Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms

Impact of bioaugmentation on psychrophilic anaerobic digestion of corn straw

In order to investigate the mechanisms by which bioaugmentation affects psychrophilic anaerobic digestion (AD), this study introduced a psychrophilic methanogenic culture into the sequencing batch of psychrophilic AD systems. The findings demonstrated that bioaugmentation boosted the abundance of Smithella (23.2 times), Syntrophobacter (9.9 times), and Methanothrix (1.4 times) in the psychrophilic AD systems, accelerating acetate and propionate degradation and improving methane production (26 %). Metagenomic analysis showed that bioaugmentation increased the relative abundance of genes related to propionate degradation and methane production, such as propionyl-CoA synthetase (45 %) and acetyl-CoA synthetase (11 %). At the cellular level, genes related to prevention of cell damage and promotion of membrane fluidity were upregulated. This study revealed the effect of bioaugmentation on microbial metabolic activities related to conversion of propionate to methane and cold tolerance in psychrophilic AD.

Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism

Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD+ through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.

A deeper investigation of membrane fouling in anaerobic membrane bioreactors for wastewater treatment: Influencing factors and fouling layer characteristics

Identifying the core parameters affecting membrane fouling and analyzing fouling layer characteristics are crucial for membrane fouling mitigation of anaerobic membrane bioreactors (AnMBRs). This study investigated the influence of various operating parameters on membrane fouling and the characteristics of different fouling layers. The ratio of flux to specific gas demand per unit of membrane area (SGD) was proposed as a key parameter for membrane fouling control and was applicable under various flux, SGD, and sludge concentration conditions. The membrane resistance and specific filtration resistance of foulants at high flux and sludge concentration reached 1.56 × 1012 m-1 and 3.56 × 1015 m-1/kg, respectively. Solid foulants accumulated on the membrane surface during rapid fouling stage. Protein-like pollutants accounted for a higher proportion (85%) of soluble foulants on the membrane surface. Humic acids were enriched on the cake/gel layer and the longitudinal enrichment process from the cake layer to the gel layer was uneven. Proteocatella (>45%) at the phylum level, Desulfovibrio (>3.1%), Syntrophobacter (>2.8%), and Treponema (>0.25%) at the genus level colonized in the gel layer and were the pioneers of membrane biofouling. Their enrichment on the membrane surface was primarily based on their own characteristics and was less sensitive to the operating conditions of AnMBRs. Therefore, this study provides a deeper understanding of membrane fouling formation process, which contributes to the long-term stable operation of AnMBR and scales up its engineering application.

Deciphering the function of Fe3O4 in alleviating propionate inhibition during high-solids anaerobic digestion: Insights of physiological response and energy conservation

Fe3O4 is a recognized addictive to enhance low solid anaerobic digestion (AD), while for high solid AD challenged by acidity inhibition, its feasibility and mechanism remain unclear. In this study, the positive effect of Fe3O4 on high-solids AD of food waste by regulating microbial physiology and energy conservation to enhance mutualistic propionate methanation was documented. The methane yield was increased by 36.7 % with Fe3O4, which because Fe3O4 alleviated propionate stress on methane generation, along with improved propionate degradation and methanogenic metabolism. Fe3O4 facilitated the production of extracellular polymeric substances and the formation of tightly bio-aggregates, fostering an enriched microbial population (e.g., Smithella and Methanosaeta) to resist propionate stress. Also, Fe3O4 up-regulated the genes in stress defense system, cytomembrane biosynthesis/function, metal irons transporter, cell division and enzyme synthesis, verifying its superiority on cellular physiology. In addition, energy-conservation strategies related to intracellular and extracellular electron transfer were enhanced by Fe3O4. Specifically, the enzyme expressions involved in reversed electron transfer and electron bifurcation coupled with direct interspecies electron transfer (DIET) were upregulated by at least 2.2 times with Fe3O4, providing sufficient energy to drive thermodynamic adverse methanogenesis from propionate-stressed condition. Consequently, the reinforced enzyme expression in the dismutation and DIET pathway make it to be the predominant drivers for enhanced methanogenic propionate metabolism. This study fills the knowledge gaps of Fe3O4-induced microbial physiological and energetic strategies to resist environmental stress, and has remarkable practical implicated for restoring inhibited bioactivities.

Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy

The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.

Disentangling microbial niche balance and intermediates' trade-offs for anaerobic digestion stability and regulation

Anaerobic digestion (AD) is a key technology for converting organic matters to methane-rich biogas. However, nutrient imbalance can destabilize the whole digestion. To realize stable operation of AD and improve its efficiency, this work considers a new strategy to control the intermediate concentrations of poor AD under nutrient stress. For this purpose, long-term digestion under different nutrient conditions was investigated. Results showed that the feedstock with a low C/N ratio (= 6) caused VFA accumulation (2072 ± 632 mg/L), leading to the inhibition of methane production. Employing a substrate with a higher C/N ratio (= 11) and/or adding NH4HCO3 (200 mg NH4+-N/Ladd) could alleviate the VFA inhibition, but excessive dosage of NH4HCO3 would induce ammonia inhibition. Through the established digestion balance between free ammonia nitrogen (FAN) between 0 and 25 mg/L, volatile fatty acid (VFA) 510-2100 mg/L, and alkalinity (ALK) 3300-7800 mg/L, an efficient methane yield of 150-250 mL/g VS was achieved and stable operation of AD under nutrient stress (low C/N ratio) was realized. Metabolic reconstruction between Euryarchaeota sp. MAG162, Methanosarcina mazei MAG53 and Mesotoga infera MAG119 highlighted that microbial niche balance was developed as a result of digestion balance, which is beneficial for stable operation of AD. These findings improved our understanding of the interaction mechanism between intermediates and microbial niches for stability control in AD.

Carbon monoxide inhibition on acidogenic glucose fermentation and aceticlastic methanogenesis

Syngas and CO-rich off-gases are key chemical platforms to produce biofuels and bioproducts. From the perspective of optimizing and up-scaling CO co-digestion with organic waste streams, this study aims at assessing and quantifying the inhibitory effects of CO on acidogenic glucose fermentation and aceticlastic methanogenesis. Mesophilic cultures were fed in two sets of batch assays, respectively, with glucose and acetate while being exposed to dissolved CO in equilibrium with partial pressures in the range of 0.25-1.00 atm. Cumulative methane production and microbial monitoring revealed that aceticlastic methanogenic archaea were significantly inhibited (2-20 % of the methane production of CO non-exposed cultures). The acidogenic glucose degrading community was also inhibited by CO, although, thanks to its functional redundancy, shifted its metabolism towards propionate production. Future work should assess the sensitivity of hereby estimated CO inhibition parameters, e.g., on the simulation output of a continuous syngas co-digestion process with organic substrates.

Magnetic porous microspheres altering interfacial thermodynamics of sewage sludge to drive metabolic cooperation for efficient methanogenesis

Controllable and recyclable magnetic porous microspheres (MPMs) have been proposed as a means for enhancing the anaerobic digestion (AD) of sludge, as they do not require continuous replenishment and can serve as carriers for anaerobes. However, the effects of MPMs on the interfacial thermodynamics of sludge and the biological responses triggered by abiotic effects in AD systems remain to be clarified. Herein, the underlying mechanisms by which MPMs alter the solid-liquid interface of sludge to drive methanogenesis were investigated. A significant increase in the contents of 13C and 2H (D) in methane molecules was observed in the presence of MPMs, suggesting that MPMs might enhance the CO2-reduction methanogenesis and participation of water in methane generation. Experimental results demonstrated that the addition of MPMs did not promote the anaerobic bioconversion of soluble organics for methanogenesis, suggesting that the enhanced methanogenesis and water participation were not achieved through promotion of the bioconversion of original liquid-state organics in sludge. Analyses of the capillary force, surface adhesion force, and interfacial proton-coupled electron transfer (PCET) of MPMs revealed that MPMs can enhance mass transfer, effective contact, and electron-proton transfer with sludge. These outcomes were confirmed by the statistical analyses of variations in the interfacial thermodynamics and PCET of sludge with and without MPMs during AD. It was thus proposed that the MPMs enhanced the PCET of sludge and PCET-driven release of protons from water by promoting the interfacial Lewis acid-base interactions of sludge, thereby resulting in the enrichment of free and attached methanogenic consortia and the high energy-conserving metabolic cooperation. This proposition was further confirmed by identifying the predominant syntrophic partners, suggesting that PCET-based efficient methanogenesis was attributable to the enrichment of genomes harbouring CO2-reducing pathway and genes encoding water-mediated proton transfer. These findings offer new insights into how substrate properties can be altered by exogenous materials to enable highly efficient methanogenesis.

Archaea oxidizing alkanes through alkyl-coenzyme M reductases

This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.

Reverse electron transfer: Novel anaerobic methanogenesis pathway regulated through exogenous CO2 synergized with biochar

Acid accumulation and carbon emission are two major challenges in anaerobic digestion. Syntrophic consortia can employ reverse electron transfer (RET) to facilitate thermodynamically unfavorable redox reactions during acetogenesis. However, the potential mechanisms and regulatory methods of RET remain unclear. This study examines the regulatory mechanisms by which exogenous CO2 affects RET and demonstrates that biochar maximizes CO2 solubility at 25.8 mmol/L to enhance effects further. CO2 synergized with biochar significantly increases cumulative methane production and propionate degradation rate. From the bioenergetic perspective, CO2 decreases energy level to a maximum of -87 kJ/mol, strengthening the thermodynamic viability. The underlying mechanism can be attributed to RET promotion, as indicated by increased formate dehydrogenase and enrichment of H2/formate-producing bacteria with their partner Methanospirillum hungatei. Moreover, the 5 % 13CH4 and methane contribution result show that CO2 accomplishes directed methanogenesis. Overall, this investigation riches the roles of CO2 and biochar in AD surrounding RET.

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

BACKGROUND

The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).

RESULTS

The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.

CONCLUSIONS

The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.

Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough

Introduction

Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions.

Methods

To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis).

Results

The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism.

Discussion

In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.

Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution

The colonization of microbes in the gut is key to establishing a healthy host-microbiome symbiosis for newborns. We longitudinally profiled the gut microbiome in a model consisting of 36 neonatal oxen from birth up to 2 months postpartum and carried out microbial transplantation to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3931 metagenomic-assembled genomes from 472 representative species, of which 184 were identified as new species when compared with existing databases of oxen. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by dynamic shifts during the first few weeks of life. Microbial transplantation was found to reshape the genetic makeup of 33 metagenomic-assembled genomes (FDR < 0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4 × 10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity were correlated with L-dopa, which was determined by single nucleotide variations via structural regulations of metabolic enzymes. The current results indicate that temporal colonization and transplantation-driven strain replacement are crucial for newborn gut development, offering insights for enhancing newborn health and growth.

Microbial granules on reactors performance during organic butyrate digestion: clean production

This critical review for anaerobic degradation of complex organic compounds like butyrate using reactors has been enormously applied for biogas production. Biogas production rate has a great impact on: reactor granulation methanogenesis, nutrient content, shear velocity, organic loading and loss of nutrients taking place in the reactor continuously. Various technologies have been applied to closed anaerobic reactors to improve biogas production and treatment efficiency. Recent reviews showed that the application of closed anaerobic reactors can accelerate the degradation of organics like volatile fatty acid-butyrate and affect microbial biofilm formation by increasing the number of methanogens and increase methane production 16.5 L-1 CH4 L-1 POME-1. The closed anaerobic reactors with stable microbial biofilm and established organic load were responsible for the improvement of the reactor and methane production. The technology mentioned in this review can be used to monitor biogas concentration, which directly correlates to organic concentrations. This review attempts to evaluate interactions among the: degradation of organics, closed anaerobic reactors system, and microbial granules. This article provides a useful picture for the improvement of the degradation of organic butyrate for COD removal, biogas and methane production in an anaerobic closed reactor.

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

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.

Hydraulic Retention Time as an Operational Tool for the Production of Short-Chain Carboxylates via Anaerobic Fermentation of Carbohydrate-Rich Waste

The carboxylate platform is a sustainable and cost-effective way to valorize wastes into biochemicals that replace those of fossil origin. Short-chain fatty acids (SCFAs) are intermediates generated during anaerobic fermentation (AF) and are considered high-value-added biochemicals among carboxylates. This investigation aimed to produce SCFAs through the AF of sugar beet molasses at 25 °C and semi-continuous feeding mode in completely stirred tank reactors. A particular focus was devoted to the role of hydraulic retention time (HRT) variation in SCFAs production and distribution profile. The highest SCFAs concentration (44.1 ± 2.3 gCOD/L) was reached at the HRT of 30 days. Caproic acid accounted for 32.5-35.5% (COD-concentration basis) at the long HRTs of 20 and 30 days due to the carbon chain elongation of shorter carboxylic acids. The findings of this study proved that HRT could be used to steer the anaerobic process toward the targeted SCFAs for specific uses. Furthermore, the successful operation at low-temperature conditions (i.e., 25 °C) makes the process economically promising.

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces as a function of the concentration of metabolic intermediates. The tool, based on thermodynamic principles and multi-objective optimisation, accounts for pathway variants in terms of different electron carriers, as well as energy conservation (proton translocating) reactions within the pathway. The method also accommodates other constraints, some of them non-linear, such as the balance of conserved moieties. The approach involves the transformation of the maximum energy yield problem into a multi-objective mixed-integer linear optimisation problem which is then subsequently solved using the epsilon-constraint method, highlighting the trade-off between yield and rate in metabolic reactions. The methodology is applied to analyse several pathway alternatives occurring during propionate oxidation in anaerobic fermentation processes, as well as to the reverse TCA cycle pathway occurring during autotrophic microbial CO2 fixation. The results obtained using the developed methodology match previously reported literature and bring about insights into the studied pathways.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments

Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.

Inhibitory mechanisms on dry anaerobic digestion: Ammonia, hydrogen and propionic acid relationship

Inhibitory pathways in dry anaerobic digestion are still understudied and current knowledge on wet processes cannot be easily transferred. This study forced instability in pilot-scale digesters by operating at short retention times (40 and 33 days) in order to understand inhibition pathways over long term operation (145 days). The first sign of inhibition at elevated total ammonia concentrations (8 g/l) was a headspace hydrogen level over the thermodynamic limit for propionic degradation, causing propionic accumulation. The combined inhibitory effect of propionic and ammonia accumulation resulted in further increased hydrogen partial pressures and n-butyric accumulation. The relative abundance of Methanosarcina increased while that of Methanoculleus decreased as digestion deteriorated. It was hypothesized that high ammonia, total solids and organic loading rate inhibited syntrophic acetate oxidisers, increasing their doubling time and resulting in its wash out, which in turn inhibited hydrogenotrophic methanogenesis and shifted the predominant methanogenic pathway towards acetoclastic methanogenesis at free ammonia over 1.5 g/l. C/N increases to 25 and 29 reduced inhibitors accumulation but did not avoid inhibition or the washout of syntrophic acetate oxidising bacteria.

Acclimation of anaerobic fermentation microbiome with acetate and ethanol for chain elongation and the biochemical response

Medium chain fatty acids (MCFAs) production is a promising method for resource recovery from organic wastes. In this study, the microbial community structure shift along the long-term acclimation experiment and the concomitant effect of H₂ level on chain elongation performance was investigated. Chain elongation microbiome could be rapidly acclimated from traditional anaerobic fermentation consortia. Genera Caproiciproducens, Clostridium sensu stricto 12, Rummeliibacillus and Oscillibacter was found to be dominant during the operation. The H₂ was accumulated in the headspace by increasing the ethanol input, which inhibited oxidation of caproate and butyrate immediately, while its inhibition effect on chain elongation was delayed. H₂ level in the headspace was positively correlated to the MCFAs production related bacteria. However, too much H₂ accumulated might be suppressive for MCFAs production in the long term. It might result from the thermodynamic barrier for discarding excess reducing equivalents under high H₂ level, which further gave rise to ethanol accumulation in this system.

Effect of Lipid Type on the Acidogenic Performance of Food Waste

Due to its high lipid content and intricate constitution, food waste poses a considerable challenge for biotreatment. This research aims to investigate the potential influence of diverse lipid species on anaerobic fermentation, induced by the varying dietary patterns observed in distinct regions. The investigation involved incorporating 5% (w/w) of beef tallow, mutton fat, soybean oil, peanut oil, and rapeseed oil, separately, into simulated food waste, and subjected it to batch mode acidogenic fermentation. The inclusion of unsaturated fatty acids resulted in a redirection of the metabolic pathway from the lactic acid type to the ethanol, acetic acid, and butyric acid types. The succession of the acidogenic metabolic pathway was highly correlated with the lipid types; beef tallow, mutton fat, soybean oil, and peanut oil delayed the metabolic process by 1, 2, 3, and 8 d, respectively, whereas rapeseed oil accelerated it by 2 d. The lipids contained within the food waste did not facilitate the buildup of soluble substances, resulting in a decrease of 14.0~59.7%. Notwithstanding, valeric acid was exclusively generated during the beef tallow and peanut oil treatments, whereas the production of lactic acid in peanut oil showed a 35.9% increase in comparison to the control.

Effect of Addition of Zero-Valent Iron (Fe) and Magnetite (Fe3O4) on Methane Yield and Microbial Consortium in Anaerobic Digestion of Food Wastewater

Direct interspecies electron transfer (DIET), which does not involve mediation by electron carriers, is realized by the addition of conductive materials to an anaerobic digester, which then activates syntrophism between acetogenic and methanogenic microorganisms. This study aimed to investigate the effect of the addition of two conductive materials, zero-valent iron (ZVI) and magnetite, on the methane production and microbial consortium via DIET in the anaerobic digestion of food wastewater. The operation of a batch reactor for food wastewater without the addition of the conductive materials yielded a biochemical methane potential (Bu), maximum methane production rate (Rm), and lag phase time (λ) of 0.380 Nm3 kg−1-VSadded, 15.73 mL day−1, and 0.541 days, respectively. Upon the addition of 1.5% ZVI, Bu and Rm increased significantly to 0.434 Nm3 kg−1-VSadded and 19.63 mL day−1, respectively, and λ was shortened to 0.065 days. Simultaneously, Methanomicrobiales increased from 26.60% to 46.90% and Methanosarcinales decreased from 14.20% to 1.50% as the ZVI input increased from 0% to 1.50%. Magnetite, at an input concentration of 1.00%, significantly increased the Bu and Rm to 0.431 Nm3 kg−1-VSadded and 18.44 mL day−1, respectively. However, although magnetite improves the efficiency of methanogenesis via DIET, the effect thereof on the methanogen community remains unclear.

Effects of initial volatile fatty acid concentrations on process characteristics, microbial communities, and metabolic pathways on solid-state anaerobic digestion

Solid-state anaerobic digestion (SSAD) is vulnerable to excess volatile fatty acids (VFA), mainly acetate and propionate. The co-effects of VFAs and microbial dynamics under VFA accumulation were investigated in SSAD of pig manure and corn straw. Adding 2 and 4 mg/g acetate or propionate caused initial increases in total VFAs, followed by decreases after day 6, resulting in 'mild' VFA accumulation, while adding 6 mg/g caused similarly increased VFAs, but with no subsequent decrease, causing 'severe' VFA accumulation and poor methanation performance. Mild propionate accumulation promoted acetate consumption, whereas acetate accumulation inhibited propionate degradation by affecting crucial redox reactions. Under severe VFA accumulation, hydrolysis and acidification mainly conducted by acid-tolerant Clostridium sp. exacerbated VFA inhibition, causing a competition between Methanosarcina and Methanosaeta, and impairments of acetoclastic and hydrogenotrophic methanogenesis and interspecies formate transfer. This study provides new insights into mechanisms of VFA accumulation in SSAD, and its effects on methanogenesis.

A Review of Biogenic Coalbed Methane Experimental Studies in China

Biogenic coalbed methane (CBM) is an important alternative energy that can help achieve carbon neutrality. Accordingly, its exploration and development have become a research hotspot in the field of fossil energy. In this review, the latest detection technologies for and experimental research on biogenic CBM in China in recent decades are summarized. The factors influencing the generation of biogenic CBM and the identification method of biogenic CBM are systematically analyzed. The technologies to detect biogas and the research methods to study microbial diversity are summarized. The literature shows that biogenic CBM is easily produced in the presence of highly abundant organic matter of low maturity, and the organic matter reaching a certain thickness can compensate for the limitation of biogenic CBM gas production due to the small abundance of organic matter to a certain extent. Biogenic CBM production could be increased in an environment with low salinity, medium alkalinity, and rich Fe²⁺ and Ni²⁺ sources. Furthermore, biogenic CBM can be identified by considering three aspects: (1) the presence of gas composition indicators; (2) the content of heavy hydrocarbon; and (3) variation in the abundance of biomarkers. In recent years, research methods to study the microbial community and diversity of CBM-producing environments in China have mainly included 16S rRNA gene library, fluorescence in situ hybridization, and high-throughput sequencing, and the dominant microorganisms have been determined in various basins in China. The results of numerous studies show that the dominant bacterial phyla are commonly Firmicutes and Proteobacteria, while the archaeal fraction mainly includes Methanoculleus, Methanobacterium, Methanocorpusculum, and Methanothrix. This review summarizes and discusses the advances in biogenic CBM production and the associated microbial community in order to promote further development of coal biotransformation and CO₂ bio-utilization to meet energy demands under carbon neutrality.

Effect of granular activated carbon adsorption and size of microbial aggregates in inoculum on stimulating direct interspecies electron transfer during anaerobic digestion of fat, oil, and grease

To investigate the effect of granular activated carbon (GAC) adsorption and size of microbial aggregates in inoculum on stimulating direct interspecies electron transfer (DIET) during anaerobic digestion of fat, oil, and grease (FOG), seed sludge was divided into two inocula (big (>0.85 mm)/small (0.15-0.85 mm)) for FOG digestion with/without GAC. More long-chain fatty acids (LCFAs) were adsorbed on GAC in the reactor with small aggregates than that with big aggregates, corresponding to 57 % and 10 % decreased methane production, respectively. Adsorption of unsaturated LCFAs (e.g., oleic acid) on GAC was found to reduce LCFA bioavailability, hinder DIET via GAC, and change community structure. Compared to pre-adsorption of oleic acid on GAC, pre-attachment of microbes on GAC resulted in 5.6-fold higher methane yield for oleic acid digestion. Together, competition of LCFA adsorption between GAC and microbial aggregates is essential for enhanced methane recovery from FOG digestion via GAC-induced DIET.

Varied promotion effects and mechanisms of biochar on anaerobic digestion (AD) under distinct food-to-microorganism (F/M) ratios and biochar dosages

Biochar (BC) promotes the performance of anaerobic digestion (AD) through different routes, such as enriching microbes, buffering pH and promoting electron transfer. However, the mechanisms and processes of AD that enhanced by BC under various food to microorganism (F/M) ratios are still unclear. The organic transformations, bioelectrochemical characteristics and microbial consortia under the different BC dosages and F/M ratios were studied to reveal the role of BC in an AD process. The electron transfer system (ETS) was proportional to BC dosage and considered to be a key for AD promotion. At the F/M ratios of 0.5 and 1.0, BC accelerated methane production mainly by promoting ETS. The most enhanced specific methanation activities (SMAs) were obtained with 10.0 g/L BC, and the promotion efficiency under the F/M ratio of 1.0 was significantly higher (P < 0.05) than that under the F/M ratio of 0.5. Under the higher F/M ratio of 2.0, BC shortened the entire AD duration for 5.0 ∼ 13.0 days and guaranteed the resilience of AD by expanding the thermodynamic window of syntrophic methanogenesis via direct interspecies electron transfer (DIET). The COD balance analysis and the ecological functional profiles of microbes demonstrated that BC promoted both the anabolism and catabolism of anaerobes, and enhanced the DIET by converting hydrotrophic methanogenesis into acetolastic methanogenesis pathway. Besides, excessive BC enhanced SMA and simultaneously triggered superfluous biomass growth and thus decreased CH₄ yield. This study provided an important reference for further application of BC under various F/M ratios and dosages in AD.

Effects of modified biochars on the shifts of short-chain fatty acid profile, iron reduction, and bacterial community in paddy soil

Biochar is well known as an effective means for soil amendment, and modification on biochar with different methods could improve the benefits for environmental remediation. In this study, two modified biochars were generated with nitric acid (NBC) and hydrogen peroxide (OBC) pretreatment, and a control biochar was produced after washing with deionized water (WBC). The dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in rice paddy soil amended with different biochars or without adding biochar (CK) were studied during 70 days of anaerobic incubation. Compared to CK treatment, the accumulation of SCFAs was largely inhibited by the amendment of biochars. Besides, OBC and WBC increased the accumulation of Fe(II) at the initial stage of incubation. Via 16S rRNA gene sequencing, modified biochars caused significant response of bacterial community in comparison to WBC at Day 0-1, and three biochars favored bacterial α-diversity in the paddy soil at the end of the incubation. Interestingly, positive and negative correlations between NBC and several bacteria taxa (e.g. Geobacter, Fonticella and Clostridium) were observed. The study revealed that modified biochars had significant effects on the shifts of SCFAs, Fe(III) reduction and bacterial diversity, which provides fundamental information for future application of modified biochars in rice cropping ecosystem.

Enhanced direct interspecies electron transfer and methane production during anaerobic digestion of fat, oil, and grease by coupling carbon-based conductive materials and exogenous hydrogen

To investigate the combination of carbon-based conductive materials and exogenous hydrogen (EH2) on methane recovery from fat, oil, and grease (FOG), granular activated carbon (GAC) and carbon cloth (CC) were chosen to collaborate with EH2, resulting in increased methane production by 59 % and 84 %, respectively. Further digestion of long chain fatty acids (LCFAs) confirms that enhanced direct interspecies electron transfer (DIET) was achieved in the reactors with GAC/CC + EH2 than those with GAC/CC only. Other evidences (such as increased microbial population and rapid degradation of volatile fatty acids) were found to support the role of GAC/CC + EH2 in promotion of DIET. Significant change of microbial community was observed using GAC/CC + EH2, which was mainly attributed to the enrichment of electrogenic species (such as Spirochaetaceae, Syntrophomonas palmitatica, and Methanosaeta), leading to some changes in metabolic pathways during acidogenesis and methanogenesis. Together, enhanced DIET was achieved by GAC/CC + EH2, thus improving the methane recovery from FOG.

Impact of combined biological hydrolysis and anaerobic digestion temperatures on the characteristics of bacterial community and digestate quality in the treatment of wastewater sludge

This work investigated the impact of temperature on the digestate water quality and bacterial community in the treatment of wastewater sludge using biological hydrolysis (BH)-anaerobic digestion (AD). The results showed that the BH 55 °C followed by AD 35 °C or 42 °C was the optimal temperature combination in terms of methane yield and digestate water quality. High-throughput sequencing revealed the key differences in bacterial communities for different BH-AD temperature combinations. Microbial source tracking showed only minor microbial migration from raw sludge and BH pre-treated sludge to the AD stage. Strong correlations between the residual sCOD, BH-AD temperature conditions, and dominant bacteria were identified. Clostridiales, Bacteroidales, Cloacimonadales, Thermotogales, and Anaerolineales were closely related to the digestate water quality and methane yield. Overall, the results showed that AD temperature exerted a dominant impact on methane yield, digestate water quality, and bacterial compositions in the BH-AD of wastewater sludge.

Lactate as an effective electron donor in the sulfate reduction: impacts on the microbial diversity

The competition between sulfate-reducing bacteria and methane-producing archaea has a major influence on organic matter removal, as well as the success of sulfidogenic systems. This study investigated the performance of six batch sulfidogenic reactors in response to different COD/sulfate ratios (1.0 and 2.0) and electron donors (cheese whey, ethanol, and sodium lactate) by evaluating the biochemical mechanisms of sulfate reduction, organic matter oxidation, and microbial structure modification. A COD/sulfate ratio of 1.0 resulted in high sulfidogenic activity for all electron donors, thereby achieving a nearly 80% sulfate removal. Lactate provided high sulfate removal rates at COD/sulfate ratios of 1.0 (80%) and 2.0 (90%). A COD/sulfate ratio of 2.0 decreased the sulfate removal rates by 25 and 28% when ethanol and cheese whey were used as substrates. The sulfate-reducing bacteria populations increased using ethanol and lactate at a COD/sulfate ratio of 1.0. Particularly, Desulfovibrio, Clostridium, and Syntrophobacter were predominant. Influent composition and COD/sulfate ratio influenced the relative abundance of the microbial communities. Therefore, controlling these parameters may facilitate the wastewater treatment with high sulfate levels through bacterial activity.

Enhancing anaerobic methane production in integrated floating-film activated sludge system filled with novel MWCNTs-modified carriers

Conductive materials can enhance anaerobic methane production by accelerating interspecies electron transfer between electroactive bacteria and methanogens. However, the daily loss or less specific surface area of small/big size of conductive materials always limits their application in anaerobic digestion. In this study, the conductive multi-walled carbon nanotubes (MWCNTs) (15 wt% and 20 wt%) were mixed with high-density polyethylene (HDPE) and novel conductive suspended carriers were prepared. Results showed the conductivity of the novel conductive suspended carriers increased by 1-2 orders of magnitude comparing with HDPE carriers, as well as the attached biomass improved from 3.93 g/m² (HDPE carriers) to 5.82 g/m² (15 wt% MWCNTs-modified carriers) and 6.67 g/m² (20 wt% MWCNTs-modified carriers). Integrated floating-film activated sludge (IFFAS) filled with MWCNT-modified carriers showed significant advantages in chemical oxygen demand (COD) removal (removal efficiency increased by 3.6-37.2%) and methanogenic performance (cumulative methane increased by 12.28-62.91%) compared with the control reactor filled with conventional HDPE carriers when treating sodium propionate wastewater at the organic loading rates (OLR) of 11.3-26.3 kg COD/(m³∙d). SEM images and high-throughput sequencing results proved potential direct interspecies electron transfer (DIET) had been established successfully on the MWCNTs-modified carriers. The syntrophic electroactive bacteria (Geobacter, Thauera) and Methanotrix were enriched by 2.28-4.58% and 9.41-16.80% respectively owning to the addition of novel conductive carriers. This study proved IFFAS process filled with novel MWCNTs-modified suspended carriers showed great potential in establishing DIET to enhance anaerobic digestion in practical application.

Enhancing the resistance to H2S toxicity during anaerobic digestion of low-strength wastewater through granular activated carbon (GAC) addition

Low-strength wastewater was treated using two laboratory-scale up-flow anaerobic sludge blankets (UASB) for 130 days under sulfate-reducing conditions. Granular activated carbon (GAC) was added to one of the reactors. The GAC addition increased the total chemical oxygen demand removal by 21-28% and total methane production by 32-78%. The sludge from the GAC-amended UASB showed higher specific methanogenic activities (SMA) and higher activities in the presence of H₂S, indicating that the GAC addition enhanced the resistance of methanogens to H₂S toxicity. Further, the microbial communities showed that the GAC addition shifted microbial communities. A robust syntrophic partnership between bacteria (i.e., Bacteroidetes_vadinHA17 and Trichococcus) and methanogens was established in the GAC-amended UASB. Sulfate-reducing bacteria (SRB) were enriched in the GAC biofilm, indicating the coexistence of competition and cooperation between SRB and methanogens. These findings provide significant insights regarding microbial community dynamics, especially SRB and methanogens, in a GAC-amended anaerobic digestion process under sulfate-reducing conditions.

Impacts of granular activated carbon addition on anaerobic granulation in blackwater treatment

Upflow anaerobic sludge blanket (UASB) reactors, with or without granular activated carbon (GAC) amendment, were applied for blackwater treatment. The impact of GAC on the formation of granules and biomethane recovery was assessed. High organic loading rates (OLRs) up to 15.7 ± 2.1 kg COD/(m³d) were achieved with both reactors. Similar chemical oxygen demand (COD) removal and methane production rate were observed with OLRs ranging from 5.1 ± 1.0 to 9.3 ± 1.5 kg COD/(m³d). Under higher OLR conditions (13.6 ± 1.1 to 15.7 ± 2.1 kg COD/(m³d)), the GAC-amended UASB achieved a higher COD reduction than the UASB without GAC addition. Interestingly, volatile suspended solids (VSS) concentrations, granule size, and extracellular polymeric substance concentrations were lower in the GAC-amended UASB reactor as compared to the UASB without GAC. The methanogenesis activity of the granules in the GAC-amended UASB reactor was significantly higher than the methanogenesis activity of the UASB granules. The microbes o_Bacteroidales and Syntrophus were predominant in both reactors. The acetoclastic methanogens dominated in the UASB reactor without GAC addition; while hydrogenotrophic methanogens dominated in the GAC-UASB reactor. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that syntrophic acetate oxidation improved with GAC addition. The co-occurrence network indicated that interactions between dominant bacteria and archaea were higher in the GAC-amended UASB reactor than in the UASB reactor without GAC addition. This study demonstrated the improved blackwater treatment performance as a result of granulation in UASB with the addition of GAC.

The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation

Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate, and H2 that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially Nε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia.

Early-stage response in anaerobic bioreactors due to high sulfate loads: Hydrogen sulfide yield and other organic volatile sulfur compounds as a sign of microbial community modifications

In this work, the early-stage response of six lab-scale biogas bioreactors fed with different amounts of a sulfate-rich organic agro-industrial effluent was investigated. Biogas characterization, gas chromatography selective for sulfur compounds and high-throughput sequencing of 16S rRNA gene were performed. Hydrogen sulfide (H₂S) yield went from transient to steady state in ∼ 2 weeks for all the studied conditions. In addition, volatile sulfur compounds (VSCs), like methanethiol (MeSH) and dimethyl sulfide (DMS), were generated at high sulfate loads. Changes were evidenced in the microbial community structures, with a higher abundance of genes involved in the dissimilatory sulfate-reduction pathway in high loaded sulfate bioreactors, as determined by PICRUSt analysis. Principal component analysis (PCA) and correlation analyses evidenced strong relationships between H₂S, VSCs and the microbial community. Sulfate-reducing bacteria (SRB) like Desulfocarbo, Desulfocella and Desulfobacteraceae might be possibly linked with methylation processes of H₂S.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

In-situ biogas upgrading assisted by bioaugmentation with hydrogenotrophic methanogens during mesophilic and thermophilic co-digestion

In this study, the effects of bioaugmentation of typically dominant hydrogenotrophic methanogens to CSTR co-digesting cheese whey and manure, under in-situ biomethanation operations were investigated. Reactors working at mesophilic (37 °C) and thermophilic (55 °C) conditions were independently treated and examined in terms of microbial composition and process dynamics. Addition of Methanoculleus bourgensis in the mesophilic reactor led to a stable biomethanation, and an improved microbial metabolism, resulting in 11% increase in CH₄ production rate. 16S rRNA and biochemical analyses revealed an enrichment in syntrophic and acidogenic species abundance. Moreover, nearly total volatile fatty acids conversion was observed. Differently, Methanothermobacter thermautotrophicus addition in the thermophilic reactor did not promote biogas upgrading performance due to incomplete H₂ conversion and inefficient community adaptation to H₂ excess, ultimately favoring acetoclastic methanogenesis. Bioaugmentation constitutes a viable tool to strengthen in-situ upgrading processes and paves the way to the development of more sophisticated and robust microbial inoculants.

Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera

Operational factors and microbial interactions affect the ecology in anaerobic digestion systems. From 12 lab-scale reactors operated under distinct engineering conditions, bacterial communities were found driven by temperature, while archaeal communities by both temperature and substrate properties. Combining the bacterial and archaeal community clustering patterns led to five sample groups (ambient, mesophilic low-solid-substrate, mesophilic, mesophilic co-digestion and thermophilic) for co-occurrence network analysis. Network topological properties were associated with substrate characteristics and hydrolysis-methanogenesis balance. The hydrolysis efficiency correlated (p < 0.05) with clustering coefficient positively and with normalized betweenness negatively. The influent particulate COD ratio and the relative differential hydrolysis-methanogenesis efficiency (D_efficiency) correlated negatively with the average path length (p < 0.05). Individual genera’s topological properties showed more connector genera in thermophilic network, representing stronger inter-module communication. Individual genera’s normalized degree and betweenness revealed that lower-abundance genera (as low as 0.1%) could perform central hub roles and communication roles, maintaining the stability and functionality of the microbial community.

Microbial community redundance in biomethanation systems lead to faster recovery of methane production rates after starvation

The Power-to-Gas concept corresponds to the use of the electric energy surplus to produce H₂ by water electrolysis, that can be further converted to methane by biomethanation. However, the fluctuant production of renewable energy sources can lead to discontinuous H₂ injections into the reactors, that may interfere with the adaptation of the microbial community to high H₂ partial pressures. In this study, the response of the microbial community to H₂ and organic feed starvation was evaluated in in-situ and ex-situ biomethanation. The fed-batch reactors were fed with acetate or glucose and H₂, and one or four weeks of starvation periods were investigated. Methane productivity was mostly affected by the four-week starvation period. However, both in-situ and ex-situ biomethanation reactors recovered their methane production rate after starvation within approximately one-week of normal operation, while the anaerobic digestion (AD) reactors did not recover their performances even after 3 weeks of normal operation. The recovery failure of the AD reactors was probably related to a slow growth of the syntrophic and methanogen microorganisms, that led to a VFA accumulation. On the contrary, the faster recovery of both biomethanation reactors was related to the replacement of Methanoculleus sp. by Methanobacterium sp., restoring the methane production in the in-situ and ex-situ biomethanation reactors. This study has shown that biomethanation processes can respond favourably to the intermittent H₂ addition without compromising their CH₄ production performance.

Saponification with calcium has different impacts on anaerobic digestion of saturated/unsaturated long chain fatty acids

Little is known about the influence of the saturation degree of long chain fatty acids (LCFAs) on the bio-methane potential of calcium-LCFAs salts. In this study, palmitic acid and oleic acid were chosen as the model compounds to investigate the impact of saponification between calcium and saturated/unsaturated LCFAs on the methane recovery from LCFAs in anaerobic digestion. A 2.2-fold enhancement of methane yield was obtained due to the formation of calcium palmitate, which was primarily attributed to the enhanced bio-aggregation and significant change of microbial community. However, saponification between calcium and oleic acid decreased the methane recovery from oleic acid digestion. Only partial saponification with excess oleic acid led to 4% increment of methane production. The low bio-accessibility of calcium oleate and the little change of microbial community may be responsible for the small difference of methane recovery due to the formation of calcium oleate.

Survival strategy of comammox bacteria in a wastewater nutrient removal system with sludge fermentation liquid as additional carbon source

Complete ammonia oxidizing (comammox) bacteria are frequently detected in wastewater biological nutrient removal (BNR) systems. This study identified "Candidatus Nitrospira nitrosa"-like comammox bacteria as the predominant ammonia oxidizers (97.5-99.4%) in a lab-scale BNR system with acetate and sludge fermentation liquid as external carbon sources. The total nitrogen and phosphorus removals of the system were 75.9% and 86.9% with minimal N₂O emission (0.27%). Low ammonia concentration, mixotrophic growth potentials and metabolic interactions with diverse heterotrophs collectively contributed to the survival of comammox bacteria in the system. The recovered draft genomes of comammox bacteria indicated their potentials in using acetate and propionate but not butyrate. Acetate and propionate indeed stimulated the transcription of comammox amoA genes (up-regulated by 4.1 folds compared with no organic addition), which was positively correlated with the ammonia oxidation rate of the community (r = 0.75, p < 0.05). Comammox bacteria could provide vitamins/cofactors (e.g., cobalamin and biotin) to heterotrophs (e.g., Burkholderiaceae), and in return receive amino acids (e.g., phenylalanine and tyrosine) from heterotrophs, which they cannot synthesize. Compared with comammox bacteria, ammonia oxidizing bacteria (AOB) exhibited lower metabolic versatility, and lacked more pathways for the synthesis of amino acids and vitamin/cofactors, leading to their washout in the studied system. BNRs with comammox bacteria as the major nitrifiers hold great potentials in achieving superior performance at low aeration cost and low N₂O emission and at full-scale plants.

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions

Anaerobic digestion is a promising method for energy recovery through conversion of organic waste to biogas and other industrial valuables. However, to tap the full potential of anaerobic digestion, deciphering the microbial metabolic pathway activities and their underlying bioenergetics is required. In addition, the behavior of organisms in consortia along with the analytical abilities to kinetically measure their metabolic interactions will allow rational optimization of the process. This review aims to explore the metabolic bottlenecks of the microbial communities adopting latest advances of profiling and ¹³C tracer-based analysis using state of the art analytical platforms (GC, GC-MS, LC-MS, NMR). The review summarizes the phases of anaerobic digestion, the role of microbial communities, key process parameters of significance, syntrophic microbial interactions and the bottlenecks that are critical for optimal bioenergetics and enhanced production of valuables. Considerations into the designing of efficient synthetic microbial communities as well as the latest advances in capturing their metabolic cross talk will be highlighted. The review further explores how the presence of additives and inhibiting factors affect the metabolic pathways. The critical insight into the reaction mechanism covered in this review may be helpful to optimize and upgrade the anaerobic digestion system.

Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MPOBT and Geobacter sulfurreducens PCAT

We established a syntrophic coculture of Syntrophobacter fumaroxidans MPOBT (SF) and Geobacter sulfurreducens PCAT (GS) growing on propionate and Fe(III). Neither of the bacteria was capable of growth on propionate and Fe(III) in pure culture. Propionate degradation by SF provides acetate, hydrogen, and/or formate that can be used as electron donors by GS with Fe(III) citrate as electron acceptor. Proteomic analyses of the SF-GS coculture revealed propionate conversion via the methylmalonyl-CoA (MMC) pathway by SF. The possibility of interspecies electron transfer (IET) via direct (DIET) and/or hydrogen/formate transfer (HFIT) was investigated by comparing the differential abundance of associated proteins in SF-GS coculture against (i) SF coculture with Methanospirillum hungatei (SF-MH), which relies on HFIT, (ii) GS pure culture growing on acetate, formate, hydrogen as propionate products, and Fe(III). We noted some evidence for DIET in the SF-GS coculture, i.e., GS in the coculture showed significantly lower abundance of uptake hydrogenase (43-fold) and formate dehydrogenase (45-fold) and significantly higher abundance of proteins related to acetate metabolism (i.e., GltA; 62-fold) compared to GS pure culture. Moreover, SF in the SF-GS coculture showed significantly lower abundance of IET-related formate dehydrogenases, Fdh3 (51-fold) and Fdh5 (29-fold), and the rate of propionate conversion in SF-GS was 8-fold lower than in the SF-MH coculture. In contrast, compared to GS pure culture, we found lower abundance of pilus-associated cytochrome OmcS (2-fold) and piliA (5-fold) in the SF-GS coculture that is suggested to be necessary for DIET. Furthermore, neither visible aggregates formed in the SF-GS coculture, nor the pili-E of SF (suggested as e-pili) were detected. These findings suggest that the IET mechanism is complex in the SF-GS coculture and can be mediated by several mechanisms rather than one discrete pathway. Our study can be further useful in understanding syntrophic propionate degradation in bioelectrochemical and anaerobic digestion systems.

Two-phase anaerobic digestion of food waste: Effect of semi-continuous feeding on acidogenesis and methane production

In present investigation, effect of diverting acidogenic off-gas from leached bed reactor (LBR) to up-flow anaerobic sludge blanket (UASB) reactor during semi-continuous food waste (FW) anaerobic digestion was evaluated. In test LBR headspace pressure (3.3 psi) was maintained with intermittent headspace gas transfer into UASB. In control, same headspace pressure was maintained without gas transfer. The semi-continuous FW addition affected the characteristics and production of leachate in control and test LBR. The cumulative COD, total soluble products and methane yields were 1.26, 1.37 and 3 times higher in the test LBR than the control. The acetate and methane yields from test LBR were 697.8 g·kgVS_added^-1 and 167.55 mL·gCOD^-1feeding. Acidogenic gas transfer maintained low partial pressure of hydrogen and the hydrogen to carbon-di-oxide ratio in the headspace of LBR, which were thermodynamically favorable for microbial metabolism and concomitant high-rate production of acetate-rich volatile fatty acid and methane-rich biogas from FW.

Patterns of syntrophic interactions in methanogenic conversion of propionate

Methanogenesis is central to anaerobic digestion processes. The conversion of propionate as a key intermediate for methanogenesis requires syntrophic interactions between bacterial and archaeal partners. In this study, a series of methanogenic enrichments with propionate as the sole substrate were developed to identify microbial populations specifically involved in syntrophic propionate conversion. These rigorously controlled propionate enrichments exhibited functional stability with consistent propionate conversion and methane production; yet, the methanogenic microbial communities experienced substantial temporal dynamics, which has important implications on the understanding of mechanisms involved in microbial community assembly in anaerobic digestion. Syntrophobacter was identified as the most abundant and consistent bacterial partner in syntrophic propionate conversion regardless of the origin of the source culture, the concentration of propionate, or the temporal dynamics of the culture. In contrast, the methanogen partners involved in syntrophic propionate conversion lacked consistency, as the dominant methanogens varied as a function of process condition and temporal dynamics. Methanoculleus populations were specifically enriched as the syntrophic partner at inhibitory levels of propionate, likely due to the ability to function under unfavorable environmental conditions. Syntrophic propionate conversion was carried out exclusively via transformation of propionate into acetate and hydrogen in enrichments established in this study. Microbial populations highly tolerant of elevated propionate, represented by Syntrophobacter and Methanoculleus, are of great significance in understanding methanogenic activities during process perturbations when propionate accumulation is frequently encountered. Key points • Syntrophobacter was the most consistent bacterial partner in propionate metabolism. • Diverse hydrogenotrophic methanogen populations could serve as syntrophic partners. • Methanoculleus emerged as a methanogen partner tolerant of elevated propionate.