Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Struvite-Driven Integration for Enhanced Nutrient Recovery from Chicken Manure Digestate

This study investigated the synergistic integration of clean technologies, specifically anaerobic digestion (AD) and struvite precipitation, to enhance nutrient recovery from chicken manure (CM). The batch experiments were conducted using (i) anaerobically digested CM digestate, referred to as raw sample (RS), (ii) filtered digestate sample (FS), and (iii) a synthetically prepared control sample (CS). The research findings demonstrated that the initial ammonia concentration variations did not significantly impact the struvite precipitation yield in the RS and FS, showcasing the materials inertness process's robustness to changing ammonia concentrations. Notably, the study revealed that the highest nitrogen (N) recovery, associated with 86% and 88% ammonia removal in the CS and FS, was achieved at pH 11, underscoring the efficiency of nutrient recovery. The RS achieved the highest nitrogen recovery efficiency at pH 10, at 86.3%. In addition, the research highlighted the positive impact of reducing heavy metal levels (Zn, Cu, Pb, Ni, Cd, Cr and Fe) and improving the composition of the microbial community in the digestate. These findings offer valuable insights into sustainable manure and nutrient management practices, emphasizing the potential benefits for the agricultural sector and the broader circular economy. Future research directions include economic viability assessments, regulatory compliance evaluations, and knowledge dissemination to promote the widespread adoption of these clean technologies on a larger scale. The study marks a significant step toward addressing the environmental concerns associated with poultry farming and underscores the potential of integrating clean technologies for a more sustainable agricultural future.

Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria

It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.

Possibility of using tannins to control greenhouse gas production during digestate storage

The presented paper deals with the testing of a possibility to reduce emissions of undesirable greenhouse gases (CH₄, CO_2; NO_x) and their mixture (biogas) during the storage of digestate using applications of secondary plant metabolites (tannins). The experiment was conducted in laboratory conditions in which the digestate was placed in fermentation chambers. Prior to the fermentation process, preparations were applied to the digestate, which contained tannins: Tanenol Antibotrytis (TA), Tanenol Clar (TC) and Tanenol Rouge (TR) in three concentrations (0.5, 1.0 and 2.0% w/w). The application of these preparations demonstrably affected the production of biogas and the contents of CH₄, CO₂ and N therein. The application of TR preparation in the concentration of 1.0% and 2.0% significantly reduced the production of biogas as compared with all variants. The preparation further inhibited the process of CH₄ development. In contrast, the other preparations with the content of different kinds of TA and TC increased the production of biogas (on average by 15%), CH₄ (on average by 7%) and CO₂ (on average by 12%) as compared with the control variant and TR variant. These two variants reduced the concentration of N in biogas on average by 38%. Thus, the tested Tanenol tannin preparations can be used in different concentrations either to control emissions of greenhouse gases during the storage of digestate or, in case of increased production of CO₂ for its reuse in order to increase methane yields in the process of anaerobic fermentation.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

A new pathway for anaerobic biotransformation of marine toxin domoic acid

Domoic acid (DA) is a harmful algal toxin produced by marine diatom Pseudo-nitzschia and seriously threatens ecosystem and human health. However, the current knowledge on its biotransformation behavior in coastal anaerobic environment is lacking. This study investigated the anaerobic biotransformation of DA by a new marine consortium GH1. The results demonstrated that 90% of DA (1 mg L^-1) was cometabolically biotransformed under sulfate-reducing condition. A new anaerobic biotransformation pathway involving DA hydration, dehydrogenation, and C-C bond cleavage was proposed, where the conjugated double-bond of DA was interrupted, resulting in the corresponding alcohols and ketones, subsequently cleaved hydrolytically, and yielding the lower molecular weight products. Desulfovibrio and Clostridiales were markedly enriched in the anaerobic biotransformation of DA, which might jointly contribute to the elevated bacterial consortium resistance and degradation to DA. This study could deepen understanding of behavior and fate for DA in marine environments.

Combined anaerobic digestion of chicken manure and corn straw: study on methanogenic potential and microbial diversity

Purpose

To explore the methane production potential and microbial community changes of combined anaerobic digestion of chicken manure and corn straw. Increase methane production, reduce the environmental pollution caused by the burning of livestock manure and straw, and provide some theoretical references for the construction and operation of actual biogas projects.

Methods

Different proportions (3%, 5%, 10%) of corn straw were added to the anaerobic digestion systems of chicken manure in order to improve the C/N ratio and to evaluate the feasibility and potential synergistic effect on the co-digestion. The key point was to use 16S rDNA sequencing to analyze the relationship between the microbial diversity and the hydrolase activity during the anaerobic digestion.

Result

The results showed that the volumetric gas production of methane in the 3% straw addition group was 227.66 ml/gVS, which was 18% higher than the cumulative methane production in the pure chicken manure experimental group. However, with the increase of straw concentration, methane production and the utilization rate of the raw materials continued to decrease. The change in activity of each hydrolase was in agreement with changes in hydrolytic acidifying bacteria, and the activity of the main hydrolase also increased with the addition of straw; the correlation coefficient was 0.9943. Sequencing results showed that the dominant strains of methanogenic archaea were Methanosarcina, Methanosaeta, Methanobacterium, and Methanospirillum. Mainly for hydrogen-eating, acetic acid-eating methanogens, its role is to use H2, methanol and acetic acid, and other substances to metabolize methane, and convert it into CH4 and CO2.

Conclusion

The addition of a small amount of straw enhanced the production capacity of hydrogen-nutritive methane to some extent, and the species richness and evenness were also improved, reducing the pollution caused by livestock manure to the environment while controlling the pollution caused by straw burning.

Graphical Abstract

Impact of biochar supported nano zero-valent iron on anaerobic co-digestion of sewage sludge and food waste: Methane production, performance stability and microbial community structure

This work evaluates the effects of biochar supported nano zero-valent iron (nZVI-BC) on anaerobic co-digestion (co-AD) of sewage sludge and food waste. Kinetic model analysis suggested that nZVI-BC addition significantly increased the methane production potential (R₀) and daily methane production rate (G_m) by 42.87% and 49.87%, while the raw biochar only increased R₀ and G_m by 5.11% and 6.73%, respectively. Supplementation of higher concentrations of nZVI-BC was not preferable as inhibition of methane productivity was appeared. nZVI-BC addition remarkably improved organics degradation efficiency, as the reduction rate of TCOD, VSS and TSS were increased by 34.93%, 11.44% and 13.96%, respectively. The microbial analysis demonstrated that nZVI-BC facilitated the growth of hydrogentrophic methanogens, while acetotrophic methanogens which can only use acetate as electron donor were restrained. The study demonstrated nZVI-BC can effectively strengthen methanogenesis mainly through the enhancement of DIET between bacteria and methanogens, and the enrichment of hydrogenotrophic methanogens.

Archaeal and bacterial community structures of rural household biogas digesters with different raw materials in Qinghai Plateau

The present study aims to investigate microbial community structures household biogas digesters with different raw materials in Qinghai Plateau rural. High-throughput 16S rRNA gene sequencing analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria are the most abundant bacterial phyla (64.08%). Prevotella group 7 was the most abundant genus in digester YL9 and YL10 (69.72% and 26.96%, respectively) using vegetable waste raw materials. Trichococcus exhibited the highest abundance (14.55%) in YL1 digester using sheep and pig manure. Clostridium sensu stricto 1 (13.89%) and Synergistaceae_uncultured (15.52%) comprised the highest abundances in digester YL5 with mixed raw materials (i.e., dairy manure, sheep manure, and human feces). In addition, Proteiniphilum and Pseudomonas exhibited the highest abundances among bacterial genera in YL4 digester using pig manure. Methanomicrobiales was the most dominant archaeal communities, ranging from 13.35% to 81.34% in abundance. Methanocorpusculum exhibited dominant abundances in all digesters using various raw materials. Methanogenium was the most abundant archaeal genera in YL4 and YL6 digesters, which consume pig manure as primary raw material. In addition, Methanosarcina and Methanosaeta exhibited the highest abundances in digester YL1 (55.03%) and YL9 (51.40%), respectively. Moreover, fermentation temperatures and pH both contributed to the archaeal and bacterial community structures in all the investigated digesters. Specially, fermentation temperature showed positive correlation with the abundances of Synergistaceae_uncultured, Methanogenium, and Methanosaeta, and pH was positively correlated with the abundances of Prevotella group 7 and Methanosarcina abundances.

Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

Metagenomics for taxonomy profiling: tools and approaches

The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

Comprehensive analysis of the microbial communities and operational parameters of two full-scale anaerobic digestion plants treating food waste in South Korea: Seasonal variation and effect of ammonia

There are about ninety full-scale anaerobic digestion (AD) plants in South Korea that treat food waste (FW); however, the key diff ;erences in the microbial communities in different seasons and the effects of ammonia in AD remain poorly understood. In this study, the seasonal changes in microbial communities associated with operational parameters of two full-scale ADs (C and W plants) treating FW were analyzed. The organic loading rate (OLR) variability had an influence on the seasonal CH₄ yield; the W plant had a lower CH₄ yield with an unstable AD performance while the C plant had a higher CH₄ yield with a stable AD performance. It was mainly due to the substantially different NH₄⁺ concentration; the W plant had a NH₄⁺ concentration nearly 1.6 times higher compared to the C plant. The high NH₄⁺ presence in the W plant led to the dominance of class Clostridia, and methanogenesis was mostly done by hydrogenotrophs (Methanomassiliicoccus luminyensis). Additionally, the members belonging to Clostridia and Bacteroidia were found at both plants in each season (share ≥0.5%) implying their indispensable role during the anaerobic digestion of FW.

Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Establishing practical strategies to run high loading corn stover anaerobic digestion: Methane production performance and microbial responses

It is significant to understand corn stover (CS) in anaerobic digestion (AD) under high organic loadings. A semi-continuous mesophilic (37 ± 1 °C) CS AD was conducted in this study with increasing loadings. The initial total solids (TS) gradually increased with 1% gradient at every 10 days from 8% to 15% until the system was acidified. Adding different ratios of cattle manure (CM) (20%, 30% and 40% (v/v)) to rescue this system back to a stable operation was adopted. The diversity of bacteria and archaea was analyzed by 16S rRNA gene sequencing technology. The results showed that when loading TS content was increased to 15%, AD system was acidized with pH value of 5.13. 30% of CM was the optimal ratio to recover biogas production. High abundance (31.07%) of Bathyarchaeota was first found in AD system. Acidification of high loading CS AD can be highly correlating with bacterial community, specially Clostridium and Caproiciproducens.

Semi-continuous fermentation of solid waste in closed artificial ecosystem: Microbial diversity, function genes evaluation

Bioregenerative Life Support System (BLSS) is a closed artificial ecosystem and could provide oxygen, food, water and other substances for space survival. Solid waste treatment is a key rate-limiting step in BLSS. In this study, solid wastes including wheat straw, human and yellow mealworm feces were disposed in a semi-continuous bio-convertor for 105 days in a ground-based experimental BLSS platform (Lunar Palace 1). Solid wastes at different periods were sampled and the microbial community variation, functional genes and metabolic pathways were analyzed. The results showed phyla Firmicutes, Bacteroidetes and Proteobacteria predominated in all samples. While microbial community structures at genus level were significantly different, indicating selective enrichment during the 105-day process. The abundance of functional gene related to carbohydrate transport and metabolism was predicted higher on 45-day and 70-day. The metabolic pathway analysis revealed the degradation mechanisms and provided evidence for metabolic regulation.

Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L⁻¹ d⁻¹ was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L⁻¹ d⁻¹ loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VS_des generation and carbon conversion efficiency (72.56 ± 3.40 mL g⁻¹ and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau

Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.

Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems

Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.

Hydrothermal treatment of Chlorella sp.: Influence on biochemical methane potential, microbial function and biochemical metabolism

This study focused on the effect of hydrothermal treatment (HTT) on biochemical methane potential (BMP) of Chlorella sp. The BMP was in the range of 119.16-485.90 mLCH₄/gVS, and increased by 80.31%-210.16% after HTT, while reduced 23.94% at hydrothermal treatment severity (HTS) 5.21. The cell wall was more greatly disrupted with increasing HTS, accompanied with the increase of volatile fatty acids (VFAs) and fermentation inhibitors (5-HMF and more complex chemical compositions) recoveries. The reducing sugar yields were 0.94-3.65% and obtained its maximum at a retention time of 30 min. Illumina MiSeq sequencing clarified that, the phylum Chloroflexi with functions of hydrolysis and acidogenesis, decreased with increasing HTS. The family Methanosaetaceae belonging to acetoclastic methanogens, had an unexpected decrease at HTS 5.21. As the response, VFAs concentration was less than 1 g/L after biochemical metabolism, while high concentrations of VFAs and inhibitors at HTS 5.21 led to the poor performance.

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome

The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.

Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum

Billions of bacteria inhabit the gastrointestinal tract. Immune-microbial cross talk is responsible for immunological homeostasis, and symbiotic microbial species induce regulatory immunity, which helps to control the inflammation levels. In this study we aimed to identify species within the equine intestinal microbiota with the potential to induce regulatory immunity. These could be future targets for preventing or treating low-grade chronic inflammation occurring as a result of intestinal microbial changes and disruption of the homeostasis. 16S rRNA gene amplicon sequencing was performed on samples of intestinal microbial content from ileum, cecum, and colon of 24 healthy horses obtained from an abattoir. Expression of genes coding for IL-6, IL-10, IL-12, IL-17, 18 s, TNFα, TGFβ, and Foxp3 in the ileum and mesenteric lymph nodes was measured by qPCR. Intestinal microbiota composition was significantly different in the cecum and colon compared to the ileum, which contains large abundances of Proteobacteria. Especially members of the Clostridiales order correlated positively with the regulatory T-cell transcription factor Foxp3 and so did the phylum Verrucomicrobia. We conclude that Clostridiales and Verrucomicrobia have the potential to induce regulatory immunity and are possible targets for intestinal microbial interventions aiming at regulatory immunity improvement.

Enhanced quinoline removal by zero-valent iron-coupled novel anaerobic processes: performance and underlying function analysis

Quinoline is toxic and difficult to degrade biologically; thus, it is a serious threat to the safety of ecosystems. To promote quinoline reduction, zero-valent iron (ZVI) was introduced into an anaerobic digestion (AD) system through batch experiments. The performance of three different types of ZVI (i.e., iron powder, iron scrap and rusty iron scrap) on quinoline degradation, methane production, formation of volatile fatty acids (VFAs) and chemical oxygen demand (COD) removal were investigated systematically. Compared to the AD system alone, quinoline and COD removal as well as the production of methane and acetic acid were effectively enhanced by ZVI, especially rusty iron scrap. The removal efficiencies of quinoline and COD were increased by 28.6% and 19.9%, respectively. The enhanced effects were attributed to the high accumulation of ferrous ions and high pH self-buffering capability, which were established by ZVI addition. Furthermore, high-throughput sequencing analysis indicated that the functional microorganisms in the ZVI-AD system were higher than in the AD system, and the added types of ZVI played important roles in structuring the innate microbial community in waste activated sludge (WAS). Especially, high enrichment of microorganisms capable of degrading quinoline, such as Pseudomonas and Bacillus, in the coupled system was detected.

Methanol metabolism and archaeal community changes in a bioelectrochemical anaerobic digestion sequencing batch reactor with copper-coated graphite cathode

In this study, the metabolism of methanol and changes in an archaeal community were examined in a bioelectrochemical anaerobic digestion sequencing batch reactor with a copper-coated graphite cathode (BEAD-SBR_Cu). Copper-coated graphite cathode produced methanol from food waste. The BEAD-SBR_Cu showed higher methanol removal and methane production than those of the anaerobic digestion (AD)-SBR. The methane production and pH of the BEAD-SBR_Cu were stable even under a high organic loading rate (OLR). The hydrogenotrophic methanogens increased from 32.2 to 60.0%, and the hydrogen-dependent methylotrophic methanogens increased from 19.5 to 37.7% in the bulk of BEAD-SBR_Cu at high OLR. Where methanol was directly injected as a single substrate into the BEAD-SBR_Cu, the main metabolism of methane production was hydrogenotrophic methanogenesis using carbon dioxide and hydrogen released by the oxidation of methanol on the anode through bioelectrochemical reactions.

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions

Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.

Co-digestion of chicken manure and microalgae Chlorella 1067 grown in the recycled digestate: Nutrients reuse and biogas enhancement

The present investigation targeted on a sustainable co-digestion system: microalgae Chlorella 1067 (Ch. 1067) was cultivated in chicken manure (CM) based digestate and then algae biomass was used as co-substrate for anaerobic digestion with CM. About 91% of the total nitrogen and 86% of the soluble organics in the digestate were recycled after the microalgae cultivation. The methane potential of co-digestion was evaluated by varying CM to Ch. 1067 ratios (0:10, 2:8, 4:6, 6:4, 8:2, 10:0 based on the volatile solids (VS)). All the co-digestion trials showed higher methane production than the calculated values, indicating synergy between the two substrates. Modified Gompertz model showed that co-digestion had more effective methane production rate and shorter lag phase. Co-digestion (8:2) achieved the highest methane production of 238.71mL⋅(g VS)^-1 and the most significant synergistic effect. The co-digestion (e.g. 8:2) presented higher and balanced content of dominant acidogenic bacteria (Firmicutes, Bacteroidetes, Proteobacterias and Spirochaetae). In addition, the archaea community Methanosaeta presented higher content than Methanosarcina, which accounted for the higher methane production. These findings indicated that the system could provide a practicable strategy for effectively recycling digestate and enhancing biogas production simultaneously.

Exogenous addition of H2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane

Biological reduction of CO₂ into CH₄ by exogenous addition of H₂ is a promising technology for upgrading biogas into higher CH₄ content. The aim of this work was to study the feasibility of exogenous H₂ addition for an in situ biogas upgrading through biological conversion of the biogas CO₂ into CH_4. Moreover, this study employed systematic study with isotope analysis for providing comprehensive evidence on the underlying pathways of CH₄ production and upstream processes. Batch reactors were inoculated with digestate originating from a full-scale biogas plant and fed once with maize leaf substrate. Periodic addition of H₂ into the headspace resulted in a completely consumption of CO₂ and a concomitant increase in CH₄ content up to 89%. The microbial community and isotope analysis shows an enrichment of hydrogenotrophic Methanobacterium and the key role of hydrogenotrophic methanogenesis for biogas upgrading to higher CH₄ content. Excess H₂ was also supplied to evaluate its effect on overall process performance. The results show that excess H₂ addition resulted in accumulation of H₂, depletion of CO₂ and inhibition of the degradation of acetate and other volatile fatty acids (VFA). A systematic isotope analysis revealed that excess H₂ supply led to an increase in dissolved H₂ to the level that thermodynamically inhibit the degradation of VFA and stimulate homo-acetogens for production of acetate from CO₂ and H₂. The inhibition was a temporary effect and acetate degradation resumed when the excess H₂ was removed as well as in the presence of stoichiometric amount of H₂ and CO₂. This inhibition mechanism underlines the importance of carefully regulating the H₂ addition rate and gas retention time to the CO₂ production rate, H₂-uptake rate and growth of hydrogenotrophic methanogens in order to achieve higher CH₄ content without the accumulation of acetate and other VFA.

Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass

The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.

The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor

The strictly anaerobic Peptoniphilaceae bacterium str. ING2-D1G (=DSM 28672=LMG 28300) was isolated from a mesophilic laboratory-scale completely stirred tank biogas reactor (CSTR) continuously co-digesting maize silage, pig and cattle manure. Based on 16S rRNA gene sequence comparison, the closest described relative to this strain is Peptoniphilus obesi ph1 showing 91.2% gene sequence identity. The most closely related species with a validly published name is Peptoniphilus indolicus DSM 20464^T whose 16S rRNA gene sequence is 90.6% similar to the one of strain ING2-D1G. The genome of the novel strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding anaerobic digestion of biomass. The strain harbors a circular chromosome with a size of 1.6 Mb that contains 1466 coding sequences, 53 tRNA genes and 4 ribosomal RNA (rrn) operons. The genome carries a 28,261bp prophage insertion comprising 47 phage-related coding sequences. Reconstruction of fermentation pathways revealed that strain ING2-D1G encodes all enzymes for hydrogen, lactate and acetate production, corroborating that it is involved in the acido- and acetogenic phase of the biogas process. Comparative genome analyses of Peptoniphilaceae bacterium str. ING2-D1G and its closest relative Peptoniphilus obesi ph1 uncovered rearrangements, deletions and insertions within the chromosomes of both strains substantiating a divergent evolution. In addition to genomic analyses, a physiological and phenotypic characterization of the novel isolate was performed. Grown in Brain Heart Infusion Broth with added yeast extract, cells were spherical to ovoid, catalase- and oxidase-negative and stained Gram-positive. Optimal growth occurred between 35 and 37°C and at a pH value of 7.6. Fermentation products were acetate, butanoate and carbon dioxide.

Technological Microbiology: Development and Applications

Over thousands of years, modernization could be predicted for the use of microorganisms in the production of foods and beverages. However, the current accelerated pace of new food production is due to the rapid incorporation of biotechnological techniques that allow the rapid identification of new molecules and microorganisms or even the genetic improvement of known species. At no other time in history have microorganisms been so present in areas such as agriculture and medicine, except as recognized villains. Currently, however, beneficial microorganisms such as plant growth promoters and phytopathogen controllers are required by various agricultural crops, and many species are being used as biofactories of important pharmacological molecules. The use of biofactories does not end there: microorganisms have been explored for the synthesis of diverse chemicals, fuel molecules, and industrial polymers, and strains environmentally important due to their biodecomposing or biosorption capacity have gained interest in research laboratories and in industrial activities. We call this new microbiology Technological Microbiology, and we believe that complex techniques, such as heterologous expression and metabolic engineering, can be increasingly incorporated into this applied science, allowing the generation of new and improved products and services.

Comparison of six methods for the recovery of PCR-compatible microbial DNA from an agricultural biogas plant

Six different commercial methods were compared to evaluate their efficiency in recovering high quantity/quality PCR compatible microbial DNA from an agricultural biogas plant. Within the last two decades, biogas plants have been developed to produce energy from organic wastes and from devoted biomass. The complex biotransformations are performed by a diverse consortium of microorganisms that is an important reserve of genes and enzymatic activities with a huge range of applications in various commercial fields. In this respect, the ability to isolate DNA from a complex matrix is of high importance. Important parameters of the recovered DNA are good yield, purity, and quality. The methods examined showed considerable differences about quantity and quality of the recovered DNA and, usually, it was observed that a higher amount was accompanied by more degradation. DNA purity was determined by its PCR amplificability. Only two methods were able to provide DNA pure enough to be directly amplified. For the rest of the methods, a few intermediate steps such as dilution and/or the addition of polyvinylpyrrolidone were necessary to remove the inhibitors present and to amplify the DNA. Real-time PCR analysis evidenced that, as expected, prokaryotic DNA was much more abundant than eukaryotic DNA, but some methods were more suited to recovering prokaryotic or eukaryotic DNA. The digestion analysis of ribosomal DNA amplicons confirmed the influence of the methods on the final output, allowing the recovery of only a fraction of the present species as determined by sequencing a small prokaryotic and eukaryotic ribosomal library.

Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge

BACKGROUND

Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry.

RESULTS

Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs.

CONCLUSIONS

Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.

Isolation of lactic acid-forming bacteria from biogas plants

Direct molecular approaches provide hints that lactic acid bacteria play an important role in the degradation process of organic material to methanogenetic substrates in biogas plants. However, their diversity in biogas fermenter samples has not been analyzed in detail yet. For that reason, five different biogas fermenters, which were fed mainly with maize silage and manure from cattle or pigs, were examined for the occurrence of lactic acid-forming bacteria. A total of 197 lactic acid-forming bacterial strains were isolated, which we assigned to 21 species, belonging to the genera Bacillus, Clostridium, Lactobacillus, Pediococcus, Streptococcus and Pseudoramibacter-related. A qualitative multiplex system and a real-time quantitative PCR could be developed for most isolates, realized by the selection of specific primers. Their role in biogas plants was discussed on the basis of the quantitative results and on physiological data of the isolates.

Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.

Biogas production from hydrothermal liquefaction wastewater (HTLWW): Focusing on the microbial communities as revealed by high-throughput sequencing of full-length 16S rRNA genes

Hydrothermal liquefaction (HTL) is an emerging and promising technology for the conversion of wet biomass into bio-crude, however, little attention has been paid to the utilization of hydrothermal liquefaction wastewater (HTLWW) with high concentration of organics. The present study investigated biogas production from wastewater obtained from HTL of straw for bio-crude production, with focuses on the analysis of the microbial communities and characterization of the organics. Batch experiments showed the methane yield of HTLWW (R-HTLWW) was 184 mL/g COD, while HTLWW after petroleum ether extraction (PE-HTLWW), to extract additional bio-crude, had higher methane yield (235 mL/g COD) due to the extraction of recalcitrant organic compounds. Sequential batch experiments further demonstrated the higher methane yield of PE-HTLWW. LC-TOF-MS, HPLC and gel filtration chromatography showed organics with molecular weight (MW) < 1000 were well degraded. Results from the high-throughput sequencing of full-length 16S rRNA genes analysis showed similar microbial community compositions were obtained for the reactors fed with either R-HTLWW or PE-HTLWW. The degradation of fatty acids were related with Mesotoga infera, Syntrophomonas wolfei et al. by species level identification. However, the species related to the degradation of other compounds (e.g. phenols) were not found, which could be due to the presence of uncharacterized microorganisms. It was also found previously proposed criteria (97% and 98.65% similarity) for species identification of 16S rRNA genes were not suitable for a fraction of 16S rRNA genes.

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes

This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production.

Preliminary study of acrylamide monomer decomposition during methane fermentation of dairy waste sludge

Polyacrylamide (PAM) used in sludge dewatering exists widely in high-solid anaerobic digestion. Acrylamide is registered in the list of chemicals demonstrating toxic, carcinogenic and mutagenic properties. Therefore, it is reasonable to ask about the mobility of such residual substances in the environment. The study was carried out to assess the impact of the mesophilic (39±1°C) and thermophilic (54±1°C) fermentation process on the level of acrylamide monomer (AMD) content in the dairy sludge. The material was analysed using high-performance liquid chromatography (HPLC) for quantification of AMD. The results indicate that the process of methane fermentation continues regardless of the temperature effects on the degradation of AMD in dairy sludge. The degree of reduction of acrylamide monomer for thermophilic fermentation is 100%, while for mesophilic fermentation it is 91%. In practice, this means that biogas technology eliminates the risk of AMD migration to plant tissue. Moreover, it should be stressed that 90% of cumulative biogas and methane production was reached one week earlier under thermophilic conditions - the dynamics of the methanisation process were over 20% faster.

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment

The genome sequence of Defluviitoga tunisiensis L3 originating from a thermophilic biogas-production plant was established and recently published as Genome Announcement by our group. The circular chromosome of D. tunisiensis L3 has a size of 2,053,097bp and a mean GC content of 31.38%. To analyze the D. tunisiensis L3 genome sequence in more detail, a phylogenetic analysis of completely sequenced Thermotogae strains based on shared core genes was performed. It appeared that Petrotoga mobilis DSM 10674(T), originally isolated from a North Sea oil-production well, is the closest relative of D. tunisiensis L3. Comparative genome analyses of P. mobilis DSM 10674(T) and D. tunisiensis L3 showed moderate similarities regarding occurrence of orthologous genes. Both genomes share a common set of 1351 core genes. Reconstruction of metabolic pathways important for the biogas production process revealed that the D. tunisiensis L3 genome encodes a large set of genes predicted to facilitate utilization of a variety of complex polysaccharides including cellulose, chitin and xylan. Ethanol, acetate, hydrogen (H2) and carbon dioxide (CO2) were found as possible end-products of the fermentation process. The latter three metabolites are considered to represent substrates for methanogenic Archaea, the key organisms in the final step of the anaerobic digestion process. To determine the degree of relatedness between D. tunisiensis L3 and dominant biogas community members within the thermophilic biogas-production plant, metagenome sequences obtained from the corresponding microbial community were mapped onto the L3 genome sequence. This fragment recruitment revealed that the D. tunisiensis L3 genome is almost completely covered with metagenome sequences featuring high matching accuracy. This result indicates that strains highly related or even identical to the reference strain D. tunisiensis L3 play a dominant role within the community of the thermophilic biogas-production plant.

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil

Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

An Esterase from Anaerobic Clostridium hathewayi Can Hydrolyze Aliphatic-Aromatic Polyesters

Recently, a variety of biodegradable polymers have been developed as alternatives to recalcitrant materials. Although many studies on polyester biodegradability have focused on aerobic environments, there is much less known on biodegradation of polyesters in natural and artificial anaerobic habitats. Consequently, the potential of anaerobic biogas sludge to hydrolyze the synthetic compostable polyester PBAT (poly(butylene adipate-co-butylene terephthalate) was evaluated in this study. On the basis of reverse-phase high-performance liquid chromatography (RP-HPLC) analysis, accumulation of terephthalic acid (Ta) was observed in all anaerobic batches within the first 14 days. Thereafter, a decline of Ta was observed, which occurred presumably due to consumption by the microbial population. The esterase Chath_Est1 from the anaerobic risk 1 strain Clostridium hathewayi DSM-13479 was found to hydrolyze PBAT. Detailed characterization of this esterase including elucidation of the crystal structure was performed. The crystal structure indicates that Chath_Est1 belongs to the α/β-hydrolases family. This study gives a clear hint that also micro-organisms in anaerobic habitats can degrade manmade PBAT.

The influence of petroleum products on the methane fermentation process

In this study the influence of the petroleum products: diesel fuel and spent engine oil on the sewage sludge digestion process and biogas production efficiency was investigated. Microbiological, chemical and enzymatic analyses were applied in the survey. It was revealed that the influence of the petroleum derivatives on the effectiveness of the methane fermentation of sewage sludge depends on the type of the petroleum product. Diesel fuel did not limit the biogas production and the methane concentration in the biogas, while spent engine oil significantly reduced the process efficacy. The changes in physical-chemical parameters, excluding COD, did not reflect the effect of the tested substances. The negative influence of petroleum products on individual bacterial groups was observed after 7 days of the process, while after 14 days probably some adaptive mechanisms appeared. The dehydrogenase activity assessment was the most relevant parameter to evaluate the effect of petroleum products contamination. Diesel fuel was probably used as a source of carbon and energy in the process, while the toxic influence was observed in case of spent engine oil.

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

BACKGROUND

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge.

RESULTS

In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway.

CONCLUSION

This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

BACKGROUND

Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest.

RESULTS

Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitoga tunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty.

CONCLUSIONS

In this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.