Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment

Enhanced Volatile Fatty Acid Production from Oil Palm Empty Fruit Bunch through Acidogenic Fermentation—A Novel Resource Recovery Strategy for Oil Palm Empty Fruit Bunch

The glucan-rich fraction, hemicellulosic compounds-rich fraction, and a mixture of both fractions obtained from organosolv pretreatment of oil palm empty fruit bunch (OPEFB) were used as substrates to produce volatile fatty acids (VFAs) in acidogenic fermentation. In this study, the effects of medium adjustment (carbon to nitrogen ratio and trace elements supplementation) and methanogenesis inhibition (through the addition of 2-bromoethanesulfonate or by heat shock) to enhance VFAs yield were investigated. The highest VFA yield was 0.50 ± 0.00 g VFAs/g volatile solid (VS), which was obtained when methanogens were inhibited by heat shock and cultivated in a mixture of glucan-rich and hemicellulosic compounds-rich fractions. Under these conditions, the fermentation produced acetic acid as the only VFA. Based on the results, the mass balance of the whole process (from pretreatment and fermentation) showed the possibility to obtain 30.4 kg acetic acid and 20.3 kg lignin with a 70% purity from 100 kg OPEFB.

The Effects of Halogenated Compounds on the Anaerobic Digestion of Macroalgae

The urgent need to replace fossil fuels has seen macroalgae advancing as a potential feedstock for anaerobic digestion. The natural methane productivity (dry weight per hectare) of seaweeds is greater than in many terrestrial plant systems. As part of their defence systems, seaweeds, unlike terrestrial plants, produce a range of halogenated secondary metabolites, especially chlorinated and brominated compounds. Some orders of brown seaweeds also accumulate iodine, up to 1.2% of their dry weight. Fluorine remains rather unusual within the chemical structure. Halogenated hydrocarbons have moderate to high toxicities. In addition, halogenated organic compounds constitute a large group of environmental chemicals due to their extensive use in industry and agriculture. In recent years, concerns over the environmental fate and release of these halogenated organic compounds have resulted in research into their biodegradation and the evidence emerging shows that many of these compounds are more easily degraded under strictly anaerobic conditions compared to aerobic biodegradation. Biosorption via seaweed has become an alternative to the existing technologies in removing these pollutants. Halogenated compounds are known inhibitors of methane production from ruminants and humanmade anaerobic digesters. The focus of this paper is reviewing the available information on the effects of halogenated organic compounds on anaerobic digestion.

Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate

Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day^-1, with a concurrent production of n-butyrate of 7.9 mM day^-1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

Suppressing methanogens and enriching electrogens in bioelectrochemical systems

Suppression of methanogens is considered as one of the main challenges in achieving the practical application of several types of bioelectrochemical system (BES). Feasibility of mixed culture as an inoculum in BES is mainly restricted by methanogenic population. Methanogens compete with electrogens (in bioanodes) or acetogens (in biocathodes) for substrate which results in diminishing Coulombic efficiency. Selection of particular inoculum pretreatment method affects the microbial diversity in anodic/cathodic microenvironments and hence the performance of BES. This review discusses various physical, chemical and biological pretreatment methods for suppressing the growth of methanogens. Selective microbial enrichment in anodic/cathodic biofilm can be promoted with bioaugmentation and/or applied external potential approach to harvest maximum Coulombs from the substrate. For field application of BES, physical pretreatment methods can be proposed with intermittent addition of chemical inhibitors and conversion of methane to electricity in order to make the process inexpensive along with recovering the maximum energy.

Rate-Limiting Mass Transfer in Micropollutant Degradation Revealed by Isotope Fractionation in Chemostat

Biodegradation of persistent micropollutants like pesticides often slows down at low concentrations (μg/L) in the environment. Mass transfer limitations or physiological adaptation are debated to be responsible. Although promising, evidence from compound-specific isotope fractionation analysis (CSIA) remains unexplored for bacteria adapted to this low concentration regime. We accomplished CSIA for degradation of a persistent pesticide, atrazine, during cultivation of Arthrobacter aurescens TC1 in chemostat under four different dilution rates leading to 82, 62, 45, and 32 μg/L residual atrazine concentrations. Isotope analysis of atrazine in chemostat experiments with whole cells revealed a drastic decrease in isotope fractionation with declining residual substrate concentration from ε(C) = -5.36 ± 0.20‰ at 82 μg/L to ε(C) = -2.32 ± 0.28‰ at 32 μg/L. At 82 μg/L ε(C) represented the full isotope effect of the enzyme reaction. At lower residual concentrations smaller ε(C) indicated that this isotope effect was masked indicating that mass transfer across the cell membrane became rate-limiting. This onset of mass transfer limitation appeared in a narrow concentration range corresponding to about 0.7 μM assimilable carbon. Concomitant changes in cell morphology highlight the opportunity to study the role of this onset of mass transfer limitation on the physiological level in cells adapted to low concentrations.

Formate and Hydrogen as Electron Shuttles in Terminal Fermentations in an Oligotrophic Freshwater Lake Sediment

The energetic situation of terminal fermentations in methanogenesis was analyzed by pool size determinations in sediment cores taken in the oligotrophic Lake Constance, Germany. Distribution profiles of fermentation intermediates and products were measured at three different water depths (2, 10, and 80 m). Methane concentrations were constant below 10 cm of sediment depth. Within the methanogenic zone, concentrations of formate, acetate, propionate, and butyrate varied between 1 and 40 μM, and hydrogen was between 0.5 and 5 Pa. From the distribution profiles of the fermentation intermediates, Gibbs free energy changes for their interconversion were calculated. Pool sizes of formate and hydrogen were energetically nearly equivalent, with -5 ± 5 kJ per mol difference of free energy change (ΔG) for a hypothetical conversion of formate to hydrogen plus CO2 The ΔG values for conversion of fatty acids to methanogenic substrates and their further conversion to methane and CO2 were calculated with hydrogen and with formate as intermediates. Syntrophic propionate oxidation reached energetic equilibrium with formate as the sole electron carrier but was sufficiently exergonic if at least some of the electrons were transferred via hydrogen. The energetic consequences of formate versus hydrogen transfer in secondary and methanogenic fermentations indicate that both carrier systems are probably used simultaneously to optimize the energy yields for the partners involved.IMPORTANCE In the terminal steps of methane formation in freshwater lake sediments, fermenting bacteria cooperate syntrophically with methanogens and homoacetogens at minimum energy increments via interspecies electron transfer. The energy yields of the partner organisms in these cooperations have so far been calculated based mainly on in situ hydrogen partial pressures. In the present study, we also analyzed pools of formate as an alternative electron carrier in sediment cores of an oligotrophic lake. The formate and hydrogen pools appeared to be energetically nearly equivalent and are likely to be used simultaneously for interspecies electron transfer. Calculations of reaction energies of the partners involved suggest that propionate degradation may also proceed through the Smithella pathway, which converts propionate via butyrate and acetate to three acetate residues, thus circumventing one energetically difficult fatty acid oxidation step.

Full-scale evaluation of methane production under oxic conditions in a mesotrophic lake

Oxic lake surface waters are frequently oversaturated with methane (CH₄). The contribution to the global CH₄ cycle is significant, thus leading to an increasing number of studies and stimulating debates. Here we show, using a mass balance, on a temperate, mesotrophic lake, that ~90% of CH₄ emissions to the atmosphere is due to CH₄ produced within the oxic surface mixed layer (SML) during the stratified period, while the often observed CH₄ maximum at the thermocline represents only a physically driven accumulation. Negligible surface CH₄ oxidation suggests that the produced 110 ± 60 nmol CH₄ L^-1 d^-1 efficiently escapes to the atmosphere. Stable carbon isotope ratios indicate that CH₄ in the SML is distinct from sedimentary CH₄ production, suggesting alternative pathways and precursors. Our approach reveals CH₄ production in the epilimnion that is currently overlooked, and that research on possible mechanisms behind the methane paradox should additionally focus on the lake surface layer.

Biogas process parameters--energetics and kinetics of secondary fermentations in methanogenic biomass degradation

Pool sizes of short-chain fatty acids (formate, acetate, propionate, and butyrate), hydrogen, and carbon monoxide were assayed in digesting sludge from four different methanogenic reactors degrading either sewage sludge or agricultural products and wastes at pH 8.0 and 40 or 47 °C. Free reaction energies were calculated for the respective degradation reactions involved, indicating that acetate, propionate, and butyrate degradation all supplied sufficient energy (-10 to -30 kJ per mol reaction) to sustain the microbial communities involved in the respective processes. Pools of formate and hydrogen were energetically equivalent as electron carriers. In the sewage sludge reactor, homoacetogenic acetate formation from H2 and CO2 was energetically feasible whereas syntrophic acetate oxidation appeared to be possible in two biogas reactors, one operating at enhanced ammonia content (4.5 g NH4 (+)-N per l) and the other one at enhanced temperature (47 °C). Maximum capacities for production of methanogenic substrates did not exceed the consumption capacities by hydrogenotrophic and aceticlastic methanogens. Nonetheless, the capacity for acetate degradation appeared to be a limiting factor especially in the reactor operating at enhanced ammonia concentration.

Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations

The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.

Alamethicin suppresses methanogenesis and promotes acetogenesis in bioelectrochemical systems

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 CO2. 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.

Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon

Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment.

Methanogenic archaea diversity in hyporheic sediments of a small lowland stream

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

Near-zero growth kinetics of Pseudomonas putida deduced from proteomic analysis

Intensive microbial growth typically observed in laboratory rarely occurs in nature. Because of severe nutrient deficiency, natural populations exhibit near-zero growth (NZG). There is a long-standing controversy about sustained NZG, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state. Using chemostat with cell retention (CCR) of Pseudomonas putida, we resolve this controversy and show that under NZG conditions, bacteria differentiate into growing and VBNC (viable but not non-culturable) forms, the latter preserving measurable catabolic activity. The proliferating cells attained a steady state, their slow growth balanced by VBNC production. Proteomic analysis revealed upregulated (transporters, stress response, self-degrading enzymes and extracellular polymers) and downregulated (ribosomal, chemotactic and primary biosynthetic enzymes) proteins in the CCR versus batch culture. Based on these profiles, we identified intracellular processes associated with NZG and generated a mathematical model that simulated the observations. We conclude that NZG requires controlled partial self-digestion and deep reconfiguration of the metabolic machinery that results in the biosynthesis of new products and development of broad stress resistance. CCR allows efficient on-line control of NZG including VBNC production. A well-nuanced understanding of NZG is important to understand microbial processes in situ and for optimal design of environmental technologies.

High concentrations of methyl fluoride affect the bacterial community in a thermophilic methanogenic sludge

To precisely control the application of methyl fluoride (CH₃F) for analysis of methanogenic pathways, the influence of 0–10% CH₃F on bacterial and archaeal communities in a thermophilic methanogenic sludge was investigated. The results suggested that CH₃F acts specifically on acetoclastic methanogenesis. The inhibitory effect stabilized at an initial concentration of 3–5%, with around 90% of the total methanogenic activity being suppressed, and a characteristic of hydrogenotrophic pathway in isotope fractionation was demonstrated under this condition. However, extended exposure (12 days) to high concentrations of CH₃F (>3%) altered the bacterial community structure significantly, resulting in increased diversity and decreased evenness, which can be related to acetate oxidation and CH₃F degradation. Bacterial clone library analysis showed that syntrophic acetate oxidizing bacteria Thermacetogenium phaeum were highly enriched under the suppression of 10% CH₃F. However, the methanogenic community did not change obviously. Thus, excessive usage of CH₃F over the long term can change the composition of the bacterial community. Therefore, data from studies involving the use of CH₃F as an acetoclast inhibitor should be interpreted with care. Conversely, CH₃F has been suggested as a factor to stimulate the enrichment of syntrophic acetate oxidizing bacteria.

Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms

Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome.

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

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.

Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

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.

Methanogenic pathway and archaeal communities in three different anoxic soils amended with rice straw and maize straw

Addition of straw is common practice in rice agriculture, but its effect on the path of microbial CH(4) production and the microbial community involved is not well known. Since straw from rice (C3 plant) and maize plants (C4 plant) exhibit different δ(13)C values, we compared the effect of these straw types using anoxic rice field soils from Italy and China, and also a soil from Thailand that had previously not been flooded. The temporal patterns of production of CH(4) and its major substrates H(2) and acetate, were slightly different between rice straw and maize straw. Addition of methyl fluoride, an inhibitor of acetoclastic methanogenesis, resulted in partial inhibition of acetate consumption and CH(4) production. The δ(13)C of the accumulated CH(4) and acetate reflected the different δ(13)C values of rice straw versus maize straw. However, the relative contribution of hydrogenotrophic methanogenesis to total CH(4) production exhibited a similar temporal change when scaled to CH(4) production irrespectively of whether rice straw or maize straw was applied. The composition of the methanogenic archaeal communities was characterized by terminal restriction fragment length polymorphism (T-RFLP) analysis and was quantified by quantitative PCR targeting archaeal 16S rRNA genes or methanogenic mcrA genes. The size of the methanogenic communities generally increased during incubation with straw, but the straw type had little effect. Instead, differences were found between the soils, with Methanosarcinaceae and Methanobacteriales dominating straw decomposition in Italian soil, Methanosarcinaceae, Methanocellales, and Methanobacteriale in China soil, and Methanosarcinaceae and Methanocellales in Thailand soil. The experiments showed that methanogenic degradation in different soils involved different methanogenic population dynamics. However, the path of CH(4) production was hardly different between degradation of rice straw versus maize straw and was also similar for the different soil types.

Quantification of the inhibitory effect of methyl fluoride on methanogenesis in mesophilic anaerobic granular systems

The inhibitory effect of CH(3)F on methanogenesis in mesophilic anaerobic granules was tested at different concentrations (0-10% v/v, in the gas phase) and verified by the stable carbon isotopic signatures of CH(4) and CO(2). The results showed that the inhibitory effect increased with the initial CH(3)F concentration up to 5%. The CH(3)F concentration causing 50% metabolic inhibition was 0.32%. Complete inhibition of acetoclastic methanogenesis with a 91% reduction in total methanogenic activity was achieved when 5% CH(3)F was initially added to the headspace, which resulted in 870 μM dissolved CH(3)F in the liquid. It was much higher than that applied in other natural anoxic non-granular systems, indicating that the layered granular structure influenced the inhibitory effect. The obvious increase in hydrogen content indicated that high concentrations of CH(3)F (≥5%) suppressed hydrogenotrophic methanogenesis as well. The stable inhibition lasted for at least 6d as the CH(3)F concentration decreased slowly with incubation time. These results suggested that CH(3)F could be used for investigating methanogenic processes in anaerobic granular systems after the CH(3)F concentration and incubation time for specific inhibition of acetoclastic methanogenesis were carefully determined. In the present system, CH(3)F concentration of 5% was suggested to be optimal.

Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil

Methane production in paddy soil is substantially suppressed after even a brief exposure of soil to oxygen. We hypothesized that the strong response of methanogen activity is reflected in the transcription of functional genes rather than in the composition of the community of methanogens. Therefore, we determined the community composition and the transcriptional response of methanogens in a rice field soil by targeting the mcrA gene (encoding the α subunit of methyl-coenzyme M reductase). Transcription of mcrA genes measured by quantitative PCR decreased by an order of magnitude after brief exposure to O2 . Terminal restriction fragment length polymorphism of mcrA genes and gene transcripts showed that although the community structure of methanogens did not change, the composition of transcripts dramatically responded to O2 exposure. In the beginning, transcripts of Methanocellales were the relatively most abundant, indicating resistance of these hydrogenotrophic methanogens against O2 stress. Later on, mcrA transcripts of acetoclastic methanogens became relatively more abundant coinciding with the turnover of acetate. The transcription of Methanosarcinaceae was relatively greater when acetate accumulated while Methanosaetaceae became more active when acetate concentrations decreased. In the presence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, mcrA transcription by Methanosaetaceae was greatly suppressed while that of Methanosarcinaceae was less affected. Our study showed that in contrast to constant community structure as revealed by DNA-based fingerprinting the transcription of functional mcrA genes strongly responded to O2 stress and the presence of inhibitor CH3 F. The response patterns reflected the genomic and physiological traits of individual methanogens.

Predominant contribution of syntrophic acetate oxidation to thermophilic methane formation at high acetate concentrations

To quantify the contribution of syntrophic acetate oxidation to thermophilic anaerobic methanogenesis under the stressed condition induced by acidification, the methanogenic conversion process of 100 mmol/L acetate was monitored simultaneously by using isotopic tracing and selective inhibition techniques, supplemented with the analysis of unculturable microorganisms. Both quantitative methods demonstrated that, in the presence of aceticlastic and hydrogenotrophic methanogens, a large percentage of methane (up to 89%) was initially derived from CO(2) reduction, indicating the predominant contribution of the syntrophic acetate oxidation pathway to acetate degradation at high acid concentrations. A temporal decrease of the fraction of hydrogenotrophic methanogenesis from more than 60% to less than 40% reflected the gradual prevalence of the aceticlastic methanogenesis pathway along with the reduction of acetate. This apparent discrimination of acetate methanization pathways highlighted the importance of the syntrophic acetate-oxidizing bacteria to initialize methanogenesis from high organic loadings.

Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research

Among the different disciplines covered by mass spectrometry, measurement of (13)C/(12)C isotopic ratio crosses a large section of disciplines from a tool revealing the origin of compounds to more recent approaches such as metabolomics and proteomics. Isotope ratio mass spectrometry (IRMS) and molecular mass spectrometry (MS) are the two most mature techniques for (13)C isotopic analysis of compounds, respectively, for high and low-isotopic precision. For the sample introduction, the coupling of gas chromatography (GC) to either IRMS or MS is state of the art technique for targeted isotopic analysis of volatile analytes. However, liquid chromatography (LC) also needs to be considered as a tool for the sample introduction into IRMS or MS for (13)C isotopic analyses of non-volatile analytes at natural abundance as well as for (13)C-labeled compounds. This review presents the past and the current processes used to perform (13)C isotopic analysis in combination with LC. It gives particular attention to the combination of LC with IRMS which started in the 1990's with the moving wire transport, then subsequently moved to the chemical reaction interface (CRI) and was made commercially available in 2004 with the wet chemical oxidation interface (LC-IRMS). The LC-IRMS method development is also discussed in this review, including the possible approaches for increasing selectivity and efficiency, for example, using a 100% aqueous mobile phase for the LC separation. In addition, applications for measuring (13)C isotopic enrichments using atmospheric pressure LC-MS instruments with a quadrupole, a time-of-flight, and an ion trap analyzer are also discussed as well as a LC-ICPMS using a prototype instrument with two quadrupoles.

Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil

Methane, which is an important greenhouse gas, is to a large part produced by methanogenic archaea in anoxic soils and sediments. Rice Cluster I methanogens have been characterized on the basis of their 16S rRNA and mcrA gene sequences, and were found to form a separate lineage within the phylogenetic radiation of Methanosarcinales and Methanomicrobiales. As isolation has not been achieved until recently, our knowledge of distribution, physiology and environmental significance of Rice Cluster I is solely based on molecular biology techniques. Rice Cluster I seems to be widely distributed, particularly in rice fields, possibly occupying different niches among the methane producers. One niche seems to be methane production on roots driven by plant photosynthesis, contributing substantially to the release of methane from rice fields into the atmosphere.