Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste

High-solid digestion - A comparison of completely stirred and plug-flow reactor systems

High-solid digestion (HSD) for biogas production is a resource-efficient and sustainable method to treat organic wastes with high total solids content and obtain renewable energy and an organic fertiliser, using a lower dilution rate than in the more common wet digestion process. This study examined the effect of reactor type on the performance of an HSD process, comparing plug-flow (PFR) type reactors developed for continuous HSD processes, and completely stirred-tank reactors (CSTRs) commonly used for wet digestion. The HSD process was operated in thermophilic conditions (52 °C), with a mixture of household waste, garden waste and agricultural residues (total solids content 27-28 %). The PFRs showed slightly better performance, with higher specific methane production and nitrogen mineralisation than the CSTRs, while the reduction of volatile solids was the same in both reactor types. Results from 16S rRNA gene sequencing showed a significant difference in the microbial population, potentially related to large differences in stirring speed between the reactor types (1 rpm in PFRs and 70-150 rpm in CSTRs, respectively). The bacterial community was dominated by the genus Defluviitoga in the PFRs and order MBA03 in the CSTRs. For the archaeal community, there was a predominance of the genus Methanoculleus in the PFRs, and of the genera Methanosarcina and Methanothermobacter in the CSTRs. Despite these shifts in microbiology, the results showed that stable digestion of substrates with high total solids content can be achieved in both reactor types, indicating flexibility in the choice of technique for HSD processes.

Deciphering the microbial interactions and metabolic shifts at different COD/sulfate ratios in electro-assisted anaerobic digestion

This research aims to investigate the influence of sulfate on the performance of microbial electrolysis cell-assisted anaerobic digester (MEC-AD) across varying sulfate conditions, including no sulfate and reduced COD/sulfate ratios from 20 to 1. The principal results indicate a gradual decline in methane yield in the MEC-AD from 78.7 ± 2.3 % under no sulfate conditions to 56.2 ± 2.0 % at a COD/sulfate ratio of 1, contrasting with a more substantial decrease in the control reactor (69.9 ± 3.6 % to 32.8 ± 1.5 %). The MEC-AD reactor exhibits heightened resilience to sulfide toxicity, showcasing higher specific methanogenic activities. Key findings suggest that the MEC-AD reactor maintains lower free sulfide concentrations, attributed to its higher pH and potential anodic sulfide oxidation. Additionally, the study reveals the promotion of syntrophic partnerships in the MEC-AD reactor, particularly between sulfate-reducing bacteria (SRB) such as Desulfovibrio, Desulfomicrobium, and Desulfobulbus, and other microbial groups, including hydrogenotrophic methanogens and electroactive bacteria. The integration of these mechanisms highlights the MEC-AD reactor's ability to effectively mitigate sulfate-induced challenges and enhance overall anaerobic digestion performance. This study presents a significant step forward in the development of resilient anaerobic digestion systems capable of efficiently handling sulfate stress.

Bioaugmentation by enriched hydrogenotrophic methanogens into trickle bed reactors for H2/CO2 conversion

Biomethanation represents a promising approach for biomethane production, with biofilm-based processes like trickle bed reactors (TBRs) being among the most efficient solutions. However, maintaining stable performance can be challenging, and both pure and mixed culture approaches have been applied to address this. In this study, inocula enriched with hydrogenotrophic methanogens were introduced to to TBRs as bioaugmentation strategy to assess their impacts on the process performance and microbial community dynamics. Metagenomic analysis revealed a metagenome-assembled genome belonging to the hydrogenotrophic genus Methanobacterium, which became dominant during enrichment and successfully colonized the TBR biofilm after bioaugmentation. The TBRs achieved a biogas production with > 96 % methane. The bioaugmented reactor consumed additional H2. This may be due to microbial species utilizing CO2 and H2 via various CO2 reduction pathways. Overall, implementing bioaugmentation in TBRs showed potential for establishing targeted species, although challenges remain in managing H2 consumption and optimizing microbial interactions.

Electro-stimulation modulates syntrophic interactions in methanogenic toluene-degrading microbiota for enhanced functionality

Syntrophy achieved via microbial cooperation is vital for anaerobic hydrocarbon degradation and methanogenesis. However, limited understanding of the metabolic division of labor and electronic interactions in electro-stimulated microbiota has impeded the development of enhanced biotechnologies for degrading hydrocarbons to methane. Here, compared to the non-electro-stimulated methanogenic toluene-degrading microbiota, electro-stimulation at 800 mV promoted toluene degradation and methane production efficiencies by 11.49 %-14.76 % and 75.58 %-290.11 %, respectively. Hydrocarbon-degrading gene bamA amplification and metagenomic sequencing analyses revealed that f_Syntrophobacteraceae MAG116 may act as a toluene degrader in the non-electro-stimulated microbiota, which was proposed to establish electron syntrophy with the acetoclastic methanogen Methanosarcina spp. (or Methanothrix sp.) through e-pili or shared acetate. In the electro-stimulated microbiota, 37.22 ± 4.33 % of Desulfoprunum sp. (affiliated f_Desulfurivibrionaceae MAG10) and 58.82 ± 3.74 % of the hydrogenotrophic methanogen Methanobacterium sp. MAG74 were specifically recruited to the anode and cathode, respectively. The potential electrogen f_Desulfurivibrionaceae MAG10 engaged in interspecies electron transfer with both syntroph f_Syntrophobacteraceae MAG116 and the anode, which might be facilitated by c-type cytochromes (e.g., ImcH, OmcT, and PilZ). Moreover, upon capturing electrons from the external circuit, the hydrogen-producing electrotroph Aminidesulfovibrio sp. MAG60 could share electrons and hydrogen with the methanogen Methanobacterium sp. MAG74, which uniquely harbored hydrogenase genes ehaA-R and ehbA-P. This study elucidates the microbial interaction mechanisms underlying the enhanced metabolic efficiency of the electro-stimulated methanogenic toluene-degrading microbiota, and emphasizes the significance of metabolic and electron syntrophic interactions in maintaining the stability of microbial community functionality.

Methylotrophic methanogenesis induced by ammonia nitrogen in an anaerobic digestion system

OBJECTIVES

This lab-scale study aimed to investigate the effect of total ammonia nitrogen (TAN) stress on the methanogenic activity and the taxonomic and functional profiles of the microbial community of anaerobic sludge (AS) from a full-scale bioreactor.

METHODS

The AS was subjected to a stepwise increase in TAN every 14 days at concentrations of 1, 2, 2.5, 3, 3.5, and 4 g TAN/L (Acclimated-AS or AAS). This acclimation stage was followed by an ammonia stress stage (4 g/L). A blank-AS (BAS) was maintained without TAN during the acclimation stage. In the second stress stage (ST), the BAS was divided into two new treatments: a control (BAS') and one that received a shock load of TAN of 4 g/L (SBAS'). Methane production was measured, and a metagenomic analysis was conducted to describe the microbial community.

RESULTS

A decrease in the relative abundance of Methanothrix soehngenii of 16 % was related to a decrease of 23 % in the methanogenic capacity of AAS when comparing with the final stage of BAS. However, recovery was observed at 3.5 g TAN/L, and a shift to methylotrophic metabolism occurred, indicated by a 4-fold increase in abundance of Methanosarcina mazei. The functional analysis of sludge metagenomes indicated that no statistical differences (p > 0.05, RM ANOVA) were found in the relative abundance of methanogenic genes that initiate acetoclastic and hydrogenotrophic pathways (acetyl-CoA synthetase, ACSS; acetate kinase, ackA; phosphate acetyltransferase, pta; and formylmethanofuran dehydrogenase subunit A, fwdA) into the BAS and AAS during the acclimation phase. The same was observed between groups of genes associated with methanogenesis from methylated compounds. In contrast, statistical differences (p < 0.05, one-way ANOVA) in the relative abundance of these genes were recorded during ST. The functional profiles of the genes involved in acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways were brought to light for acclimatation and stress experimental stages.

CONCLUSIONS

TAN inhibited methanogenic activity and acetoclastic metabolism. The gradual acclimatization to TAN leads to metabolic and taxonomic changes that allow for the subsequent recovery of methanogenic functionality. The study highlights the importance of adequate management of anaerobic bioprocesses with high nitrogen loads to maintain the methanogenic functionality of the microbial community.

Effect of Stepwise Exposure to High-Level Erythromycin on Anaerobic Digestion

High-level erythromycin (ERY) fermentation wastewater will pose serious threats to lake environments. Anaerobic digestion (AD) has advantages in treating high-level antibiotic wastewater. However, the fate of antibiotic resistance genes (ARGs) and microbial communities in AD after stepwise exposure to high-level ERY remains unclear. In this study, an AD reactor was first exposed to 0, 5, 10, 50, 100 and 200 mg/L ERY and then re-exposed to 0, 50, 200 and 500 mg/L ERY to investigate the effect of ERY on AD. The results show that AD could adapt to the presence of high-level ERY (500 mg/L) and could maintain efficient CH4 production after domestication with low-level ERY (50 mg/L). The AD process could achieve higher removal of ERY (>94%), regardless of the initial ERY concentration. ErmB and mefA, conferring resistance through target alteration and efflux pumps, respectively, were dominant in the AD process. The first exposure to ERY stimulated an increase in the total ARG abundance, while the AD process seemed to discourage ARG maintenance following re-exposure to ERY. ERY inhibited the process of acetoclastic methanogenesis, but strengthened the process of hydrogenotrophic methanogenesis. This work provides useful information for treating high-level ERY fermentation wastewater by the AD process.

Metataxonomic characterization of the microbial present in the anaerobic digestion of turkey litter waste with the addition of two inocula: allochthonous and commercial

Turkey litter waste is lignocellulosic waste that can be sustainably used as an energy source through anaerobic digestion (AD). The 16S ribosomal RNA technique helps to unravel microbial diversity and predominant metabolic pathways. The assays were performed in 600-mL-glass bottles with 400 mL volume, for 60 days at 37 °C. The study evaluated the physicochemical parameters, the composition of the microbiota, and the functional inference in AD of different concentrations of turkey litter (T) using two inocula: granular inoculum (S) and commercial inoculum (B). The highest accumulated methane production (633 mL CH4·L-1) was observed in the test containing 25.5 g VS·L-1 of turkey litter with the addition of the two inocula (T3BS). In tests without inoculum (T3) and with commercial inoculum (T3B), there was an accumulation of acids and consequent inhibition of methane production 239 mL CH4·L-1 and 389 mL CH4·L-1, respectively. Bacteroidota, Firmicutes, and Actinobacteria were the main phyla identified. The presence of archaea Methanobacterium, Methanocorpusculum, and Methanolinea highlighted the hydrogenotrophic metabolic pathway in T3BS. Functional prediction showed enzymes involved in three metabolic pathways in turkey litter biodigestion: acetotrophic, hydrogenotrophic, and methylotrophic methanogenesis. The predominant hydrogenotrophic pathway can be observed by analyzing the microbiota, archaea involved in this specific pathway, genes involved, and relative acid consumption for T3S and T3BS samples with higher methane production. Molecular tools help to understand the main groups of microorganisms and metabolic pathways involved in turkey litter AD, such as the use of different inocula, allowing the development of strategies for the sustainable disposal of turkey litter.

Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities

BACKGROUND

Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.

RESULTS

In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.

CONCLUSION

Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.

Comprehensive insights into the effects of acidogenic off-gas utilization on successive biogas production, microbial community structure and metabolite distribution during two-stage anaerobic digestion

Although two-stage anaerobic digestion (TSAD) technology has been investigated, the mechanisms regarding the impact of acidogenic off-gas (AOG) on successive methane production have not been well addressed. In this study, a novel TSAD system was designed. Food waste, as the main substrate, was co-digested with chicken manure and corn straw. The acidogenic gas beyond atmospheric pressure was introduced into the bottom of the methanogenesis reactor through a stainless steel diffuser. Results showed the addition of AOG increased the methane yield from 435.2 to 597.1 mL/g VSin in successive methanogenesis stage, improved by 37.2 %, and increased the energy yield from 9.0 to 11.3 kJ/g VSsubstrate. However, the theoretical contribution of hydrogenotrophic methanogenesis using H2 contained in AOG was only 15.2 % of the increased methane yield. After the addition of AOG, the decreased levels of ammonia nitrogen and butyrate indicate that the stability of the AD system was improved. The electron transfer system and co-enzyme F420 activity were enhanced; however, the decrease in acetate kinase activity indicates aceticlastic methanogenesis may have been weakened. The microbial diversity and species richness were improved by the added AOG. Methanosarcina was more competitive than Methanothermobacter, enhancing the syntrophic effect. The relative abundance of protein degradation bacteria norank_f_Anaerolineaceae and lipid degradation bacteria Syntrophomonas was increased. Metabolite analysis confirmed that the addition of AOG promoted amino acid metabolism, the biosynthesis of other secondary metabolism and lipid metabolism. The improved degradation of recalcitrant organic components (lipids and proteins) in food waste was responsible for the increased methane yield. This study provides an in-depth understanding of the impact of AOG utilization on successive methane production and has practical implications for the treatment of food waste.

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Two-stage conversion of syngas and pyrolysis aqueous condensate into L-malate

Hybrid thermochemical-biological processes have the potential to enhance the carbon and energy recovery from organic waste. This work aimed to assess the carbon and energy recovery potential of multifunctional processes to simultaneously sequestrate syngas and detoxify pyrolysis aqueous condensate (PAC) for short-chain carboxylates production. To evaluate relevant process parameters for mixed culture co-fermentation of syngas and PAC, two identical reactors were run under mesophilic (37 °C) and thermophilic (55 °C) conditions at increasing PAC loading rates. Both the mesophilic and the thermophilic process recovered at least 50% of the energy in syngas and PAC into short-chain carboxylates. During the mesophilic syngas and PAC co-fermentation, methanogenesis was completely inhibited while acetate, ethanol and butyrate were the primary metabolites. Over 90% of the amplicon sequencing variants based on 16S rRNA were assigned to Clostridium sensu stricto 12. During the thermophilic process, on the other hand, Symbiobacteriales, Syntrophaceticus, Thermoanaerobacterium, Methanothermobacter and Methanosarcina likely played crucial roles in aromatics degradation and methanogenesis, respectively, while Moorella thermoacetica and Methanothermobacter marburgensis were the predominant carboxydotrophs in the thermophilic process. High biomass concentrations were necessary to maintain stable process operations at high PAC loads. In a second-stage reactor, Aspergillus oryzae converted acetate, propionate and butyrate from the first stage into L-malate, confirming the successful detoxification of PAC below inhibitory levels. The highest L-malate yield was 0.26 ± 2.2 molL-malate/molcarboxylates recorded for effluent from the mesophilic process at a PAC load of 4% v/v. The results highlight the potential of multifunctional reactors where anaerobic mixed cultures perform simultaneously diverse process roles, such as carbon fixation, wastewater detoxification and carboxylates intermediate production. The recovered energy in the form of intermediate carboxylates allows for their use as substrates in subsequent fermentative stages.

Assessing microbial stability and predicting biogas production in full-scale thermophilic dry methane fermentation of municipal solid waste

Compared to typical anaerobic digestion processes, little is known about both sludge microbial compositions and biogas production models for full-scale dry methane fermentation treating municipal solid waste (MSW). The anaerobic sludge composed of one major hydrogenotrophic methanogen (Methanoculleus) and syntrophic acetate oxidizing bacteria (e.g., Caldicoprobacter), besides enrichment of MSW degraders such as Clostridia. The core population remained phylogenetically unchanged during the fermentation process, regardless of amounts of MSW supplied (∼35 ton/d) or biogas produced (∼12000 Nm3/d). Based on the correlations observed between feed amounts of MSW from 6 days in advance to the current day and biogas output (the strongest correlation: r = 0.77), the best multiple linear regression (MLR) model incorporating the temperature factor was developed with a good prediction for validation data (R2 = 0.975). The proposed simple MLR method with only data on the feedstock amounts will help decision-making processes to prevent low-efficient biogas production.

New insights on ecological roles of waste activated sludge in nutrient-stressed co-digestion

There have been extensive applications of waste activated sludge (WAS) in anaerobic co-digestion (AcoD). Nonetheless, mechanisms through which AcoD systems maintain stability, particularly under nutrient-stressed conditions, are under-appreciated. In this study, the role of WAS in a nutrient-stressed WAS-food waste AcoD system was re-evaluated. Our findings demonstrated that WAS-based co-digestion increased methane production (by 20-60%) as WAS bolsters such systems' resilience via establishing a core niche-based microbial balance. The carbon utilization investigation suggested a microbial niche balance is attainable if two conditions are satisfied: 1) hydrolysis efficiency is greater than 50%; and 2) both the acidogenesis-to-hydrolysis and acetogenesis-to-hydrolysis efficiencies surpass 0.5. Metagenomic assembly genome (MAG) analysis indicated that the versatile metabolic characteristics strengthened the microbial niche balance, rendering the system resilient and efficient through a syntrophic mode, contributing to both acidogenesis and acetogenesis. The findings of this study provide new insights into the ecological effects of WAS on AcoD.

Enhancement of Biodegradability of Chicken Manure via the Addition of Zeolite in a Two-Stage Dry Anaerobic Digestion Configuration

Leach bed reactors (LBRs) are dry anaerobic systems that can handle feedstocks with high solid content, like chicken manure, with minimal water addition. In this study, the chicken manure was mixed with zeolite, a novel addition, and packed in the LBR to improve biogas production. The resulting leachate was then processed in a continuous stirred tank reactor (CSTR), where most of the methane was produced. The supernatant of the CSTR was returned to the LBR. The batch mode operation of the LBR led to a varying methane production rate (MPR) with a peak in the beginning of each batch cycle when the leachate was rich in organic matter. Comparing the MPR in both systems, the peaks in the zeolite system were higher and more acute than in the control system, which was under stress, as indicated by the acetate accumulation at 2328 mg L-1. Moreover, the presence of zeolite in the LBR played a crucial role, increasing the overall methane yield from 0.142 (control experiment) to 0.171 NL CH4 per g of volatile solids of chicken manure entering the system at a solid retention time of 14 d. Zeolite also improved the stability of the system. The ammonia concentration increased gradually due to the little water entering the system and reached 3220 mg L-1 (control system) and 2730 mg L-1 (zeolite system) at the end of the experiment. It seems that zeolite favored the accumulation of the ammonia at a lower rate (14.0 mg L-1 d-1) compared to the control experiment (17.3 mg L-1 d-1). The microbial analysis of the CSTR fed on the leachate from the LBR amended with zeolite showed a higher relative abundance of Methanosaeta (83.6%) compared to the control experiment (69.1%). Both CSTRs established significantly different bacterial profiles from the inoculum after 120 days of operation (p < 0.05). Regarding the archaeal communities, there were no significant statistical differences between the CSTRs and the inoculum (p > 0.05).

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).

Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Significance of homogeneous operation in light-assisted fixed-bed bioprocess under ammonia stress: Optimization, long-term operation and metagenomic analysis

Activating microbes with light is a promising strategy for addressing ammonia-stressed anaerobic digestion (AD). However, as a critical in-process parameter, homogenous operation, in light-assisted AD amended by bio-fixed bed has received limited attention. This research endeavors to establish a uniform-illuminated biosystem and assess its practical feasibility through a 90-day semi-continuous operation at pilot scale under solar light illumination. With optimal stirring mode (intermittent stirring for 3 min every 15 min), robust methane yields were achieved across various organic loads, reaching 88.7-94.3% of theoretical yield under high ammonium stress (3500 mg/L). The metagenomic analysis unveiled that uniform illumination triggered synergistic effects in AD, fostering a diversified microbial consortium, enhancing carbohydrate and methane metabolism, and facilitating the formation of an electroactive bio-cluster. This study underscores the significance of homogenous illumination in AD systems for efficient waste-to-energy conversion, highlighting the implementation of solar light as a greener approach for scale-up application.

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Insight into using hydrochar to alleviate ammonia nitrogen inhibition during anaerobic digestion of waste activated sludge: Performance, metagenomic and metabolomic signatures

In this study, hydrochar (HCR) was used to alleviate high ammonia inhibition to the anaerobic digestion (AD) of waste activated sludge (WAS) and to elucidate the inner microorganism mechanism. After HCR addition, the cumulative methane yield increased by 73.6 % and 35.6 % under ammonia inhibition levels of 3000 and 6000 mg/L, respectively. Metagenomic analysis showed that HCR enriched the diversity of hydrogenotrophic methanotrophs, and the relative abundances of functional microorganisms with electron transfer capabilities (Geobacteraceae bacterium etc.) were 1.5-7.8 times higher than those without HCR addition. Metabolomics analysis implied that metabolites related to fatty acid degradation, such as glutaric acid and hexadecanal, were downregulated (2.9-15.7 %) under ammonia inhibition conditions and that HCR regulates metabolites in the methane metabolic pathway. Moreover, HCR changed the methanogenic pathway from hydrogenotrophic methanogenesis to multiple pathways under ammonia inhibition conditions, especially methanolic and methylotrophic methanogenesis, which facilitated the methane yield. This study provides valuable information for understanding the inner microbial mechanism of HCR addition on alleviating high ammonia inhibition to AD of WAS, and gives basic knowledge for the application of AD of WAS under ammonia inhibition conditions.

Microbiome assembly and stability during start-up of a full-scale, two-phase anaerobic digester fed cow manure and mixed organic feedstocks

Carbon transformations during anaerobic digestion are mediated by complex microbiomes, but their assembly is poorly understood, especially in full-scale digesters. Gene-centric metagenomics combining functional and taxonomic classification was performed for an on-farm digester during start-up. Cow manure and organic waste pre-treated in a hydrolysis tank were fed to the methane-producing digester and the volatile solids loading rate was slowly increased from 0 to 3.5 kg volatile solids m-3 d-1 over one year. The microbial community in the anaerobic digester exhibited a high ratio of archaea, which were dominated by hydrogenotrophic methanogens. Bacteria in the anaerobic digester had a high abundance of genes for ferredoxin cycling, H2 generation, and more metabolically complex fermentations than in the hydrolysis tank. In total, the results show that a functionally stable microbiome was achieved quickly during start-up and that the microbiome created in the low-pH hydrolysis tank did not persist in the downstream anaerobic digester.

Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics

Ammonia release from proteinaceous feedstocks represents the main inhibitor of the anaerobic digestion (AD) process, which can result in a decreased biomethane yield or even complete failure of the process. The present study focused on the adaptation of mesophilic AD communities to a stepwise increase in the concentration of ammonium chloride in synthetic medium with casein used as the carbon source. An adaptation process occurring over more than 20 months allowed batch reactors to reach up to 20 g of NH4+ N/L without collapsing in acidification nor ceasing methane production. To decipher the microbial dynamics occurring during the adaptation and determine the genes mostly exposed to selective pressure, a combination of biochemical and metagenomics analyses was performed, reconstructing the strains of key species and tracking them over time. Subsequently, the adaptive metabolic mechanisms were delineated by following the single nucleotide variants (SNVs) characterizing the strains and prioritizing the associated genes according to their function. An in-depth exploration of the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacteria Acetomicrobium sp. ma133 identified positively selected SNVs on genes involved in stress adaptation. The intraspecies diversity with multiple coexisting strains in a temporal succession pattern allows us to detect the presence of an additional level of diversity within the microbial community beyond the species level.

Acclimation of microbial communities to low and moderate salinities in anaerobic digestion

In recent years anaerobic digestion (AD) has been investigated as suitable biotechnology to treat wastewater at elevated salinities. However, when starting up AD reactors with inocula that are not adapted to salinity, low concentrations of sodium (Na+) in the influent can already cause disintegration of microbial aggregates and wash-out. This study investigated biomass acclimation to 5 g Na+/L of two different non-adapted inocula in two lab-scale hybrid expanded granular sludge bed (EGSB)-anaerobic filter (AF) reactors fed with synthetic wastewater. After an initial biomass disintegration, new aggregates were formed relatively fast (i.e., after 95 days of operation), indicating microbial community adaptation. The newly formed microbial aggregates accumulated Na+ at the expense of calcium (Ca2+), but this did not hamper biomass retention or process performance. The hybrid reactor configuration, including a pumice stone filter in the upper section, and the low up-flow velocities applied, were key features for retaining the biomass within the system. This reactor configuration can be easily applied and represents a low-cost alternative for acclimating biomass to saline effluents, even in existing digesters. When the acclimated biomass was transferred from EGSB to an up-flow anaerobic sludge blanket (UASB) reactor configuration also fed with saline synthetic wastewater, more dense aggregates in the form of granules were obtained. The performances of the UASB inoculated with the acclimated biomass were comparable to another reactor seeded with saline-adapted granular sludge from a full-scale plant. Regardless of the inoculum origin, a defined core microbiome of Bacteria (Thermovirga, Bacteroidetes vadinHA17, Blvii28 wastewater-sludge group, Mesotoga, and Synergistaceae) and Archaea (Methanosaeta and Methanobacterium) was detected, highlighting the importance of these microbial groups in developing halotolerance and maintaining AD process stability.

Efficacy of bioaugmentation with nondomesticated mixed microbial consortia under ammonia inhibition in anaerobic digestion

Bioaugmentation shows promise in mitigating ammonia-induced microbial inhibition in anaerobic digestion processes. However, the advanced technical requirements and high costs associated with pure strain cultivation, as well as the time-consuming and labor-intensive process of domesticating consortia, present challenges for industrial applications. Herein, the efficacy of bioaugmentation with nondomesticated mixed microbial consortia was evaluated, which resulted in a significant methane production improvement of 5.6%-11.7% and 10.3%-13.5% under total ammonia nitrogen concentrations of 2.0 and 4.9 g-N/L, respectively. Microbial analysis revealed that at high ammonium levels, the bioaugmented culture facilitated a transition in the methanogenic pathway from acetoclastic to hydrogenotrophic by regulating symbiotic relationships between propionate- and acetate-oxidizing bacteria and methanogens. Consortium type and dose applied were identified as crucial factors determining bioaugmentation effectiveness. Overall, nondomesticated mixed microbial consortia demonstrate potential as cost-effective bioaugmentation agents for mitigating ammonia-induced inhibition.

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.

Wheat bran inclusion level impacts its net energy by shaping gut microbiota and regulating heat production in gestating sows

An accurate estimation of net energy (NE) of wheat bran is essential for precision feeding of sows. However, the effects of inclusion level on NE of wheat bran have not been reported. Inclusion level was hypothesized to impact NE of wheat bran by regulating gut microbiota and partitioning of heat production. Therefore, twelve multiparous sows (Yorkshire × Landrace; 2 to 4 parity) were assigned to a replicated 3 × 6 Youden square with 3 successive periods and 6 diets in each square. The experiment included a corn-soybean meal diet (WB0) and five diets including 9.8% (WB10), 19.5% (WB20), 29.2% (WB30), 39.0% (WB40) and 48.7% wheat bran (WB50), respectively. Each period included 6 d of adaptation to diets followed by 6 d for heat production measurement using open-circuit respiration chambers. Compared with other groups, WB30, WB40, and WB50 enriched different fiber-degrading bacteria genera (P < 0.05). Apparent total tract digestibility of neutral detergent fiber and acid detergent fiber of wheat bran were greater in WB30 and WB40 (P < 0.05). Physical activity (standing and sitting) decreased as inclusion level increased (P = 0.04), which tended to decrease related heat production (P = 0.07). Thermic effect of feeding (TEF) was higher in WB50 than other treatments (P < 0.01). Metabolizable energy of wheat bran was similar among treatment groups (except for WB10). NE of wheat bran conformed to a quadratic regression equation with inclusion level (R2 = 0.99, P < 0.01) and peaked at an inclusion level of 35.3%. In conclusion, increasing inclusion level decreased energy expenditure of sows on physical activity and promoted growth of fiber-degrading bacteria, which improved energy utilization of fiber. Fermentation of wheat bran fiber by Prevotellaceae_UCG-003 and norank_f__Paludibacteraceae might increase TEF. Consequently, sows utilized energy in wheat bran most efficiently at an inclusion level of 35.3%.

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

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

Presence and role of viruses in anaerobic digestion of food waste under environmental variability

BACKGROUND

The interaction among microorganisms in the anaerobic digestion of food waste (ADFW) reactors lead to the degradation of organics and the recycling of energy. Viruses are an important component of the microorganisms involved in ADFW, but are rarely investigated. Furthermore, little is known about how viruses affect methanogenesis.

RESULTS

Thousands of viral sequences were recovered from five full-scale ADFW reactors. Gene-sharing networks indicated that the ADFW samples contained substantial numbers of unexplored anaerobic-specific viruses. Moreover, the viral communities in five full-scale reactors exhibited both commonalities and heterogeneities. The lab-scale dynamic analysis of typical ADFW scenarios suggested that the viruses had similar kinetic characteristics to their prokaryotic hosts. By associating with putative hosts, a majority of the bacteria and archaea phyla were found to be infected by viruses. Viruses may influence prokaryotic ecological niches, and thus methanogenesis, by infecting key functional microorganisms, such as sulfate-reducing bacteria (SRB), syntrophic acetate-oxidizing bacteria (SAOB), and methanogens. Metabolic predictions for the viruses suggested that they may collaborate with hosts at key steps of sulfur and long-chain fatty acid (LCFA) metabolism and could be involved in typical methanogenesis pathways to participate in methane production.

CONCLUSIONS

Our results expanded the diversity of viruses in ADFW systems and suggested two ways that viral manipulated ADFW biochemical processes. Video Abstract.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman

Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H₂ and CH₄. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO₂, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.

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.

Bioaugmentation of the green alga to enhance biogas production in an anaerobic hollow-fiber membrane bioreactor

Anaerobic membrane reactors (AnMBRs) offer an alternative wastewater treatment system, presenting both reclamation of value through biogas production, and efficient treatment of recalcitrant contaminants such as antibiotics from wastewater. The effects of bioaugmentation with the green alga Haematococcus pluvialis on anaerobic treatment of pharmaceutical wastewaters, alleviating membrane biofouling, biogas production and impact on the indigenous microbial communities were evaluated using AnMBRs. The outputs of the bioreactor experiments revealed that bioaugmentation strategies with the green alga increased removal of chemical oxygen demand by 12% and delayed membrane fouling by 25% and increased biogas production by 40%. Furthermore, bioaugmentation with the green alga led to a significant change in relative abundance of archaea and the main methanogenesis pathway shifted from Methanothermobacter to Methanosaeta, accompanied by their respective syntrophic bacteria.

Enhanced hydrolysis/acidogenesis and potential mechanism in thermal-alkali-biofilm synergistic pretreatment of high-solid and low-organic-content sludge

Improving the anaerobic digestion (AD) of high-solid and low-organic-content sludge is imperative for sustainable waste activated sludge (WAS) management. Here, a thermal-alkali-biofilm pretreatment (TAB) was established to treat high-solid and low-organic-content sludge and compared with thermal and thermal-alkali methods. The results showed that TAB drastically improved WAS reduction, hydrolysis/acidogenesis efficiency, and biochemical methane potential. TAB possessed the lowest sludge particle size and the highest surface charge due to the stimulated proteolysis and WAS solubilization, supported by the protease activity test and secondary substrate identification. In addition, the biofilm assistance noticeably accelerated the elimination of autochthonous bacteria in WAS (e.g., Proteobacteria) and facilitated the enrichment of specialized fermentative microorganisms (e.g., Firmicutes) along with relevant functional genes, lying molecular foundation for the enhanced hydrolysis/acidogenesis in TAB. These findings could expand the application of biofilm in the AD of WAS and provide new insight into the pretreatment strategy of high-solid and low-organic-content sludge.

Comparative effect of conductive and dielectric materials on methanogenesis from highly concentrated volatile fatty acids

Various conductive materials and their dielectric counterparts were used to get deeper insights into contribution of direct interspecies electron transfer (DIET) in improving methanogenesis from highly concentrated volatile fatty acids (12.5 g/L). Potential CH₄ yield, maximum CH₄ production rate and lag phase were significantly (up to 1.4, 3.9 and 2.0 times, respectively) improved with addition of stainless-steel mesh (SM) and carbon felt (CF) compared to both control and dielectric counterparts (p < 0.05). k_app increased by 82% for SM and 63% for CF compared to control (p < 0.05). Short thick pili-like structures up to 150 nm in width were formed only in CF and SM biofilms, however, were more abundant for SM. Ureibacillus and Limnochordia specific for SM biofilms, and Coprothermobacter and Ca. Caldatribacterium for CF biofilms, were considered electrogenic. Promotion of DIET by conductive materials is governed by many factors, including specificity of electrogenic groups to material surface.

Biomethane production and microbial strategies corresponding to high organic loading treatment for molasses wastewater in an upflow anaerobic filter reactor

Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. In this study, an upflow anaerobic filter (UAF) reactor was employed to establish a high organic loading treatment system for molasses wastewater and further investigated the microbial community dynamics in response to this stressful operation. The biogas production increased with an increase in total organic carbon (TOC) loading rate from 1.0 to 14 g/L/day, and then it decreased with further TOC loading rate addition until 16 g/L/day. The UAF reactor achieved a maximum biogas production of 6800 mL/L/day with a TOC removal efficiency of 66.5% at a TOC loading rate of 14 g/L/day. Further microbial analyses revealed that both the bacterial and archaeal communities developed multiple strategies to maintain stable operation of the reactor at high organic loading (e.g., Proteiniphilum and Defluviitoga maintained high abundances throughout the operation; Tissierella temporarily dominated the bacterial community at TOC loading rates of 8.0 to 14 g/L/day; and multi-trophic Methanosarcina shifted as the dominant methanogen at the TOC loading rates of 8.0 to 16 g/L/day). This study presents insights into a high organic loading molasses wastewater treatment system and the microbial flexibility in methane fermentation in response to process disturbances.

Culture adaptation for enhanced biogas production from birch wood applying stable carbon isotope analysis to monitor changes in the microbial community

Birch wood is a potential feedstock for biogas production in Northern Europe; however, the lignocellulosic matrix is recalcitrant preventing efficient conversion to methane. To improve digestibility, birch wood was thermally pre-treated using steam explosion at 220 °C for 10 min. The steam-exploded birch wood (SEBW) was co-digested with cow manure for a period of 120 days in continuously fed CSTRs where the microbial community adapted to the SEBW feedstock. Changes in the microbial community were tracked by stable carbon isotopes- and 16S r RNA analyses. The results showed that the adapted microbial culture could increase methane production up to 365 mL/g VS day, which is higher than previously reported methane production from pre-treated SEBW. This study also revealed that the microbial adaptation significantly increased the tolerance of the microbial community against the inhibitors furfural and HMF which were formed during pre-treatment of birch. The results of the microbial analysis indicated that the relative amount of cellulosic hydrolytic microorganisms (e.g. Actinobacteriota and Fibrobacterota) increased and replaced syntrophic acetate bacteria (e.g. Cloacimonadota, Dethiobacteraceae, and Syntrophomonadaceae) as a function of time. Moreover, the stable carbon isotope analysis indicated that the acetoclastic pathway became the main route for methane production after long-term adaptation. The shift in methane production pathway and change in microbial community shows that for anaerobic digestion of SEBW, the hydrolysis step is important. Although acetoclastic methanogens became dominant after 120 days, a potential route for methane production could also be a direct electron transfer among Sedimentibacter and methanogen archaea.

Molecular characterization of microorganisms with industrial potential for methane production in sludge from Kangemi sewage treatment plant, Nyeri county-Kenya

Microbial consortia under anaerobic conditions are involved in oxidizing organic matter in the sludge to produce methane gas. However, in developing countries like Kenya, these microbes have not been fully identified to target them for the efficient harnessing of biofuel. This study collected wet sludge from two anaerobic digestion lagoons 1 and 2 that were operational during sampling at Kangemi Sewage Treatment Plant, in Nyeri County, Kenya. DNA was extracted from samples using commercially available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for identifying microorganisms directly involved in various stages of methanogenesis pathways. The study found hydrogenotrophic methanogens, such as Methanospirillum (32%), Methanobacterium (27%), Methanobrevibacter (27%), and Methanosarcina (32%), being predominant in the lagoon communities, whereas acetoclastic microorganisms such as the Methanoregula (22%) and the acetate oxidazing bacteria such as Clostridia (68%) were the key microbes for that pathway in the sewage digester sludge. Furthermore, Methanothermobacter (18%), Methanosarcina (21%), Methanosaeta (15%), and Methanospirillum (13%) carried out the methylotrophic pathway. In contrast, Methanosarcina (23%),Methanoregula (14%), methanosaeta (13%), and methnanoprevibacter (13%) seemed to play an important role in the final step of methane release. This study concluded that the sludge produced from the Nyeri-Kangemi WWTP harbors microbes with significant potential for biogas production. The study recommends a pilot study to investigate the efficiency of the identified microbes for biogas production.

Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw

High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.

Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion

Aromatic compounds like phenyl acids (PA) can accumulate during anaerobic digestion (AD) of organic wastes due to an increased entry of lignocellulose, secondary plant metabolites or proteins, and thermodynamic challenges in degrading the benzene ring. The effects of aromatic compounds can be various - from being highly toxic to be stimulating for methanogenesis - depending on many parameters like inoculum or molecular characteristics of the aromatic compound. To contribute to a better understanding of the consequences of PA exposure during AD, the aim was to evaluate the effects of 10 mM PA on microbial communities degrading different, degradation phase-specific substrates in thermophilic batch reactors within 28  days: Microcrystalline cellulose (MCC, promoting hydrolytic to methanogenic microorganisms), butyrate or propionate (promoting syntrophic volatile fatty acid (VFA) oxidisers to methanogens), or acetate (promoting syntrophic acetate oxidisers to methanogens). Methane production, VFA concentrations and pH were evaluated, and microbial communities and extracellular polymeric substances (EPS) were assessed. The toxicity of PA depended on the type of substrate which in turn determined the (i) microbial diversity and composition and (ii) EPS quantity and quality. Compared with the respective controls, methane production in MCC reactors was less impaired by PA than in butyrate, propionate and acetate reactors which showed reductions in methane production of up to 93%. In contrast to the controls, acetate concentrations were high in all PA reactors at the end of incubation thus acetate was a bottle-neck intermediate in those reactors. Considerable differences in EPS quantity and quality could be found among substrates but not among PA variants of each substrate. Methanosarcina spp. was the dominant methanogen in VFA reactors without PA exposure and was inhibited when PA were present. VFA oxidisers and Methanothermobacter spp. were abundant in VFA assays with PA exposure as well as in all MCC reactors. As MCC assays showed higher methane yields, a higher microbial diversity and a higher EPS quantity and quality than VFA reactors when exposed to PA, we conclude that EPS in MCC reactors might have been beneficial for absorbing/neutralising phenyl acids and keeping (more susceptible) microorganisms shielded in granules or biofilms.

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.

Biomethane recovery through co-digestion of cheese whey and glycerol in a two-stage anaerobic fluidized bed reactor: Effect of temperature and organic loading rate on methanogenesis

Anaerobic digestion for CH₄ recovery in wastewater treatment has been carried out with different strategies to increase process efficiency, among which co-digestion and the two-stage process can be highlighted. In this context, this study aimed at evaluating the co-digestion of cheese whey and glycerol in a two-stage process using fluidized bed reactors, verifying the effect of increasing the organic loading rate (OLR) (2-20 g-COD.L^-1.d^-1) and temperature (thermophilic and mesophilic) in the second stage methanogenic reactor. The mesophilic methanogenic reactor (R-Meso) (mean temperature of 22 °C) was more tolerant to high OLR and its best performance was at 20 g-COD.L^-1.d^-1, resulting in methane yield (MY) and methane production (MPR) of 273 mL-CH₄.g-COD^-1 and 5.8 L-CH₄.L^-1.d^-1 (with 67% of CH₄), respectively. Through 16S rRNA gene massive sequencing analysis, a greater diversity of microorganisms was identified in R-Meso than in R-Thermo (second stage methanogenic reactor, 55 °C). Firmicutes was the phyla with higher relative abundance in R-Thermo, while in R-Meso the most abundant ones were Proteobacteria and Bacteroidetes. Regarding the Archaea domain, a predominance of hydrogenotrophic microorganisms could be observed, being the genera Methanothermobacter and Methanobacterium the most abundant in R-Thermo and R-Meso, respectively. The two-stage system composed with a thermophilic acidogenic reactor + R-Meso was more adequate for the co-digestion of cheese whey and glycerol than the single-stage process, promoting increases of up to 47% in the energetic yield (10.3 kJ.kg-COD^-1) and 14% in organic matter removal (90.5%).

Microbial Behavior and Influencing Factors in the Anaerobic Digestion of Distiller: A Comprehensive Review

Anaerobic digestion technology is regarded as the most ideal technology for the treatment of a distiller in terms of environmental protection, resource utilization, and cost. However, there are some limitations to this process, the most prominent of which is microbial activity. The purpose of this paper is to provide a critical review of the microorganisms involved in the anaerobic digestion process of a distiller, with emphasis on the archaea community. The effects of operating parameters on microbial activity and process, such as pH, temperature, TAN, etc., are discussed. By understanding the activity of microorganisms, the anaerobic treatment technology of a distiller can be more mature. Aiming at the problem that anaerobic treatment of a distiller alone is not effective, the synergistic effect of different substrates is briefly discussed. In addition, the recent literature on the use of microorganisms to purify a distiller was collected in order to better purify the distiller and reduce harm. In the future, more studies are needed to elucidate the interactions between microorganisms and establish the mechanisms of microbial interactions in different environments.

Active microbial communities during biodegradation of biodegradable plastics by mesophilic and thermophilic anaerobic digestion

Biodegradable plastics, if they are not properly managed at their end-of-life, can have the same hazardous environmental consequences as conventional plastics. This study investigates the treatment of the main biodegradable plastics under mesophilic and thermophilic anaerobic digestion using biochemical methane potential test and the microorganisms involved in the process using amplicon sequencing of the 16 S rRNA. Here we showed that, only PHB and TPS undergone important and rapid biodegradation under mesophilic condition (38 °C). By contrast, PCL and PLA exhibited very low biodegradation rate as 500 days were required to reach the ultimate methane yield. Little or no degradation occurred for PBAT and PBS at 38 °C. Under thermophilic conditions (58 °C), TPS, PHB, and PLA reached high levels of biodegradation in a relatively short period (&lt; 100 d). While PBS, PBAT, and PCL could not be converted into methane at 58 °C. PHB degraders (Enterobacter and Cupriavidus) and lactate-utilizing bacteria (Moorella and Tepidimicrobium) appeared to play an important role in the PHB and PLA degradation, respectively. This work not only provides crucial data on the anaerobic digestion of the main biodegradable plastics but also enriches the understanding of the microorganisms involved in this process, which are of great importance for future development of the treatment of biodegradable plastics in anaerobic digestion systems.

Maximizing the energy recovery from rice straw through two-step conversion using eggshell-catalytic pyrolysis followed by enhanced anaerobic digestion using calcium-rich biochar

Anaerobic digestion of lignocelluloses for biogas production is greatly restricted by the poor biomass degradability. Herein, a novel approach is suggested to enhance the energy recovery from rice straw through a two-step conversion using eggshell-based catalytic pyrolysis followed by biochar-based anaerobic co-digestion. Pyrolysis with eggshell significantly enhanced the crude bio-oil yield by 4.6 %. Anaerobic digestion of rice straw using 4 g L^-1 of rice straw biochar (RB) showed the highest recorded biogas yield of 503.7 L kg^-1 VS, with 268.6 L kg^-1 VS biomethane yield. However, 4 g L^-1 of calcium-enriched eggshell rice straw biochar (ERB) enhanced the biomethane yield to 281.8 L kg^-1 VS, which represented 95.6 % higher than the control. It was attributed to enhancement of biomethanation, which resulted in 74.5 % maximum recorded biomethane content at the 7th day of anaerobic digestion. Microbial analysis confirmed that Methanosarciniales was the most dominant Archael group in the control (14.84 %), which increased sharply to 73.91 % and 91.66 % after addition of 4 g L^-1 RB and ERB, respectively. The suggested route enhanced the energy recovery in the form of bio-oil and biomethane by 41.6 %.

Methanogenic consortia from thermophilic molasses-fed structured-bed reactors: microbial characterization and responses to varying food-to-microorganism ratios

The heterogeneous character of fixed-film reactors may create highly specialized zones with a stratified distribution of microbial groups and varying capabilities to withstand high organic loads in anaerobic digestion (AD) systems. The microbial distribution and methane-producing potential of biomass from different regions (feeding zone and structured bed) of two second-stage thermophilic (55 ºC) fixed-film reactors were assessed. Three levels of food-to-microorganism (F/M) ratio (0.4, 1.0 and 3.0 g-COD g⁻¹VS) using fermented (two-stage AD) and fresh (single-stage AD) sugarcane molasses were tested in batch reactors, simulating low to high organic loads. Specific methane production rates increased as the F/M increased when using fermented molasses, maintaining efficient methanogenesis at substrate availability levels threefold higher than single-stage schemes (3.0 vs. 1.0 g-COD g⁻¹VS). Success in methane production derived from the homogenous establishment (similar in both feeding zone and bed) of syntrophic associations between acetogens (Pelotomaculum, Syntrophothermus, Syntrophomonas and Thermodesulfovibrio), acetate oxidizers (Thermoacetogenium, Mesotoga and Pseudothermotoga) and hydrogenotrophic methogens (Methanothermobacter and Methanoculleus) replacing acetoclastic methanogens (Methanosaeta). Phase separation under thermophilic conditions was demonstrated to boost methane production from sugar-rich substrates, because the process depends on microbial groups (hydrogenotrophs) that grow faster and are less susceptible to low pH values compared to acetotrophs.

Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology

The present work evaluated the impacts of microbial communities, biomass activity and sludge morphology on anaerobic syntrophic reactions. Experiments were conducted using mature floc sludge and granular sludge under different food/microbes ratios, and with different sludge types (floc sludge, concentrated floc sludge and granular sludge) and sludge morphology (granules, vortexed granules, and granules with different particle sizes). The results show that the intact granules achieved the most effective syntrophic reaction among all sludge types. The granule structure facilitated the enrichment of syntrophic acetate oxidation bacteria (g_Syner-01 and g_Mesotoga) and methanogens, which corresponds to their superior specific methanogenic activity and high production of communication compounds. Despite the high diffusion and substrate uptake capacities, the disintegrated granules had low H₂ consumption rates, which led to poor syntrophic activities. The results underline the importance of sludge spatial structures in promoting excellent syntrophic activities and the development of diverse microbial communities.

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.

High-efficiency anaerobic co-digestion of food waste and mature leachate using expanded granular sludge blanket reactor

Anaerobic digestion of food waste receives more and more attention for waste-to-energy conversion, while easy acidification and limited efficiency hinder its wide application. To improve anaerobic digestion of food waste, its anaerobic co-digestion with mature leachate was performed using an expanded granular sludge blanket reactor. With the chemical oxidation demand (COD) removal of around 80%, the methane production and organic loading rate of the reactor reached 5.87 ± 0.45 L/L/d and 23.6 g COD/L/d, respectively. The rate of COD converted to methane was ranging from 74% to 87%. The addition of mature leachate provided ammonium to avoid acidification and trace metals for microbial growth, and the efficiencies of four stages of anaerobic digestion were all enhanced. The predominant methanogenic genera were shifted to adapt the changing condition, thus stabilizing the system. These findings support high-efficiency bioenergy recovery from food waste and leachate in practice.

Influence of NH3 and NH4+ on anaerobic digestion and microbial population structure at increasing total ammonia nitrogen concentrations

Despite the extensive research dedicated to ammonia inhibition, the effect of NH₃ and NH₄⁺ on each anaerobic digestion stage and the associated microorganisms is still not completely understood. In the past, the focus was mainly on methanogenesis and either on NH₃ or total ammonia nitrogen (TAN). Here, anaerobic digestion of two defined substrates, namely starch/NH₄Cl and casein, was investigated particularly regarding the effects of different NH₃/NH₄⁺ ratios on the involved microorganisms. TAN affected bacteria, primarily gram-positive ones, whereas archaea responded largely to the NH₃ concentration. These sensitivity differences are attributed to differences in the corresponding cell-membrane structures. A TAN decrease via stripping performed in two full-scale agricultural biogas plants resulted in increased bacterial diversity, with a pronounced increase in the propionate acetogens' abundance. Based on these data, it is suggested that inhibition can be avoided and processes stabilized in biogas plants by adjusting the NH₃/NH₄⁺ ratio, when feeding nitrogen-rich substrates.