterina; Yamamoto, Yoko; Tajima, Yoshinori; Yokoyama, Keiichi; Katashkina, Joanna; Nishio, Yousuke

2017-09-01

The inhibition of mevalonate kinase (MVK) by downstream metabolites is an important mechanism in the regulation of isoprenoid production in a broad range of organisms. The first feedback-resistant MVK was previously discovered in the methanogenic archaeon Methanosarcinamazei. Here, we report the cloning, expression, purification, kinetic characterization and inhibition analysis of MVKs from two other methanogens, Methanosaetaconcilii and Methanocellapaludicola. Similar to the M. mazei MVK, these enzymes were not inhibited by diphosphomevalonate (DPM), dimethylallyl diphosphate (DMAPP), isopentenyldiphosphate (IPP), geranylpyrophosphate (GPP) or farnesylpyrophosphate (FPP). However, they exhibited significantly higher affinity to mevalonate and higher catalytic efficiency than the previously characterized enzyme.

Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

NASA Astrophysics Data System (ADS)

Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C. M.; Zeng, Raymond J.

2014-06-01

The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 +/- 0.06, 1.0 +/- 0.13 and 0.4 +/- 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.

Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

PubMed Central

Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C. M.; Zeng, Raymond J.

2014-01-01

The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 ± 0.06, 1.0 ± 0.13 and 0.4 ± 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation. PMID:24920064

Phylogenetic identification of methanogens assimilating acetate-derived carbon in dairy and swine manures.

PubMed

Barret, Maialen; Gagnon, Nathalie; Morissette, Bruno; Kalmokoff, Martin L; Topp, Edward; Brooks, Stephen P J; Matias, Fernando; Neufeld, Josh D; Talbot, Guylaine

2015-02-01

In order to develop approaches for reducing the carbon footprint of the swine and dairy industries, it is important first to identify the methanogenic communities that drive methane emissions from stored manure. In this study, the metabolically active methanogens in substrate-starved manure samples taken from two dairy and one swine manure storage tanks were identified using [(13)C]-acetate and DNA stable-isotope probing (DNA-SIP). Molecular analysis of recovered genomic [(13)C]-DNA revealed that two distinct clusters of unclassified methanogen populations affiliated with the Methanoculleus genus, and the populations affiliated with Methanoculleus chikugoensis assimilated acetate-derived carbon (acetate-C) in swine and dairy starved manure samples, respectively. Furthermore, carbon flow calculations indicated that these populations were the primary contributors to methane emissions during these anoxic SIP incubations. Comparative analysis of mcrA gene abundance (coding for a key enzyme of methanogenesis) for Methanoculleus spp. in fresh feces and a wider range of stored dairy or swine manure samples, by real-time quantitative PCR using newly designed specific primers, demonstrated that the abundance of this genus significantly increased during storage. The findings supported the involvement of these particular methanogen populations as methane emitters from swine and dairy manure storage tanks. The study revealed that the ability to assimilate acetate-C for growth in manure differed within the Methanoculleus genus. Crown Copyright © 2014. Published by Elsevier GmbH. All rights reserved.

Comparative Proteomic Analysis of Methanothermobacter themautotrophicus ΔH in Pure Culture and in Co-Culture with a Butyrate-Oxidizing Bacterium

PubMed Central

Enoki, Miho; Shinzato, Naoya; Sato, Hiroaki; Nakamura, Kohei; Kamagata, Yoichi

2011-01-01

To understand the physiological basis of methanogenic archaea living on interspecies H2 transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain ΔH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H2 supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F420-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that α subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic methanogens to syntrophic growth is more complicated than that of hitherto proposed. PMID:21904627

Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste.

PubMed

Sasaki, Daisuke; Hori, Tomoyuki; Haruta, Shin; Ueno, Yoshiyuki; Ishii, Masaharu; Igarashi, Yasuo

2011-01-01

The methanogenic pathway and microbial community in a thermophilic anaerobic digestion process of organic solid waste were investigated in a continuous-flow stirred-tank reactor using artificial garbage slurry as a feedstock. The decomposition pathway of acetate, a significant precursor of CH(4) and a key intermediate metabolite in the anaerobic digestion process, was analyzed by using stable isotopes. A tracer experiment using (13)C-labeled acetate revealed that approximately 80% of the acetate was decomposed via a non-aceticlastic oxidative pathway, whereas the remainder was converted to methane via an aceticlastic pathway. Archaeal 16S rRNA analyses demonstrated that the hydrogenotrophic methanogens Methanoculleus spp. accounted for >90% of detected methanogens, and the aceticlastic methanogens Methanosarcina spp. were the minor constituents. The clone library targeting bacterial 16S rRNA indicated the predominance of the novel Thermotogales bacterium (relative abundance: ~53%), which is related to anaerobic acetate oxidizer Thermotoga lettingae TMO, although the sequence similarity was low. Uncultured bacteria that phylogenetically belong to municipal solid waste cluster I were also predominant in the microflora (~30%). These results imply that the microbial community in the thermophilic degrading process of organic solid waste consists exclusively of unidentified bacteria, which efficiently remove acetate through a non-aceticlastic oxidative pathway. Copyright © 2010 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effects of mineral salt supplement on enteric methane emissions, ruminal fermentation and methanogen community of lactating cows.

PubMed

Li, Xiaohua; Liu, Chong; Chen, Yongxing; Shi, Rongguang; Cheng, Zhenhua; Dong, Hongmin

2017-08-01

We evaluated the effects of mineral salt supplement on enteric methane emissions, ruminal fermentation and methanogen community of dairy cows over a whole lactation period. Ten Holstein cows fed a total mixed ration (TMR) diet were randomly allocated into two groups, one supplied with mineral salts as the treatment group and the other as the control group. The methane measurement showed that the ingestion of mineral salts lowered enteric methane emissions significantly (P < 0.05), with an average of 10.5% reduction over the whole lactation period. Ruminal fermentation analysis showed the mineral salt intake could significantly decrease the acetate : propionate ratio (P < 0.05). Real-time PCR assay showed that rumen methanogen abundance significantly reduced in the treatment group (P < 0.05) but was not significantly influenced by mineral salt intake over the whole lactation period. Intergroup methanogen community composition was influenced slightly by mineral salt intake; however, significantly different intragroup profiles were apparent throughout the whole lactation period, according to denaturing gradient gel electrophoresis analysis. In conclusion, these results suggested that the effective mitigation of enteric methane emissions by mineral salt intake could be attributed to decreased density of methanogenic archaea and that fluctuations in methane emission over the lactation period might be related to Methanobrevibacter diversity. © 2016 Japanese Society of Animal Science.

Effect of sludge age on methanogenic and glycogen accumulating organisms in an aerobic granular sludge process fed with methanol and acetate

PubMed Central

Pronk, M; Abbas, B; Kleerebezem, R; van Loosdrecht, M C M

2015-01-01

The influence of sludge age on granular sludge formation and microbial population dynamics in a methanol- and acetate-fed aerobic granular sludge system operated at 35°C was investigated. During anaerobic feeding of the reactor, methanol was initially converted to methane by methylotrophic methanogens. These methanogens were able to withstand the relatively long aeration periods. Lowering the anaerobic solid retention time (SRT) from 17 to 8 days enabled selective removal of the methanogens and prevented unwanted methane formation. In absence of methanogens, methanol was converted aerobically, while granule formation remained stable. At high SRT values (51 days), γ-Proteobacteria were responsible for acetate removal through anaerobic uptake and subsequent aerobic growth on storage polymers formed [so called metabolism of glycogen-accumulating organisms (GAO)]. When lowering the SRT (24 days), Defluviicoccus-related organisms (cluster II) belonging to the α-Proteobacteria outcompeted acetate consuming γ-Proteobacteria at 35°C. DNA from the Defluviicoccus-related organisms in cluster II was not extracted by the standard DNA extraction method but with liquid nitrogen, which showed to be more effective. Remarkably, the two GAO types of organisms grew separately in two clearly different types of granules. This work further highlights the potential of aerobic granular sludge systems to effectively influence the microbial communities through sludge age control in order to optimize the wastewater treatment processes. PMID:26059251

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.

Reduction of structural Fe(III) in nontronite by methanogen Methanosarcina barkeri

USGS Publications Warehouse

Liu, D.; Dong, Hailiang H.; Bishop, M.E.; Wang, Hongfang; Agrawal, A.; Tritschler, S.; Eberl, D.D.; Xie, S.

2011-01-01

Clay minerals and methanogens are ubiquitous and co-exist in anoxic environments, yet it is unclear whether methanogens are able to reduce structural Fe(III) in clay minerals. In this study, the ability of methanogen Methanosarcina barkeri to reduce structural Fe(III) in iron-rich smectite (nontronite NAu-2) and the relationship between iron reduction and methanogenesis were investigated. Bioreduction experiments were conducted in growth medium using three types of substrate: H2/CO2, methanol, and acetate. Time course methane production and hydrogen consumption were measured by gas chromatography. M. barkeri was able to reduce structural Fe(III) in NAu-2 with H2/CO2 and methanol as substrate, but not with acetate. The extent of bioreduction, as measured by the 1,10-phenanthroline method, was 7-13% with H2/CO2 as substrate, depending on nontronite concentration (5-10g/L). The extent was higher when methanol was used as a substrate, reaching 25-33%. Methanogenesis was inhibited by Fe(III) reduction in the H2/CO2 culture, but enhanced when methanol was used. High charge smectite and biogenic silica formed as a result of bioreduction. Our results suggest that methanogens may play an important role in biogeochemical cycling of iron in clay minerals and may have important implications for the global methane budget. ?? 2010 Elsevier Ltd.

Stress management skills in the subsurface: H2 stress on thermophilic heterotrophs and methanogens

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Holden, J. F.

2017-12-01

Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in subsurface environments such as coal and shale beds, marine sediments, and oil reservoirs where they encounter H2 stress conditions. It is important to study the H2 stress survival strategies of these organisms and their cooperation with one another for survival to better understand their biogeochemical impact in hot subsurface environments. In this study, we have shown that H2 inhibition changed the growth kinetics and the transcriptome of Thermococcus paralvinellae. We observed a significant decrease in batch phase growth rates and cell concentrations with high H2 background. Produced metabolite production measurements, RNA-seq analyses of differentially expressed genes and in silico experiments we performed with the T. paralvinellae metabolic model showed that T. paralvinellae produces formate by a formate hydrogenlyase to survive H2 inhibition. We have also shown that H2 limitation caused a significant decrease in batch phase growth rates and methane production rates of the methanogen, Methanocaldococcus jannaschii. H2 stress of both organisms can be ameliorated by syntrophic growth. H2 syntrophy was demonstrated in microcosm incubations for a natural assemblage of Thermococcus and hyperthermophilic methanogens present in hydrothermal fluid samples. This project aims to describe how a hyperthermophilic heterotroph and a hyperthermophilic methanogen eliminate H2 stress and explore cooperation among thermophiles in the hot subsurface.

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...

DEPENDENCE OF A HIGH-RATE, PCE-DECHLORINATING ENRICHMENT CULTURE ON METHANOGENIC ACTIVITY. (R825549C053)

EPA Science Inventory

The role served by the presence of methanogenic activity within a tetrachloroethene (PCE)-dechlorinating culture was investigated through a series of supplementation experiments. An acclimated lactate-enrichment culture (LEC 1) capable of rapidly converting PCE to ethene was s...

MICROBIAL REDUCTIVE DECHLORINATION OF HEXACHLORO-1,3-BUTADIENE IN A METHANOGENIC ENRICHMENT CULTURE. (R825513C007)

EPA Science Inventory

Sequential reductive dechlorination of hexachloro-1,3-butadiene (HCBD) was achieved by a mixed, methanogenic culture enriched from a contaminated estuarine sediment. Both methanol and lactate served as carbon and electron sources. Methanol was stoichiometrically converted to m...

Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis▿

PubMed Central

Yu, Zhongtang; García-González, Rubén; Schanbacher, Floyd L.; Morrison, Mark

2008-01-01

Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples. PMID:18083874

Metagenome changes in the biogas producing community during anaerobic digestion of rice straw.

PubMed

Pore, Soham D; Shetty, Deepa; Arora, Preeti; Maheshwari, Sneha; Dhakephalkar, Prashant K

2016-08-01

The present investigation was undertaken to study the microbial community succession in a sour and healthy digester. Ion torrent next-generation sequencing (NGS)-based metagenomic approach indicated abundance of hydrolytic bacteria and exclusion of methanogens and syntrophic bacteria in sour digester. Functional gene analysis revealed higher abundance of enzymes involved in acidogenesis and lower abundance of enzymes associated with methanogenesis like Methyl coenzyme M-reductase, F420 dependent reductase and Formylmethanofuran dehydrogenase in sour digester. Increased abundance of methanogens (Methanomicrobia) and genes involved in methanogenesis was observed in the restored/healthy digester highlighting revival of pH sensitive methanogenic community. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thioredoxin-linked redox control of metabolism in Methanocaldococcus jannaschii, an evolutionarily deeply-rooted hyperthermophilic methanogenic archaeon

USDA-ARS?s Scientific Manuscript database

Thioredoxin (Trx), a small redox protein, controls multiple processes in eukaryotes and bacteria by changing the thiol redox status of selected proteins. We have investigated this aspect in methanarchaea. These ancient methanogens produce methane almost exclusively from H2 plus CO2 carried approxima...

Ruminal fermentation of anti-methanogenic nitrate- and nitro-containing forages in vitro

USDA-ARS?s Scientific Manuscript database

Nitrate, 3-nitro-1-propionic acid (NPA), and 3-nitro-1-propanol (NPOH) can accumulate in forages and be poisonous to animals if fed at high enough amounts. These chemicals are also recognized as potent anti-methanogenic compounds, but plants naturally containing these chemicals have been studied li...

Hydrolysis, adsorption, and biodegradation of bensulfuron methyl under methanogenic conditions.

PubMed

Zhu, Fan-Ping; Duan, Jian-Lu; Yuan, Xian-Zheng; Shi, Xiao-Shuang; Han, Zhen-Lian; Wang, Shu-Guang

2018-05-01

Bensulfuron methyl (BSM), one of the most widely used herbicides in paddy soils, is frequently detected in natural and artificial aquatic systems. However, BSM transformation under methanogenic conditions has not been given sufficient attention. In this study, BSM elimination and transformation by anaerobic enrichment cultures were investigated. The results showed that BSM can be mineralized to methane through hydrolysis, adsorption, and biodegradation under a methanogenic environment. The adsorption led to protein static quenching in the extracellular polymeric substances (EPSs) of the enrichment cultures. Specifically, BSM mainly reacted with the amine, amide, amino acid, and amino sugar functional groups in proteins. BSM hydrolysis and biodegradation occurred through the breakage of the sulfonylurea bridge and sulfonyl amide linkage. The cleavage of the sulfonylurea bridge occurred in both hydrolysis and biodegradation, while the cleavage of the sulfonyl amide linkage only occurred in hydrolysis. These results elucidated the complex transformation of BSM under methanogenic conditions, which will advance the studies on sulfonylurea herbicide biotransformation and hazard assessment in the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of different ammonia sources on aceticlastic and hydrogenotrophic methanogens.

PubMed

Tian, Hailin; Fotidis, Ioannis A; Kissas, Konstantinos; Angelidaki, Irini

2018-02-01

Ammonium chloride (NH 4 Cl) was usually used as a model ammonia source to simulate ammonia inhibition during anaerobic digestion (AD) of nitrogen-rich feedstocks. However, ammonia in AD originates mainly from degradation of proteins, urea and nucleic acids, which is distinct from NH 4 Cl. Thus, in this study, the inhibitory effect of a "natural" ammonia source (urea) and NH 4 Cl, on four pure methanogenic strains (aceticlastic: Methanosarcina thermophila, Methanosarcina barkeri; hydrogenotrophic: Methanoculleus bourgensis, Methanoculleus thermophilus), was assessed under mesophilic (37 °C) and thermophilic (55 °C) conditions. The results showed that urea hydrolysis increased pH significantly to unsuitable levels for methanogenic growth, while NH 4 Cl had a negligible effect on pH. After adjusting initial pH to 7 and 8, urea was significantly stronger inhibitor with longer lag phases to methanogenesis compared to NH 4 Cl. Overall, urea seems to be more toxic on both aceticlastic and hydrogenotrophic methanogens compared to NH 4 Cl under the same total and free ammonia levels. Copyright © 2017 Elsevier Ltd. All rights reserved.

The effect of organic loading rate and retention time on hydrogen production from a methanogenic CSTR.

PubMed

Pakarinen, O; Kaparaju, P; Rintala, J

2011-10-01

The possibility of shifting a methanogenic process for hydrogen production by changing the process parameters viz., organic loading rate (OLR) and hydraulic retention time (HRT) was evaluated. At first, two parallel semi-continuously fed continuously stirred tank reactors (CSTR) were operated as methanogenic reactors (M1 and M2) for 78 days. Results showed that a methane yield of 198-218 L/kg volatile solids fed (VS(fed)) was obtained when fed with grass silage at an OLR of 2 kgVS/m³/d and HRT of 30 days. After 78 days of operation, hydrogen production was induced in M2 by increasing the OLR from 2 to 10 kgVS/m³/d and shortening the HRT from 30 to 6 days. The highest H₂ yield of 42 L/kgVS(fed) was obtained with a maximum H₂ content of 24%. The present results thus demonstrate that methanogenic process can be shifted towards hydrogen production by increasing the OLR and decreasing HRT. Copyright © 2011 Elsevier Ltd. All rights reserved.

Anaerobic digestion of food waste stabilized by lime mud from papermaking process.

PubMed

Zhang, Jishi; Wang, Qinqing; Zheng, Pengwei; Wang, Yusong

2014-10-01

The effects of lime mud from papermaking process (LMP) addition as buffer agent and inorganic nutrient on the anaerobic digestion stability of food waste (FW) were investigated under mesophilic conditions with the aim of avoiding volatile fatty acids accumulation, and inorganic elements deficiency. When LMP concentration ranged from 6.0 to 10g/L, the FW anaerobic digestion could maintain efficient and stable state. These advantages are attributed to the existence of Ca, Na, Mg, K, Fe, and alkaline substances that favor the methanogenic process. The highest CH4 yield of 272.8mL/g-VS was obtained at LMP and VS concentrations of 10.0 and 19.8g/L, respectively, with the corresponding lag-phase time of 3.84d and final pH of 8.4. The methanogens from residue digestates mainly consisted of Methanobrevibacter, coccus-type and sarcina-type methanogens with LMP addition compared to Methanobacteria in control. However, higher concentration of LMP inhibited methanogenic activities and methane production. Copyright © 2014 Elsevier Ltd. All rights reserved.

Response of anaerobes to methyl fluoride, 2-bromoethanesulfonate and hydrogen during acetate degradation.

PubMed

Hao, Liping; Lü, Fan; Li, Lei; Shao, Liming; He, Pinjing

2013-05-01

To use the selective inhibition method for quantitative analysis of acetate metabolism in methanogenic systems, the responses of microbial communities and metabolic activities, which were involved in anaerobic degradation of acetate, to the addition of methyl fluoride (CH3F), 2-bromoethanesulfonate (BES) and hydrogen were investigated in a thermophilic batch experiment. Both the methanogenic inhibitors, i.e., CH3F and BES, showed their effectiveness on inhibiting CH4 production, whereas acetate metabolism other than acetoclastic methanogenesis was stimulated by BES, as reflected by the fluctuated acetate concentration. Syntrophic acetate oxidation was thermodynamically blocked by hydrogen (H2), while H2-utilizing reactions as hydrogenotrophic methanogenesis and homoacetogenesis were correspondingly promoted. Results of PCR-DGGE fingerprinting showed that, CH3F did not influence the microbial populations significantly. However, the BES and hydrogen notably altered the bacterial community structures and increased the diversity. BES gradually changed the methanogenic community structure by affecting the existence of different populations to different levels, whilst H2 greatly changed the abundance of different methanogenic populations, and induced growth of new species.

Kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash.

PubMed

Acharya, Bhavik K; Pathak, Hilor; Mohana, Sarayu; Shouche, Yogesh; Singh, Vasdev; Madamwar, Datta

2011-08-01

Anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. Treatment efficiency of the bioreactor was investigated at different hydraulic retention times (HRT) and organic loading rates (OLR 5-20 kg COD m⁻³ d⁻¹). Applying the modified Stover-Kincannon model to the reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 2 kg m⁻³ d⁻¹ and 1.69 kg m⁻³ d⁻¹ respectively. Bacterial community structures of acidogenic and methanogenic reactors were assessed using culture-independent analyses. Sequencing of 16S rRNA genes exhibited a total of 123 distinct operational taxonomic units (OTUs) comprising 49 from acidogenic reactor and 74 (28 of eubacteria and 46 of archaea) from methanogenic reactor. The findings reveal the role of Lactobacillus sp. (Firmicutes) as dominant acid producing organisms in acidogenic reactor and Methanoculleus sp. (Euryarchaeotes) as foremost methanogens in methanogenic reactor. Copyright © 2011 Elsevier Ltd. All rights reserved.

The anaerobic digestion process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivard, C.J.; Boone, D.R.

1996-01-01

The microbial process of converting organic matter into methane and carbon dioxide is so complex that anaerobic digesters have long been treated as {open_quotes}black boxes.{close_quotes} Research into this process during the past few decades has gradually unraveled this complexity, but many questions remain. The major biochemical reactions for forming methane by methanogens are largely understood, and evolutionary studies indicate that these microbes are as different from bacteria as they are from plants and animals. In anaerobic digesters, methanogens are at the terminus of a metabolic web, in which the reactions of myriads of other microbes produce a very limited rangemore » of compounds - mainly acetate, hydrogen, and formate - on which the methanogens grow and from which they form methane. {open_quotes}Interspecies hydrogen-transfer{close_quotes} and {open_quotes}interspecies formate-transfer{close_quotes} are major mechanisms by which methanogens obtain their substrates and by which volatile fatty acids are degraded. Present understanding of these reactions and other complex interactions among the bacteria involved in anaerobic digestion is only now to the point where anaerobic digesters need no longer be treated as black boxes.« less

Assessment of microbial communities associated with fermentative-methanogenic biodegradation of aromatic hydrocarbons in groundwater contaminated with a biodiesel blend (B20).

PubMed

Ramos, Débora Toledo; da Silva, Márcio Luís Busi; Nossa, Carlos Wolfgang; Alvarez, Pedro J J; Corseuil, Henry Xavier

2014-09-01

A controlled field experiment was conducted to assess the potential for fermentative-methanogenic biostimulation (by ammonium-acetate injection) to enhance biodegradation of benzene, toluene, ethylbenzene and xylenes (BTEX) as well as polycyclic aromatic hydrocarbons (PAHs) in groundwater contaminated with biodiesel B20 (20:80 v/v soybean biodiesel and diesel). Changes in microbial community structure were assessed by pyrosequencing 16S rRNA analyses. BTEX and PAH removal began 0.7 year following the release, concomitantly with the increase in the relative abundance of Desulfitobacterium and Geobacter spp. (from 5 to 52.7 % and 15.8 to 37.3 % of total Bacteria 16S rRNA, respectively), which are known to anaerobically degrade hydrocarbons. The accumulation of anaerobic metabolites acetate and hydrogen that could hinder the thermodynamic feasibility of BTEX and PAH biotransformations under fermentative/methanogenic conditions was apparently alleviated by the growing predominance of Methanosarcina. This suggests the importance of microbial population shifts that enrich microorganisms capable of interacting syntrophically to enhance the feasibility of fermentative-methanogenic bioremediation of biodiesel blend releases.

Free acetic acid as the key factor for the inhibition of hydrogenotrophic methanogenesis in mesophilic mixed culture fermentation.

PubMed

Zhang, Wei; Dai, Kun; Xia, Xiu-Yang; Wang, Hua-Jie; Chen, Yun; Lu, Yong-Ze; Zhang, Fang; Zeng, Raymond Jianxiong

2018-05-18

The inhibition of acetate under acidic pH is an ideal way to reduce methanogenesis in mesophilic mixed culture fermentation (MCF). However, the effects of acetate concentration and acidic pH on methanogenesis remain unclear. Besides, although hydrogenotrophic methanogens can be suitable targets in MCF, they are generally ignored. Therefore, we intentionally enriched hydrogenotrophic methanogens and found that free acetic acid (FAA, x) concentration and specific methanogenic activity (SMA, y) were correlated according to the equation: y = 0.86 × 0.31/(0.31 + x) (R 2  = 0.909). The SMA was decreased by 50% and 90% at the FAA concentrations of 0.31 and 2.36 g/L, respectively. The coenzyme M concentration and relative electron transport activity agreed well with the FAA concentration. Moreover, the methanogenic activity could not be recovered when the FAA concentration exceeded 0.81 g/L. These findings indicated that neither acetate nor acidic pH, but FAA was the key factor to inhibit methanogenesis in MCF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inhibition of Acetoclastic Methanogenesis in Crude Oil- and Creosote-Contaminated Groundwater

USGS Publications Warehouse

Warren, E.; Bekins, B.A.; Godsy, E.M.; Smith, V.K.

2003-01-01

The inhibition of acetoclastic methanogenesis in crude oil- and creosote-contaminated groundwater was studied. The crude oil and water-soluble components of creosote contributed to the inhibition of acetoclastic methanogens. Acetoclastic methanogenesis was much more susceptible to the toxic inhibition of crude oil and creosote than either hydrogen- or formate-utilizing methanogenesis. The effect of this toxic inhibition was apparent in the population of the methanogenic trophic groups near nonaqueous crude oil at the Bemidji, MN, site. At a crude oil-contaminated site, numbers of acetoclastic methanogens found close to crude oil were 100 times fewer than those of hydrogen- and formate-utilizing methanogens. In laboratory toxicity assays, crude oil collected from the site inhibited methane production from acetate but not from formate or hydrogen. Toxicity assays with aqueous creosote extract completely inhibited acetate utilization over the range of tested dilutions but only mildly affected formate and hydrogen utilization. Wastewater reactor studies indicated that this toxicity would result in a decrease in the biodegradation rate of contaminants at sites where toxic compounds are present.

Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China.

PubMed

Qin, Huibin; Lang, Huihua; Yang, Hongjiang

2013-09-01

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

[Impact of liquid volume of recycled methanogenic effluent on anaerobic hydrolysis].

PubMed

Hao, Li-ping; Lü, Fan; He, Pin-jing; Shao, Li-ming

2008-09-01

Methanogenic effluent was recycled to regulate hydrolysis during two-phase anaerobic digestion of organic solid wastes. In order to study the impact of recycled effluent's volume on hydrolysis, four hydrolysis reactors filled with vegetable and flower wastes were constructed, with different liquid volumes of recycled methanogenic effluent, i.e., 0.1, 0.5, 1.0, 2.0 m3/(m3 x d), respectively. The parameters related to hydrolytic environment (pH, alkalinity, ORP, concentrations of ammonia and reducing sugar), microbial biomass and hydrolysis efficiency (accumulated SCOD, accumulated reducing sugar, and hydrolysis rate constants) were monitored. This research shows that recycling methanogenic effluent into the hydrolysis reactor can enhance its buffer capability and operation stability; higher recycled volume is favorable for microbial anabolism and further promotes hydrolysis. After 9 days of reaction, the accumulated SCOD in the hydrolytic effluent reach 334, 407, 413, 581 mg/g at recycled volumes of 0.1, 0.5, 1.0, 2.0 m3/(m3 x d) and their first-order hydrolysis rate kinetic constants are 0.065, 0.083, 0.089, 0.105 d(-1), respectively.

Ammonia inhibition on hydrogen enriched anaerobic digestion of manure under mesophilic and thermophilic conditions.

PubMed

Wang, Han; Zhang, Yifeng; Angelidaki, Irini

2016-11-15

Capturing of carbon dioxide by hydrogen derived from excess renewable energy (e.g., wind mills) to methane in a microbially catalyzed process offers an attractive technology for biogas production and upgrading. This bioconversion process is catalyzed by hydrogenotrophic methanogens, which are known to be sensitive to ammonia. In this study, the tolerance of the biogas process under supply of hydrogen, to ammonia toxicity was studied under mesophilic and thermophilic conditions. When the initial hydrogen partial pressure was 0.5 atm, the methane yield at high ammonia load (7 g NH 4 + -N L -1 ) was 41.0% and 22.3% lower than that at low ammonia load (1 g NH 4 + -N L -1 ) in mesophilic and thermophilic condition, respectively. Meanwhile no significant effect on the biogas composition was observed. Moreover, we found that hydrogentrophic methanogens were more tolerant to the ammonia toxicity than acetoclastic methanogens in the hydrogen enriched biogas production and upgrading processes. The highest methane production yield was achieved under 0.5 atm hydrogen partial pressure in batch reactors at all the tested ammonia levels. Furthermore, the thermophilic methanogens at 0.5 atm of hydrogen partial pressure were more tolerant to high ammonia levels (≥5 g NH 4 + -N L -1 ), compared with mesophilic methanogens. The present study offers insight in developing resistant hydrogen enriched biogas production and upgrading processes treating ammonia-rich waste streams. Copyright © 2016 Elsevier Ltd. All rights reserved.

Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants▿

PubMed Central

Nettmann, E.; Bergmann, I.; Pramschüfer, S.; Mundt, K.; Plogsties, V.; Herrmann, C.; Klocke, M.

2010-01-01

Knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic Archaea in the reactor samples. In addition, quantitative real-time PCR (Q-PCR) was used to support and complete the FISH analysis. Five of the six biogas reactors were dominated by hydrogenotrophic Methanomicrobiales. The average values were between 60 to 63% of archaeal cell counts (FISH) and 61 to 99% of archaeal 16S rRNA gene copies (Q-PCR). Within this order, Methanoculleus was found to be the predominant genus as determined by amplified rRNA gene restriction analysis. The aceticlastic family Methanosaetaceae was determined to be the dominant methanogenic group in only one biogas reactor, with average values for Q-PCR and FISH between 64% and 72%. Additionally, in three biogas reactors hitherto uncharacterized but potentially methanogenic species were detected. They showed closest accordance with nucleotide sequences of the hitherto unclassified CA-11 (85%) and ARC-I (98%) clusters. These results point to hydrogenotrophic methanogenesis as a predominant pathway for methane synthesis in five of the six analyzed biogas plants. In addition, a correlation between the absence of Methanosaetaceae in the biogas reactors and high concentrations of total ammonia (sum of NH3 and NH4+) was observed. PMID:20154117

Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil ▿

PubMed Central

Peng, Jingjing; Lü, Zhe; Rui, Junpeng; Lu, Yahai

2008-01-01

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH4 production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH4 was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH4 production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H2) seems to be the key factor that regulates the shift of methanogenic community. PMID:18344350

Syntrophic acetate oxidation in two-phase (acid-methane) anaerobic digesters.

PubMed

Shimada, T; Morgenroth, E; Tandukar, M; Pavlostathis, S G; Smith, A; Raskin, L; Kilian, R E

2011-01-01

The microbial processes involved in two-phase anaerobic digestion were investigated by operating a laboratory-scale acid-phase (AP) reactor and analyzing two full-scale, two-phase anaerobic digesters operated under mesophilic (35 °C) conditions. The digesters received a blend of primary sludge and waste activated sludge (WAS). Methane levels of 20% in the laboratory-scale reactor indicated the presence of methanogenic activity in the AP. A phylogenetic analysis of an archaeal 16S rRNA gene clone library of one of the full-scale AP digesters showed that 82% and 5% of the clones were affiliated with the orders Methanobacteriales and Methanosarcinales, respectively. These results indicate that substantial levels of aceticlastic methanogens (order Methanosarcinales) were not maintained at the low solids retention times and acidic conditions (pH 5.2-5.5) of the AP, and that methanogenesis was carried out by hydrogen-utilizing methanogens of the order Methanobacteriales. Approximately 43, 31, and 9% of the archaeal clones from the methanogenic phase (MP) digester were affiliated with the orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales, respectively. A phylogenetic analysis of a bacterial 16S rRNA gene clone library suggested the presence of acetate-oxidizing bacteria (close relatives of Thermacetogenium phaeum, 'Syntrophaceticus schinkii,' and Clostridium ultunense). The high abundance of hydrogen consuming methanogens and the presence of known acetate-oxidizing bacteria suggest that acetate utilization by acetate oxidizing bacteria in syntrophic interaction with hydrogen-utilizing methanogens was an important pathway in the second-stage of the two-phase digestion, which was operated at high ammonium-N concentrations (1.0 and 1.4 g/L). A modified version of the IWA Anaerobic Digestion Model No. 1 (ADM1) with extensions for syntrophic acetate oxidation and weak-acid inhibition adequately described the dynamic profiles of volatile acid production/degradation and methane generation observed in the laboratory-scale AP reactor. The model was validated with historical data from the full-scale digesters.

Microbiological characterization and specific methanogenic activity of anaerobe sludges used in urban solid waste treatment.

PubMed

Lozano, Claudia Johanna Sandoval; Mendoza, Marisol Vergara; de Arango, Mariela Carreño; Monroy, Edgar Fernando Castillo

2009-02-01

This study presents the microbiological characterization of the anaerobic sludge used in a two-stage anaerobic reactor for the treatment of organic fraction of urban solid waste (OFUSW). This treatment is one alternative for reducing solid waste in landfills at the same time producing a biogas (CH(4) and CO(2)) and an effluent that can be used as biofertilizer. The system was inoculated with sludge from a wastewater treatment plant (WWTP) (Río Frío Plant in Bucaramanga-Colombia) and a methanogenic anaerobic digester for the treatment of pig manure (Mesa de los Santos in Santander). Bacterial populations were evaluated by counting groups related to oxygen sensitivity, while metabolic groups were determined by most probable number (MPN) technique. Specific methanogenic activity (SMA) for acetate, formate, methanol and ethanol substrates was also determined. In the acidogenic reactor (R1), volatile fatty acids (VFA) reached values of 25,000 mg L(-1) and a concentration of CO(2) of 90%. In this reactor, the fermentative population was predominant (10(5)-10(6)MPN mL(-1)). The acetogenic population was (10(5)MPN mL(-1)) and the sulphate-reducing population was (10(4)-10(5)MPN mL(-1)). In the methanogenic reactor (R2), levels of CH(4) (70%) were higher than CO(2) (25%), whereas the VFA values were lower than 4000 mg L(-1). Substrate competition between sulphate-reducing (10(4)-10(5)MPN mL(-1)) and methanogenic bacteria (10(5)MPN mL(-1)) was not detected. From the SMA results obtained, acetoclastic (2.39 g COD-CH(4)g(-1)VSS(-1)day(-1)) and hydrogenophilic (0.94 g COD-CH(4)g(-1)VSS(-1)day(-1)) transformations as possible metabolic pathways used by methanogenic bacteria is suggested from the SMA results obtained. Methanotrix sp., Methanosarcina sp., Methanoccocus sp. and Methanobacterium sp. were identified.

Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

PubMed Central

Kaur, Parwinder; Appels, Rudi; Bayer, Philipp E.; Keeble-Gagnere, Gabriel; Wang, Jiankang; Hirakawa, Hideki; Shirasawa, Kenta; Vercoe, Philip; Stefanova, Katia; Durmic, Zoey; Nichols, Phillip; Revell, Clinton; Isobe, Sachiko N.; Edwards, David; Erskine, William

2017-01-01

Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia’s key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production. PMID:28928752

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.

PubMed

Sorokin, Dimitry Y; Merkel, Alexander Y; Abbas, Ben; Makarova, Kira S; Rijpstra, W Irene C; Koenen, M; Sinninghe Damsté, Jaap S; Galinski, Erwin A; Koonin, Eugene V; van Loosdrecht, Mark C M

2018-05-21

Methanogenic enrichments from hypersaline lakes at moderate thermophilic conditions have resulted in the cultivation of an unknown deep lineage of euryarchaeota related to the class Halobacteria. Eleven soda lake isolates and three salt lake enrichment cultures were methyl-reducing methanogens that utilize C1 methylated compounds as electron acceptors and H2 or formate as electron donors, but they were unable to grow on either substrates alone or to form methane from acetate. They are extreme halophiles, growing optimally at 4 M total Na + and the first representatives of methanogens employing the 'salt-in' osmoprotective mechanism. The salt lake subgroup is neutrophilic, whereas the soda lake isolates are obligate alkaliphiles, with an optimum around pH 9.5. Both grow optimally at 50 °C. The genetic diversity inside the two subgroups is very low, indicating that the soda and salt lake clusters consist of a single genetic species each. The phylogenetic distance between the two subgroups is in the range of distant genera, whereas the distance to other euryarchaea is below 83 % identity of the 16S rRNA gene. These isolates and enriched methanogens, together with closely related environmental clones from hypersaline habitats (the SA1 group), form a novel class-level clade in the phylum Euryarchaeota. On the basis of distinct phenotypic and genetic properties, the soda lake isolates are classified into a new genus and species, Methanonatronarchaeum thermophilum, with the type strain AMET1 T (DSM 26684 T =NBRC 110805 T =UNIQEM U982 T ), and the salt lake methanogens into a candidate genus and species 'Candidatus Methanohalarchaeum thermophilum'. These organisms are proposed to form novel family, order and class Methanonatronarchaeaceae fam. nov., Methanonatronarchaeales ord. nov. and Methanonatronarchaeia classis nov., within the phylum Euryarchaeota.

Estimation of methanogen biomass via quantitation of coenzyme M

USGS Publications Warehouse

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.

Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luthey-Schulten, Zaida

The methanogenic archaea, anaerobic microbes that convert CO2 and H2 and/or other small organic fermentation products into methane, play an unusually large role in the global carbon cycle. As they perform the final step in the anaerobic breakdown of biomass, methanogens are a biogenic source of an estimated one billion tons methane each year. Depending on the location, produced methane can be considered as either a greenhouse gas (agricultural byproduct), sequestered carbon storage (methane hydrate deposits), or a potential energy source (organic wastewater treatment). These microbes therefore represent an important target for biotechnology applications. Computational models of methanogens with predictivemore » power are useful aids in the adaptation of methanogenic systems, but need to connect processes of wide-ranging time and length scales. In this project, we developed several computational methodologies for modeling the dynamic behavior of entire cells that connects stochastic reaction-diffusion dynamics of individual biochemical pathways with genome-scale modeling of metabolic networks. While each of these techniques were in the realm of well-defined computational methods, here we integrated them to develop several entirely new approaches to systems biology. The first scientific aim of the project was to model how noise in a biochemical pathway propagates into cellular phenotypes. Genetic circuits have been optimized by evolution to regulate molecular processes despite stochastic noise, but the effect of such noise on a cellular biochemical networks is currently unknown. An integrated stochastic/systems model of Escherichia coli species was created to analyze how noise in protein expression gives—and therefore noise in metabolic fluxes—gives rise to multiple cellular phenotype in isogenic population. After the initial work developing and validating methods that allow characterization of the heterogeneity in the model organism E. coli, the project shifted toward investigations of the methanogen Methanosarcina acetivorans. By integrating an unprecedented transcriptomics dataset for growth of the methanogen on many substrates with an in silico model, heterogeneity in metabolic pathway usage and methane production were examined. This lent insight into the physiological requirements of the organism under different environmental conditions and uncovered the unique regulatory role that mRNA half-life has in shaping metabolic flux distributions in this organism.« less

Methane production potential and microbial community structure for different forest soils

NASA Astrophysics Data System (ADS)

Matsumoto, Y.; Ueyama, M.; Kominami, Y.; Endo, R.; Tokumoto, H.; Hirano, T.; Takagi, K.; Takahashi, Y.; Iwata, H.; Harazono, Y.

2017-12-01

Forest soils are often considered as a methane (CH4) sink, but anaerobic microsites potentially decrease the sink at the ecosystem scale. In this study, we measured biological CH4 production potential of soils at various ecosystems, including upland forests, a lowland forest, and a bog, and analyzed microbial community structure using 16S ribosomal RNA (rRNA) genes. Three different types of soil samples (upland, bank of the stream, and center of the stream) were collected from Yamashiro forest meteorology research site (YMS) at Kyoto, Japan, on 11 May 2017. The soils were incubated at dark and anaerobic conditions under three different temperatures (37°C, 25°C, and 10°C) from 9 June 2017. The upland soils emitted CH4 with largest yields among the three soils at 37°C and 25°C, although no CH4 emission was observed at 10°C. For all temperature ranges, the emission started to increase with a 14- to 20-days lag after the start of the incubation. The lag indicates a slow transition to anaerobic conditions; as dissolved oxygen in water decreased, the number and/or activity of anaerobic bacteria like methanogens increased. The soils at the bank and center of the stream emitted CH4 with smaller yields than the upland soils in the three temperature ranges. The microbial community analyses indicate that methanogenic archaea presented at the three soils including the aerobic upland soil, but compositions of methanogenic archaea were different among the soils. In upland soils, hydrogenotrophic methanogens, such as Methanobacterium and Methanothermobacter, consisted almost all of the total methanogen detected. In the bank and center of the stream, soils contained approximately 10-25% of acetoclastic methanogens, such as Methanosarcina and Methanosaeta, among the total methanogen detected. Methanotrophs, a genus of Methanobacteriaceae, was appeared in the all types of soils. We will present results from same incubation and 16S rRNA analyses for other ecosystems, including a larch forest on volcanic soils, a young larch forest on Gleyic Cambisol, and a boreal bog and a lowland forest on permafrost. Comparing various soils from temperate and boreal ecosystems, we will discuss differences of biogenic CH4 production potential among the soils with the microbial community analyses.

Molecular Diversity and Activity of Methanogens in the Subseafloor at Deep-Sea Hydrothermal Vents of the Pacific Ocean (Invited)

NASA Astrophysics Data System (ADS)

Huber, J. A.; Merkel, A.; Holden, J. F.; Lilley, M. D.; Butterfield, D. A.

2009-12-01

Methanogenesis is thought to represent one of the most ancient metabolic pathways on Earth, and methanogens may serve as important primary producers in warm crustal habitats at deep-sea hydrothermal vents. Many of these obligate chemolithoautotrophs depend solely on geochemically-derived energy and carbon sources and grow at high temperatures under strictly anaerobic conditions. A combined geochemical and microbiological approach was used to determine the distribution and molecular diversity of methanogens in low temperature diffuse vent fluids from the Endeavour Segment R2K ISS site, as well as Axial Seamount and volcanoes of the Mariana Arc. Geochemical data from hot and adjacent warm diffuse vent fluids provided chemical indicators to guide sample selection for detailed polymerase chain reaction (PCR)-based analysis of the key enzyme for methane formation, methyl-coenzyme M reductase (mcrA), as well as archaeal 16S rRNA genes. At most Endeavour vent sites, hydrogen concentrations were too low to support hydrogenotrophic methanogensis directly and only one diffuse site, Easter Island, had a positive signal for the mcrA gene. These sequences were most closely related to members of the order Methanococcales, as well as anaerobic methane oxidizers (ANME-1). The presence of ANME, which are rarely found in non-sedimented marine environments, is another line of evidence supporting the occurrence of buried sediments at Endeavour. At Axial, a number of diffuse vents have strong chemical indicators of methanogenesis. Methanogenic communities were detected at 3 sites on the southeast side of the caldera: the northern end of the 1998 lava flow, the International District, and on the pre-1987 lava flow. Time series work at Marker 113 showed that in 4 different years over the last 6 years methanogenic communities are active and abundant, suggesting a stable anaerobic, warm subseafloor habitat. Results show that members of the order Methanococcales dominate at this site, including mesophiles and hyper/thermophiles, but that some methanogens recovered from Marker 113 are surviving at low or sub-optimal hydrogen levels. Vent 9m had a community composition similar to Marker 113, dominated by Methanococcales, and Zen Gardens, also at Axial, had a population of methanogens very different from either site. The community there was composed of members of the order Methanomicrobiales, including mesophilic methanogens previously only found in terrestrial environments. Along the Mariana Arc, Shrimp City vent at NW Rota-1 had some of the highest levels of methane detected on the entire arc, and mcrA analysis indicates members of the Methanococcales were present, as well as Methanosarcinales and anaerobic methane oxidizers. An integrated comparison of organismal and geochemical diversity will be presented to link energy transfer in these diverse hydrothermal systems from mantle to microbes.

Group specific quantitative real-time polymerase chain reaction (qRT-PCR) analysis of methanogenic archaea in stored swine manure

USDA-ARS?s Scientific Manuscript database

Consolidated storage of swine manure is associated with the production of a variety of odors and emissions which result from anaerobic digestion of materials present in the manure. Methanogenic archaea are a diverse group of anaerobic microorganisms responsible for the production of methane. In th...

Evaluation of support matrices for immobilization of anaerobic consortia for efficient carbon cycling in waste regeneration.

PubMed

Chauhan, Ashvini; Ogram, Andrew

2005-02-18

Efficient metabolism of fatty acids during anaerobic waste digestion requires development of consortia that include "fatty acid consuming H(2) producing bacteria" and methanogenic bacteria. The objective of this research was to optimize methanogenesis from fatty acids by evaluating a variety of support matrices for use in maintaining efficient syntrophic-methanogenic consortia. Tested matrices included clays (montmorillonite and bentonite), glass beads (106 and 425-600mum), microcarriers (cytopore, cytodex, cytoline, and cultispher; conventionally employed for cultivation of mammalian cell lines), BioSep beads (powdered activated carbon), and membranes (hydrophilic; nylon, polysulfone, and hydrophobic; teflon, polypropylene). Data obtained from headspace methane (CH(4)) analyses as an indicator of anaerobic carbon cycling efficiency indicated that material surface properties were important in maintenance and functioning of the anaerobic consortia. Cytoline yielded significantly higher CH(4) than other matrices as early as in the first week of incubation. 16S rRNA gene sequence analysis from crushed cytoline matrix showed the presence of Syntrophomonas spp. (butyrate oxidizing syntrophs) and Syntrophobacter spp. (propionate oxidizing syntrophs), with Methanosaeta spp. (acetate utilizing methanogen), and Methanospirillum spp. (hydrogen utilizing methanogen) cells. It is likely that the more hydrophobic surfaces provided a suitable surface for adherence of cells of syntrophic-methanogenic consortia. Cytoline also appeared to protect entrapped consortia from air, resulting in rapid methanogenesis after aerial exposure. Our study suggests that support matrices can be used in anaerobic digestors, pre-seeded with immobilized or entrapped consortia on support matrices, and may be of value as inoculant-adsorbents to rapidly initiate or recover proper system functioning following perturbation.

Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils.

PubMed

Radl, Viviane; Gattinger, Andreas; Chronáková, Alica; Nemcová, Anna; Cuhel, Jiri; Simek, Miloslav; Munch, Jean Charles; Schloter, Michael; Elhottová, Dana

2007-09-01

In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.

Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity.

PubMed

Cadena, Santiago; García-Maldonado, José Q; López-Lozano, Nguyen E; Cervantes, Francisco J

2018-05-01

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H 2 S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.

Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.

PubMed

Costa, Kyle C; Wong, Phoebe M; Wang, Tiansong; Lie, Thomas J; Dodsworth, Jeremy A; Swanson, Ingrid; Burn, June A; Hackett, Murray; Leigh, John A

2010-06-15

In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir.

PubMed

Pan, Pan; Hong, Bo; Mbadinga, Serge Maurice; Wang, Li-Ying; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-09-01

Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe 3 O 4 ), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe 3 O 4 ) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, β-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe 3 O 4 ) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/β-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of β-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.

Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.

PubMed

Aydin, Sevcan; Ince, Bahar; Ince, Orhan

2015-06-01

This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of microbial community composition in thermophilic methane-producing incubation of production water from a high-temperature oil reservoir.

PubMed

Zhou, Fang; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

2013-01-01

Investigation of petroleum microbes is fundamental for the development and utilization of oil reservoirs' microbial resources, and also provides great opportunities for research and development of bio-energy. Production water from a high-temperature oil reservoir was incubated anaerobically at 55 degrees C for more than 400 days without amendment of any nutrients. Over the time of incubation, about 1.6 mmol of methane and up to 107 micromol of hydrogen (H2) were detected in the headspace. Methane formation indicated that methanogenesis was likely the predominant process in spite of the presence of 23.4 mM SO4(2-) in the production water. Microbial community composition of the incubation was characterized by means of 16S rRNA gene clone libraries construction. Bacterial composition changed from Pseudomonales as the dominant population initially to Hydrogenophilales-related microorganisms affiliated to Petrobacter spp. closely. After 400 days of incubation, other bacterial members detected were related to Anareolineales, beta-, gamma-, and delta-Proteobacteria. The archaeal composition of the original production water was essentially composed of obligate acetoclastic methanogens of the genus Methanosaeta, but the incubation was predominantly composed of CO2-reducing methanogens of the genus Methanothermobacter and Crenarchaeotes-related microorganisms. Our results suggest that methanogenesis could be more active than expected in oil reservoir environments and methane formation from CO2-reduction played a significant role in the methanogenic community. This conclusion is consistent with the predominant role played by H2-oxidizing methanogens in the methanogenic conversion of organic matter in high-temperature petroleum reservoirs.

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

PubMed Central

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-01-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life. PMID:21654849

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor.

PubMed

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-12-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

Reductive Dehalogenation of a Nitrogen Heterocyclic Herbicide in Anoxic Aquifer Slurries

PubMed Central

Adrian, Neal R.; Suflita, Joseph M.

1990-01-01

We studied the metabolic fate of bromacil in anaerobic aquifer slurries held under denitrifying, sulfate-reducing, or methanogenic conditions. Liquid chromatograhy-mass spectrometry of the slurries confirmed that bromacil was debrominated under methanogenic conditions but was not degraded under the other incubation conditions. This finding extends the range of aryl reductive dehalogenation reactions to include nitrogen heterocyclic compounds. PMID:16348103

Forensic fingerprinting of oil-spill hydrocarbons in a methanogenic environment-Mandan, ND and Bemidji, MN

USGS Publications Warehouse

Hostettler, F.D.; Wang, Y.; Huang, Y.; Cao, W.; Bekins, B.A.; Rostad, C.E.; Kulpa, C.F.; Laursen, Andrew E.

2007-01-01

In recent decades forensic fingerprinting of oil-spill hydrocarbons has emerged as an important tool for correlating oils and for evaluating their source and character. Two long-term hydrocarbon spills, an off-road diesel spill (Mandan, ND) and a crude oil spill (Bemidji, MN) experiencing methanogenic biodegradation were previously shown to be undergoing an unexpected progression of homologous n-alkane and n-alkylated cyclohexane loss. Both exhibited degradative losses proceeding from the high-molecular-weight end of the distributions, along with transitory concentration increases of lower-molecular-weight homologs. Particularly in the case of the diesel fuel spill, these methanogenic degradative patterns can result in series distributions that mimic lower cut refinery fuels or admixture with lower cut fuels. Forensic fingerprinting in this long-term spill must therefore rely on more recalcitrant series, such as polycyclic aromatic hydrocarbon or drimane sesquiterpane profiles, to prove if the spilled oil is single-sourced or whether there is verifiable admixture with other extraneous refinery fuels. Degradation processes impacting n-alkanes and n-alkylated ring compounds, which make these compounds unsuitable for fingerprinting, nevertheless are of interest in understanding methanogenic biodegradation. Copyright ?? Taylor & Francis Group, LLC.

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau

PubMed Central

Huang, Xiao Dan; Martinez-Fernandez, Gonzalo; Padmanabha, Jagadish; Long, Ruijun; Denman, Stuart E.; McSweeney, Christopher S.

2016-01-01

Host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. A study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (yak and Tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude Tibetan Plateau. The methylotrophic Methanomassiliicoccaceae was the predominant archaeal group in all animals even though Methanobrevibacter are usually present in greater abundance in ruminants globally. Furthermore, within the Methanomassiliicoccaceae family members from Mmc. group 10 and Mmc. group 4 were dominant in Tibetan Plateau ruminants compared to Mmc. group 12 found to be highest in other ruminants studied. Small ruminants presented the highest number of sequences that belonged to Methanomassiliicoccaceae compared to the larger ruminants. Although the methanogen community structure was different among the ruminant species, there were striking similarities between the animals in this environment. This indicates that factors such as the extreme environmental conditions and diet on the Tibetan Plateau might have a greater impact on rumen methanogen community compared to host differences. PMID:27274707

Methane production from formate, acetate and H2/CO2; focusing on kinetics and microbial characterization.

PubMed

Pan, Xiaofang; Angelidaki, Irini; Alvarado-Morales, Merlin; Liu, Houguang; Liu, Yuhong; Huang, Xu; Zhu, Gefu

2016-10-01

For evaluating the methanogenesis from typical methanogenic precursors (formate, acetate and H2/CO2), CH4 production kinetics were investigated at 37±1°C in batch anaerobic digestion tests and stimulated by modified Gompertz model. The results showed that maximum methanation rate from formate, acetate and H2/CO2 were 19.58±0.49, 42.65±1.17 and 314.64±3.58NmL/gVS/d in digested manure system and 6.53±0.31, 132.04±3.96 and 640.16±19.92NmL/gVS/d in sewage sludge system during second generation incubation. Meanwhile the model could not fit well in granular sludge system, while the rate of formate methanation was faster than from H2/CO2 and acetate. Considering both the kinetic results and microbial assay we could conclude that H2/CO2 methanation was the fastest methanogenic step in digested manure and sewage sludge system with Methanomicrobiales as dominant methanogens, while granular sludge with Methanobacteriales as dominant methanogens contributed to the fastest formate methanation. Copyright © 2016. Published by Elsevier Ltd.

Effect of sulfate and nitrate on acetate conversion by anaerobic microorganisms in a freshwater sediment.

PubMed

Scholten, Johannes C M; Bodegom, Peter M; Vogelaar, Jaap; Ittersum, Alexander; Hordijk, Kees; Roelofsen, Wim; Stams, Alfons J M

2002-12-01

Acetate is quantitatively the most important substrate for methane production in a freshwater sediment in The Netherlands. In the presence of alternative electron acceptors the conversion of acetate by methanogens was strongly inhibited. By modelling the results, obtained in experiments with and without (13)C-labelled acetate, we could show that the competition for acetate between methanogens and sulfate reducers is the main cause of inhibition of methanogenesis in the sediment. Although nitrate led to a complete inhibition of methanogenesis, acetate-utilising nitrate-reducing bacteria hardly competed with methanogens for the available acetate in the presence of nitrate. Most-probable-number enumerations showed that methanogens (2x10(8) cells cm(-3) sediment) and sulfate reducers (2x10(8) cells cm(-3) sediment) were the dominant acetate-utilising organisms in the sediment, while numbers of acetate-utilising nitrate reducers were very low (5x10(5) cells cm(-3) sediment). However, high numbers of sulfide-oxidising nitrate reducers were detected. Denitrification might result in the formation of toxic products. We speculate that the accumulation of low concentrations of NO (<0.2 mM) may result in an inhibition of methanogenesis.

Evaluation of stable isotope fingerprinting techniques for the assessment of the predominant methanogenic pathways in anaerobic digesters.

PubMed

Nikolausz, M; Walter, R F H; Sträuber, H; Liebetrau, J; Schmidt, T; Kleinsteuber, S; Bratfisch, F; Günther, U; Richnow, H H

2013-03-01

Laboratory biogas reactors were operated under various conditions using maize silage, chicken manure, or distillers grains as substrate. In addition to the standard process parameters, the hydrogen and carbon stable isotopic composition of biogas was analyzed to estimate the predominant methanogenic pathways as a potential process control tool. The isotopic fingerprinting technique was evaluated by parallel analysis of mcrA genes and their transcripts to study the diversity and activity of methanogens. The dominant hydrogenotrophs were Methanomicrobiales, while aceticlastic methanogens were represented by Methanosaeta and Methanosarcina at low and high organic loading rates, respectively. Major changes in the relative abundance of mcrA transcripts were observed compared to the results obtained from DNA level. In agreement with the molecular results, the isotope data suggested the predominance of the hydrogenotrophic pathway in one reactor fed with chicken manure, while both pathways were important in the other reactors. Short-term changes in the isotopic composition were followed, and a significant change in isotope values was observed after feeding a reactor digesting maize silage. This ability of stable isotope fingerprinting to follow short-term activity changes shows potential for indicating process failures and makes it a promising technology for process control.

Effects of Subsurface Microbial Ecology on Geochemical Evolution of a Crude-Oil Contaminated Aquifer

NASA Astrophysics Data System (ADS)

Bekins, B. A.; Cozzarelli, I. M.; Godsy, E. M.; Warren, E.; Hostettler, F. D.

2001-12-01

We have identified several subsurface habitats for microorganisms in a crude oil contaminated located near Bemidji, Minnesota. These aquifer habitats include: 1) the unsaturated zone contaminated by hydrocarbon vapors, 2) the zones containing separate-phase crude oil, and 3) the aqueous-phase contaminant plume. The surficial glacial outwash aquifer was contaminated when a crude oil pipeline burst in 1979. We analyzed sediment samples from the contaminated aquifer for the most probable numbers of aerobes, iron reducers, fermenters, and three types of methanogens. The microbial data were then related to gas, water, and oil chemistry, sediment extractable iron, and permeability. The microbial populations in the various contaminated subsurface habitats each have special characteristics and these affect the aquifer and contaminant chemistry. In the eight-meter-thick, vapor-contaminated vadose zone, a substantial aerobic population has developed that is supported by hydrocarbon vapors and methane. Microbial numbers peak in locations where access to both hydrocarbons and nutrients infiltrating from the surface is maximized. The activity of this population prevents hydrocarbon vapors from reaching the land surface. In the zone where separate-phase crude oil is present, a consortium of methanogens and fermenters dominates the populations both above and below the water table. Moreover, gas concentration data indicate that methane production has been active in the oily zone since at least 1986. Analyses of the extracted separate-phase oil show that substantial degradation of C15 -C35 n-alkanes has occurred since 1983, raising the possibility that significant degradation of C15 and higher n-alkanes has occurred under methanogenic conditions. However, lab and field data suggest that toxic inhibition by crude oil results in fewer acetate-utilizing methanogens within and adjacent to the separate-phase oil. Data from this and other sites indicate that toxic inhibition of acetoclastic methanogenesis in the proximity of separate phase contaminant sources may result in build-up of acetate in contaminant plumes. Within the aqueous-phase contaminant plume steep vertical hydrocarbon concentration gradients are associated with sharp transitions in the dominant microbial population. In the 20 years since the aquifer became contaminated, sediment iron oxides have been depleted and the dominant physiologic type has changed in areas of high contaminant flux from iron reducing to methanogenic. Thus, methanogens are found in high permeability horizons down gradient from the oil while iron reducers persist in low permeability zones. Expansion of the methanogenic zone over time has resulted in a concomitant increase in the aquifer volume contaminated with the highest concentrations of benzene and ethylbenzene.

Molecular Biology and Physiology of Methanogenic Archaebacteria

DTIC Science & Technology

1989-06-27

anaerobic food chains, the methanogens contribute to the mineralization of large amounts of organic matter. The end product of their metabolism...of radiolabelled substrate to product [8; Worrell and Nagle, in preparation]. Strain RT103, a formate auxotroph was isolated from the kanamycin...methylmercaptopurine riboside 0. 16 Bacteriocidald 8-aza-2, 6-diaminopurine 0.0011 6-thioguanine 0.0004 8-azaguanine 0.0004 6- mercaptopurine 0 8

Methane-Cycling Microbial Communities and Methane Emission in Natural and Restored Peatlands

PubMed Central

Hynninen, Anu; Nieminen, Mika; Tuomivirta, Tero T.; Tuittila, Eeva-Stiina; Nousiainen, Hannu; Kell, Dana K.; Yrjälä, Kim; Tervahauta, Arja; Fritze, Hannu

2012-01-01

We addressed how restoration of forestry-drained peatlands affects CH4-cycling microbes. Despite similar community compositions, the abundance of methanogens and methanotrophs was lower in restored than in natural sites and correlated with CH4 emission. Poor establishment of methanogens may thus explain low CH4 emissions on restored peatlands even 10 to 12 years after restoration. PMID:22752167

Multiple evidence for methylotrophic methanogenesis as the dominant methanogenic pathway in hypersaline sediments from the Orca Basin, Gulf of Mexico

NASA Astrophysics Data System (ADS)

Zhuang, Guang-Chao; Elling, Felix J.; Nigro, Lisa M.; Samarkin, Vladimir; Joye, Samantha B.; Teske, Andreas; Hinrichs, Kai-Uwe

2016-08-01

Among the most extreme habitats on Earth, dark, deep, anoxic brines host unique microbial ecosystems that remain largely unexplored. As the terminal step of anaerobic degradation of organic matter, methanogenesis is a potentially significant but poorly constrained process in deep-sea hypersaline environments. We combined biogeochemical and phylogenetic analyses with incubation experiments to unravel the origin of methane in the hypersaline sediments of Orca Basin in the northern Gulf of Mexico. Substantial concentrations of methane, up to 3.4 mM, coexisted with high concentrations of sulfate from 16 to 43 mM in two sediment cores retrieved from the northern and southern parts of Orca Basin. The strong depletion of 13C in methane (-77‰ to -89‰) points towards a biological source. While low concentrations of competitive substrates limited the significance of hydrogenotrophic and acetoclastic methanogenesis, the presence of non-competitive methylated substrates (methanol, trimethylamine, dimethyl sulfide, dimethylsulfoniopropionate) supported the potential for methane generation through methylotrophic methanogenesis. Thermodynamic calculations demonstrated that hydrogenotrophic and acetoclastic methanogenesis were unlikely to occur under in situ conditions, while methylotrophic methanogenesis from a variety of substrates was highly favorable. Likewise, carbon isotope relationships between methylated substrates and methane suggested methylotrophic methanogenesis was the major source of methane. Stable and radio-isotope tracer experiments with 13C-labeled bicarbonate, acetate and methanol and 14C-labeled methylamine indicated that methylotrophic methanogenesis was the predominant methanogenic pathway. Based on 16S rRNA gene sequences, halophilic methylotrophic methanogens related to the genus Methanohalophilus dominated the benthic archaeal community in the northern basin and also occurred in the southern basin. High abundances of methanogen lipid biomarkers such as intact polar and polyunsaturated hydroxyarchaeols were detected in sediments from the northern basin, with lower abundances in the southern basin. Strong 13C-depletion of saturated and monounsaturated hydroxyarchaeol were consistent with methylotrophic methanogenesis as the major methanogenic pathway. Collectively, the availability of methylated substrates, thermodynamic calculations, experimentally determined methanogenic activity as well as lipid and gene biomarkers support the hypothesis that methylotrophic methanogenesis is the predominant pathway of methane formation in the presence of sulfate in Orca Basin sediments.

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions

PubMed Central

Hagen, Live H.; Ishaq, Suzanne L.; Zamanzadeh, Mirzaman; Wright, André-Denis G.; Pope, Phillip B.; Sundset, Monica A.

2016-01-01

Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes. In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16–38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer. PMID:27159387

Analyses of n-alkanes degrading community dynamics of a high-temperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques.

PubMed

Zhou, Lei; Li, Kai-Ping; Mbadinga, Serge Maurice; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2012-08-01

Despite the knowledge on anaerobic degradation of hydrocarbons and signature metabolites in the oil reservoirs, little is known about the functioning microbes and the related biochemical pathways involved, especially about the methanogenic communities. In the present study, a methanogenic consortium enriched from high-temperature oil reservoir production water and incubated at 55 °C with a mixture of long chain n-alkanes (C(15)-C(20)) as the sole carbon and energy sources was characterized. Biodegradation of n-alkanes was observed as methane production in the alkanes-amended methanogenic enrichment reached 141.47 μmol above the controls after 749 days of incubation, corresponding to 17 % of the theoretical total. GC-MS analysis confirmed the presence of putative downstream metabolites probably from the anaerobic biodegradation of n-alkanes and indicating an incomplete conversion of the n-alkanes to methane. Enrichment cultures taken at different incubation times were subjected to microbial community analysis. Both 16S rRNA gene clone libraries and DGGE profiles showed that alkanes-degrading community was dynamic during incubation. The dominant bacterial species in the enrichment cultures were affiliated with Firmicutes members clustering with thermophilic syntrophic bacteria of the genera Moorella sp. and Gelria sp. Other represented within the bacterial community were members of the Leptospiraceae, Thermodesulfobiaceae, Thermotogaceae, Chloroflexi, Bacteroidetes and Candidate Division OP1. The archaeal community was predominantly represented by members of the phyla Crenarchaeota and Euryarchaeota. Corresponding sequences within the Euryarchaeota were associated with methanogens clustering with orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. On the other hand, PCR amplification for detection of functional genes encoding the alkylsuccinate synthase α-subunit (assA) was positive in the enrichment cultures. Moreover, the appearance of a new assA gene sequence identified in day 749 supported the establishment of a functioning microbial species in the enrichment. Our results indicate that n-alkanes are converted to methane slowly by a microbial community enriched from oilfield production water and fumarate addition is most likely the initial activation step of n-alkanes degradation under thermophilic methanogenic conditions.

Methanogenic community development in anaerobic granular bioreactors treating trichloroethylene (TCE)-contaminated wastewater at 37 °C and 15 °C.

PubMed

Siggins, Alma; Enright, Anne-Marie; O'Flaherty, Vincent

2011-04-01

Four expanded granular sludge bed (EGSB) bioreactors were seeded with a mesophilically-grown granular sludge and operated in duplicate for mesophilic (37 °C; R1 & R2) and low- (15°; R3 & R4) temperature treatment of a synthetic volatile fatty acid (VFA) based wastewater (3 kg COD m(-3) d(-1)) with one of each pair (R1 & R3) supplemented with increasing concentrations of trichloroethylene (TCE; 10, 20, 40, 60 mg l(-1)) and one acting as a control. Bioreactor performance was evaluated by % COD removal efficiency and % biogas methane (CH(4)) content. Quantitative Polymerase Chain Reaction (qPCR) was used to investigate the methanogenic community composition and dynamics in the bioreactors during the trial, while specific methanogenic activity (SMA) and toxicity assays were utilized to investigate the activity and TCE/dichloroethylene (DCE) toxicity thresholds of key trophic groups, respectively. At both 37 °C and 15 °C, TCE levels of 60 mg l(-1) resulted in the decline of % COD removal efficiencies to 29% (Day 235) and 37% (Day 238), respectively, and in % biogas CH(4) to 54% (Day 235) and 5% (Day 238), respectively. Despite the inhibitory effect of TCE on the anaerobic digestion process, the main drivers influencing methanogenic community development, as determined by qPCR and Non-metric multidimensional scaling analysis, were (i) wastewater composition and (ii) operating temperature. At the apical TCE concentration both SMA and qPCR of methanogenic archaea suggested that acetoclastic methanogens were somewhat inhibited by the presence of TCE and/or its degradation derivatives, while competition by dechlorinating organisms may have limited the availability of H(2) for hydrogenotrophic methanogenesis. In addition, there appeared to be an inverse correlation between SMA levels and TCE tolerance, a finding that was supported by the analysis of the inhibitory effect of TCE on two additional biomass sources. The results indicate that low-temperature anaerobic digestion is a feasible approach for the treatment of TCE-containing wastewater. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

PubMed Central

Seedorf, Henning; Kittelmann, Sandra

2014-01-01

Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ± standard deviation, 89.6% ± 9.8%) and Methanomassiliicoccales (10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ± 6.7%) and Methanosphaera sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens. PMID:25416771

Changes in the ratio of tetraether to diether lipids in cattle feces in response to altered dietary ratio of grass silage and concentrates.

PubMed

McCartney, C A; Dewhurst, R J; Bull, I D

2014-09-01

The distinctive membrane lipids of the archaea can contain a wide range of chemical structures. The membrane lipid composition of ruminal methanogenic archaea has not yet been characterized. In this study, we analyzed proportions of the core archaeal membrane lipids dialkyl glycerol diethers (DGDG) and glycerol dialkyl glycerol tetraether (GDGT). We analyzed the feces of beef steers consuming diets that promoted differences in ruminal conditions that were either favorable (i.e., grass silage) or challenging (i.e., concentrates) for the methanogenic archaea. There was significantly less total ether lipid in the feces of cattle consuming the concentrate diet in comparison to the grass silage diet (97 vs. 218 mg/kg DM, respectively), reflecting the inhibitory effect of dietary concentrate on methanogens. Additionally, the proportion of fecal ether lipids as GDGT was much greater in feces from cattle consuming the concentrate diet than in feces from cattle fed grass silage (90% vs. 67% GDGT). A possible explanation for this adaptation is that membrane lipids composited of GDGT lipids are less permeable to protons, thereby protecting the methanogens against low ruminal pH and helping to maintain the chemiosmotic potential (which is important for ATP production, methanogenesis, and growth). The greater proportion of fecal ether lipids as GDGT may reflect adaptation of membrane lipids within the same species, a shift toward methanogens that have a greater proportion of GDGT (e.g., Thermoplasmata), or both. The effect of ruminal environment on membrane composition means that it will be important to consider the production of both DGDG and GDGT lipids when developing a proxy for methanogenesis.

Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen

USGS Publications Warehouse

Kiene, R.P.; Oremland, Ronald S.; Catena, Anthony; Miller, Laurence G.; Capone, D.G.

1986-01-01

Addition of dimethylsulfide (DMS), dimethyldisulfide (DMDS), or methane thiol (MSH) to a diversity of anoxic aquatic sediments (e.g., fresh water, estuarine, alkaline/hypersaline) stimulated methane production. The yield of methane recovered from DMS was often 52 to 63%, although high concentrations of DMS (as well as MSH and DMDS) inhibited methanogenesis in some types of sediments. Production of methane from these reduced methylated sulfur compounds was blocked by 2-bromoethanesulfonic acid. Sulfate did not influence the metabolism of millimolar levels of DMS, DMDS, or MSH added to sediments. However, when DMS was added at ∼2-μM levels as [14C]DMS, metabolism by sediments resulted in a 14CH4/14CO2 ratio of only 0.06. Addition of molybdate increased the ratio to 1.8, while 2-bromoethanesulfonic acid decreased it to 0, but did not block 14CO2 production. These results indicate the methanogens and sulfate reducers compete for DMS when it is present at low concentrations; however, at high concentrations, DMS is a “noncompetitive” substrate for methanogens. Metabolism of DMS by sediments resulted in the appearance of MSH as a transient intermediate. A pure culture of an obligately methylotrophic estuarine methanogen was isolated which was capable of growth on DMS. Metabolism of DMS by the culture also resulted in the transient appearance of MSH, but the organism could grow on neither MSH nor DMDS. The culture metabolized [14C]-DMS to yield a 14CH4/14CO2 ratio of ∼2.8. Reduced methylated sulfur compounds represent a new class of substrates for methanogens and may be potential precursors of methane in a variety of aquatic habitats.

The composition, localization and function of low-temperature-adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils.

PubMed

Dai, Y; Yan, Z; Jia, L; Zhang, S; Gao, L; Wei, X; Mei, Z; Liu, X

2016-07-01

To reveal the microbial communities from Qinghai-Tibetan Plateau wetland soils that have the potential to be used in the utilization of cellulosic and chitinous biomass at low temperatures (≤25°C). Soil samples collected from six wetlands on Qinghai-Tibetan Plateau were supplemented with or without cellulose and chitin flakes, and anaerobically incubated at 25 and 15°C; high-throughput 16S rRNA gene sequencing was used to access the composition and localization (in the slurry and on the surface) of enriched microbial communities; a hypothetical model was constructed to demonstrate the functional roles of involved microbes mainly at genus level. Overall, microbial communities from Qinghai-Tibetan Plateau wetlands showed significant potential to convert both cellulose and chitin to methane at low temperatures; Clostridium III, Clostridium XIVa, Paludibacter, Parcubacteria, Saccharofermentans, Pelotomaculum, Methanosaeta, Methanobrevibacter, Methanoregula, Methanospirillum and Methanosarcina participated in methanogenic degradation of both cellulose and chitin through the roles of hydrolytic, saccharolytic and secondary fermenters and methanogens respectively. Acetotrophic methanogens were mainly enriched in the slurries, while hydrogenotrophic methanogens could be both in the slurries and on the surface. The composition and localization of microbial communities that could effectively convert cellulose and chitin to methane at low temperatures have been revealed by high-throughput 16S rRNA gene sequencing methods, and reviewing the literatures on the microbial pure culture helped to elucidate functional roles of significantly enriched microbes. This study will contribute to the understanding of carbon and nitrogen cycling of cellulose and chitin in cold-area wetlands and provide fundamental information to obtain microbial resources for the utilization of biomass wastes at low temperatures. © 2016 The Society for Applied Microbiology.

Isolation, identification and fibrolytic characteristics of rumen fungi grown with indigenous methanogen from yaks (Bos grunniens) grazing on the Qinghai-Tibetan Plateau.

PubMed

Wei, Y-Q; Yang, H-J; Luan, Y; Long, R-J; Wu, Y-J; Wang, Z-Y

2016-03-01

To obtain co-cultures of anaerobic fungi and their indigenously associated methanogens from the rumen of yaks grazing on the Qinghai-Tibetan Plateau and investigate their morphology features and ability to degrade lignocellulose. Twenty fungus-methanogen co-cultures were obtained by Hungate roll-tube technique. The fungi were identified as Orpinomyces, Neocallimastix and Piromyces genera based on the morphological characteristics and internal transcribed spacer 1 sequences analysis. All methanogens were identified as Methanobrevibacter sp. by 16S rRNA gene sequencing. There were four types of co-cultures: Neocallimastix with Methanobrevibacter ruminantium, Orpinomyces with M. ruminantium, Orpinomyces with Methanobrevibacter millerae and Piromyces with M. ruminantium among 20 co-cultures. In vitro studies with wheat straw as substrate showed that the Neocallimastix with M. ruminantium co-cultures and Piromyces with M. ruminantium co-cultures exhibited higher xylanase, filter paper cellulase (FPase), ferulic acid esterase, acetyl esterase activities, in vitro dry matter digestibility, gas, CH4 , acetate production, ferulic acid and p-coumaric acid releases. The Neocallimastix frontalis Yak16 with M. ruminantium co-culture presented the strongest lignocellulose degradation ability among 20 co-cultures. Twenty fungus-methanogen co-cultures were obtained from the rumen of grazing yaks. The N. frontalis with M. ruminantium co-cultures were highly effective combination for developing a fermentative system that bioconverts lignocellulose to high activity fibre-degrading enzyme, CH4 and acetate. The N. frontalis with M. ruminantium co-cultures from yaks grazing on the Qinghai-Tibetan Plateau present great potential in lignocellulose biodegradation industry. © 2015 The Society for Applied Microbiology.

The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

PubMed Central

Kessler, Peter S.; Blank, Carrine; Leigh, John A.

1998-01-01

Nitrogen fixation occurs in two domains, Archaea and Bacteria. We have characterized a nif (nitrogen fixation) gene cluster in the methanogenic archaeon Methanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order, nifH, ORF105 (similar to glnB), ORF121 (similar to glnB), nifD, nifK, nifE, nifN, and nifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of the glnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kb nif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ to nifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens. PMID:9515920

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

Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations.

PubMed

Klieve, A V; Ouwerkerk, D; Maguire, A J

2012-11-01

To investigate, using culture-independent techniques, the presence and diversity of methanogenic archaea in the foregut of kangaroos. DNA was extracted from forestomach contents of 42 kangaroos (three species), three sheep and three cattle. Four qualitative and quantitative PCR assays targeting the archaeal domain (16S rRNA gene) or the functional methanogenesis gene, mcrA, were used to determine the presence and population density of archaea in kangaroos and whether they were likely to be methanogens. All ruminal samples were positive for archaea, produced PCR product of expected size, contained high numbers of archaea and high numbers of cells with mcrA genes. Kangaroos were much more diverse and contradictory. Fourteen kangaroos had detectable archaea with numbers 10- to 1000-fold fewer than sheep and cattle. Many kangaroos that did not possess archaea were positive for the mcrA gene and had detectable numbers of cells with this gene and vice versa. DNA sequence analysis of kangaroos' archaeal 16S rRNA gene clones show that many methanogens were related to Methanosphaera stadmanae. Other sequences were related to non-methanogenic archaea (Thermoplasma sp.), and a number of kangaroos had mcrA gene sequences related to methane oxidising archaea (ANME). Discrepancies between qualitative and quantitative PCR assays for archaea and the mcrA gene suggest that the archaeal communities are very diverse and it is possible that novel species exist. Archaea (in general) were below detectable limits in many kangaroos, especially Red kangaroos; when present they are in lower numbers than in ruminants, and the archaea are not necessarily methanogenic. The determination of why this is the case in the kangaroo foregut could assist in reducing emissions from other ecosystems in the future. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Methanolobus taylorii sp nov, a new methylotropic, estuarine methanogen

USGS Publications Warehouse

Oremland, Ronald S.; Boone, David R.

1994-01-01

Strain GS-16T (T = type strain) is a methylotrophic methanogen that was isolated from estuarine sediments from San Francisco Bay (4) and has been deposited in the Oregon Collection of Methanogens (Oregon Graduate Institute, Portland) as strain OCM 5ST. This strain was isolated by using dimethyl sulfide as the catabolic substrate (4), but it can also grow on methylamines (13) and methanethiol (8, 9) and grew when it was inoculated into MSHA medium (6) supplemented with 20 mM methanol as the sole catabolic substrate. Strain GS-16T cells form methane from methylmercury (12) and dimethylselenide (16), although they cannot grow on these substrates, and form traces of ethane from diethyl sulfide (15). Methanogenesis from trimethylamine is inhibited by methyl fluoride (11) and methyl bromide (14), but not by dimethyl ether (1 1).

Methods for Detecting Microbial Methane Production and Consumption by Gas Chromatography.

PubMed

Aldridge, Jared T; Catlett, Jennie L; Smith, Megan L; Buan, Nicole R

2016-04-05

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO 2 . Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al. , 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al. , 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al. , 2015). Here we describe the end point and kinetic assays that can be used to measure methane production by methanogens or methane consumption by methanotrophic microbes. The protocols can be used for measuring methane production or consumption by microbial pure cultures or by enrichment cultures.

Application of Methanobrevibacter acididurans in anaerobic digestion.

PubMed

Savant, D V; Ranade, D R

2004-01-01

To operate anaerobic digesters successfully under acidic conditions, hydrogen utilizing methanogens which can grow efficiently at low pH and tolerate high volatile fatty acids (VFA) are desirable. An acid tolerant hydrogenotrophic methanogen viz. Methanobrevibacter acididurans isolated from slurry of an anaerobic digester running on alcohol distillery wastewater has been described earlier by this lab. This organism could grow optimally at pH 6.0. In the experiments reported herein, M. acididurans showed better methanogenesis under acidic conditions with high VFA, particularly acetate, than Methanobacterium bryantii, a common hydrogenotrophic inhabitant of anaerobic digesters. Addition of M. acididurans culture to digesting slurry of acidogenic as well as methanogenic digesters running on distillery wastewater showed increase in methane production and decrease in accumulation of volatile fatty acids. The results proved the feasibility of application of M. acididurans in anaerobic digesters.

Shifts in Methanogenic Subpopulations Measured with Antibody Probes in a Fixed-Bed Loop Anaerobic Bioreactor Treating Sulfite Evaporator Condensate

PubMed Central

Macario, Alberto J. L.; de Macario, Everly Conway; Ney, Ulrich; Schoberth, Siegfried M.; Sahm, Hermann

1989-01-01

A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbations, such as restarting and relocating the biomass into a different tank. Methanogens related to Methanobacterium bryantii MoHG and Methanobrevibacter smithii ALI were numerous throughout the observation period, while Methanosarcina mazei S6 and Methanosarcina thermophila TM1 were found in the early and late samples, respectively. Also, Methanobacterium formicicum was more numerous at the top portion of the bioreactor, while Methanobrevibacter arboriphilus AZ and DC were at the bottom. Sample formalinization required for prolonged storage proved suitable for antigen preservation. Images PMID:16347990

Shifts in methanogenic subpopulations measured with antibody probes in a fixed-bed loop anaerobic bioreactor treating sulfite evaporator condensate.

PubMed

Macario, A J; Conway de Macario, E; Ney, U; Schoberth, S M; Sahm, H

1989-08-01

A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbations, such as restarting and relocating the biomass into a different tank. Methanogens related to Methanobacterium bryantii MoHG and Methanobrevibacter smithii ALI were numerous throughout the observation period, while Methanosarcina mazei S6 and Methanosarcina thermophila TM1 were found in the early and late samples, respectively. Also, Methanobacterium formicicum was more numerous at the top portion of the bioreactor, while Methanobrevibacter arboriphilus AZ and DC were at the bottom. Sample formalinization required for prolonged storage proved suitable for antigen preservation.

Does lead affect microbial metabolism in aquifer sediments under different terminal electron accepting conditions?

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Vroblesky, D.A.

1993-01-01

In groundwater from a petroleum hydrocarbon-contaminated aquifer. Substantial accumulation of aliphatic organic acids occurred only in methanogenic microcosms, and only trace amounts of acetic acid were detected in sulfate-reducing microcosms. This pattern parallels field observations in which high organic acid concentrations were detected in methanogenic zones, but only low concentrations of acetic acid were detected in sulfate-reducing zones. -from Authors

Choline and N,N-dimethylethanolamine as direct substrates for methanogens.

PubMed

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

2012-12-01

Choline (N,N,N-trimethylethanolamine), which is widely distributed in membrane lipids and is a component of sediment biota, has been shown to be utilized anaerobically by mixed prokaryote cultures to produce methane but not by pure cultures of methanogens. Here, we show that five recently isolated Methanococcoides strains from a range of sediments (Aarhus Bay, Denmark; Severn Estuary mudflats at Portishead, United Kingdom; Darwin Mud Volcano, Gulf of Cadiz; Napoli mud volcano, eastern Mediterranean) can directly utilize choline for methanogenesis producing ethanolamine, which is not further metabolized. Di- and monomethylethanolamine are metabolic intermediates that temporarily accumulate. Consistent with this, dimethylethanolamine was shown to be another new growth substrate, but monomethylethanolamine was not. The specific methanogen inhibitor 2-bromoethanesulfonate (BES) inhibited methane production from choline. When choline and trimethylamine are provided together, diauxic growth occurs, with trimethylamine being utilized first, and then after a lag (∼7 days) choline is metabolized. Three type strains of Methanococcoides (M. methylutens, M. burtonii, and M. alaskense), in contrast, did not utilize choline. However, two of them (M. methylutens and M. burtonii) did metabolize dimethylethanolamine. These results extend the known substrates that can be directly utilized by some methanogens, giving them the advantage that they would not be reliant on bacterial syntrophs for their substrate supply.

Choline and N,N-Dimethylethanolamine as Direct Substrates for Methanogens

PubMed Central

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

2012-01-01

Choline (N,N,N-trimethylethanolamine), which is widely distributed in membrane lipids and is a component of sediment biota, has been shown to be utilized anaerobically by mixed prokaryote cultures to produce methane but not by pure cultures of methanogens. Here, we show that five recently isolated Methanococcoides strains from a range of sediments (Aarhus Bay, Denmark; Severn Estuary mudflats at Portishead, United Kingdom; Darwin Mud Volcano, Gulf of Cadiz; Napoli mud volcano, eastern Mediterranean) can directly utilize choline for methanogenesis producing ethanolamine, which is not further metabolized. Di- and monomethylethanolamine are metabolic intermediates that temporarily accumulate. Consistent with this, dimethylethanolamine was shown to be another new growth substrate, but monomethylethanolamine was not. The specific methanogen inhibitor 2-bromoethanesulfonate (BES) inhibited methane production from choline. When choline and trimethylamine are provided together, diauxic growth occurs, with trimethylamine being utilized first, and then after a lag (∼7 days) choline is metabolized. Three type strains of Methanococcoides (M. methylutens, M. burtonii, and M. alaskense), in contrast, did not utilize choline. However, two of them (M. methylutens and M. burtonii) did metabolize dimethylethanolamine. These results extend the known substrates that can be directly utilized by some methanogens, giving them the advantage that they would not be reliant on bacterial syntrophs for their substrate supply. PMID:23001649

Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems

PubMed Central

Sleutels, Tom H. J. A.; Molenaar, Sam D.; Heijne, Annemiek Ter; Buisman, Cees J. N.

2016-01-01

A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future. PMID:27681899

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

PubMed Central

Walter, Andreas; Knapp, Brigitte A.; Farbmacher, Theresa; Ebner, Christian; Insam, Heribert; Franke‐Whittle, Ingrid H.

2012-01-01

Summary To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year. PMID:22950603

Molecular sequences derived from Paleocene Fort Union Formation coals vs. associated produced waters: Implications for CBM regeneration

USGS Publications Warehouse

Klein, Donald A.; Flores, Romeo M.; Venot, Christophe; Gabbert, Kendra; Schmidt, Raleigh; Stricker, Gary D.; Pruden, Amy; Mandernack, Kevin

2008-01-01

Coalbed methane regeneration is of increasing interest, and is gaining global attention with respect to enhancement of gas recovery. The objective of this study is to determine if there are differences in methanogen nucleic acid sequences associated with low rank coals from the Powder River Basin, Wyoming, in comparison with sequences that can be recovered from coal bed-associated produced waters. Based on results obtained to date, the sequences from the coals appear to be associated with putatively deep-rooted thermophilic autotrophic methanogens, whereas the sequences from the waters are associated with thermophilic autotrophic and heterotrophic methanogens. The recovered sequences associated with coal thus appear to be both phylogenetically and functionally distinct from those that are more closely associated with the produced water. To be able to relate such recovered sequences to organisms that might be present and possibly active in these environments, it is suggested that direct observation, followed by isolation and single cell-based physiological/molecular analyses, be used to characterize methanogenic consortia possibly associated with coals and/or produced waters. It is also important to characterize the microenvironment where these microbes might be found, in both ecological and geological contexts, to be able to develop effective, ecologically relevant coalbed methane regeneration processes.

Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems.

PubMed

Sleutels, Tom H J A; Molenaar, Sam D; Heijne, Annemiek Ter; Buisman, Cees J N

2016-01-05

A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future.

Effect of feeding palm oil by-products based diets on total bacteria, cellulolytic bacteria and methanogenic archaea in the rumen of goats.

PubMed

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats.

Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates

PubMed Central

Khan, Munawwar A.; Patel, Poojabahen G.; Ganesh, Arpitha G.; Rais, Naushad; Faheem, Sultan M.; Khan, Shams T.

2018-01-01

Introduction: Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique. Methods & Materials: Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies. Results and Discussion: In general, the aceticlastic organisms (Methanosarcinaceae & Methanosaetaceae) were more abundant than the hydrogenotrophic organisms (Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that family Methanosaetaceae was the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters. Conclusion: Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters. PMID:29785219

Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation.

PubMed

Zhuang, Li; Tang, Jia; Wang, Yueqiang; Hu, Min; Zhou, Shungui

2015-08-15

Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments. Copyright © 2015 Elsevier B.V. All rights reserved.

Methane producing bacteria: Immunological characterization: Progress report, April 1, 1984--June 30, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conway de Macario, E.; Macario, A.J.L.; Wolin, M.J.

1988-01-01

A major contribution of this research has been a significant advance of the immunology of methanogens and other archaebacteria (e.g., extreme halophiles). The foundations have been laid to begin the immunologic study of microbes which are non-methanogens themselves but are important for the fermentation process. This work helped to make clear that bacterial immunology goes beyond the study of pathogens for man, animals, or plants. Immunology can be applied successfully to the study of isolates of importance to understand evolution, phylogeny, ecology, bio-conversion systems, and to advance methanogenic biotechnology. Immunology holds considerable potential to aid in genetic and genetic engineeringmore » manipulations as well as in in situ handling of microbes relevant to methanogenesis. Thus, antibodies can help in the discovery of useful microbes, the generation of improved stains, the selection of desirable microorganisms, and in the monitoring and controlling of bioreactors. Immunogolic work in this new field should generate knowledge and devices relevant to areas such as Biological Energy Research, Ecology of Microorganisms, and Environmental (Sanitary) Engineering. In this regard, this work has contributed a comprehensive antiserum bank, a large panel of calibrated polyclonal antibody probes, and techniques for producing and utilizing these probes in the study of methanogens and related bacteria. 67 refs.« less

Anaerobic consumers of monosaccharides in a moderately acidic fen.

PubMed

Hamberger, Alexandra; Horn, Marcus A; Dumont, Marc G; Murrell, J Colin; Drake, Harold L

2008-05-01

16S rRNA-based stable isotope probing identified active xylose- and glucose-fermenting Bacteria and active Archaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH(4)-emitting fen. Xylose and glucose were converted to fatty acids, CO(2), H(2), and CH(4) under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermenters, as well as moderately acid-tolerant methanogens. Organisms of the families Acidaminococcaceae, Aeromonadaceae, Clostridiaceae, Enterobacteriaceae, and Pseudomonadaceae and the order Actinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facultative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. Uncultured Euryarchaeota (i.e., Methanosarcinaceae and Methanobacteriaceae) and Crenarchaeota species were identified by 16S rRNA analysis of anoxic slurries, demonstrating that the acidic fen harbors novel methanogens and Crenarchaeota organisms capable of anaerobiosis. Fermentation-derived molecules are conceived to be the primary drivers of methanogenesis when electron acceptors other than CO(2) are absent, and the collective findings of this study indicate that fen soils harbor diverse, acid-tolerant, and novel xylose-utilizing as well as glucose-utilizing facultative aerobes and obligate anaerobes that form trophic links to novel moderately acid-tolerant methanogens.

Atypical one-carbon metabolism of an acetogenic and hydrogenogenic Moorella thermoacetica strain.

PubMed

Jiang, Bo; Henstra, Anne-Meint; Paulo, Paula L; Balk, Melike; van Doesburg, Wim; Stams, Alfons J M

2009-02-01

A thermophilic spore-forming bacterium (strain AMP) was isolated from a thermophilic methanogenic bioreactor that was fed with cobalt-deprived synthetic medium containing methanol as substrate. 16S rRNA gene analysis revealed that strain AMP was closely related to the acetogenic bacterium Moorella thermoacetica DSM 521(T) (98.3% sequence similarity). DNA-DNA hybridization showed 75.2 +/- 4.7% similarity to M. thermoacetica DSM 521(T), suggesting that strain AMP is a M. thermoacetica strain. Strain AMP has a unique one-carbon metabolism compared to other Moorella species. In media without cobalt growth of strain AMP on methanol was only sustained in coculture with a hydrogen-consuming methanogen, while in media with cobalt it grew acetogenically in the absence of the methanogen. Addition of thiosulfate led to sulfide formation and less acetate formation. Growth of strain AMP with CO resulted in the formation of hydrogen as the main product, while other CO-utilizing Moorella strains produce acetate as product. Formate supported growth only in the presence of thiosulfate or in coculture with the methanogen. Strain AMP did not grow with H(2)/CO(2), unlike M. thermoacetica (DSM 521(T)). The lack of growth with H(2)/CO(2) likely is due to the absence of cytochrome b in strain AMP.

Conductive iron oxides accelerate thermophilic methanogenesis from acetate and propionate.

PubMed

Yamada, Chihaya; Kato, Souichiro; Ueno, Yoshiyuki; Ishii, Masaharu; Igarashi, Yasuo

2015-06-01

Anaerobic digester is one of the attractive technologies for treatment of organic wastes and wastewater, while continuous development and improvements on their stable operation with efficient organic removal are required. Particles of conductive iron oxides (e.g., magnetite) are known to facilitate microbial interspecies electron transfer (termed as electric syntrophy). Electric syntrophy has been reported to enhance methanogenic degradation of organic acids by mesophilic communities in soil and anaerobic digester. Here we investigated the effects of supplementation of conductive iron oxides (magnetite) on thermophilic methanogenic microbial communities derived from a thermophilic anaerobic digester. Supplementation of magnetite accelerated methanogenesis from acetate and propionate under thermophilic conditions, while supplementation of ferrihydrite also accelerated methanogenesis from propionate. Microbial community analysis revealed that supplementation of magnetite drastically changed bacterial populations in the methanogenic acetate-degrading cultures, in which Tepidoanaerobacter sp. and Coprothermobacter sp. dominated. These results suggest that supplementation of magnetite induce electric syntrophy between organic acid-oxidizing bacteria and methanogenic archaea and accelerate methanogenesis even under thermophilic conditions. Findings from this study would provide a possibility for the achievement of stably operating thermophilic anaerobic digestion systems with high efficiency for removal of organics and generation of CH4. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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. © 2016 S. Karger AG, Basel.

A Flexible System for Cultivation of Methanococcus and Other Formate-Utilizing Methanogens

PubMed Central

Wang, Liangliang; Lupa, Boguslaw

2017-01-01

Many hydrogenotrophic methanogens use either H2 or formate as the major electron donor to reduce CO2 for methane production. The conventional cultivation of these organisms uses H2 and CO2 as the substrate with frequent replenishment of gas during growth. H2 is explosive and requires an expensive gassing system to handle safely. Formate is as an ideal alternative substrate from the standpoints of both economy and safety but leads to large changes in the culture pH during growth. Here, we report that glycylglycine is an inexpensive and nontoxic buffer suitable for growth of Methanococcus maripaludis and Methanothermococcus okinawensis. This cultivation system is suitable for growth on liquid as well as solid medium in serum bottles. Moreover, it allows cultivation of liter scale cultures without expensive fermentation equipment. This formate cultivation system provides an inexpensive and flexible alternative for the growth of formate-utilizing, hydrogenotrophic methanogens. PMID:29348732

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.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy.

PubMed

Brazelton, William J; Thornton, Christopher N; Hyer, Alex; Twing, Katrina I; Longino, August A; Lang, Susan Q; Lilley, Marvin D; Früh-Green, Gretchen L; Schrenk, Matthew O

2017-01-01

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.

Salinity and Temperature Constraints on Microbial Methanogenesis in the Lei-Gong-Huo Mud Volcano of Eastern Taiwan

NASA Astrophysics Data System (ADS)

Sun, W.; Lin, L.; Wang, P.

2012-12-01

Terrestrial mud volcano is thought to be one of the most important natural sources of methane emission. Previous studies have shown that methane cycling in terrestrial mud volcanoes involves a complex reaction network driven by the interactions between subsurface and surface abiotic and microbial processes. In situ methanogenesis appears to produce methane at quantities exceeding those of deeply-sourced thermogenic methane and the capacities of anaerobic methanotrophy at shallow depth levels, thereby contributing significantly to the methane emission. Various degrees of evaporation at surface also lead to the enhancement of chloride concentrations in pore water, favoring the proliferation of halo-tolerant and/or halophilic methanogens. The goal of this study is to investigate the extent of methanogenesis in terrestrial mud volcanoes by incubating mud slurries with various precursors (H2/CO2, acetate, methanol, and methylamine) at different salinities (up to 2000 mM) and temperatures (up to 50 oC). Methane concentrations were monitored through time and molecular analyses were applied to investigate the changes of methanogenic communities. Methanogenesis was stimulated by any investigated precursor at room temperature. However, the methanogenic response to salinity varied. Of the investigated precursors, H2/CO2 and methyl-compounds (methanol and methylamine) stimulated methanogenesis at all investigated salinities. The rates and yields of hydrogen- and methyl-utilizing methanogenesis declined significantly at salinities greater than 1500 mM. Acetate-utilizing methanogenesis proceeded at salinities less than 700 mM. At 40 oC, methanogenesis was stimulated by all investigated precursors at the in situ salinity (~400 mM). At 50 oC, only H2-utilizing methanogenesis was stimulated. Analyses of terminal restriction fragment length polymorphism (TRFLP) for 16S rRNA genes revealed various patterns upon different precursors and salinities. The TRFLP results combined with clone library analyses indicated that major RFs recovered from incubations with methyl-compounds at room temperature and 40 oC were represented by sequences affiliated with Methanococcoides spp., Methanosarcina spp., and Methanolobus spp. In particular, only Methanosarcina- and Methanococcoides-related members were detected at salinities greater than 1000 mM or at 40 oC. RFs recovered from incubations with H2/CO2 at room temperature and 40 oC were represented by sequences related to different Methanococcus spp. Overall, methanogens utilizing H2/CO2 and methyl-compounds appear to be capable of actively producing methane at salinities greater than acetate-utilizing methanogens could tolerate. These methanogens might adapt better to the fluctuation of salinity or extremely high salinity induced by the surface evaporation in terrestrial mud volcanoes. When considering the overall methane emission from terrestrial mud volcanoes, these halo-tolerant methanogens become a significant factor. Key words: mud volcano, Methane, Methanogenesis, Salinity

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

PubMed Central

Elling, Felix J.; Yoshinaga, Marcos Y.; Söllinger, Andrea; Urich, Tim; Hinrichs, Kai-Uwe

2016-01-01

ABSTRACT A new clade of archaea has recently been proposed to constitute the seventh methanogenic order, the Methanomassiliicoccales, which is related to the Thermoplasmatales and the uncultivated archaeal clades deep-sea hydrothermal vent Euryarchaeota group 2 and marine group II Euryarchaeota but only distantly related to other methanogens. In this study, we investigated the membrane lipid composition of Methanomassiliicoccus luminyensis, the sole cultured representative of this seventh order. The lipid inventory of M. luminyensis comprises a unique assemblage of novel lipids as well as lipids otherwise typical for thermophilic, methanogenic, or halophilic archaea. For instance, glycerol sesterpanyl-phytanyl diether core lipids found mainly in halophilic archaea were detected, and so were compounds bearing either heptose or methoxylated glycosidic head groups, neither of which have been reported so far for other archaea. The absence of quinones or methanophenazines is consistent with a biochemistry of methanogenesis different from that of the methanophenazine-containing methylotrophic methanogens. The most distinctive characteristic of the membrane lipid composition of M. luminyensis, however, is the presence of tetraether lipids in which one glycerol backbone is replaced by either butane- or pentanetriol, i.e., lipids recently discovered in marine sediments. Butanetriol dibiphytanyl glycerol tetraether (BDGT) constitutes the most abundant core lipid type (>50% relative abundance) in M. luminyensis. We have thus identified a source for these unusual orphan lipids. The complementary analysis of diverse marine sediment samples showed that BDGTs are widespread in anoxic layers, suggesting an environmental significance of Methanomassiliicoccales and/or related BDGT producers beyond gastrointestinal tracts. IMPORTANCE Cellular membranes of members of all three domains of life, Archaea, Bacteria, and Eukarya, are largely formed by lipids in which glycerol serves as backbone for the hydrophobic alkyl chains. Recently, however, archaeal tetraether lipids with either butanetriol or pentanetriol as a backbone were identified in marine sediments and attributed to uncultured sediment-dwelling archaea. Here we show that the butanetriol-based dibiphytanyl tetraethers constitute the major lipids in Methanomassiliicoccus luminyensis, currently the only isolate of the novel seventh order of methanogens. Given the absence of these lipids in a large set of archaeal isolates, these compounds may be diagnostic for the Methanomassiliicoccales and/or closely related archaea. PMID:27208108

Effects of dietary supplementation of active dried yeast on fecal methanogenic archaea diversity in dairy cows.

PubMed

Jin, Dingxing; Kang, Kun; Wang, Hongze; Wang, Zhisheng; Xue, Bai; Wang, Lizhi; Xu, Feng; Peng, Quanhui

2017-04-01

This study aimed to investigate the effects of dietary supplementation of different dosages of active dried yeast (ADY) on the fecal methanogenic archaea community of dairy cattle. Twelve multiparous, healthy, mid-lactating Holstein dairy cows (body weight: 584 ± 23.2 kg, milk produced: 26.3 ± 1.22 kg/d) were randomly assigned to one of three treatments (control, ADY2, and ADY4) according to body weight with four replicates per treatment. Cows in the control group were fed conventional rations without ADY supplementation, while cows in the ADY2 and ADY4 group were fed rations supplemented with ADY at 2 or 4 g/d/head. Real-time PCR analysis showed the populations of total methanogens in the feces were significantly decreased (P < 0.05) in the ADY4 group compared with control. High-throughput sequencing technology was applied to examine the differences in methanogenic archaea diversity in the feces of the three treatment groups. A total of 155,609 sequences were recovered (a mean of 12,967 sequences per sample) from the twelve fecal samples, which consisted of a number of operational taxonomic units (OTUs) ranging from 1451 to 1,733, were assigned to two phyla, four classes, five orders, five families and six genera. Bioinformatic analyses illustrated that the natural fecal archaeal community of the control group was predominated by Methanobrevibacter (86.9% of the total sequence reads) and Methanocorpusculum (10.4%), while the relative abundance of the remaining four genera were below 1% with Methanosphaera comprising 0.8%, Thermoplasma composing 0.4%, and the relative abundance of Candidatus Nitrososphaera and Halalkalicoccus being close to zero. At the genus level, the relative abundances of Methanocorpusculum and Thermoplasma were increased (P < 0.05) with increasing dosage of ADY. Conversely, the predominant methanogen genus Methanobrevibacter was decreased with ADY dosage (P < 0.05). Dietary supplementation of ADY had no significant effect (P > 0.05) on the abundances of genera unclassified, Candidatus Nitrososphaera, and Halalkalicoccus. In conclusion, supplementation of ADY to the rations of dairy cattle could alter the population sizes and composition of fecal methanogenic archaea in the feces of dairy cattle. The decrease in Methanobrevibacter happened with a commensurate increase in the genera Methanocorpusculum and Thermoplasma. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children

PubMed Central

van de Pol, Jeroen A. A.; van Best, Niels; Mbakwa, Catherine A.; Thijs, Carel; Savelkoul, Paul H.; Arts, Ilja C. W.; Hornef, Mathias W.; Mommers, Monique; Penders, John

2017-01-01

The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity. Archaea have been shown to be absent during infancy while omnipresent in school-aged children, suggesting that colonization may result from environmental exposure during childhood. The factors that determine the acquisition of methanogenic archaea, however, have remained undefined. Therefore, we aimed to explore determinants associated with the acquisition of the two main gastrointestinal archaeal species, Methanobrevibacter smithii and Methanosphaera stadtmanae, in children. Within the context of the KOALA Birth Cohort Study, fecal samples from 472 children aged 6–10 years were analyzed for the abundance of M. smithii and M. stadtmanae using qPCR. Environmental factors such as diet, lifestyle, hygiene, child rearing, and medication were recorded by repeated questionnaires. The relationship between these determinants and the presence and abundance of archaea was analyzed by logistic and linear regression respectively. Three hundred and sixty-nine out of the 472 children (78.2%) were colonized by M. smithii, and 39 out of the 472 children (8.3%) by M. stadtmanae. The consumption of organic yogurt (odds ratio: 4.25, CI95: 1.51; 11.95) and the consumption of organic milk (odds ratio: 5.58, CI95: 1.83; 17.01) were positively associated with the presence of M. smithii. We subsequently screened raw milk, processed milk, and yogurt samples for methanogens. We identified milk products as possible source for M. smithii, but not M. stadtmanae. In conclusion, M. smithii seems present in milk products and their consumption may determine archaeal gut colonization in children. For the first time, a large variety of determinants have been explored in association with gut colonization by methanogenic archaea. Although more information is needed to confirm and unravel the mechanisms in detail, it provides new insights on microbial colonization processes in early life. PMID:28344572

Long-Term Incubation Reveals Methanogenic Biodegradation of C5 and C6 iso-Alkanes in Oil Sands Tailings.

PubMed

Siddique, Tariq; Mohamad Shahimin, Mohd Faidz; Zamir, Saima; Semple, Kathleen; Li, Carmen; Foght, Julia M

2015-12-15

iso-Alkanes are major components of petroleum and have been considered recalcitrant to biodegradation under methanogenic conditions. However, indigenous microbes in oil sands tailings ponds exposed to solvents rich in 2-methylbutane, 2-methylpentane, 3-methylpentane, n-pentane, and n-hexane produce methane in situ. We incubated defined mixtures of iso- or n-alkanes with mature fine tailings from two tailings ponds of different ages historically exposed to different solvents: one, ~10 years old, receiving C5-C6 paraffins and the other, ~35 years old, receiving naphtha. A lengthy incubation (>6 years) revealed iso-alkane biodegradation after lag phases of 900-1800 and ~280 days, respectively, before the onset of methanogenesis, although lag phases were shorter with n-alkanes (~650-1675 and ~170 days, respectively). 2-Methylpentane and both n-alkanes were completely depleted during ~2400 days of incubation, whereas 2-methylbutane and 3-methylpentane were partially depleted only during active degradation of 2-methylpentane, suggesting co-metabolism. In both cases, pyrotag sequencing of 16S rRNA genes showed codominance of Peptococcaceae with acetoclastic (Methanosaeta) and hydrogenotrophic (Methanoregula and Methanolinea) methanogens. These observations are important for predicting long-term greenhouse-gas emissions from oil sands tailings ponds and extend the known range of hydrocarbons susceptible to methanogenic biodegradation in petroleum-impacted anaerobic environments.

An advanced anaerobic biofilter with effluent recirculation for phenol removal and methane production in treatment of coal gasification wastewater.

PubMed

Li, Yajie; Tabassum, Salma; Zhang, Zhenjia

2016-09-01

An advanced anaerobic biofilter (AF) was introduced for the treatment of coal gasification wastewater (CGW), and effluent recirculation was adopted to enhance phenol removal and methane production. The results indicated that AF was reliable in treating diluted CGW, while its efficiency and stability were seriously reduced when directly treating raw CGW. However, its performance could be greatly enhanced by effluent recirculation. Under optimal effluent recirculation of 0.5 to the influent, concentrations of chemical oxygen demand (COD) and total phenol in the effluent could reach as low as 234.0 and 14.2mg/L, respectively. Also, the rate of methane production reached 169.0mLCH4/L/day. Though CGW seemed to restrain the growth of anaerobic microorganisms, especially methanogens, the inhibition was temporary and reversible, and anaerobic bacteria presented strong tolerance. The activities of methanogens cultivated in CGW could quickly recover on feeding with glucose wastewater (GW). However, the adaptability of anaerobic bacteria to the CGW was very poor and the activity of methanogens could not be improved by long-term domestication. By analysis using the Haldane model, it was further confirmed that high effluent recirculation could result in high activity for hydrolytic bacteria and substrate affinity for toxic matters, but only suitable effluent recirculation could result in high methanogenic activity. Copyright © 2016. Published by Elsevier B.V.

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.

PubMed

Wagner, Robert; Zona, Donatella; Oechel, Walter; Lipson, David

2017-08-01

While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Draft Genome of the Non-Host-Associated Methanobrevibacter arboriphilus Strain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins

PubMed Central

Poehlein, Anja; Daniel, Rolf

2017-01-01

Methanobrevibacter arboriphilus strain DH1 is an autotrophic methanogen that was isolated from the wetwood of methane-emitting trees. This species has been of considerable interest for its unusual oxygen tolerance and has been studied as a model organism for more than four decades. Strain DH1 is closely related to other host-associated Methanobrevibacter species from intestinal tracts of animals and the rumen, making this strain an interesting candidate for comparative analysis to identify factors important for colonizing intestinal environments. Here, the genome sequence of M. arboriphilus strain DH1 is reported. The draft genome is composed of 2.445.031 bp with an average GC content of 25.44% and predicted to harbour 1964 protein-encoding genes. Among the predicted genes, there are also more than 50 putative genes for the so-called adhesin-like proteins (ALPs). The presence of ALP-encoding genes in the genome of this non-host-associated methanogen strongly suggests that target surfaces for ALPs other than host tissues also need to be considered as potential interaction partners. The high abundance of ALPs may also indicate that these types of proteins are more characteristic for specific phylogenetic groups of methanogens rather than being indicative for a particular environment the methanogens thrives in. PMID:28634433

Effect of Feeding Palm Oil By-Products Based Diets on Total Bacteria, Cellulolytic Bacteria and Methanogenic Archaea in the Rumen of Goats

PubMed Central

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats. PMID:24756125

Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands.

PubMed

Martinson, Guntars O; Pommerenke, Bianca; Brandt, Franziska B; Homeier, Jürgen; Burneo, Juan I; Conrad, Ralf

2018-02-01

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH 4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH 4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH 4 -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH 4 production potential, stable carbon isotope fractionation and pathway of CH 4 formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH 4 emissions from type-I tank bromeliads but to higher CH 4 production potentials in type-I tank bromeliad slurries. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Characterisation of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.

PubMed

Salami, Saheed A; Valenti, Bernardo; Bella, Marco; O'Grady, Michael N; Luciano, Giuseppe; Kerry, Joseph P; Jones, Eleanor; Priolo, Alessandro; Newbold, Charles J

2018-05-01

This study characterised the response of ruminal fermentation and the rumen microbiome in lambs fed commercial vegetal sources of hydrolysable tannins (HT) and condensed tannins (CT). Forty-four lambs (19.56 ± 2.06 kg) were randomly assigned to either a concentrate diet (CON, n = 8) or CON supplemented with 4% of two HT [chestnut (Castanea sativa, HT-c) and tara (Caesalpinia spinosa, HT-t)] and CT [mimosa (Acacia negra, CT-m) and gambier (Uncaria gambir, CT-g)] extracts (all, n = 9) for 75 days pre-slaughter. Tannin supplementation did not influence ruminal fermentation traits. Quantitative PCR demonstrated that tannins did not affect the absolute abundance of ruminal bacteria or fungi. However, CT-m (-12.8%) and CT-g (-11.5%) significantly reduced the abundance of methanogens, while HT-t (-20.7%) and CT-g (-20.8%) inhibited protozoal abundance. Ribosomal amplicon sequencing revealed that tannins caused changes in the phylogenetic structure of the bacterial and methanogen communities. Tannins inhibited the fibrolytic bacterium, Fibrobacter and tended to suppress the methanogen genus, Methanosphaera. Results demonstrated that both HT and CT sources could impact the ruminal microbiome when supplemented at 4% inclusion level. HT-t, CT-m and CT-g extracts displayed specific antimicrobial activity against methanogens and protozoa without compromising ruminal fermentation in a long-term feeding trial.

Low-Temperature (10°C) Anaerobic Digestion of Dilute Dairy Wastewater in an EGSB Bioreactor: Microbial Community Structure, Population Dynamics, and Kinetics of Methanogenic Populations

PubMed Central

Cysneiros, Denise; O'Flaherty, Vincent

2013-01-01

The feasibility of anaerobic digestion of dairy wastewater at 10°C was investigated in a high height : diameter ratio EGSB reactor. Stable performance was observed at an applied organic loading rate (OLR) of 0.5–2 kg COD m−3 d−1 with chemical oxygen demand (COD) removal efficiencies above 85%. When applied OLR increased to values above 2 kg COD m−3 d−1, biotreatment efficiency deteriorated, with methanogenesis being the rate-limiting step. The bioreactor recovered quickly (3 days) after reduction of the OLR. qPCR results showed a reduction in the abundance of hydrogenotrophic methanogenic Methanomicrobiales and Methanobacteriales throughout the steady state period followed by a sharp increase in their numbers (111-fold) after the load shock. Specific methanogenic activity and maximum substrate utilising rate (A max) of the biomass at the end of trial indicated increased activity and preference towards hydrogenotrophic methanogenesis, which correlated well with the increased abundance of hydrogenotrophic methanogens. Acetoclastic Methanosaeta spp. remained at stable levels throughout the trial. However, increased apparent half-saturation constant (K m) at the end of the trial indicated a decrease in the specific substrate affinity for acetate of the sludge, suggesting that Methanosaeta spp., which have high substrate affinity, started to be outcompeted in the reactor. PMID:24089597

Low-temperature (10°C) anaerobic digestion of dilute dairy wastewater in an EGSB bioreactor: microbial community structure, population dynamics, and kinetics of methanogenic populations.

PubMed

Bialek, Katarzyna; Cysneiros, Denise; O'Flaherty, Vincent

2013-01-01

The feasibility of anaerobic digestion of dairy wastewater at 10°C was investigated in a high height : diameter ratio EGSB reactor. Stable performance was observed at an applied organic loading rate (OLR) of 0.5-2 kg COD m(-3) d(-1) with chemical oxygen demand (COD) removal efficiencies above 85%. When applied OLR increased to values above 2 kg COD m(-3) d(-1), biotreatment efficiency deteriorated, with methanogenesis being the rate-limiting step. The bioreactor recovered quickly (3 days) after reduction of the OLR. qPCR results showed a reduction in the abundance of hydrogenotrophic methanogenic Methanomicrobiales and Methanobacteriales throughout the steady state period followed by a sharp increase in their numbers (111-fold) after the load shock. Specific methanogenic activity and maximum substrate utilising rate (A(max)) of the biomass at the end of trial indicated increased activity and preference towards hydrogenotrophic methanogenesis, which correlated well with the increased abundance of hydrogenotrophic methanogens. Acetoclastic Methanosaeta spp. remained at stable levels throughout the trial. However, increased apparent half-saturation constant (K(m)) at the end of the trial indicated a decrease in the specific substrate affinity for acetate of the sludge, suggesting that Methanosaeta spp., which have high substrate affinity, started to be outcompeted in the reactor.

Quick-start of full-scale anaerobic digestion (AD) using aeration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lagerkvist, Anders, E-mail: al@ltu.se; Pelkonen, Markku; Wikström, Tommy

Highlights: • A fast, and original, start up procedure for anaerobic digestors has been applied at full scale. • The development of a methanogenic culture has been documented using fluorescent in situ hybridization. • The technique can be widely applied. - Abstract: A conventional 1300 m{sup 3} continuously stirred anaerobic tank reactor at the city of Boden, north Sweden, which was receiving a feed of both sewage sludge and food waste, was put out of operation due to the build-up of a float phase. The reactor was emptied and cleaned. At start-up there was no methanogenic sludge available, so anmore » unconventional start-up procedure was applied: The reactor was rapidly (8 days with 1200 kg of total solids (TS) added daily) filled with thickened, and slightly acidic sewage sludge, showing only slight methane generation, which was subsequently heated to 55 °C. Then compressed air was blown into the digester and within a month a fully functional methanogenic culture was established. The transfer from acidogenic to methanogenic conditions happened in about one week. As a start-up technique this is fast and cost efficient, it only requires the access of a compressor, electricity and a source of air. In total, about 16 tonnes of oxygen were used. It is proposed that this method may also be used as an operational amendment technique, should a reactor tend to acidify.« less

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation.

PubMed

Chojnacka, Aleksandra; Szczęsny, Paweł; Błaszczyk, Mieczysław K; Zielenkiewicz, Urszula; Detman, Anna; Salamon, Agnieszka; Sikora, Anna

2015-01-01

Anaerobic digestion is a complex process involving hydrolysis, acidogenesis, acetogenesis and methanogenesis. The separation of the hydrogen-yielding (dark fermentation) and methane-yielding steps under controlled conditions permits the production of hydrogen and methane from biomass. The characterization of microbial communities developed in bioreactors is crucial for the understanding and optimization of fermentation processes. Previously we developed an effective system for hydrogen production based on long-term continuous microbial cultures grown on sugar beet molasses. Here, the acidic effluent from molasses fermentation was used as the substrate for methanogenesis in an upflow anaerobic sludge blanket bioreactor. This study focused on the molecular analysis of the methane-yielding community processing the non-gaseous products of molasses fermentation. The substrate for methanogenesis produces conditions that favor the hydrogenotrophic pathway of methane synthesis. Methane production results from syntrophic metabolism whose key process is hydrogen transfer between bacteria and methanogenic Archaea. High-throughput 454 pyrosequencing of total DNA isolated from the methanogenic microbial community and bioinformatic sequence analysis revealed that the domain Bacteria was dominated by Firmicutes (mainly Clostridia), Bacteroidetes, δ- and γ-Proteobacteria, Cloacimonetes and Spirochaetes. In the domain Archaea, the order Methanomicrobiales was predominant, with Methanoculleus as the most abundant genus. The second and third most abundant members of the Archaeal community were representatives of the Methanomassiliicoccales and the Methanosarcinales. Analysis of the methanogenic sludge by scanning electron microscopy with Energy Dispersive X-ray Spectroscopy and X-ray diffraction showed that it was composed of small highly heterogeneous mineral-rich granules. Mineral components of methanogenic granules probably modulate syntrophic metabolism and methanogenic pathways. A rough functional analysis from shotgun data of the metagenome demonstrated that our knowledge of methanogenesis is poor and/or the enzymes responsible for methane production are highly effective, since despite reasonably good sequencing coverage, the details of the functional potential of the microbial community appeared to be incomplete.

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water.

PubMed

Oko, Bonahis J; Tao, Yu; Stuckey, David C

2017-01-01

Oil field produced water (OFPW) is widely produced in large volumes around the world. Transforming the organic matter in OFPW into bioenergy, such as biomethane, is one promising way to sustainability. However, OFPW is difficult to biologically degrade because it contains complex compounds such as naphthenic acids (NAs), or polycyclic aromatic hydrocarbons (PAHs). Although active microbial communities have been found in many oil reservoirs, little is known about how an exotic microbiome, e.g. the one which originates from municipal wastewater treatment plants, would evolve when incubated with OFPW. In this study, we harvested methanogenic biomass from two sources: a full-scale anaerobic digester (AD) treating oil and gas processing wastewater (named O&G sludge), and from a full-scale AD reactor treating multiple fractions of municipal solid wastes (named MS, short for mixed sludge). Both were incubated in replicate microcosms fed with PAHs, NAs, or OFPW. The results showed that the PAHs, NAs, and OFPW feeds could rapidly alter the methanogenic microbiomes, even after 14 days, while the O&G sludge adapted faster than the mixed sludge in all the incubations. Two rarely reported microorganisms, a hydrogenotrophic methanogen Candidatus methanoregula and a saccharolytic fermenter Kosmotoga , were found to be prevalent in the PAHs and OFPW microcosms, and are likely to play an important role in the syntrophic degradation of PAHs and OFPW, cooperating with methanogens such as Methanoregula, Methanosarcina, or Methanobacterium . The dominant phyla varied in certain patterns during the incubations, depending on the biomass source, feed type, and variation in nutrients. The sludge that originated from the oil and gas processing wastewater treatment (O&G) reactor adapted faster than the one from municipal solid waste reactors, almost certainly because the O&G biomass had been "pre-selected" by the environment. This study reveals the importance of biomass selection for other crude oil-waste-related bioengineering studies, such as bioaugmentation and bioremediation.

Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio

PubMed Central

Dar, Shabir A.; Kleerebezem, Robbert; Stams, Alfons J. M.; Kuenen, J. Gijs

2008-01-01

The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol−1, i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80–85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10–15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol−1, i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40–45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic Archaea accounted for 10% of the total microbial community. PMID:18305937

Abundance and diversity of methanogens: potential role in high arsenic groundwater in Hetao Plain of Inner Mongolia, China.

PubMed

Wang, Y H; Li, P; Dai, X Y; Zhang, R; Jiang, Z; Jiang, D W; Wang, Y X

2015-05-15

To investigate the community diversity and abundance of methanogens and their potential role in high arsenic groundwater, 17 groundwater samples from Hetao Plain of Inner Mongolia were investigated with an integrated method including 16S rRNA gene clone library, quantitative polymerase chain reaction and geochemistry analyses. Total arsenic (AsTot) concentrations were 82.7-1088.7 μg/L and arsenite (AsIII) mostly dominated in these samples with percentages of 0.04-0.79. CH₄ concentrations ranged from 0.01 to 292 μg/L and distinctly elevated only when AsTot were relatively high and SO₄(2-) were distinctly low. Principal component analysis indicated that these samples were divided into three groups according to the variations of AsTot, CH₄ and SO₄(2-). AsTot concentrations were distinctly high in the group with high CH₄ and low SO₄(2-) comparing to the other two groups (one with high CH₄ and high SO₄(2-), the other with low CH₄ and SO₄(2-)). The mcrA gene (methyl coenzyme-M reductase gene) based phylogenetic analysis of methanogens population showed that methanogenic archaea was diverse but mainly composed of Methanomicrobiales, Methanosarcinales, Methanobacteria and unidentified groups, with Methanomicrobiales being distinctly dominant (50.6%). The mcrA gene abundance in high arsenic groundwater ranged from 3.01 × 10(3) to 3.80 × 10(6)copies/L and accounted for 0-30.2% of total archaeal 16S rRNA genes. The abundance of mcrA genes was positively correlated with the concentrations of AsTot (R=0.59), AsIII (R=0.57) and FeII (R=0.79), while it was negatively correlated with oxidation-reduction potential (R=-0.66) and SO₄(2-) concentration (R=-0.64). These results implied that methanogenic archaea might accelerate As release in groundwater aquifers in Hetao Plain. Copyright © 2015. Published by Elsevier B.V.

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation

PubMed Central

Chojnacka, Aleksandra; Szczęsny, Paweł; Błaszczyk, Mieczysław K.; Zielenkiewicz, Urszula; Detman, Anna; Salamon, Agnieszka; Sikora, Anna

2015-01-01

Anaerobic digestion is a complex process involving hydrolysis, acidogenesis, acetogenesis and methanogenesis. The separation of the hydrogen-yielding (dark fermentation) and methane-yielding steps under controlled conditions permits the production of hydrogen and methane from biomass. The characterization of microbial communities developed in bioreactors is crucial for the understanding and optimization of fermentation processes. Previously we developed an effective system for hydrogen production based on long-term continuous microbial cultures grown on sugar beet molasses. Here, the acidic effluent from molasses fermentation was used as the substrate for methanogenesis in an upflow anaerobic sludge blanket bioreactor. This study focused on the molecular analysis of the methane-yielding community processing the non-gaseous products of molasses fermentation. The substrate for methanogenesis produces conditions that favor the hydrogenotrophic pathway of methane synthesis. Methane production results from syntrophic metabolism whose key process is hydrogen transfer between bacteria and methanogenic Archaea. High-throughput 454 pyrosequencing of total DNA isolated from the methanogenic microbial community and bioinformatic sequence analysis revealed that the domain Bacteria was dominated by Firmicutes (mainly Clostridia), Bacteroidetes, δ- and γ-Proteobacteria, Cloacimonetes and Spirochaetes. In the domain Archaea, the order Methanomicrobiales was predominant, with Methanoculleus as the most abundant genus. The second and third most abundant members of the Archaeal community were representatives of the Methanomassiliicoccales and the Methanosarcinales. Analysis of the methanogenic sludge by scanning electron microscopy with Energy Dispersive X-ray Spectroscopy and X-ray diffraction showed that it was composed of small highly heterogeneous mineral-rich granules. Mineral components of methanogenic granules probably modulate syntrophic metabolism and methanogenic pathways. A rough functional analysis from shotgun data of the metagenome demonstrated that our knowledge of methanogenesis is poor and/or the enzymes responsible for methane production are highly effective, since despite reasonably good sequencing coverage, the details of the functional potential of the microbial community appeared to be incomplete. PMID:26000448

Impact of fulvic acids on bio-methanogenic treatment of municipal solid waste incineration leachate.

PubMed

Dang, Yan; Lei, Yuqing; Liu, Zhao; Xue, Yiting; Sun, Dezhi; Wang, Li-Ying; Holmes, Dawn E

2016-12-01

A considerable amount of leachate with high fulvic acid (FA) content is generated during the municipal solid waste (MSW) incineration process. This incineration leachate is usually processed by downstream bio-methanogenic treatment. However, few studies have examined the impact that these compounds have on methanogenesis and how they are degraded and transformed during the treatment process. In this study, a laboratory-scale expanded granular sludge bed (EGSB) reactor was operated with MSW incineration leachate containing various concentrations of FA (1500 mg/L to 8000 mg/L) provided as the influent. We found that FA degradation rates decreased from 86% to 72% when FA concentrations in the reactor were increased, and that molecular size, level of humification and aromatization of the residual FA macromolecules all increased after bio-methanogenic treatment. Increasing FA influent concentrations also inhibited growth of hydrogenotrophic methanogens from the genus Methanobacterium and syntrophic bacteria from the genus Syntrophomonas, which resulted in a decrease in methane production and a concomitant increase in CO 2 content in the biogas. Sequences most similar to species from the genus Anaerolinea went up as FA concentrations increased. Bacteria from this genus are capable of extracellular electron transfer and may be using FA as an electron acceptor for growth or as a shuttle for syntrophic exchange with other microorganisms in the reactor. In order to determine whether FA could serve as an electron shuttle to promote syntrophy in an anaerobic digester, co-cultures of Geobacter metallireducens and G. sulfurreducens were grown in the presence of FA from raw leachate or from residual bioreactor effluent. While raw FA stimulated electron transfer between these two bacteria, residual FA did not have any electron shuttling abilities, indicating that FA underwent a significant transformation during the bio-methanogenic treatment process. These results are significant and should be taken into consideration when optimizing anaerobic bioreactors used to treat MSW incineration leachate high in FA content. Copyright © 2016 Elsevier Ltd. All rights reserved.

Discovery of a novel rumen methanogen in the anaerobic fungal culture and its distribution in the rumen as revealed by real-time PCR

PubMed Central

2014-01-01

Background The novel archaea belonging to Rumen Cluster C (RCC), which may play an important role in methane production in the rumen have received increased attention. However, the present information on RCC in the rumen is limited by the unsuccessful isolation of axenic pure RCC from the rumen. In the present study, RCC grown in anaerobic fungal subcultures was identified by the molecular and culture methods. Results A novel RCC species existing in the fungal subcultures was identified and demonstrated by the 16S rRNA gene clone library. Interestingly, the novel RCC species survived in the fungal cultures over all the subculture transferring, even in the 62nd subculture, in contrast to the other methanogens, which disappeared during subcultures. Further work showed that subculture transfer frequency significantly affected the relative abundance of the novel RCC species in the fungal subcultures. The five-day and seven-day transfer frequencies increased the relative abundance of the RCC species (P<0.05). In addition, quantitative real-time PCR revealed that high concentrate diets did not affect the abundance of archaea, but numerically reduced the abundance of the novel RCC species in the rumen. In addition, the relative abundance of the RCC species was numerically higher in the rumen liquid fraction than in the rumen epithelium and solid fractions. Finally, a purified fungal culture containing the RCC species was successfully obtained. PCR and sequencing analysis showed that the novel RCC species contained a mcrA gene, which is known to play a crucial role in methanogenesis, and thus could be identified as a methanogen. Conclusion In this study, a novel RCC species was identified as a methanogen and closely associated with anaerobic fungi. This novel approach by using co-culture with anaerobic fungi may provide a feasible way to culture and investigate not yet identified methanogens. PMID:24758319

Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea

NASA Astrophysics Data System (ADS)

Zhuang, Guang-Chao; Heuer, Verena B.; Lazar, Cassandre S.; Goldhammer, Tobias; Wendt, Jenny; Samarkin, Vladimir A.; Elvert, Marcus; Teske, Andreas P.; Joye, Samantha B.; Hinrichs, Kai-Uwe

2018-03-01

Microbial production of methane is an important terminal metabolic process during organic matter degradation in marine sediments. It is generally acknowledged that hydrogenotrophic and acetoclastic methanogenesis constitute the dominant pathways of methane production; the importance of methanogenesis from methylated compounds remains poorly understood. We conducted various biogeochemical and molecular genetic analyses to characterize substrate availability, rates of methanogenesis, and methanogen community composition, and further evaluated the contribution of different substrates and pathways for methane production in deltaic surface and subsurface sediments of the Western Mediterranean Sea. Major substrates representing three methanogenic pathways, including H2, acetate, and methanol, trimethylamine (TMA), and dimethylsulfide (DMS), were detected in the pore waters and sediments, and exhibited variability over depth and between sites. In accompanying incubation experiments, methanogenesis rates from various 14C labeled substrates varied as well, suggesting that environmental factors, such as sulfate concentration and organic matter quality, could significantly influence the relative importance of individual pathway. In particular, methylotrophic and hydrogenotrophic methanogenesis contributed to the presence of micromolar methane concentrations in the sulfate reduction zone, with methanogenesis from methanol accounting for up to 98% of the total methane production in the topmost surface sediment. In the sulfate-depleted zone, hydrogenotrophic methanogenesis was the dominant methanogenic pathway (67-98%), and enhanced methane production from acetate was observed in organic-rich sediment (up to 31%). Methyl coenzyme M reductase gene (mcrA) analysis revealed that the composition of methanogenic communities was generally consistent with the distribution of methanogenic activity from different substrates. This study provides the first quantitative assessment of methylotrophic methanogenesis in marine sediments and has important implications for marine methane cycling. The occurrence of methylotrophic methanogenesis in surface sediments could fuel the anaerobic oxidation of methane (AOM) in the shallow sulfate reduction zone. Release of methane produced from methylotrophic methanogenesis could be a source of methane efflux to the water column, thus influencing the benthic methane budgets.

Discovery of a novel rumen methanogen in the anaerobic fungal culture and its distribution in the rumen as revealed by real-time PCR.

PubMed

Jin, Wei; Cheng, Yan Fen; Mao, Sheng Yong; Zhu, Wei Yun

2014-04-23

The novel archaea belonging to Rumen Cluster C (RCC), which may play an important role in methane production in the rumen have received increased attention. However, the present information on RCC in the rumen is limited by the unsuccessful isolation of axenic pure RCC from the rumen. In the present study, RCC grown in anaerobic fungal subcultures was identified by the molecular and culture methods. A novel RCC species existing in the fungal subcultures was identified and demonstrated by the 16S rRNA gene clone library. Interestingly, the novel RCC species survived in the fungal cultures over all the subculture transferring, even in the 62nd subculture, in contrast to the other methanogens, which disappeared during subcultures. Further work showed that subculture transfer frequency significantly affected the relative abundance of the novel RCC species in the fungal subcultures. The five-day and seven-day transfer frequencies increased the relative abundance of the RCC species (P<0.05). In addition, quantitative real-time PCR revealed that high concentrate diets did not affect the abundance of archaea, but numerically reduced the abundance of the novel RCC species in the rumen. In addition, the relative abundance of the RCC species was numerically higher in the rumen liquid fraction than in the rumen epithelium and solid fractions. Finally, a purified fungal culture containing the RCC species was successfully obtained. PCR and sequencing analysis showed that the novel RCC species contained a mcrA gene, which is known to play a crucial role in methanogenesis, and thus could be identified as a methanogen. In this study, a novel RCC species was identified as a methanogen and closely associated with anaerobic fungi. This novel approach by using co-culture with anaerobic fungi may provide a feasible way to culture and investigate not yet identified methanogens.

Warmer and drier conditions and nitrogen fertilizer application altered methanotroph abundance and methane emissions in a vegetable soil.

PubMed

Ran, Yu; Xie, Jianli; Xu, Xiaoya; Li, Yong; Liu, Yapeng; Zhang, Qichun; Li, Zheng; Xu, Jianming; Di, Hongjie

2017-01-01

Methane (CH 4 ) is a potent greenhouse gas, and soil can both be a source and sink for atmospheric CH 4 . It is not clear how future climate change may affect soil CH 4 emissions and related microbial communities. The aim of this study was to determine the interactive effects of a simulated warmer and drier climate scenarios and the application of different nitrogen (N) sources (urea and manure) on CH 4 emissions and related microbial community abundance in a vegetable soil. Greenhouses were used to control simulated climate conditions which gave 2.99 °C warmer and 6.2% lower water content conditions. The field experiment was divided into two phases. At the beginning of phase II, half of the greenhouses were removed to study possible legacy effects of the simulated warmer and drier conditions. The responses in methanogen and methanotroph abundance to a simulated climate change scenario were determined using real-time PCR. The results showed that the simulated warmer and drier conditions in the greenhouses significantly decreased CH 4 emissions largely due to the lower soil moisture content. For the same reason, CH 4 emissions of treatments in phase I were much lower than the same treatments in phase II. The abundance of methanotrophs showed a more significant response than methanogens to the simulated climate change scenario, increasing under simulated drier conditions. Methanogenic community abundance remained low, except where manure was applied which provided a source of organic C that stimulated methanogen growth. Soil moisture content was a major driver for methanotroph abundance and strongly affected CH 4 emissions. The application of N source decreased CH 4 emissions probably because of increased methanotrophic activity. CH 4 emissions were positively correlated to methanogenic abundance and negatively correlated to methanotrophic abundance. These results demonstrate that projected future climate change conditions can have a feedback impact on CH 4 emissions from the soil by altering soil conditions (particularly soil moisture) and related microbial communities.

Solute concentrations influence microbial methanogenesis in coal-bearing strata of the Cherokee basin, USA

DOE PAGES

Kirk, Matthew F.; Wilson, Brien H.; Marquart, Kyle A.; ...

2015-11-18

In this study, microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% R o) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Clmore » type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L –1. Gas dryness values [C 1/(C 2 + C 3)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirk, Matthew F.; Wilson, Brien H.; Marquart, Kyle A.

In this study, microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% R o) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Clmore » type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L –1. Gas dryness values [C 1/(C 2 + C 3)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.« less

Biomethane potential of industrial paper wastes and investigation of the methanogenic communities involved.

PubMed

Walter, Andreas; Silberberger, Sandra; Juárez, Marina Fernández-Delgado; Insam, Heribert; Franke-Whittle, Ingrid H

2016-01-01

Cellulose-containing waste products from the agricultural or industrial sector are potentially one of the largest sources of renewable energy on earth. In this study, the biomethane potential (BMP) of two types of industrial paper wastes, wood and pulp residues (WR and PR, respectively), were evaluated under both mesophilic and thermophilic conditions, and various pretreatment methods were applied in the attempt to increase the methane potential during anaerobic digestion. The methanogenic community composition was investigated with denaturing gradient gel electrophoresis (DGGE) and the ANAEROCHIP microarray, and dominant methanogens were quantitated using quantitative PCR. All pretreatments investigated in this study with the exception of the alkaline pretreatment of PR were found to increase the BMP of two paper industry wastes. However, the low recalcitrance level of the PR resulted in the pretreatments being less effective in increasing BMP when compared with those for WR. These results were supported by the physico-chemical data. A combined application of ultrasound and enzymatic pretreatment was found to be the best strategy for increasing methane yields. The retention time of substrates in the reactors strongly influenced the BMP of wastes subjected to the different pretreatments. In sludges from both paper wastes subjected to the various pretreatments, mixotrophic Methanosarcina species were found to dominate the community, accompanied by a consortium of hydrogenotrophic genera. Pretreating industrial paper wastes could be a potentially viable option for increasing the overall degradation efficiency and decreasing reactor retention time for the digestion of complex organic matter such as lignocellulose or hemicellulose. This would help reduce the environmental burden generated from paper production. Although there were minor differences in the methanogenic communities depending on the temperature of anaerobic digestion, there was little effect of substrate and pretreatment type on the community composition. Thus, methanogen community dynamics would not seem to be an appropriate indicator regarding BMP in the AD processes investigated.

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 the mentioned potential habitats.

Methane production and methanogen levels in steers that differ in residual gain.

PubMed

Freetly, H C; Lindholm-Perry, A K; Hales, K E; Brown-Brandl, T M; Kim, M; Myer, P R; Wells, J E

2015-05-01

Methane (CH4) gas released by cattle isa product of fermentation in the digestive tract. The 2 primary sites of CH4 production in ruminants are the reticulum-rumen complex and the cecum. Methane release from cattle represents a 2% to 12% loss of the energy intake. Reducing the proportion of feed energy lost as CH4 has the potential of improving feed efficiency as well as decreasing the contribution of cattle to greenhouse gas production. Feed intake and growth were measured on 132 fall-born steers for 70 d. Seven steers with extreme positive residual gain (RG) and 7 steers with extreme negative RG whose DMI was within 0.32 SD of the mean intake were selected for subsequent measurements. Enteric CH4 production was measured via indirect calorimetry. Rumen, cecum, and rectal contents were obtained from steers at slaughter for measurement of in vitro CH4 production and methanogen 16S rRNA levels. Enteric CH4 production did not differ (P = 0.11) between the positive RG (112 ± 13 L/d)and the negative RG (74 ± 13 L/d) steers. In vitro rumen methane production did not differ between positive RG(64.26 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (61.49 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1)DM∙min(-1); P = 0.86). In vitro cecum methane production did not differ between positive RG (4.24 ×10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (4.35 × 10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1); P = 0.97). Methanogen 16S rRNA as a percentage of the total bacteria16S rRNA did not differ between RG groups (P = 0.18). The methanogen 16S rRNA as a percentage of rumen fluid total bacteria 16S rRNA (5.3% ±3.1%) did not differ from the methanogen 16S rRNA asa percentage of cecum content total bacteria 16S rRNA(11.8% ± 3.1%; P = 0.14). The methanogen 16S rRNA as a percentage of the rectum content total bacteria 16SrRNA (0.7% ± 3.1%) was not different from the rumen content (P = 0.29) but was less than the cecum content(P = 0.01). Methanomicrobiales 16S rRNA as a percentage of total methanogen 16S rRNA did not differ across sample sites (P = 0.81); however, steers with positive RG (10.5% ± 1.6%) were more numerous than steers with negative RG (5.1% ± 1.6%; P = 0.02). Cattle that differ in RG at the same DMI do not differ in characteristics associated with CH4 production.

Salinity Responses of Benthic Microbial Communities in a Solar Saltern (Eilat, Israel)

PubMed Central

Sørensen, Ketil Bernt; Canfield, Donald E.; Oren, Aharon

2004-01-01

The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries. The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120‰, and sulfate reduction was strongly inhibited at an in situ salinity of 215‰. Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget. Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust. In slurries with a salinity of 180‰ or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria. Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120‰. PMID:15006785

Evidence of active methanogen communities in shallow sediments of the sonora margin cold seeps.

PubMed

Vigneron, Adrien; L'Haridon, Stéphane; Godfroy, Anne; Roussel, Erwan G; Cragg, Barry A; Parkes, R John; Toffin, Laurent

2015-05-15

In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and application of a synthetic DNA standard for real-time PCR analysis of microbial communities in a biogas digester.

PubMed

May, T; Koch-Singenstreu, M; Ebling, J; Stantscheff, R; Müller, L; Jacobi, F; Polag, D; Keppler, F; König, H

2015-08-01

A synthetic DNA fragment containing primer binding sites for the quantification of ten different microbial groups was constructed and evaluated as a reliable enumeration standard for quantitative real-time PCR (qPCR) analyses. This approach has been exemplary verified for the quantification of several methanogenic orders and families in a series of samples drawn from a mesophilic biogas plant. Furthermore, the total amounts of bacteria as well as the number of sulfate-reducing and propionic acid bacteria as potential methanogenic interaction partners were successfully determined. The obtained results indicated a highly dynamic microbial community structure which was distinctly affected by the organic loading rate, the substrate selection, and the amount of free volatile fatty acids in the fermenter. Methanosarcinales was the most predominant methanogenic order during the 3 months of observation despite fluctuating process conditions. During all trials, the modified quantification standard indicated a maximum of reproducibility and efficiency, enabling this method to open up a wide range of novel application options.

Improved Monitoring of Semi-Continuous Anaerobic Digestion of Sugarcane Waste: Effects of Increasing Organic Loading Rate on Methanogenic Community Dynamics

PubMed Central

Leite, Athaydes Francisco; Janke, Leandro; Lv, Zuopeng; Harms, Hauke; Richnow, Hans-Hermann; Nikolausz, Marcell

2015-01-01

The anaerobic digestion of filter cake and its co-digestion with bagasse, and the effect of gradual increase of the organic loading rate (OLR) from start-up to overload were investigated. Understanding the influence of environmental and technical parameters on the development of particular methanogenic pathway in the biogas process was an important aim for the prediction and prevention of process failure. The rapid accumulation of volatile organic acids at high OLR of 3.0 to 4.0 gvs·L−1·day−1 indicated strong process inhibition. Methanogenic community dynamics of the reactors was monitored by stable isotope composition of biogas and molecular biological analysis. A potential shift toward the aceticlastic methanogenesis was observed along with the OLR increase under stable reactor operating conditions. Reactor overloading and process failure were indicated by the tendency to return to a predominance of hydrogenotrophic methanogenesis with rising abundances of the orders Methanobacteriales and Methanomicrobiales and drop of the genus Methanosarcina abundance. PMID:26404240

Anaerobic biodegradation of soybean biodiesel and diesel blends under methanogenic conditions.

PubMed

Wu, Shuyun; Yassine, Mohamad H; Suidan, Makram T; Venosa, Albert D

2015-12-15

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic biodegradation of soybean biodiesel B100 (biodiesel only) with different petrodiesel loads was studied using biomass pre-acclimated to B100 and B80 (80% biodiesel and 20% petrodiesel). The results indicated that the biodiesel fraction of the blend could be effectively biodegraded, whereas petrodiesel was not biodegraded at all under methanogenic conditions. The presence of petrodiesel in blends with biodiesel had a greater inhibitory effect on the rate of biodegradation than the biodegradation efficiency (defined as the efficiency of methane production). Both the biodegradation rate coefficient and the methane production efficiency increased almost linearly with the increasing fraction of biodiesel. With the increasing fraction of petrodiesel, the biodegradation rate and efficiency were correlated with the concentration of soluble FAMEs in the water. Copyright © 2015 Elsevier Ltd. All rights reserved.

Toluene inhibition on an anaerobic reactor sludge in terms of potential activity and composition of acetoclastic methanogens.

PubMed

Ince, Orhan; Kolukirik, Mustafa; Cetecioglu, Zeynep; Eyice, Ozge; Inceoglu, Ozgul; Ince, Bahar

2009-12-01

The aim of this study was to determine the effect of toluene on an anaerobic sludge taken from a full-scale upflow anaerobic sludge blanket (UASB) reactor in terms of potential activity and composition of acetoclastic methanogens. Specific methanogenic activity (SMA) test results showed that 5%, 9.5%, 14%, 24%, 29%, 38% and 62% inhibition occurred in the potential methane production (PMP) rate of the sludge at toluene concentrations of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM and 1 mM, respectively. Fluorescence in situ hybridization (FISH) results showed that relative abundance of archaeal cells was approx. 19% throughout the SMA tests. The anaerobic sludge was dominated by acetoclastic genus Methanosaeta which were slightly affected by increasing toluene concentrations do not have any effect on relative abundance of Methanosaeta spp., which was between 73% +/- 1.6 and 68% +/- 2.1 of the archaeal population.

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

PubMed Central

Kono, Takunari; Mehrotra, Sandhya; Endo, Chikako; Kizu, Natsuko; Matusda, Mami; Kimura, Hiroyuki; Mizohata, Eiichi; Inoue, Tsuyoshi; Hasunuma, Tomohisa; Yokota, Akiho; Matsumura, Hiroyoshi; Ashida, Hiroki

2017-01-01

Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown. PMID:28082747

Analysis of a bio-electrochemical reactor containing carbon fiber textiles for the anaerobic digestion of tomato plant residues.

PubMed

Hirano, Shin-Ichi; Matsumoto, Norio

2018-02-01

A bio-electrochemical system packed with supporting material can promote anaerobic digestion for several types of organic waste. To expand the target organic matters of a BES, tomato plant residues (TPRs), generated year-round as agricultural and cellulosic waste, were treated using three methanogenic reactors: a continuous stirred tank reactor (CSTR), a carbon fiber textile (CFT) reactor, and a bio-electrochemical reactor (BER) including CFT with electrochemical regulation (BER + CFT). CFT had positive effects on methane fermentation and methanogen abundance. The microbial population stimulated by electrochemical regulation, including hydrogenotrophic methanogens, cellulose-degrading bacteria, and acetate-degrading bacteria, suppressed acetate accumulation, as evidenced by the low acetate concentration in the suspended fraction in the BER + CFT. These results indicated that the microbial community in the BER + CFT facilitated the efficient decomposition of TPR and its intermediates such as acetate to methane. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of Nitrooxy Compounds with Different Molecular Structures on the Rumen Methanogenesis, Metabolic Profile, and Methanogenic Community.

PubMed

Jin, Wei; Meng, Zhenxiang; Wang, Jing; Cheng, Yanfen; Zhu, Weiyun

2017-08-01

Rumen in vitro fermentation was used to evaluate the capacity of nitrooxy compounds to mitigate rumen methane production. The following three nitrooxy compounds, each with different molecular structures, were evaluated: 2,2-dimethyl-3-(nitrooxy) propanoic (DNP), N-[2-(Nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), and nitroglycerin (NG). All three compounds substantially decreased the total gas production, methane production, and the acetate:propionate ratio, while increasing hydrogen production. The growth of methanogens was specifically inhibited by all three compounds, without affecting the abundance of bacteria, anaerobic fungi, or protozoa. However, inhibition of methanogenesis required a much higher dose of DNP when compared to NPD or NG. Further investigations were conducted on NG to determine its effects on the methanogenic community. NG reduced the relative abundance of Methanomassiliicoccales, while increasing the relative abundance of Methanobrevibacter and Methanosphaera. Overall, the results suggested that all three of these nitrooxy compounds could specifically inhibit rumen methanogenesis, but NPD and NG were much more efficient than DNP at rumen methane mitigation.

Ex-situ biogas upgrading and enhancement in different reactor systems.

PubMed

Kougias, Panagiotis G; Treu, Laura; Benavente, Daniela Peñailillo; Boe, Kanokwan; Campanaro, Stefano; Angelidaki, Irini

2017-02-01

Biogas upgrading is envisioned as a key process for clean energy production. The current study evaluates the efficiency of different reactor configurations for ex-situ biogas upgrading and enhancement, in which externally provided hydrogen and carbon dioxide were biologically converted to methane by the action of hydrogenotrophic methanogens. The methane content in the output gas of the most efficient configuration was >98%, allowing its exploitation as substitute to natural gas. Additionally, use of digestate from biogas plants as a cost efficient method to provide all the necessary nutrients for microbial growth was successful. High-throughput 16S rRNA sequencing revealed that the microbial community was resided by novel phylotypes belonging to the uncultured order MBA08 and to Bacteroidales. Moreover, only hydrogenotrophic methanogens were identified belonging to Methanothermobacter and Methanoculleus genera. Methanothermobacter thermautotrophicus was the predominant methanogen in the biofilm formed on top of the diffuser surface in the bubble column reactor. Copyright © 2016 Elsevier Ltd. All rights reserved.

Methane-producing microbial community in a coal bed of the Illinois basin.

PubMed

Strapoc, Dariusz; Picardal, Flynn W; Turich, Courtney; Schaperdoth, Irene; Macalady, Jennifer L; Lipp, Julius S; Lin, Yu-Shih; Ertefai, Tobias F; Schubotz, Florence; Hinrichs, Kai-Uwe; Mastalerz, Maria; Schimmelmann, Arndt

2008-04-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.

Effects of biopretreatment on pyrolysis behaviors of corn stalk by methanogen.

PubMed

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

2014-07-01

The study investigated the effects of methanogen pretreatment on pyrolysis behaviors of corn stalk (CS) by using Py-GC/MS analysis and thermogravimetric analysis. Results indicated that biopretreatment changed considerably the pyrolysis behaviors of CS from four weight loss stages to two weight loss stages. Increasing biopretreatment time from 5 days to 25 days enhanced the kinds and contents of chemicals in volatile products. In pyrolysis products, the contents of sugars, linear ketones and furans decreased from 1.43%, 12.60% and 7.38% to 1.25%, 10.22% and 3.25%, respectively, and the contents of phenols increased from 15.08% to 27.84%. The most content change from 6.83% to 13.63% indicated that methanogen pretreatment improved the pyrolysis selectivity of CS to product the 4-VP, but it was disadvantageous to 5-hydroxymethyl furfural, levoglucose and furfural. The changes of chemical compositions and structure of CS after biopretreatment were the main reason of the differences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

PubMed Central

Thornton, Christopher N.; Hyer, Alex; Twing, Katrina I.; Longino, August A.; Lang, Susan Q.; Lilley, Marvin D.; Früh-Green, Gretchen L.; Schrenk, Matthew O.

2017-01-01

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif. PMID:28149702

Biodegradation of trichloroethylene and its anaerobic daughter products in freshwater wetland sediments

USGS Publications Warehouse

Lorah, M.M.; Olsen, L.D.

2001-01-01

Laboratory microcosms were prepared under methanogenic, sulfate-reducing, and aerobic conditions using sediment and groundwater from a freshwater wetland that is a discharge area for a trichloroethylene (TCE) to evaluate potential biodegradation rates of TCE and its anaerobic daughter products (cis-1,2-dichloroethylene, trans-1,2-dichloroethylene, and vinyl chloride (VC)). Anaerobic degradation of TCE was about an order of magnitude faster under methanogenic conditions than under sulfate-reducing conditions. Both 12DCE and VC were found under sulfate-reducing conditions in the microcosms containing the wetland sediment, but their production, especially for VC, was substantially slower than under methanogenic conditions. Methane concentrations remained approximately constant (when losses in the formalin-amended controls are considered) in the microcosms amended with TCE and increased in the microcosms amended with the 12DCE isomers and VC during the first 18-25 days of incubation. The most rapid decrease in concentrations of TCE, cis-12DCE, trans-12DCE, and VC was found after aerobic methane-oxidizing conditions were definitely established.

Biological methane production under putative Enceladus-like conditions.

PubMed

Taubner, Ruth-Sophie; Pappenreiter, Patricia; Zwicker, Jennifer; Smrzka, Daniel; Pruckner, Christian; Kolar, Philipp; Bernacchi, Sébastien; Seifert, Arne H; Krajete, Alexander; Bach, Wolfgang; Peckmann, Jörn; Paulik, Christian; Firneis, Maria G; Schleper, Christa; Rittmann, Simon K-M R

2018-02-27

The detection of silica-rich dust particles, as an indication for ongoing hydrothermal activity, and the presence of water and organic molecules in the plume of Enceladus, have made Saturn's icy moon a hot spot in the search for potential extraterrestrial life. Methanogenic archaea are among the organisms that could potentially thrive under the predicted conditions on Enceladus, considering that both molecular hydrogen (H 2 ) and methane (CH 4 ) have been detected in the plume. Here we show that a methanogenic archaeon, Methanothermococcus okinawensis, can produce CH 4 under physicochemical conditions extrapolated for Enceladus. Up to 72% carbon dioxide to CH 4 conversion is reached at 50 bar in the presence of potential inhibitors. Furthermore, kinetic and thermodynamic computations of low-temperature serpentinization indicate that there may be sufficient H 2 gas production to serve as a substrate for CH 4 production on Enceladus. We conclude that some of the CH 4 detected in the plume of Enceladus might, in principle, be produced by methanogens.

Two-phase anaerobic digestion within a solid waste/wastewater integrated management system

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Gioannis, G.; Diaz, L.F.; Muntoni, A.

2008-07-01

A two-phase, wet anaerobic digestion process was tested at laboratory scale using mechanically pre-treated municipal solid waste (MSW) as the substrate. The proposed process scheme differs from others due to the integration of the MSW and wastewater treatment cycles, which makes it possible to avoid the recirculation of process effluent. The results obtained show that the supplying of facultative biomass, drawn from the wastewater aeration tank, to the solid waste acidogenic reactor allows an improvement of the performance of the first phase of the process which is positively reflected on the second one. The proposed process performed successfully, adopting mesophilicmore » conditions and a relatively short hydraulic retention time in the methanogenic reactor, as well as high values of organic loading rate. Significant VS removal efficiency and biogas production were achieved. Moreover, the methanogenic reactor quickly reached optimal conditions for a stable methanogenic phase. Studies conducted elsewhere also confirm the feasibility of integrating the treatment of the organic fraction of MSW with that of wastewater.« less

Methyl Fluoride Affects Methanogenesis Rather than Community Composition of Methanogenic Archaea in a Rice Field Soil

PubMed Central

Daebeler, Anne; Gansen, Martina; Frenzel, Peter

2013-01-01

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens. PMID:23341965

[Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang Oilfield (China)].

PubMed

Nazina, T N; Shestakova, N M; Grigor'ian, A A; Mikhaĭlova, E M; Turova, T P; Poltaraus, A B; Feng, C; Ni, F; Beliaev, S S

2006-01-01

The number of microorganisms of major metabolic groups and the rates of sulfate-reducing and methanogenic processes in the formation waters of the high-temperature horizons of Dagang oilfield have been determined. Using cultural methods, it was shown that the microbial community contained aerobic bacteria oxidizing crude oil, anaerobic fermentative bacteria, sulfate-reducing bacteria, and methanogenic bacteria. Using cultural methods, the possibility of methane production from a mixture of hydrogen and carbon dioxide (H2 + CO2) and from acetate was established, and this result was confirmed by radioassays involving NaH14CO3 and 14CH3COONa. Analysis of 16S rDNA of enrichment cultures of methanogens demonstrated that these microorganisms belong to Methanothermobacter sp. (M. thermoautotrophicus), which consumes hydrogen and carbon dioxide as basic substrates. The genes of acetate-utilizing bacteria were not identified. Phylotypes of the representatives of Thermococcus spp. were found among 16S rDNAs of archaea. 16S rRNA genes of bacterial clones belong to the orders Thermoanaerobacteriales (Thermoanaerobacter, Thermovenabulum, Thermacetogenium, and Coprothermobacter spp.), Thermotogales, Nitrospirales (Thermodesulfovibrio sp.) and Planctomycetales. 16S rDNA of a bacterium capable of oxidizing acetate in the course of syntrophic growth with H2-utilizing methanogens was found at high-temperature petroleum reservoirs for the first time. These results provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs, indicating that syntrophic processes play an important part in acetate degradation accompanied by methane production.

Isolation and characterization of new strains of methanogens from cold terrestrial habitats.

PubMed

Simankova, Maria V; Kotsyurbenko, Oleg R; Lueders, Tillmann; Nozhevnikova, Alla N; Wagner, Bianca; Conrad, Ralf; Friedrich, Michael W

2003-06-01

Five strains of methanogenic archaea (MT, MS, MM, MSP, ZB) were isolated from permanently and periodically cold terrestrial habitats. Physiological and morphological studies, as well as phylogenetic analyses of the new isolates were performed. Based on sequences of the 16S rRNA and methyl-coenzyme M reductase a-subunit (mcrA) genes all new isolates are closely related to known mesophilic and psychrotolerant methanogens. Both, phylogenetic analyses and phenotypic properties allow to classify strains MT, MS, and MM as members of the genus Methanosarcina. Strain MT is a new ecotype of Methanosarcina mazei, whereas strains MM and MS are very similar to each other and can be assigned to the recently described psychrotolerant species Methanosarcina lacustris. The hydrogenotrophic strain MSP is a new ecotype of the genus Methanocorpusculum. The obligately methylotrophic strain ZB is closely related to Methanomethylovorans hollandica and can be classified as new ecotype of this species. All new isolates, including the strains from permanently cold environments, are not true psychrophiles according to their growth temperature characteristics. In spite of the ability of all isolates to grow at temperatures as low as 1-5 degrees C, all of them have their growth optima in the range of moderate temperatures (25-35 degrees C). Thus, they can be regarded as psychrotolerant organisms. Psychrotolerant methanogens are thought to play an important role in methane production in both, habitats under seasonal temperature variations or from permanently cold areas.

Survival in the hot subsurface: Hydrogen stress on hyperthermophilic heterotrophs and methanogens

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Holden, J. F.

2017-12-01

Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in hot subsurface environments such as hydrothermal vents, marine sediments, and oil reservoirs. This project aims to make fundamental advances in our understanding of interspecies microbe-microbe interactions in hot subsurface environments by integrating metabolic network modeling, transcriptomic analyses and continuous cultivation of hyperthermophiles and describe how heterotrophs and methanogens eliminate H2 stress. Some subsurface environments may lack alternative electron acceptors (e.g., S°) for the heterotroph and sufficient environmental flux rates to draw in fresh energy sources or remove excess metabolic products. We observed a decrease in growth rates for the H2-producer Thermococcus paralvinellae when grown with an aqueous H2 background of 65 µM relative to no added H2. Metabolite analysis showed increased formate production during H2 inhibition. Differential gene expression analyses coupled with metabolic network modeling showed that T. paralvinellae oxidized H2 and made formate by a formate hydrogenlyase to survive H2 inhibition. Low H2 concentrations (20 µM) also caused a decrease in growth and CH4 production rates for the H2-consuming methanogen Methanocaldococcus jannaschii. H2 stress in both organisms was ameliorated when the organisms were grown together syntrophically. CH4 was produced without any added H2 during syntrophic growth, and there was no formate produced by T. paralvinellae. These organisms may impact the biogeochemistry, especially natural gas production, in saline, organic-rich subsurface environments when both are present.

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds.

PubMed

Mohamad Shahimin, Mohd Faidz; Foght, Julia M; Siddique, Tariq

2016-05-15

Oil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (n-pentane and n-hexane) or four (n-pentane, n-hexane, n-octane and n-decane) n-alkanes under methanogenic conditions for ~600 d. Microbes in Albian MFT began methane production by ~80 d, achieving complete depletion of n-pentane and n-hexane in the two-alkane mixture and their preferential biodegradation in the four-alkane mixture. Microbes in CNRL MFT preferentially metabolized n-octane and n-decane in the four-alkane mixture after a ~80 d lag but exhibited a lag of ~360 d before commencing biodegradation of n-pentane and n-hexane in the two-alkane mixture. 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. Anaerolineaceae sequences increased only in cultures amended with the four-alkane mixture and only during n-octane and n-decane biodegradation. The dominant methanogens were acetoclastic Methanosaetaceae. These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation. Copyright © 2016 Elsevier B.V. All rights reserved.

Unexpected competitiveness of Methanosaeta populations at elevated acetate concentrations in methanogenic treatment of animal wastewater.

PubMed

Chen, Si; Cheng, Huicai; Liu, Jiang; Hazen, Terry C; Huang, Vicki; He, Qiang

2017-02-01

Acetoclastic methanogenesis is a key metabolic process in anaerobic digestion, a technology with broad applications in biogas production and waste treatment. Acetoclastic methanogenesis is known to be performed by two archaeal genera, Methanosaeta and Methanosarcina. The conventional model posits that Methanosaeta populations are more competitive at low acetate levels (<1 mM) than Methanosarcina and vice versa at higher acetate concentrations. While this model is supported by an extensive body of studies, reports of inconsistency have grown that Methanosaeta were observed to outnumber Methanosarcina at elevated acetate levels. In this study, monitoring of anaerobic digesters treating animal wastewater unexpectedly identified Methanosaeta as the dominant acetoclastic methanogen population at both low and high acetate levels during organic overloading. The surprising competitiveness of Methanosaeta at elevated acetate was further supported by the enrichment of Methanosaeta with high concentrations of acetate (20 mM). The dominance of Methanosaeta in the methanogen community could be reproduced in anaerobic digesters with the direct addition of acetate to above 20 mM, again supporting the competitiveness of Methanosaeta over Methanosarcina at elevated acetate levels. This study for the first time systematically demonstrated that the dominance of Methanosaeta populations in anaerobic digestion could be linked to the competitiveness of Methanosaeta at elevated acetate concentrations. Given the importance of acetoclastic methanogenesis in biological methane production, findings from this study could have major implications for developing strategies for more effective control of methanogenic treatment processes.

A Reactive-Transport Model Describing Methanogen Growth and Methane Production in Diffuse Flow Vents at Axial Seamount

NASA Astrophysics Data System (ADS)

Algar, C. K.

2015-12-01

Hydrogenotrophic methanogenesis is an important mode of metabolism in deep-sea hydrothermal vents. Diffuse vent fluids often show a depletion in hydrogen with a corresponding increase in methane relative to pure-mixing of end member fluid and seawater, and genomic surveys show an enrichment in genetic sequences associated with known methanogens. However, because we cannot directly sample the subseafloor habitat where these organisms are living, constraining the size and activity of these populations remains a challenge and limits our ability to quantify the role they play in vent biogeochemistry. Reactive-transport modeling may provide a useful tool for approaching this problem. Here we present a reactive-transport model describing methane production along the flow-path of hydrothermal fluid from its high temperature end-member to diffuse venting at the seafloor. The model is set up to reflect conditions at several diffuse vents in the Axial Seamount. The model describes the growth of the two dominant thermophilic methanogens, Methanothermococcus and Methanocaldococcus, observed at Axial seamount. Monod and Arrhenius constants for Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii were obtained for the model using chemostat and bottle experiments at varying temperatures. The model is used to investigate the influence of different mixing regimes on the subseafloor populations of these methanogens. By varying the model flow path length and subseafloor cell concentrations, and fitting to observed hydrogen and methane concentrations in the venting fluid, the subseafloor biomass, fluid residence time, and methane production rate can be constrained.

Enhanced Radiation Resistance of Methanosarcina soligelidi SMA-21, a New Methanogenic Archaeon Isolated from a Siberian Permafrost-Affected Soil in Direct Comparison to Methanosarcina barkeri.

PubMed

Morozova, Daria; Moeller, Ralf; Rettberg, Petra; Wagner, Dirk

2015-11-01

Permafrost-affected soils are characterized by a high abundance and diversity of methanogenic communities, which are considered suitable model organisms for potential life on Mars. Methanogens from Siberian permafrost have been proven to be highly resistant against divers stress conditions such as subzero temperatures, desiccation, and simulated thermophysical martian conditions. Here, we studied the radiation resistance of the currently described new species Methanosarcina soligelidi SMA-21, which was isolated from a Siberian permafrost-affected soil, in comparison to Methanosarcina barkeri, which is used as a reference organism from a nonpermafrost soil environment. Both strains were exposed to solar UV and ionizing radiation to assess their limits of survival. Methanosarcina soligelidi exhibit an increase in radiation resistance to UV (2.5- to 13.8-fold) and ionizing radiation (46.6-fold) compared to M. barkeri. The F10 (UVC) and D10 (X-rays) values of M. soligelidi are comparable to values for the well-known, highly radioresistant species Deinococcus radiodurans. In contrast, the radiation response of M. barkeri was highly sensitive to UV and ionizing radiation comparably to Escherichia coli and other radiosensitive microorganisms. This study showed that species of the same genus respond differently to UV and ionizing radiation, which might reflect the adaptation of Methanosarcina soligelidi SMA-21 to the harsh environmental conditions of the permafrost habitat. Methanogenic archaea-Environmental UV-Ionizing radiation-Permafrost-Radiation resistance-Mars.

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

PubMed

Reumer, Max; Harnisz, Monika; Lee, Hyo Jung; Reim, Andreas; Grunert, Oliver; Putkinen, Anuliina; Fritze, Hannu; Bodelier, Paul L E; Ho, Adrian

2018-02-01

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities. IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects. Copyright © 2018 American Society for Microbiology.

Effect of sudden addition of PCE and bioreactor coupling to ZVI filters on performance of fluidized bed bioreactors operated in simultaneous electron acceptor modes.

PubMed

Moreno-Medina, C U; Poggi-Varaldo, Hector M; Breton-Deval, L; Rinderknecht-Seijas, N

2017-11-01

The present work evaluated the effects of (i) feeding a water contaminated with 80 mg/L PCE to bioreactors seeded with inoculum not acclimated to PCE, (ii) coupling ZVI side filters to bioreactors, and (iii) working in different biological regimes, i.e., simultaneous methanogenic aeration and simultaneous methanogenic-denitrifying regimes, on fluidized bed bioreactor performance. Simultaneous electron acceptors refer to the simultaneous presence of two compounds operating as final electron acceptors in the biological respiratory chain (e.g., use of either O 2 or NO 3 - in combination with a methanogenic environment) in a bioreactor or environmental niche. Four lab-scale, mesophilic, fluidized bed bioreactors (bioreactors) were implemented. Two bioreactors were operated as simultaneous methanogenic-denitrifying (MD) units, whereas the other two were operated in partially aerated methanogenic (PAM) mode. In the first period, all bioreactors received a wastewater with 1 g chemical oxygen demand of methanol per liter (COD-methanol/L). In a second period, all the bioreactors received the wastewater plus 80 mg perchloroethylene (PCE)/L; at the start of period 2, one MD and one PAM were coupled to side sand-zero valent iron filters (ZVI). All bioreactors were inoculated with a microbial consortium not acclimated to PCE. In this work, the performance of the full period 1 and the first 60 days of period 2 is reported and discussed. The COD removal efficiency and the nitrate removal efficiency of the bioreactors essentially did not change between period 1 and period 2, i.e., upon PCE addition. On the contrary, specific methanogenic activity in PAM bioreactors (both with and without coupled ZVI filter) significantly decreased. This was consistent with a sharp fall of methane productivity in those bioreactors in period 2. During period 2, PCE removals in the range 86 to 97 % were generally observed; the highest removal corresponded to PAM bioreactors along with the highest dehalogenation efficiency (94 %). Principal component analysis as well as cluster analysis confirmed the trends mentioned above, i.e., the better performance of PAM over MD, and the unexpected no effect of the ZVI side filters on PCE removal and dehalogenation efficiencies. To the best of our knowledge, this is the first report on the combined treatment ZVI-biological of a water polluted with PCE, where the biological operation relied on simultaneous electron acceptors.

Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

PubMed Central

Gao, Beile; Gupta, Radhey S

2007-01-01

Background The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood. Results We have carried out comprehensive analyses on each open reading frame (ORFs) in the genomes of 11 archaea (3 Crenarchaeota – Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota – Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus) to search for proteins that are unique to either all Archaea or for its main subgroups. These studies have identified 1448 proteins or ORFs that are distinctive characteristics of Archaea and its various subgroups and whose homologues are not found in other organisms. Six of these proteins are unique to all Archaea, 10 others are only missing in Nanoarchaeum equitans and a large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobales and Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens). Of particular importance is the observation that 31 proteins are uniquely present in virtually all methanogens (including M. kandleri) and 10 additional proteins are only found in different methanogens as well as A. fulgidus. In contrast, no protein was exclusively shared by various methanogen and any of the Halobacteriales or Thermoplasmatales. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. In contrast to the phylogenomics studies, a monophyletic grouping of archaea is not supported by phylogenetic analyses based on protein sequences. Conclusion The identified archaea-specific proteins provide novel molecular markers or signature proteins that are distinctive characteristics of Archaea and all of its major subgroups. The species distributions of these proteins provide novel insights into the evolutionary relationships among different groups within Archaea, particularly regarding the origin of methanogenesis. Most of these proteins are of unknown function and further studies should lead to discovery of novel biochemical and physiological characteristics that are unique to either all archaea or its different subgroups. PMID:17394648

Detection of the osmoregulator betaine in methanogens.

PubMed

Robertson, D E; Noll, D; Roberts, M F; Menaia, J A; Boone, D R

1990-02-01

Trimethyl glycine (glycine betaine) was detected by 13C nuclear magnetic resonance spectroscopy at high intracellular concentrations in several methanogens (Methanogenium cariaci, "Methanogenium anulus" AN9, Methanohalophilus zhilinae, Methanohalophilus mahii, and Methanococcus voltae) grown on marine media containing yeast extract. 13C labeling studies with Methanogenium cariaci suggested that the betaine which accumulated inside the cells was not synthesized de novo but was transported in from the medium. Proof of such a transport system was provided by growing Methanogenium cariaci on yeast-free medium supplemented with betaine. Under these conditions, betaine was the dominant osmoregulator.

Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture.

PubMed

Sundset, Monica A; Edwards, Joan E; Cheng, Yan Fen; Senosiain, Roberto S; Fraile, Maria N; Northwood, Korinne S; Praesteng, Kirsti E; Glad, Trine; Mathiesen, Svein D; Wright, André-Denis G

2009-02-01

The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.

Trace Elements Induce Predominance among Methanogenic Activity in Anaerobic Digestion

PubMed Central

Wintsche, Babett; Glaser, Karin; Sträuber, Heike; Centler, Florian; Liebetrau, Jan; Harms, Hauke; Kleinsteuber, Sabine

2016-01-01

Trace elements (TE) play an essential role in all organisms due to their functions in enzyme complexes. In anaerobic digesters, control, and supplementation of TEs lead to stable and more efficient methane production processes while TE deficits cause process imbalances. However, the underlying metabolic mechanisms and the adaptation of the affected microbial communities to such deficits are not yet fully understood. Here, we investigated the microbial community dynamics and resulting process changes induced by TE deprivation. Two identical lab-scale continuous stirred tank reactors fed with distiller’s grains and supplemented with TEs (cobalt, molybdenum, nickel, tungsten) and a commercial iron additive were operated in parallel. After 72 weeks of identical operation, the feeding regime of one reactor was changed by omitting TE supplements and reducing the amount of iron additive. Both reactors were operated for further 21 weeks. Various process parameters (biogas production and composition, total solids and volatile solids, TE concentration, volatile fatty acids, total ammonium nitrogen, total organic acids/alkalinity ratio, and pH) and the composition and activity of the microbial communities were monitored over the total experimental time. While the methane yield remained stable, the concentrations of hydrogen sulfide, total ammonia nitrogen, and acetate increased in the TE-depleted reactor compared to the well-supplied control reactor. Methanosarcina and Methanoculleus dominated the methanogenic communities in both reactors. However, the activity ratio of these two genera was shown to depend on TE supplementation explainable by different TE requirements of their energy conservation systems. Methanosarcina dominated the well-supplied anaerobic digester, pointing to acetoclastic methanogenesis as the dominant methanogenic pathway. Under TE deprivation, Methanoculleus and thus hydrogenotrophic methanogenesis was favored although Methanosarcina was not overgrown by Methanoculleus. Multivariate statistics revealed that the decline of nickel, cobalt, molybdenum, tungsten, and manganese most strongly influenced the balance of mcrA transcripts from both genera. Hydrogenotrophic methanogens seem to be favored under nickel- and cobalt-deficient conditions as their metabolism requires less nickel-dependent enzymes and corrinoid cofactors than the acetoclastic and methylotrophic pathways. Thus, TE supply is critical to sustain the activity of the versatile high-performance methanogen Methanosarcina. PMID:28018337

mcrA Gene abundance correlates with hydrogenotrophic methane production rates in full-scale anaerobic waste treatment systems.

PubMed

Morris, R L; Tale, V P; Mathai, P P; Zitomer, D H; Maki, J S

2016-02-01

Anaerobic treatment is a sustainable and economical technology for waste stabilization and production of methane as a renewable energy. However, the process is under-utilized due to operational challenges. Organic overload or toxicants can stress the microbial community that performs waste degradation, resulting in system failure. In addition, not all methanogenic microbial communities are equally capable of consistent, maximum biogas production. Opinion varies as to which parameters should be used to monitor the fitness of digester biomass. No standard molecular tools are currently in use to monitor and compare full-scale operations. It was hypothesized that determining the number of gene copies of mcrA, a methanogen-specific gene, would positively correlate with specific methanogenic activity (SMA) rates from biomass samples from six full-scale anaerobic digester systems. Positive correlations were observed between mcrA gene copy numbers and methane production rates against H2  : CO2 and propionate (R(2)  = 0·67-0·70, P < 0·05) but not acetate (R(2)  = 0·49, P > 0·05). Results from this study indicate that mcrA gene targeted qPCR can be used as an alternate tool to monitor and compare certain methanogen communities in anaerobic digesters. Using quantitative PCR (qPCR), we demonstrate that the abundance of mcrA, a gene specific to methane producing archaea, correlated with specific methanogenic activity (SMA) measurements when H2 and CO2 , or propionate were provided as substrates. However, mcrA abundance did not correlate with SMA with acetate. SMA values are often used as a fitness indicator of anaerobic biomass. Results from qPCR can be obtained within a day while SMA analysis requires days to weeks to complete. Therefore, qPCR for mcrA abundance is a sensitive and fast method to compare and monitor the fitness of certain anaerobic biomass. As a monitoring tool, qPCR of mcrA will help anaerobic digester operators optimize treatment and encourage more widespread use of this valuable technology. © 2015 The Society for Applied Microbiology.

Growth and Survivability of Microorganisms at Martian Temperatures and Pressures

NASA Astrophysics Data System (ADS)

Mickol, Rebecca Lynne

The discovery of methane in the martian atmosphere via numerous ground- and space-based sources has prompted the study of methanogens as models for life on Mars. Methanogens are microorganisms within the domain Archaea, many of which utilize carbon dioxide (CO2) and hydrogen to produce methane. The non-photosynthetic nature of methanogens indicates that they could exist in sub-surface environments, protected from harmful UV and ionizing radiation on the surface of Mars. These organisms also do not require organics, which are sparse on the planet. Additionally, the wide variety of environments we find life in on Earth, as well as evidence for liquid brines on the surface of Mars, suggest that habitable environments may still exist on the planet. However, there are a variety of conditions that any extant life on Mars would need to endure, including wide variations in temperature over one sol, a low-pressure atmosphere, and a limited availability of liquid water, among others. This dissertation encompasses various experiments that examined the ability of four species of methanogens (Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis, and Methanothermobacter wolfeii) to survive and/or grow under 1) low-pressure conditions and 2) freeze/thaw cycles. Low pressure studies include both survival and active growth experiments conducted between 7 mbar (the average surface pressure on Mars) and 143 mbar. Freeze/thaw experiments utilized short- and long-term cycles varying in temperature between the organisms' growth temperatures (22 °C, M. maripaludis; 37 °C, M. barkeri and M. formicicum; 55 °C, M. wolfeii ) and -80 °C, encompassing Mars-relevant temperature changes. As a comparison to methanogen growth and survivability, additional experiments were conducted using a non-spore-forming bacterium, Serratia liquefaciens , previously shown capable of growth at 7 mbar, 0 °C and within an anoxic CO2 atmosphere. The experiments described here assessed the survivability of S. liquefaciens exposed to martian UV irradiation within liquid brines and ices. The experiments discussed here demonstrate the ability of Earth microorganisms to withstand certain extreme conditions on Mars and suggest that the planet may contain relatively habitable microenvironments within the near subsurface.

Morphology and Phylogeny of a New Species of Anaerobic Ciliate, Trimyema finlayi n. sp., with Endosymbiotic Methanogens.

PubMed

Lewis, William H; Sendra, Kacper M; Embley, T Martin; Esteban, Genoveva F

2018-01-01

Many anaerobic ciliated protozoa contain organelles of mitochondrial ancestry called hydrogenosomes. These organelles generate molecular hydrogen that is consumed by methanogenic Archaea, living in endosymbiosis within many of these ciliates. Here we describe a new species of anaerobic ciliate, Trimyema finlayi n. sp., by using silver impregnation and microscopy to conduct a detailed morphometric analysis. Comparisons with previously published morphological data for this species, as well as the closely related species, Trimyema compressum , demonstrated that despite them being similar, both the mean cell size and the mean number of somatic kineties are lower for T. finlayi than for T. compressum , which suggests that they are distinct species. This was also supported by analysis of the 18S rRNA genes from these ciliates, the sequences of which are 97.5% identical (6 substitutions, 1479 compared bases), and in phylogenetic analyses these sequences grouped with other 18S rRNA genes sequenced from previous isolates of the same respective species. Together these data provide strong evidence that T. finlayi is a novel species of Trimyema , within the class Plagiopylea. Various microscopic techniques demonstrated that T. finlayi n. sp. contains polymorphic endosymbiotic methanogens, and analysis of the endosymbionts' 16S rRNA gene showed that they belong to the genus Methanocorpusculum , which was confirmed using fluorescence in situ hybridization with specific probes. Despite the degree of similarity and close relationship between these ciliates, T. compressum contains endosymbiotic methanogens from a different genus, Methanobrevibacter . In phylogenetic analyses of 16S rRNA genes, the Methanocorpusculum endosymbiont of T. finlayi n. sp. grouped with sequences from Methanomicrobia, including the endosymbiont of an earlier isolate of the same species, ' Trimyema sp.,' which was sampled approximately 22 years earlier, at a distant (∼400 km) geographical location. Identification of the same endosymbiont species in the two separate isolates of T. finlayi n. sp. provides evidence for spatial and temporal stability of the Methanocorpusculum-T. finlayi n. sp. endosymbiosis. T. finlayi n. sp. and T. compressum provide an example of two closely related anaerobic ciliates that have endosymbionts from different methanogen genera, suggesting that the endosymbionts have not co-speciated with their hosts.

In situ permafrost thaw due to climate change drives holistic microbial community shifts with implications for methane cycling

NASA Astrophysics Data System (ADS)

Mondav, Rhiannon; McCalley, Carmody; Hodgkins, Suzanne; Rich, Virginia; Frolking, Steve; Saleska, Scott; Barnes, Andrew; Chanton, Jeff; Crill, Patrick

2014-05-01

Thawing permafrost is a potentially significant source of radiative forcing feedback due to increased emissions of methane, a biogenic greenhouse gas (GHG). This study investigated changes in the microbial community along a permafrost thaw gradient at Stordalen Mire, Sweden using 16S rRNA gene amplicon and metagenomic methods. In situ measurements of geochemical parameters, including CH4 and C isotopes, enabled linkage of community dynamics to significant shifts in C balance. The thaw gradient ranged from intact at a palsa (low productivity and GHG emissions), through partially thawed in a bog (high productivity, low GHG emissions) to a completely thawed fen (high productivity and GHG emissions). Microbial assemblages in both the palsa and fen were highly diverse (in both richness and evenness), consistent with climax communities. The microbial community in the bog had distinctly lower diversity, characteristic of ecosystem disturbance. The palsa community was dominated by Acidobacteria and Proteobacteria, as is typical of a range of soils including permafrost. Methanogens dominated both the bog and fen and were most abundant within the zone of water table fluctuation. Inferring methanogens' production pathway from phylogeny showed a shift from mostly hydrogenotrophic methanogens in the bog towards acetotrophic methanogens in the fen. This corroborated porewater and flux emitted CH4 and CO2 carbon isotopic 13C signatures of CH4 and CO2. The fen, where the highest CH4 flux was recorded, was significantly richer in methanogenic archaea. A novel archaea, Candidatus Methanoflorens stordalenmirensis, was present at up to 70% relative abundance in the bog, enabling recovery of a population genome. The genome (and associated metaproteome) of 'M. stordalenmirensis' indicates that hydrogenotrophic methane production is its main energy conservation pathway. 'Methanoflorens' may be an indicator species of permafrost thaw, it is globally ubiquitous, and appears a major contributor to global methane production. Our results revealed a distinct difference in the microbial community structure and membership at each site, which can be directly associated with increasing methane emission and thaw state.

Hydrogen and carbon isotope systematics in hydrogenotrophic methanogenesis under H2-limited and H2-enriched conditions: implications for the origin of methane and its isotopic diagnosis

NASA Astrophysics Data System (ADS)

Okumura, Tomoyo; Kawagucci, Shinsuke; Saito, Yayoi; Matsui, Yohei; Takai, Ken; Imachi, Hiroyuki

2016-12-01

Hydrogen and carbon isotope systematics of H2O-H2-CO2-CH4 in hydrogenotrophic methanogenesis and their relation to H2 availability were investigated. Two H2-syntrophic cocultures of fermentatively hydrogenogenic bacteria and hydrogenotrophic methanogens under conditions of <102 Pa-H2 and two pure cultures of hydrogenotrophic methanogens under conditions of 105 Pa-H2 were tested. Carbon isotope fractionation between CH4 and CO2 during hydrogenotrophic methanogenesis was correlated with pH2, as indicated in previous studies. The hydrogen isotope ratio of CH4 produced during rapid growth of the thermophilic methanogen Methanothermococcus okinawensis under high pH2 conditions ( 105 Pa) was affected by the isotopic composition of H2, as concluded in a previous study of Methanothermobacter thermautotrophicus. This " {δ D}_{{H}_2} effect" is a possible cause of the diversity of previously reported values for hydrogen isotope fractionation between CH4 and H2O examined in H2-enriched culture experiments. Hydrogen isotope fractionation between CH4 and H2O, defined by (1000 + {δ D}_{{CH}_4} )/(1000 + {δ D}_{{H}_2O} ), during hydrogenotrophic methanogenesis of the H2-syntrophic cocultures was in the range 0.67-0.69. The hydrogen isotope fractionation of our H2-syntrophic dataset overlaps with those obtained not only from low- pH2 experiments reported so far but also from natural samples of "young" methane reservoirs (0.66-0.74). Conversely, such hydrogen isotope fractionation is not consistent with that of "aged" methane in geological samples (≥0.79), which has been regarded as methane produced via hydrogenotrophic methanogenesis from the carbon isotope fractionation. As a possible process inducing the inconsistency in hydrogen isotope signatures between experiments and geological samples, we hypothesize that the hydrogen isotope signature of CH4 imprinted at the time of methanogenesis, as in the experiments and natural young methane, may be altered by diagenetic hydrogen isotope exchange between extracellular CH4 and H2O through reversible reactions of the microbial methanogenic pathway in methanogenic region and/or geological methane reservoirs.

Analysis of Microbial Community Composition and Methane Production From Northern Peatlands Across a Climate Gradient

NASA Astrophysics Data System (ADS)

Sarno, A. F.; Humphreys, E.; Olefeldt, D.; Heffernan, L.; Roman, T. D.; Sebestyen, S.; Kolka, R.; Yavitt, J. B.; Finn, D.; Cadillo-Quiroz, H.

2017-12-01

Northern peatland ecosystems allow for the accumulation of a carbon (C) pool as the rate of photosynthesis exceeds the rate of organic carbon decomposition. Under current climate conditions, many northern peatlands act as a C sink; however, changes in climate and other environmental conditions, such as soil permafrost melting, are capable of changing the decomposition cascade. Here we take advantage of four peatlands situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess how the relative abundance of microbial functional groups and substrate availability within the microbial community might impact the decomposition of soil organic matter to methane. The four peatlands had similar hydrology and geochemistry and were poor fen types. Soil, water and gas samples were collected at the water table level. Microbial community composition, derived from Illumina amplicon sequencing of the 16S rRNA gene, and geochemical and climate variables were analyzed with principal component regression analysis to determine major drivers of community variation. Mean annual temperature (r2=0.53), mean annual precipitation (r2=0.36), water table level (r2=0.43) and soil temperature (r2=0.49), were all statistically significant drivers of both general microbial and methanogen community composition (p value < 0.001). The relative abundance of Methanocella, Methanosarcina and Methanobacterium varied significantly across the climate gradient (p value < 0.05), however the majority of methanogen genera did not. Interestingly, dissolved methane (r2=0.24) was statistically significant at the general community level (p value < 0.001), but not significant when tested against only the methanogen community. The results demonstrate that environmental factors predicted to change over time due to climate change will have a significant impact on microbial community composition and C sinks within Northern peatlands. Further analyses of microbial processes that produce methanogenic substrates such as fermentation and syntrophic reactions, in tandem with the further identification and quantification of methanogens, will elucidate other drivers of methane production in Northern peatlands.

Quantitative microbiological analysis of bacterial community shifts in a high-rate anaerobic bioreactor treating sulfite evaporator condensate.

PubMed

Ney, U; Macario, A J; Conway de Macario, E; Aivasidis, A; Schoberth, S M; Sahm, H

1990-08-01

The bacterial population of a high-rate, anaerobic, fixed-bed loop reactor treating sulfite evaporator condensate from the pulp industry was studied over a 14-month period. This period was divided into seven cycles that included a startup at the beginning of each cycle. Some 82% of the total biomass was immobilized on and between the porous glass rings filling the reactor. The range of the total number of microorganisms in these biofilms was 2 x 10 to 7 x 10 cells per ml. Enumeration and characterization by microbiological methods and by phase-contrast, epifluorescence, and electron microscopy showed that the samples consisted mainly of the following methanogens: a Methanobacterium sp., a Methanosarcina sp., a Methanobrevibacter sp., and a Methanothrix sp., as well as furfural-degrading sulfate-reducing bacteria resembling Desulfovibrio furfuralis. Viable counts of hydrogenotrophic methanogens were relatively stable (mostly within the range of 3.2 x 10 to 7.5 x 10 cells per ml), but Methanobrevibacter cells increased from <5 to 30% of the total hydrogenotrophic count after transfer of the fixed bed into a second reactor vessel. Acetotrophic methanogens reached their highest numbers of 1.3 x 10 to 2.6 x 10 cells per ml in the last fermentation cycles. They showed a morphological shift from sarcinalike packets in early samples to single coccoid forms in later phases of the fermentation. Furfural-degrading sulfate reducers reached counts of 1 x 10 to 5.8 x 10 cells per ml. The distribution of the chief metabolic groups between free fluid and biofilms was analyzed in the fifth fermentation cycle: 4.5 times more furfural degraders were found in the free fluid than in the biofilms. In contrast, 5.8 times more acetotrophic and 16.6 times more hydrogenotrophic methanogens were found in the biofilms than in the free liquid. The data concerning time shifts of morphotypes among the trophic groups of methanogens corroborated the trends observed by using immunological assays on the same samples.

Quantitative Microbiological Analysis of Bacterial Community Shifts in a High-Rate Anaerobic Bioreactor Treating Sulfite Evaporator Condensate

PubMed Central

Ney, U.; Macario, A. J. L.; de Macario, E. Conway; Aivasidis, A.; Schoberth, S. M.; Sahm, H.

1990-01-01

The bacterial population of a high-rate, anaerobic, fixed-bed loop reactor treating sulfite evaporator condensate from the pulp industry was studied over a 14-month period. This period was divided into seven cycles that included a startup at the beginning of each cycle. Some 82% of the total biomass was immobilized on and between the porous glass rings filling the reactor. The range of the total number of microorganisms in these biofilms was 2 × 109 to 7 × 109 cells per ml. Enumeration and characterization by microbiological methods and by phase-contrast, epifluorescence, and electron microscopy showed that the samples consisted mainly of the following methanogens: a Methanobacterium sp., a Methanosarcina sp., a Methanobrevibacter sp., and a Methanothrix sp., as well as furfural-degrading sulfate-reducing bacteria resembling Desulfovibrio furfuralis. Viable counts of hydrogenotrophic methanogens were relatively stable (mostly within the range of 3.2 × 108 to 7.5 × 108 cells per ml), but Methanobrevibacter cells increased from <5 to 30% of the total hydrogenotrophic count after transfer of the fixed bed into a second reactor vessel. Acetotrophic methanogens reached their highest numbers of 1.3 × 108 to 2.6 × 108 cells per ml in the last fermentation cycles. They showed a morphological shift from sarcinalike packets in early samples to single coccoid forms in later phases of the fermentation. Furfural-degrading sulfate reducers reached counts of 1 × 107 to 5.8 × 107 cells per ml. The distribution of the chief metabolic groups between free fluid and biofilms was analyzed in the fifth fermentation cycle: 4.5 times more furfural degraders were found in the free fluid than in the biofilms. In contrast, 5.8 times more acetotrophic and 16.6 times more hydrogenotrophic methanogens were found in the biofilms than in the free liquid. The data concerning time shifts of morphotypes among the trophic groups of methanogens corroborated the trends observed by using immunological assays on the same samples. Images PMID:16348253

Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor

NASA Astrophysics Data System (ADS)

Imachi, H.; Tasumi, E.; Morono, Y.; Ito, M.; Takai, K.; Inagaki, F.

2013-12-01

Deep subseafloor environments associated with hydrocarbon reservoirs have been least explored by previous scientific drilling and hence the nature of deep subseafloor life and its ecological roles in the carbon cycle remain largely unknown. In this study, we performed cultivation of subseafloor methanogenic communities using a continuous-flow bioreactor with polyurethane sponges, called down-flow hanging sponge (DHS) reactor. The sample used for the reactor cultivation was obtained from 2 km-deep coalbeds off the Shimokita Peninsula of Japan, the northwestern Pacific, during the Integrated Ocean Drilling Program (IODP) Expedition 337 using a riser drilling technology of the drilling vessel Chikyu. The coalbed samples were incubated anaerobically in the DHS reactor at the in-situ temperature of 40°C. Synthetic seawater supplemented with a tiny amount of yeast extract, acetate, propionate and butyrate was provided into the DHS reactor. After 34 days of the bioreactor operation, a small production of methane was observed. The methane concentration was gradually increased and the stable carbon isotopic composition of methane was consistency 13C-depleted during the bioreactor operation, indicating the occurrence of microbial methanogenesis. Microscopic observation showed that the enrichment culture contained a variety of microorganisms, including methanogen-like rod-shaped cells with F420 auto-fluorescence. Interestingly, many spore-like particles were observed in the bioreactor enrichment. Phylogenetic analysis of 16S rRNA genes showed the growth of phylogenetically diverse bacteria and archaea in the DHS reactor. Predominant archaeal components were closely related to hydrogenotrophic methanogens within the genus Methanobacterium. Some predominant bacteria were related to the spore-formers within the class Clostridia, which are overall in good agreement with microscopic observations. By analyzing ion images using a nano-scale secondary ion mass spectrometry (NanoSIMS), 13C-bicarbonate incorporation of rod-shaped methanogens, as well as 13C-acetate incorporation of other cells, was observed. These microbiological data obtained from the DHS reactor generally support a geochemical indication that microbial processes contribute to the biogeochemical carbon cycle associated with 2 km-coalbeds in the deep subseafloor biosphere.

Single-cell analysis of the methanogenic archaeon Methanosarcina soligelidi from Siberian permafrost by means of confocal Raman microspectrocopy for astrobiological research

NASA Astrophysics Data System (ADS)

Serrano, Paloma; Wagner, Dirk; Böttger, Ute; de Vera, Jean-Pierre; Lasch, Peter; Hermelink, Antje

2014-08-01

Methanogenic archaea from Siberian permafrost are suitable model organisms that meet many of the preconditions for survival on the martian subsurface. These microorganisms have proven to be highly resistant when exposed to diverse stress factors such as desiccation, radiation and other thermo-physical martian conditions. In addition, the metabolic requirements of methanogenic archaea are in principle compatible with the environmental conditions of the Red Planet. The ExoMars mission will deploy a rover carrying a Raman spectrometer among the analytical instruments in order to search for signatures of life and to investigate the martian geochemistry. Raman spectroscopy is known as a powerful nondestructive optical technique for biosignature detection that requires only little sample preparation. In this study, we describe the use of confocal Raman microspectroscopy (CRM) as a rapid and sensitive technique for characterization of the methanogenic archaeon Methanosarcina soligelidi SMA-21 at the single cell level. These studies involved acquisition of Raman spectra from individual cells isolated from microbial cultures at different stages of growth. Spectral analyses indicated a high degree of heterogeneity between cells of individual cultures and also demonstrated the existence of growth-phase specific Raman patterns. For example, besides common Raman patterns of microbial cells, CRM additionally revealed the presence of lipid vesicles and CaCO3 particles in microbial preparations of M. soligelidi SMA-21, a finding that could be confirmed by electron microscopy. The results of this study suggest that heterogeneity and diversity of microorganisms have to be considered when using Raman-based technologies in future space exploration missions.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

PubMed Central

2012-01-01

Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world. PMID:22691113

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

PubMed

Roy Chowdhury, Anindya; Dutta, Chitra

2012-06-12

Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples.

PubMed

Barret, Maialen; Gagnon, Nathalie; Kalmokoff, Martin L; Topp, Edward; Verastegui, Yris; Brooks, Stephen P J; Matias, Fernando; Neufeld, Josh D; Talbot, Guylaine

2013-01-01

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-(13)C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of (13)C into DNA was detectable at in situ acetate concentrations (~7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the (13)C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.

Methanogenic activity tests by Infrared Tunable Diode Laser Absorption Spectroscopy.

PubMed

Martinez-Cruz, Karla; Sepulveda-Jauregui, Armando; Escobar-Orozco, Nayeli; Thalasso, Frederic

2012-10-01

Methanogenic activity (MA) tests are commonly carried out to estimate the capability of anaerobic biomass to treat effluents, to evaluate anaerobic activity in bioreactors or natural ecosystems, or to quantify inhibitory effects on methanogenic activity. These activity tests are usually based on the measurement of the volume of biogas produced by volumetric, pressure increase or gas chromatography (GC) methods. In this study, we present an alternative method for non-invasive measurement of methane produced during activity tests in closed vials, based on Infrared Tunable Diode Laser Absorption Spectroscopy (MA-TDLAS). This new method was tested during model acetoclastic and hydrogenotrophic methanogenic activity tests and was compared to a more traditional method based on gas chromatography. From the results obtained, the CH(4) detection limit of the method was estimated to 60 ppm and the minimum measurable methane production rate was estimated to 1.09(.)10(-3) mg l(-1) h(-1), which is below CH(4) production rate usually reported in both anaerobic reactors and natural ecosystems. Additionally to sensitivity, the method has several potential interests compared to more traditional methods among which short measurements time allowing the measurement of a large number of MA test vials, non-invasive measurements avoiding leakage or external interferences and similar cost to GC based methods. It is concluded that MA-TDLAS is a promising method that could be of interest not only in the field of anaerobic digestion but also, in the field of environmental ecology where CH(4) production rates are usually very low. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Biologically Produced Methane as a Renewable Energy Source.

PubMed

Holmes, D E; Smith, J A

2016-01-01

Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO 2 . However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person. Copyright © 2016 Elsevier Inc. All rights reserved.

Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates.

PubMed

Morita, Masahiko; Malvankar, Nikhil S; Franks, Ashley E; Summers, Zarath M; Giloteaux, Ludovic; Rotaru, Amelia E; Rotaru, Camelia; Lovley, Derek R

2011-01-01

Mechanisms for electron transfer within microbial aggregates derived from an upflow anaerobic sludge blanket reactor converting brewery waste to methane were investigated in order to better understand the function of methanogenic consortia. The aggregates were electrically conductive, with conductivities 3-fold higher than the conductivities previously reported for dual-species aggregates of Geobacter species in which the two species appeared to exchange electrons via interspecies electron transfer. The temperature dependence response of the aggregate conductance was characteristic of the organic metallic-like conductance previously described for the conductive pili of Geobacter sulfurreducens and was inconsistent with electron conduction through minerals. Studies in which aggregates were incubated with high concentrations of potential electron donors demonstrated that the aggregates had no significant capacity for conversion of hydrogen to methane. The aggregates converted formate to methane but at rates too low to account for the rates at which that the aggregates syntrophically metabolized ethanol, an important component of the reactor influent. Geobacter species comprised 25% of 16S rRNA gene sequences recovered from the aggregates, suggesting that Geobacter species may have contributed to some but probably not all of the aggregate conductivity. Microorganisms most closely related to the acetate-utilizing Methanosaeta concilii accounted for more than 90% of the sequences that could be assigned to methane producers, consistent with the poor capacity for hydrogen and formate utilization. These results demonstrate for the first time that methanogenic wastewater aggregates can be electrically conductive and suggest that direct interspecies electron transfer could be an important mechanism for electron exchange in some methanogenic systems.

Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

PubMed

FitzGerald, Jamie A; Allen, Eoin; Wall, David M; Jackson, Stephen A; Murphy, Jerry D; Dobson, Alan D W

2015-01-01

Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

Effect of the Associated Methanogen Methanobrevibacter thaueri on the Dynamic Profile of End and Intermediate Metabolites of Anaerobic Fungus Piromyces sp. F1.

PubMed

Li, Yuanfei; Jin, Wei; Cheng, Yanfen; Zhu, Weiyun

2016-09-01

Although the scheme of metabolic pathways involved in the production of the major end products has been described, the dynamic profile of metabolites of anaerobic fungi co-cultured with methanogens is limited, especially for the intermediate metabolites. In the present study, the fermentation of the co-culture of Piromyces sp. F1 and Methanobrevibacter thaueri on glucose was investigated. The presence of methanogens shortened the growth lag time of anaerobic fungi and enhanced the total gas production. The occurrence of the maximum cell dry weight and the disappearance of most of the substrate were observed at 24 h for the co-culture and 48 h for the fungal mono-culture. In the co-culture, hydrogen was detected at a very low level during fermentation, and formate transitorily accumulated at 24 h and disappeared at 48 h, resulting in an increase of pH. Acetate was higher during the fermentation in the co-culture (P < 0.05), while lactate and ethanol were higher only in the initial stage of fermentation (P < 0.05). After 48 h, lactate in the mono-culture became much higher than that in the co-culture (P < 0.05), and ethanol tended to remain the same in both cultures. Moreover, malate tended to be exhausted in the co-culture, while it accumulated in the mono-culture. Citrate was also detected in both co-culture and mono-culture. Collectively, these results suggest that methanogen enhanced the malate pathway and weakened the lactate pathway of anaerobic fungus.

Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

PubMed Central

Barret, Maialen; Gagnon, Nathalie; Kalmokoff, Martin L.; Topp, Edward; Verastegui, Yris; Brooks, Stephen P. J.; Matias, Fernando; Neufeld, Josh D.

2013-01-01

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-13C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of 13C into DNA was detectable at in situ acetate concentrations (∼7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the 13C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis. PMID:23104405

Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China.

PubMed

Li, Zhi Peng; Liu, Han Lu; Jin, Chun Ai; Cui, Xue Zhe; Jing, Yi; Yang, Fu He; Li, Guang Yu; Wright, André-Denis G

2013-11-01

Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.

Bioaugmentation of overloaded anaerobic digesters restores function and archaeal community.

PubMed

Tale, V P; Maki, J S; Zitomer, D H

2015-03-01

Adding beneficial microorganisms to anaerobic digesters for improved performance (i.e. bioaugmentation) has been shown to decrease recovery time after organic overload or toxicity upset. Compared to strictly anaerobic cultures, adding aerotolerant methanogenic cultures may be more practical since they exhibit higher methanogenic activity and can be easily dried and stored in ambient air for future shipping and use. In this study, anaerobic digesters were bioaugmented with both anaerobic and aerated, methanogenic propionate enrichment cultures after a transient organic overload. Digesters bioaugmented with anaerobic and moderately aerated cultures recovered 25 and 100 days before non-bioaugmented digesters, respectively. Increased methane production due to bioaugmentation continued a long time, with 50-120% increases 6 to 12 SRTs (60-120 days) after overload. In contrast to the anaerobic enrichment, the aerated enrichments were more effective as bioaugmentation cultures, resulting in faster recovery of upset digester methane and COD removal rates. Sixty days after overload, the bioaugmented digester archaeal community was not shifted, but was restored to one similar to the pre-overload community. In contrast, non-bioaugmented digester archaeal communities before and after overload were significantly different. Organisms most similar to Methanospirillum hungatei had higher relative abundance in well-operating, undisturbed and bioaugmented digesters, whereas organisms similar to Methanolinea tarda were more abundant in upset, non-bioaugmented digesters. Bioaugmentation is a beneficial approach to increase digester recovery rate after transient organic overload events. Moderately aerated, methanogenic propionate enrichment cultures were more beneficial augments than a strictly anaerobic enrichment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils

PubMed Central

Li, Fuyan; Zheng, Fengfeng; Wang, Yongli; Liu, Weiguo; Zhang, Chuanlun L.

2017-01-01

Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea. PMID:28717356

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments.

PubMed

Zheng, Shiling; Wang, Bingchen; Liu, Fanghua; Wang, Oumei

2017-11-01

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNA-based terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The results also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

PubMed

Hagen, Live Heldal; Vivekanand, Vivekanand; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

2015-07-01

A new biogas process is initiated by adding a microbial community, typically in the form of a sample collected from a functional biogas plant. This inoculum has considerable impact on the initial performance of a biogas reactor, affecting parameters such as stability, biogas production yields and the overall efficiency of the anaerobic digestion process. In this study, we have analyzed changes in the microbial composition and performance of an inoculum during storage using barcoded pyrosequencing of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, and determination of the biomethane potential, respectively. The inoculum was stored at room temperature, 4 and -20 °C for up to 11 months and cellulose was used as a standard substrate to test the biomethane potential. Storage up to 1 month resulted in similar final methane yields, but the rate of methane production was reduced by storage at -20 °C. Longer storage times resulted in reduced methane yields and slower production kinetics for all storage conditions, with room temperature and frozen samples consistently giving the best and worst performance, respectively. Both storage time and temperature affected the microbial community composition and methanogenic activity. In particular, fluctuations in the relative abundance of Bacteroidetes were observed. Interestingly, a shift from hydrogenotrophic methanogens to methanogens with the capacity to perform acetoclastic methanogensis was observed upon prolonged storage. In conclusion, this study suggests that biogas inocula may be stored up to 1 month with low loss of methanogenic activity, and identifies bacterial and archaeal species that are affected by the storage.

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

Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

PubMed

Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

2007-09-01

Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

PubMed

Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

2015-11-01

The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Methane-producing microbial community in a coal bed of the Illinois Basin

USGS Publications Warehouse

Strapoc, D.; Picardal, F.W.; Turich, C.; Schaperdoth, I.; Macalady, J.L.; Lipp, J.S.; Lin, Y.-S.; Ertefai, T.F.; Schubotz, F.; Hinrichs, K.-U.; Mastalerz, Maria; Schimmelmann, A.

2008-01-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H 2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H2-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H 2-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

PubMed Central

Ivarsson, Magnus; Schnürer, Anna; Bengtson, Stefan; Neubeck, Anna

2016-01-01

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes. PMID:27433154

Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nayak, Dipti D.; Mahanta, Nilkamal; Mitchell, Douglas A.

Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather thanmore » thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.« less

Engineered heat treated methanogenic granules: a promising biotechnological approach for extreme thermophilic biohydrogen production.

PubMed

Abreu, Angela A; Alves, Joana I; Pereira, M Alcina; Karakashev, Dimitar; Alves, M Madalena; Angelidaki, Irini

2010-12-01

In the present study, two granular systems were compared in terms of hydrogen production rate, stability and bacterial diversity under extreme thermophilic conditions (70 degrees C). Two EGSB reactors were individually inoculated with heat treated methanogenic granules (HTG) and HTG amended with enrichment culture with high capacity of hydrogen production (engineered heat treated methanogenic granules - EHTG), respectively. The reactor inoculated with EHTG (R(EHTG)) attained a maximum production rate of 2.7l H(2)l(-1)day(-1) in steady state. In comparison, the R(HTG) containing the HTG granules was very unstable, with low hydrogen productions and only two peaks of hydrogen (0.8 and 1.5l H(2)l(-1)day(-1)). The presence of active hydrogen producers in the R(EHTG) system during the reactor start-up resulted in the development of an efficient H(2)-producing bacterial community. The results showed that "engineered inocula" where known hydrogen producers are co-inoculated with HTG is an efficient way to start up biohydrogen-producing reactors. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Improving methane yield from organic fraction of municipal solid waste (OFMSW) with magnetic rice-straw biochar.

PubMed

Qin, Yong; Wang, Haoshu; Li, Xiangru; Cheng, Jay Jiayang; Wu, Weixiang

2017-12-01

Magnetic biochar is a potential economical anaerobic digestion (AD) additive. To better understand the possible role of magnetic biochar for the improvement of biomethanization performance and the retention of methanogens, magnetic biochar fabricated under different precursor concentrations were introduced into organic fraction of municipal solid waste (OFMSW) slurry AD system. Results showed that methane production in AD treatment with magnetic biochar fabricated under 3.2g FeCl 3 :100g rice-straw ratio increased by 11.69% compared with control treatment without biochar addition, due to selective enrichment of microorganisms participating in anaerobic digestion on magnetic biochar. AD treatment with magnetic biochar fabricated under 32g FeCl 3 :100g rice-straw ratio resulted in 38.34% decreasement of methane production because of the competition of iron oxide for electron. Furthermore, 25% of total methanogens were absorbed on magnetic biochar and can be harvested with magnet, which can offer a potential solution for preventing the methanogens loss in the anaerobic digesters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Methanogenic degradation of acetone by an enrichment culture.

PubMed

Platen, H; Schink, B

1987-01-01

An anaerobic enrichment culture degraded 1 mol of acetone to 2 mol of methane and 1 mol of carbon dioxide. Two microorganisms were involved in this process, a filament-forming rod similar to Methanothrix sp. and an unknown rod with round to slightly pointed ends. Both organisms formed aggregates up to 300 micron in diameter. No fluorescing bacteria were observed indicating that hydrogen or formate-utilizing methanogens are not involved in this process. Acetate was utilized in this culture by the Methanothrix sp. Inhibition of methanogenesis by bromoethanesulfonic acid or acetylene decreased the acetone degradation rate drastically and led to the formation of 2 mol acetate per mol of acetone. Streptomycin completely inhibited acetone degradation, and neither acetate nor methane was formed. 14CO2 was incorporated exclusively into the C-1 atom of acetate indicating that acetone is degraded via carboxylation to an acetoacetate residue. It is concluded that acetone is degraded by a coculture of an eubacterium and an acetate-utilizing methanogen and that acetate is the only intermediate transferred between both. The energetical problems of the eubacterium converting acetone to acetate are discussed.

Squalenes, phytanes and other isoprenoids as major neutral lipids of methanogenic and thermoacidophilic 'archaebacteria'

NASA Technical Reports Server (NTRS)

Tornabene, T. G.; Langworthy, T. A.; Holzer, G.; Oro, J.

1979-01-01

The neutral lipids from nine species of methanogenic bacteria (five methanobacilli, two methanococci, a methanospirillum and a methanosarcina) and two thermoacidophilic bacteria (Thermo-plasma and Sulfolobus) have been analyzed. The neutral lipids were found to comprise a wide range (C14 to C30) of polyisoprenyl hydrocarbons with varying degrees of saturation. The principal components represented the three major isoprenoid series (C20 phytanyl, C25 pentaisoprenyl, and C30 squalenyl), in contrast with the neutral lipids of extreme halophiles, which consist predominantly of C2O (phytanyl, geranylgeraniol), C30 (squalenes), C40 (carotenes) and C50 (bacterioruberins compounds), as reported by Kates (1978). These results, which indicate strong general similarities between genetically diverse organisms, support the classification of these organisms in a separate phylogenetic group. The occurrence of similar isoprenoid compounds in petroleum and ancient sediments and the fact that the methanogens, halophiles and thermoacidophiles live in conditions presumed to have prevailed in archaen times suggest that the isoprenoid compounds in petroleum compounds and sediment may have been directly synthesized by organisms of this type

Methanogenic degradation of toilet-paper cellulose upon sewage treatment in an anaerobic membrane bioreactor at room temperature.

PubMed

Chen, Rong; Nie, Yulun; Kato, Hiroyuki; Wu, Jiang; Utashiro, Tetsuya; Lu, Jianbo; Yue, Shangchao; Jiang, Hongyu; Zhang, Lu; Li, Yu-You

2017-03-01

Toilet-paper cellulose with rich but refractory carbon sources, are the main insoluble COD fractions in sewage. An anaerobic membrane bioreactor (AnMBR) was configured for sewage treatment at room temperature and its performance on methanogenic degradation of toilet paper was highlighted. The results showed, high organic removal (95%), high methane conversion (90%) and low sludge yield (0.08gVSS/gCOD) were achieved in the AnMBR. Toilet-paper cellulose was fully biodegraded without accumulation in the mixed liquor and membrane cake layer. Bioconversion efficiency of toilet paper approached 100% under a high organic loading rate (OLR) of 2.02gCOD/L/d and it could provide around 26% of total methane generation at most of OLRs. Long sludge retention time and co-digestion of insoluble/soluble COD fractions achieving mutualism of functional microorganisms, contributed to biodegradation of toilet-paper cellulose. Therefore the AnMBR successfully implemented simultaneously methanogenic bioconversion of toilet-paper cellulose and soluble COD in sewage at room temperature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Self-adaption of methane-producing communities to pH disturbance at different acetate concentrations by shifting pathways and population interaction.

PubMed

Hao, Liping; Lü, Fan; Li, Lei; Wu, Qing; Shao, Liming; He, Pinjing

2013-07-01

To investigate the competition among acetate-utilizing microorganisms at different acetate levels, bioconversion processes of 50, 100, 150 and 200 mM acetate in the presence and absence of methanogenic inhibitor CH3F were monitored in thermophilic methanogenic system. The successive response of methane-producing community during the deteriorative and recovery phases caused by pH disturbance was analyzed. High acetate concentration (>50mM) inhibited the activity of acetoclastic methanogenesis (AM). The increasing pH (>7.5) enhanced this inhibition. The syntrophic acetate oxidizing (SAO) bacteria and hydrogenotrophic methanogens including Methanomicrobiales and Methanobacteirales were more tolerant to the stress from high acetate concentration and high pH. Resumption from alkali condition to normal pH stimulated the growth of acetate oxidizing syntrophs. The reaction rate of SAO-HM was lower than that of AM. These results point to the possibility to regenerate the deteriorated anaerobic digesters by addition of acclimatized inocula rich in acetate-oxidizing syntrophs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

DOE PAGES

Nayak, Dipti D.; Mahanta, Nilkamal; Mitchell, Douglas A.; ...

2017-09-07

Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather thanmore » thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.« less

Thermophilic methanogenesis in a hot-spring algal-bacterial mat (71 to 30/sup 0/C)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, D.M.

1978-06-01

Algal-bacterial mats which grow in the effluent channels of alkaline hot springs provided an environment suitable for studying natural thermophilic methane-producing bacteria. Methane was rapidly produced in cores taken from the mat and appeared to be an end product of decomposition of the algal-bacterial organic matter. Formaldehyde prevented production of methane. Initial methanogenic rate was lower and methanogenesis became exponential when samples were permitted to cool before laboratory incubation. Methanogenesis occurred and methanogenic bateria were present over a range of 68 to 30/sup 0/C, with optimum methanogenesis near 45/sup 0/C. The temperature distribution of methanogenesis in the mat is discussedmore » relative to published results on standing crop, primary production, and decomposition in the thermal gradient. The depth distribution of methanogenesis was similar to that of freshwater sediments, with a zone of intense methanogenesis near the mat surface. Methanogenesis in deeper mat layers was very low or undetectable despite large numbers of viable methanogenic bacteria and could not be stimulated by addition of anoxic source water, sulfide, or a macronutrient solution.« less

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

2016-05-11

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.

Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge.

PubMed

Liu, Can; Li, Huan; Zhang, Yuyao; Si, Dandan; Chen, Qingwu

2016-09-01

High-solids anaerobic digestion (HSAD), a promising method with smaller reactor and less heating energy consumption, showed relatively lower digestion efficiency sometimes and higher tolerance to some inhibitors. To investigate the phenomena, the archaeal and bacterial communities in four anaerobic digesters treating sewage sludge with total solids (TS) of 10-19% were investigated. Although acetoclastic methanogenesis conducted mainly by genus Methanosarcina was still the main pathway producing methane, the total ratio of acetoclastic methanogens decreased along with the increased TS. In contrary, the relative abundance of hydrogenotrophic methanogens increased from 6.8% at TS 10% to 22.3% at TS 19%, and methylotrophic methanogens from 10.4% to 20.9%. The bacterial community was dominated by five phyla. Acidogenic and acetogenic bacteria affiliated to Firmicutes decreased following the increase of TS; while the proteolysis phylum Bacteroidetes increased, with a tolerant family ST-12K33 notably existing in the digesters at TS 17% and 19%. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Characterization of a Methanogenic Community within an Algal Fed Anaerobic Digester

PubMed Central

Ellis, Joshua T.; Tramp, Cody; Sims, Ronald C.; Miller, Charles D.

2012-01-01

The microbial diversity and metabolic potential of a methanogenic consortium residing in a 3785-liter anaerobic digester, fed with wastewater algae, was analyzed using 454 pyrosequencing technology. DNA was extracted from anaerobic sludge material and used in metagenomic analysis through PCR amplification of the methyl-coenzyme M reductase α subunit (mcrA) gene using primer sets ML, MCR, and ME. The majority of annotated mcrA sequences were assigned taxonomically to the genera Methanosaeta in the order Methanosarcinales. Methanogens from the genus Methanosaeta are obligate acetotrophs, suggesting this genus plays a dominant role in methane production from the analyzed fermentation sample. Numerous analyzed sequences within the algae fed anaerobic digester were unclassified and could not be assigned taxonomically. Relative amplicon frequencies were determined for each primer set to determine the utility of each in pyrosequencing. Primer sets ML and MCR performed better quantitatively (representing the large majority of analyzed sequences) than primer set ME. However, each of these primer sets was shown to provide a quantitatively unique community structure, and thus they are of equal importance in mcrA metagenomic analysis. PMID:23724331

Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages.

PubMed

Shi, Yu; Huang, Zhou; Han, Shuai; Fan, Shuo; Yang, Hong

2015-08-01

Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Boosting methane generation by co-digestion of sludge with fruit and vegetable waste: Internal environment of digester and methanogenic pathway.

PubMed

Di Maria, Francesco; Barratta, Martino

2015-09-01

The effects of anaerobic co-digestion of waste-mixed sludge with fruit and vegetable waste (FVW) on the methane generation of a mesophilic digester was investigated. Organic loading rates (OLR) were 1.46kgVS/m(3)day, 2.1kgVS/m(3)day and 2.8kgVS/m(3)day. Increase in the OLR due to FVW co-digestion caused modification of the internal environment of the digester, mainly in terms of N-NH4 (mg/L). Corresponding microbial populations were investigated by metagenomic high-throughput sequencing. Maximum specific bio-methane generation of 435 NLCH4 per kgVS feed was achieved for an OLR of 2.1kgVS/m(3)day, which corresponded to a biomethane generation per kgVS removed of about 1700 NLCH4. In these conditions the methanogenic pathway was dominated by aceticlastic Methanosaeta and hydrogenotrophic/aceticlastic Methanoscarcinae. Ammonia concentration in the digester resulted a key parameter for enhancing syntrophic acetate oxidation, enabling a balanced aceticlastic and hydrogenotrophic/aceticlastic methanogenic pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial communities involved in methane production from hydrocarbons in oil sands tailings.

PubMed

Siddique, Tariq; Penner, Tara; Klassen, Jonathan; Nesbø, Camilla; Foght, Julia M

2012-09-04

Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

Biosorption of Cu(II) by powdered anaerobic granular sludge from aqueous medium.

PubMed

Zhou, Xu; Chen, Chuan; Wang, Aijie; Jiang, Guangming; Liu, Lihong; Xu, Xijun; Yuan, Ye; Lee, Duu-Jung; Ren, Nanqi

2013-01-01

Copper(II) biosorption processes by two pre-treated powdered anaerobic granular sludges (PAGS) (original sludges were methanogenic anaerobic granules and denitrifying sulfide removal (DSR) anaerobic granules) were investigated through batch tests. Factors affecting the biosorption process, such as pH, temperature and initial copper concentrations, were examined. Also, the physico-chemical characteristics of the anaerobic sludge were analyzed by Fourier transform infrared spectroscopy, scanning electron microscopy image, surface area and elemental analysis. A second-order kinetic model was applied to describe the biosorption process, and the model could fit the biosorption process. The Freundlich model was used for describing the adsorption equilibrium data and could fit the equilibrium data well. It was found that the methanogenic PAGS was more effective in Copper(II) biosorption process than the DSR PAGS, whose maximum biosorption capacity was 39.6% lower. The mechanisms of the biosorption capacities for different PAGS were discussed, and the conclusion suggested that the environment and biochemical reactions during the growth of biomass may have affected the structure of the PAGS. The methanogenic PAGS had larger specific surface area and more biosorption capacity than the DSR PAGS.

Antibiotic degradation and microbial community structures during acidification and methanogenesis of swine manure containing chlortetracycline or oxytetracycline.

PubMed

Yin, Fubin; Dong, Hongmin; Zhang, Wanqin; Zhu, Zhiping; Shang, Bin

2018-02-01

Anaerobic digestion (AD) has been applied to animal manure stabilization, and antibiotics is frequently found in animal manure. However, antibiotic degradation and microbial community structures during two-stage AD (acidification and methanogenesis) remain poorly understood. This experiments on two-stage anaerobic swine manure digesters were performed to investigate the degradation mechanisms and effects of chlortetracycline (CTC) and oxytetracycline (OTC) on microbial community structures. Results showed that acidification and methanogenesis showed good degradation performance for manure containing CTC and OTC at 60 and 40 mg/kg·TS, respectively. CTC and OTC were degraded by 59.8% and 41.3% in the acidogenic stage and by 76.3% and 78.3% in the methanogenic stage, respectively. CTC and OTC negatively affected bacterial community in methanogenic and acidogenic stages, respectively. They also adversely influenced the archaeal species in the methanogenic stage. Two-stage AD was proposed to treat manure containing antibiotics and to reduce the negative effects of antibiotics on AD. Copyright © 2017 Elsevier Ltd. All rights reserved.

Changes in microbial community structures due to varying operational conditions in the anaerobic digestion of oxytetracycline-medicated cow manure.

PubMed

Turker, Gokhan; Aydin, Sevcan; Akyol, Çağrı; Yenigun, Orhan; Ince, Orhan; Ince, Bahar

2016-07-01

Management of manure containing veterinary antibiotics is a major concern in anaerobic treatment systems because of their possible adverse effects on microbial communities. Therefore, the aim of study was to investigate how oxytetracycline (OTC) influences bacteria and acetoclastic and hydrogenotrophic methanogens under varying operational conditions in OTC-medicated and non-medicated anaerobic cow manure digesters. Concentrations of OTC and its metabolites throughout the anaerobic digestion were determined using ultraviolet-high-performance liquid chromatography (UV-HPLC) and tandem liquid chromatography-mass spectrometry (LC/MS/MS), respectively. Fluorescent in situ hybridization, denaturing gradient gel electrophoresis, cloning, and sequencing analyses were used to monitor changes in microbial community structures. According to the results of analytical and molecular approaches, operating conditions highly influence active microbial community dynamics and associate with biogas production and elimination of OTC and its metabolites during anaerobic digestion of cow manure in the presence of an average initial concentration of 2.2 mg OTC/L. The impact of operating conditions has a drastic effect on acetoclastic methanogens than hydrogenotrophic methanogens and bacteria.

Quantifying the percentage of methane formation via acetoclastic and syntrophic acetate oxidation pathways in anaerobic digesters.

PubMed

Jiang, Ying; Banks, Charles; Zhang, Yue; Heaven, Sonia; Longhurst, Philip

2018-01-01

Ammonia concentration is one of the key factors influencing the methanogenic community composition and dominant methanogenic pathway in anaerobic digesters. This study adopted a radiolabelling technique using [2- 14 C] acetate to investigate the relationship between total ammonia nitrogen (TAN) and the methanogenic pathway. The radiolabelling experiments determined the ratio of 14 CO 2 and 14 CH 4 in the biogas which was used to quantitatively determine the percentage of CH 4 derived from acetoclastic and syntrophic acetate oxidation routes, respectively. This technique was performed on a selection of mesophilic digesters representing samples of low to high TAN concentrations (0.2-11.1gkg -1 wet weight). In high TAN digesters, the ratio between 14 CO 2 and 14 CH 4 was in the range 2.1-3.0; indicating 68-75% of methane was produced via the hydrogenotrophic route; whereas in low ammonia samples the ratio was 0.1-0.3, indicating 9-23% of methane was produced by the hydrogenotrophic route. These findings have been confirmed further by phylogenetic studies. Copyright © 2017. Published by Elsevier Ltd.

Anaerobic biodegradability and methanogenic toxicity of key constituents in copper chemical mechanical planarization effluents of the semiconductor industry.

PubMed

Hollingsworth, Jeremy; Sierra-Alvarez, Reyes; Zhou, Michael; Ogden, Kimberly L; Field, Jim A

2005-06-01

Copper chemical mechanical planarization (CMP) effluents can account for 30-40% of the water discharge in semiconductor manufacturing. CMP effluents contain high concentrations of soluble copper and a complex mixture of organic constituents. The aim of this study is to perform a preliminary assessment of the treatability of CMP effluents in anaerobic sulfidogenic bioreactors inoculated with anaerobic granular sludge by testing individual compounds expected in the CMP effluents. Of all the compounds tested (copper (II), benzotriazoles, polyethylene glycol (M(n) 300), polyethylene glycol (M(n) 860) monooleate, perfluoro-1-octane sulfonate, citric acid, oxalic acid and isopropanol) only copper was found to be inhibitory to methanogenic activity at the concentrations tested. Most of the organic compounds tested were biodegradable with the exception of perfluoro-1-octane sulfonate and benzotriazoles under sulfate reducing conditions and with the exception of the same compounds as well as Triton X-100 under methanogenic conditions. The susceptibility of key components in CMP effluents to anaerobic biodegradation combined with their low microbial inhibition suggest that CMP effluents should be amenable to biological treatment in sulfate reducing bioreactors.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

PubMed

Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

2018-05-01

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

Detection of methanogenic archaea in the pitchers of the Northern pitcher plant (Sarracenia purpurea ).

PubMed

Krieger, Joseph R; Kourtev, Peter S

2012-02-01

Carnivorous plants of the genus Sarracenia rely on microorganisms in their pitchers to decompose drowned insects. The environment inside pitchers is considered to be aerobic; however, there might be zones, such as at the bottom of the pitcher, where anaerobic conditions develop. Samples of the sediment at the bottom of Sarracenia purpurea pitchers were analyzed for the presence of archaea, using PCR and sequencing of the 16S rRNA gene. Archaeal DNA was detected in 20% of sampled pitchers. All sequences were closely related to Methanobrevibacter . Therefore, pitchers may contain anoxic zones inhabited by methanogens.

Detection of the osmoregulator betaine in methanogens.

PubMed Central

Robertson, D E; Noll, D; Roberts, M F; Menaia, J A; Boone, D R

1990-01-01

Trimethyl glycine (glycine betaine) was detected by 13C nuclear magnetic resonance spectroscopy at high intracellular concentrations in several methanogens (Methanogenium cariaci, "Methanogenium anulus" AN9, Methanohalophilus zhilinae, Methanohalophilus mahii, and Methanococcus voltae) grown on marine media containing yeast extract. 13C labeling studies with Methanogenium cariaci suggested that the betaine which accumulated inside the cells was not synthesized de novo but was transported in from the medium. Proof of such a transport system was provided by growing Methanogenium cariaci on yeast-free medium supplemented with betaine. Under these conditions, betaine was the dominant osmoregulator. PMID:2306094

Microbial methane from in situ biodegradation of coal and shale: A review and reevaluation of hydrogen and carbon isotope signatures

USGS Publications Warehouse

Vinson, David S.; Blair, Neal E.; Martini, Anna M.; Larter, Steve; Orem, William H.; McIntosh, Jennifer C.

2017-01-01

Stable carbon and hydrogen isotope signatures of methane, water, and inorganic carbon are widely utilized in natural gas systems for distinguishing microbial and thermogenic methane and for delineating methanogenic pathways (acetoclastic, hydrogenotrophic, and/or methylotrophic methanogenesis). Recent studies of coal and shale gas systems have characterized in situ microbial communities and provided stable isotope data (δD-CH4, δD-H2O, δ13C-CH4, and δ13C-CO2) from a wider range of environments than available previously. Here we review the principal biogenic methane-yielding pathways in coal beds and shales and the isotope effects imparted on methane, document the uncertainties and inconsistencies in established isotopic fingerprinting techniques, and identify the knowledge gaps in understanding the subsurface processes that govern H and C isotope signatures of biogenic methane. We also compare established isotopic interpretations with recent microbial community characterization techniques, which reveal additional inconsistencies in the interpretation of microbial metabolic pathways in coal beds and shales. Collectively, the re-assessed data show that widely-utilized isotopic fingerprinting techniques neglect important complications in coal beds and shales.Isotopic fingerprinting techniques that combine δ13C-CH4 with δD-CH4 and/or δ13C-CO2have significant limitations: (1) The consistent ~ 160‰ offset between δD-H2O and δD-CH4 could imply that hydrogenotrophic methanogenesis is the dominant metabolic pathway in microbial gas systems. However, hydrogen isotopes can equilibrate between methane precursors and coexisting water, yielding a similar apparent H isotope signal as hydrogenotrophic methanogenesis, regardless of the actual methane formation pathway. (2) Non-methanogenic processes such as sulfate reduction, Fe oxide reduction, inputs of thermogenic methane, anaerobic methane oxidation, and/or formation water interaction can cause the apparent carbon isotope fractionation between δ13C-CH4 and δ13C-CO2(α13CCO2-CH4) to differ from the true methanogenic fractionation, complicating interpretation of methanogenic pathways. (3) Where little-fractionating non-methanogenic bacterial processes compete with highly-fractionating methanogenesis, the mass balance between CH4 and CO2 is affected. This has implications for δ13C values and provides an alternative interpretation for net C isotope signatures than solely the pathways used by active methanogens. (4) While most of the reviewed values of δD-H2O - δD-CH4 and α13CCO2-CH4 are apparently consistent with hydrogenotrophic methanogenesis as the dominant pathway in coal beds and shales, recent microbial community characterization techniques suggest a possible role for acetoclastic or methylotrophic methanogenesis in some basins.

Methane cycling in alpine wetlands - an interplay of microbial communities and vascular plants

NASA Astrophysics Data System (ADS)

Henneberger, Ruth; Cheema, Simrita; Zeyer, Josef

2014-05-01

Wetland environments play an important role for the global climate, as they represent a major terrestrial carbon store. These environments are potential sinks for atmospheric carbon due to reduced decomposition rates of plant material in the waterlogged, anoxic subsurface. In contrast, wetlands are also a major source of the highly potent greenhouse gas methane (CH4), which is produced in the anoxic zones through methanogenic archaea (methanogens) degrading organic matter. The CH4 emitted into the pore water diffuses upwards towards the surface, and is partially oxidized in the oxic zones by aerobic methanotrophic bacteria (methanotrophs) before reaching the atmosphere. Nonetheless, global emissions of atmospheric CH4 from natural wetlands are estimated to range from 100 to 230 Tg a-1. Natural wetlands can be found around the globe, and are also common in temperate-cold climates in the Northern hemisphere. Methane release from these environments is influenced by many factors (e.g., vegetation, water table, temperature, pH) and shows high seasonal and spatial variability. To comprehend these variations and further predict potential responses to climate change, the biotic and abiotic processes involved in CH4 turnover need to be understood in detail. Many research projects focus on (sub-)arctic wetland areas, while studies on CH4 emissions from alpine wetlands are scarce, despite similar processes occurring in these different regions. Recently, we conducted a survey of 14 wetlands (i.e., fens vegetated with vascular plants) located in the Swiss Alps, showing CH4 emissions between 74 ± 43 and 711 ± 212 mg CH4 m-2 d-1 (Franchini et al., in press). A detailed study of one fen also revealed that CH4 emission was highest immediately after snowmelt, followed by a decrease in CH4 emission throughout the snow-free period (Liebner et al., 2012). Even though the CH4 cycle is largely driven by microbially mediated processes, vascular plants also play a crucial role in CH4 emissions from wetlands, as CH4 generated in the deeper layers can bypass the oxic, methanotrophic zones through the plant aerenchyma. In addition, O2 transported to the root system facilitates CH4 oxidation in the rhizosphere. To further comprehend these complex processes, the present study focused on selected fens dominated by different plants (i.e., Carex spp. or Eriophorum spp.). We combined field-measurements of overall CH4 emissions, CH4 and O2 pore water concentrations and plant-mediated bypass with molecular biological analyses of methanogenic and methanotrophic subpopulations at different soil depths. Methane emissions and pore water concentrations varied with location and dominating plant species. Nevertheless, in all fens we observed the presence of active methanogens and methanotrophs throughout the depth profile, independently of O2 and CH4 concentrations, with active methanogens being highly abundant even in the oxic layers indicating the presence of microniches. The often described spatial separation of methanogenic activity in anoxic zones and methanotrophic activity in oxic zones and oxic-anoxic interfaces could not be observed. The composition of the methanogenic and methanotrophic subpopulations that are active at different depths is currently analyzed in detail, providing new insights into the complex processes involved in CH4 turnover in alpine regions.

Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event.

PubMed

Konhauser, Kurt O; Pecoits, Ernesto; Lalonde, Stefan V; Papineau, Dominic; Nisbet, Euan G; Barley, Mark E; Arndt, Nicholas T; Zahnle, Kevin; Kamber, Balz S

2009-04-09

It has been suggested that a decrease in atmospheric methane levels triggered the progressive rise of atmospheric oxygen, the so-called Great Oxidation Event, about 2.4 Gyr ago. Oxidative weathering of terrestrial sulphides, increased oceanic sulphate, and the ecological success of sulphate-reducing microorganisms over methanogens has been proposed as a possible cause for the methane collapse, but this explanation is difficult to reconcile with the rock record. Banded iron formations preserve a history of Precambrian oceanic elemental abundance and can provide insights into our understanding of early microbial life and its influence on the evolution of the Earth system. Here we report a decline in the molar nickel to iron ratio recorded in banded iron formations about 2.7 Gyr ago, which we attribute to a reduced flux of nickel to the oceans, a consequence of cooling upper-mantle temperatures and decreased eruption of nickel-rich ultramafic rocks at the time. We measured nickel partition coefficients between simulated Precambrian sea water and diverse iron hydroxides, and subsequently determined that dissolved nickel concentrations may have reached approximately 400 nM throughout much of the Archaean eon, but dropped below approximately 200 nM by 2.5 Gyr ago and to modern day values ( approximately 9 nM) by approximately 550 Myr ago. Nickel is a key metal cofactor in several enzymes of methanogens and we propose that its decline would have stifled their activity in the ancient oceans and disrupted the supply of biogenic methane. A decline in biogenic methane production therefore could have occurred before increasing environmental oxygenation and not necessarily be related to it. The enzymatic reliance of methanogens on a diminishing supply of volcanic nickel links mantle evolution to the redox state of the atmosphere.

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

PubMed Central

Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

2016-01-01

Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions. PMID:27600710

Genetic resources for methane production from biomass described with the Gene Ontology.

PubMed

Purwantini, Endang; Torto-Alalibo, Trudy; Lomax, Jane; Setubal, João C; Tyler, Brett M; Mukhopadhyay, Biswarup

2014-01-01

Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing "gold standards" for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).

Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii

PubMed Central

Susanti, Dwi; Wong, Joshua H.; Vensel, William H.; Loganathan, Usha; DeSantis, Rebecca; Schmitz, Ruth A.; Balsera, Monica; Buchanan, Bob B.; Mukhopadhyay, Biswarup

2014-01-01

Thioredoxin (Trx), a small redox protein, controls multiple processes in eukaryotes and bacteria by changing the thiol redox status of selected proteins. The function of Trx in archaea is, however, unexplored. To help fill this gap, we have investigated this aspect in methanarchaea—strict anaerobes that produce methane, a fuel and greenhouse gas. Bioinformatic analyses suggested that Trx is nearly universal in methanogens. Ancient methanogens that produce methane almost exclusively from H2 plus CO2 carried approximately two Trx homologs, whereas nutritionally versatile members possessed four to eight. Due to its simplicity, we studied the Trx system of Methanocaldococcus jannaschii—a deeply rooted hyperthermophilic methanogen growing only on H2 plus CO2. The organism carried two Trx homologs, canonical Trx1 that reduced insulin and accepted electrons from Escherichia coli thioredoxin reductase and atypical Trx2. Proteomic analyses with air-oxidized extracts treated with reduced Trx1 revealed 152 potential targets representing a range of processes—including methanogenesis, biosynthesis, transcription, translation, and oxidative response. In enzyme assays, Trx1 activated two selected targets following partial deactivation by O2, validating proteomics observations: methylenetetrahydromethanopterin dehydrogenase, a methanogenesis enzyme, and sulfite reductase, a detoxification enzyme. The results suggest that Trx assists methanogens in combating oxidative stress and synchronizing metabolic activities with availability of reductant, making it a critical factor in the global carbon cycle and methane emission. Because methanogenesis developed before the oxygenation of Earth, it seems possible that Trx functioned originally in metabolic regulation independently of O2, thus raising the question whether a complex biological system of this type evolved at least 2.5 billion years ago. PMID:24505058

Bacterial metabolism of aromatic compounds and a complex hazardous waste under anaerobic conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Connor, O.A.

1992-01-01

The biological fate of organic chemicals in the environment depends upon a variety of physical/chemical factors. In the absence of molecular oxygen, the importance of terminal electron acceptors has been often overlooked. Since anaerobic microbial consortia are dependent upon the availability of particular electron acceptors, these conditions can play an important role in influencing the fate of environmental pollutants. In this research, different electron acceptors were evaluated for their effects on the biodegradation of environmental toxicants. Two anaerobic bioassays, the Biochemical Methane Potential (BMP) and the Anaerobic Toxicity Assay (ATA), were used to evaluate a series of phthalic acid estersmore » (PAEs), substituted phenols and a landfill leachate, for their methanogenic biodegradability and toxicity. Many of the PAEs and phenols could be stoichiometrically mineralized. In addition, the landfill leachate was found to be inhibitory at concentrations greater than 10%, and partially mineralized in approximately 50 weeks. Based upon these assays, 6 different functional groups and their isomers were evaluated for their effect on the biodegradability and toxicity of phenol under methanogenic and denitrifying conditions. These results indicated that nitro- and chloro-substituted phenols were persistent under denitrifying conditions. Under methanogenic conditions, these compounds were metabolized to a more reduced intermediate with less toxicity. Conversely, amino-substituted phenols were not readily mineralized under methanogenic conditions, but were metabolized after minimal lag under denitrifying conditions. From active denitrifying phenol degrading cultures, a pure culture was obtained which could grow on phenol and on a variety of other alkyl-substituted aromatic compounds. Additional studies have tentatively identified several alicyclic metabolites including cyclohexanol, 2-cyclohexene-1-ol, cyclohexanone and 2-cyclohexene-1-one from phenol catabolism.« less

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume.

PubMed

Ma, Jie; Nossa, Carlos W; Alvarez, Pedro J J

2015-09-01

The capacity of groundwater ecosystem to recover from contamination by organic chemicals is a vital concern for environmental scientists. A pilot-scale aquifer system was used to investigate the long-term dynamics of contaminants, groundwater geochemistry, and microbial community structure (by 16S rRNA gene pyrosequencing and quantitative real-time PCR) throughout the 5-year life cycle of a surrogate ethanol blend fuel plume (10% ethanol + 50 mg/L benzene + 50 mg/L toluene). Two-year continuous ethanol-blended release significantly changed the groundwater geochemistry (resulted in anaerobic, low pH, and organotrophic conditions) and increased bacterial and archaeal populations by 82- and 314-fold respectively. Various anaerobic heterotrophs (fermenters, acetogens, methanogens, and hydrocarbon degraders) were enriched. Two years after the release was shut off, all contaminants and their degradation byproducts disappeared and groundwater geochemistry completely restored to the pre-release states (aerobic, neutral pH, and oligotrophic). Bacterial and archaeal populations declined by 18- and 45-fold respectively (relative to the time of shut off). Microbial community structure reverted towards the pre-release states and alpha diversity indices rebounded, suggesting the resilience of microbial community to ethanol blend releases. We also found shifts from O2-sensitive methanogens (e.g., Methanobacterium) to methanogens that are not so sensitive to O2 (e.g., Methanosarcina and Methanocella), which is likely to contribute to the persistence of methanogens and methane generation following the source removal. Overall, the rapid disappearance of contaminants and their metabolites, rebound of geochemical footprints, and resilience of microbial community unequivocally document the natural capacity of groundwater ecosystem to attenuate and recover from a large volume of catastrophic spill of ethanol-based biofuel. Copyright © 2015 Elsevier Ltd. All rights reserved.

Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

PubMed Central

Toth, Courtney R. A.; Gieg, Lisa M.

2018-01-01

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems. PMID:29354103

Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate.

PubMed

Mei, R; Narihiro, T; Nobu, M K; Liu, W-T

2016-11-01

In anaerobic digesters, temperature fluctuation could lead to process instability and failure. It is still not well understood how digester microbiota as a whole respond to heat shock, and what specific organisms are vulnerable to perturbation or responsible for process recovery after perturbation. To address these questions, a mesophilic benzoate-degrading methanogenic culture enriched from digester was subjected to different levels of heat shock. Three types of methane production profiles after perturbation were observed in comparison to the control: uninhibited, inhibited with later recovery, and inhibited without recovery. These responses were correlated with the microbial community compositions based on the analyses of 16S rRNA and 16S rRNA gene. Specifically, the primary benzoate-degrading syntroph was highly affected by heat shock, and its abundance and activity were both crucial to the restoration of benzoate degradation after heat shock. In contrast, methanogens were stable regardless whether methane production was inhibited. Populations related to 'Candidatus Cloacimonetes' and Firmicutes showed stimulated growth. These observations indicated distinct physiological traits and ecological niches associated with individual microbial groups. The results obtained after exposure to heat shock can be critical to more comprehensive characterization of digester ecology under perturbations. Anaerobic digestion is an essential step in municipal wastewater treatment owing to its striking capacity of reducing wasted sludge and recovering energy. However, as an elaborate microbial process, it requires constant temperature control and is sensitive to heat shock. In this study, we explored the microbial response to heat shock of a methanogenic culture enriched from anaerobic digester sludge. Microorganisms that were vulnerable to perturbation or responsible for process recovery after perturbation were identified. © 2016 The Society for Applied Microbiology.

Genetic resources for methane production from biomass described with the Gene Ontology

PubMed Central

Purwantini, Endang; Torto-Alalibo, Trudy; Lomax, Jane; Setubal, João C.; Tyler, Brett M.; Mukhopadhyay, Biswarup

2014-01-01

Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/). PMID:25520705

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

PubMed

Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

2016-09-29

Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities

PubMed Central

FitzGerald, Jamie A.; Allen, Eoin; Wall, David M.; Jackson, Stephen A.; Murphy, Jerry D.; Dobson, Alan D. W.

2015-01-01

Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation. PMID:26555136

Impact of recycled effluent on the hydrolysis during anaerobic digestion of vegetable and flower waste.

PubMed

Lü, F; He, P J; Hao, L P; Shao, L M

2008-01-01

Two trials were established to investigate the effect of recycled effluent on hydrolysis during anaerobic co-digestion of vegetable and flower waste. Trial I evaluated the effect by regulating the flow rate of recycled effluent, while Trial II regulated the ratio of hydrolytic effluent to methanogenic effluent, which were recycled to hydrolysis reactor. Results showed that the recirculation of methanogenic effluent could enhance the buffer capability and operation stability of hydrolysis reactor. Higher recycled flow rate was favourable for microbial anabolism and further promoted hydrolysis. After 9 days of hydrolysis, the cumulative SCOD in the hydrolytic effluent reached 334, 407, 413, 581 mg/g at recycled flow rates of 0.1, 0.5, 1.0, 2.0 m3/(m3 x d), respectively. It was feasible to recycling a mixture of hydrolytic and methanogenic effluent to the hydrolysis reactor. This research showed that partially introducing hydrolytic effluent into the recycled liquid could enhance hydrolysis, while excessive recirculation of hydrolytic effluent will inhibit the hydrolysis. The flow ratio 1:3 of hydrolytic to methanogenic effluent was found to provide the highest hydrolysis efficiency and degradation rate of lignocelluloses-type biomass, among four ratios of 0:1, 1:3, 1:1 and 3:1. Under this regime, after 9 days of hydrolysis, the cumulative TOC and TN in the hydrolytic effluent reached 162 mg/g and 15 mg/g, the removal efficiency of TS, VS, C and cellulose in the solid phase were 60.66%, 62.88%, 58.35% and 49.12%, respectively. The flow ratio affected fermentation pathways, i.e. lower ratio favoured propionic acid fermentation and the generation of lactic acid while higher ratio promoted butyric acid fermentation. IWA Publishing 2008.

Role of microorganisms for cycling of atmospheric constituents, emphasizing the greenhouse gas methane (Invited)

NASA Astrophysics Data System (ADS)

Conrad, R.

2013-12-01

Microorganisms have contributed significantly to the formation of the atmosphere and the habitability of Earth. Microbial methanogenesis probably helped overcoming the faint sun problem on young Earth. Later on, cyanobacterial photosynthesis produced oxygen and thus restricted the life zone of methanogenic microbial communities, which nowadays contribute only about 1% to total carbon cycle. Nevertheless, methanogenesis still dominates the budget of atmospheric methane and contributes significantly to the greenhouse effect. There are numerous habitats, which exchange methane with the atmosphere, and even more in which methane is intensively cycled albeit little emitted. Methane can be a byproduct of chemical reactions in plant leaves, or of aerobic methyl phosphonate consumption in ocean water. Most commonly, however, methane is a stoichiometric catabolic product in the degradation of organic matter by anaerobic microorganisms. The degradation is achieved by a complex microbial community consisting of various species of hydrolytic and fermentative Bacteria that produce hydrogen, carbon dioxide and acetate as major end products, and of methanogenic Archaea that eventually convert these compounds to methane and carbon dioxide. The composition of such methanogenic microbial communities, the rates and paths of methane formation, and the isotopic composition of the produced methane all exhibit quite some variability across the different habitats in which methane is produced from organic matter decomposition, such as flooded soils, lake sediments, peatlands, animal gut systems. The structure of the microbial communities often strongly affects their function. It is a challenging task to understand the environmental and biochemical basis of the interactions of abiotic factors and microorganisms shaping the structure and function of the microbial communities in the different methanogenic habitats.

Microbial community activities during establishment, performance, and decline of bench-scale passive treatment systems for mine drainage.

PubMed

Logan, Miranda V; Reardon, Kenneth F; Figueroa, Linda A; McLain, Jean E T; Ahmann, Dianne M

2005-11-01

Permeable reactive barrier (PRB) technology, in which sulfate-reducing bacteria (SRB) facilitate precipitation of metal sulfides, is a promising approach for remediation of sulfate- and metal-laden mine drainage. While PRBs are easily established, they often decline for reasons not well understood. SRB depend on or compete with multiple dynamic microbial populations within a PRB; as a result, performance depends on the changing PRB chemical composition and on succession and competition within the microbial community. To investigate these interactions, we constructed and monitored eight bench-scale PRBs to define periods of establishment, performance, and decline. We then conducted short-term batch studies, using substrate-supplemented column materials, on Days 0 (pre-establishment), 27 (establishment), 41 (performance), and 99 (decline) to reveal potential activities of cellulolytic bacteria, fermenters + anaerobic respirers, SRB, and methanogens. PRBs showed active sulfate reduction, with sulfate removal rates (SRR) of approximately 1-3 mol/m3/d, as well as effective removal of Zn2+. Potential activities of fermentative + anaerobic respiratory bacteria were initially high but diminished greatly during establishment and dropped further during performance and decline. In contrast, potential SRB activity rose during establishment, peaked during performance, and diminished as performance declined. Potential methanogen activity was low; in addition, SRB-methanogen substrate competition was shown not to limit SRB activity. Cellulolytic bacteria showed no substrate limitation at any time. However, fermenters experienced substrate limitation by Day 0, SRB by Day 27, and methanogens by Day 41, showing the dependence of each group on upstream populations to provide substrates. All potential activities, except methanogenesis, were ultimately limited by cellulose hydrolysis; in addition, all potential activities except methanogenesis declined substantially by Day 99, showing that long-term substrate deprivation strongly diminished the intrinsic capacity of the PRB community to perform.

Comparison of surficial CO2 efflux to other measures of subsurface crude oil degradation.

PubMed

Warren, Ean; Sihota, Natasha J; Hostettler, Frances D; Bekins, Barbara A

2014-08-01

At a spill site near Bemidji, Minnesota, crude oil at the water table has been undergoing anaerobic biodegradation for over 30years. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. To compare microbial activity measurement methods from multiple locations in the oil body, surficial carbon dioxide efflux, methanogen and methanotroph concentrations, and oil degradation state were collected. Carbon dioxide effluxes over the oil body averaged more than four times those at the background site. Methanotrophic bacteria concentrations measured using pmoA were over 10(5) times higher above the oil-contaminated sediments compared with the background site. Methanogenic archaea measured using mcrA ranged from 10(5) to over 10(7) in the oil and were below detection in the background. Methanogens correlated very well with methanotroph concentrations (r=0.99), n-alkylcyclohexane losses as a proxy for degradation state (r=-0.96), and somewhat less well with carbon dioxide efflux (r=0.92). Carbon dioxide efflux similarly correlated to methanotroph concentrations (r=0.90) and n-alkylcyclohexane losses (r=-0.91). Published by Elsevier B.V.

Thermo-alkaline pretreatment of waste activated sludge at low-temperatures: effects on sludge disintegration, methane production, and methanogen community structure.

PubMed

Kim, Jaai; Yu, Youngseob; Lee, Changsoo

2013-09-01

Low-temperature thermo-alkaline pretreatment of waste activated sludge (WAS) was studied, within the region of 0-0.2 M NaOH and 60-90°C, for the effects of NaOH concentration and temperature on sludge degradability in anaerobic digestion (AD). Significant disintegration of sludge solids (up to 75.6%) and an increase in methane production (up to 70.6%) were observed in the pretreatment trials. Two quadratic models were successfully generated by response surface analysis (R(2)>0.9, p<0.05) to approximate how the degree of sludge disintegration (SD) and methane production (MP) respond to changes in the pretreatment conditions. The maximum responses of SD (77.8%) and MP (73.9% increase over the control) were shown at [0.16 M NaOH, 90°C] and [0.10 M NaOH, 73.7°C], respectively. NaOH addition showed a significant influence on the evolution of methanogen community structure during AD, whereas temperature did not. Aceticlastic Methanosaeta and Methanosarcina speceies were likely the major methanogens. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids.

PubMed

Sousa, Diana Z; Smidt, Hauke; Alves, Maria M; Stams, Alfons J M

2009-06-01

Syntrophic relationships are the key for biodegradation in methanogenic environments. We review the ecological and physiological features of syntrophic communities involved in the degradation of saturated and unsaturated long-chain fatty acids (LCFA), as well as their potential application to convert lipids/fats containing waste to biogas. Presently, about 14 species have been described with the ability to grow on fatty acids in syntrophy with methanogens, all belonging to the families Syntrophomonadaceae and Syntrophaceae. The principle pathway of LCFA degradation is through beta-oxidation, but the initial steps in the conversion of unsaturated LCFA are unclear. Communities enriched on unsaturated LCFA also degrade saturated LCFA, but the opposite generally is not the case. For efficient methane formation, the physical and inhibitory effects of LCFA on methanogenesis need to be considered. LCFA adsorbs strongly to biomass, which causes encapsulation of active syntrophic communities and hampers diffusion of substrate and products in and out of the biomass. Quantification of archaea by real-time PCR analysis suggests that potential LCFA inhibitory effect towards methanogens might be reversible. Rather, the conversion of adsorbed LCFA in batch assays was shown to result in a significant increase of archaeal cell numbers in anaerobic sludge samples.

Decolorization of a reactive copper-phthalocyanine dye under methanogenic conditions.

PubMed

Beydili, M I; Matthews, R D; Pavlostathis, S G

2001-01-01

The objective of this research was to assess the biological decolorization of the copper-phthalocyanine dye Reactive Blue 7 (RB7) under methanogenic conditions using a mixed, methanogenic culture in a repetitive dye addition batch assay. The initial rate of decolorization was 13.2 mg/L-d and 5.7 mg/L-d for the first and second dye addition, respectively. For an initial RB7 concentration of ca. 300 mg/L, the extent of decolorization remained constant (about 62%) for each repetitive RB7 addition and resulted in a residual color build up. Declining absorbance ratio values (A664/A620) with increasing incubation time confirmed that the observed color removal was due to transformation as opposed to adsorption on the biomass. Chemical decolorization assays using sodium dithionite as the reducing agent resulted in similar absorbance spectra to that obtained after biological decolorization. In addition, in both the chemical and biological decolorization assays, partial oxidation of the reduced dye solution upon exposure to air resulted in higher residual color, indicating that the reduction and decolorization of RB7 are partially reversible. These results also suggest that RB7 reduction and decolorization both chemically and biologically most likely followed a similar reduction mechanism.

Biogeochemistry of microbial coal-bed methane

USGS Publications Warehouse

Strc, D.; Mastalerz, Maria; Dawson, K.; MacAlady, J.; Callaghan, A.V.; Wawrik, B.; Turich, C.; Ashby, M.

2011-01-01

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane gas or uplifted coals containing older, thermogenic gas mixed with more recently produced microbial methane. Recent advances in genomics have allowed further evaluation of the source of microbial methane, through the use of high-throughput phylogenetic sequencing and fluorescent in situ hybridization, to describe the diversity and abundance of bacteria and methanogenic archaea in these subsurface formations. However, the anaerobic metabolism of the bacteria breaking coal down to methanogenic substrates, the likely rate-limiting step in biogenic gas production, is not fully understood. Coal molecules are more recalcitrant to biodegradation with increasing thermal maturity, and progress has been made in identifying some of the enzymes involved in the anaerobic degradation of these recalcitrant organic molecules using metagenomic studies and culture enrichments. In recent years, researchers have attempted lab and subsurface stimulation of the naturally slow process of methanogenic degradation of coal. Copyright ?? 2011 by Annual Reviews. All rights reserved.

Comparison of surficial CO2 efflux to other measures of subsurface crude oil degradation

USGS Publications Warehouse

Warren, Ean; Sihota, Natasha J.; Hostettler, Frances D.; Bekins, Barbara A.

2014-01-01

At a spill site near Bemidji, Minnesota, crude oil at the water table has been undergoing anaerobic biodegradation for over 30 years. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. To compare microbial activity measurement methods from multiple locations in the oil body, surficial carbon dioxide efflux, methanogen and methanotroph concentrations, and oil degradation state were collected. Carbon dioxide effluxes over the oil body averaged more than four times those at the background site. Methanotrophic bacteria concentrations measured using pmoA were over 105 times higher above the oil-contaminated sediments compared with the background site. Methanogenic archaea measured using mcrA ranged from 105 to over 107 in the oil and were below detection in the background. Methanogens correlated very well with methanotroph concentrations (r = 0.99), n-alkylcyclohexane losses as a proxy for degradation state (r = − 0.96), and somewhat less well with carbon dioxide efflux (r = 0.92). Carbon dioxide efflux similarly correlated to methanotroph concentrations (r = 0.90) and n-alkylcyclohexane losses (r = − 0.91).

Inoculum selection influences the biochemical methane potential of agro-industrial substrates

PubMed Central

De Vrieze, Jo; Raport, Linde; Willems, Bernard; Verbrugge, Silke; Volcke, Eveline; Meers, Erik; Angenent, Largus T; Boon, Nico

2015-01-01

Obtaining a reliable estimation of the methane potential of organic waste streams in anaerobic digestion, for which a biochemical methane potential (BMP) test is often used, is of high importance. Standardization of this BMP test is required to ensure inter-laboratory repeatability and accuracy of the BMP results. Therefore, guidelines were set out; yet, these do not provide sufficient information concerning origin of and the microbial community in the test inoculum. Here, the specific contribution of the methanogenic community on the BMP test results was evaluated. The biomethane potential of four different substrates (molasses, bio-refinery waste, liquid manure and high-rate activated sludge) was determined by means of four different inocula from full-scale anaerobic digestion plants. A significant effect of the selected inoculum on the BMP result was observed for two out of four substrates. This inoculum effect could be attributed to the abundance of methanogens and a potential inhibiting effect in the inoculum itself, demonstrating the importance of inoculum selection for BMP testing. We recommend the application of granular sludge as an inoculum, because of its higher methanogenic abundance and activity, and protection from bulk solutions, compared with other inocula. PMID:25756301

Methane emission from sewers.

PubMed

Liu, Yiwen; Ni, Bing-Jie; Sharma, Keshab R; Yuan, Zhiguo

2015-08-15

Recent studies have shown that sewer systems produce and emit a significant amount of methane. Methanogens produce methane under anaerobic conditions in sewer biofilms and sediments, and the stratification of methanogens and sulfate-reducing bacteria may explain the simultaneous production of methane and sulfide in sewers. No significant methane sinks or methanotrophic activities have been identified in sewers to date. Therefore, most of the methane would be emitted at the interface between sewage and atmosphere in gravity sewers, pumping stations, and inlets of wastewater treatment plants, although oxidation of methane in the aeration basin of a wastewater treatment plant has been reported recently. Online measurements have also revealed highly dynamic temporal and spatial variations in methane production caused by factors such as hydraulic retention time, area-to-volume ratio, temperature, and concentration of organic matter in sewage. Both mechanistic and empirical models have been proposed to predict methane production in sewers. Due to the sensitivity of methanogens to environmental conditions, most of the chemicals effective in controlling sulfide in sewers also suppress or diminish methane production. In this paper, we review the recent studies on methane emission from sewers, including the production mechanisms, quantification, modeling, and mitigation. Copyright © 2015 Elsevier B.V. All rights reserved.

Biomarker Evidence for Widespread Anaerobic Methane Oxidation in Mediterranean Sediments by a Consortium of Methanogenic Archaea and Bacteria†

PubMed Central

Pancost, Richard D.; Sinninghe Damsté, Jaap S.; de Lint, Saskia; van der Maarel, Marc J. E. C.; Gottschal, Jan C.

2000-01-01

Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible Nautile. Geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in 13C (δ13C values are as low as −95‰). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of 13C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, our results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings is the predominant microbiological process. PMID:10698781

Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer.

PubMed

Tischer, Karolin; Kleinsteuber, Sabine; Schleinitz, Kathleen M; Fetzer, Ingo; Spott, Oliver; Stange, Florian; Lohse, Ute; Franz, Janett; Neumann, Franziska; Gerling, Sarah; Schmidt, Christian; Hasselwander, Eyk; Harms, Hauke; Wendeberg, Annelie

2013-09-01

Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Effect of didecyl dimethyl ammonium chloride on nitrate reduction in a mixed methanogenic culture.

PubMed

Tezel, U; Pierson, J A; Pavlostathis, S G

2008-01-01

The effect of the quaternary ammonium compound, didecyl dimethyl ammonium chloride (DDAC), on nitrate reduction was investigated at concentrations up to 100 mg/L in a batch assay using a mixed, mesophilic (35 degrees C) methanogenic culture. Glucose was used as the carbon and energy source and the initial nitrate concentration was 70 mg N/L. Dissimilatory nitrate reduction to ammonia (DNRA) and to dinitrogen (denitrification) were observed at DDAC concentrations up to 25 mg/L. At and above 50 mg DDAC/L, DNRA was inhibited and denitrification was incomplete resulting in accumulation of nitrous oxide. At DDAC concentrations above 10 mg/L, production of nitrous oxide, even transiently, resulted in complete, long-term inhibition of methanogenesis and accumulation of volatile fatty acids. Fermentation was inhibited at and above 75 mg DDAC/L. DDAC suppressed microbial growth and caused cell lysis at a concentration 50 mg/L or higher. Most of the added DDAC was adsorbed on the biomass. Over 96% of the added DDAC was recovered from all cultures at the end of the 100-days incubation period, indicating that DDAC did not degrade in the mixed methanogenic culture under the conditions of this study.

Modeling steady-state methanogenic degradation of phenols in groundwater

USGS Publications Warehouse

Bekins, Barbara A.; Godsy, E. Michael; Goerlitz, Donald F.

1993-01-01

Field and microcosm observations of methanogenic phenolic compound degradation indicate that Monod kinetics governs the substrate disappearance but overestimates the observed biomass. In this paper we present modeling results from an ongoing multidisciplinary study of methanogenic biodegradation of phenolic compounds in a sand and gravel aquifer contaminated by chemicals and wastes used in wood treatment. Field disappearance rates of four phenols match those determined in batch microcosm studies previously performed by E.M. Godsy and coworkers. The degradation process appears to be at steady-state because even after a sustained influx over several decades, the contaminants still are disappearing in transport downgradient. The existence of a steady-state degradation profile of each substrate together with a low biomass density in the aquifer indicate that the bacteria population is exhibiting no net growth. This may be due to the oligotrophic nature of the biomass population in which utilization and growth are approximately independent of concentration for most of the concentration range. Thus a constant growth rate should exist over much of the contaminated area which may in turn be balanced by an unusually high decay or maintenance rate due to hostile conditions or predation.

Optimisation of single-phase dry-thermophilic anaerobic digestion under high organic loading rates of industrial municipal solid waste: population dynamics.

PubMed

Zahedi, S; Sales, D; Romero, L I; Solera, R

2013-10-01

Different high feed organic loading rates (OLRs) (from 5.7 g to 46.0 g TVS/l/d) or hydraulic retention times (HRTs) (from 15 d to 2 d) in single-phase dry-thermophilic anaerobic digestion (AD) of organic fraction municipal solid waste (OFMSW) were investigated. The specific gas production (SGP) values (0.25-0.53 m(3)/kg TVS) and the percentages of Eubacteria, Archaea, H2-utilising methanogens (HUMs) and acetate-utilising methanogens (AUMs) were stable within the ranges 80.2-91.1%, 12.4-18.5%, 4.4-9.8% and 5.5-10.9%, respectively. A HUM/AUM ratio greater than 0.7 seems to be necessary to maintain very low partial pressures of H2 required for dry AD process. Increasing OLR resulted in an increase in all the populations, except for propionate-utilising acetogens (PUAs). Optimal conditions were obtained at 3d HRT (OLR=30.7 g TVS/l/d), which is lower than the doubling time of acetogens and methanogens. The methane production (MP) was clearly higher than those reported in AD of OFMSW. Copyright © 2013 Elsevier Ltd. All rights reserved.

Anaerobic biodegradability of alkylphenols and fuel oxygenates in the presence of alternative electron acceptors.

PubMed

Puig-Grajales, L; Tan, N G; van der Zee, F; Razo-Flores, E; Field, J A

2000-11-01

Alkylphenols and fuel oxygenates are important environmental pollutants produced by the petrochemical industry. A batch biodegradability test was conducted with selected ortho-substituted alkylphenols (2-cresol, 2,6-dimethylphenol and 2-ethylphenol), fuel oxygenates (methyl tert-butyl ether, ethyl tert-butyl ether and tert-amylmethyl ether) and tert-butyl alcohol (TBA) as model compounds. The ortho-substituted alkylphenols were not biodegraded after 100 days of incubation under methanogenic, sulfate-, or nitrate-reducing conditions. However, biodegradation of 2-cresol and 2-ethylphenol (150 mg l(-1)) was observed in the presence of Mn (IV) as electron acceptor. The biodegradation of these two compounds took place in less than 15 days and more than 90% removal was observed for both compounds. Mineralization was indicated since no UV-absorbing metabolites accumulated after 23 days of incubation. These alkylphenols were also slowly chemically oxidized by Mn (IV). No biodegradation of fuel oxygenates or TBA (1 g l(-1)) was observed after 80 or more days of incubation under methanogenic, Fe (III)-, or Mn (IV)-reducing conditions, suggesting that these compounds are recalcitrant under anaerobic conditions. The fuel oxygenates caused no toxicity towards acetoclastic methanogens activity in anaerobic granular sludge.

Evaluating host-associated sources of marine methane supersaturation

NASA Astrophysics Data System (ADS)

Blanton, J. M.; Pieper, L. M.; Allen, E. E.

2013-12-01

Methane can be found in surface ocean waters at levels from 5% to 75% greater than expected from exchange with the atmosphere. Because oceanic emissions account for up to 4% of the planet's annual methane inventory, understanding marine sources and sinks is relevant to global greenhouse gas budgets. These methane levels are presumed to result from the activity of microorganisms in the water column, yet this presents a paradox: how can biotic methanogensis, primarily understood as an anaerobic process, take place in oxic waters? One working theory is that methanogens find safe harbor in the gastrointestinal tracts of marine animals. We investigate the possibility that microbial communities within fish, and the fecal material they produce, contribute to in-situ methane production in the open ocean. Using genetic markers, we test the GI tracts of benthic and pelagic marine teleosts for the presence of methanogenic organisms and for components of the methanogenesis pathway. Our results indicate that methanogens may be present in fish, but in low numbers. This work sets the scene for measurement of methane production rates from these gut-associated communities in order to elucidate their contribution to oceanic methane supersaturation.

Microbial aggregates in anaerobic wastewater treatment.

PubMed

Kosaric, N; Blaszczyk, R

1990-01-01

The phenomenon aggregation of anaerobic bacteria gives an opportunity to speed up the digestion rate during methanogenesis. The aggregates are mainly composed of methanogenic bacteria which convert acetate and H2/CO2 into methane. Other bacteria are also included in the aggregates but their concentration is rather small. The aggregates may also be formed during acetogenesis or even hydrolysis but such aggregates are not stable and disrupt quickly when not fed. A two stage process seems to be suitable when high concentrated solid waste must be treated. Special conditions are necessary to promote aggregate formation from methanogenic bacteria but aggregates once formed are stable without feeding even for a few years. The structure, texture and activity of bacterial aggregates depend on several parameters: (1)--temperature and pH, (2)--wastewater composition and (3)--hydrodynamic conditions within the reactor. The common influence of all these parameters is still rather unknown but some recommendations may be given. Temperature and pH should be maintained in the range which is optimal for methanogenic bacteria e.g. a temperature between 32 and 50 degrees C and a value pH between 6.5 and 7.5. Wastewaters should contain soluble wastes and the specific loading rate should be around one kgCOD(kgVSS)-1 d-1. The concentration of the elements influences aggregate composition and probably structure and texture. At high calcium concentration a change in the colour of the granules has been observed. Research is necessary to investigate the influence of other elements and organic toxicants on maintenance of the aggregates. Hydrodynamic conditions seem to influence the stability of the granules over long time periods. At low liquid stream rates, aggregates may starve and lysis within the aggregates is possible which results in hollowing of aggregates and their floating. At high liquid stream rates the aggregates may be disrupted and washed out of the reactor as a flocculent sludge. Methanogenic bacterial aggregates have been successfully applied in many full scale installations, especially for sugar beet, potato, pulp and paper mill, and other soluble wastes. The UASB reactors used for these treatments are simple in construction and handling which result in rather low total costs. A further and wider application of UASB reactors and methanogenic aggregates for various industrial wastewaters is expected.

A Ferredoxin- and F 420 H 2 -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Zhen; Wang, Mingyu; Ferry, James G.

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; but, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO 2-reducing methanogenic anaerobes (methanogens) from the domainArchaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogenMethanosarcina acetivoranswith unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologsmore » of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domainsBacteriaandArchaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes inEscherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F 420(F 420H 2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420H 2and reduction of ferredoxin with the exergonic oxidation of F 420H 2and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) byM. acetivoransand uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth ofM. acetivoransand proposed to be essential for growth in the environment when acetate is limiting.IMPORTANCEDiscovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2-reducing methanogens to include diverse prokaryotes from the domainsBacteriaandArchaea. Furthermore, the unprecedented coenzyme F 420-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH 4-oxidizing pathways. Our results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth’s biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.« less

A Ferredoxin- and F 420 H 2 -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

DOE PAGES

Yan, Zhen; Wang, Mingyu; Ferry, James G.; ...

2017-02-07

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; but, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO 2-reducing methanogenic anaerobes (methanogens) from the domainArchaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogenMethanosarcina acetivoranswith unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologsmore » of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domainsBacteriaandArchaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes inEscherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F 420(F 420H 2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420H 2and reduction of ferredoxin with the exergonic oxidation of F 420H 2and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) byM. acetivoransand uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth ofM. acetivoransand proposed to be essential for growth in the environment when acetate is limiting.IMPORTANCEDiscovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2-reducing methanogens to include diverse prokaryotes from the domainsBacteriaandArchaea. Furthermore, the unprecedented coenzyme F 420-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH 4-oxidizing pathways. Our results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth’s biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.« less

A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea.

PubMed

Yan, Zhen; Wang, Mingyu; Ferry, James G

2017-02-07

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO 2 -reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F 420 (F 420 H 2 ) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420 H 2 and reduction of ferredoxin with the exergonic oxidation of F 420 H 2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2 -reducing methanogens to include diverse prokaryotes from the domains Bacteria and Archaea The unprecedented coenzyme F 420 -dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH 4 -oxidizing pathways. The results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth's biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation. Copyright © 2017 Yan et al.

Survivability and growth kinetics of methanogenic archaea at various pHs and pressures: Implications for deep subsurface life on Mars

NASA Astrophysics Data System (ADS)

Sinha, Navita; Nepal, Sudip; Kral, Timothy; Kumar, Pradeep

2017-02-01

Life as we know it requires liquid water and sufficient liquid water is highly unlikely on the surface of present-day Mars. However, according to thermal models there is a possibility of liquid water in the deep subsurface of Mars. Thus, the martian subsurface, where the pressure and temperature is higher, could potentially provide a hospitable environment for a biosphere. Also, methane has been detected in the Mars' atmosphere. Analogous to Earth's atmospheric methane, martian methane could also be biological in origin. The carbon and energy sources for methanogenesis in the subsurface of Mars could be available by downwelling of atmospheric CO2 into the regolith and water-rock reactions such as serpentinization, respectively. Corresponding analogs of the martian subsurface on Earth might be the active sites of serpentinization at depths where methanogenic thermophilic archaea are the dominant species. Methanogens residing in Earth's hydrothermal environments are usually exposed to a variety of physiological stresses including a wide range of pressures, temperatures, and pHs. Martian geochemical models imply that the pH of probable groundwater varies from 4.96 to 9.13. In this work, we used the thermophilic methanogen, Methanothermobacter wolfeii, which grows optimally at 55oC. Therefore, a temperature of 55oC was chosen for these experiments, possibly simulating Mars' subsurface temperature. A martian geophysical model suggests depth and pressure corresponding to a temperature of 55 °C would be between 1-30 km and 100-3,000 atm respectively. Here, we have simulated Mars deep subsurface pH, pressure, and temperature conditions and have investigated the survivability, growth rate, and morphology of M. wolfeii after exposure to a wide range of pH 5-9) and pressure (1-1200 atm) at a temperature of 55 °C. Interestingly, in this study we have found that M. wolfeii was able to survive at all the pressures and pHs tested at 55 °C. In order to understand the effect of different pHs and pressures on the metabolic activities of M. wolfeii, we also calculated their growth rate by measuring methane concentration in the headspace gas samples at regular intervals. In acidic conditions, the growth rate (γ) of M. wolfeii increased with the increase in pressure. In neutral and alkaline conditions, the growth rate (γ) of M. wolfeii initially increased with pressure, but decreased upon further increase of pressure. To investigate the effect of combined pH, pressure, and temperature on the morphology of M. wolfeii, we took phase contrast images of the cells. We did not find any obvious significant alteration in the morphology of M. wolfeii cells. Methanogens, chemolithoautotrophic anaerobic microorganisms, are considered as ideal model microorganisms for Mars. In light of research presented here, we suggest that at least one methanogen, M. wolfeii, could survive in the deep subsurface environment of Mars.

Competition between Methanogens and Acetogens in Biocathodes: A Comparison between Potentiostatic and Galvanostatic Control

PubMed Central

Molenaar, Sam D.; Saha, Pradip; Mol, Annemerel R.; Sleutels, Tom H. J. A.; ter Heijne, Annemiek; Buisman, Cees J. N.

2017-01-01

Microbial electrosynthesis is a useful form of technology for the renewable production of organic commodities from biologically catalyzed reduction of CO2. However, for the technology to become applicable, process selectivity, stability and efficiency need strong improvement. Here we report on the effect of different electrochemical control modes (potentiostatic/galvanostatic) on both the start-up characteristics and steady-state performance of biocathodes using a non-enriched mixed-culture inoculum. Based on our results, it seems that kinetic differences exist between the two dominant functional microbial groups (i.e., homoacetogens and methanogens) and that by applying different current densities, these differences may be exploited to steer product selectivity and reactor performance. PMID:28106846

Competition between Methanogens and Acetogens in Biocathodes: A Comparison between Potentiostatic and Galvanostatic Control.

PubMed

Molenaar, Sam D; Saha, Pradip; Mol, Annemerel R; Sleutels, Tom H J A; Ter Heijne, Annemiek; Buisman, Cees J N

2017-01-19

Microbial electrosynthesis is a useful form of technology for the renewable production of organic commodities from biologically catalyzed reduction of CO₂. However, for the technology to become applicable, process selectivity, stability and efficiency need strong improvement. Here we report on the effect of different electrochemical control modes (potentiostatic/galvanostatic) on both the start-up characteristics and steady-state performance of biocathodes using a non-enriched mixed-culture inoculum. Based on our results, it seems that kinetic differences exist between the two dominant functional microbial groups (i.e., homoacetogens and methanogens) and that by applying different current densities, these differences may be exploited to steer product selectivity and reactor performance.

Photoenhanced anaerobic digestion of organic acids

DOEpatents

Weaver, Paul F.

1990-01-01

A process is described for rapid conversion of organic acids and alcohols anaerobic digesters into hydrogen and carbon dioxide, the optimal precursor substrates for production of methane. The process includes addition of photosynthetic bacteria to the digester and exposure of the bacteria to radiant energy (e.g., solar energy). The process also increases the pH stability of the digester to prevent failure of the digester. Preferred substrates for photosynthetic bacteria are the organic acid and alcohol waste products of fermentative bacteria. In mixed culture with methanogenic bacteria or in defined co-culture with non-aceticlastic methanogenic bacteria, photosynthetic bacteria are capable of facilitating the conversion or organic acids and alcohols into methane with low levels of light energy input.

Organic loading rate and food-to-microorganism ratio shape prokaryotic diversity in a demo-scale up-flow anaerobic sludge blanket reactor treating domestic wastewater.

PubMed

Cardinali-Rezende, Juliana; Araújo, Juliana C; Almeida, Paulo G S; Chernicharo, Carlos A L; Sanz, José L; Chartone-Souza, Edmar; Nascimento, Andréa M A

2013-12-01

We investigated the microbial community in an up-flow anaerobic sludge blanket (UASB) reactor treating domestic wastewater (DW) during two different periods of organic loading rate (OLR) and food-to-microorganism (F/M) ratio. 16S rDNA clone libraries were generated, and quantitative real-time PCR (qPCR) analyses were performed. Fluctuations in the OLR and F/M ratio affected the abundance and the composition of the UASB prokaryotic community, mainly at the species level, as well as the performance of the UASB reactor. The qPCR analysis suggested that there was a decrease in the bacterial cell number during the rainy season, when the OLR and F/M ratio were lower. However, the bacterial diversity was higher during this time, suggesting that the community degraded more diversified substrates. The diversity and the abundance of the archaeal community were higher when the F/M ratio was lower. Shifts in the methanogenic community composition might have influenced the route of methane production, with methane produced by acetotrophic methanogens (dry season), and by hydrogenotrophic, methylotrophic and acetotrophic methanogens (rainy season). This study revealed higher levels of bacterial diversity, metabolic specialization and chemical oxygen demand removal efficiency of the DW UASB reactor during the rainy season.

Involvement of formate as an interspecies electron carrier in a syntrophic acetate-oxidizing anaerobic microorganism in coculture with methanogens.

PubMed

Hattori, S; Luo, H; Shoun, H; Kamagata, Y

2001-01-01

To determine whether formate is involved in interspecies electron transfer between substrate-oxidizing bacteria and hydrogenotrophic microorganisms under anaerobic conditions, a syntrophic acetate-oxidizing bacterium Thermacetogenium phaeum strain PB was cocultured either with a formate /H2-utilizing methanogen strain TM (designated as PB/TM coculture), or an H2-utilizing methanogen strain deltaH (designated as PB/deltaH coculture). Acetate oxidation and subsequent methanogenesis in PB/TM coculture were found to be significantly faster than in PB/deltaH coculture. Formate dehydrogenase and hydrogenase were both detected in strains PB and TM. H2 partial pressures in the PB/TM coculture were kept lower (20 to 40 Pa) than those of the PB/deltaH coculture (40 to 60 Pa) during the exponential growth phase. Formate was also detected in both PB/TM and PB/deltaH cocultures, and the concentration of formate was maintained at a lower level in the PB/TM coculture (5 to 9 microM) than in the PB/deltaH coculture. Thermodynamic calculations revealed that the concentrations of both H2 and formate severely affect the syntrophic oxidation of acetate. These results strongly indicate that not only H2 but also formate may be involved in interspecies electron transfer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hornibrook, E.R.C.; Longstaffe, F.J.; Fyfe, W.S.

The identity and distribution of substrates that support CH{sub 4} production in wetlands is poorly known at present. Organic compounds are the primary methanogenic precursor at all depths within anoxic wetland soils; however, the distribution of microbial processes by which these compounds are ultimately converted to CH{sub 4} is uncertain. Based on stable isotope measurements of CH{sub 4} and {Sigma}CO{sub 2} extracted from soil porewaters in two temperate zone wetlands, we present evidence that a systematic spatial distribution of microbial methanogenic pathways can exist in certain anoxic, organic-rich soils. CH{sub 4} production by the acetate fermentation pathway is favored inmore » the shallow subsurface. while methanogenesis from the reduction of CO{sub 2} with H{sub 2} becomes more predominant in older, less reactive peat at depth. This distribution can account for many of the reported CH{sub 4} emission characteristics of wetlands, in particular, their sensitivity to changes in primary productivity, temperature, and hydrology. These factors play an important role in controlling the short-term supply of labile substrates to fermentive methanogens in the shallow subsurface where the most intense CH{sub 4} production occurs. Predominance of the CO{sub 2}-reduction pathway at depth may help to explain reports of CH{sub 4} with a semifossil age in lower peat layers. 60 refs., 7 figs., 1 tab.« less

Reactor performance of a 750 m(3) anaerobic digestion plant: varied substrate input conditions impacting methanogenic community.

PubMed

Wagner, Andreas Otto; Malin, Cornelia; Lins, Philipp; Gstraunthaler, Gudrun; Illmer, Paul

2014-10-01

A 750 m(3) anaerobic digester was studied over a half year period including a shift from good reactor performance to a reduced one. Various abiotic parameters like volatile fatty acids (VFA) (formic-, acetic-, propionic-, (iso-)butyric-, (iso-)valeric-, lactic acid), total C, total N, NH4 -N, and total proteins, as well as the organic matter content and dry mass were determined. In addition several process parameters such as temperature, pH, retention time and input of substrate and the concentrations of CH4, H2, CO2 and H2S within the reactor were monitored continuously. The present study aimed at the investigation of the abundance of acetogens and total cell numbers and the microbial methanogenic community as derived from PCR-dHPLC analysis in order to put it into context with the determined abiotic parameters. An influence of substrate quantity on the efficiency of the anaerobic digestion process was found as well as a shift from a hydrogenotrophic in times of good reactor performance towards an acetoclastic dominated methanogenic community in times of reduced reactor performance. After the change in substrate conditions it took the methano-archaeal community about 5-6 weeks to be affected but then changes occurred quickly. Copyright © 2014 Elsevier Ltd. All rights reserved.

Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens

PubMed Central

Rezadehbashi, Maryam; Baldwin, Susan A.

2018-01-01

Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. PMID:29473875

Hydrogen or formate: Alternative key players in methanogenic degradation.

PubMed

Schink, Bernhard; Montag, Dominik; Keller, Anja; Müller, Nicolai

2017-06-01

Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

PubMed Central

Ozbayram, Emine Gozde; Ince, Orhan; Ince, Bahar; Harms, Hauke

2018-01-01

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass. PMID:29443879

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars.

PubMed

Mickol, R L; Kral, T A

2017-12-01

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species (Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar - 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days - 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.

Anaerobic Biodegradation of Soybean Biodiesel and Diesel ...

EPA Pesticide Factsheets

Biotransformation of soybean biodiesel and the inhibitory effect of petrodiesel were studied under methanogenic conditions. Biodiesel removal efficiency of more than 95% was achieved in a chemostat with influent biodiesel concentrations up to 2.45 g/L. The kinetics of anaerobic biodegradation of soybean biodiesel B100 (biodiesel only) with different petrodiesel loads were studied using biomass pre-acclimated to B100 and B80 (80% biodiesel and 20 petrodiesel). The results indicated that the biodiesel fraction of the blend could be effectively biodegraded, whereas petrodiesel was not biodegraded at all under methanogenic conditions. The presence of petrodiesel in blends with biodiesel had a greater inhibitory effect on the rate of biodegradation than the biodegradation efficiency (defined as the efficiency of methane production). Both the biodegradation rate coefficient and the methane production efficiency increased almost linearly with the increasing fraction of biodiesel. With the increasing fraction of petrodiesel, the biodegradation rate and efficiency were correlated with the concentration of soluble FAMEs in the water. The objective of this study was to investigate the anaerobic biodegradation of soybean biodiesel blends under methanogenic conditions. Biological methane potential (BMP) tests were conducted in serum bottles to determine the anaerobic biodegradation kinetics of biodiesel in the absence and presence of different concentrations of petrod

Start-up of an anaerobic fluidized bed reactor treating synthetic carbohydrate rich wastewater.

PubMed

Yeshanew, Martha M; Frunzo, Luigi; Luongo, Vincenzo; Pirozzi, Francesco; Lens, Piet N L; Esposito, Giovanni

2016-12-15

The present work studied the start-up process of a mesophilic (37 ± 2 °C) anaerobic fluidized bed reactor (AFBR) operated at a hydraulic retention time (HRT) of 20 days using synthetic carbohydrate rich wastewater. Anox Kaldness-K1 carriers were used as biofilm carrier material. The reactor performance and biofilm formation were evaluated during the process. The start-up process at lower liquid recirculation flow rate enhanced the biofilm formation and reactor performance. The organic substrate composition had a major impact on early colonization of methanogenic archaea onto the surface of the Kaldness carriers during the start-up process. Specific organic substrates favouring the growth of methanogenic archaea, such as acetate, are preferred in order to facilitate the subsequent biofilm formation and AFBR start-up. The supply of 'bio-available' nutrients and trace elements, in particular iron, had an important role on optimal methanogenic activity and speeding-up of the biofilm development on the Kaldness carriers. This paper provides possible strategies to optimize the various operational parameters that influence the initial biofilm formation and development in an AFBR and similar high rate anaerobic reactors, hence can be used to reduce the long time required for process start-up. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pyrosequencing reveals the key microorganisms involved in sludge alkaline fermentation for efficient short-chain fatty acids production.

PubMed

Zheng, Xiong; Su, Yinglong; Li, Xiang; Xiao, Naidong; Wang, Dongbo; Chen, Yinguang

2013-05-07

Short-chain fatty acids (SCFAs) have been regarded as the excellent carbon source of wastewater biological nutrient removal, and sludge alkaline (pH 10) fermentation has been reported to achieve highly efficient SCFAs production. In this study, the underlying mechanisms for the improved SCFAs production at pH 10 were investigated by using 454 pyrosequencing and fluorescent in situ hybridization (FISH) to analyze the microbial community structures in sludge fermentation reactors. It was found that sludge fermentation at pH 10 increased the abundances of Pseudomonas sp. and Alcaligenes sp., which were able to excrete extracellular proteases and depolymerases, and thus enhanced the hydrolysis of insoluble sludge protein and polyhydroxyalkanoates (PHA). Meanwhile, the abundance of acid-producing bacteria (such as Clostridium sp.) in the reactor of pH 10 was also higher than that of uncontrolled pH, which benefited the acidification of soluble organic substrates. Further study indicated that sludge fermentation at pH 10 significantly decreased the number of methanogenic archaea, resulting in lower SCFAs consumption and lower methane production. Therefore, anaerobic sludge fermentation under alkaline conditions increased the abundances of bacteria involved in sludge hydrolysis and acidification, and decreased the abundance of methanogenic archaea, which favored the competition of bacteria over methanogens and resulted in the efficient production of SCFAs.

A novel bioaugmentation strategy to accelerate methanogenesis via adding Geobacter sulfurreducens PCA in anaerobic digestion system.

PubMed

Zhang, Shuo; Chang, Jiali; Liu, Wei; Pan, Yiran; Cui, Kangping; Chen, Xi; Liang, Peng; Zhang, Xiaoyuan; Wu, Qing; Qiu, Yong; Huang, Xia

2018-06-12

Based on the new syntrophic methanogenesis route via direct interspecies electron transfer (DIET), a novel bioaugmentation method by adding exoelectrogenic Geobacter species to accelerate methanogenesis was developed in this study. Geobacter sulfurreducens PCA, type exoelectrogenic strain of Geobacter species was chosen for the research. To clarify the effect of G. sulfurreducens on methanogenesis, batch tests of CH 4 production were carried out. Acetate, the most typical precursor of methanogenesis was chosen as the substrate of batch tests. Amendment of G. sulfurreducens accelerated CH 4 production remarkably. The lag phase of CH 4 production was shortened, and the maximum CH 4 production rate was increased by 78%. Fluorescence in situ hybridization showed that G. sulfurreducens closely gathered with methanogens. For the archaeal communities, the high-throughput sequencing results demonstrated that Methanosaetaceae and Methanobacteriaceae were potential bioaugmented methanogens. We speculated that the accelerated methanogenesis by adding G. sulfurreducens may result from the syntrophic association between G. sulfurreducens and methanogens affiliated with Methanosaetaceae and Methanobacteriaceae. This research provides a new route to enhance methanogenesis through the utilization of G. sulfurreducens. Through this study, the role of Geobacter in the anaerobic engineering and carbon cycling of nature should be paid more attention. Copyright © 2018. Published by Elsevier B.V.

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters.

PubMed

Ozbayram, Emine Gozde; Ince, Orhan; Ince, Bahar; Harms, Hauke; Kleinsteuber, Sabine

2018-02-14

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma . Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

Thermophilic anaerobic degradation of butyrate by a butyrate-utilizing bacterium in coculture and triculture with methanogenic bacteria.

PubMed

Ahring, B K; Westermann, P

1987-02-01

We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was beta-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in the triculture, in which both hydrogen and acetate were utilized, than in the coculture, in which acetate accumulated. Yeast extract, rumen fluid, and clarified digestor fluid stimulated butyrate degradation, while the effect of Trypticase was less pronounced. Penicillin G, d-cycloserine, and vancomycin caused complete inhibition of butyrate utilization by the cultures. No growth or degradation of butyrate occurred when 2-bromoethanesulfonic acid or chloroform, specific inhibitors of methanogenic bacteria, was added to the cultures and common electron acceptors such as sulfate, nitrate, and fumarate were not used with butyrate as the electron donor. Addition of hydrogen or oxygen to the gas phase immediately stopped growth and butyrate degradation by the cultures. Butyrate was, however, metabolized at approximately the same rate when hydrogen was removed from the cultures and was metabolized at a reduced rate in the cultures previously exposed to hydrogen.

Effect of volumetric organic loading rate (OLR) on H2 and CH4 production by two-stage anaerobic co-digestion of food waste and brown water.

PubMed

Paudel, Sachin; Kang, Youngjun; Yoo, Yeong-Seok; Seo, Gyu Tae

2017-03-01

Two-stage anaerobic digestion system consisting of two continuously stirred tank reactors (CSTRs) operating at mesophillic conditions (37°C) were studied. The aim of this study is to determine optimum Hydraulic Retention Time (HRT) of the two-stage anaerobic digester system for hydrogen and methane production. This paper also discusses the effect of OLR with change in HRT on the system. Four different HRTs of 48, 24, 12, 8h were monitored for acidogenic reactor, which provided OLR of 17.7, 34.8, 70.8, 106gVS/L·d respectively. Two HRTs of 15days and 20days were studied with OLR of 1.24 and 1.76gVS/L·d respectively in methanogenic reactor. Hydrogen production at higher OLR and shorter HRT seemed favorable 106gVS/L·d (8h) in acidogenic reactor system. In methanogenic reactor system HRT of 20day with OLR of 1.24gVS/L·d was found optimum in terms of methane production and organic removal. The result of this study illustrated the optimum HRT of 8h and 20days in acidogenic stage and methanogenic stage for maximum hydrogen and methane production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars

NASA Astrophysics Data System (ADS)

Mickol, R. L.; Kral, T. A.

2017-12-01

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species ( Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar - 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days - 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

PubMed Central

Manzoor, Shahid; Bongcam-Rudloff, Erik; Schnürer, Anna; Müller, Bettina

2016-01-01

Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle. PMID:27851830

Enhanced biomethane production rate and yield from lignocellulosic ensiled forage ley by in situ anaerobic digestion treatment with endogenous cellulolytic enzymes.

PubMed

Speda, Jutta; Johansson, Mikaela A; Odnell, Anna; Karlsson, Martin

2017-01-01

Enzymatic treatment of lignocellulosic material for increased biogas production has so far focused on pretreatment methods. However, often combinations of enzymes and different physicochemical treatments are necessary to achieve a desired effect. This need for additional energy and chemicals compromises the rationale of using enzymes for low energy treatment to promote biogas production. Therefore, simpler and less energy intensive in situ anaerobic digester treatment with enzymes is desirable. However, investigations in which exogenous enzymes are added to treat the material in situ have shown mixed success, possibly because the enzymes used originated from organisms not evolutionarily adapted to the environment of anaerobic digesters. In this study, to examine the effect of enzymes endogenous to methanogenic microbial communities, cellulolytic enzymes were instead overproduced and collected from a dedicated methanogenic microbial community. By this approach, a solution with very high endogenous microbial cellulolytic activity was produced and tested for the effect on biogas production from lignocellulose by in situ anaerobic digester treatment. Addition of enzymes, endogenous to the environment of a mixed methanogenic microbial community, to the anaerobic digestion of ensiled forage ley resulted in significantly increased rate and yield of biomethane production. The enzyme solution had an instant effect on more readily available cellulosic material. More importantly, the induced enzyme solution also affected the biogas production rate from less accessible cellulosic material in a second slower phase of lignocellulose digestion. Notably, this effect was maintained throughout the experiment to completely digested lignocellulosic substrate. The induced enzyme solution collected from a microbial methanogenic community contained enzymes that were apparently active and stable in the environment of anaerobic digestion. The enzymatic activity had a profound effect on the biogas production rate and yield, comparable with the results of many pretreatment methods. Thus, application of such enzymes could enable efficient low energy in situ anaerobic digester treatment for increased biomethane production from lignocellulosic material.

Physiological and isotopic characteristics of nitrogen fixation by hyperthermophilic methanogens: Key insights into nitrogen anabolism of the microbial communities in Archean hydrothermal systems

NASA Astrophysics Data System (ADS)

Nishizawa, Manabu; Miyazaki, Junichi; Makabe, Akiko; Koba, Keisuke; Takai, Ken

2014-08-01

Hyperthermophilic hydrogenotrophic methanogens are considered to be one of the most predominant primary producers in hydrogen (H2)-abundant hydrothermal environments in the present-day ocean and throughout the history of the Earth. However, the nitrogen sources supporting the development of microbial communities in hydrothermal environments remain poorly understood. We have investigated, for the first time, methanogenic archaea commonly found in deep-sea hydrothermal environments to understand their physiological properties (growth kinetics, energetics, and metal requirements) and isotopic characteristics during the fixation of dinitrogen (N2), which is an abundant but less-bioavailable compound in hydrothermal fluids. Culture experiments showed that Methanocaldococcus strain (Mc 1-85N) (Topt = 85 °C) and Methanothermococcus strain (Mt 5-55N) (Topt = 55 °C) assimilated N2 and ammonium, but not nitrate. Previous phylogenetic studies have predicted that the Methanocaldococcus and Methanothermococcus lineages have nitrogenases, key enzymes for N2 fixation, with biochemically uncharacterised active site metal cofactors. We showed that Mt 5-55N required molybdenum for the nitrogenase to function, implying a molybdenum-bearing cofactor in the strain. Molybdenum also stimulated diazotrophic (i.e., N2-fixing) growth of Mc 1-85N, though further experiments are required to test whether the strain contains a molybdenum-dependent nitrogenase. Importantly, Mc 1-85N exhibited an apparently lower requirement of and higher tolerance to molybdenum and iron than Mt 5-55N. Furthermore, both strains produced more 15N-depleted biomass (-4‰ relative to N2) than that previously reported for diazotrophic photosynthetic prokaryotes. These results demonstrate that diazotrophic hyperthermophilic methanogens can be broadly distributed in seafloor and subseafloor hydrothermal environments, where the availability of transition metals is variable and where organic carbon, organic nitrogen, and ammonium are generally scarce. The emergence and function of diazotrophy, coupled with methanogenesis, in the early Earth is also consistent with the nitrogen isotopic records of 3.5 billion-year-old hydrothermal deposits.

Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors.

PubMed

Shehab, Noura; Li, Dong; Amy, Gary L; Logan, Bruce E; Saikaly, Pascal E

2013-11-01

A large percentage of organic fuel consumed in a microbial fuel cell (MFC) is lost as a result of oxygen transfer through the cathode. In order to understand how this oxygen transfer affects the microbial community structure, reactors were operated in duplicate using three configurations: closed circuit (CC; with current generation), open circuit (OC; no current generation), and sealed off cathodes (SO; no current, with a solid plate placed across the cathode). Most (98 %) of the chemical oxygen demand (COD) was removed during power production in the CC reactor (maximum of 640 ± 10 mW/m(2)), with a low percent of substrate converted to current (coulombic efficiency of 26.5 ± 2.1 %). Sealing the cathode reduced COD removal to 7 %, but with an open cathode, there was nearly as much COD removal by the OC reactor (94.5 %) as the CC reactor. Oxygen transfer into the reactor substantially affected the composition of the microbial communities. Based on analysis of the biofilms using 16S rRNA gene pyrosequencing, microbes most similar to Geobacter were predominant on the anodes in the CC MFC (72 % of sequences), but the most abundant bacteria were Azoarcus (42 to 47 %) in the OC reactor, and Dechloromonas (17 %) in the SO reactor. Hydrogenotrophic methanogens were most predominant, with sequences most similar to Methanobacterium in the CC and SO reactor, and Methanocorpusculum in the OC reactors. These results show that oxygen leakage through the cathode substantially alters the bacterial anode communities, and that hydrogenotrophic methanogens predominate despite high concentrations of acetate. The predominant methanogens in the CC reactor most closely resembled those in the SO reactor, demonstrating that oxygen leakage alters methanogenic as well as general bacterial communities.

Enhancing methane production from food waste fermentate using biochar: the added value of electrochemical testing in pre-selecting the most effective type of biochar.

PubMed

Cruz Viggi, Carolina; Simonetti, Serena; Palma, Enza; Pagliaccia, Pamela; Braguglia, Camilla; Fazi, Stefano; Baronti, Silvia; Navarra, Maria Assunta; Pettiti, Ida; Koch, Christin; Harnisch, Falk; Aulenta, Federico

2017-01-01

Recent studies have suggested that addition of electrically conductive biochar particles is an effective strategy to improve the methanogenic conversion of waste organic substrates, by promoting syntrophic associations between acetogenic and methanogenic organisms based on interspecies electron transfer processes. However, the underlying fundamentals of the process are still largely speculative and, therefore, a priori identification, screening, and even design of suitable biochar materials for a given biotechnological process are not yet possible. Here, three charcoal-like products (i.e., biochars) obtained from the pyrolysis of different lignocellulosic materials, (i.e., wheat bran pellets, coppiced woodlands, and orchard pruning) were tested for their capacity to enhance methane production from a food waste fermentate. In all biochar-supplemented (25 g/L) batch experiments, the complete methanogenic conversion of fermentate volatile fatty acids proceeded at a rate that was up to 5 times higher than that observed in the unamended (or sand-supplemented) controls. Fluorescent in situ hybridization analysis coupled with confocal laser scanning microscopy revealed an intimate association between archaea and bacteria around the biochar particles and provided a clear indication that biochar also shaped the composition of the microbial consortium. Based on the application of a suite of physico-chemical and electrochemical characterization techniques, we demonstrated that the positive effect of biochar is directly related to the electron-donating capacity (EDC) of the material, but is independent of its bulk electrical conductivity and specific surface area. The latter properties were all previously hypothesized to play a major role in the biochar-mediated interspecies electron transfer process in methanogenic consortia. Collectively, these results of this study suggest that for biochar addition in anaerobic digester operation, the screening and identification of the most suitable biochar material should be based on EDC determination, via simple electrochemical tests.

Hydrocarbon Degradation in Caspian Sea Sediment Cores Subjected to Simulated Petroleum Seepage in a Newly Designed Sediment-Oil-Flow-Through System.

PubMed

Mishra, Sonakshi; Wefers, Peggy; Schmidt, Mark; Knittel, Katrin; Krüger, Martin; Stagars, Marion H; Treude, Tina

2017-01-01

The microbial community response to petroleum seepage was investigated in a whole round sediment core (16 cm length) collected nearby natural hydrocarbon seepage structures in the Caspian Sea, using a newly developed Sediment-Oil-Flow-Through (SOFT) system. Distinct redox zones established and migrated vertically in the core during the 190 days-long simulated petroleum seepage. Methanogenic petroleum degradation was indicated by an increase in methane concentration from 8 μM in an untreated core compared to 2300 μM in the lower sulfate-free zone of the SOFT core at the end of the experiment, accompanied by a respective decrease in the δ 13 C signal of methane from -33.7 to -49.5‰. The involvement of methanogens in petroleum degradation was further confirmed by methane production in enrichment cultures from SOFT sediment after the addition of hexadecane, methylnapthalene, toluene, and ethylbenzene. Petroleum degradation coupled to sulfate reduction was indicated by the increase of integrated sulfate reduction rates from 2.8 SO 4 2- m -2 day -1 in untreated cores to 5.7 mmol SO 4 2- m -2 day -1 in the SOFT core at the end of the experiment, accompanied by a respective accumulation of sulfide from 30 to 447 μM. Volatile hydrocarbons (C2-C6 n -alkanes) passed through the methanogenic zone mostly unchanged and were depleted within the sulfate-reducing zone. The amount of heavier n -alkanes (C10-C38) decreased step-wise toward the top of the sediment core and a preferential degradation of shorter (C30) was seen during the seepage. This study illustrates, to the best of our knowledge, for the first time the development of methanogenic petroleum degradation and the succession of benthic microbial processes during petroleum passage in a whole round sediment core.

Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent-Contaminated Aquifer Undergoing Intrinsic Bioremediation

PubMed Central

Dojka, Michael A.; Hugenholtz, Philip; Haack, Sheridan K.; Pace, Norman R.

1998-01-01

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association. PMID:9758812

Effects of Vegetation Composition and Trophic Structure on Pathways of Mercury Methylation in Alaskan Peatlands

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Barkay, T.; Krabbenhoft, D. P.; Liu, X.

2016-12-01

Methyl mercury (MeHg) can be produced by diverse microbes including syntrophs, methanogens, and fermenters, besides sulfate (SO42-, SRB) and iron- reducing bacteria. Many freshwater wetlands are deficient in electron acceptors that support the traditional respiratory pathways of methylation, yet high levels of MeHg can accumulate. To investigate methylation pathways in these wetlands and to connect these pathways with surface vegetation and microbial communities, experiments were conducted using peats from 28 sites in Alaska collected during the summer of 2015. The sites were clustered using multiple factor analysis based on pH, temp, CH4 and volatile fatty acids production rates, and surface vegetation composition. Three clusters were generated and corresponded to three trophic levels that were manifested by three pH levels (4.2, 5.3, and 5.8). Hg methylation activity in laboratory incubations was determined using the short-lived radioisotope 197Hg. In the low pH, Sphagnum fuscum dominated cluster, methylation rates were less than 0.1% day-1. Conversely, the high pH trophic cluster dominated by Carex aquatilis, Carex tenuiflora, and active syntrophy, exhibited Hg methylation rates as high as 10% day-1. In intermediate sites, rich in Sphagnum magellanicum with less Carex, a gradient in syntrophy and Hg methylation paths was observed. Amendments with SO42- showed very active sulfate reduction but no stimulation of methylation; another set of amendments with methanogenic inhibitors greatly reduced methylation rates at intermediate and high trophic clusters. These results suggested that SRB, metabolizing either syntrophically with methanogens and/or by fermentation, likely methylated Hg. While metatranscriptomics studies are being conducted to verify the role of syntrophs, fermenters, and methanogens as methylators, these incubation results revealed that Hg methylation pathways change greatly along trophic gradients with a dominance of respiratory pathways in rich fens, syntrophy dominance in intermediate sites, and fermentation dominance in poor bogs.

A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

PubMed Central

Yan, Zhen

2017-01-01

ABSTRACT Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. PMID:28174314

Factors that control the stable carbon isotopic composition of methane produced in an anoxic marine sediment

NASA Technical Reports Server (NTRS)

Alperin, M. J.; Blair, Neal E.; Albert, D. B.; Hoehler, T. M.; Martens, C. S.

1993-01-01

The carbon isotopic composition of methane produced in anoxic marine sediment is controlled by four factors: (1) the pathway of methane formation, (2) the isotopic composition of the methanogenic precursors, (3) the isotope fractionation factors for methane production, and (4) the isotope fractionation associated with methane oxidation. The importance of each factor was evaluated by monitoring stable carbon isotope ratios in methane produced by a sediment microcosm. Methane did not accumulate during the initial 42-day period when sediment contained sulfate, indicating little methane production from 'noncompetitive' substrates. Following sulfate depletion, methane accumulation proceeded in three distinct phases. First, CO2 reduction was the dominant methanogenic pathway and the isotopic composition of the methane produced ranged from -80 to -94 per thousand. The acetate concentration increased during this phase, suggesting that acetoclastic methanogenic bacteria were unable to keep pace with acetate production. Second, acetate fermentation became the dominant methanogenic pathway as bacteria responded to elevated acetate concentrations. The methane produced during this phase was progressively enriched in C-13, reaching a maximum delta(C-13) value of -42 per thousand. Third, the acetate pool experienced a precipitous decline from greater than 5 mM to less than 20 micro-M and methane production was again dominated by CO2 reduction. The delta(C-13) of methane produced during this final phase ranged from -46 to -58 per thousand. Methane oxidation concurrent with methane production was detected throughout the period of methane accumulation, at rates equivalent to 1 to 8 percent of the gross methane production rate. Thus methane oxidation was too slow to have significantly modified the isotopic signature of methane. A comparison of microcosm and field data suggests that similar microbial interactions may control seasonal variability in the isotopic composition of methane emitted from undisturbed Cape Lookout Bight sediment.

Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation

USGS Publications Warehouse

Dojka, M.A.; Hugenholtz, P.; Haack, S.K.; Pace, N.R.

1998-01-01

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OPS, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.

Mercury methylation and sulfate reduction rates in mangrove sediments, Rio de Janeiro, Brazil: The role of different microorganism consortia.

PubMed

Correia, Raquel Rose Silva; Guimarães, Jean Remy Davée

2017-01-01

Recent studies have shown Hg methylation in mangrove sediments, however, little is known about the different microorganism consortia involved. We investigated the participation of prokaryotes in general, iron-reducing bacteria-IRB, sulfate-reducing bacteria-SRB, methanogens and fungi in Hg methylation and sulfate reduction rates (SRR) in mangrove sediments using iron amendments for IRB and specific inhibitors for the other microorganisms. Sediment samples were collected from two mangrove zones, tidal flat and mangrove forest (named root sediments). Samples were incubated with 203 Hg or 35 SO 4 2- and Me 203 Hg/ 35 Sulfur were measured by liquid scintillation. Methylmercury (MeHg) formation was significantly reduced when SRB (87.7%), prokaryotes (76%) and methanogens (36.5%) were inhibited in root sediments, but only SRB (51.6%) and prokaryotes (57.3%) in tidal flat. However, in the tidal flat, inhibition of methanogens doubled Hg methylation (104.5%). All inhibitors (except fungicide) significantly reduced SRR in both zones. In iron amended tidal flat samples, Hg methylation increased 56.5% at 100 μg g -1 and decreased at 500 and 1000 μg g -1 (57.8 and 82%). In the roots region, however, MeHg formation gradually decreased in response to Fe amendments from 100 μg g -1 (37.7%) to 1000 μg g -1 (93%). SRR decreased in all iron amendments. This first simultaneous evaluation of Hg methylation and sulfate-reduction and of the effect of iron and inhibitors on both processes suggest that SRB are important Hg methylators in mangrove sediments. However, it also suggests that SRB activity could not explain all MeHg formation. This implies the direct or indirect participation of other microorganisms such as IRB and methanogens and a complex relationship among these groups. Copyright © 2016. Published by Elsevier Ltd.

Hydrocarbon Degradation in Caspian Sea Sediment Cores Subjected to Simulated Petroleum Seepage in a Newly Designed Sediment-Oil-Flow-Through System

PubMed Central

Mishra, Sonakshi; Wefers, Peggy; Schmidt, Mark; Knittel, Katrin; Krüger, Martin; Stagars, Marion H.; Treude, Tina

2017-01-01

The microbial community response to petroleum seepage was investigated in a whole round sediment core (16 cm length) collected nearby natural hydrocarbon seepage structures in the Caspian Sea, using a newly developed Sediment-Oil-Flow-Through (SOFT) system. Distinct redox zones established and migrated vertically in the core during the 190 days-long simulated petroleum seepage. Methanogenic petroleum degradation was indicated by an increase in methane concentration from 8 μM in an untreated core compared to 2300 μM in the lower sulfate-free zone of the SOFT core at the end of the experiment, accompanied by a respective decrease in the δ13C signal of methane from -33.7 to -49.5‰. The involvement of methanogens in petroleum degradation was further confirmed by methane production in enrichment cultures from SOFT sediment after the addition of hexadecane, methylnapthalene, toluene, and ethylbenzene. Petroleum degradation coupled to sulfate reduction was indicated by the increase of integrated sulfate reduction rates from 2.8 SO42-m-2 day-1 in untreated cores to 5.7 mmol SO42-m-2 day-1 in the SOFT core at the end of the experiment, accompanied by a respective accumulation of sulfide from 30 to 447 μM. Volatile hydrocarbons (C2–C6 n-alkanes) passed through the methanogenic zone mostly unchanged and were depleted within the sulfate-reducing zone. The amount of heavier n-alkanes (C10–C38) decreased step-wise toward the top of the sediment core and a preferential degradation of shorter (C30) was seen during the seepage. This study illustrates, to the best of our knowledge, for the first time the development of methanogenic petroleum degradation and the succession of benthic microbial processes during petroleum passage in a whole round sediment core. PMID:28503172

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

NASA Astrophysics Data System (ADS)

Lorah, Michelle M.; Voytek, Mary A.

2004-05-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

The effect of temperature and retention time on methane production and microbial community composition in staged anaerobic digesters fed with food waste.

PubMed

Gaby, John Christian; Zamanzadeh, Mirzaman; Horn, Svein Jarle

2017-01-01

Food waste is a large bio-resource that may be converted to biogas that can be used for heat and power production, or as transport fuel. We studied the anaerobic digestion of food waste in a staged digestion system consisting of separate acidogenic and methanogenic reactor vessels. Two anaerobic digestion parameters were investigated. First, we tested the effect of 55 vs. 65 °C acidogenic reactor temperature, and second, we examined the effect of reducing the hydraulic retention time (HRT) from 17 to 10 days in the methanogenic reactor. Process parameters including biogas production were monitored, and the microbial community composition was characterized by 16S amplicon sequencing. Neither organic matter removal nor methane production were significantly different for the 55 and 65 °C systems, despite the higher acetate and butyrate concentrations observed in the 65 °C acidogenic reactor. Ammonium levels in the methanogenic reactors were about 950 mg/L NH 4 + when HRT was 17 days but were reduced to 550 mg/L NH 4 + at 10 days HRT. Methane production increased from ~ 3600 mL/day to ~ 7800 when the HRT was decreased. Each reactor had unique environmental parameters and a correspondingly unique microbial community. In fact, the distinct values in each reactor for just two parameters, pH and ammonium concentration, recapitulate the separation seen in microbial community composition. The thermophilic and mesophilic digesters were particularly distinct from one another. The 55 °C acidogenic reactor was mainly dominated by Thermoanaerobacterium and Ruminococcus , whereas the 65 °C acidogenic reactor was initially dominated by Thermoanaerobacterium but later was overtaken by Coprothermobacter . The acidogenic reactors were lower in diversity (34-101 observed OTU 0.97 , 1.3-2.5 Shannon) compared to the methanogenic reactors (472-513 observed OTU 0.97 , 5.1-5.6 Shannon). The microbial communities in the acidogenic reactors were > 90% Firmicutes, and the Euryarchaeota were higher in relative abundance in the methanogenic reactors. The digestion systems had similar biogas production and COD removal rates, and hence differences in temperature, NH 4 + concentration, and pH in the reactors resulted in distinct but similarly functioning microbial communities over this range of operating parameters. Consequently, one could reduce operational costs by lowering both the hydrolysis temperature from 65 to 55 °C and the HRT from 17 to 10 days.

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.

2004-01-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction.Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: Biogeochemical controls and associations with microbial communities

USGS Publications Warehouse

Lorah, M.M.; Voytek, M.A.

2004-01-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea

PubMed Central

Duszenko, Nikolas

2017-01-01

ABSTRACT Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri. The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans. Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh. IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport systems and supramolecular complexes to optimize electron and carbon flow to control biomass synthesis and the production of methane. Worldwide, methanogens are used to generate renewable methane for heat, electricity, and transportation. Our observations suggest Methanosarcina acetivorans, but not Methanosarcina barkeri, has electrically quantized membranes. Escherichia coli, a model facultative anaerobe, has optimal electron transport at the stationary phase but not during exponential growth. This study also suggests the metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. The enhancement of methanogen electron transport through methanophenazine has the potential to increase renewable methane production at an industrial scale. PMID:28710268

Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea.

PubMed

Duszenko, Nikolas; Buan, Nicole R

2017-09-15

Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri The concentration of MPh suggests the cell membrane of M. acetivorans , but not of M. barkeri , is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh. IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport systems and supramolecular complexes to optimize electron and carbon flow to control biomass synthesis and the production of methane. Worldwide, methanogens are used to generate renewable methane for heat, electricity, and transportation. Our observations suggest Methanosarcina acetivorans , but not Methanosarcina barkeri , has electrically quantized membranes. Escherichia coli , a model facultative anaerobe, has optimal electron transport at the stationary phase but not during exponential growth. This study also suggests the metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. The enhancement of methanogen electron transport through methanophenazine has the potential to increase renewable methane production at an industrial scale. Copyright © 2017 American Society for Microbiology.

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

DOE PAGES

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

Effects of Nickel and Cobalt on Kinetics of Methanol Conversion by Methanogenic Sludge as Assessed by On-Line CH4 Monitoring

PubMed Central

Gonzalez-Gil, Graciela; Kleerebezem, Robbert; Lettinga, Gatze

1999-01-01

When metals were added in a pulse mode to methylotrophic-methanogenic biomass, three methane production rate phases were recognized. Increased concentrations of Ni and Co accelerated the initial exponential and final arithmetic increases in the methane production rate and reduced the temporary decrease in the rate. When Ni and Co were added continuously, the temporary decrease phase was eliminated and the exponential production rate increased. We hypothesize that the temporary decrease in the methane production rate and the final arithmetic increase in the methane production rate were due to micronutrient limitations and that the precipitation-dissolution kinetics of metal sulfides may play a key role in the biovailability of these compounds. PMID:10103284

Anaerobic treatability of wastewater contaminated with propylene glycol.

PubMed

Sezgin, Naim; Tonuk, Gulseven Ubay

2013-09-01

The purpose of this study was to investigate the biodegradability of propylene glycol in anaerobic conditions by using methanogenic culture. A master reactor was set up to develop a culture that would be acclimated to propylene glycol. After reaching steady-state, culture was transferred to serum bottles. Three reactors with same initial conditions were run for consistency. Propylene glycol was completely biodegradable under anaerobic methanogenic conditions. Semi-continuous reactors operated at a temperature of 35°C had consistently achieved a propylene glycol removal of higher than 95 % based on chemical oxygen demand (COD). It was found that in semi-continuous reactors, anaerobic treatment of propylene glycol at concentrations higher than 1,500 mg COD m(-3) day(-1) was not convenient due to instable effluent COD.

Methanogenic burst in the end-Permian carbon cycle.

PubMed

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

2014-04-15

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.

Effects of nickel and cobalt on kinetics of methanol conversion by methanogenic sludge as assessed by on-line CH4 monitoring.

PubMed

Gonzalez-Gil, G; Kleerebezem, R; Lettinga, G

1999-04-01

When metals were added in a pulse mode to methylotrophic-methanogenic biomass, three methane production rate phases were recognized. Increased concentrations of Ni and Co accelerated the initial exponential and final arithmetic increases in the methane production rate and reduced the temporary decrease in the rate. When Ni and Co were added continuously, the temporary decrease phase was eliminated and the exponential production rate increased. We hypothesize that the temporary decrease in the methane production rate and the final arithmetic increase in the methane production rate were due to micronutrient limitations and that the precipitation-dissolution kinetics of metal sulfides may play a key role in the biovailability of these compounds.

Enhancement of methane production in anaerobic digestion of sewage sludge by thermal hydrolysis pretreatment.

PubMed

Choi, Jae-Min; Han, Sun-Kee; Lee, Chae-Young

2018-07-01

This study was performed to optimize thermal hydrolysis pretreatment (THP) of sewage sludge for enhanced anaerobic digestion (AD). Using the response surface methodology (RSM), the optimal conditions were found 180 °C of reaction temperature and 76 min of reaction time. Through THP under optimal conditions, high molecular substances in sewage sludge such as soluble microbial by-products (SMPs) and extracellular polymeric substances (EPSs) were hydrolyzed into low molecular ones without the generation of refractory compounds. The microbial community analysis revealed that relative abundances of Methanomicrobia such as Methanosarcina, Methanosaeta (acetoclastic methanogens), and Methanoculleus (hydrogenotrophic methanogens) in AD with THP were higher than those in conventional AD. Copyright © 2018. Published by Elsevier Ltd.

Evaluation of various cheese whey treatment scenarios in single-chamber microbial electrolysis cells for improved biohydrogen production.

PubMed

Rivera, Isaac; Bakonyi, Péter; Cuautle-Marín, Manuel Alejandro; Buitrón, Germán

2017-05-01

In this study single-chamber microbial electrolysis cells (MECs) were applied to treat cheese whey (CW), an industrial by-product, and recover H 2 gas. Firstly, this substrate was fed directly to the MEC to get the initial feedback about its H 2 generation potential. The results indicated that the direct application of CW requires an adequate pH control to realize bioelectrohydrogenesis and avoid operational failure due to the loss of bioanode activity. In the second part of the study, the effluents of anaerobic (methanogenic) digester and hydrogenogenic (dark fermentative H 2 -producing) reactor utilizing the CW were tested in the MEC process (representing the concept of a two-stage technology). It turned out that the residue of the methanogenic reactor - with its relatively lower carbohydrate- and higher volatile fatty acid contents - was more suitable to produce hydrogen bioelectrochemically. The MEC operated with the dark fermentation effluent, containing a high portion of carbohydrates and low amount of organic acids, produced significant amount of undesired methane simultaneously with H 2 . Overall, the best MEC behavior was attained using the effluent of the methanogenic reactor and therefore, considering a two-stage system, methanogenesis is an advisable pretreatment step for the acidic CW to enhance the H 2 formation in complementary microbial electrohydrogenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of dissolved and vapor‐phase gases to investigate methanogenic degradation of petroleum hydrocarbon contamination in the subsurface

USGS Publications Warehouse

Amos, Richard T.; Mayer, K. Ulrich; Bekins, Barbara A.; Delin, Geoffrey N.; Williams, Randi L.

2005-01-01

At many sites contaminated with petroleum hydrocarbons, methanogenesis is a significant degradation pathway. Techniques to estimate CH4 production, consumption, and transport processes are needed to understand the geochemical system, provide a complete carbon mass balance, and quantify the hydrocarbon degradation rate. Dissolved and vapor‐phase gas data collected at a petroleum hydrocarbon contaminated site near Bemidji, Minnesota, demonstrate that naturally occurring nonreactive or relatively inert gases such as Ar and N2 can be effectively used to better understand and quantify physical and chemical processes related to methanogenic activity in the subsurface. In the vadose zone, regions of Ar and N2 depletion and enrichment are indicative of methanogenic and methanotrophic zones, and concentration gradients between the regions suggest that reaction‐induced advection can be an important gas transport process. In the saturated zone, dissolved Ar and N2 concentrations are used to quantify degassing driven by methanogenesis and also suggest that attenuation of methane along the flow path, into the downgradient aquifer, is largely controlled by physical processes. Slight but discernable preferential depletion of N2 over Ar, in both the saturated and unsaturated zones near the free‐phase oil, suggests reactivity of N2 and is consistent with other evidence indicating that nitrogen fixation by microbial activity is taking place at this site.

Low pressure microenvironments: Methane production at 50 mbar and 100 mbar by methanogens

NASA Astrophysics Data System (ADS)

Mickol, Rebecca L.; Kral, Timothy A.

2018-04-01

Low pressure is often overlooked in terms of possible biocidal effects when considering a habitable environment on Mars. Few experiments have investigated the ability for microorganisms to actively grow under low pressure conditions, despite the atmosphere being a location on Earth where organisms could be exposed to these pressures. Three species of methanogens (Methanobacterium formicicum, Methanosarcina barkeri, Methanococcus maripaludis) were tested for their ability to actively grow (demonstrate an increase in methane production and optical density) within low-pressure microenvironments at 50 mbar or 100 mbar. M. formicicum was the only species to demonstrate both an increase in methane and an increase in optical density during the low-pressure exposure period for experiments conducted at 50 mbar and 100 mbar. In certain experiments, M. barkeri showed an increase in optical density during the low-pressure exposure period, likely due to the formation of multicellular aggregates, but minimal methane production (<1%). During incubation following exposure to low pressure, cultures of all species resumed methane production and increased in optical density. Thus, low pressure may not be a biocidal factor for certain methanogen species, with growth possible under low-pressure conditions. Results indicate that low pressure exposure may just be inhibitory during the exposure itself, and metabolism may resume following incubation under more ideal conditions. Further work is needed to address growth/survival under Mars surface pressures.

Effects of an applied voltage on direct interspecies electron transfer via conductive materials for methane production.

PubMed

Lee, Jung-Yeol; Park, Jeong-Hoon; Park, Hee-Deung

2017-10-01

Direct interspecies electron transfer (DIET) between exoelectrogenic bacteria and methanogenic archaea via conductive materials is reported as an efficient method to produce methane in anaerobic organic waste digestion. A voltage can be applied to the conductive materials to accelerate the DIET between two groups of microorganisms to produce methane. To evaluate this hypothesis, two sets of anaerobic serum bottles with and without applied voltage were used with a pair of graphite rods as conductive materials to facilitate DIET. Initially, the methane production rate was similar between the two sets of serum bottles, and later the serum bottles with an applied voltage of 0.39V showed a 168% higher methane production rate than serum bottles without an applied voltage. In cyclic voltammograms, the characteristic redox peaks for hydrogen and acetate oxidation were identified in the serum bottles with an applied voltage. In the microbial community analyses, hydrogenotrophic methanogens (e.g. Methanobacterium) were observed to be abundant in serum bottles with an applied voltage, while methanogens utilizing carbon dioxide (e.g., Methanosaeta and Methanosarcina) were dominant in serum bottles without an applied voltage. Taken together, the applied voltage on conductive materials might not be effective to promote DIET in methane production. Instead, it appeared to generate a condition for hydrogenotrophic methanogenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacterial ethane formation from reduced, ethylated sulfur compounds in anoxic sediments

USGS Publications Warehouse

Oremland, R.S.; Whiticar, Michael J.; Strohmaier, F.E.; Kiene, R.P.

1988-01-01

Trace levels of ethane were produced biologically in anoxic sediment slurries from five chemically different aquatic environments. Gases from these locations displayed biogenic characteristics, having 12C-enriched values of ??13CH4 (-62 to -86%.), ??13C2H6 (-35 to -55%.) and high ratios (720 to 140,000) of CH4 [C2H6 + C3H8]. Endogenous production of ethane by slurries was inhibited by autoclaving or by addition of the inhibitor of methanogenic bacteria, 2-bromoethanesulfonic acid (BES). Ethane formation was stimulated markedly by ethanethiol (ESH), and, to a lesser extent, by diethylsulfide (DES). Formation of methane and ethane in ESH- or DES-amended slurries was blocked by BES. Experiments showed that ethionine (or an analogous compound) could be a precursor of ESH. Ethylamine or ethanol additions to slurries caused only a minor stimulation of ethane formation. Similarly, propanethiol additions resulted in only a minor enhancement of propane formation. Cell suspensions of a methyltrophic methanogen produced traces of ethane when incubated in the presence of DES, although the organism did not grow on this compound. These results indicate that methanogenic bacteria produce ethane from the traces of ethylated sulfur compounds present in recent sediments. Preliminary estimates of stable carbon isotope fractionation associated with sediment methane formation from dimethylsulfide was about 40%., while ethane formation from DES and ESH was only 4. 6 and 6.5%., respectively. ?? 1988.

Bioelectrochemical enhancement of anaerobic methanogenesis for high organic load rate wastewater treatment in a up-flow anaerobic sludge blanket (UASB) reactor.

PubMed

Zhao, Zhiqiang; Zhang, Yaobin; Chen, Shuo; Quan, Xie; Yu, Qilin

2014-10-17

A coupling process of anaerobic methanogenesis and electromethanogenesis was proposed to treat high organic load rate (OLR) wastewater. During the start-up stage, acetate removal efficiency of the electric-biological reactor (R1) reached the maximization about 19 percentage points higher than that of the control anaerobic reactor without electrodes (R2), and CH4 production rate of R1 also increased about 24.9% at the same time, while additional electric input was 1/1.17 of the extra obtained energy from methane. Coulombic efficiency and current recorded showed that anodic oxidation contributed a dominant part in degrading acetate when the metabolism of methanogens was low during the start-up stage. Along with prolonging operating time, aceticlastic methanogenesis gradually replaced anodic oxidation to become the main pathway of degrading acetate. When the methanogens were inhibited under the acidic conditions, anodic oxidation began to become the main pathway of acetate decomposition again, which ensured the reactor to maintain a stable performance. FISH analysis confirmed that the electric field imposed could enrich the H2/H(+)-utilizing methanogens around the cathode to help for reducing the acidity. This study demonstrated that an anaerobic digester with a pair of electrodes inserted to form a coupling system could enhance methanogenesis and reduce adverse impacts.

Involvement of thermophilic archaea in the biocorrosion of oil pipelines.

PubMed

Davidova, Irene A; Duncan, Kathleen E; Perez-Ibarra, B Monica; Suflita, Joseph M

2012-07-01

Two thermophilic archaea, strain PK and strain MG, were isolated from a culture enriched at 80°C from the inner surface material of a hot oil pipeline. Strain PK could ferment complex organic nitrogen sources (e.g. yeast extract, peptone, tryptone) and was able to reduce elemental sulfur (S°), Fe(3+) and Mn(4+) . Phylogenetic analysis revealed that the organism belonged to the order Thermococcales. Incubations of this strain with elemental iron (Fe°) resulted in the abiotic formation of ferrous iron and the accumulation of volatile fatty acids during yeast extract fermentation. The other isolate, strain MG, was a H(2) :CO(2) -utilizing methanogen, phylogenetically affiliated with the genus Methanothermobacter family. Co-cultures of the strains grew as aggregates that produced CH(4) without exogenous H(2) amendment. The co-culture produced the same suite but greater concentrations of fatty acids from yeast extract than did strain PK alone. Thus, the physiological characteristics of organisms both alone and in combination could conceivably contribute to pipeline corrosion. The Thermococcus strain PK could reduce elemental sulfur to sulfide, produce fatty acids and reduce ferric iron. The hydrogenotrophic methanogen strain MG enhanced fatty acid production by fermentative organisms but could not couple the dissolution Fe° with the consumption of water-derived H(2) like other methanogens. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

PubMed Central

Santana, Priscila Bessa; Junior, Rubens Ghilardi; Alves, Claudio Nahum; Silva, Jeronimo Lameira; McCulloch, John Anthony; Schneider, Maria Paula Cruz; da Costa da Silva, Artur

2012-01-01

Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the α subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified - the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous. PMID:22481885

Methane production and simultaneous sulphate reduction in anoxic, salt marsh sediments

USGS Publications Warehouse

Oremland, R.S.; Marsh, L.M.; Polcin, S.

1982-01-01

It has been generally believed that sulphate reduction precludes methane generation during diagenesis of anoxic sediments1,2. Because most biogenic methane formed in nature is thought to derive either from acetate cleavage or by hydrogen reduction of carbon dioxide3-6, the removal of these compounds by the energetically more efficient sulphate-reducing bacteria can impose a substrate limitation on methanogenic bacteria 7-9. However, two known species of methanogens, Methanosarcina barkeri and Methanococcus mazei, can grow on and produce methane from methanol and methylated amines10-13. In addition, these compounds stimulate methane production by bacterial enrichments from the rumen11,14 and aquatic muds13,14. Methanol can enter anaerobic food webs through bacterial degradation of lignins15 or pectin16, and methylated amines can be produced either from decomposition of substances like choline, creatine and betaine13,14 or by bacterial reduction of trimethylamine oxide17, a common metabolite and excretory product of marine animals. However, the relative importance of methanol and methylated amines as precursors of methane in sediments has not been previously examined. We now report that methanol and trimethylamine are important substrates for methanogenic bacteria in salt marsh sediments and that these compounds may account for the bulk of methane produced therein. Furthermore, because these compounds do not stimulate sulphate reduction, methanogenesis and sulphate reduction can operate concurrently in sulphate-containing anoxic sediments. ?? 1982 Nature Publishing Group.