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Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH ₄) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH ₄ production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH ₄ production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH ₄ production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H ₂-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae . Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH ₄ is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa. Significance Microorganisms are key players in emissions of the greenhouse gas (GHG) methane from anoxic carbon-rich peat soils of the Arctic permafrost region. Although available data and modeling suggest a significant temperature-induced increase of GHG emissions from these regions by the end of this century, the controls of and interactions within the underlying microbial networks are largely unknown. This temperature-gradient study of an Arctic peat soil using integrated omics techniques reveals critical temperatures at which microbial adaptations cause changes in metabolic bottlenecks of anaerobic carbon-degradation pathways. In particular taxonomic shifts within functional guilds at different levels of the carbon degradation cascade enable a fast adaptation of the microbial system resulting in high methane emissions at all temperatures.

Anaerobic digestion is considered a key technology for the future bio-based economy. The microbial consortium carrying out the anaerobic digestion process is quite complex, and its exact role in terms of “elasticity”, i.e., the ability to rapidly adapt to changing conditions, is still unknown. In this study, the role of the initial microbial community in terms of operational stability and stress tolerance was evaluated during a 175-day experiment. Five different inocula from stable industrial anaerobic digesters were fed a mixture of waste activated sludge and glycerol. Increasing ammonium pulses were applied to evaluate stability and stress tolerance. A different response in terms of start-up and ammonium tolerance was observed among the different inocula. Methanosaetaceae were the dominant acetoclastic methanogens, yet, Methanosarcinaceae increased in abundance at elevated ammonium concentrations. A shift from a Firmicutes to a Proteobacteria dominated bacterial community was observed in failing digesters. Methane production was strongly positively correlated with Methanosaetaceae , but also with Bacteria related to Anaerolinaceae , Clostridiales , and Alphaproteobacteria . Volatile fatty acids were strongly positively correlated with Betaproteobacteria and Bacteroidetes , yet ammonium concentration only with Bacteroidetes . Overall, these results indicate the importance of inoculum selection to ensure stable operation and stress tolerance in anaerobic digestion.

Ammonia is a major environmental factor influencing biomethanation in full-scale anaerobic digesters. In this study, the effect of different ammonia levels on methanogenic pathways and methanogenic community composition of full-scale biogas plants was investigated. Eight full-scale digesters operating under different ammonia levels were sampled, and the residual biogas production was followed in fed-batch reactors. Acetate, labelled in the methyl group, was used to determine the methanogenic pathway by following the 14 CH 4 and 14 CO 2 production. Fluorescence in situ hybridisation was used to determine the methanogenic communities’ composition. Results obtained clearly demonstrated that syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis was the dominant pathway in all digesters with high ammonia levels (2.8–4.57 g NH 4 + -N L −1 ), while acetoclastic methanogenic pathway dominated at low ammonia (<1.21 g NH 4 + -N L −1 ). Thermophilic Methanomicrobiales spp. and mesophilic Methanobacteriales spp. were the most abundant methanogens at free ammonia concentrations above 0.44 g NH 3 -N L −1 and total ammonia concentrations above 2.8 g NH 4 + -N L −1 , respectively. Meanwhile, in anaerobic digesters with low ammonia (<1.21 g NH 4 + -N L −1 ) and free ammonia (<0.07 g NH 3 -N L −1 ) levels, mesophilic and thermophilic Methanosaetaceae spp. were the most abundant methanogens.

Among different conversion processes for biomass, biological anaerobic digestion is one of the most economic ways to produce biogas from various biomass substrates. In addition to hydrolysis of polymeric substances, the activity and performance of the methanogenic bacteria is of paramount importance during methanogenesis. The aim of this paper is primarily to review the recent literature about the occurrence of both acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of particulate biomass to methane (not wastewater treatment), while this review does not cover the activity of the acetate oxidizing bacteria. Both acetotrophic and hydrogenotrophic methanogens are essential for the last step of methanogenesis, but the reports about their roles during this phase of the process are very limited. Despite, some conclusions can still be drawn. At low concentrations of acetate, normally filamentous Methanosaeta species dominate, e.g., often observed in sewage sludge. Apparently, high concentrations of toxic ionic agents, like ammonia, hydrogen sulfide (H 2 S) and volatile fatty acids (VFA), inhibit preferably Methanosaetaceae and especially allow the growth of Methanosarcina species consisting of irregular cell clumps, e.g., in cattle manure. Thermophilic conditions can favour rod like or coccoid hydrogenotrophic methanogens. Thermophilic Methanosarcina species were also observed, but not thermophilic Methanosaetae. Other environmental factors could favour hydrogentrophic bacteria, e.g., short or low retention times in a biomass reactor. However, no general rules regarding process parameters could be derivated at the moment, which favours hydrogenotrophic methanogens. Presumably, it depends only on the hydrogen concentration, which is generally not mentioned in the literature.

The search for renewable energies has been one of the biggest challenges of the last decades. Sludge and solid wastes of many sources have been used to produce biogas of high calorific value. Thus, this work aimed to evaluate the biogas production of solid waste originating from a tannery that uses chromium salts as a tanning agent and to characterize the physicochemical parameters and microbial composition of the biogas-producing biomass. Wastes were collected and the parameters were evaluated at the initial and final time points of the anaerobic incubation process. At the end of 150 days, there was a production of 26.1 mL g−1 VSS of biogas with 52% of methane. The highest amount of biomethane observed was related to the archaeal family Methanosaetaceae and bacterial order Bacteroidales. Knowledge about changes in the microbial composition can provide tools for manipulation, isolation, and inoculation of the microorganisms inside the bioreactors to maximize methane production.

We studied the methanogenic pathway and archaeal community composition in the sediment of two clearwater lakes, Lake Batata and Lake Mussura, in Amazonia. We measured CH sub(4) production and d super(13)C of CO sub(2), CH sub(4), and acetate-methyl in the presence and absence of CH sub(3)F, an inhibitor of acetotrophic methanogenesis. The fractionation factor of methanogenesis from CO sub(2) was rather high in both lake sediments, which was consistent with the low concentrations of H sub(2) and the small negative Gibbs free energy of hydrogenotrophic methanogenesis. The d super(13)C of acetate-methyl was relatively low compared to that of organic matter and decreased further upon inhibition of acetate consumption by CH super(3)F. Collectively, the data possibly suggest involvement of syntrophic acetate oxidation besides acetotrophic methanogenesis. The isotopic data were used to calculate the percent contribution of CO super(2) reduction to total methanogenesis, which was rather high (approximately 53-63%). Copy numbers of bacterial and archaeal 16S ribosomal ribonucleic acid (rRNA) genes were about 10-fold higher in Lake Mussura than in Lake Batata, indicating that microbial numbers were not a limiting factor for production rates of CH super(4), which were similar in both lake sediments. The composition of the archaeal community was analyzed by cloning and sequencing of the genes coding for 16S rRNA and methyl coenzyme M reductase (mcrA), demonstrating the presence of acetotrophic Methanosaetaceae and different hydrogenotrophic methanogenic orders (Methanomicrobiales, Methanobacteriales, Methanocellales) in both lake sediments. Although methanogenic communities and pathways were principally comparable to those found in lake sediments of the midlatitudes, there were several particularities, e.g., the possible involvement of syntrophic acetate oxidation.

Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3− through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

Background The fact that microalgae perform very efficiently photosynthetic conversion of sunlight into chemical energy has moved them into the focus of regenerative fuel research. Especially, biogas generation via anaerobic digestion is economically attractive due to the comparably simple apparative process technology and the theoretical possibility of converting the entire algal biomass to biogas/methane. In the last 60 years, intensive research on biogas production from microalgae biomass has revealed the microalgae as a rather challenging substrate for anaerobic digestion due to its high cell wall recalcitrance and unfavorable protein content, which requires additional pretreatment and co-fermentation strategies for sufficient fermentation. However, sustainable fuel generation requires the avoidance of cost/energy intensive biomass pretreatments to achieve positive net-energy process balance. Results Cultivation of microalgae in replete and limited nitrogen culture media conditions has led to the formation of protein-rich and low protein biomass, respectively, with the last being especially optimal for continuous fermentation. Anaerobic digestion of nitrogen limited biomass (low-N BM) was characterized by a stable process with low levels of inhibitory substances and resulted in extraordinary high biogas, and subsequently methane productivity [750 ± 15 and 462 ± 9 mLN g−1 volatile solids (VS) day−1, respectively], thus corresponding to biomass-to-methane energy conversion efficiency of up to 84%. The microbial community structure within this highly efficient digester revealed a clear predominance of the phyla Bacteroidetes and the family Methanosaetaceae among the Bacteria and Archaea, respectively. The fermentation of replete nitrogen biomass (replete-N BM), on the contrary, was demonstrated to be less productive (131 ± 33 mLN CH4 g−1VS day−1) and failed completely due to acidosis, caused through high ammonia/ammonium concentrations. The organization of the microbial community of the failed (replete-N) digester differed greatly compared to the stable low-N digester, presenting a clear shift to the phyla Firmicutes and Thermotogae, and the archaeal population shifted from acetoclastic to hydrogenotrophic methanogenesis. Conclusions The present study underlines the importance of cultivation conditions and shows the practicability of microalgae biomass usage as mono-substrate for highly efficient continuous fermentation to methane without any pretreatment with almost maximum practically achievable energy conversion efficiency (biomass to methane).

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH 4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH 4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH 4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

The aim of this study was to determine the impact of using mineral fertilizers on biogas production from vegetable waste. A mixture of wastes from a fruit and vegetable processing plant was used in the experiments, together with two commercial fertilizers, Substral and Agrecol. Experiments were conducted in 5-L anaerobic reactors operated semi-continuously at 35 °C. The application of Substral at a dose of 1 g/kg increased the production of methane and hydrogen by 40% and 78%, up to 420 LCH4/kgVS and 34 LH2/kgVS, respectively. In contrast, with Agrecol supplementation, the average yields of methane and hydrogen were 365 LCH4/kgVS and 27.7 LH2/kgVS, respectively. The beneficial effects of supplementation were due to the compositions of the mineral fertilizers, which contained nutrients and metals that stimulate the growth of microorganisms and build the structures of enzymes. The addition of mineral fertilizers changed the microbial communities of the digestates. At a family level, the main bacteria groups reported were Lactobacillaceae, Anaerolineaceae, Clostridiaceae, Synergistaceae, and Bacteroidetes vadin HA17. The predominant methanogens were Methanosarcinaceae and Methanosaetaceae. There was no clear relationship between the supplementation type and dose and the growth of individual microbial groups. However, the addition of mineral fertilizers increased the relative abundance of Lactobacillaceae and Anaerolineaceae, which are responsible for the hydrolysis and fermentation of polysaccharides into lactic acid, hydrogen, and acetic acid.