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

Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring

DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.

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

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

Blackwater biomethane recovery using a thermophilic upflow anaerobic sludge blanket reactor: Impacts of effluent recirculation on reactor performance

Thermophilic anaerobic digestion is a promising process for high-solid blackwater (BW) treatment due to improved hydrolysis rates, high methanogenesis efficiency, and pathogen removal, when compared with mesophilic treatment. In the present work, the effects of effluent recirculation (i.e., mixing) on thermophilic blackwater treatment were studied. A laboratory-scale thermophilic upflow anaerobic sludge blanket reactor was operated with and without effluent recirculation. The methanogenesis efficiency of the BW treatment increased from 45.0 ± 2.9% when effluent recirculation was applied to 56.7 ± 5.5% without effluent recirculation. Without effluent recirculation, the COD accumulation in the bioreactor was reduced from 17.2 to 3.8% and the effluent volatile fatty acids (VFA) concentration was reduced from 0.64 ± 0.18 to 0.15 ± 0.10 g/L. Further, both acetoclastic and hydrogenotrophic methanogenic activity increased from 101.3 ± 10.8 and 93.9 ± 6.1 to 120.4 ± 9.4 and 118.2 ± 13.2 mg CH₄-COD/(gVSS⋅d), respectively, after effluent recirculation was discontinued. The predominant methanogens changed from Methanothermobacter (67%) with effluent recirculation to Methanosarcina (62%) without effluent recirculation. As compared to the effluent recirculation conditions, the enhanced biomethane recovery and treatment performance without effluent recirculation can be attributed to the close proximity of bacteria and archaea groups and the reduced VFA accumulation. Predicted functional gene comparison showed higher prevalence of function for intermediate metabolite transportation (transporters, ATP-binding cassette (ABC) transporters, and two-component system) after discontinuing effluent circulation, which contributed to improved syntrophic propionate oxidation and syntrophic acetate oxidization and enhanced hydrogenotrophic methanogenesis.

Enhancement of syntrophic acetate oxidation pathway via single walled carbon nanotubes addition under high acetate concentration and thermophilic condition

The effect of single walled carbon nanotubes (SWCNT) on methane production under high acetate concentration and thermophilic condition was evaluated. An isotope labeling experiment verified that >85% of methane was generated from syntrophic acetate oxidation (SAO) at 50, 100 and 150 mM acetate and almost 100% at 200 mM. SWCNT addition had little effect on the methanogenesis pathway, whereas it accelerated methane production via decreasing lag phase times and increasing maximum methane production rates. Electrochemical impedance spectroscopy (EIS) results revealed the electrical resistivity of sludge in groups of SWCNT was distinctly smaller than CK groups, indicating higher sludge conductivity was achieved. Further, the results of communities described that Coprothermobacter and Thermacetogenium played the most important role in SAO under all conditions. Meanwhile, the enriched Thermacetogenium and direct interspecies electron transfer (DIET) pathway in SAO consortia contributed to the acceleration of methane production via SWCNT addition.

Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO

In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20–70 °C), pH (6.0–8.5), and CO (0–10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers

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

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments

Coastal sediments are rich in conductive particles, possibly affecting microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate-oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure, and their survival depends on successful partnership. Here, we demonstrate that conductive particles enable the partnership between SAO bacteria (i.e., Geobacter spp.) and methanogens (Methanosarcina spp.) from the coastal sediments of the Bothnian Bay of the Baltic Sea. Baltic methanogenic sediments were rich in conductive minerals, had an apparent isotopic fractionation characteristic of CO₂-reductive methanogenesis, and were inhabited by Geobacter and Methanosarcina. As long as conductive particles were delivered, Geobacter and Methanosarcina persisted, whereas exclusion of conductive particles led to the extinction of Geobacter. Baltic Geobacter did not establish a direct electric contact with Methanosarcina, necessitating conductive particles as electrical conduits. Within SAO consortia, Geobacter was an efficient [¹³C]acetate utilizer, accounting for 82% of the assimilation and 27% of the breakdown of acetate. Geobacter benefits from the association with the methanogen, because in the absence of an electron acceptor it can use Methanosarcina as a terminal electron sink. Consequently, inhibition of methanogenesis constrained the SAO activity of Geobacter as well. A potential benefit for Methanosarcina partnering with Geobacter is that together they competitively exclude acetoclastic methanogens like Methanothrix from an environment rich in conductive particles. Conductive particle-mediated SAO could explain the abundance of acetate oxidizers like Geobacter in the methanogenic zone of sediments where no electron acceptors other than CO₂ are available.

Acetate-oxidizing bacteria are known to thrive in mutualistic consortia in which H₂ or formate is shuttled to a methane-producing Archaea partner. Here, we discovered that such bacteria could instead transfer electrons via conductive minerals. Mineral SAO (syntrophic acetate oxidation) could be a vital pathway for CO₂-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-facilitated SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.

In-situ sludge pretreatment in a single-stage anaerobic digester

This study aimed to develop an in-situ sludge pretreatment method by increasing the temperature from thermophilic to extreme thermophilic condition in a single-stage anaerobic digester. The results revealed that a stable performance was obtained within the temperature range of 55-65°C, and the maximum methane yield of 208.51±13.66mL/g VS was obtained at 65°C. Moreover, the maximum extent of hydrolysis (33%) and acidification (27.1%) was also observed at 65°C. However, further increase of temperature to 70°C did not improve the organic conversion efficiency. Microbial community analysis revealed that Coprothermobacter, highly related to acetate oxidisers, appeared to be the abundant bacterial group at higher temperature. A progressive shift in methanogenic members from Methanosarcina to Methanothermobacter was observed upon increasing the temperature. This work demonstrated single-stage sludge digestion system can be successfully established at high temperature (65°C) with stable performance, which can eliminate the need of conventional thermophilic pretreatment step.