Isolation of a novel acidiphilic methanogen from an acidic peat bog

Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states

Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.

Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure

The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F₄₂₀ content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils

Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an ana­lysis of microbial communities using 16S rRNA gene sequencing and the mole­cular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH₄ production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.

Spatial distribution and biogeochemistry of redox active species in arctic sedimentary porewaters and seeps

Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn(II), Fe(II), O₂, and Fe(III)-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe(II) oxidation and reductive dissolution of Fe(III) and Mn(IV) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe(III) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe(II) and soluble Fe(III) in a highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle.

Bio-Based Processes for Material and Energy Production from Waste Streams under Acidic Conditions

The revolutionary transformation from petrol-based production to bio-based production is becoming urgent in line with the rapid industrialization, depleting resources, and deterioration of the ecosystem. Bio-based production from waste-streams is offering a sustainable and environmentally friendly solution. It offers several advantages, such as a longer operation period, less competition for microorganisms, higher efficiency, and finally, lower process costs. In the current study, several bio-based products (organic acids, biomethane, biohydrogen, and metal leachates) produced under acidic conditions are reviewed regarding their microbial pathways, processes, and operational conditions. Furthermore, the limitations both in the production process and in the scale-up are evaluated with future recommendations.

Effects of biochar on methane emission from paddy soil: Focusing on DOM and microbial communities

Biochar can be used as a soil amendment. However, it generally possesses unique physicochemical properties and complex organics, which could affect soil methanogenesis. In this study，straw-based biochars obtained at 300 °C (BC300), 500 °C (BC500) and 700 °C (BC700) were added to the paddy soil. Compared with the blank group, BC300 significantly increased paddy soil methane emissions by about 38%. However, this promoting effect gradually disappeared with the increase of pyrolysis temperature, and the inhibition even appeared in the BC700 group with the methane reduction by 18.2%. This might be related to the organics released from biochar. Van Krevelen (VK) diagram showed that the aromaticity of BC700 and BC500 were significantly higher than BC300. Fluorescent analysis further revealed that BC300 increased the amount of degradable fluorescent organics in the soil, which could provide more substrate for methane production. Moreover, as pyrolysis temperature increased, the fluorescent organics released were more likely to be non-biodegradable humus. In addition, it was shown that BC700 could adsorb some inherent organics in the soil, and thus reduced the total organic content and inhibited soil methane emissions. Microbial analysis showed that methanogenesis had a positive correlation with the abundance of syntrophic bacteria (e.g. Desulfobacca and Clostridium) which had ability to further degrade various types of organics and provided substrates to the methanogens. This article provides a deeper understanding regarding for the effects of biochar on methane emission from paddy soil in terms of organics and microbial perspectives.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Molecular and microbial insights towards understanding the effects of hydrochar on methane emission from paddy soil

Directly returning rice straw to the paddy soil would significantly stimulate methane emission, and hydrochar has potential to be used as soil conditioner. However, the effects of hydrochar on the methane emission from paddy soil and the related mechanisms are still unclear. In the present study, straw-based hydrochar obtained at 200 °C (HC200), 250 °C (HC250) and 300 °C (HC300) and hydrochar after removal of bio-oil at these temperatures (CHC200, CHC250, and CHC300) were prepared and added to the paddy soil. The application of HC200, HC250 and HC300 resulted in the enhanced methane production compared to the control, showing 4.3, 1.6 and 1.5-fold higher methane production, respectively. It was related to the large amount of dissolved organic matter (DOM) released from hydrochar. Excitation-emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC) showed that the hydrochar-derived DOM mainly included humic-like, phenolic and less aromatic structures, and with the increase of hydrothermal temperature, the content of humic-like substances and phenols increased, while biodegradable organics decreased. This was consistent with the maximum methane production by HC200. After incubation, there was no low-aromatic structures observed in the soil leachate, and the residual organics were mainly humus. The EEM-PARAFAC results were supported by compositional characterization of soil leachate by high-resolution mass spectrometry, and the refractory organics released from hydrochar was mainly lignins or (CRAM)-like structures in the range of H/C = 0.8-1.6 and O/C = 0.1-0.5. The organics dissolved from the washed hydrochar was significantly reduced, and some washed hydrochar (CHC250 and CHC300) even inhibited methane emission possibly due to their ability to adsorb organics. Microbial analysis further showed that the increased methane production resulted from hydrochar was associated with the enrichment of Janibacter, Anaeromyxobacter, Anaerolinea and Sporacetigenium. This present study provided a better understanding to the effect of hydrochar on methanogenesis in paddy soil.

A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor

Acid crisis characterized by acid accumulation and/or low pH is a common reason for the failure of anaerobic digestion (AD), which is usually applied for wastewater and waste treatment. Acid-tolerant methanogens are rarely reported to be active in the artificial anaerobic digester. In this study, we observed that the thermophilic methanogenesis by a consortium in the form of flocs and not granules could still be recovered during long-term operation at acetate concentration of up to 104 mM and pH 5.5 by adjusting the pH gradually or directly to pH 5.5 or 5.0. The acclimation process involving the gradual decrease in pH could enhance the resistance of the consortium against extreme acidification. The stable isotopic signature analysis of biogas revealed that Methanosarcina, which produced methane through acetoclastic methanogenesis (AM) pathway, was the predominant methane producer when the pH was decreased gradually to 5.0. Meanwhile, the abundance of Coprothermobacter increased with a decrease in pH. Contrastingly, when directly subjected to an environment of pH 5.5 and 104 mM acetate (15.84-mM free acetic acid) after a 42-day lag phase, Methanothermobacter was the predominant methanogen. Methanothermobacter initiated methane production through the hydrogenotrophic pathway and formed syntrophic relationship/consortium with the potential acetate-oxidizing bacteria, Thermacetogenium and Coprothermobacter. Comparative metagenomic and metatranscriptomic analysis on this self-adapted and acid-tolerant consortium revealed that the genes, such as GroEL, DnaK, CheY, and flagellum-related genes (FlaA, FlgE, and FliC) from Anaerobaculum, Thermacetogenium, and Coprothermobacter were highly overexpressed in response to system acidification. Microbial self-adaptation patterns (community structure adjustment, methanogenesis pathway shift, and transcriptional regulation) of thermophilic methanogenic consortium to gradual and sudden acidification were evaluated by integrated stable isotopic signature and comparative meta-omic approaches. The study elucidated the acid-resistant mechanism of thermophilic methanogenic consortium and deepened our knowledge of the function, interaction, and microbial characteristics of Methanosarcina, Methanothermobacter, and Coprothermobacter under extreme acidic environment.

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

Effect of different initial low pH conditions on biogas production, composition, and shift in the aceticlastic methanogenic population

Anaerobic digestion (AD) reactors often encounter low pH inhibition during startup and high organic loading periods. The use of a large amount of NaOH in order to raise and buffer the low pH, is reported to be inhibitory to methanogens. In order to address this problem, we acclimatized aceticlastic methanogens to low pH. Methanogens were successfully acclimatized to initial low pH down to 3.5 in a lengthy, five months, acclimatization period. The aceticlastic methanogen, Methanothrix soehngenii which was 96.3% of the total methanogenic population at pH 4.5 and 86.75% at pH 3.5, demonstrated that they were the most tolerant aceticlastic methanogens to low pH. After acclimatization, methane yield at pH 4.5 was comparable to neutral pH. Methanosaeta maintained its dominance over Methanosarcina at an elevated level of acetate (66 mM), and a negative correlation was observed between them. There was a positive correlation between the CH₄ content and pH.

A Real-Time Multiplexed Microbial Growth Intervalometer for Capturing High-Resolution Growth Curves

Batch cultures are a low maintenance and routine culturing method in microbiology. Automated tools that measure growth curves from microorganisms grown in traditional laboratory glassware, such as Balch-type tubes, are not commercially available. Here, we present a new MicrobiAl Growth Intervalometer (MAGI) that measures optical density as it correlates to microbial growth by utilizing photo-conduction as opposed to photo-attenuation used by traditional OD measurement equipment. Photo-attenuation occurs when biomass in suspension within a medium blocks and/or diffuses light directed at the detector, such that an increase in biomass results in a decrease in the measured signal. Photo-conduction differs in which the biomass contained in a medium conducts light from the emitter to the detector, where an increase in the biomass results in a corresponding increase in the measured signal. MAGI features software-driven automation that provides investigators with a highly sensitive, low-background noise growth measurement instrument with added capabilities for remote visualization and data acquisition. It is a low maintenance, cost effective, versatile, and robust platform for aerobic/anaerobic cultivation. We demonstrate the versatility of this device by obtaining growth curves from two common laboratory organisms Escherichia coli K-12 and Bacillus subtilis. We show that growth rates and generation times in E. coli K-12 are reproducible to previously published results and that morphological changes of B. subtilis during growth can be detected as a change in the slope of the growth curve, which is a function of the effects of cell size on photo-conduction through the medium. We also test MAGI to capture growth curves from an environmental organism, Intrasporangium calvum C5, under various media compositions. Our results demonstrate that the MAGI platform accurately measures growth curves in media under various redox conditions (aerobic, microaerobic, and anaerobic), complex and minimal medias, and resolving diauxic growth curves when I. calvum is grown on a disaccharide. Lastly, we demonstrate that the device can resolve growth curves for μM concentrations of resources that yield low biomass. This research advances the tools available to microbiologists aiming to monitor growth curves in a variety of disciplines, such as environmental microbiology, clinical microbiology, and food sciences.

Applying bio-electric field of microbial fuel cell-upflow anaerobic sludge blanket reactor catalyzed blast furnace dusting ash for promoting anaerobic digestion

In this study, a novel manner of bio-electric field (BEF) which generated by upflow anaerobic sludge blanket (UASB)-microbial fuel cell (MFC) integrated system facilitated iron-carbon micro-electrolysis in blast furnace dusting ash (BFDA) was proposed for the reinforcement of anaerobic digestion in UASB. The responses of COD removal efficiency and biogas production with (0.1-0.4 V) BEF catalyzed 5 g BFDA(R_{MFC-5gBFDA-UASB}) were much higher than the other tests, and maximum reached 86% and 240 ml/d respectively. Ultra-fast acidogenesis was achieved with 0.3 V BEF supplied to BFDA and the time shortened 94 h compared controlled (R_UASB) with R_{MFC-5gBFDA-UASB}. With the electrochemical and microbial community analysis, the redox ability and direct interspecies electron transfer accumulated with BEF catalyzed. The abundance of Firmicutes which could generate bio-hydrogen was highest in R_{MFC-5gBFDA-UASB} (44.58%) compared to R_UASB (31.36%) and R_5gBFDA-UASB (40.04%). In addition, the structure and morphology variation of BFDA revealed that the synergistic effects of BEF stimulated iron-carbon micro-electrolysis for electron transferring and enhanced the activities of methanogens and acetogens with high relative abundance to biotransform organic compounds, as well as adsorption and precipitation of iron oxides (hematite and magnetite) promoting anaerobic digestion. The MFC-BFDA-UASB integrated system provides a promising and cost-effective way to enhance anaerobic digestion and recycled functionalized waste effectively.

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities

In lotic ecosystems highly susceptible to anthropogenic activities, the influences of environmental variables on microbial communities and their functions remain poorly understood, despite our rapidly increasing sequencing ability. In this study, we profiled the microbial communities in the hyporheic sediments of a watershed undergoing intensive anthropogenic activities via next-generation sequencing of 16S rRNA V4-V5 hypervariable regions on Illumina MiSeq platform. Tidal impacts on microbial communities were investigated via co-occurrence networks. In addition, the influences of physicochemical variables including salinity, and the concentrations of nutrients, organic matter and heavy metals on the microbial communities were explored via canonical correspondence analyses. The sediment samples were collected from 19 sites covering the whole main river stem of the target watershed (n = 19; Maozhou river watershed, Shenzhen, China). The samples were sub-divided in the field for microbiological analyses and measurements of physicochemical variables. The results indicated that core microbiome was associated with archaea methanogens and bacteria members from Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Synergistetes and Firmicutes, among which, gram-negative and anaerobic bacteria genera contributing to the cycling of carbon, nitrogen and sulfur were predominant. Site-specific microbiomes were revealed that may serve as indicators of local environmental conditions (e.g., members affiliated to Oceanospirillales were abundant at sites with salt intrusion). Distinct microbial co-occurrence networks were identified for non-tidal, inter-tidal and tidal sites. Major environmental factors influencing microbial community composition included the concentrations of nitrate and bicarbonate in river water, pore water concentrations of sulfate, dissolved organic carbon and electrical conductivity, as well as manganese concentrations associated with the solid sediment. Collectively, the results of this study provide fundamental insights into the influence of environmental perturbations on microbial community composition in a lotic system, which may aid in the design of effective remediation and/or restoration strategies in the target watershed and beyond.

Methanogens: biochemical background and biotechnological applications

Since fossil sources for fuel and platform chemicals will become limited in the near future, it is important to develop new concepts for energy supply and production of basic reagents for chemical industry. One alternative to crude oil and fossil natural gas could be the biological conversion of CO2 or small organic molecules to methane via methanogenic archaea. This process has been known from biogas plants, but recently, new insights into the methanogenic metabolism, technical optimizations and new technology combinations were gained, which would allow moving beyond the mere conversion of biomass. In biogas plants, steps have been undertaken to increase yield and purity of the biogas, such as addition of hydrogen or metal granulate. Furthermore, the integration of electrodes led to the development of microbial electrosynthesis (MES). The idea behind this technique is to use CO2 and electrical power to generate methane via the microbial metabolism. This review summarizes the biochemical and metabolic background of methanogenesis as well as the latest technical applications of methanogens. As a result, it shall give a sufficient overview over the topic to both, biologists and engineers handling biological or bioelectrochemical methanogenesis.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

About half of the global methane (CH₄ ) 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 CH₄ 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.

Distinct and diverse anaerobic respiration of methanogenic community in response to MnO2 nanoparticles in anaerobic digester sludge

Recently, the influence of metal oxide nanoparticles (NPs) on methanogenesis in anaerobic digestion has drawn much attention, however, the changes in NPs and functioning consortia within the methanogenic community are usually not investigated. Therefore, the methanogenesis performance, NPs transformation and methanogenic community development in anaerobic digester sludge under MnO₂ NP supplementation were demonstrated in this study. MnO₂ NPs (400 mg/gVSS) stimulated the methane (CH₄) yield by 42% for a final CH₄ proportion of 81.8% of the total gas production. Meanwhile, the coenzyme F₄₂₀ and INT-electron transport system activities showed positive correlation with MnO₂ concentration. Microbial Mn reduction and oxidation occurred in conjunction with methanogenesis, resulting in transformation of the shape of the MnO₂ NPs from wire-like to globular particles. Microbial community analysis indicated that the relative abundances of genera Methanobacterium, Methanosaeta, and Methanosarcina were higher in the presence of MnO₂ NPs. Moreover, a new and different crucial synergy within the methanogenic community was formed with low-abundance consortia driving Mn respiration coupled to methanogenesis in anaerobic digestion. To our knowledge, this is the first report on transformation of metal oxides NPs combined with syntrophic community development in studies focusing on methanogenesis in response to NPs.

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain

As surface temperatures are expected to rise in the future, ice-rich permafrost may thaw, altering soil topography and hydrology and creating a mosaic of wet and dry soil surfaces in the Arctic. Arctic wetlands are large sources of CH₄ , and investigating effects of soil hydrology on CH₄ fluxes is of great importance for predicting ecosystem feedback in response to climate change. In this study, we investigate how a decade-long drying manipulation on an Arctic floodplain influences CH₄ -associated microorganisms, soil thermal regimes, and plant communities. Moreover, we examine how these drainage-induced changes may then modify CH₄ fluxes in the growing and nongrowing seasons. This study shows that drainage substantially lowered the abundance of methanogens along with methanotrophic bacteria, which may have reduced CH₄ cycling. Soil temperatures of the drained areas were lower in deep, anoxic soil layers (below 30 cm), but higher in oxic topsoil layers (0-15 cm) compared to the control wet areas. This pattern of soil temperatures may have reduced the rates of methanogenesis while elevating those of CH₄ oxidation, thereby decreasing net CH₄ fluxes. The abundance of Eriophorum angustifolium, an aerenchymatous plant species, diminished significantly in the drained areas. Due to this decrease, a higher fraction of CH₄ was alternatively emitted to the atmosphere by diffusion, possibly increasing the potential for CH₄ oxidation and leading to a decrease in net CH₄ fluxes compared to a control site. Drainage lowered CH₄ fluxes by a factor of 20 during the growing season, with postdrainage changes in microbial communities, soil temperatures, and plant communities also contributing to this reduction. In contrast, we observed CH₄ emissions increased by 10% in the drained areas during the nongrowing season, although this difference was insignificant given the small magnitudes of fluxes. This study showed that long-term drainage considerably reduced CH₄ fluxes through modified ecosystem properties.

A Modified Approach for in Situ Chemical Oxidation Coupled to Biodegradation Enhances Light Nonaqueous Phase Liquid Source-Zone Remediation

Field and batch experiments were conducted to assess whether a modified approach for in situ chemical oxidation (ISCO) (with MgO₂ and Fe₂O₃ particles recovered from acid mine drainage treatment) can enhance LNAPL (light nonaqueous phase liquid) dissolution and produce bioavailable soluble compounds. This modified ISCO approach was coupled to biodegradation to further remove residual compounds by microbially mediated processes. Pure palm biodiesel (B100) was chosen to represent a poorly water-soluble compound that behaves like LNAPLs, and 100 L was released to a 2 m² area excavated down to the water table. A past adjacent B100-field experiment under natural attenuation was conducted as a baseline control. Results demonstrated the enhancement of organic compound dissolution and production of soluble compounds due to the modified in situ chemical oxidation. The slow release of H₂O₂ by MgO₂ decomposition (termed partial chemical oxidation) and production of soluble compounds allowed the stimulation of microbial growth and promoted a beneficial response in microbial communities involved in oxidized biodiesel compound biodegradation. This is the first field experiment to demonstrate that this modified ISCO approach coupled to biodegradation could be a feasible strategy for the removal of poorly water-soluble compounds (e.g., biodiesel) and prevent the long-term effects generally posed in source zones.

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H₂-CO₂ utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H⁺ rather than Na⁺ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na⁺ and H⁺ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume

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.

Effect of influent COD/SO4(2-) ratios on UASB treatment of a synthetic sulfate-containing wastewater

The effect of the chemical oxygen demand/sulfate (COD/SO4(2-)) ratio on the anaerobic treatment of synthetic chemical wastewater containing acetate, ethanol, and sulfate, was investigated using a UASB reactor. The experimental results show that at a COD/SO4(2-) ratio of 20 and a COD loading rate of 25.2gCODL(-1)d(-1), a COD removal of as high as 87.8% was maintained. At a COD/SO4(2-) ratio of 0.5 (sulfate concentration 6000mgL(-1)), however, the COD removal was 79.2% and the methane yield was 0.20LCH4gCOD(-1). The conversion of influent COD to methane dropped from 80.5% to 54.4% as the COD/SO4(2-) ratio decreased from 20 to 0.5. At all the COD/SO4(2-) ratios applied, over 79.4% of the total electron flow was utilized by methane-producing archaea (MPA), indicating that methane fermentation was the predominant reaction. The majority of the methane was produced by acetoclastic MPA at high COD/SO4(2-) ratios and both acetoclastic and hydrogenthrophic MPA at low COD/SO4(2-) ratios. Only at low COD/SO4(2-) ratios were SRB species such as Desulfovibrio found to play a key role in ethanol degradation, whereas all the SRB species were found to be incomplete oxidizers at both high and low COD/SO4(2-) ratios.

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

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 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.

Microbially influenced corrosion communities associated with fuel-grade ethanol environments

Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these “newer fuels” as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

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

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.

Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments

Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette

Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. (13)CO2 mofette soil incubations showed high label incorporations with ∼512 ng (13)C g (dry weight (dw)) soil(-1) d(-1) into the bulk soil and up to 10.7 ng (13)C g (dw) soil(-1) d(-1) into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of (13)CO2. Subdivision 1 Acidobacteriaceae assimilated (13)CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.

Southern Appalachian peatlands support high archaeal diversity

Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.

Sulfate reduction at low pH to remediate acid mine drainage

Industrial activities and the natural oxidation of metallic sulfide-ores produce sulfate-rich waters with low pH and high heavy metals content, generally termed acid mine drainage (AMD). This is of great environmental concern as some heavy metals are highly toxic. Within a number of possibilities, biological treatment applying sulfate-reducing bacteria (SRB) is an attractive option to treat AMD and to recover metals. The process produces alkalinity, neutralizing the AMD simultaneously. The sulfide that is produced reacts with the metal in solution and precipitates them as metal sulfides. Here, important factors for biotechnological application of SRB such as the inocula, the pH of the process, the substrates and the reactor design are discussed. Microbial communities of sulfidogenic reactors treating AMD which comprise fermentative-, acetogenic- and SRB as well as methanogenic archaea are reviewed.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO₂) and methane (CH₄) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH₄ or CO₂ production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.

Pyrosequencing reveals the key microorganisms involved in sludge alkaline fermentation for efficient short-chain fatty acids production

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.

Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales

Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models.

Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration

Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.