Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

Biomineralization of phosphorus during anaerobic treatment of distillery wastewaters

This study addresses the pressing environmental concerns associated with the rapidly growing distillery industry, which is a significant contributor to wastewater generation. By focusing on the treatment of distillery wastewater using anaerobic digestion, this research explores the potential to convert organic materials into biofuels (methane). Moreover, the study aims to recover both methane and phosphorus from distillery wastewater in a single anaerobic reactor, which represents a novel and unexplored approach. Laboratory-scale experiments were conducted using mesophilic and thermophilic upflow anaerobic sludge blanket reactors. A key aspect of the study involved the implementation of a unique strategy: the mixing of centrate and spent caustic wastewater streams. This approach was intended to enhance treatment performance, manipulate the microbial community structure, and thereby optimizing the overall treatment performance. The integration of the centrate and spent caustic streams yielded remarkable co-benefits, resulting in significant biomethane production and efficient phosphorus precipitation. The study demonstrated a phosphorus removal efficiency of ∼60 % throughout the 130-140 days operation period. The recovery of phosphorus via the reactor sludge offers exciting opportunities for its utilization as a fertilizer or as a raw material within the phosphorus refinery industry. The biomethane produced during the treatment exhibits significant energy potential, estimated at 0.5 GJ/(m3 distillery wastewater).

Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions

Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

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.

Pilot-scale two-phase anaerobic digestion of deoiled food waste and waste activated sludge: Effects of mixing ratios and functional analysis

Anaerobic co-digestion of deoiled food waste (dFW) and waste activated sludge (WAS) can address the challenges derived from mono-digestion of FW. In the present study, a pilot-scale methanogenic bioreactor of a two-phase anaerobic digestion system was developed to explore the impact of dFW/WAS volatile solids ratios on the overall performance, microbial community, and metabolic pathways. Besides, the tech-economic of the system was analyzed. The results showed that the degradation efficiency of soluble chemical oxygen demand (SCOD) was more than 84.90% for all the dFW/WAS ratios (v/v) (1:0, 39:1, 29:1, 19:1 and 9:1). Moreover, the dominant genus of bacteria and archaea with different ratios were Lactobacillus (66.84-98.44%) and Methanosaeta (53.66-80.09%), respectively. Co-digestion of dFW and WAS (29: 1 in v/v ratios) obtained the highest yield of methane (0.41 L CH₄/L_added) with approximately 90% of SCOD being removed. In the pilot-scale experiment, the co-digestion of FW and WAS makes positive contribution to reusing solid waste for improving solid management.

Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale

Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.

Bioaugmentation potential of inoculum derived from anaerobic digestion feedstock for enhanced methane production using water hyacinth

The utilisation of water hyacinth for production of biogas is considered to be a solution to both its control and the global renewable energy challenge. In this instance, an investigation was conducted to evaluate the potential of water hyacinth inoculum to enhance methane production during anaerobic digestion (AD). Chopped whole water hyacinth (10% (w/v)) was digested to prepare an inoculum consisting mainly of water hyacinth indigenous microbes. The inoculum was incorporated in the AD of freshly chopped whole water hyacinth to set up different ratios of water hyacinth inoculum and water hyacinth mixture with appropriate controls. The results of batch tests with water hyacinth inoculum showed a maximal cumulative volume of 211.67 ml of methane after 29 days of AD as opposed to 88.6 ml of methane generated from the control treatment without inoculum. In addition to improving methane production, inclusion of water hyacinth inoculum reduced the electrical conductivity (EC) values of the resultant digestate, and, amplification of nifH and phoD genes in the digestate accentuates it as a potential soil ameliorant. This study provides an insight into the potential of water hyacinth inoculum to enhance methane production and contribute to the feasibility of the digestate as a soil fertility enhancer.

Start-up strategies of electromethanogenic reactors for methane production from cattle manure

This study qualitatively assessed the impacts of different start-up strategies on the performance of methane (CH₄) production from cattle manure (CM) in electromethanogenic reactors. Single chamber MECs were operated with an applied voltage of 0.7 V and the impact of electrode acclimatization with a simple substrate, acetate (ACE) vs a complex waste, CM, was compared. Upon biofilm formation on the sole carbon source (ACE or CM), several MECs (ACE_CM and CM_ACE) were subjected to cross-feeding (switching substrate to CM or ACE) during the test period to evaluate the impact of the primary substrate. Even though there was twice as much peak current density via feeding ACE during biofilm formation, this did not translate into higher CH₄ production during the test period, when reactors were fed with CM. Higher or similar CH₄ production was recorded in CM_CM reactors compared to ACE_CM at various soluble chemical oxygen demand (sCOD) concentrations. Additionally, feeding ACE as primary substrate did not significantly impact either COD removals or coulombic efficiencies. On the other hand, the use of anaerobic digester (AD) seed as an inoculum in CM-fed MECs (CM_CM), relative to no inoculum added MECs (Blank), increased the initial CH₄ production rate by 45% and reduced the start-up time by 20%. In CM-fed MECs, Geobacter dominated bacterial communities of bioanodes and hydrogenotrophic methanogen Methanoculleus dominated archaeal communities of biocathodes. Community cluster analysis revealed the significance of primary substrate in shaping electrode biofilm; thus, it should be carefully selected for successful start-up of electromethanogenic reactors treating wastes.

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

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

Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress

Microorganisms in anaerobic digestion (AD) are easily affected by ammonia, especially acetoclastic methanogens. Thus, in ammonia-suppressed AD systems, acetate degradation is reported to be carried out mainly by the cooperation of syntrophic acetate oxidizers and hydrogenotrophic methanogens. Previous studies have revealed ammonia inhibition on microbial flora by AD performance, but the effect mechanism of ammonia on microbial metabolism remains poorly understood. In this study, we constructed a mesophilic chemostat fed with acetate as the sole carbon source, gradually increased the total ammonia nitrogen (TAN) concentration from 1 g L^-1 to 6 g L^-1, and employed the 16S rRNA gene, metagenomics, and metatranscriptomics analysis to characterize the microbial community structure and metabolic behavior. The results showed that even at the TAN of 6 g L^-1 (pH 7.5), the methanogenesis kept normal, the biogas production was approximately 92% of that at TAN of 1 g L^-1 and the acetate degradation ratio reached 99%, suggesting the strong TAN tolerance of the microbial community enriched. 16S rRNA gene analysis suggested that the microbial community structure changed along with the TAN concentration. Methanothrix predominated in methanogens all the time, in which the dominant species was gradually replaced from M. soehngenii to M. harundinacea with the increased TAN. Dominant bacterial species also changed and Proteiniphilum showed a significant positive correlation with increased TAN. Meta-omics analysis showed that the absolute dominant microorganisms at TAN of 6 g L^-1 were M. harundinacea and Proteiniphilum, both of which highly expressed genes for anti-oxidative stress. M. harundinacea and the second dominant methanogen Methanosarcina highly expressed both acetate cleavage and CO₂ reduction pathways, suggesting the possibility that these two pathways contributed to methanogenesis together. Proteiniphilum and some other species in Firmicutes and Synergistetes were likely acetate oxidizers in the community as they highly expressed genes for syntrophic acetate oxidization, H₂ generation, and electron transfer. These results suggested that Proteiniphilum as well as M. harundinacea have strong ammonia tolerance and played critical roles in acetate degradation under ammonia-suppressed conditions. The achievements of the study would contribute to the regulation and management of the AD process.

Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy

Syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis (HM) plays a vital role in the anaerobic digestion of protein-rich feedstocks such as food wastes. However, current knowledge of the biodiversity and genetic potential of the involved microbial participants, especially syntrophic acetate-oxidizing bacteria (SAOB), is limited due to the low abundance of these microorganisms and challenges in their isolation. The intent of this study was to enrich and identify potential SAOB. Therefore, we conducted continuous acetate feeding under high ammonia concentrations using two separate inoculum consortia of microorganisms that originated from full-scale mesophilic food waste digesters, which lasted for more than 200 days. Using 16S rRNA gene amplicon and metagenomic analyses, we observed a convergence of the experimental microbial communities during the enrichment regarding taxonomic composition and metabolic functional composition. Stable carbon isotope analyses of biogas indicated that SAO-HM was the dominant methanogenic pathway during the enrichment process. The hydrogenotrophic methanogen Methanoculleus dominated the archaeal community. The enriched SAO community featured high biodiversity and metabolic functional redundancy. By analyzing the metagenome-assembled genomes, the known SAOB Syntrophaceticus schinkii and six uncultured populations were identified to have the genetic potential to perform SAO through the conventional reversed Wood-Ljungdahl pathway, while another six bacteria were found to encode the reversed Wood-Ljungdahl pathway combined with a glycine cleavage system as novel SAOB candidates. These results showed that the food waste anaerobic digesters harbor diverse SAOB and highlighted the importance of the glycine cleavage system for acetate oxidation. IMPORTANCE Syntrophic acetate oxidation to CO₂ and H₂, together with hydrogenotrophic methanogenesis, contributes to much of the carbon flux in the anaerobic digestion of organic wastes, especially at high ammonia concentrations. A deep understanding of the biodiversity, metabolic genetic potential, and ecology of the SAO community can help to improve biomethane production from wastes for clean energy production. Here, we enriched the SAO-HM functional guild obtained from full-scale food waste anaerobic digesters and recorded dynamic changes in community taxonomic composition and functional profiles. By reconstructing the metabolic pathways, diverse known and novel bacterial members were found to have SAO potential via the reversed Wood-Ljungdahl (WL) pathway alone, or via the reversed WL pathway with a glycine cleavage system (WLP-GCS), and those catalyzing WLP-GCS showed higher microbial abundance. This study revealed the biodiversity and metabolic functional redundancy of SAOB in full-scale anaerobic digester systems and provided inspiration for further genome-centric studies.

Enrichment of Anaerobic Microbial Communities from Midgut and Hindgut of Sun Beetle Larvae (Pachnoda marginata) on Wheat Straw: Effect of Inoculum Preparation

The Pachnoda marginata larva have complex gut microbiota capable of the effective conversion of lignocellulosic biomass. Biotechnological utilization of these microorganisms in an engineered system can be achieved by establishing enrichment cultures using a lignocellulosic substrate. We established enrichment cultures from contents of the midgut and hindgut of the beetle larva using wheat straw in an alkaline medium at mesophilic conditions. Two different inoculation preparations were used: procedure 1 (P1) was performed in a sterile bench under oxic conditions using 0.4% inoculum and small gauge needles. Procedure 2 (P2) was carried out under anoxic conditions using more inoculum (4%) and bigger gauge needles. Higher methane production was achieved with P2, while the highest acetic acid concentrations were observed with P1. In the enrichment cultures, the most abundant bacterial families were Dysgonomonadaceae, Heliobacteriaceae, Ruminococcaceae, and Marinilabiliaceae. Further, the most abundant methanogenic genera were Methanobrevibacter, Methanoculleus, and Methanosarcina. Our observations suggest that in samples processed with P1, the volatile fatty acids were not completely converted to methane. This is supported by the finding that enrichment cultures obtained with P2 included acetoclastic methanogens, which might have prevented the accumulation of acetic acid. We conclude that differences in the inoculum preparation may have a major influence on the outcome of enrichment cultures from the P. marginata larvae gut.

Miniphocaeibacter halophilus sp. nov., an ammonium-tolerant acetate-producing bacterium isolated from a biogas system

An anaerobic bacterial strain, designated AMB_01T, recovered from mesophilic propionate enrichment of a high-ammonia biogas digester, was characterised using phenotypic and molecular taxonomic methods. Cells of AMB_01T are coccus-shaped and often occur arranged as diplococci or sarcina. Growth occurred at 20–45 °C, initial pH 5.5–8.5 and with up to 0.7 M NH4Cl, with optimum growth at 37–42 °C and pH 8.0. AMB_01T achieved high cell density and highest acetate production when grown on carbohydrates, including monomers, disaccharides and polysaccharides, such as glucose, maltose, cellobiose and starch. The strain was also able to use amino acids and some organic acids and alcoholic compounds for growth. Acetate was formed as the main product and yeast was not required for growth. The major cellular fatty acids were summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B), C18 : 1ω7, C14 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7 and/or iso-C15 : 0 2OH). The highest 16S rRNA gene sequence similarity found was with Miniphocaeibacter massiliensis (96.6 %), within the family Peptoniphilaceae , phylum Bacillota (Firmicutes). The genomic DNA G+C content was 29.0 mol%. An almost complete set of genes for the acetyl-CoA pathway was found. Genome comparisons between AMB_01T and close relatives showed highest digital DNA–DNA hybridisation to Finegoldia magna (23 %), highest average nucleotide identity with genome nucleotide and amino acid sequences to M. massiliensis (72 and 73 %, respectively) and highest average nucleotide identity (87 %) with Schnuerera ultunensis , indicating that AMB_01T represents a novel species. Analysis of genomic, chemotaxonomic, biochemical and physiological data confirmed that strain AMB_01T represents a novel species, for which the name Miniphocaeibacter halophilus sp. nov. is proposed. The type strain is AMB_01T (=DSM 110247T=JCM 39107 T).

Calcium hypochlorite pretreatment improves thermophilic digestion of waste activated sludge in an upflow anaerobic sludge blanket reactor

Anaerobic wasted activated sludge (WAS) digestion has been widely applied to reduce sludge volume and generate bioenergy in the form of methane. However, anaerobic WAS digestion performance is often challenged with poor hydrolysis of biomass cellular structures. In the present study, the feasibility of using calcium hypochlorite (Ca(ClO)₂) to improve the thermophilic digestion of WAS was studied. Two thermophilic upflow anaerobic sludge bed (UASB) reactors (one with and one without Ca(ClO)₂ pretreatment) were operated for 120 days under low and high organic loading rate (OLR) conditions, corresponding hydraulic retention time (HRT) of 10 days and 6 days, respectively. Both reactors achieved satisfied performance during the studied period. Under the low OLR condition, Ca(ClO)₂ pretreatment significantly improved WAS total volatile solids (VS) removal efficiency (from 48.06 ± 2.63% to 57.34 ± 3.54%) and methane yield (from 289.2 ± 27.6 to 362.2 ± 36.7 N mL/g VS). However, no significant improvement was observed under the high OLR condition. g_S1 and g_Fervidobacterium were predominant bacteria in the thermophilic UASB reactor fed with Ca(ClO)₂ pretreated WAS. Methanosarcina was dominant archaea in both reactors. The treatment mechanism and application potential of using Ca(ClO)₂ to enhance the WAS digestibility were further discussed.

Impact of Granular Activated Carbon on Anaerobic Process and Microbial Community Structure during Mesophilic and Thermophilic Anaerobic Digestion of Chicken Manure

In this work, the impact of granular activated carbon (GAC) on the mesophilic and thermophilic anaerobic digestion of chicken manure and the structure of microbial communities was investigated. These results demonstrated that GAC supplementation effectively enhanced the consumption of produced organic acids in the mesophilic and thermophilic batch tests, accompanied by faster biomethane production in the presence of GAC than from reactors without GAC. However, since the free ammonia level was 3–6 times higher in the thermophilic reactors, this led to the instability of the anaerobic digestion process of the nitrogen-rich substrate at thermophilic temperatures. Bacteroidia and Clostridia were the two main bacterial classes in the mesophilic reactors, whereas the class Clostridia had a competitive advantage over other groups in the thermophilic systems. The archaeal communities in the mesophilic reactors were mainly represented by representatives of the genera Methanosarcina, Methanobacterium, and Methanotrix, whereas the archaeal communities in the thermophilic reactors were mainly represented by members of the genera Methanosarcina, Methanoculleus, and Methanothermobacter. New data obtained in this research will help control and manage biogas reactors in the presence of GAC at different temperatures.

Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions

During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.

Gradual development of ammonia-induced syntrophic acetate-oxidizing activities under mesophilic and thermophilic conditions quantitatively tracked using multiple isotopic approaches

Insights into microbiota adaptation to increased ammonia stress, and identification of indicator microorganisms can help to optimize the operation of anaerobic digesters. To identify microbial indicators and investigate their metabolic contribution to acetoclastic methanogenesis (AM), syntrophic acetate oxidation (SAO) or hydrogenotrophic methanogenesis (HM), 40 anaerobic batch reactors fed with acetate of 110 mmol/L were set up at NH₄⁺-N concentrations of 0.14 g/L, 5.00 g/L or 7.00 g/L, inoculated with thermophilic or mesophilic microbiota with or without pre-exposure to ammonia stress. Four stable carbon isotope probing approaches were applied in parallel, with [1,2-¹³C]-CH₃COOH, [2-¹³C]-CH₃COOH, [¹³C]NaHCO₃ or non-labeled CH₃COOH used individually. The last three approaches were used to quantify the methanogenic pathways by tracking labeled ¹³C or natural ¹³C signatures in the resulting CH₄ and CO₂, and consistently detected the dynamic transition of dominant pathways from AM to SAO-HM under ammonia stress. Results of quantitative PCR and fluorescence in-situ hybridization illustrated the procedure, acetotrophic methanogens being outcompeted by acetate-oxidizing syntrophs. The first and last isotope-labeling approaches were designed to probe the active acetate-mineralizing microbes with DNA-SIP. Known acetate-oxidizing bacteria like Syntrophaceticus and Tepidanaerobacter, as well as novel members of Pseudomonas, Bacillus and Symbiobacteraceae were detected, with Methanoculleus as the predominant H₂/CO₂-utilizing partner. Using NanoSIMS, some bacterial cells were observed to be fixing CO₂ from [¹³C]NaHCO₃. In this study, Methanosaeta was only active with ammonia < 200 mg-N/L; the syntrophs catalyzing SAO-HM started to compete with AM-conducting Methanosarcina at intermediate concentrations of ammonia, i.e. 200-500 mg-N/L, and outcompeted the acetotrophic methanogens with ammonia > 500 mg-N/L. Under ammonia stress, diverse known and novel microbial taxa were involved in acetate mineralization, comparable with those identified in previous studies.

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

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

Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments

Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. However, the impact of these organic and inorganic compounds on biogeochemical processes including microbial redox reactions, mineral transformations, and microbial community transitions in urban subsurface environments is poorly understood. Here we conducted a microcosm experiment with soil samples from an urban construction site to investigate the possible biotic and abiotic processes impacted when sulfate and acetate or lactate were introduced into an urban subsurface environment. In the top-layer soil (0-0.3 m) microcosms, which were highly alkaline (pH > 10), the major impact was on abiotic processes such as secondary mineral precipitation. In the mid-layer (2-3 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were greatly impacted by the specific organic acid added, and sulfate-reduction was not observed until after Fe(III)-reduction was complete. Near the end of the incubation, some genera related to syntrophic acetate oxidation and methanogenesis were observed in the lactate-amended microcosms. In the bottom-layer (7-8 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were affected by the concentration of amended sulfate. Sulfate-reduction was concurrent with Fe(III)-reduction, suggesting that Fe(II) production was likely due to abiotic reduction of Fe(III) by sulfide produced by microbial sulfate reduction. The slightly acidic initial pH (~5.8) of the mid-soil system was a major factor controlling sequential microbial Fe(III) and sulfate reduction versus parallel Fe(III) and sulfate reduction in the bottom soil system, which had a neutral initial pH (~7.2). 16S rRNA gene-based community analysis revealed a variety of indigenous microbial groups including alkaliphiles, dissimilatory iron and sulfate reducers, syntrophes, and methanogens tightly coupled with, and impacted by, these complex abiotic and biogeochemical processes occurring in urban subsurface environments.

A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions

Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.

The transition temperature (42 °C) from mesophilic to thermophilic micro-organisms enhances biomethane potential of corn stover

Mesophilic and thermophilic digestion has long been considered as preferred temperature ranges for anaerobic digestion. However, in this study, the effects of temperatures (37, 42, 47, and 55 °C) on the biomethane potential of corn stover were conducted with batch experiments, and the highest biomethane potential was at 42 °C. It was inferred that the change of feed materials, e.g., pretreatment caused by acidification (pH 6.0) during the lag time (4 days), was the main driver for higher biomethane potential. The natural pretreatment stimulated by a slight digestive temperature increase to 42 °C can enhance the biomethane potential of corn stover without adding extra acid. Meanwhile, metabolic pathways of methanogens changed from acetoclastic to mixotrophic and hydrogenotrophic methanogenesis. Based on these results, the transition temperature (42 °C) from mesophilic to thermophilic micro-organisms could be a promising option for corn stover anaerobic digestion.

Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis

Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.

Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level

Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high-ammonia anaerobic digesters, but propionate-degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia-tolerant syntrophic propionate-oxidising bacteria using propionate enrichment at high ammonia levels (0.7-0.8 g NH₃ L^-1 ) in continuously-fed reactors. We reconstructed 30 high-quality metagenome-assembled genomes (MAGs) from the propionate-fed reactors, which revealed two novel species from the families Peptococcaceae and Desulfobulbaceae as syntrophic propionate-oxidising candidates. Both MAGs possess genomic potential for the propionate oxidation and electron transfer required for syntrophic energy conservation and, similar to ammonia-tolerant acetate degrading syntrophs, both MAGs contain genes predicted to link to ammonia and pH tolerance. Based on relative abundance, a Peptococcaceae sp. appeared to be the main propionate degrader and has been given the provisional name "Candidatus Syntrophopropionicum ammoniitolerans". This bacterium was also found in high-ammonia biogas digesters, using quantitative PCR. Acetate was degraded by syntrophic acetate-oxidising bacteria and the hydrogenotrophic methanogenic community consisted of Methanoculleus bourgensis and a yet to be characterised Methanoculleus sp. This work provides knowledge of cooperating syntrophic species in high-ammonia systems and reveals that ammonia-tolerant syntrophic propionate-degrading populations share common features, but diverge genomically and taxonomically from known species.

Enhancing anaerobic digestion for rural wastewater treatment with granular activated carbon (GAC) supplementation

Notwithstanding many efforts to increase the efficiency of anaerobic digestion at low-temperature (winter) conditions, a cost-effective and efficient method is lacking. This study proposes a low-cost method of low-temperature (<35 °C) anaerobic digestion of wastewater, involving supplementation with granular activated carbon (GAC). Supplementation with GAC was found to reduce the lag time by 29.8% (from 15.1 to 10.6 days) and increase the maximum methane production rate by 23.4% (from 6.4 to 7.9 mL/day) at 25 °C. Network analysis demonstrated a strong co-occurrence of Syntrophobacteriales and hydrogenotrophic methanogens (Methanobacteriaceae; WSA2; Methanoregulaceae). GAC supplementation can drastically reduce the time required for organic matter decomposition and methane production, thereby increase the efficiency of wastewater treatment.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste

BACKGROUND

Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited.

RESULTS

A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected.

CONCLUSIONS

Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.

Comparative study of industrial-scale high-solid biogas production from food waste: Process operation and microbiology

Anaerobic high-solid treatment (HST) for processing food waste and biogas production is a viable technology with considerable commercial potential. In this study, we examined and compared mesophilic and thermophilic industrial-scale plug-flow digesters. The HSTs demonstrated reasonable biogas yields from food waste (0.4-0.6 Nm³ CH₄/kg volatile solids). However, during operation at thermophilic conditions ammonia inhibition (~2 g NH₃-N/L) and acid accumulation (6-14 g/L) caused severe process disturbance. Microbial community structures diverged between the processes, with temperature appearing to be a strong driver. A unique feature of the thermophilic HSTs was high abundance of the uncultivated Clostridia group MBA03 and temperature fluctuations in one mesophilic HST were linked to drastically decreased abundance of methanogens and relative abundance of Cloacimonetes. The process data obtained in this study clearly demonstrate both potential and challenges in HST of food waste but also possibilities for management approaches to tackle process imbalance and restore process function.

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.

Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

Anaerobic digestion

Worldwide waste generation has become a topic of interest since the accumulation of this waste has prompted environmental hazards. Among which, anaerobic digestion provides green and efficient alternate solution for removal of toxic waste and energy production. Therefore, this review emphasizes on the recent data published in 2018 on topics related to anaerobic process, enhancement of biogas production, and fermentation efficiency. Furthermore, more focus was made on the factors influencing anaerobic digestion and the effect of trace elements as ionic salts as well as nanoparticles on overall biogas production, respectively. PRACTITIONER POINTS: Anaerobic digestion provide green and efficient alternate solution to deal with. This review focused on the conditions related to anaerobic process to improve biogas production and fermentation efficiency. The trace elements were focused on how to influence biogas production during anaerobic digestion.

Methanogenesis stimulation and inhibition for the production of different target electrobiofuels in microbial electrolysis cells through an on-demand control strategy using the coenzyme M and 2-bromoethanesulfonate

Electron allocation through the suppression or the stimulation of methanogenesis is critical for microbial electrolysis cells (MECs) to produce the desired target product (e.g., CH₄ or H₂). In this study, selective methanogenesis control using the coenzyme M (CoM) and 2-bromoethanesulfonate (2-BES) was investigated in a two-chambered MEC to evaluate the effect of CoM and 2-BES on the production of different electrobiofuels, net energy conversion efficiency and microbial community structure. Because the CoM is a crucial methyl-group carrier in the final process of methanogenesis, it was postulated that CoM would stimulate methanogenic activity at the anode, while a structural analog of the CoM (i.e., 2-BES) was expected to improve cathodic H₂ yield using electrons conserved because of methanogen inhibition (electron equivalence: 8 mol e^- = 1 mol CH₄ = 4 mol H₂). CoM injection in MECs significantly enhanced their CH₄ production rate, purity, and yield by 4.5-fold, 14.5%, and 76.1%, respectively, compared to the control. Moreover, microbial community analysis indicated that Methanosaeta, the major acetoclastic methanogen, continued to dominate the microbial community but steadily decreased in relative abundance after the CoM injection. On the other hand, drastic increases in hydrogenotrophic methanogens, such as Methanoculleus and Methanolinea, were observed along with potential syntrophic acetate-oxidizing bacteria. In contrast, CH₄ production in the 2-BES injected trials was significantly inhibited by 79.5%, resulting in a corresponding increase of H₂ production by 145.5% compared to the control. Unlike the CoM, the microbial community did not noticeably change when 2-BES was injected, although the population size gradually decreased over time. Also, a single injection of CoM and 2-BES, even at low concentrations (500 μM), enabled the desired allocation of electrons as characterized by a high sensitivity, fast response, and negligible interference. In terms of energy conversion efficiency, methanogenesis stimulation approach resulted in higher net energy production than inhibition approach, whereas the remained electrons were not fully converted to hydrogen in case of the inhibition trial, thus producing less energy.

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers

Syntrophic acetate oxidation (SAO) plays a pivotal role in biogas production processes when aceticlastic methanogens are inhibited. Despite the importance of SAO, the metabolic interactions and syntrophic growth of the organisms involved are still poorly understood. Therefore, we studied growth parameters and interactions within constructed defined cocultures comprising the methanogen Methanoculleus bourgensis and one, or several, of the syntrophic acetate oxidizers Syntrophaceticus schinkii, [ Clostridium] ultunense, and Tepidanaerobacter acetatoxydans and a novel, uncharacterized bacterium. Cultivation experiments in a design-of-experiment approach revealed positive effects on methane production rate of increased ammonium levels (up to 0.2 M), temperature (up to 45 °C), and acetate concentrations (0.15-0.30 M). Molecular analyses and thermodynamic calculations demonstrated close interlinkages between the microorganisms, with available energies of -10 kJ/mol for acetate oxidation and -20 kJ/mol for hydrogenotrophic methanogenesis. The estimated generation time varied between 3 and 20 days for all syntrophic microorganisms involved, and the acetate minimum threshold level was 0.40-0.45 mM. The rate of methanogenesis depended on the SAO bacteria present in the culture. These data are beneficial for interpretation of SAO prevalence and competiveness against aceticlastic methanogens in anaerobic environments.

Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula

The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20°C). A methane yield (based on mL-CH₄/g-COD_added) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20°C but not at 10°C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role of Methanosaeta (acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the family Syntrophaceae (Syntrophus and uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10°C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10°C) from lipid-containing wastewaters.

Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions

Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g^-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.

Effects of various feedstocks on isotope fractionation of biogas and microbial community structure during anaerobic digestion

Feedstock type influences bacterial and methanogenic communities in anaerobic digestion. These two communities work tightly to maintain the stability of anaerobic digestion. How to quick report the changes of microbial community structure especially methanogenesis is the key issue for optimizing anaerobic digestion process. In this study, ¹³C isotope fractionations of CH₄ and CO₂ in biogas and microbial community composition were analyzed in 5 different feedstocks. Our results showed that grass silage, maize silage and swine manure fed reactors had similar δ ¹³C values and methanogenic community composition, dominated by Methanosarcinaceae. The lowest δ ¹³CH₄ values were detected in straw and chicken manure fed reactors, reflecting reduced microbial degradation of material or the presence of toxic components in these feedstocks. The straw fed bioreactor lead to low δ ¹³CH₄ values, probably reflecting relatively high levels of the syntrophic acetate oxidizing bacteria, Synergistaceae and Syntrophaceae, which might work collectively with hydrogenotrophic methanogens, resulting in the low δ ¹³CH₄ values in this bioreactor. Significantly, all core microbes in the 5 different feedstock fed bioreactors were either Clostridia species or related to the Synergistaceae (syntrophic acetate oxidizing bacteria).

Acetoclastic methanogenesis led by Methanosarcina in anaerobic co-digestion of fats, oil and grease for enhanced production of methane

Fats, oil and grease (FOG) are energy-dense wastes that substantially increase biomethane recovery. Shifts in the microbial community during anaerobic co-digestion of FOG was assessed to understand relationships between substrate digestion and microbial adaptations. Excessive addition of FOG inhibited the methanogenic activity during initial phase; however, it enhanced the ultimate methane production by 217% compared to the control. The dominance of Proteobacteria was decreased with a simultaneous increase in Firmicutes, Bacteriodetes, Synergistetes and Euryarchaeota during the co-digestion. A significant increase in Syntrophomonas (0.18-11%), Sporanaerobacter (0.14-6%) and Propionispira (0.02-19%) was observed during co-digestion, which substantiated their importance in acetogenesis. Among methanogenic Archaea, the dominance of Methanosaeta (94%) at the beginning of co-digestion was gradually replaced by Methanosarcina (0.52-95%). The absence/relatively low abundance of syntrophic acetate oxidizers and hydrogenotrophic methanogens, and dominance of acetoclastic methanogens suggested that methane generation during co-digestion of FOG was predominantly conducted through acetoclastic pathway led by Methanosarcina.

Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities

Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens.

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.

Effect of Start-Up Strategies and Electrode Materials on Carbon Dioxide Reduction on Biocathodes

The enrichment of CO₂-reducing microbial biocathodes is challenging. Previous research has shown that a promising approach could be to first enrich bioanodes and then lower the potential so the electrodes are converted into biocathodes. However, the effect of such a transition on the microbial community on the electrode has not been studied. The goal of this study was thus to compare the start-up of biocathodes from preenriched anodes with direct start-up from bare electrodes and to investigate changes in microbial community composition. The effect of three electrode materials on the long-term performance of the biocathodes was also investigated. In this study, preenrichment of acetate-oxidizing bioanodes did not facilitate the start-up of biocathodes. It took about 170 days for the preenriched electrodes to generate substantial cathodic current, compared to 83 days for the bare electrodes. Graphite foil and carbon felt cathodes produced higher current at the beginning of the experiment than did graphite rods. However, all electrodes produced similar current densities at the end of the over 1-year-long study (2.5 A/m²). Methane was the only product detected during operation of the biocathodes. Acetate was the only product detected after inhibition of the methanogens. Microbial community analysis showed that Geobacter sp. dominated the bioanodes. On the biocathodes, the Geobacter sp. was succeeded by Methanobacterium spp., which made up more than 80% of the population. After inhibition of the methanogens, Acetobacterium sp. became dominant on the electrodes (40% relative abundance). The results suggested that bioelectrochemically generated H₂ acted as an electron donor for CO₂ reduction.

IMPORTANCE In microbial electrochemical systems, living microorganisms function as catalysts for reactions on the anode and/or the cathode. There is a variety of potential applications, ranging from wastewater treatment and biogas generation to production of chemicals. Systems with biocathodes could be used to reduce CO₂ to methane, acetate, or other high-value chemicals. The technique can be used to convert solar energy to chemicals. However, enriching biocathodes that are capable of CO₂ reduction is more difficult and less studied than enriching bioanodes. The effect of different start-up strategies and electrode materials on the microbial communities that are enriched on biocathodes has not been studied. The purpose of this study was to investigate two different start-up strategies and three different electrode materials for start-up and long-term operation of biocathodes capable of reducing CO₂ to valuable biochemicals.

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

To enrich syntrophic acetate‐oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)‐dominated systems and continuously supplied with acetate (0.4 or 7.5 g l⁻¹) at high‐ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64–69% and effluent acetate level of 0.4–1.0 g l⁻¹ were recorded in chemostats fed high acetate. Low methane production in the low‐acetate chemostats indicated that the substrate supply was below the threshold for methanization of acetate via SAO. Novel representatives within the family Clostridiales and genus Syntrophaceticus (class Clostridia) were identified to represent putative SAOB candidates in mesophilic and thermophilic conditions respectively. Known SAOB persisted at low relative abundance in all chemostats. The hydrogenotrophic methanogens Methanoculleus bourgensis (mesophilic) and Methanothermobacter thermautotrophicus (thermophilic) dominated archaeal communities in the high‐acetate chemostats. In line with the restricted methane production in the low‐acetate chemostats, methanogens persisted at considerably lower abundance in these chemostats. These findings strongly indicate involvement in SAO and tolerance to high ammonia levels of the species identified here, and have implications for understanding community function in stressed anaerobic processes.