Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste

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

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

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.

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 (< 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.

New insights into the mechanisms underlying biochar-assisted sustained high-efficient co-digestion: Reducing thermodynamic constraints and enhancing extracellular electron transfer flux

To clarify the roles of biochar in the anaerobic co-digestion of waste activated sludge (WAS) and food waste (FW), batch tests were conducted coupled with thermodynamics, extracellular electron transfer flux and microbial community analysis. Compared with the control group, biochar significantly facilitated the co-digestion at three periods, but its sustainable facilitation was mainly in the syntrophic methanogenesis of volatile fatty acids (VFAs). The thermodynamic analysis confirmed that biochar could alleviate limitations imposed by high hydrogen partial pressure during interspecies hydrogen transfer (IHT), the thermodynamic windows was expanded 137% and 92% in the syntrophic methanogenesis of acetate and propionate, respectively. Meanwhile, due to the redox capacity of biochar (4.85 and 0.35 μmol e^-/g biochar), the equivalent current of direct interspecies electron transfer (DIET) flux for syntrophic methanogenesis of acetate and propionate obtained were 1.0 × 10^-4 A and 0.9 × 10^-4 A, which were 10⁸ times than that of IHT. It should be noticed that the functional microorganisms like Methanosarcina which could participate DIET were only enriched on the surface of biochar, the dominant Methanothermobacter in suspended sludge probably indicate IHT was still the main pathway for syntrophic methanogenesis. Nevertheless, the DIET triggered by the redox-active moieties on the surface of biochar and the enhanced IHT by alleviating thermodynamic restrictions, promoted the syntrophic methanogenesis synergistically.

Iocasia fonsfrigidae NS-1 gen. nov., sp. nov., a Novel Deep-Sea Bacterium Possessing Diverse Carbohydrate Metabolic Pathways

Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362^T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.

Comparison of decabromodiphenyl ether degradation in long-term operated anaerobic bioreactors under thermophilic and mesophilic conditions and the pathways involved

Anaerobic digestion of decabromodiphenyl ether was carried out and compared in two continuously stirred anaerobic bioreactors for 210 days under thermophilic and mesophilic conditions. Results show that the degradation of decabromodiphenyl ether followed the first-order reaction kinetics, which exhibited a higher removal rate in the thermophilic reactor when compared to the mesophilic one, reaching its maximum of 1.1 μg·day^-1. The anaerobic digestion of decabromodiphenyl ether was found to involve the replacement of bromines from polybrominated diphenyl ether by hydrogen atoms, gradually forming nona-, octa- and hepta-brominated diphenyl ether, respectively. Under the thermophilic condition, the reactors were dominated by Bacillus sp. and Methanosarcina sp. with high bioactivity and high concentrations of debromination microorganisms.

Methane production and active microbial communities during anaerobic digestion of three commercial biodegradable coffee capsules under mesophilic and thermophilic conditions

Biodegradable plastics market is increasing these last decades, including for coffee capsules. Anaerobic digestion, as a potential end-of-life scenario for plastic waste, has to be investigated. For this purpose, mesophilic (38 °C) and thermophilic (58 °C) anaerobic digestion tests on three coffee capsules made up with biodegradable plastic (Beanarella®, Launay® or Tintoretto®) and spent coffee (control) were compared by their methane production and the microbial communities active during the process. Mesophilic biodegradation of the capsules was slow and did not reach completion after 100 days, methane production ranged between 67 and 127 NL (CH₄) kg^-1 (VS). Thermophilic anaerobic digestion resulted in a better biodegradation and reached completion around 100 days, methane productions were between 257 and 294 NL (CH₄) kg^-1 (VS). The microbial populations from the reactors fed with plastics versus spent coffee grounds were significantly different, under both the mesophilic and the thermophilic conditions. However, the different biodegradable plastics only had a small impact on the main microbial community composition at a similar operational temperature and sampling time. Interestingly, the genus Tepidimicrobium was identified as a potential key microorganisms involved in the thermophilic conversion of biodegradable plastic in methane.

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.

Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco)

Both molecular analyses and culture-dependent isolation were combined to investigate the diversity of sulfate-reducing prokaryotes and explore their role in sulfides production in full-scale anaerobic digesters (Marrakech, Morocco). At global scale, using 16S rRNA gene sequencing, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Synergistetes, and Euryarchaeota were the most dominant phyla. The abundance of Archaea (3.1–5.7%) was linked with temperature. The mcrA gene ranged from 2.18 × 105 to 1.47 × 107 gene copies.g−1 of sludge. The sulfate-reducing prokaryotes, representing 5% of total sequences, involved in sulfides production were Peptococcaceae, Syntrophaceae, Desulfobulbaceae, Desulfovibrionaceae, Syntrophobacteraceae, Desulfurellaceae, and Desulfobacteraceae. Furthermore, dsrB gene ranged from 2.18 × 105 to 1.92 × 107 gene copies.g−1 of sludge. The results revealed that exploration of diversity and function of sulfate-reducing bacteria may play a key role in decreasing sulfide production, an undesirable by-product, during anaerobic digestion.

Microbial community in an anaerobic membrane bioreactor and its performance in treating organic solid waste under controlled and deteriorated conditions

The adoption of anaerobic membrane bioreactors (AnMBRs) for organic solid waste management is important for the recovery of energy and high-quality treated water. However, few studies have focused on AnMBR treatment of high-strength organic solid waste and the microorganisms involved under deteriorated operating conditions. In the present study, a 15-L bench-scale AnMBR was operated using a model slurry of high-strength organic solid waste with the organic loading rate (OLR) increasing from 2.3 g chemical oxygen demand (COD) L^-1 day^-1 (represented as a controlled condition) to 11.6 g COD L^-1 day^-1 (represented as a deteriorated condition), and microbial community dynamics over 120 days of operation were analyzed. The abundances of methanogens and bacteria that were dominant under the controlled condition decreased as a result of both high organic loading and sludge withdrawal under the deteriorated condition and did not recover thereafter. Instead, numbers of putative volatile fatty acid (VFA)-producing bacterial operational taxonomic units (OTUs) related to the genus Prevotella increased rapidly, reaching a relative abundance of 43.2%, leading to the deterioration of methanogenic AnMBR operation. Considering that the sequences of these OTUs exhibited relatively low sequence identity (91-95%) to those of identified Prevotella species, the results strongly suggest that the accumulation of VFAs by novel VFA-producing bacteria in the digestion sludge promotes the disruption of the methanogen community under deteriorated conditions.

Unexpected diversity of acetate degraders in anaerobic membrane bioreactor treating organic solid waste revealed by high-sensitivity stable isotope probing

In anaerobic membrane bioreactor (AnMBR) treating organic solid waste, acetate is one of the most important precursors to CH₄. However, the identity and diversity of anaerobic acetate degraders are largely unknown, possibly due to their slow growth rates and low abundances. Here, we identified acetate-degrading microorganisms in the AnMBR sludges by high-sensitivity stable isotope probing. Degradation of the amended ¹³C-acetate coincided with production of ¹³CH₄ and ¹³CO₂ during the sludge incubation. High-throughput sequencing of RNA density fractions indicated that the aceticlastic and hydrogenotrophic methanogens, i.e., Methanosaeta sp. (acetate dissimilator) and Methanolinea sp. (acetate assimilator), incorporated ¹³C-acetate significantly. Remarkably, 22 bacterial species incorporating ¹³C-acetate were identified, whereas their majority was distantly related to the cultured representatives. Only two of them were the class Deltaproteobacteria-affiliated lineages with syntrophic volatile fatty acid oxidation activities. Phylogenetic tree analysis and population dynamics tracing revealed that novel species of the hydrolyzing and/or fermenting taxa, such as the phyla Bacteroidetes, Chloroflexi and Lentisphaerae, exhibited low relative abundances comparable to that of Methanolinea sp. (0.00011%) during the AnMBR operation, suggesting that these bacteria were involved in anaerobic acetate assimilation. Meanwhile, novel species of the phyla Firmicutes, Synergistetes and Caldiserica, the candidate phyla Aminicenantes and Atribacteria and the candidate division GOUTA4-related clade, as well as the known Deltaproteobacteria members, existed at relatively high abundances (0.00031%-0.31121%) in the reactor, suggesting that these bacterial species participated in anaerobic dissimilation of acetate, e.g., syntrophic acetate oxidation. The results of this study demonstrated the unexpected diversity and ecophysiological features of the anaerobic acetate degraders in the AnMBR treating organic solid waste.

Methane production from food waste via mesophilic anaerobic digestion with ethanol pre-fermentation: Methanogenic pathway and microbial community analyses

To investigate the methanogenic pathway and microbial community in a mesophilic anaerobic digestion (AD) system with food waste (FW) ethanol pre-fermentation (EP), two semi-continuous AD systems were operated by feeding FW with (PSR) and without EP (control). In this study, δ¹³C-ethanol was supplemented as solo substrate for AD sludge when the reactors operation stabilized to analyze the methanogenic pathways. The results suggested that approximately 59.3% of methane was produced from acetotrophic methanogens, while 40.7% was formed by hydrogenotrophic methanogens in the PSR group. On the other hand, compared with control, methane produced via CO₂ reduction pathway was increased by 4.70%. Meanwhile, the composition variations of the microbial community in AD supported the above conclusion, since the relative abundances of Clostridium and Methanobacterium were enhanced by 7.6% and 10.2%, respectively in PSR reactor. These results provided a theoretical basis for AD applications and biogas yield improvements with EP process.

Enhanced biomethane recovery from fat, oil, and grease through co-digestion with food waste and addition of conductive materials

In this study, the effect of conductive additives on co-digestion of fat, oil, and grease (FOG) and food waste (FW) was evaluated. Initially, biochemical methane potential (BMP) test was conducted for optimization of mixing ratio of FW and FOG. The optimal methane production (800 L (kg VS)^-1) was obtained from co-digestion of 70% FW + 30% FOG (w/w), which was 1.2 times and 12 times of that obtained from mono-digestion of FW and FOG, respectively. This optimal mixing ratio was used for subsequent fed-batch studies with the addition of two conductive additives, granular activated carbon (GAC) and magnetite. The addition of GAC significantly shortened the lag phase (from 7 to 3 d), reduced accumulation of various volatile fatty acids (VFAs), and enhanced methane production rate (50-80% increase) compared to the control and magnetite-amended bioreactor. Fourier transformation infrared (FTIR) analysis suggested that the degradation of lipids, protein and carbohydrates was the highest in GAC amended reactor, followed by magnetite and control reactors. GAC addition also enriched more abundant and diverse bacteria and methanogens than control. Magnetite addition also showed similar trends but to a lesser degree. The substantial enrichment of syntrophic LCFA β-oxidizing bacteria (e.g. Syntrophomonas) and methanogenic archaea in the GAC-amended bioreactor likely attributed to the superior methanogenesis kinetics in GAC amended bioreactor. Our findings suggest that the addition of GAC could provide a sustainable strategy to enrich kinetically efficient syntrophic microbiome to favor methanogenesis kinetics in co-digestion of FW and FOG.

Metabolic analysis of efficient methane production from food waste with ethanol pre-fermentation using carbon isotope labeling

Anaerobic digestion (AD) has been widely applied as an economic option for food waste (FW) treatment. In this study, the group treated with ethanol pre-fermentation (EP) for 12 h (EP12) exhibited the highest cumulative biogas yield (206 mL/g-volatile solid) during AD process and therefore it was used to illuminate the underlying metabolic processes of AD with EP. Carbon isotope labeled glucose was supplemented to FW substrate, and the EP process was found to alleviate the acidification inhibition with conducting extremely high carbon flux towards ethanol formation (43.7%). Then an efficient acetogenesis phase was also observed in EP12 group, because of high carbon conversion rate from ethanol to acetate. Overall, higher carbon conversion rate to methane (90.1%) during methanogenesis was found in the AD system with EP than in the control experiment (80.3%). Thus, we quantitatively confirmed that EP affects the AD metabolism of FW in terms of carbon flow distribution.

Thermophilic anaerobic digestion of cattail and hydrothermal carbonization of the digestate for co-production of biomethane and hydrochar

Thermophilic anaerobic digestion (AD) of cattail followed by hydrothermal carbonization (HTC) was studied. The intent of the research was to develop agricultural waste-based biorefining technologies for bioenergy production along with value-added products. Cattail was anaerobically digested at 55 °C for 14 days and protein and cellulose components were partially degraded. The average methane yield was 230-280 mL/g volatile solids and the total solids decreased by 33-55%. When the particle size of cattail was reduced from 1 in. to 1 mm, the lag phase was shortened from 1.48 to 0 d. Following the AD process of cattail, the AD digestate was hydrothermally carbonized at 250 °C for 4 h, yielding approximately 6.7-7.5 wt % gaseous products, 64 wt % liquid products and 28 wt % hydrochar. The gaseous products contained >5000 ppm H₂S and liquid products possessed fewer chemicals and higher ratio of phenolic compounds compared to the liquid products from HTC of original cattail. The hydrochar had a higher carbon content (76.8-79.8%) and a higher specific surface area (∼10 m²/g) than those of the feedstock. Hydrochar was further activated by using Na₂CO₃, NaHCO₃ and NaCl. The activation process increased the carbon content and specific surface area to 84-93% and 250-630 m²/g, respectively.

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.

Two-stage thermophilic anaerobic co-digestion of corn stover and cattle manure to enhance biomethane production

Two-stage thermophilic anaerobic co-digestion of cattle manure and corn stover was conducted to increase biomethane production. The first stage pre-digestion of corn stover was studied based on the following treatment variables: corn stover to liquid fraction of digestate (CS:LFD) ratio (1:7, 1:10, 1:13, 1:14), digestion temperature (55 °C, 60 °C) and digestion time (3, 7, 14 days). The reduction in lignin, cellulose and hemicellulose (LCH) was between 3.97% and 11.98%, which increased the biodegradability of corn stover. Corn stover pre-digested with a CS:LFD ratio of 1:10 at 55 °C for a period of 3 and 7 days was subjected to anaerobic co-digestion with cattle manure. The highest biomethane yield was observed on day 21 with a value of 357.41 mL/g volatile solids (VS) for untreated corn stover, 446.84 mL/g VS for corn stover pre-digested for 3 days and 518.58 mL/g VS for corn stover pre-digested for 7 days with LFD. The VS conversion efficiency for co-digestion of cattle manure with untreated corn stover, corn stover pre-digested for 3 days and 7 days was 42.8%, 43.3% and 51.8%, respectively, on day 21, which was higher than that (34.0%) of cattle manure only.

Instability diagnosis and syntrophic acetate oxidation during thermophilic digestion of vegetable waste

Effective process monitoring and instability diagnosis are important for stable anaerobic digestion (AD) of vegetable waste (VW). In order to evaluate the performance of thermophilic digestion of VW, to make early diagnosis for instability after organic overload, and to reveal the dynamics of microbial community under different running states, thermophilic AD of VW was carried out under improved organic loading rates (OLR) of 0.5-2.5 g volatile solid (VS)/(L ∙ d) in this study. Gaseous parameters including volumetric methane production rate (VMPR), CH₄, CO₂, and H₂ concentrations, and liquid parameters including pH, oxidation-reduction potential, volatile fatty acid (VFA), and total alkalinity (TA), bicarbonate alkalinity (BA), intermediate alkalinity (IA), and ammonia, were monitored. The coupling parameters, such as the CH₄/CO₂, VFA/BA, and BA/TA ratios were also used to evaluate stability. The dynamics of syntrophic acetate-oxidizing bacteria (SAOB), acetoclastic methanogens (AM), and hydrogenotrophic methanogens (HM) were analyzed by high-throughput sequencing. The main methanogenic bacteria were HM (Methanothermobacter) during the start-up period of OLR 0.5 gVS/(L ∙ d), while they were AM (Methanosarcina) during the stable period of OLR of 1.0 gVS/(L ∙ d). The VMPR of stable period was about 0.29 L/(L · d) with total VFA concentration below 100 mg/L, CH₄/CO₂ > 1.3, and BA/TA>0.9. The first instability due to the accumulation of VFA and self-recovery due to syntrophic acetate oxidation occurred at an OLR of 1.5 gVS/(L ∙ d). The syntrophic acetate-oxidizing bacteria probably belong to genus S1 (family Thermotogaceae). The digestion failed at an OLR of 2.0 g VS/(L · d). H₂ was only detected during collapsed period instead of instable period. The total ammonia nitrogen loss and bicarbonate alkalinity (BA) reduction were the primary causes for the instability of AD of VW without effluent recirculation. Compared with single parameters, the CH₄/CO₂ and BA/total alkalinity (TA) ratios are recommended as early warning indicators for engineering applications of thermophilic AD of VW.

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste

During anaerobic digestion of municipal solid waste, organic matter is converted to methane, carbon dioxide, and other organic and inorganic compounds through a complex cooperation among different microbial groups with different metabolic activities. Here, culture-dependent and independent approaches provided evidence for examining the relationship between bacterial and archaeal communities and methane production in a pilot-scale anaerobic digestion. The abundance of aerobic and anaerobic functional groups of C and N cycles, such as cellulolytic, pectinolytic, amylolytic and proteolytic bacteria, was high at the beginning of the experiment and was drastically decreased after anaerobic digestion. In contrast, the ammonifiers increased in the biogas producing reactors in a higher pH environment. The methanogenic archaeal genera recovered were Methanobrevibacter, Methanobacterium, Methanoculleus and Methanocorpusculum, thus indicating that methane was formed primarily by the hydrogenotrophic pathway in the reactors. Moreover, the mechanical pretreatment effects, as well as the effect of pelleted manure as inoculum, were considered. The highest methane production was detected in the biodigesters with minced organic waste, thus indicating that pre-treatment of a heterogeneous starting matrix was essential for improving biogas production and stabilizing the process.

Do microbial communities in an anaerobic bioreactor change with continuous feeding sludge into a full-scale anaerobic digestion system?

Microbial communities of sludge samples from a full-scale anaerobic digestion (AD) fed with primary sludge (PS) and excess sludge (ES) were analyzed using qPCR and MiSeq. The results showed that the microbial composition of digested sludge remained relatively stable but was partially changed by microbial immigration from feeding sludge. The dominant archaea in the digested sludge were largely the same as those in the feeding sludge, but their abundances differed markedly. The dominant fungal genera in the digested sludge were different from those in PS but were similar to those in ES. Various differences in bacterial community differences between digested sludge and PS/ES were observed. Notably, this study is the first to suggest Verrucomicrobia is the predominant bacterial phylum in the digested sludge, and that numerous unreported microorganisms belonging to the order LD1-PB3 existed in this AD system and potentially played roles in the processes of hydrolysis, fermentation, and acetogenesis.

Biochar assisted thermophilic co-digestion of food waste and waste activated sludge under high feedstock to seed sludge ratio in batch experiment

Batch experiments were conducted using biochar (BC) to promote stable and efficient methane production from thermophilic co-digestion of food waste (FW) and waste activated sludge (WAS) at feedstock/seed sludge (F/S) ratios of 0.25, 0.75, 1.5, 2.25, and 3. The results showed that the presence of BC dramatically shortened the lag time of methane production and increased the methane production rate with increased organic loading. The higher buffer capacity and large specific surface area of BC promoted microorganism growth and adaption to VFAs accumulation. Additionally, the electron exchange in syntrophic oxidation of butyrate and acetate as intermediate products was significantly facilitated by BC possibly due to the selective succession of bacteria and methanogens which may have participated in direct interspecies electron transfer, in contrast with the control group with low-efficient electron ferried between syntrophic oxidizers and methanogens using hydrogen as the electron carrier.

Correlation between system performance and bacterial composition under varied mixing intensity in thermophilic anaerobic digestion of food waste

This study examines the stability and efficiency of thermophilic anaerobic digesters treating food waste under various mixing velocities (50-160 rpm). The results showed that high velocities (120 and 160 rpm) were harmful to the digestion process with 18-30% reduction in methane generation and 1.8 to 3.8 times increase in volatile fatty acids (VFA) concentrations, compared to mild mixing (50 and 80 rpm). Also, the removal rate of soluble COD dropped from 75 to 85% (at 50-80 rpm) to 20-59% (at 120-160 rpm). Similarly, interrupted mixing caused adverse impacts and led to near-failure conditions with excessive VFA accumulation (15.6 g l^-1), negative removal rate of soluble COD and low methane generation (132 ml gVS^-1). The best efficiency and stability were achieved under mild mixing (50 and 80 rpm). In particular, the 50 rpm stirring speed resulted in the highest methane generation (573 ml gVS^-1). High-throughput sequencing of 16S rRNA genes revealed that the digesters were dominated by one bacterial genus (Petrotoga; phylym Thermotogae) at all mixing velocities except at 0 rpm, where the community was dominated by one bacterial genus (Anaerobaculum; phylum Synergistetes). The Petrotoga genus seems to have played a major role in the degradation of organic matter.

A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria

Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed ¹³C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of ¹³C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed ¹³C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in ¹³C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in ¹³C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge

High solid anaerobic digestion (HSAD) is a rapidly developed anaerobic digestion technique for treating municipal sludge, and has been widely used in Europe and Asia. Recently, the enhanced HSAD process with thermal treatment showed its advantages in both methane production and VS reduction. However, the understanding of the microbial community is still poor. This study investigated microbial communities in a pilot enhanced two-stage HSAD system that degraded waste activated sludge at 9% solid content. The system employed process “thermal pre-treatment (TPT) at 70 °C, thermophilic anaerobic digestion (TAD), and mesophilic anaerobic digestion (MAD)”. Hydrogenotrophic methanogens Methanothermobacter spp. dominated the system with relative abundance up to about 100% in both TAD and MAD. Syntrophic acetate oxidation (SAO) bacteria were discovered in TAD, and they converted acetate into H₂ and CO₂ to support hydrogenotrophic methanogenesis. The microbial composition and conversion route of this system are derived from the high solid content and protein content in raw sludge, as well as the operational conditions. This study could facilitate the understanding of the enhanced HSAD process, and is of academic and industrial importance.

Assessment of the degradation efficiency of full-scale biogas plants: A comparative study of degradation indicators

Increasing popularity and applications of the anaerobic digestion (AD) process has necessitated the development and identification of tools for obtaining reliable indicators of organic matter degradation rate and hence evaluate the process efficiency especially in full-scale, commercial biogas plants. In this study, four biogas plants (A1, A2, B and C) based on different feedstock, process configuration, scale and operational performance were selected and investigated. Results showed that the biochemical methane potential (BMP) based degradation rate could be use in incisively gauging process efficiency in lieu of the traditional degradation rate indicators. The BMP degradation rates ranged from 70 to 90% wherein plants A2 and C showed the highest throughput. This study, therefore, corroborates the feasibility of using the BMP degradation rate as a practical tool for evaluating process performance in full-scale biogas processes and spots light on the microbial diversity in full-scale biogas processes.

Exogenous addition of H2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane

Biological reduction of CO₂ into CH₄ by exogenous addition of H₂ is a promising technology for upgrading biogas into higher CH₄ content. The aim of this work was to study the feasibility of exogenous H₂ addition for an in situ biogas upgrading through biological conversion of the biogas CO₂ into CH_4. Moreover, this study employed systematic study with isotope analysis for providing comprehensive evidence on the underlying pathways of CH₄ production and upstream processes. Batch reactors were inoculated with digestate originating from a full-scale biogas plant and fed once with maize leaf substrate. Periodic addition of H₂ into the headspace resulted in a completely consumption of CO₂ and a concomitant increase in CH₄ content up to 89%. The microbial community and isotope analysis shows an enrichment of hydrogenotrophic Methanobacterium and the key role of hydrogenotrophic methanogenesis for biogas upgrading to higher CH₄ content. Excess H₂ was also supplied to evaluate its effect on overall process performance. The results show that excess H₂ addition resulted in accumulation of H₂, depletion of CO₂ and inhibition of the degradation of acetate and other volatile fatty acids (VFA). A systematic isotope analysis revealed that excess H₂ supply led to an increase in dissolved H₂ to the level that thermodynamically inhibit the degradation of VFA and stimulate homo-acetogens for production of acetate from CO₂ and H₂. The inhibition was a temporary effect and acetate degradation resumed when the excess H₂ was removed as well as in the presence of stoichiometric amount of H₂ and CO₂. This inhibition mechanism underlines the importance of carefully regulating the H₂ addition rate and gas retention time to the CO₂ production rate, H₂-uptake rate and growth of hydrogenotrophic methanogens in order to achieve higher CH₄ content without the accumulation of acetate and other VFA.

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box." We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester.

Non-autotrophic methanogens dominate in anaerobic digesters

Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.

A novel high-throughput multi-parameter flow cytometry based method for monitoring and rapid characterization of microbiome dynamics in anaerobic systems

A novel multidimensional flow cytometry based method has been demonstrated to monitor and rapidly characterize the dynamics of the complex anaerobic microbiome associated with perturbations in external environmental factors. While community fingerprinting provides an estimate of the meta genomic structure, flow cytometry provides a fingerprint of the community morphology including its autofluorescence spectrum in a high-throughput manner. Using anaerobic microbial consortia perturbed with the controlled addition of various carbon sources, it is possible to quantitatively discriminate between divergent microbiome analogous to community fingerprinting techniques using automated ribosomal intergenic spacer analysis (ARISA). The utility of flow cytometry based method has also been demonstrated in a fully functional industry scale anaerobic digester to distinguish between microbiome composition caused by varying hydraulic retention time (HRT). This approach exploits the rich multidimensional information from flow cytometry for rapid characterization of the dynamics of microbial communities.

Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB)

Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions. The genome encodes further 44 tRNA genes and three rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation features as well as genomic traits related to ammonia tolerance and methanogenesis.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

High-rate, High Temperature Acetotrophic Methanogenesis Governed by a Three Population Consortium in Anaerobic Bioreactors

A combination of acetate oxidation and acetoclastic methanogenesis has been previously identified to enable high-rate methanogenesis at high temperatures (55 to 65°C), but this capability had not been linked to any key organisms. This study combined RNA–stable isotope probing on ¹³C-labelled acetate and 16S amplicon sequencing to identify the active micro-organisms involved in high-rate methanogenesis. Active biomass was harvested from three bench-scale thermophilic bioreactors treating waste activated sludge at 55, 60 and 65°C, and fed with ¹³-C labelled and ¹²C-unlabelled acetate. Acetate uptake and cumulative methane production were determined and kinetic parameters were estimated using model-based analysis. Pyrosequencing performed on ¹³C- enriched samples indicated that organisms accumulating labelled carbon were Coprothermobacter (all temperatures between 55 and 65°C), acetoclastic Methanosarcina (55 to 60°C) and hydrogenotrophic Methanothermobacter (60 to 65°C). The increased relative abundance of Coprothermobacter with increased temperature corresponding with a shift to syntrophic acetate oxidation identified this as a potentially key oxidiser. Methanosarcina likely acts as both a hydrogen utilising and acetoclastic methanogen at 55°C, and is replaced by Methanothermobacter as a hydrogen utiliser at higher temperatures.

Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure

In recent years, anaerobic co-digestion (AcoD) has been widely used to improve reactor performance, especially methane production. In this study, we applied two different operating temperatures (thermophilic and mesophilic) and gradually increased the load of food wastewater (FWW) to investigate the bacterial communities during the AcoD of waste activated sludge (WAS) and FWW. As the load of FWW was increased, methane production rate (MPR; L CH4/L d) and methane content (%) in both Thermophilic AcoD (TAcoD) and Mesophilic AcoD (MAcoD) increased significantly; the highest MPR and methane content in TAcoD (1.423 L CH4/L d and 68.24%) and MAcoD (1.233 L CH4/L d and 65.21%) were observed when the FWW mixing ratio was 75%. However, MPR and methane yield in both reactors decreased markedly and methane production in TAcoD ceased completely when only FWW was fed into the reactor, resulting from acidification of the reactor caused by accumulation of organic acids. Pyrosequencing analysis revealed a decrease in bacterial diversity in TAcoD and a markedly different composition of bacterial communities between TAcoD and MAcoD with an increase in FWW load. For example, Bacterial members belonging to two genera Petrotoga (assigned to phylum Thermotogae) and Petrimonas (assigned to phylum Bacteroidetes) became dominant in TAcoD and MAcoD with an increase in FWW load, respectively. In addition, quantitative real-time PCR (qPCR) results showed higher bacterial and archaeal populations (expressed as 16S rRNA gene concentration) in TAcoD than MAcoD with an increase in FWW load and showed maximum population when the FWW mixing ratio was 75% in both reactors. Collectively, this study demonstrated the dynamics of key bacterial communities in TAcoD and MAcoD, which were highly affected by the load of FWW.

Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

This study aimed to reveal how antibiotic resistance genes (ARGs) and their horizontal and vertical transfer-related items (mobilome and bacterial hosts) respond to the transformation of anaerobic digestion (AD) from mesophilic to thermophilic using one-step temperature increase. The resistomes and mobilomes of mesophilic and thermophilic sludge were investigated using metagenome sequencing, and the changes in 24 representative ARGs belonging to three categories, class 1 integron and bacterial genera during the transition period were further followed using quantitative PCR and 454-pyrosequencing. After the temperature increase, resistome abundance in the digested sludge decreased from 125.97 ppm (day 0, mesophilic) to 50.65 ppm (day 57, thermophilic) with the reduction of most ARG types except for the aminoglycoside resistance genes. Thermophilic sludge also had a smaller mobilome, including plasmids, insertion sequences and integrons, than that of mesophilic sludge, suggesting the lower horizontal transfer potential of ARGs under thermophilic conditions. On the other hand, the total abundance of 18 bacterial genera, which were suggested as the possible hosts for 13 ARGs through network analysis, decreased from 23.27% in mesophilic sludge to 11.92% in thermophilic sludge, indicating fewer hosts for the vertical expansion of ARGs after the increase in temperature. These results indicate that the better reduction of resistome abundance by thermophilic AD might be associated with the decrease of both the horizontal and vertical transferability of ARGs.

Biologically Produced Methane as a Renewable Energy Source

Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO₂. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.

Effect of organic loading on the microbiota in a temperature-phased anaerobic digestion (TPAD) system co-digesting dairy manure and waste whey

Temperature-phased anaerobic digestion (TPAD) has gained increasing attention because it provides the flexibility to operate digesters under conditions that enhance overall digester performance. However, research on impact of organic overloading rate (OLR) to microbiota of TPAD systems was limited. In this study, we investigated the composition and successions of the microbiota in both the thermophilic and the mesophilic digesters of a laboratory-scale TPAD system co-digesting dairy manure and waste whey before and during organic overloading. The thermophilic and the mesophilic digesters were operated at 50 and 35 °C, respectively, with a hydraulic retention time (HRT) of 10 days for each digester. High OLR (dairy manure with 5 % total solid and waste whey of ≥60.4 g chemical oxygen demand (COD)/l/day) resulted in decrease in pH and in biogas production and accumulation of volatile fatty acids (VFAs) in the thermophilic digester, while the mesophilic digester remained unchanged except a transient increase in biogas production. Both denaturant gradient gel electrophoresis (DGGE) and Illumina sequencing of 16S ribosomal RNA (rRNA) gene amplicons showed dramatic change in microbiota composition and profound successions of both bacterial and methanogenic communities. During the overloading, Thermotogae was replaced by Proteobacteria, while Methanobrevibacter and archaeon classified as WCHD3-02 grew in predominance at the expense of Methanoculleus in the thermophilic digester, whereas Methanosarcina dominated the methanogenic community, while Methanobacterium and Methanobrevibacter became less predominant in the mesophilic digester. Canonical correspondence analysis (CCA) revealed that digester temperature and pH were the most influential environmental factors that explained much of the variations of the microbiota in this TPAD system when it was overloaded.

Comparison of metabolomic profiles of microbial communities between stable and deteriorated methanogenic processes

Central metabolite profiles from glucose in microbial communities during methanogenic process were compared between a stable methanogenic reactor (MR) and a deteriorated reactor (DR). The concentrations of intracellular metabolites related to the Embden-Meyerhof and pentose phosphate pathways, with the exception of pyruvate, remained high in the MR, showing increased carbon flux in the glycolysis pathway during stable methanogenesis. Extracellular acetate temporarily accumulated in the MR, consistent with higher ATP level in the MR. Intracellular concentrations of the intermediates in the reductive branch of tricarboxylic acid cycle, malate, fumarate, and succinate were higher in the DR. Low NADH/NAD(+) ratio both in the MR and DR would suggest NADH consumption during acetate and lactate/succinate production in the MR and DR, respectively. Intracellular glutamate levels were higher in the MR, correlating with lower NADPH/NADP(+) ratio concentrations in the MR. These findings contribute to a better understanding of the metabolic state during stable methanogenesis.