Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing

Ex-situ biomethanation for CO2 valorization: State of the art, recent advances, challenges, and future prospective

Ex-situ biomethanation is an emerging technology that facilitates the use of surplus renewable electricity and valorizes carbon dioxide (CO2) for biomethane production by hydrogenotrophic methanogens. This review offers an up-to-date overview of the current state of ex-situ biomethanation and thoroughly analyzes key operational parameters affecting hydrogen (H2) gas-liquid mass transfer and biomethanation performance, along with an in-depth discussion of the technical challenges. To the best of our knowledge, this is the first review article to discuss microbial community structure in liquid and biofilm phases and their responses after exposure to H2 starvation during ex-situ biomethanation. In addition, future research in areas such as reactor configuration and optimization of operational parameters for improving the H2 mass transfer rate, inhibiting opportunistic homoacetogens, integration of membrane technology, and use of conductive packing material is recommended to overcome challenges and improve the efficiency of ex-situ biomethanation. Furthermore, this review presents a techno-economic analysis for the future development and facilitation of industrial implementation. The insights presented in this review will offer useful information to identify state-of-the-art research trends and realize the full potential of this emerging technology for CO2 utilization and biomethane production.

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.

Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview

Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.

Diversity of endophytic fungal community in Huperzia serrata from different ecological areas and their correlation with Hup A content

Background

Huperzine A (Hup A) has attracted considerable attention as an effective therapeutic candidate drug used to treat Alzheimer’s disease. Whereas, the production of Hup A from wild plants faced a major challenge, which is the wild Huperzia Serrata harbor a low Hup A content, has a long-life cycle, and has a small yield. At present, several reports showed that Hup A is produced by various endophytic fungal strains isolated from H. serrata, thereby providing an alternative method to produce the compound and reduce the consumption of this rare and endangered plant. However, till now, very few comprehensive studies are available on the biological diversity and structural composition of endophytic fungi and the effects of endophytic fungi on the Hup A accumulation in H. serrata.

Results

In this research, the composition and diversity of fungal communities in H. serrata were deciphered based on high-throughput sequencing technology of fungal internal transcribed spacer regions2 (ITS2). The correlation between endophytic fungal community and Hup A content was also investigated. Results revealed that the richness and the diversity of endophytic fungi in H. serrata was various according to different tissues and different ecological areas. The endophytic fungal communities of H. serrata exhibit species-specific, ecological-specific, and tissue-specific characteristics. There are 6 genera (Ascomycota_unclassified, Cyphellophora, Fungi_unclassified, Sporobolomyces, and Trichomeriaceae_unclassified) were significantly positively correlated with Hup A content in all two areas, whereas, there are 6 genera (Auricularia, Cladophialophora, Cryptococcus, Mortierella, and Mycena) were significantly negatively correlated with Hup A content of in all two areas.

Conclusions

This study indicated a different composition and diverse endophytic fungal communities in H. serrata from different organs and ecological areas. The current study will provide the realistic basis and theoretical significance for understanding the biological diversity and structural composition of endophytic fungal communities in H. serrata, as well as providing novel insights into the interaction between endophytic fungi and Hup A content.

Biofilm formation as a method of improved treatment during anaerobic digestion of organic matter for biogas recovery

The efficiency of anaerobic digestion could be increased by promoting microbial retention through biofilm development. The inclusion of certain types of biofilm carriers has differentiated existing AD biofilm reactors through their respective mode of biofilm growth. Bacteria and archaea engaged in methanogenesis during anaerobic processes potentially build biofilms by adhering or attaching to biofilm carriers. Meta-analyzed results depicted varying degrees of biogas enhancement within AD biofilm reactors. Furthermore, different carrier materials highly induced the dynamicity of the dominant microbial population in each system. It is suggested that the promotion of surface contact and improvement of interspecies electron transport have greatly impacted the treatment results. Modern spectroscopy techniques have been and will continue to give essential information regarding biofilm's composition and structural organization which can be useful in elucidating the added function of this special layer of microbial cells.

Thermophilic co-digestion of blackwater and organic kitchen waste: Impacts of granular activated carbon and different mixing ratios

Biogas (methane) as a source of renewable energy, was produced in the anaerobic co-digestion of blackwater (BW, municipal toilet wastewater) and organic kitchen waste (KW). The impact on methane production of various BW to KW mixing ratios, with and without the addition of granular activated carbon (GAC), were studied under thermophilic (55 °C) temperatures. GAC is reported to enhance methane production in such digestions through direct interspecies electron transfer. The results showed that the co-digestion of BW and KW under the 1:2 VS ratio significantly improved the biomethane potential (BMP). In the absence of GAC, an optimal BW:KW ratio was found to be 1:2, achieving a BMP of 0.76 g CH₄-COD/g feed-COD. With GAC addition, the BMP increased to 0.81 g CH₄-COD/g feed-COD, the lag phase in the digestion was significantly reduced, and the methane production rate increased. Microbial communities in the BW-KW anaerobic digestion were analyzed with and without the addition of GAC. Methanothermobacter and Methanosarcina were predominant archaea in BW-KW digests, with and without GAC amendment, while a third methanogen, Methanomassiliicoccus, was enriched with the addition of GAC to the digest. Further, through SEM image, the enrichment of pili-like stucture was observed in GAC surface.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Succession of endophytic fungi and arbuscular mycorrhizal fungi associated with the growth of plant and their correlation with secondary metabolites in the roots of plants

BACKGROUND

To decipher the root and microbial interaction, secondary metabolite accumulation in roots and the microbial community's succession model during the plant's growth period demands an in-depth investigation. However, till now, no comprehensive study is available on the succession of endophytic fungi and arbuscular mycorrhizal fungi (AMF) with roots of medicinal licorice plants and the effects of endophytic fungi and AMF on the secondary metabolite accumulation in licorice plant's root.

RESULTS

In the current study, interaction between root and microbes in 1-3 years old medicinal licorice plant's root and rhizospheric soil was investigated. Secondary metabolites content in licorice root was determined using high-performance liquid chromatography (HPLC). The composition and diversity of endophytic and AMF in the root and soil were deciphered using high-throughput sequencing technology. During the plant's growth period, as compared to AMF, time and species significantly affected the diversity and richness of endophytic fungi, such as Ascomycota, Basidiomycota, Fusarium, Cladosporium, Sarocladium. The growth period also influenced the AMF diversity, evident by the significant increase in the relative abundance of Glomus and the significant decrease in the relative abundance of Diversispora. It indicated a different succession pattern between the endophytic fungal and AMF communities. Meanwhile, distance-based redundancy analysis and Mantel tests revealed root's water content and secondary metabolites (glycyrrhizic acid, liquiritin, and total flavonoids), which conferred endophytic fungi and AMF diversity. Additionally, plant growth significantly altered soil's physicochemical properties, which influenced the distribution of endophytic fungal and AMF communities.

CONCLUSIONS

This study indicated a different succession pattern between the endophytic fungal and AMF communities. During the plant's growth period, the contents of three secondary metabolites in roots increased per year, which contributed to the overall differences in composition and distribution of endophytic fungal and AMF communities. The endophytic fungal communities were more sensitive to secondary metabolites than AMF communities. The current study provides novel insights into the interaction between rhizospheric microbes and root exudates.

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.

Microbial composition of a hydropower cooling water system reveals thermophilic bacteria with a possible role in primary biofilm formation

Microfouling, ie biofilm formation on surfaces, can have an economic impact and requires costly maintenance in water-powered energy generation systems. In this study, the microbiota of a cooling system (filter and heat exchanger) in the Irapé hydroelectric power plant in Brazil was examined. The goal was to identify bacteria that could be targeted to more efficiently reduce biofilm formation. Two sampling campaigns were made corresponding to two well-defined seasons of the Brazilian Cerrado biome: the dry (campaign 1) and the wet (campaign 2). Microfouling communities varied considerably over time in samples obtained at different times after the last clearance of the heat exchanger. The thermophilic bacteria Meiothermus, Thermomonas and Symbiobacterium were exclusive and abundant in the microfouling of the heat exchanger in campaign 2, while methanotrophs and iron-reducing bacteria were abundant only in filter sediments. These findings could help to guide strategies for ecofriendly measures to reduce biofilm fouling in hydroelectric power plants, minimizing environmental and economic losses.

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

Mesophilic and thermophilic anaerobic digestion of soybean curd residue for methane production: Characterizing bacterial and methanogen communities and their correlations with organic loading rate and operating temperature

To find the optimal operation parameters and provide an explanation of methanogenic pathway for methane production in mesophilic (35 °C) and thermophilic (55 °C) anaerobic digestion (MAD, TAD) of soybean curd residue (SCR), MAD and MAD were contrastively investigated for 95 days. The maximum available OLR was identified as 3.3 gVS/L for both MAD and TAD. Compared to MAD, TAD exhibited a 20% higher average methane yield (0.591 L/gVS) and a 7.5% higher volatile solids removal efficiency (74.1 ± 10.4%). Bacterial phyla Bacteroidetes, Firmicutes and Proteobacteria dominated in MAD digesters while genus Defluviitoga was selectively enriched in TAD digesters due to higher temperature and organic loading pressure. Principal coordinates analysis of methanogen community showed that both temperature and OLR were crucial environmental variables shifting the taxonomic patterns of the methanogens. The enriched methanogen genus Methanothermobacter (93%) with a hydrogenotrophic methanogenic pathway had a close correlation with the TAD performance.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.

A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants

BACKGROUND

In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline.

RESULTS

Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers. Mapping of identified metaproteins with process steps described by the Anaerobic Digestion Model 1 confirmed its main assumptions and also proposed some extensions such as syntrophic acetate oxidation or fermentation of alcohols. Results indicate that the microbial communities were shaped by syntrophy as well as competition and phage-host interactions causing cell lysis. For the families Bacillaceae, Enterobacteriaceae, and Clostridiaceae, the number of phages exceeded up to 20-fold the number of host cells.

CONCLUSION

Phage-induced cell lysis might slow down the conversion of substrates to biogas, though, it could support the growth of auxotrophic microbes by cycling of nutrients.

Process performance and microbial community structure in thermophilic trickling biofilter reactors for biogas upgrading

This study evaluated the process performance and determined the microbial community structure of two lab-scale thermophilic trickling biofilter reactors used for biological methanation of hydrogen and carbon-dioxide for a total period of 94 days. Stable and robust operation was achieved by means of a single-pass gas flow. The quality of the output gas (>97%) was comparable to the methane purity achieved by commercial biogas upgrading systems fulfilling the specifications to be used as substitute to natural gas. The reactors' methane productivity reached >1.7 L_CH4/(L_R·d) at hydrogen loading rate of 7.2 L_H2/(L_R·d). The spatial distribution of the microbial consortia localized in the liquid media and biofilm enabled us to gain a deeper understanding on how the microbiome is structured inside the trickling biofilter. Sequencing results revealed a significant predominance of Methanothermobacter sp. in the biofilm. Unknown members of the class Clostridia were highly abundant in biofilm and liquid media, while acetate utilising bacteria predominated in liquid samples.

SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples

Metaproteomics represent an important tool for the taxonomic and functional investigation of microbial communities in humans, environment, and technical applications. Due to the high complexity of the microbial communities, protein, and peptide fractionation is applied to improve the characterization of taxonomic and functional composition of microbial communities. In order to target scientific questions regarding taxonomic and functional composition adequately, a tradeoff between the number of fractions analyzed and the required depth of information has to be found. Two samples of a biogas plant were analyzed by either single LC-MS/MS measurement (1D) or LC-MS/MS measurements of fractions obtained after SDS-PAGE (2D) separation. Fractionation with SDS-PAGE increased the number of identified spectra by 273%, the number of peptides by 95%, and the number of metaproteins by 59%. Rarefaction plots of species and metaproteins against identified spectra showed that 2D separation was sufficient to identify most microbial families but not all metaproteins. More reliable quantitative comparison could be achieved with 2D. 1D separation enabled high-throughput analysis of samples, however, depth in functional descriptions and reliability of quantification were lost. Nevertheless, the proteotyping of multiple samples was still possible. 2D separations provided more reliable quantitative data combined with a deeper insight into the taxonomic and functional composition of the microbial communities. Regarding taxonomic and functional composition, metaproteomics based on 2D is just the tip of an iceberg.

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.

Proteiniborus indolifex sp. nov., isolated from a thermophilic industrial-scale biogas plant

A novel strictly anaerobic bacterium, designated strain BA2-13^T, was isolated from a thermophilic industrial-scale biogas plant. Cells were rod-shaped and Gram-stain-positive. Growth occurred at temperatures of 25 to 50 °C and between pH 6.3 and 9.5. Strain BA2-13^T produced indole. Cell growth was stimulated by yeast extract, peptone, meat extract, a mixture of 20 amino acids, glucose, pyruvate and ribose. When grown on peptone and yeast extract, the main fermentation products were acetic acid, H₂ and CO₂. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_14 : 0 3-OH. Major polar lipids were diphosphatidylglycerol, glycolipids, phospholipids and phosphatidylgycerol. Phylogenetic analysis based on 16S rRNA gene nucleotide sequence analysis placed strain BA2-13^T within the order Clostridiales showing closest affiliation with Proteiniborusethanoligenes with 95.9 % sequence identity. Physiological, genotypic and chemotaxonomic differences of strain BA2-13^T from P. ethanoligenes support the description of a new species within the genus Proteiniborus for which we suggest the name Proteiniborusindolifex sp. nov. (type strain BA2-13^T=DSM 103060^T=LMG 29818^T).

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

BACKGROUND

Previous studies on the Miscellaneous Crenarchaeota Group, recently assigned to the novel archaeal phylum Bathyarchaeota, reported on the dominance of these Archaea within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail.

RESULTS

Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system. Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Individual metagenome assemblies followed by genome binning resulted in the reconstruction of five metagenome-assembled genomes (MAGs) of Bathyarchaeota. MAGs were estimated to be 65-92% complete, ranging in their genome sizes from 1.1 to 2.0 Mb. Phylogenetic classification based on core gene sets confirmed their placement within the phylum Bathyarchaeota clustering as a separate group diverging from most of the recently known Bathyarchaeota clusters. The genetic repertoire of these MAGs indicated an energy metabolism based on carbohydrate and amino acid fermentation featuring the potential for extracellular hydrolysis of cellulose, cellobiose as well as proteins. In addition, corresponding transporter systems were identified. Furthermore, genes encoding enzymes for the utilization of carbon monoxide and/or carbon dioxide via the Wood-Ljungdahl pathway were detected.

CONCLUSIONS

For the members of Bathyarchaeota detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that Bathyarchaeota members contribute presumably to hydrolysis and subsequent fermentation of organic substrates within biotechnological biogas production processes.

Effect of ensiling and silage additives on biogas production and microbial community dynamics during anaerobic digestion of switchgrass

Silage processing has a crucial positive impact on the methane yield of anaerobic treated substrates. Changes in the characteristics of switchgrass after ensiling with different additives and their effects on methane production and microbial community changes during anaerobic digestion were investigated. After ensiling (CK), methane yield was increased by 33.59% relative to that of fresh switchgrass (FS). In comparison with the CK treatment, methane production was improved by 17.41%, 13.08% and 8.72% in response to ensiling with LBr+X, LBr and X, respectively. A modified Gompertz model predicted that the optimum treatment was LBr+X, with a potential cumulative methane yield of 178.31mL/g total solids (TS) and a maximum biogas production rate of 44.39mL/g TS·d. Firmicutes and Bacteroidetes were the predominant bacteria in FS and silage switchgrass; however, the switchgrass treated with LBr+X was rich in Synergistetes, which was crucial for methane production.

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.

Effects of organic loading rate on biogas production from macroalgae: Performance and microbial community structure

Macroalgae biomass has been considered as a promising feedstock for biogas production. In order to improve the efficiency of anaerobic digestion (AD) of macroalgae, semi-continuous fermentation was conducted to examine the effects of organic loading rate (OLR) on biogas production from Macrocystis pyrifer. Results showed that, under OLRs of 1.37, 2.74, 4.12 and 6.85kgVS_substrate/(m³·d), the average unit biogas yields were 438.9, 477.3, 480.1 and 188.7mL/(gVS_substrated), respectively. It indicated that biogas production was promoted by the increased OLR in an appropriate range while inhibited by the OLR beyond the appropriate range. The investigation on physical-chemical parameters revealed that unfavorable VFAs concentration, pH and salinity might be the main causes for system failure due to the overrange OLR, while the total phenols failed to reach the inhibitory concentration. Microbial community analysis demonstrated that several bacterial and archaeal phyla altered with increase in OLR apparently.

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.

Non-autotrophic methanogens dominate in anaerobic digesters

Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.

Methodological flaws introduce strong bias into molecular analysis of microbial populations

AIMS

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results.

METHODS AND RESULTS

Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach.

CONCLUSIONS

The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured.

Ex-situ biogas upgrading and enhancement in different reactor systems

Biogas upgrading is envisioned as a key process for clean energy production. The current study evaluates the efficiency of different reactor configurations for ex-situ biogas upgrading and enhancement, in which externally provided hydrogen and carbon dioxide were biologically converted to methane by the action of hydrogenotrophic methanogens. The methane content in the output gas of the most efficient configuration was >98%, allowing its exploitation as substitute to natural gas. Additionally, use of digestate from biogas plants as a cost efficient method to provide all the necessary nutrients for microbial growth was successful. High-throughput 16S rRNA sequencing revealed that the microbial community was resided by novel phylotypes belonging to the uncultured order MBA08 and to Bacteroidales. Moreover, only hydrogenotrophic methanogens were identified belonging to Methanothermobacter and Methanoculleus genera. Methanothermobacter thermautotrophicus was the predominant methanogen in the biofilm formed on top of the diffuser surface in the bubble column reactor.

Anaerobic digestion of nitrogen rich poultry manure: Impact of thermophilic biogas process on metal release and microbial resistances

Poultry manure is a nitrogen rich fertilizer, which is usually recycled and spread on agricultural fields. Due to its high nutrient content, chicken manure is considered to be one of the most valuable animal wastes as organic fertilizer. However, when chicken litter is applied in its native form, concerns are raised as such fertilizers also include high amounts of antibiotic resistant pathogenic Bacteria and heavy metals. We studied the impact of an anaerobic thermophilic digestion process on poultry manure. Particularly, microbial antibiotic resistance profiles, mobile genetic elements promoting the resistance dissemination in the environment as well as the presence of heavy metals were focused in this study. The initiated heat treatment fostered a community shift from pathogenic to less pathogenic bacterial groups. Phenotypic and molecular studies demonstrated a clear reduction of multiple resistant pathogens and self-transmissible plasmids in the heat treated manure. That treatment also induced a higher release of metals and macroelements. Especially, Zn and Cu exceeded toxic thresholds. Although the concentrations of a few metals reached toxic levels after the anaerobic thermophilic treatment, the quality of poultry manure as organic fertilizer may raise significantly due to the elimination of antibiotic resistance genes (ARG) and self-transmissible plasmids.

Comparison of dry and wet milling pre-treatment methods for improving the anaerobic digestion performance of the Pennisetum hybrid

A planetary ball mill increased the specific methane yield of thePennisetumhybrid by 42%.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

BACKGROUND

One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.

RESULTS

The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis.

CONCLUSIONS

Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

BACKGROUND

Methane yield and biogas productivity of biogas plants (BGPs) depend on microbial community structure and function, substrate supply, and general biogas process parameters. So far, however, relatively little is known about correlations between microbial community function and process parameters. To close this knowledge gap, microbial communities of 40 samples from 35 different industrial biogas plants were evaluated by a metaproteomics approach in this study.

RESULTS

Liquid chromatography coupled to tandem mass spectrometry (Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer) of all 40 samples as triplicate enabled the identification of 3138 different metaproteins belonging to 162 biological processes and 75 different taxonomic orders. The respective database searches were performed against UniProtKB/Swiss-Prot and seven metagenome databases. Subsequent clustering and principal component analysis of these data allowed for the identification of four main clusters associated with mesophile and thermophile process conditions, the use of upflow anaerobic sludge blanket reactors and BGP feeding with sewage sludge. Observations confirm a previous phylogenetic study of the same BGP samples that was based on 16S rRNA gene sequencing by De Vrieze et al. (Water Res 75:312-323, 2015). In particular, we identified similar microbial key players of biogas processes, namely Bacillales, Enterobacteriales, Bacteriodales, Clostridiales, Rhizobiales and Thermoanaerobacteriales as well as Methanobacteriales, Methanosarcinales and Methanococcales. For the elucidation of the main biomass degradation pathways, the most abundant 1 % of metaproteins was assigned to the KEGG map 1200 representing the central carbon metabolism. Additionally, the effect of the process parameters (i) temperature, (ii) organic loading rate (OLR), (iii) total ammonia nitrogen (TAN), and (iv) sludge retention time (SRT) on these pathways was investigated. For example, high TAN correlated with hydrogenotrophic methanogens and bacterial one-carbon metabolism, indicating syntrophic acetate oxidation.

CONCLUSIONS

This is the first large-scale metaproteome study of BGPs. Proteotyping of BGPs reveals general correlations between the microbial community structure and its function with process parameters. The monitoring of changes on the level of microbial key functions or even of the microbial community represents a well-directed tool for the identification of process problems and disturbances.Graphical abstractCorrelation between the different orders and process parameter, as well as principle component analysis of all investigated biogas plants based on the identified metaproteins.

Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems

Anaerobic digestion (AD) is a microbial process widely used to treat organic wastes. While the microbes involved in digestion of municipal sludge are increasingly well characterized, the taxonomic and functional compositions of AD digesters treating industrial wastewater have been understudied. This study examined metagenomes from a biogas-producing digester treating municipal sludge in Shek Wu Hui (SWH), Hong Kong and an industrial wastewater digester in Guangzhou (GZ), China, and compared their taxonomic composition and reconstructed biochemical pathways. Genes encoding carbohydrate metabolism and protein metabolism functions were overrepresented in GZ, while genes encoding functions related to fatty acids, lipids and isoprenoids were overrepresented in SWH, reflecting the plants' feedstocks. Mapping of genera to functions in each community indicated that both digesters had a high level of functional redundancy, and a more even distribution of genera in GZ suggested that it was more functionally stable. While fermentation in both samples was dominated by Clostridia, SWH had an overrepresentation of Proteobacteria, including syntrophic acetogens, reflecting its more complex substrate. Considering the growing importance of biogas as an alternative fuel source, a detailed mechanistic understanding of AD is important and this report will be a basis for further study of industrial wastewater AD.

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.

Enhancing metaproteomics--The value of models and defined environmental microbial systems

Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.

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.

Digester performance and microbial community changes in thermophilic and mesophilic sequencing batch reactors fed with the fine sieved fraction of municipal sewage

This study investigates the start-up and operation of bench-scale mesophilic (35 °C) and thermophilic (55 °C) anaerobic sequencing batch reactor (SBR) digesters treating the fine sieved fraction (FSF) from raw municipal sewage. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter equipped with a 350 micron mesh. For the given wastewater, the major component of FSF was toilet paper, which is estimated to be 10-14 kg per year per average person in the western European countries. A seven months adaptation time was allowed for the thermophilic and mesophilic digesters in order to adapt to FSF as the sole substrate with varying dry solids content of 10-25%. Different SBR cycle durations (14, 9 and 2 days) were applied for both temperature conditions to study methane production rates, volatile fatty acids (VFAs) dynamics, lag phases, as well as changes in microbial communities. The prevailing sludge in the two digesters consisted of very different bacterial and archaeal communities, with OP9 lineage and Methanothermobacter being pre-dominant in the thermophilic digester and Bacteroides and Methanosaeta dominating the mesophilic one. Eventually, decreasing the SBR cycle period, thus increasing the FSF load, resulted in improved digester performances, particularly with regard to the thermophilic digester, i.e. shortened lag phases following the batch feedings, and reduced VFA peaks. Over time, the thermophilic digester outperformed the mesophilic one with 15% increased volatile solids (VS) destruction, irrespective to lower species diversity found at high temperature.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Impact of temperature on feed-flow characteristics and filtration performance of an upflow anaerobic sludge blanket coupled ultrafiltration membrane treating municipal wastewater

The objective of this study was to assess the operational feasibility of an anaerobic membrane bioreactor (AnMBR), consisting of an upflow anaerobic sludge blanket (UASB) reactor coupled to an ultrafiltration membrane unit, at two operational temperatures (25°C and 15°C) for the treatment of municipal wastewater. The results showed that membrane fouling at 15°C was more severe than that at 25°C. Higher chemical oxygen demand (COD) and soluble microbial products (SMP) concentrations, lower mean particle diameter, and higher turbidity in the UASB effluent at lower temperature aggravated membrane fouling compared to the 25°C operation. However, the overall AnMBR treatment performance was not significantly affected by temperature, which was attributed to the physical membrane barrier. Cake resistance was found responsible for over 40% of the total fouling in both cases. However, an increase was observed in the contribution of pore blocking resistance at 15°C related to the larger amount of fine particles in the UASB effluent compared to 25°C. Based on the overall results, it is concluded that an AnMBR, consisting of a UASB coupled membrane unit, is not found technically feasible for the treatment of municipal wastewater at 15°C, considering the rapid deterioration of the filtration performance.

Metaproteomics of complex microbial communities in biogas plants

Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.

Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor

Taxonomic and functional profiling based on metagenome analyses frequently revealed that members of the class Clostridia dominate biogas reactor communities and perform different essential metabolic pathways in the biogas fermentation process. Clostridium bornimense strain M2/40(T) was recently isolated from a mesophilic two-phase lab-scale biogas reactor continuously fed with maize silage and wheat straw. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding carbohydrate active enzyme production and fermentation of organic compounds for consolidated biofuel production from biomass. The C. bornimense M2/40(T) genome consists of a chromosome (2,917,864bp in size) containing 2613 protein coding sequences, and a 699,161bp chromid (secondary replicon) harboring 680 coding sequences. Both replicons feature very similar GC-contents of approximately 29%. The complex genome comprises three prophage regions, two CRISPR-cas systems and a putative cellulosomal gene cluster that is located on the second replicon (chromid) of the strain. The overexpressed glycosyl hydrolases (GH) CelK (GH9) and CelA (GH48) encoded in the cellulosomal gene cluster were shown to be active on the substrates xylan and xyloglucan whereas XghA (GH74) is highly active on xyloglucan. Reconstruction of fermentation pathways from genome sequence data revealed that strain M2/40(T) encodes all enzymes for hydrogen, acetate, formate, lactate, butyrate, and ethanol production, leading to the classification of the isolate as acidogenic bacterium. Phylogenetic analyses uncovered that the closest characterized relative of C. bornimense is C. cellulovorans. Comparative analyses of the C. bornimense and C. cellulovorans genomes revealed considerable rearrangements within their chromosomes suggesting that both species evolved separately for a relatively long period of time and adapted to specific tasks within microbial consortia responsible for anaerobic digestion.