Showing papers on "Methanogen published in 2015"

Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

Abstract: Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7-17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25-100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement. Despite proposed strategies to increase rice productivity and reduce methane emissions, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies.

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy.

Abstract: The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at the 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula) and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.

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

Abstract: 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.

Pyrosequencing of mcrA and archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters.

Abstract: 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.

Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate oxidizing bacteria

Abstract: Ammonia-rich substrates can cause inhibition on anaerobic digestion process Syntrophic acetate-oxidizing bacteria (SAOB) and hydrogenotrophic methanogens are important for the ammonia inhibitory mechanism on anaerobic digestion The roles and interactions of SAOB and hydrogenotrophic methanogens to ammonia inhibition effect are still unclear The aim of the current study was to determine the ammonia toxicity levels of various pure strains of SAOB and hydrogenotrophic methanogens Moreover, ammonia toxicity on the syntrophic-cultivated strains of SAOB and hydrogenotrophic methanogens was tested Thus, four hydrogenotrophic methanogens (ie Methanoculleus bourgensis, Methanobacterium congolense, Methanoculleu thermophilus and Methanothermobacter thermautotrophicus), two SAOB (ie Tepidanaerobacter acetatoxydans and Thermacetogenium phaeum) and their syntrophic cultivation were assessed under 026, 3, 5 and 7 g NH4 (+)-N L(-1) The results showed that some hydrogenotrophic methanogens were equally, or in some cases, more tolerant to high ammonia levels compared to SAOB Furthermore, a mesophilic hydrogenotrophic methanogen was more sensitive to ammonia toxicity compared to thermophilic methanogens tested in the study, which is contradicting to the general belief that thermophilic methanogens are more vulnerable to high ammonia loads compared to mesophilic This unexpected finding underlines the fact that the complete knowledge of ammonia inhibition effect on hydrogenotrophic methanogens is still absent

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

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

Potential of tannin-rich plants for modulating ruminal microbes and ruminal fermentation in sheep.

Abstract: The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 × 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest that TRP fed as pellets could be used to decrease methane production.

A microbial functional group-based module for simulating methane production and consumption: Application to an incubated permafrost soil

Abstract: Accurately estimating methane (CH4) flux in terrestrial ecosystems is critically important for investigating and predicting biogeochemistry-climate feedbacks. Improved simulations of CH4 flux require explicit representations of the microbial processes that account for CH4 dynamics. A microbial functional group-based module was developed, building on the decomposition subroutine of the Community Land Model 4.5. This module considers four key mechanisms for CH4 production and consumption: methanogenesis from acetate or from single-carbon compounds and CH4 oxidation using molecular oxygen or other inorganic electron acceptors. Four microbial functional groups perform these processes: acetoclastic methanogens, hydrogenotrophic methanogens, aerobic methanotrophs, and anaerobic methanotrophs. This module was used to simulate dynamics of carbon dioxide (CO2) and CH4 concentrations from an incubation experiment with permafrost soils. The results show that the model captures the dynamics of CO2 and CH4 concentrations in microcosms with top soils, mineral layer soils, and permafrost soils under natural and saturated moisture conditions and three temperature conditions of −2°C, 3°C, and 5°C (R2 > 0.67; P < 0.001). The biases for modeled results are less than 30% across the soil samples and moisture and temperature conditions. Sensitivity analysis confirmed the importance of acetic acid's direct contribution as substrate and indirect effects through pH feedback on CO2 and CH4 production and consumption. This study suggests that representing the microbial mechanisms is critical for modeling CH4 production and consumption; it is urgent to incorporate microbial mechanisms into Earth system models for better predicting trace gas dynamics and the behavior of the climate system.

Persistence of Methanosaeta populations in anaerobic digestion during process instability

Abstract: Anaerobic digestion is a sustainable technology for the treatment of organic waste and production of biogas. Acetoclastic methanogenesis accounts for the majority of methane production in anaerobic digestion. Therefore, sustaining robust acetoclastic methanogens is important for stable process performance. Due to faster growth kinetics at high acetate concentrations, it has been considered that Methanosarcina would be more prevalent than Methanosaeta in unstable anaerobic digestion processes which frequently experience high acetate levels. Methanogen population dynamics were monitored in multiple continuous anaerobic digesters for 500 days. Results from quantitative polymerase chain reaction analysis show that Methanosaeta dominated over Methanosarcina in anaerobic digestion at high acetate levels up to 44 mM, suggesting the potential of Methanosaeta as a robust and efficient acetoclastic candidate for resilient anaerobic methane conversion. Further efforts are needed to identify mechanisms contributing to the unexpected competitiveness of these methanogens at high acetate levels observed in this study.

Effect of temperature on the structure and activity of a methanogenic archaeal community during rice straw decomposition

Abstract: In recent years, the rice fields in Sanjiang Plain of Northeast China have drawn more and more attention because of the unique high-latitude location and the important contributions to rice production and methane emission. In the present study, a rice field soil in Sanjiang Plain was anaerobically incubated in presence and absence of rice straw at three temperatures (10 °C, 30 °C and 45 °C). The community structure and activity dynamics of methanogenic archaea were investigated by the terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of mcrA genes and transcripts and archaeal 16S rRNA genes. We found rice straw addition significantly shortened the lag phase of methanogenesis and enhanced the production of CH 4 and the accumulation of methanogenic precursors (CO 2 , H 2 and acetate). The T-RFLP analysis of mcrA gene revealed that structure of methanogenic archaeal community was relatively stable during the anoxic incubation. By contrast, analysis at the transcript level showed a highly dynamic composition of the active methanogens. In the beginning and early stages of incubation, Methanosarcinaceae actively utilized the accumulated acetate and H 2 /CO 2 for CH 4 production. Then the different methanogenic community developed along with the incubation time, and each representative methanogen group became predominant in different temperatures and treatments. At 10 °C, Methanobacteriales became more abundant in the soil without straw, while Methanosarcinaceae dominated in the soil with straw. The acetoclastic Methanosaetaceae , in particular, appeared to be active at 30 °C, probably due to the low concentration of acetate. High temperature of 45 °C significantly favored the hydrogenotrophic methanogens, with the increasing abundance of Methanobacteriales early and then the Methanocellales in the later stages.

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA.

Abstract: 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 %Ro) 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-Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L-1. Gas dryness values [C1/(C2+C3)] 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.

RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis.

Abstract: Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that are key to using these tools to further define the science of ruminal methanogenesis.

Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing

Abstract: 2-Phase anaerobic digestion (AD), where the acidogenic phase was operated at 2day hydraulic retention time (HRT) and the methanogenic phase at 10days HRT, had been evaluated to determine if it could provide higher organic reduction and methane production than the conventional single-stage AD (also operated at 12days HRT). 454 pyrosequencing was performed to determine and compare the microbial communities. The acidogenic reactor of the 2-phase system yielded a unique bacterial community of the lowest richness and diversity, while bacterial profiles of the methanogenic reactor closely followed the single-stage reactor. All reactors were predominated by hydrogenotrophic methanogens, mainly Methanolinea. Unusually, the acidogenic reactor contributed up to 24% of total methane production in the 2-phase system. This could be explained by the presence of Methanosarcina and Methanobrevibacter, and their activities could also help regulate reactor alkalinity during high loading conditions through carbon dioxide production. The enrichment of hydrolytic and acidogenic Porphyromonadaceae, Prevotellaceae, Ruminococcaceae and unclassified Bacteroidetes in the acidogenic reactor would have contributed to the improved sludge volatile solids degradation, and ultimately the overall 2-phase system's performance. Syntrophic acetogenic microorganisms were absent in the acidogenic reactor but present in the downstream methanogenic reactor, indicating the retention of various metabolic pathways also found in a single-stage system. The determination of key microorganisms further expands our understanding of the complex biological functions in AD process.

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

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

The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.

Abstract: Methanosarcina species are the most metabolically versatile of the methanogenic Archaea and can obtain energy for growth by producing methane via the hydrogenotrophic, acetoclastic or methylotrophic pathways. Methanosarcina barkeri CM1 was isolated from the rumen of a New Zealand Friesian cow grazing a ryegrass/clover pasture, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. The 4.5 Mb chromosome has an average G + C content of 39 %, and encodes 3523 protein-coding genes, but has no plasmid or prophage sequences. The gene content is very similar to that of M. barkeri Fusaro which was isolated from freshwater sediment. CM1 has a full complement of genes for all three methanogenesis pathways, but its genome shows many differences from those of other sequenced rumen methanogens. Consequently strategies to mitigate ruminant methane need to include information on the different methanogens that occur in the rumen.

Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps

Abstract: Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro-organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate-reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing Deltaproteobacteria (SRB) recovered from deep-sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (e_(lipid–water)) for D. multivorans grown under different carbon assimilation conditions, with more D-enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of e_(lipid–water) values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D-enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in e_(lipid–water) values.

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

Abstract: 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.

Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester.

Abstract: A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.

Alamethicin Suppresses Methanogenesis and Promotes Acetogenesis in Bioelectrochemical Systems

Abstract: Microbial electrosynthesis (MES) systems with mixed cultures often generate a variety of gaseous and soluble chemicals. Methane is the primary end product in mixed-culture MES because it is the thermodynamically most favorable reduction product of CO 2 . Here, we show that the peptaibol alamethicin selectively suppressed the growth of methanogens in mixed-culture MES systems, resulting in a shift of the solution and cathode communities to an acetate-producing system dominated by Sporomusa, a known acetogenic genus in MES systems. Archaea in the methane-producing control were dominated by Methanobrevibacter species, but no Archaea were detected in the alamethicin-treated reactors. No methane was detected in the mixed-culture reactors treated with alamethicin over 10 cycles (∼3 days each). Instead, acetate was produced at an average rate of 115 nmol ml −1 day −1 , similar to the rate reported previously for pure cultures of Sporomusa ovata on biocathodes. Mixed-culture control reactors without alamethicin generated methane at nearly 100% coulombic recovery, and no acetate was detected. These results show that alamethicin is effective for the suppression of methanogen growth in MES systems and that its use enables the production of industrially relevant organic compounds by the inhibition of methanogenesis.

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

Abstract: In methanogenic habitats, volatile fatty acids (VFA), such as propionate and butyrate, are major intermediates in organic matter degradation. VFA are further metabolized to H2, acetate and CO2 by syntrophic fatty acid-degrading bacteria (SFAB) in association with methanogenic archaea. Despite their indispensable role in VFA degradation, little is known about SFAB abundance and their environmental distribution. To facilitate ecological studies, we developed four novel genus-specific quantitative PCR (qPCR) assays, with primer sets targeting known SFAB: Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas. Primer set specificity was confirmed using in silico and experimental (target controls, clone libraries and melt-curve analysis) approaches. These qPCR assays were applied to quantify SFAB in a variety of mesophilic methanogenic habitats, including a laboratory propionate enrichment culture, pilot- and full-scale anaerobic reactors, cow rumen, horse faeces, an experimental rice paddy soil, a bog stream and swamp sediments. The highest SFAB 16S rRNA gene copy numbers were found in the propionate enrichment culture and anaerobic reactors, followed by the bog stream and swamp sediment samples. In addition, it was observed that SFAB and methanogen abundance varied with reactor configuration and substrate identity. To our knowledge, this research represents the first comprehensive study to quantify SFAB in methanogenic habitats using qPCR-based methods. These molecular tools will help investigators better understand syntrophic microbial communities in engineered and natural environments.

Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades.

Abstract: To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.