Methanogenic archaea database containing physiological and biochemical characteristics

Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments

Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.

Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

Scale-up of biomass production by Methanococcus maripaludis

The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD₅₇₈) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h^-1 and the highest recorded OD₅₇₈ of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.

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.

Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review

In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.

Long-Term Assessment of Temperature Management in an Industrial Scale Biogas Plant

Temperature management is one of the primary considerations of biogas plant operation, and influences physical and biochemical processes. An increase in the temperature leads to an increase in the hydrolysis rate of the feedstock, while it can inhibit microorganisms taking part in different stages of anaerobic digestion. Because of the complexity of the biochemical processes within the anaerobic digestion process, there is a lack of knowledge about the effects of temperature and temperature change on efficiency. Moreover, the impact of stirring directly affects the temperature distribution in the anaerobic digestion reactors. In this study, the temperature management in an industrial-scale biogas plant was examined, and the effect of small temperature changes (from the operation temperature 42 °C) on the efficiency was studied in a laboratory under two different conditions: with stirring (at 40 and 44 °C) and without stirring (at 40 and 44 °C). The examination results from the biogas plant showed that heat transfer in the reactor was not sufficient at the bottom of the digester. Adaptation of the post-digester samples to the temperature changes was more challenging than that of the digester samples. From digestate samples, higher biomethane generation could be obtained, resulting from sufficient contact between microorganisms, enzymes, and substrates. Overall, differences between these changing conditions (approx. 6 NmL CH4 g VS−1) were not significant and could be adapted by the process.

Effect of low-thermal pretreatment on the methanogenic performance and microbiome population of continuous high-solid anaerobic digester treating dewatered sludge

Undigested and dewatered sludge at 10% total solids was pretreated at 60 °C for 3 h and fed to a lab-scale horizontal anaerobic bioreactor for 130 days with solids retention time (SRTs) from 25 to 16 d. The low-thermal pretreatment enabled higher net energy production, improved sludge treatment efficiency, and enhanced digestion stability. The highest average biomethane yield and production rate were 138.5 mL/g VS and 0.43 L/L.d, respectively, and the economic benefit was expected to be the maximum at SRT 16 d. Pretreatment did not increase the specific methanogenic activity per unit methanogen, but resulted in higher abundance of methanogenic archaea and hydrolytic bacteria. Methanogenic population shifted from hydrogenotrophic to acetoclastic, consistent with predicted gene expression at SRT equal or below 20 d. Anaerobic digestion along with low-thermal could be a feasible management strategy for undigested dewatered sludge from small WWTPs.

Understanding methane emission from stored animal manure: A review to guide model development

National inventories of methane (CH₄ ) emission from manure management are based on guidelines from the Intergovernmental Panel on Climate Change using country-specific emission factors. These calculations must be simple and, consequently, the effects of management practices and environmental conditions are only crudely represented in the calculations. The intention of this review is to develop a detailed understanding necessary for developing accurate models for calculating CH₄ emission from liquid manure, with particular focus on the microbiological conversion of organic matter to CH₄ . Themes discussed are (a) the liquid manure environment; (b) methane production processes from a modeling perspective; (c) development and adaptation of methanogenic communities; (d) mass and electron conservation; (e) steps limiting CH₄ production; (f) inhibition of methanogens; (g) temperature effects on CH₄ production; and (h) limits of existing estimation approaches. We conclude that a model must include calculation of microbial response to variations in manure temperature, substrate availability and age, and management system, because these variables substantially affect CH₄ production. Methane production can be reduced by manipulating key variables through management procedures, and the effects may be taken into account by including a microbial component in the model. When developing new calculation procedures, it is important to include reasonably accurate algorithms of microbial adaptation. This review presents concepts for these calculations and ideas for how these may be carried out. A need for better quantification of hydrolysis kinetics is identified, and the importance of short- and long-term microbial adaptation is highlighted.

A mechanistic model of methane emission from animal slurry with a focus on microbial groups

Liquid manure (slurry) from livestock releases methane (CH4) that contributes significantly to global warming. Existing models for slurry CH4 production-used for mitigation and inventories-include effects of organic matter loading, temperature, and retention time but cannot predict important effects of management, or adequately capture essential temperature-driven dynamics. Here we present a new model that includes multiple methanogenic groups whose relative abundance shifts in response to changes in temperature or other environmental conditions. By default, the temperature responses of five groups correspond to those of four methanogenic species and one uncultured methanogen, although any number of groups could be defined. We argue that this simple mechanistic approach is able to describe both short- and long-term responses to temperature where other existing approaches fall short. The model is available in the open-source R package ABM (https://github.com/sashahafner/ABM) as a single flexible function that can include effects of slurry management (e.g., removal frequency and treatment methods) and changes in environmental conditions over time. Model simulations suggest that the reduction of CH4 emission by frequent emptying of slurry pits is due to washout of active methanogens. Application of the model to represent a full-scale slurry storage tank showed it can reproduce important trends, including a delayed response to temperature changes. However, the magnitude of predicted emission is uncertain, primarily as a result of sensitivity to the hydrolysis rate constant, due to a wide range in reported values. Results indicated that with additional work-particularly on the magnitude of hydrolysis rate-the model could be a tool for estimation of CH4 emissions for inventories.

Integration of Artificial Intelligence into Biogas Plant Operation

In the biogas plants, organic material is converted to biogas under anaerobic conditions through physical and biochemical processes. From supply of the raw material to the arrival of the products to customers, there are serial processes which should be sufficiently monitored for optimizing the efficiency of the whole process. In particular, the anaerobic digestion process, which consists of sequential complex biological reactions, requires improved monitoring to prevent inhibition. Conventional implemented methods at the biogas plants are not adequate for monitoring the operational parameters and finding the correlation between them. As Artificial Intelligence has been integrated in different areas of life, the integration of it into the biogas production process will be inevitable for the future of the biogas plant operation. This review paper first examines the need for monitoring at the biogas plants with giving details about the process and process monitoring as well. In the following sections, the current situation of implementations of Artificial Intelligence in the biogas plant operation and in the similar industries will be represented. Moreover, considering that all the information gathered from literature and operational needs, an implementation model will be presented.

Insight into the intestinal microbiome of farrowing sows following the administration of garlic (Allium sativum) extract and probiotic bacteria cultures under farming conditions

Background

Due to the tendency to reduce antibiotic use in humans and animals, more attention is paid to feed additives as their replacement. Crucial role of feed additives is to improve the health status, production efficiency and performance. In this original research, we estimate the potential influence of garlic (Allium sativum) extract and probiotic formula including Enterococcus faecium, Lactobacillus rhamnosus and Lactobacillus fermentum on the intestinal microbiota of sows, using the next generation sequencing method (NGS).

Results

Our results indicate that the overall species richness as well as the composition of swine gut microbiota may be shaped by regular feeding with supplemented additives. On the Family and Genus level both additives (garlic extract and probiotics) seem to decrease microbiome diversity and richness. However, when it comes to garlic supplementation, we found the opposite trend on the Species level.

Conclusions

The analysis of the selected microbial function indicates that both additives used in this study (garlic extract and composition of probiotics) seem to create a greater metabolic potential than estimated in a control group of sows. A general trend of losing or decreasing members of pathogenic species in the swine microbiome seems to occur in relation to both supplemented additives. In the prevention of some bacterial diseases supplemented additives could be considered for future use.

An Unexpectedly Broad Thermal and Salinity-Tolerant Estuarine Methanogen Community

Moderately thermophilic (T_max, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (T_opt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (<48 h) revealing methanogens with optimal activity reaching 70 °C in a temperate estuary sediment (in situ temperature 4–5 °C). While 30 °C enrichments amended with acetate, H₂ or methanol selected for corresponding mesophilic trophic groups, at 60 °C, only hydrogenotrophs (genus Methanothermobacter) were observed. Since these methanogens are not known to be active under in situ temperatures, we conclude constant dispersal from high temperature habitats. The likely provenance of the thermophilic methanogens was studied by enrichments covering a range of temperatures and salinities. These enrichments indicated that the estuarine sediment hosted methanogens encompassing the global activity envelope of most cultured species. We suggest that estuaries are fascinating sink and source environments for microbial function study.

Operational Parameters of Biogas Plants: A Review and Evaluation Study

The biogas production technology has improved over the last years for the aim of reducing the costs of the process, increasing the biogas yields, and minimizing the greenhouse gas emissions. To obtain a stable and efficient biogas production, there are several design considerations and operational parameters to be taken into account. Besides, adapting the process to unanticipated conditions can be achieved by adequate monitoring of various operational parameters. This paper reviews the research that has been conducted over the last years. This review paper summarizes the developments in biogas design and operation, while highlighting the main factors that affect the efficiency of the anaerobic digestion process. The study’s outcomes revealed that the optimum operational values of the main parameters may vary from one biogas plant to another. Additionally, the negative conditions that should be avoided while operating a biogas plant were identified.

Selective Enrichment of Clostridium Spp. by Nutrition Control from Sihe Coal Geological Microbial Communities

In the coal biogasification, butyric acid is an important intermediate product. The enrichment of butyric acid-producing bacteria in coal geological methanogens is critical to confirm this assertion. Therefore, to study a method for enrichment of butyric acid-producing bacteria and to explore characteristic factors for evaluating the enrichment effect would be the basis for further strain isolation and metabolomics research. In this study, the nutrition control method was used for the butyric acid-producing bacteria enrichment from concentrated bacteria solution in Sihe coal seam. The characteristic factors' changes in gas production, gas composition, butyric acid concentration, and pH were observed and analyzed in the experiment. High-throughput sequencing was used as a verification method to validate the medium and genera enrichment effect that can be used for the butyric acid-producing bacteria. Through experimental research and analysis, it was identified that the glucose-sucrose-maltose medium was the beneficial medium to the enrichment of butyric acid-producing bacteria, and the high-throughput sequencing determined that the enriched genera were Clostridium spp. Glucose-sucrose-maltose medium experimental data confirmed that the decrease of CO₂ and H₂ daily yield, the increase of butyric acid concentration, and the decrease of pH value had a significant positive correlation with the enrichment of Clostridium spp.

A synthesis of bacterial and archaeal phenotypic trait data

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources

Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.

Volatile Fatty Acids Production from Microalgae Biomass: Anaerobic Digester Performance and Population Dynamics during Stable Conditions, Starvation, and Process Recovery

Disturbances in anaerobic digestion (AD) negatively impact the overall reactor performance. These adverse effects have been widely investigated for methane generation. However, AD recently appeared as a potential technology to obtain volatile fatty acids (VFAs) and thus, the impact of process disturbances must be evaluated. In this sense, microbial response towards a starvation period of two weeks was investigated resulting in a conversion of organic matter into VFAs of 0.39 ± 0.03 COD-VFAs/CODin. However, the lack of feeding reduced the yield to 0.30 ± 0.02 COD-VFAs/CODin. Microbial analysis revealed that the starvation period favored the syntrophic acetate-oxidizing bacteria coupled with hydrogenotrophic methanogens. Finally, the system was fed at 9 g COD/Ld resulting in process recovery (0.39 ± 0.04 COD-VFAs/CODin). The different microbiome obtained at the end of the process was proved to be functionally redundant, highlighting the AD robustness for VFAs production.

Rabbit manure as a potential inoculum for anaerobic digestion

The potential of using rabbit manure as inoculum for biogas production was evaluated through batch assays using bean straw as substrate. The microbial diversity in the rabbit manure included lignin-degrading bacteria (classes Bacteroidia, Bacilli and Clostridia) as well as key acetoclastic (Matheanosarcina and Methanosaeta), and hydrogenotrophic (Methanobacterium, Methanolinea, and Methanovebribacter) archaea. The effects of particle size, substrate to inoculum ratio (S/X) and pH adjustment were studied to improve the inoculum activity. The adjustment of the pH entailed the highest improvement in methane production (515%) and rate (164%). However, high S/X, (3-4), resulted in the acidification of the processes, denoting an imbalance between hydrolytic bacteria and methanogenic archaea in the rabbit manure. This confirmed that the use of rabbit manure as inoculum could sustain anaerobic digestion from agricultural residues, although a proper enrichment and adaptation is necessary to ensure an appropriate methane production.

Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions

Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g^-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

BACKGROUND

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

RESULTS

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

CONCLUSIONS

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.

Effect of Mechanical Pre-Treatment of the Agricultural Substrates on Yield of Biogas and Kinetics of Anaerobic Digestion

The effect of mechanical pre-treatment of nine different agricultural substrates minced to particle sizes of 1.5 mm, 5 mm and 10 mm on biogas and methane yields and fermentation kinetics was investigated. The results showed, that for five of the nine tested substrates (grass, Progas rye, Palazzo rye, tall wheatgrass, beet), a higher biogas production was obtained for the degree of fragmentation of 10 mm compared to fragmentation of 5 mm and 1.5 mm. For fragmentation of 5 mm, the highest biogas production was achieved for sorghum silage, Atletico maize and Cannavaro maize—649.80, 735.59 and 671.83 Nm3/Mg VS, respectively. However, for the degree of fragmentation of 1.5 mm, the highest biogas production (510.43 Nm3/Mg volatile solid (VS)) was obtained with Topinambur silage. The modified Gompertz model fitted well the kinetics of anaerobic digestion of substrates and show a significant dependence of the model parameters Hmax (biogas production potential) and Rmax (maximum rate of biogas production) on the degree of substrate fragmentation.

Physiology and methane productivity of Methanobacterium thermaggregans

Accumulation of carbon dioxide (CO2), associated with global temperature rise, and drastically decreasing fossil fuels necessitate the development of improved renewable and sustainable energy production processes. A possible route for CO2 recycling is to employ autotrophic and hydrogenotrophic methanogens for CO2-based biological methane (CH4) production (CO2-BMP). In this study, the physiology and productivity of Methanobacterium thermaggregans was investigated in fed-batch cultivation mode. It is shown that M. thermaggregans can be reproducibly adapted to high agitation speeds for an improved CH4 productivity. Moreover, inoculum size, sulfide feeding, pH, and temperature were optimized. Optimization of growth and CH4 productivity revealed that M. thermaggregans is a slightly alkaliphilic and thermophilic methanogen. Hitherto, it was only possible to grow seven autotrophic, hydrogenotrophic methanogenic strains in fed-batch cultivation mode. Here, we show that after a series of optimization and growth improvement attempts another methanogen, M. thermaggregas could be adapted to be grown in fed-batch cultivation mode to cell densities of up to 1.56 g L-1. Moreover, the CH4 evolution rate (MER) of M. thermaggregans was compared to Methanothermobacter marburgensis, the CO2-BMP model organism. Under optimized cultivation conditions, a maximum MER of 96.1 ± 10.9 mmol L-1 h-1 was obtained with M. thermaggregans-97% of the maximum MER that was obtained utilizing M. marburgensis in a reference experiment. Therefore, M. thermaggregans can be regarded as a CH4 cell factory highly suited to be applicable for CO2-BMP.

A comparative study of single- and two-phase anaerobic digestion of food waste under uncontrolled pH conditions

This study compared single- versus two-phase systems for semi-continuous anaerobic digestion of food waste without pH control at varying organic loading rates (OLRs). The methanogenic reactors of both systems required trace element supplementation for stable operation at 3.0 g VS (volatile solids)/L∙d or higher OLRs. Under trace-element supplemented conditions, both systems achieved stable and efficient performance at OLRs up to 4.0 g VS/L∙d. The two-phase system outperformed the single-phase system at 1.0-4.0 g VS/L∙d OLRs, but it failed at an OLR of 5.0 g VS/L∙d. Meanwhile, the single-phase system maintained the stable performance and reached its maximum methane production at this OLR. These results suggest that a single-phase configuration is more advantageous for robust treatment of food waste without pH control at high organic and hydraulic loads. Hydrogenotrophic methanogens dominated the methanogen community throughout the experiment in both systems. Microbial community structure shifts correlated with reactor operation and performance characteristics.

PhyMet2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens

The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet² , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet² with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.

Full-scale agricultural biogas plant metal content and process parameters in relation to bacterial and archaeal microbial communities over 2.5 year span

A start-up of 4 MW agricultural biogas plant in Vučja vas, Slovenia, was monitored from 2011 to 2014. The start-up was carried out in 3 weeks with the intake of biomass from three operating full-scale 1-2 MW donor agricultural biogas plants. The samples were taken from donor digesters and from two serial digesters during the start-up over the course of 2.5 years. Bacterial and Archaeal microbial communities progressively diverged from the composition of donor digesters during the start-up phase. The rate of change of Bacterial community decreased exponentially over the first 2.5 years as dynamics within the first 70 days was comparable to that of the next 1.5 years, whereas approximately constant rate was observed for Archaea. Despite rearrangements, the microbial communities remained functionally stable and produced biogas throughout the whole 2.5 years of observation. All systems parameters measured were ordered according to their Kernel density (Gaussian function) ranging from the most dispersed (substrate categories used as cosubstrates, quantities of each cosubstrate, substate dry and volatile matter, process parameters) towards progressively least dispersed (trace metal and ion profiles, aromatic-polyphenolic compounds, biogas plant functional output (energy)). No deficiency was detected in trace metal content as the distribution of metals and elements fluctuated within the suggested limits for biogas over 2.5 year observation. In contrast to the recorded process variables, Bacterial and Archaeal microbial communities exhibited directed changes oriented in time. Variation partitioning showed that a large fraction of variability in the Bacterial and Archaeal microbial communities (55% and 61%, respectively) remained unexplained despite numerous measured variables (n = 44) and stable biogas production. Our results show that the observed reorganization of microbial communities was not directly associated with impact on the full-scale biogas reactor performance. Novel parameters need to be determined to elucidate the variables directly associated with the reorganization of microbial communities and those relevant for sustained function such as the more in-depth interaction between TSOC, trace metal profiles, aromatic-polyphenolic compounds and ionic strength (e.g. electrical conductivity).

Core promoter information content correlates with optimal growth temperature

The subtle mechanisms by which protein-DNA interactions remain functional across a wide range of temperatures are largely unknown. In this work, we manually curated available information relating fully sequenced archaeal genomes with organism growth temperatures. We built a motif that represents the core promoter of each species and calculated its information content. We then studied the relation between optimal growth temperature (OGT) and information content (IC) in the promoter region.We found a positive correlation between G + C content and OGT in tRNA regions and not in overall genome. Furthermore, we found that there is a positive correlation between information content and optimal growth temperatures in Archaea. This can't be explained by an increased C+G composition nor by other obvious mechanisms. These findings suggest that increased information content could produce a positive fitness in organisms living at high temperatures. We suggest that molecular information theory may need to be adapted for hyperthermophiles.

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle

BACKGROUND

Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors.

RESULTS

Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes, Firmicutes, Proteobacteria, Synergistetes, Actinobacteria, Spirochaetes, Tenericutes, Caldithrix, Verrucomicrobia, Thermotogae, Chloroflexi, Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate-oxidizing metabolic machinery homologous to those of Acetobacterium woodii and Desulfovibrio vulgaris. Furthermore, genes for enzymes of the reductive acetyl-CoA pathway were present in the microbial communities.

CONCLUSIONS

The results indicate that lactate is oxidized mainly to acetate during the acetogenic step of AD and this comprises the acetotrophic pathway of methanogenesis. The genes for lactate utilization under anaerobic conditions are widespread in the domain Bacteria. Lactate oxidation to the substrates for methanogens is the most energetically attractive process in comparison to butyrate, propionate, or ethanol oxidation.

Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment

The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

Methane Seepage on Mars: Where to Look and Why

Methane on Mars is a topic of special interest because of its potential association with microbial life. The variable detections of methane by the Curiosity rover, orbiters, and terrestrial telescopes, coupled with methane's short lifetime in the martian atmosphere, may imply an active gas source in the planet's subsurface, with migration and surface emission processes similar to those known on Earth as "gas seepage." Here, we review the variety of subsurface processes that could result in methane seepage on Mars. Such methane could originate from abiotic chemical reactions, thermogenic alteration of abiotic or biotic organic matter, and ancient or extant microbial metabolism. These processes can occur over a wide range of temperatures, in both sedimentary and igneous rocks, and together they enhance the possibility that significant amounts of methane could have formed on early Mars. Methane seepage to the surface would occur preferentially along faults and fractures, through focused macro-seeps and/or diffuse microseepage exhalations. Our work highlights the types of features on Mars that could be associated with methane release, including mud-volcano-like mounds in Acidalia or Utopia; proposed ancient springs in Gusev Crater, Arabia Terra, and Valles Marineris; and rims of large impact craters. These could have been locations of past macro-seeps and may still emit methane today. Microseepage could occur through faults along the dichotomy or fractures such as those at Nili Fossae, Cerberus Fossae, the Argyre impact, and those produced in serpentinized rocks. Martian microseepage would be extremely difficult to detect remotely yet could constitute a significant gas source. We emphasize that the most definitive detection of methane seepage from different release candidates would be best provided by measurements performed in the ground or at the ground-atmosphere interface by landers or rovers and that the technology for such detection is currently available. Key Words: Mars-Methane-Seepage-Clathrate-Fischer-Tropsch-Serpentinization. Astrobiology 17, 1233-1264.

Ulva biomass as a co-substrate for stable anaerobic digestion of spent coffee grounds in continuous mode

Ulva biomass was evaluated as a co-substrate for anaerobic digestion of spent coffee grounds at varying organic loads (0.7-1.6g chemical oxygen demand (COD)/Ld) and substrate compositions. Co-digestion with Ulva (25%, COD basis) proved beneficial for SCG biomethanation in both terms of process performance and stability. The beneficial effect is much more pronounced at higher organic and hydraulic loads, with the highest COD removal and methane yield being 51.8% and 0.19L/g COD fed, respectively. The reactor microbial community structure changed dynamically during the experiment, and a dominance shift from hydrogenotrophic to aceticlastic methanogens occurred with increase in organic loading rate. Network analysis provides a comprehensive view of the microbial interactions involved in the system and confirms a direct positive correlation between Ulva input and methane productivity. A group of populations, including Methanobacterium- and Methanoculleus-related methanogens, was identified as a possible indicator for monitoring the biomethanation performance.

Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation

Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark

Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.

Enhancing biogas plant production using pig manure and corn silage by adding wheat straw processed with liquid hot water and steam explosion

BACKGROUND

Pig manure utilization and valorization is an important topic with tightening regulations focused on ecological and safety issues. By itself pig manure is a poor substrate for biogas production because of its excessive nitrogen content relative to available organic carbon. Such substrate is alkaline, and methanogenesis can be suppressed, and so additional substrates with high organic carbon must be added. The most promising is straw, which is available from adjacent biogas plant cultures. However, the abundant lignocellulosic biomass of wheat straw undergoes slow decomposition, and only a fraction of the chemical energy can be converted into biogas; thus economical methods for pretreatment increasing bioavailability are sought.

RESULTS

A method was investigated to increase the methane yield in a full-scale plant for co-fermenting pig manure with corn silage, which was the default substrate in the original source reactors. Increased lignocellulosic bioavailability of wheat straw was achieved by combining liquid hot water (LHW) and steam explosion (SE). According to FT-IR analysis, the treatment resulted in hemicellulose hydrolysis, partial cellulose depolymerization, and lignin bond destruction. Low-mass polysaccharides (0.6 × 10³ g mol^-1) had significantly higher concentration in the leachate of LHW-SE wheat straw than raw wheat straw. The methanogenic potential was evaluated using inoculum from two different biogas plants to study the influence of microorganism consortia. The yield was 24-34% higher after the pretreatment process. In a full-scale biogas plant, the optimal conditions were ~ 165 °C, ~ 2.33 MPa, and 10 min in LHW and ~ 65 °C and ~ 0.1 MPa for SE. The processes did not generate detectable inhibitors according to GC-MS analysis, such as furfural and 5-hydroxymethylfurfural.

CONCLUSIONS

The LHW-SE combined pretreatment process increases the bioavailability of carbohydrates from wheat straw. The LHW-SE treated wheat straw gave similar biogas yields to corn silage, thus enables at least partial replacement of corn silage and is good for diversification of substrates. Surprisingly, microorganisms consortia from other biogas plant fed with other substrates may have higher efficiency in utilization of tested substrate. Thus, methanogenic consortia may be considered in the process of optimization at industrial scale. The efficiency was calculated, and the LHW-SE may be profitable at full industrial scale and further optimization is proposed.

Stability of peatland carbon to rising temperatures

Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.

Performance, kinetics behaviors and microbial community of internal circulation anaerobic reactor treating wastewater with high organic loading rate: Role of external hydraulic circulation

Performance of internal circulation anaerobic reactor (IC) treating wastewater at high organic loading rate (OLR) and role of external hydraulic circulation were evaluated. When the OLR was increased from 2.50 to 18.94kgCOD/m³/d, COD removal decreased to 85% slightly and methane production increased to 4.49L/L/d with the upflow velocity of 1.0m/h resulted from the additional hydraulic circulation. Withdrawal of external hydraulic circulation led to decrease of COD removal to lower than 60% drastically and methane production by 81%. Accumulation of volatile fatty acids caused decline of pH to below 6.0 and the shift of substrate metabolic pathway to the hybrid fermentation. In addition, both maximum methane production rate and maximum substrate degradation rate obtained from mathematical models decreased significantly. Hydrogenotrophic methanogens including Methanobacterium and Methanocorpusculum predominated in the anaerobic sludge and the shift of microbial community was also observed.

Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance: Implications from microbial community shift

To elucidate the enhanced methane yield from organic wastes, the effects of low-strength ultrasonication on the microbial community structures in upflow anaerobic sludge blanket reactors were for the first time analyzed using pyrosequencing. Interestingly, a more even microbial community was observed in the ultrasonicated granules than in the control, which could compensate for the decreased richness and resulted in comparable (archaea) or even higher (bacteria) diversity. The ultrasonicated granules contained higher levels of δ-Proteobacteria, of which many are reportedly potential syntrophs, as well as methanogenic genera Methanosaeta, Methanotorris, and Methanococcus. The increased presence of syntrophic bacteria with their methanogenic partners was discussed with respect to hydrogen flux; their selective proliferation seems to be responsible for the enhanced anaerobic performance. This study is the first research shedding light on the novel function of low-strength ultrasound shifting the microbial structure towards better biogas production performance, and will facilitate application of low-strength ultrasound to other bioprocesses.

Response of a continuous anaerobic digester to temperature transitions: A critical range for restructuring the microbial community structure and function

Temperature is a crucial factor that significantly influences the microbial activity and so the methanation performance of an anaerobic digestion (AD) process. Therefore, how to control the operating temperature for optimal activity of the microbes involved is a key to stable AD. This study examined the response of a continuous anaerobic reactor to a series of temperature shifts over a wide range of 35-65 °C using a dairy-processing byproduct as model wastewater. During the long-term experiment for approximately 16 months, the reactor was subjected to stepwise temperature increases by 5 °C at a fixed HRT of 15 days. The reactor showed stable performance within the temperature range of 35-45 °C, with the methane production rate and yield being maximum at 45 °C (18% and 26% greater, respectively, than at 35 °C). However, the subsequent increase to 50 °C induced a sudden performance deterioration with a complete cessation of methane recovery, indicating that the temperature range between 45 °C and 50 °C had a critical impact on the transition of the reactor's methanogenic activity from mesophilic to thermophilic. This serious process perturbation was associated with a severe restructuring of the reactor microbial community structure, particularly of methanogens, quantitatively as well as qualitatively. Once restored by interrupted feeding for about two months, the reactor maintained fairly stable performance under thermophilic conditions until it was upset again at 65 °C. Interestingly, in contrast to most previous reports, hydrogenotrophs largely dominated the methanogen community at mesophilic temperatures while acetotrophs emerged as a major group at thermophilic temperature. This implies that the primary methanogenesis route of the reactor shifted from hydrogen- to acetate-utilizing pathways with the temperature shifts from mesophilic to thermophilic temperatures. Our observations suggest that a mesophilic digester may not need to be cooled at up to 45 °C in case of undesired temperature rise, for example, by excessive self-heating, which offers a possibility to reduce operating costs.

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

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