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

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester

Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

BACKGROUND

The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.

RESULTS

The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.

CONCLUSIONS

This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.

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.

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H₂/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Background

Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced.

Results

In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes.

Conclusion

High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.

Cobalt oxide nanoparticles as a new strategy for enhancing methane production from anaerobic digestion of noxious aquatic weeds

This study investigated the effect of cobalt oxide nanoparticles (Co₃O₄-NPs) supplementation on anaerobic microbial population changes and anaerobic digestion (AD) performance and production. Co₃O₄-NPs (3 mg/L) showed the maximum enhancement of biogas yield over the cow dung (CD) as control and the co-digestion process of CD with water hyacinth (WH) by 58.9 and 27.2 %, respectively. Furthermore, methane (CH₄) yield was enhanced by 89.96 and 43.4 % over CD and co-digestion processes, respectively. Additionally, the microbiological assessment analysis using VIT® gene probe technology showed that Co₃O₄-NPs enhance the viability of total bacterial cells by 9 %. The techno-economic analysis reflects the revenue of this strategy on the highest net energy content of biogas, which was achieved with 3 mg/L Co₃O₄-NPs and was 428.05 kWh with a net profit of 67.66 USD/m³ of the substrate. Therefore, nanoparticle supplementation to the AD process can be considered a promising approach to enhance biogas and CH₄.

Current Trends in Biological Valorization of Waste-Derived Biomass: The Critical Role of VFAs to Fuel A Biorefinery

The looming climate and energy crises, exacerbated by increased waste generation, are driving research and development of sustainable resource management systems. Research suggests that organic materials, such as food waste, grass, and manure, have potential for biotransformation into a range of products, including: high-value volatile fatty acids (VFAs); various carboxylic acids; bioenergy; and bioplastics. Valorizing these organic residues would additionally reduce the increasing burden on waste management systems. Here, we review the valorization potential of various sustainably sourced feedstocks, particularly food wastes and agricultural and animal residues. Such feedstocks are often micro-organism-rich and well-suited to mixed culture fermentations. Additionally, we touch on the technologies, mainly biological systems including anaerobic digestion, that are being developed for this purpose. In particular, we provide a synthesis of VFA recovery techniques, which remain a significant technological barrier. Furthermore, we highlight a range of challenges and opportunities which will continue to drive research and discovery within the field. Analysis of the literature reveals growing interest in the development of a circular bioeconomy, built upon a biorefinery framework, which utilizes biogenic VFAs for chemical, material, and energy applications.

Deterministic processes drive the microbial assembly during the recovery of an anaerobic digester after a severe ammonia shock

Anaerobic digestion allows to produce sustainable energy but the microbial community involved in this process is highly sensitive to perturbations. In this study, a longitudinal experiment was performed in two sets of triplicate bioreactors to evaluate the influence of ammonia addition on AD microbiome and its recovery. Zeolite was added in three reactors to mitigate the inhibition. Microbial dynamics were monitored with 16S rRNA sequencing at 15 time points. Dominant methanogenic pathways were determined with gas isotopic signature analysis. Zeolite addition did not enable to reduce ammonia inhibition or improve the process under the conditions tested. In all the bioreactors, ammonia inhibition sharply decreased the methane production but the process could restart thanks to the increase of hydrogenotrophic archaea and syntrophic bacteria. Interestingly, similar behaviour was observed in the six reactors. Neutral modelling and null model were used and showed that a deterministic process governed the recovery of AD microbiome after failure.

Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways

Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.

Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches

Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms under anaerobic conditions. Methane gas, a beneficial by-product of the AD process, is a renewable energy source that can replace fossil fuels following purification. However, detailed functional roles and metabolic interactions between microbial populations involved in organic waste removal and methanogenesis are yet to be known. Recent metagenomic approaches based on advanced high-throughput sequencing techniques have enabled the exploration of holistic microbial taxonomy and functionality of complex microbial populations involved in the AD process. Gene-centric and genome-centric analyses based on metagenome-assembled genomes are a platform that can be used to study the composition of microbial communities and their roles during AD. This review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the AD process.

Microbial community assembly and dynamics in Granular, Fixed-Biofilm and planktonic microbiomes valorizing Long-Chain fatty acids at 20 °C

Distinct microbial assemblages evolve in anaerobic digestion (AD) reactors to drive sequential conversions of organics to methane. The spatio-temporal development of three such assemblages (granules, biofilms, planktonic) derived from the same inoculum was studied in replicated bioreactors treating long-chain fatty acids (LCFA)-rich wastewater at 20 °C at hydraulic retention times (HRTs) of 12-72 h. We found granular, biofilm and planktonic assemblages differentiated by diversity, structure, and assembly mechanisms; demonstrating a spatial compartmentalisation of the microbiomes from the initial community reservoir. Our analysis linked abundant Methanosaeta and Syntrophaceae-affiliated taxa (Syntrophus and uncultured) to their putative, active roles in syntrophic LCFA bioconversion. LCFA loading rates (stearate, palmitate), and HRT, were significant drivers shaping microbial community dynamics and assembly. This study of the archaea and syntrophic bacteria actively valorising LCFAs at short HRTs and 20 °C will help uncover the microbiology underpinning anaerobic bioconversions of fats, oil and grease.

Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste

Bacterial community structure and dynamics in anaerobic digesters are primarily influenced by feedstock composition. It is therefore important to unveil microbial traits that explain microbiome variations in response to substrate changes. Here, gene and genome-centric metagenomics were used to examine microbiome dynamics in four laboratory-scale reactors, in which sewage sludge was co-digested with increasing amounts of food waste. A co-occurrence network revealed microbiome shifts in response to changes in substrate composition and concentration. Food waste concentration correlated with extracellular enzymes and metagenome-assembled genomes (MAGs) involved in the degradation of complex carbohydrates commonly found in fruits and plant cell walls as well as with the abundance of hydrolytic MAGs. A key role was attributed to Proteiniphillum for being the only bacteria that encoded the complete pectin degradation pathway. These results suggest that changes of feedstock composition establish new microbial niches for bacteria with the capacity to degrade newly added substrates.

The metabolic process of methane production by combined fermentation of coal and corn straw

The anaerobic degradation of coal combined with straw biomass can promote the methane production. The biogas production potential and metabolic pathway were explored via the co-digestion simulation experiment of coal and corn straw. The results showed that 2 g of corn straw combined respectively with 4 g of bituminous coal A, 6 g of bituminous coal B and 4 g of bituminous coal C resulted in highest methane yields. The structure of lignocellulose in corn straw was partially degraded into guaiacyl and syringyl units. Meanwhile, the content of biodegradable tyrosine like protein and soluble microbial by-products in liquid phase significantly decreased. Significantly, the structure of archaea altered from aceticlastic to hydrogenotrophic methanogens when the fermentation substrate changed from high to low rank coal. The proportion of hydrogenotrophic methanogens was significantly higher than that of aceticlastic and methylotrophic methanogens, and the hydrogenotrophic pathway was dominant than the aceticlastic pathway.

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.

Enhancement of Biogas Production via Co-Digestion of Wastewater Treatment Sewage Sludge and Brewery Spent Grain: Physicochemical Characterization and Microbial Community

The present study intends to evaluate a synergy towards enhanced biogas production by co-digesting municipal sewage sludge (SS) with brewery spent grain (BSG). To execute this, physicochemical and metagenomics analysis was conducted on the sewage sludge substrate. The automatic methane potential test system II (AMPTS II) biochemical methane potential (BMP) batch setup was operated at 35 ± 5 °C, pH range of 6.5–7.5 for 30 days’ digestion time on AMPTS II and 150 days on semi-continuous setup, where the organic loading rate (OLR) was guided by pH and the volatile fatty acids to total alkalinity (VFA/TA) ratio. Metagenomics analysis revealed that Proteobacteria was the most abundant phyla, consisting of hydrolytic and fermentative bacteria. The archaea community of hydrogenotrophic methanogen genus was enriched by methanogens. The highest BMP was obtained with co-digestion of SS and BSG, and 9.65 g/kg of VS. This not only increased biogas production by 104% but also accelerated the biodegradation of organic matters. However, a significant reduction in the biogas yield, from 10.23 NL/day to 2.02 NL/day, was observed in a semi-continuous process. As such, it can be concluded that different species in different types of sludge can synergistically enhance the production of biogas. However, the operating conditions should be optimized and monitored at all times. The anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment works (WWTWs) and sustainable waste management. It is recommended to upscale co-digestion of the feed for the pilot biogas plant. This will also go a long way in curtailing and minimizing the impacts of sludge disposal in the environment.

Sustained effect of zero-valent iron nanoparticles under semi-continuous anaerobic digestion of sewage sludge: Evolution of nanoparticles and microbial community dynamics

The effects of adding zero-valent iron nanoparticles (nZVI) on the physicochemical, biological and biochemical responses of a semi-continuous anaerobic digestion of sewage sludge have been assessed. Two sets of consecutive experiments of 103 and 116 days, respectively, were carried out in triplicate. nZVI were magnetically retained in the reactors, and the effect of punctual doses (from 0.27 to 4.33 g L^-1) over time was studied. Among the different parameters monitored, only methane content in the biogas was significantly higher when nZVI was added. However, this effect was progressively lost after the addition, and in 5-7 days, the methane content returned to initial values. The increase in the oxidation state of nanoparticles seems to be related to the loss of effect over time. Higher dose (4.33 g L^-1) sustained positive effects for a longer time along with higher methane content, but this fact seems to be related to microbiome acclimation. Changes in microbial community structure could also play a role in the mechanisms involved in methane enhancement. In this sense, the microbial consortium analysis reported a shift in the balance among acetogenic eubacterial communities, and a marked increase in the relative abundance of members assigned to Methanothrix genus, recognized as acetoclastic species showing high affinity for acetate, which explain the rise in methane content in the biogas. This research demonstrates that biogas methane enrichment in semicontinuous anaerobic digesters can be achieved by using nZVI nanoparticles, thus increasing energy production or reducing costs of a later biogas upgrading process.

Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics

BACKGROUND

The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.

RESULTS

The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.

CONCLUSIONS

External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.

Sludge digestibility and functionally active microorganisms in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking

Methanogenic sludge digestion plays a pivotal role in attenuating and hygienizing the massively-produced waste activated sludge (WAS), which is predominantly composed of microbial cells and extracellular polymeric substances (EPS). The efficient sludge digestion requires a variety of functionally active microorganisms working together closely to convert sludge organic matter into biogas. Nonetheless, the digestion efficiency (or digestibility quantified as carbon removal efficiency) of major sludge constituents (i.e., microbial cells and EPS) and associated functionally active microorganisms in sludge digesters remain elusive. In this study, we identified the digestibility of sludge microbial cells and the associated functionally active microorganisms by using Escherichia coli (E. coli)-fed digestion and microbial source tracking. The average carbon removals in four digesters fed with fresh WAS (WAS-AD), thermal pretreated WAS (Thermal-WAS-AD), E. coli cells (E.coli-AD) and thermal pretreated E. coli cells (Thermal-E.coli-AD) were 30.6 ± 3.4%, 45.8 ± 2.9%, 69.0 ± 3.4% and 68.9 ± 4.6%, respectively. Compared to WAS-AD and Thermal-WAS-AD, the significantly higher carbon removals in E. coli-AD and Thermal-E. coli-AD suggested the remarkably higher digestibility of microbial cells than EPS, and releasing organic matter from EPS might be a rate-limiting step in sludge digestion. Functionally active microorganisms for microbial cell digestion predominantly included fermenters (e.g., Petrimonas and Lentimicrobium), syntrophic acetogens (e.g., Synergistaceae) and methanogens (e.g., Methanosaeta and Methanosarcina). Microbial source tracking estimation showed that the microbial cell-digesting populations accounted for 35.6 ± 9.1% and 70.3 ± 10.1% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively. Accordingly, the functionally active microorganisms for digestion of both microbial cells and EPS accounted for 64.5 ± 12.1% and 97.3 ± 2.0% of total digestion sludge microbiome in WAS-AD and Thermal-WAS-AD, respectively. By contrast, feeding WAS-derived microorganisms accounted for 23.2 ± 4.4% and 2.3 ± 1.2% of total microbial communities in the WAS-AD and Thermal-WAS-AD, respectively.

A microbial gene catalog of anaerobic digestion from full-scale biogas plants

BACKGROUND

Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood.

FINDINGS

In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination.

CONCLUSIONS

This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

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.

Microbial invasions in sludge anaerobic digesters

Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.

Intermittent aeration of landfill simulation bioreactors: Effects on emissions and microbial community

Landfill simulation experiments were run at lab-scale to compare the effects of intermittent and continuous aeration on the evolution of leachate composition and biogas production. The experiments were carried out using six reactors; two of them under continuous aeration, two under intermitted aeration and two anaerobic as a control. Different aeration regimes produced different effects on reactors. As expected, carbon discharge via biogas was higher in reactors under continuous aeration than under intermittent aeration. The evolution of leachate quality was affected by the aeration regimes; however, at test end very similar concentration were ascertained for relevant leachate parameters in all aerated reactors. A comprehensive description of the aerobic and anaerobic landfill microbiome is provided, using a metagenomic approach focused on the microbial genome reconstruction. A time course investigation evidenced the modification of the microbiome and revealed taxa and specific microbes more strictly connected to the environmental parameters of the reactors. Methanoculleus, Syntrophomonas and Parabacteroides were identified as the genera more strictly connected to biogas production, while numerous species belonging to Thiomonas, Nitrosomonas, Xanthomonadaceae, Myxococcales and Alcaligenaceae were found to be connected with NH₄⁺ oxidation.

Enhancement of anaerobic digestion of phoenix tree leaf by mild alkali pretreatment: Optimization by Taguchi orthogonal design and semi-continuous operation

This study aimed at evaluating the valorization of a typical yard waste, phoenix tree leaf (PTL), through mild alkali pretreatment followed by anaerobic digestion (AD). To this end, L₉ Taguchi orthogonal biochemical methane potential (BMP) tests and semi-continuous AD experiments were conducted to examine the optimum pretreatment condition and the long term effect of alkali pretreatment on AD. The community structure evolutions were analyzed by high throughput 16S rRNA gene pyrosequencing. The results indicated that alkali pretreatment was effective on decrystallization and releasing more surface of PTL for enzyme attacking. The methane yield was positively correlated with lignin removal (R²=0.8242). In semi-continuous mode, 151.5±7.9 mL/g VS of the methane yield was obtained for alkali pretreated PTL, which was 80% higher than that of untreated one. Microbial community analysis indicated that alkali pretreatment led to a higher abundance of dominated bacteria (Bacteroidetes and Clostridia) and archaea of Methanosaeta.

PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning

PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter. Using a PacBio platform, 1.58 million long reads (19.6 Gb) were produced with an average length of 7,604 bp. Using an Illumina HiSeq platform, 151.2 million read pairs (45.4 Gb) were produced. Hybrid assemblies using PacBio long reads and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length, contig N50 size, and number of large contigs. Interestingly, depth-based hybrid assemblies generated a higher percentage of complete genes (98.86%) compared to those based on HiSeq contigs only (40.29%), because the PacBio reads were long enough to cover many repeating short elements and capture multiple genes in a single read. Additionally, the incorporation of PacBio long reads led to considerable advantages regarding reducing contig numbers and increasing the completeness of the genome reconstruction, which was poorly assembled and binned when using HiSeq data alone. From this comparison of PacBio long reads with Illumina HiSeq short reads related to complex microbiome samples, we conclude that PacBio long reads can produce longer contigs, more complete genes, and better genome binning, thereby offering more information about metagenomic samples.

Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

BACKGROUND

Biomethanation is a promising solution to upgrade the CH₄ content in biogas. This process consists in the injection of H₂ into an anaerobic digester, using the capacity of indigenous hydrogenotrophic methanogens for converting the injected H₂ and the CO₂ generated from the anaerobic digestion process into CH₄. However, the injection of H₂ could cause process disturbances by impacting the microbial communities of the anaerobic digester. Better understanding on how the indigenous microbial community can adapt to high H₂ partial pressures is therefore required.

RESULTS

Seven microbial inocula issued from industrial bioprocesses treating different types of waste were exposed to a high H₂ partial pressure in semi-continuous reactors. After 12 days of operation, even though both CH₄ and volatile fatty acids (VFA) were produced as end products, one of them was the main product. Acetate was the most abundant VFA, representing up to 94% of the total VFA production. VFA accumulation strongly anti-correlated with CH₄ production according to the source of inoculum. Three clusters of inocula were distinguished: (1) inocula leading to CH₄ production, (2) inocula leading to the production of methane and VFA in a low proportion, and (3) inocula leading to the accumulation of mostly VFA, mainly acetate. Interestingly, VFA accumulation was highly correlated to a low proportion of archaea in the inocula, a higher amount of homoacetogens than hydrogenotrophic methanogens and, the absence or the very low abundance in members from the Methanosarcinales order. The best methanogenic performances were obtained when hydrogenotrophic methanogens and Methanosarcina sp. co-dominated all along the operation.

CONCLUSIONS

New insights on the microbial community response to high H₂ partial pressure are provided in this work. H₂ injection in semi-continuous reactors showed a significant impact on microbial communities and their associated metabolic patterns. Hydrogenotrophic methanogens, Methanobacterium sp. or Methanoculleus sp. were highly selected in the reactors, but the presence of co-dominant Methanosarcinales related species were required to produce higher amounts of CH₄ than VFA.

The next frontier of the anaerobic digestion microbiome: From ecology to process control

The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.

Assessment of the microbial interplay during anaerobic co-digestion of wastewater sludge using common components analysis

Anaerobic digestion (AD) is used to minimize solid waste while producing biogas by the action of microorganisms. To give an insight into the underlying microbial dynamics in anaerobic digesters, we investigated two different AD systems (wastewater sludge mixed with either fish or grass waste). The microbial activity was characterized by 16S RNA sequencing. 16S data is sparse and dispersed, and existent data analysis methods do not take into account this complexity nor the potential microbial interactions. In this line, we proposed a data pre-processing pipeline addressing these issues while not restricting only to the most abundant microorganisms. The data were analyzed by Common Components Analysis (CCA) to decipher the effect of substrate composition on the microorganisms. CCA results hinted the relationships between the microorganisms responding similarly to the AD physicochemical parameters. Thus, in overall, CCA allowed a better understanding of the inter-species interactions within microbial communities.

Biomethane Potential Test: Influence of Inoculum and the Digestion System

High precision of measurement of methane potential is important for the economic operation of biogas plants in the future. The biochemical methane potential (BMP) test based on the VDI 4630 protocol is the state-of-the-art method to determine the methane potential in Germany. The coefficient of variation (CV) of methane yield was >10% in several previous inter-laboratory tests. The aim of this work was to investigate the effects of inoculum and the digestion system on the measurement variability. Methane yield and methane percentage of five substrates were investigated in a Hohenheim biogas yield test (D-HBT) by using five inocula, which were used several times in inter- laboratory tests. The same substrates and inocula were also tested in other digestion systems. To control the quality of the inocula, the effect of adding trace elements (TE) and the microbial community was investigated. Adding TE had no influence for the selected, well- supplied inocula and the community composition depended on the source of the inocula. The CV of the specific methane yield was <4.8% by using different inocula in one D-HBT (D-HBT1) and <12.8% by using different digestion systems compared to D-HBT1. Incubation time between 7 and 14 days resulted in a deviation in CV of <4.8%.

The microbiome driving anaerobic digestion and microbial analysis

The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.

Illustration of the microbial community selected by optimized process and nutritional parameters resulting in enhanced biomethanation of rice straw without thermo-chemical pretreatment

Effects of different process and nutritional parameters on microbial community structure and function were investigated to enhance the biomethanation of rice straw without any thermochemical pre-treatment. The study was performed in a mesophilic anaerobic digester with cattle dung slurry as inoculum. The highest methane yield of 274 ml g^-1 volatile solids was obtained from particulate rice straw (1 mm size, 7.5% solids loading rate) at 37 °C, pH-7, when supplemented with urea (carbon: nitrogen ratio, 25:1) and zinc as trace element (100 µM) at 21 days hydraulic retention time. The optimization of conditions selected Clostridium, Bacteroides, and Ruminococcus as dominant hydrolytic bacteria and Methanosarcina as the methanogen. Analysis of metagenome and metatranscriptome revealed wide array of bacterial lignocellulolytic enzymes that efficiently hydrolyzed the rice straw. The methane yield was >80% of the theoretical yield, making this green process a sustainable choice for efficient extraction of energy from rice straw.

Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

Prospective Approach to the Anaerobic Bioconversion of Benzo- and Dibenzothiophene Sulfones to Sulfide

Sulfur recovery from organic molecules such as toxic sulfones is an actual problem, and its solution through the use of environmentally friendly and nature-like processes looks attractive for research and application. For the first time, the possible bioconversion of organic sulfones (benzo-and dibenzothiophene sulfones) to inorganic sulfide under anaerobic conditions with simultaneous biogas production from glucose within a methanogenesis process is demonstrated. Biogas with a methane content of 50.7%-82.1% was obtained without H2S impurities. Methanogenesis with 99.7%-100% efficiency and 97.8%-100% conversion of benzo- and dibenzothiophene sulfones (up to 0.45 mM) to inorganic sulfide were obtained in eight days by using a combination of various anaerobic biocatalysts immobilized in a poly(vinyl alcohol) cryogel. Pure cell cultures of sulfate-reducing bacteria and/or H2-producing bacteria were tested as additives to the methanogenic activated sludge. The immobilized activated sludge "enhanced" by bacterial additives appeared to retain its properties and be usable multiple times for the conversion of sulfones under batch conditions.

Effects of H2:CO2 ratio and H2 supply fluctuation on methane content and microbial community composition during in-situ biological biogas upgrading

BACKGROUND

Commercial biogas upgrading facilities are expensive and consume energy. Biological biogas upgrading may serve as a low-cost approach because it can be easily integrated with existing facilities at biogas plants. The microbial communities found in anaerobic digesters typically contain hydrogenotrophic methanogens, which can use hydrogen (H₂) as a reducing agent for conversion of carbon dioxide (CO₂) into methane (CH₄). Thus, biological biogas upgrading through the exogenous addition of H₂ into biogas digesters for the conversion of CO₂ into CH₄ can increase CH₄ yield and lower CO₂ emission.

RESULTS

The addition of 4 mol of H₂ per mol of CO₂ was optimal for batch biogas reactors and increased the CH₄ content of the biogas from 67 to 94%. The CO₂ content of the biogas was reduced from 33 to 3% and the average residual H₂ content was 3%. At molar H₂:CO₂ ratios > 4:1, all CO₂ was converted into CH₄, but the pH increased above 8 due to depletion of CO₂, which negatively influenced the process stability. Additionally, high residual H₂ content in these reactors was unfavourable, causing volatile fatty acid accumulation and reduced CH₄ yields. The reactor microbial communities shifted in composition over time, which corresponded to changes in the reactor variables. Numerous taxa responded to the H₂ inputs, and in particular the hydrogenotrophic methanogen Methanobacterium increased in abundance with addition of H₂. In addition, the apparent rapid response of hydrogenotrophic methanogens to intermittent H₂ feeding indicates the suitability of biological methanation for variable H₂ inputs, aligning well with fluctuations in renewable electricity production that may be used to produce H₂.

CONCLUSIONS

Our research demonstrates that the H₂:CO₂ ratio has a significant effect on reactor performance during in situ biological methanation. Consequently, the H₂:CO₂ molar ratio should be kept at 4:1 to avoid process instability. A shift toward hydrogenotrophic methanogenesis was indicated by an increase in the abundance of the obligate hydrogenotrophic methanogen Methanobacterium.

Long-Term Storage and Use of Artificially Immobilized Anaerobic Sludge as a Powerful Biocatalyst for Conversion of Various Wastes Including Those Containing Xenobiotics to Biogas

The aim of this paper is to demonstrate the possibilities of anaerobic sludge cells immobilized into poly(vinyl alcohol) cryogel for the methanogenic conversion of various lignocellulosic waste and other media containing antibiotics (ampicillin, kanamycin, benzylpenicillin) or pesticides (chlorpyrifos or methiocarb and its derivatives). It was established that the immobilized cells of the anaerobic consortium can be stored frozen for at least three years while preserving a high level of metabolic activity. The cells after the long-term storage in an immobilized and frozen state were applied for the methanogenesis of a wide number of wastes, and an increase in both methane yield and methane portion in the produced biogas as compared to the conventionally used suspended anaerobic sludge cells, was ensured. It was shown that the “additional” introduction of bacterial Clostridium acetobutylicum, Pseudomonas sp., Enterococcus faecalis cells (also immobilized using same support) improves characteristics of methanogenesis catalyzed by immobilized anaerobic sludge.

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics

In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.

The Future Agricultural Biogas Plant in Germany: A Vision

After nearly two decades of subsidized and energy crop-oriented development, agricultural biogas production in Germany is standing at a crossroads. Fundamental challenges need to be met. In this article we sketch a vision of a future agricultural biogas plant that is an integral part of the circular bioeconomy and works mainly on the base of residues. It is flexible with regard to feedstocks, digester operation, microbial communities and biogas output. It is modular in design and its operation is knowledge-based, information-driven and largely automated. It will be competitive with fossil energies and other renewable energies, profitable for farmers and plant operators and favorable for the national economy. In this paper we discuss the required contribution of research to achieve these aims.

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia

Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.

Evaluation of the digestibility of steam-exploded wheat straw by ruminal fermentation, sugar yield and microbial structurein vitro

Wheat straw is considered an abundant lignocellulosic biomass source in China. However, its recalcitrance hinders the degradation of wheat straw by enzymes and microbes. In this study, we investigated the optimum steam explosion conditions of pretreated wheat straw by response surface methodology to improve its nutrition level as a feedstuff for the ruminant industry or as a feedstock for biofuel production. The highest volatile fatty acid (VFA) yield (30.50 mmol L⁻¹) was obtained at 2.3 MPa, 90 s and a moisture content of 36.46%. Under optimal conditions, steam explosion significantly altered the fermentation parameters in vitro. Ionic chromatography showed that pretreating wheat straw could improve the production of fermentable sugar, which was ascribed to the degradation of cellulose and hemicellulose. In addition, high throughput 16S rRNA amplicon sequencing analysis revealed that steam explosion changed the microbial community and enhanced the colonization of cellulolytic bacteria. Our findings demonstrated that steam explosion pretreatment could greatly improve the digestibility of wheat straw by facilitating sugar production and microbial colonization.

Wheat straw is considered an abundant lignocellulosic biomass source in China.

Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.

Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion

BACKGROUND

Demand-driven biogas production could play an important role for future sustainable energy supply. However, feeding a biogas reactor according to energy demand may lead to organic overloading and, thus, to process failures. To minimize this risk, digesters need to be actively steered towards containing more robust microbial communities. This study focuses on acetogenesis and methanogenesis as crucial process steps for avoiding acidification. We fed lab-scale anaerobic digesters with volatile fatty acids under various feeding regimes and disturbances. The resulting microbial communities were analyzed on DNA and RNA level by terminal restriction fragment length polymorphism of the mcrA gene, 16S rRNA gene amplicon sequencing, and a [2-13C]-acetate assay. A modified Anaerobic Digestion Model 1 (ADM1) that distinguishes between the acetoclastic methanogens Methanosaeta and Methanosarcina was developed and fitted using experimental abiotic and biotic process parameters.

RESULTS

Discontinuous feeding led to more functional resilience than continuous feeding, without loss in process efficiency. This was attributed to a different microbial community composition. Methanosaeta dominated the continuously fed reactors, while its competitor Methanosarcina was washed out. With discontinuous feeding, however, the fluctuating acetic acid concentrations provided niches to grow and co-exist for both organisms as shown by transcription analysis of the mcrA gene. Our model confirmed the higher functional resilience due to the higher abundance of Methanosarcina based on its higher substrate uptake rate and higher resistance to low pH values. Finally, we applied our model to maize silage as a more complex and practically relevant substrate and showed that our model is likely transferable to the complete AD process.

CONCLUSIONS

The composition of the microbial community determined the AD functional resilience against organic overloading in our experiments. In particular, communities with higher share of Methanosarcina showed higher process stability. The share of these microorganisms can be purposefully increased by discontinuous feeding. A model was developed that enables derivation of the necessary feeding regime for a more robust community with higher share of Methanosarcina.

Genetic repertoires of anaerobic microbiomes driving generation of biogas

BACKGROUND

Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters. Currently, most of the efforts on microbial management system (MiMaS) are focused on process-specific marker species and community dynamics, but a practical implementation is in its infancy. The high number of unknown and uncharacterized microorganisms in general is one of the reasons hindering further advancements.

RESULTS

A Biogas Metagenomics Hybrid Assembly (BioMETHA) database, derived from microbiomes of biogas plants, was generated using a dedicated assembly strategy for different metagenomic datasets. Long reads from nanopore sequencing (MinION) were combined with short, more accurate second-generation sequencing reads (Illumina). The hybrid assembly resulted in 231 genomic bins each representing a taxonomic unit with an average completeness of 47%. Functional annotation identified 13,190 non-redundant genes covering roughly 207 k coding sequences. Mapping rates of metagenomics DNA derived from diverse biogas plants and laboratory reactors increased up to 73%. In addition, an EC (enzyme commission) reference sequence collection (ERSC) was generated whose genes are crucial for biogas-related processes, consisting of 235 unique EC numbers organized in 52 metabolic modules. Mapping rates of metatranscriptomic data to this ERSC revealed coverages of up to 93%. Process parameters and imbalances of laboratory reactors could be reconstructed by evaluating abundance of biogas-specific metabolic modules using metatranscriptomic data derived from various fermenter systems.

CONCLUSION

This newly established metagenomic hybrid assembly in combination with an EC reference sequence collection might help to shed light on the microbial dark matter of biogas plants by contributing to the development of a reference for biogas plant microbiome-specific gene sequences. Considering a biogas microbiome as a complex meta-organism expressing a meta-transcriptome, the approach established here could lay the foundation for a function-based microbial management system.

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.

Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics

The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the Bacteroidetes are able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCE This work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales Even though structural elements of cellulosome were restricted to Clostridiales species, our study identified a putative mechanism in Bacteroidetes species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.

Metagenome Sequences of a Thermophilic Anaerobic Digester Adapted to a Low C/N Ratio, High-Ammonia Feedstock (Poultry Litter)

We sequenced the metagenome of a pilot-scale thermophilic digester with long-term, stable performance on poultry litter feedstock which has a very low C/N ratio, a high ammonia level, and high lignocellulose content. Firmicutes were the dominant phylum (68.9%). Other abundant phyla included Bacteroidetes, Euryarchaeota, and Thermotogae This microbiome represents a hydrogenotrophic methanogenic community with high diversity.

Comparative evaluation of sludge surface charge as an indicator of process fluctuations in a biogas reactor

The current political situation imposes high demands on the economic feasibility of biogas plants. High prizes for biogas substrates and a trend to reduced feed-in tariffs generated an increasing need to optimize substrate exploitation and operation conditions. This includes a comprehensive and reliable biogas process monitoring. For that purpose a number of different process monitoring methods like CH₄ production rate, FOS/TAC (ratio of organic acid/total inorganic carbon alkalinity), pH or (auto)fluorescence are successfully applied. This paper will evaluate whether the surface charge - a parameter, which has not been in use so far - might also be suitable for biogas process monitoring. Since it is known that the surface charge is correlated with the adherence and floc formation capability of microbial cells, a change in surface charge might also reflect a change in the biogas process efficiency, or vice versa. To test this hypothesis, samples for the investigations were taken from a continuously stirred laboratory-scale tank biogas reactor with continuously increased substrate load. The impact of the load change was measured with both, surface charge and a number of more established monitoring parameters as given above. It was found that the "surface charge" reflected well short-term process changes (within hours) caused by an increasing substrate load in the reactor, though the highest short-term monitoring sensitivity was obtained with the "FOS/TAC" monitoring. Different from other monitoring parameters like CH₄, pH, or FOS/TAC the value of the parameter "surface charge" decreased with every feeding, eventually indicating a continuous deterioration of the biogas process conditions. Surface charge might therefore be of particular use as a complementary tool especially for the long-term monitoring of biogas process conditions.