Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization

The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities.

Evolution mechanism of microbial community structure and metabolic activity in aquatic nutrient-poor sedimentary environments driven by 17β-estradiol pollution

17β-Estradiol (E2) is a novel micro-pollutant that is widely distributed in aquatic sediments and has a universal toxicological effect on aquatic organisms. However, its ecological impact on aquatic microorganisms is not yet clear. In this study, we designed a simulation system for oligotrophic water deposition in the laboratory, analyzed the impact of different concentrations of E2 pollution on the carbon metabolism activity (carbon gas emission rate) of water microorganisms. Based on high-throughput sequencing results, we revealed the impact of E2 pollution on the community structure succession and metabolic function of bacteria, archaea, and methanogens in the simulated system, explored the impact mechanism of E2 pollution on microbial carbon metabolism in water bodies. Our results suggested that E2 significantly impacts the bacterial and archaeal community rather than the methanogen community, thereby indirectly inhibiting methane production. The achievements will bridge the theoretical gap between estrogen metabolism and carbon metabolism in sedimentary environments and contribute to enriching the ecological toxicology theory of steroid estrogen.

Electron-transfer-driven spatial optimisation of anaerobic consortia for efficient methanogenesis: Neglected inductive effect of conductive materials

The inductive effect of conductive materials (CMs) on enhancing methanogenesis metabolism has been overlooked. Herein, we highlight role of CMs in inducing the spatial optimisation of methanogenic consortia by altering the Lewis acid-base (AB) interactions within microbial aggregates. In the presence of CMs and after their removal, the methane production and methane proportion in biogas significantly increase, with no significant difference between the two situations. Analyses of interactions between CMs and extracellular polymer substances (EPSs) with and without D2O reveal that CMs promote release and transfer potential of electron in EPSs, which induce and enhance the role of water molecules being primarily as proton acceptors in the hydrogen bonding between EPSs and water, thereby changing the electron-donor- and electron-acceptor-based AB interactions. Investigations of succession dynamics of microbial communities, co-occurrence networks, and metagenomics further indicate that electron transfer drives the microbial spatial optimisation for efficient methanogenesis through intensive interspecies interactions.

From waste management to circular economy: Leveraging thermophiles for sustainable growth and global resource optimization

Waste of any origin is one of the most serious global and man-made concerns of our day. It causes climate change, environmental degradation, and human health problems. Proper waste management practices, including waste reduction, safe handling, and appropriate treatment, are essential to mitigate these consequences. It is thus essential to implement effective waste management strategies that reduce waste at the source, promote recycling and reuse, and safely dispose of waste. Transitioning to a circular economy with policies involving governments, industries, and individuals is essential for sustainable growth and waste management. The review focuses on diverse kinds of environmental waste sources around the world, such as residential, industrial, commercial, municipal services, electronic wastes, wastewater sewerage, and agricultural wastes, and their challenges in efficiently valorizing them into useful products. It highlights the need for rational waste management, circularity, and sustainable growth, and the potential of a circular economy to address these challenges. The article has explored the role of thermophilic microbes in the bioremediation of waste. Thermophiles known for their thermostability and thermostable enzymes, have emerged to have diverse applications in biotechnology and various industrial processes. Several approaches have been explored to unlock the potential of thermophiles in achieving the objective of establishing a zero-carbon sustainable bio-economy and minimizing waste generation. Various thermophiles have demonstrated substantial potential in addressing different waste challenges. The review findings affirm that thermophilic microbes have emerged as pivotal and indispensable candidates for harnessing and valorizing a range of environmental wastes into valuable products, thereby fostering the bio-circular economy.

Microbiome dynamics and products profiles of biowaste fermentation under different organic loads and additives

Biowaste fermentation is a promising technology for low-carbon print bioenergy and biochemical production. Although it is believed that the microbiome determines both the fermentation efficiency and the product profiles of biowastes, the explicit mechanisms of how microbial activity controls fermentation processes remained to be unexplored. The current study investigated the microbiome dynamics and fermentation product profiles of biowaste fermentation under different organic loads (5, 20, and 40 g-VS/L) and with additives that potentially modulate the fermentation process via methanogenesis inhibition (2-bromoethanesulfonate) or electron transfer promotion (i.e., reduced iron, magnetite iron, and activated carbon). The overall fermentation products yields were 440, 373 and 208 CH4-eq/g-VS for low-, medium- and high-load fermentation. For low- and medium-load fermentation, volatile fatty acids (VFAs) were first accumulated and were gradually converted to methane. For high-load fermentation, VFAs were the main fermentation products during the entire fermentation period, accounting for 62% of all products. 16S rRNA-based analyses showed that both 2-bromoethanesulfonate addition and increase of organic loads inhibited the activity of methanogens and promoted the activity of distinct VFA-producing bacterial microbiomes. Moreover, the addition of activated carbon promoted the activity of H2-producing Bacteroides, homoacetogenic Eubacteriaceae and methanogenic Methanosarcinaceae, whose activity dynamics during the fermentation led to changes in acetate and methane production. The current results unveiled mechanisms of microbiome activity dynamics shaping the biowaste fermentation product profiles and provided the fundamental basis for the development of microbiome-guided engineering approaches to modulate biowaste fermentation toward high-value product recovery.

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.

Carbon/nitrogen flows and associated microbial communities in full-scale foodwaste treatment plants

Microorganisms play key roles in the conversion of organic matter in foodwaste. However, both the microbially-mediated element (carbon/C and nitrogen/N) flows and associated microbial communities in foodwaste treatment plants (FWTPs) remain unclear. This study collected samples of different foodwaste treatment units from five full-scale FWTPs to analyze the C/N flows and microbial communities in foodwaste treatment processes. Results showed that 39.8-45.0% of organic carbon in foodwaste was converted into biogas. Hydrolytic acidogenic bacteria (e.g., Lactobacillus and Limosilactobacillus) and eukaryota (e.g., Cafeteriaceae, Saccharomycetales, and Agaricomycetes) were more abundant in feedstock and pretreatment units. Redundancy analyses showed that acidogens were major players in the transformation of foodwaste organic matter. Populations of W27 and Tepidanaerobacter were major contributors to the difference in conversion of C/N in these FWTPs. This study could support foodwaste treatment efficiencies improvement by providing insights into C/N flows and associated microbiota in FWTPs.

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics

The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.

Comparison of Thermophilic-Mesophilic and Mesophilic-Thermophilic Two-Phase High-Solid Sludge Anaerobic Digestion at Different Inoculation Proportions: Digestion Performance and Microbial Diversity

This study investigated the performance of thermophilic-mesophilic (T-M) and mesophilic-thermophilic (M-T) two-phase sludge anaerobic digestion at different inoculation proportions after a change in digestion temperature. After temperature change, the pH, total ammonia nitrogen (TAN), free ammonia nitrogen (FAN), solubility chemical oxygen demand (SCOD), and total alkalinity (TA) levels of two-phase digesters were between thermophilic control digesters and mesophilic control digesters. However, the volatile fatty acid (VFA) levels of two-phase digesters were higher than those of thermophilic or mesophilic control digesters. The bacteria communities of M-T two-phase digesters were more diverse than those of T-M. After a change in digestion temperature, the bacterial community was dominated by Coprothermobacter. After a change of digestion temperature, the relative abundance (RA) of Methanobacterium, Methanosaeta, and Methanospirillum of M-T two-phase digesters was higher than that of T-M two-phase digesters. In comparison, the RA of Methanosarcina of T-M two-phase digesters was higher than that of M-T two-phase digesters. The ultimate methane yields of thermophilic control digesters were greater than those of mesophilic control digesters. Nevertheless, the ultimate methane yield levels of M-T two-phase digesters were greater than those of T-M two-phase digesters. The ultimate methane yields of all two-phase digesters presented an earlier increase and later decrease trend with the increasing inoculation proportion. Optimal methane production condition was achieved when 15% of sludge (T-M15) was inoculated under mesophilic-thermophilic conditions, which promoted 123.6% (based on mesophilic control) or 27.4% (based on thermophilic control). An optimal inoculation proportion (about 15%) balanced the number and activity of methanogens of high-solid sludge anaerobic digestion.

Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype

The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.

Understanding the mechanism of enhanced anaerobic biodegradation of biodegradable plastics after alkaline pretreatment

Biodegradable plastics (BPs) tend to replace conventional plastics, which increases the amount of BP waste entering the environment. The anaerobic environment exists extensively in nature, and anaerobic digestion has become a widely used technique for organic waste treatment. Many kinds of BPs have low biodegradability (B_D) and biodegradation rates under anaerobic condition due to the limitation of hydrolysis, so they still have harmful environmental consequences in anaerobic environment. There is an urgent need to find an intervention method to improve the biodegradation of BPs. Therefore, this study aimed to investigate the effectiveness of alkaline pretreatment in accelerating the thermophilic anaerobic degradation of ten widely used BPs, such as poly (lactic acid) (PLA), poly (butylene adipate-co-terephthalate) (PBAT), thermoplastic starch (TPS), poly (butylene succinate-co-butylene adipate) (PBSA), cellulose diacetate (CDA), etc. The results showed that NaOH pretreatment significantly improved the solubility of PBSA, PLA, poly (propylene carbonate) (PPC), and TPS. Except for PBAT, pretreatment with an appropriate NaOH concentration could improve the B_D and degradation rate. The pretreatment also reduced the lag phase in the anaerobic degradation of BPs such as PLA, PPC, and TPS. Specifically, for CDA and PBSA, the B_D increased from 4.6 % and 30.5 % to 85.2 % and 88.7 %, with increments of 1752.2 % and 190.8 %, respectively. Microbial analysis indicated that NaOH pretreatment promoted the dissolution and hydrolysis of PBSA and PLA and the deacetylation of CDA, which contributed to rapid and complete degradation. This work not only provides a promising method for improving the degradation of BP waste but also lays the foundation for its large-scale application and safe disposal.

Response mechanisms of anaerobic fermentative sludge to zinc oxide nanoparticles during medium-chain carboxylates production from waste activated sludge

The conversion of waste activated sludge (WAS) into medium chain carboxylates (MCCs) has attracted much attention, while investigations of the impacts of ZnO nanoparticles (NPs) on this process are sparse. The present study showed that 8 mg/g-TSS of ZnO NPs have little effects on all key steps and the activity of anaerobes, and finally leading to unchanged MCCs production. Although 30 mg/g-TSS of ZnO NPs weakly inhibited the hydrolysis, acidogenesis, and chain elongation process, WAS solubilization was enhanced, thus, the improvement was enough to offset inhibition, also resulting in an insignificant impact on overall MCCs production. However, the improvement with ZnO NPs dosages above 100 mg/g-TSS was not sufficient to offset the biological inhibition, thus inducing negative impact on overall MCCs production. The decline of EPS induced by Zn²⁺ and generation of excessive reactive oxygen species (ROS) were the main factors responsible for the inhibitory effects of ZnO NPs on lower activity of anaerobes. For chain elongation process, the discriminative Clostridium IV (as MCCs-forming bacteria) with a strong adaptation to ZnO NPs (300 mg/g-TSS) was observed. The present study provided a deep understanding related to the effects of ZnO NPs on the production of MCCs production from WAS and identified a zinc resistance anaerobe, which would be significant for the evaluation of influence and alleviation of inhibition induced by ZnO NPs on the carbon cycle of organic wastes.

Nonmonotonic effect of CuO nanoparticles on medium-chain carboxylates production from waste activated sludge

The growing applications of CuO nanoparticles (NPs) in industrial and agriculture has increased their concentrations in wastewater and subsequently accumulated in waste activated sludge (WAS), raising concerns about their impact on reutilization of WAS, especially on the medium-chain carboxylates (MCCs) production from anaerobic fermentation of WAS. Here we showed that CuO NPs at 10-50 mg/g-TS can significantly inhibit MCCs production, and reactive oxygen species generation was revealed to be the key factor linked to the phenomena. At lower CuO NPs concentrations (0.5-2.5 mg/g-TS), however, MCCs production was enhanced, with a maximum level of 37% compared to the control. The combination of molecular approaches and metaproteomic analysis revealed that although low dosage CuO NPs (2.5 mg/g-TS) weakly inhibited chain elongation process, they displayed contributive characteristics both in WAS solubilization and transport/metabolism of carbohydrate. These results demonstrated that the complex microbial processes for MCCs production in the anaerobic fermentation of WAS can be affected by CuO NPs in a dosage-dependent manner via regulating microbial protein expression level. Our findings can provide new insights into the influence of CuO NPs on anaerobic fermentation process and shed light on the treatment option for the resource utilization of CuO NPs polluted WAS.

Degradation of biodegradable plastics by anaerobic digestion: Morphological, micro-structural changes and microbial community dynamics

The serious environmental problem caused by traditional plastics has stimulated the popularization of biodegradable plastics (BPs). However, the rigorous prerequisite for the efficient degradation of BPs has not eliminated its potential hazard to nature. In most biosystems exists the anaerobic environment, but it is still controversial whether BPs can be degraded under such condition. Therefore, this study systematically assessed the anaerobic degradation performance of ten common BPs under mesophilic and thermophilic conditions. Results showed that four BPs were degraded evidently under mesophilic condition with the biodegradability of 57.9%-84.6%, while during thermophilic condition, five BPs showed remarkable degradation performance with the biodegradability of 53.0% to 95.7%. According to morphological and micro-structural analysis, the biodegradation of the BPs probably proceeded via bulk and/or surface erosion. Under mesophilic condition, Anaerolineales, Bacteroidales, Clostridiales, SBR1031, and Synergistales appeared to play an important role. During thermophilic condition, the hydrolysis, acidogenesis, and methanogenesis of most BPs were mainly conducted by Coprothermobacter and the archaea Methanothermobacter. This work not only provides crucial data on the anaerobic biodigestibility of BPs but also enriches the understanding of the BPs degradation mechanisms, which are of great importance for future popularization of BP products and simultaneously relieving the environmental pollution.

Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.

Lignocellulolytic microbiomes for augmenting lignocellulose degradation in anaerobic digestion

Bioaugmenting lignocellulose digestion with potent lignocellulolytic microbiomes (LMs) facilitates efficient biomethanation. Assessing the metabolic roles of microbial communities of the LMs and their complex interactions with the indigenous anaerobic digester microbiome is pivotal in implementing bioaugmentation. Multiple meta-omics are the frontline approaches to investigating gene functions, metabolic roles, and the ecological niches of LMs.

The Relationship Between the Gut Microbiome and Neurodegenerative Diseases

Many recent studies have shown that the gut microbiome plays important roles in human physiology and pathology. Also, microbiome-based therapies have been used to improve health status and treat diseases. In addition, aging and neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, have become topics of intense interest in biomedical research. Several researchers have explored the links between these topics to study the potential pathogenic or therapeutic effects of intestinal microbiota in disease. But the exact relationship between neurodegenerative diseases and gut microbiota remains unclear. As technology advances, new techniques for studying the microbiome will be developed and refined, and the relationship between diseases and gut microbiota will be revealed. This article summarizes the known interactions between the gut microbiome and neurodegenerative diseases, highlighting assay techniques for the gut microbiome, and we also discuss the potential therapeutic role of microbiome-based therapies in diseases.

Experimental systems biology approaches reveal interaction mechanisms in model multispecies communities

Interactions between microorganisms in multispecies communities are thought to have substantial consequences for the community. Identifying the molecules and genetic pathways that contribute to such interplay is thus crucial to understand as well as modulate community dynamics. Here I focus on recent studies that utilize experimental systems biology techniques to study these phenomena in simplified model microbial communities. These unbiased biochemical and genomic approaches have identified novel interactions and described the underlying genetic and molecular mechanisms. I discuss the insights provided by these studies, describe innovative strategies used to investigate less tractable organisms and environments, and highlight the utility of integrating these and more targeted methods to comprehensively characterize interactions between species in microbial communities.

Effect of proton pump inhibitor on microbial community, function, and kinetics in anaerobic digestion with ammonia stress

The proton pump is a convincing mechanism for ammonia inhibition in anaerobic digestion, which explained how the ammonia accumulated intercellularly due to diffusion of free ammonia. Proton pump inhibitor (PPI) was dosed for mitigating the accumulation in anaerobic digestion with ammonia stress, with respect to kinetics. Results show PPI inhibited β-oxidation of fatty acids by targeting ATPase in anaerobic digestion with ammonia stress. Alternatively, PPI stimulated syntrophic acetate oxidization. Random forest located key genera as syntrophic consortia. Methane increased 18.72 ± 7.39% with 20 mg/L PPI at the first peak, consistent with microbial results. The deterministic Gompertz kinetics and stochastic Gaussian processes contributed 97.63 ± 8.93% and 2.37 ± 8.93% in accumulated methane production, respectively. Thus, the use of PPI for anaerobic digestion allowed mitigate ammonia inhibition based on the mechanism of proton pump, facilitate intercellularly ammonia accumulation, stimulate syntrophic consortia, and eliminate uncertainty of process failure, which resulted in efficient methane production under ammonia stress.

Stabilization of anaerobic co-digestion of biowaste using activated carbon of coffee ground biomass

Process instability commonly encountered in anaerobic co-digestion (AcoD) of organic fractions of municipal solid wastes (OFMSWs) is addressed by utilizing hydrochar (CB-HTC) and activated hydrochar (ACB-HTC) derived from coffee ground biomass. Addition of CB-HTC or ACB-HTC shortened the lag phase resulting in high biogas yield of 68.57 Nl/kg oTS or 102.86 Nl/kg oTS, respectively within the first week. Improvement in biogas yield (~5% higher than the control) was due to unique properties which prevented washout of consortia of bacteria useful for AcoD and subsequently led to a more stable process. An increase in either OLR [1.0 kg oTS/(m³*d) to 1.5 kg oTS/(m³*d)] or temperature (36.5 °C to 42.5 °C) did not lead to increase in ammonium-nitrogen or TKN in reactors amended with hydrochars. Likewise, ratio of VFA/TA was within 0.2-0.3 after the fourth week in ACB-HTC treated reactor. Addition of ACB-HTC greatly improved nutrient retention in the digestate.

Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters

Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRTs (5-25 days) on the performance of the co-digestion system was investigated and state-of-the-art genome-centric metagenomic analysis was employed to uncover the dynamics and metabolic network of the key players underlying the well-functioned and poorly-functioned co-digestion microbial communities. The results of the microbial analyses indicated that SRT largely shaped microbial community structure by enriching the syntrophic specialist Syntrophomonas and CO₂/H₂ ( formate)-using methanogen Methanocorpusculum in the well-functioned co-digester operated at SRT of 25 days, while selecting acid-tolerant populations Lactobacillus at SRT of 5 days. The metagenome assembled genomes (MAGs) of key players, such as Syntrophomonadaceae, Methanocorpusculum, and Mesotoga, were retrieved, additionally, the syntrophic acetate oxidation plus hydrogenotrophic methanogenesis (SAO-HM) were proposed as the dominant pathway for methane production. The metabolic interaction in the co-digestion microbial consortia was profiled by assigning MAGs into functional guilds. Functional redundancy was found in the bacterial groups in hydrolysis step, and the members in these groups reduced the direct competition by niche differentiation.

Simultaneous H2S mitigation and methanization enhancement of chicken manure through the introduction of the micro-aeration approach

The impact on H₂S alleviation and methane yield enhancement after submitting the anaerobic digestion of chicken manure to a finite amount of air was investigated. The largest reduction in the H₂S biogas content (58% lower) occurred when air intensity of 30 ml/g VS_in was injected into the reactors. Consequently, a maximum methane yield (335 mL-g VS_in^-1), which was 77% higher than the control, was concurrently achieved. Slight sulfate accumulation (<330 mg L^-1) was observed inside the micro-aerated digesters with higher air intensities, suggesting a suppression of sulfide inhibition. Bacterial diversity/richness was enhanced in these digesters while the relative abundance of Methanocelleus increased by 36%. The most important contributing factor to enhancement was the synergistic effect resulting from increments in the hydrolysis rate and the suppression of sulfide inhibition. The results highlighted the potential of in situ H₂S mitigation with the added benefit of methane yield enhancement.

Biochar for Wastewater Treatment—Conversion Technologies and Applications

Biochar as a stable carbon-rich material shows incredible potential to handle water/wastewater contaminants. Its application is gaining increasing interest due to the availability of feedstock, the simplicity of the preparation methods, and their enhanced physico-chemical properties. The efficacy of biochar to remove organic and inorganic pollutants depends on its surface area, pore size distribution, surface functional groups, and the size of the molecules to be removed, while the physical architecture and surface properties of biochar depend on the nature of feedstock and the preparation method/conditions. For instance, pyrolysis at high temperatures generally produces hydrophobic biochars with higher surface area and micropore volume, allowing it to be more suitable for organic contaminants sorption, whereas biochars produced at low temperatures own smaller pore size, lower surface area, and higher oxygen-containing functional groups and are more suitable to remove inorganic contaminants. In the field of water/wastewater treatment, biochar can have extensive application prospects. Biochar have been widely used as an additive/support media during anaerobic digestion and as filter media for the removal of suspended matter, heavy metals and pathogens. Biochar was also tested for its efficiency as a support-based catalyst for the degradation of dyes and recalcitrant contaminants. The current review discusses on the different methods for biochar production and provides an overview of current applications of biochar in wastewater treatment.

Hydrochar-Facilitated Anaerobic Digestion: Evidence for Direct Interspecies Electron Transfer Mediated through Surface Oxygen-Containing Functional Groups

Acceleration of the anaerobic digestion (AD) process is crucial to achieving energy-efficient recycling of organic wastes. Hydrochar is produced by hydrothermal liquefaction of biomass, yet its application in the AD process is rarely reported. The present study showed that sewage sludge-derived hydrochar (SH) enhanced the methane production rate of glucose by 37%. SH increased the methane production rate from acetate but did not affect acidification and the methane production rate from H₂/CO₂. SH enhanced hydrogenotrophic methanogenesis, which could be due to direct interspecies electron transfer (DIET) by converting H⁺, e^-, and CO₂ to methane. Trichococcus and Methanosaeta were dominant in the AD process with SH. Label-free proteomic analysis showed Methanosaeta was involved in DIET as reflected by the up-regulation of proteins involved in hydrogenotrophic methanogenesis. Hydrochars derived from corn straw (CH), Enteromorpha algae (EH), and poplar wood (PH), as well as activated carbon (AC), were also tested in the AD process. SH, CH, and EH obviously increased the methane production rates, which were 39%, 15%, and 20% higher than the control experiment, respectively. It was neither electrical conductivity nor the total redox property of hydrochars and AC but the abundances of surface oxygen-containing functional groups that correlated to the methane production rates.

Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology

Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.

pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion

pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H₂. Methanosarcina thermophila, the predominant methanogen prior to H₂ addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H₂, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.

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.

A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor

Acid crisis characterized by acid accumulation and/or low pH is a common reason for the failure of anaerobic digestion (AD), which is usually applied for wastewater and waste treatment. Acid-tolerant methanogens are rarely reported to be active in the artificial anaerobic digester. In this study, we observed that the thermophilic methanogenesis by a consortium in the form of flocs and not granules could still be recovered during long-term operation at acetate concentration of up to 104 mM and pH 5.5 by adjusting the pH gradually or directly to pH 5.5 or 5.0. The acclimation process involving the gradual decrease in pH could enhance the resistance of the consortium against extreme acidification. The stable isotopic signature analysis of biogas revealed that Methanosarcina, which produced methane through acetoclastic methanogenesis (AM) pathway, was the predominant methane producer when the pH was decreased gradually to 5.0. Meanwhile, the abundance of Coprothermobacter increased with a decrease in pH. Contrastingly, when directly subjected to an environment of pH 5.5 and 104 mM acetate (15.84-mM free acetic acid) after a 42-day lag phase, Methanothermobacter was the predominant methanogen. Methanothermobacter initiated methane production through the hydrogenotrophic pathway and formed syntrophic relationship/consortium with the potential acetate-oxidizing bacteria, Thermacetogenium and Coprothermobacter. Comparative metagenomic and metatranscriptomic analysis on this self-adapted and acid-tolerant consortium revealed that the genes, such as GroEL, DnaK, CheY, and flagellum-related genes (FlaA, FlgE, and FliC) from Anaerobaculum, Thermacetogenium, and Coprothermobacter were highly overexpressed in response to system acidification. Microbial self-adaptation patterns (community structure adjustment, methanogenesis pathway shift, and transcriptional regulation) of thermophilic methanogenic consortium to gradual and sudden acidification were evaluated by integrated stable isotopic signature and comparative meta-omic approaches. The study elucidated the acid-resistant mechanism of thermophilic methanogenic consortium and deepened our knowledge of the function, interaction, and microbial characteristics of Methanosarcina, Methanothermobacter, and Coprothermobacter under extreme acidic environment.

Acclimatised rumen culture for raw microalgae conversion into biogas: Linking microbial community structure and operational parameters in anaerobic membrane bioreactors (AnMBR)

Ruminal fluid was inoculated in an Anaerobic Membrane Reactor (AnMBR) to produce biogas from raw Scenedesmus. This work explores the microbial ecology of the system during stable operation at different solids retention times (SRT). The 16S rRNA amplicon analysis revealed that the acclimatised community was mainly composed of Anaerolineaceae, Spirochaetaceae, Lentimicrobiaceae and Cloacimonetes fermentative and hydrolytic members. During the highest biodegradability achieved in the AnMBR (62%) the dominant microorganisms were Fervidobacterium and Methanosaeta. Different microbial community clusters were observed at different SRT conditions. Interestingly, syntrophic bacteria Gelria and Smithella were enhanced after increasing 2-fold the organic loading rate, suggesting their importance in continuous systems producing biogas from raw microalgae.

Molecular microbial ecology of stable versus failing rice straw anaerobic digesters

Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1  day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1  day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.

Semi-Continuous Anaerobic Digestion of Orange Peel Waste: Effect of Activated Carbon Addition and Alkaline Pretreatment on the Process

The valorization of orange peel waste (OPW) is sought worldwide mainly via anaerobic digestion. A common problem encountered during the biological treatment is the seasonality of its production and the presence of d-Limonene. The latter is a typical anti-microbial compound. This work aims to evaluate the effect of the use of granular activated carbon (GAC) combined with alkaline pretreatment to enhance methane generation during semi-continuous anaerobic digestion of OPW. The experimental design consisted of two groups of experiments, A and B. Experiment A was designed to verify the maximum OPW loading and to assess the effect of pH and nutrients on the process. Experiment B was designed to study the effect of alkaline pretreatment alone and of alkaline pretreatment aided by biochar addition to the process. Apart from the methane yields, the d-Limonene contents were measured in all experiments. The preliminary results showed that OPW alkaline pretreatment after the addition of a moderate amount of GAC can render anaerobic digestion of OPW sustainable as long as the organic loading does not exceed 2 gVS·L−1·day−1 and nutrients are supplemented. The experiment in which GAC was added after alkaline pretreatment resulted in the highest methane yield and reactor stability.

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.

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.

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated toward community degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure

Anaerobic digestion (AD) uses a range of substrates to generate biogas, including energy crops such as globally abundant rice straw (RS). Unfortunately, RS is high in lignocellulosic material and has high to C:N ratios (~80:1), which makes it (alone) a comparatively poor substrate for AD. Co-digestion with dairy manure (DM) has been promoted as a method for balancing C:N ratios to improve RS AD whilst also treating another farm waste and co-producing a potentially useful fertiliser. However, past co-digestion studies have not directly compared RS AD microbial communities with and without DM additions, which has made it hard to assess all impacts of DM addition to RS AD processes. Here, four RS:DM ratios were contrasted in identical semi-continuous-fed AD bioreactors, and 100% RS was found to produce the highest specific methane yields (112 mL CH4/g VS/day; VS, volatile solids), which is over double yields achieved in the reactor with the highest DM content (30:70 RS:DM by mass; 48 mL CH4/g VS/day). To underpin these data, microbial communities were sequenced and characterised across the four reactors. Dominant operational taxonomic units (OTUs) in the 100% RS unit were Bacteroidetes/Firmicutes, whereas the 30:70 RS:DM unit was dominated by Proteobacteria/Spirochaetes, suggesting major microbial community shifts occur with DM additions. However, community richness was lowest with 100% RS (despite higher specific yields), suggesting particular OTUs may be more important to yields than microbial diversity. Further, ambient VFA and VS levels were significantly higher when no DM was added, suggesting DM-amended reactors may cope better with higher organic loading rates (OLR). Results show that RS AD without DM addition is feasible, although co-digestion with DM will probably allow higher OLRs, resulting in great RS throughput in farm AD units.

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

BACKGROUND

The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web.

RESULTS

Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype.

CONCLUSIONS

Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.

Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times

BACKGROUND

Anaerobic fermentation of lignocellulose occurs in both natural and managed environments, and is an essential part of the carbon cycle as well as a promising route to sustainable production of fuels and chemicals. Lignocellulose solubilization by mixed microbiomes is important in these contexts.

RESULTS

Here, we report the development of stable switchgrass-fermenting enrichment cultures maintained at various residence times and moderately high (55 °C) temperatures. Anaerobic microbiomes derived from a digester inoculum were incubated at 55 °C and fed semi-continuously with medium containing 30 g/L mid-season harvested switchgrass to achieve residence times (RT) of 20, 10, 5, and 3.3 days. Stable, time-invariant cellulolytic methanogenic cultures with minimal accumulation of organic acids were achieved for all RTs. Fractional carbohydrate solubilization was 0.711, 0.654, 0.581 and 0.538 at RT = 20, 10, 5 and 3.3 days, respectively, and glucan solubilization was proportional to xylan solubilization at all RTs. The rate of solubilization was described well by the equation r = k(C - C₀f_r), where C represents the concentration of unutilized carbohydrate, C₀ is the concentration of carbohydrate (cellulose and hemicellulose) entering the bioreactor and f_r is the extrapolated fraction of entering carbohydrate that is recalcitrant at infinite residence time. The 3.3 day RT is among the shortest RT reported for stable thermophilic, methanogenic digestion of a lignocellulosic feedstock. 16S rDNA phylotyping and metagenomic analyses were conducted to characterize the effect of RT on community dynamics and to infer functional roles in the switchgrass to biogas conversion to the various microbial taxa. Firmicutes were the dominant phylum, increasing in relative abundance from 54 to 96% as RT decreased. A Clostridium clariflavum strain with genetic markers for xylose metabolism was the most abundant lignocellulose-solubilizing bacterium. A Thermotogae (Defluviitoga tunisiensis) was the most abundant bacterium in switchgrass digesters at RT = 20 days but decreased in abundance at lower RTs as did multiple Chloroflexi. Synergistetes and Euryarchaeota were present at roughly constant levels over the range of RTs examined.

CONCLUSIONS

A system was developed in which stable methanogenic steady-states were readily obtained with a particulate biomass feedstock, mid-season switchgrass, at laboratory (1 L) scale. Characterization of the extent and rate of carbohydrate solubilization in combination with 16S rDNA and metagenomic sequencing provides a multi-dimensional view of performance, species composition, glycoside hydrolases, and metabolic function with varying residence time. These results provide a point of reference and guidance for future studies and organism development efforts involving defined cultures.

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures

Temperature has different effects on anaerobic digestion (AD) of various biomasses, which could bring out changes in microbial communities. The relationship between microbial community and methane production at 35 °C (R35), 38 °C (R38), 41 °C (R41), and 44 °C (R44) was analyzed during AD of corn stover (CS). The results showed that the daily biogas and methane production from R44 were 16.6%-42.4% and 16.2%-40.6% higher than yields from R35, R38 and R41, respectively. The abundance of Bacteroidetes in R35, R38 and R41 was relatively close (30.70%-39.36%), which was low in R44 (16.00%). The abundance of Firmicutes in R35 was 32.30%, however, Firmicutes was the most dominant phylum at R44 (66.58%). The abundance of Miscellaneous_Crenarchaeotic_Group and Euryarchaeota were 54.63 ± 6.47% and 44.43 ± 6.73% across all digesters. This research demonstrated that among all temperatures studied, 44 °C could enhance the conversion efficiency of the substrates to methane and be recommended for better conversion of CS in AD process.

Comprehensive analysis of microbial communities in full-scale mesophilic and thermophilic anaerobic digesters treating food waste-recycling wastewater

Microbes were sampled for a year in a full-scale mesophilic anaerobic digester (MD) and a thermophilic anaerobic digester (TD) treating food waste-recycling wastewater (FRW), then microbial community structure, dynamics and diversity were quantified. In the MD, Fastidiosipila, Petrimonas, vadinBC27, Syntrophomonas, and Proteiniphilum were dominant bacterial genera; they may contribute to hydrolysis and fermentation. In the TD, Defluviitoga, Gelria and Tepidimicrobium were dominant bacteria; they may be responsible for hydrolysis and acid production. In the MD, dominant methanogens changed from Methanobacterium (17.1 ± 16.9%) to Methanoculleus (67.7 ± 17.8%) due to the increase in ammonium concentration. In the TD, dominant methanogens changed from Methanoculleus (42.8 ± 13.6%) to Methanothermobacter (49.6 ± 11.0%) due to the increase of pH. Bacteria and archaea were more diverse in the MD than in the TD. These results will guide development of microbial management methods to improve the process stability of MD and TD treating FRW.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells

BACKGROUND

Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole.

RESULTS

To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 ± 3.3%) during initial biofilm formation to dominance by Deltaproteobacteria, particularly Geobacter (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition.

CONCLUSIONS

The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.

Performance of direct anaerobic digestion of dewatered sludge in long-term operation

Direct anaerobic digestion of dewatered sludge with total solids (TS) content of 15-20% was tested in a horizontal digester for one and half years. The system kept stable with pH 7-8. The concentration of volatile fatty acids was lower than 800 mg/L, free ammonia nitrogen was lower than 200 mg/L, and total alkalinity kept higher than 6000 mg/L. The performance was influenced by organic load rate (OLR) and organic content in feed sludge. When volatile solids (VS) in TS of feed sludge reached 60-65% at OLR 3.50-3.70 g/(L·d), the process exhibited the best performance with organic removal rate of 32.19 ± 7.73% and methane production of 156.86 ± 13.05 ml/g VS added. Microbial analyses indicated that Methanosarcina became predominant and Methanosaeta almost disappeared. Moreover, hydrogenotrophic and methylotrophic methanogens accounted for 18.13-29.40% and 11.58-29.56% of the total, respectively. These provide a new guideline for small-scale or centralized sludge treatment.