Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing

Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant

Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.

Antibiotics inhibit methanogenesis during municipal solid waste decomposition

Municipal solid waste (MSW) landfills are significant sources of antibiotics. However, the effects of antibiotics on MSW decomposition process and methanogenesis during solid waste decomposition remain insufficiently characterized. This study investigated the effects of environmentally relevant concentrations (ERCs) of antibiotics (200 μg/kg for each antibiotic) on MSW decomposition and methanogenesis in bioreactors treated with and without eight antibiotics (three tetracyclines, three sulfonamides, and two macrolides). The key phases of MSW decomposition, namely the aerobic, anaerobic acid, and methanogenic phases, were determined by analyzing the key physiochemical parameters of the leachate, including pH, chemical oxygen demand, and biochemical oxygen demand. We assessed the bacterial and archaeal compositions, along with the abundance of the gene encoding the alpha subunit of methyl-coenzyme M reductase (mcrA), during MSW decomposition using high throughput 16S ribosomal RNA (rRNA) gene sequencing and quantitative polymerase chain reactions, respectively. Our results revealed that antibiotics significantly altered the compositions of bacteria and methanogens, leading to decreased mcrA abundance and methanogenesis. Specifically, antibiotics inhibited cellulose-degrading bacteria (Firmicutes) and archaea (E2) in the anaerobic acid phase and hydrolytic bacteria (Proteobacteria) in the methanogenic phase, resulting in lower degradation of biodegradable matter than that of the biodegradation without antibiotics treatment. However, the typical MSW decomposition process indicated by the key decomposition phases was successfully separated in both bioreactors, suggesting that antibiotics did not affect overall MSW decomposition process development or the associated individual decomposition phases establishment. These findings suggest that antibiotics at ERCs may inhibit methanogenesis during MSW decomposition, thereby providing fundamental information for methane management and climate change studies.

Comparison of mesophilic and thermophilic anaerobic digestions of thermal hydrolysis pretreated swine manure: Process performance, microbial communities and energy balance

Anaerobic digestion (AD) of swine manure (SM) commonly shows low biogas output and unsatisfactory economic performance. In this study, thermophilic AD (TAD, 50 ± 1 °C) was combined with thermal hydrolysis pretreatment (THP, 170 °C/10 bar), to investigate its potential for maximizing biogas yield, securing successful digestion and microbial diversity, as well as improving energy balance. Four lab-scale continuously stirred tank reactors were operated for 300 days and compared with each other, i.e., reactor 1 (raw SM fed in mesophilic AD: RSM-MAD), reactor 2 (THP-treated SM fed in MAD: TSM-MAD), reactor 3 (RSM-TAD), and reactor 4 (TSM-TAD). The results showed that THP was efficient to increase methane production of SM, TSM-TAD mode led to the highest methane yield (129.8 ± 40.5 mL-CH₄/g-VS/day) among the tests (p < 0.05). Although TAD was more likely to induce free ammonia (> 700 mg/L) or volatile fatty acids (> 6000 mg/L) accumulation compared with MAD in start-up phase, TSM-TAD treatment mode behaved a sustainable digestion process in a long-term operation. For TSM-TAD scenario, higher Shannon-Weaver (3.873) and lower Simpson index (0.061) indicated this mode ensured and enlarged the diversity of bacteria communities. Phylum Bathyarchaeota was dominant (59.3%-90.0%) in archaea community, followed by Euryarchaeota in the four reactors. RSM-MAD treatment mode achieved the highest energy output (4.65 GJ/day), TSM-TAD was less effective (-17.38 GJ/day) due to increased energy demands. Thus improving the energetic efficiency of THP units is recommended for the development of TSM-TAD treatment mode.

Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion

Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.

Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes

Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na⁺). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as N^ε-acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments.

IMPORTANCE Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be a halotolerant acetoclastic methanogen with the flexibility for adaptation in the anaerobic digestion process both at low (5 g/L Na⁺) and high salinity conditions (20 g/L Na⁺). Annotation of the recovered M. harundinacea genome revealed salinity stress-related functions, including the modification of EPS glycoconjugates and the production of compatible solutes. This is the first study reporting these genomic features within a Methanothrix sp., a milestone further supporting previous studies that identified M. harundinacea as a key-driver in anaerobic granulation under high salinity stress.

Exploring the role of microbial biofilm for industrial effluents treatment

Biofilm formation on biotic or abiotic surfaces is caused by microbial cells of a single or heterogeneous species. Biofilm protects microbes from stressful environmental conditions, toxic action of chemicals, and antimicrobial substances. Quorum sensing (QS) is the generation of autoinducers (AIs) by bacteria in a biofilm to communicate with one other. QS is responsible for the growth of biofilm, synthesis of exopolysaccharides (EPS), and bioremediation of environmental pollutants. EPS is used for wastewater treatment due to its three-dimensional matrix which is composed of proteins, polysaccharides, humic-like substances, and nucleic acids. Autoinducers mediate significantly the degradation of environmental pollutants. Acyl-homoserine lactone (AHL) producing bacteria as well as quorum quenching enzyme or bacteria can effectively improve the performance of wastewater treatment. Biofilms-based reactors due to their economic and ecofriendly nature are used for the treatment of industrial wastewaters. Electrodes coated with electro-active biofilm (EAB) which are obtained from sewage sludge, activated sludge, or industrial and domestic effluents are getting popularity in bioremediation. Microbial fuel cells are involved in wastewater treatment and production of energy from wastewater. Synthetic biological systems such as genome editing by CRISPR-Cas can be used for the advanced bioremediation process through modification of metabolic pathways in quorum sensing within microbial communities. This narrative review discusses the impacts of QS regulatory approaches on biofilm formation, extracellular polymeric substance synthesis, and role of microbial community in bioremediation of pollutants from industrial effluents.

Methanogenic performance and microbial community during thermophilic digestion of food waste and sewage sludge in a high-solid anaerobic membrane bioreactor

The methanogenic performance and microbial community of the thermophilic anaerobic mono-digestion and co-digestion of food waste and sewage sludge in a high-solid membrane bioreactor were investigated by a continuous experiment. The methane recovery rate of the system reached 98.0% and 89.0% when the substrate was pure food waste and 25% sewage sludge substitution, respectively. Kinetics characterization showed that hydrolysis was the rate-limiting step in both mono-digestion and co-digestion while methanogenic performance and microbial community were significantly affected by feed condition. The dominant archaea for methane generation shifted from Methanothermobacter thermophilus (72.82%) to Methanosarcina thermophila (96.25%) with sewage sludge gradually added from 0% to 100% in the substrate. The relationships between digestion performance, such as the accumulation of soluble proteins in the reactor, and functional microbial groups were also carefully analyzed. Finally, reasonable metabolic pathways for mono-digestion and co-digestion were summarized.

Methanogen Community Dynamics and Methanogenic Function Response to Solid Waste Decomposition

Methane production during solid waste decomposition is a typical methanogen-mediated and enzyme-catalyzed anaerobic digestion (AD). Methanogen community dynamics and metabolic diversity during the decomposition are not known. In this study, we investigated methanogen community dynamics and methanogenic pathways during solid waste decomposition in a bioreactor using high-throughput Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), respectively. We also related the methanogen community differences with solid waste and leachate physiochemical parameters. Results showed that the percentage of biodegradable matter (BDM) in solid waste decreased from 55 ± 5% in aerobic phase (AP) to 30 ± 2% in anaerobic acid phase (ACP), and to 13 ± 11% in methanogenic phase (MP), resulting in 76% BDM consumption by microbes. Methanogen community structure varied in AP, ACP, and MP, showing that Methanomicrobiales and Methanosarcinales were dominant in AP and MP and archaea E2 was abundant in ACP. Each phase had abundant core methanogen orders, genera, and species with significant difference (p < 0.05). Redundancy analysis showed that biochemical oxygen demand (BOD₅) and nitrate significantly influenced methanogen community composition, suggesting that methanogen community structure is nutrient-dependent. Two methanogenic pathways including acetoclastic and hydrogenotrophic pathways with associated functional genes differed at three phases. ACP had the lowest abundance of these genes, indicating that methanogenesis was inhibited in acidogenesis. Abundant hydrogenotrophic and acetoclastic methanogenesis functional genes in MP and AP are in response to the abundance of Methanomicrobiales and Methanosarcinales. The findings provide previously unidentified insight into the mechanism of methanogen community structure and function during solid waste bioconversion for methane.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers

Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.

Methanobacterium Capable of Direct Interspecies Electron Transfer

Direct interspecies electron transfer (DIET) from bacteria to methanogens is a revolutionary concept for syntrophic metabolism in methanogenic soils/sediments and anaerobic digestion. Previous studies have indicated that the potential for DIET is limited to methanogens in the Methanosarcinales, leading to the assumption that an abundance of other types of methanogens, such as Methanobacterium species, indicates a lack of DIET. We report here on a strain of Methanobacterium, designated strain YSL, that grows via DIET in defined cocultures with Geobacter metallireducens. The cocultures formed aggregates, in which cells of strain YSL and G. metallireducens were uniformly dispersed throughout. This close association of the two species is the likely explanation for the ability of a strain of G. metallireducens that could not express electrically conductive pili to grow in coculture with strain YSL. Granular activated carbon promoted the initial formation of the DIET-based cocultures. The discovery of DIET in Methanobacterium, the genus of methanogens that has been the exemplar for interspecies electron transfer via H₂, suggests that the capacity for DIET is much more broadly distributed among methanogens than previously considered. More innovative approaches to microbial isolation and characterization are needed in order to better understand how methanogenic communities function.

Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment

Over the past decades, anaerobic biotechnology is commonly used for treating high-strength wastewaters from different industries. This biotechnology depends on interactions and co-operation between microorganisms in the anaerobic environment where many pollutants’ transformation to energy-rich biogas occurs. Properties of wastewater vary across industries and significantly affect microbiome composition in the anaerobic reactor. Methanogenic archaea play a crucial role during anaerobic wastewater treatment. The most abundant acetoclastic methanogens in the anaerobic reactors for industrial wastewater treatment are Methanosarcina sp. and Methanotrix sp. Hydrogenotrophic representatives of methanogens presented in the anaerobic reactors are characterized by a wide species diversity. Methanoculleus sp., Methanobacterium sp. and Methanospirillum sp. prevailed in this group. This work summarizes the relation of industrial wastewater composition and methanogen microbial communities present in different reactors treating these wastewaters.

Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation

The microbes present in bioethanol production processes have been previously studied in laboratory-scale experiments, but there is a lack of information on full-scale industrial processes. In this study, the microbial communities of three industrial bioethanol production processes were characterized using several methods. The samples originated from second-generation bioethanol plants that produce fuel ethanol from biowaste, food industry side streams, or sawdust. Amplicon sequencing targeting bacteria, archaea, and fungi was used to explore the microbes present in biofuel production and anaerobic digestion of wastewater and sludge. Biofilm-forming lactic acid bacteria and wild yeasts were identified in fermentation samples of a full-scale plant that uses biowaste as feedstock. During the 20-month monitoring period, the anaerobic digester adapted to the bioethanol process waste with a shift in methanogen profile indicating acclimatization to high concentrations of ammonia. Amplicon sequencing does not specifically target living microbes. The same is true for indirect parameters, such as low pH, metabolites, or genes of lactic acid bacteria. Since rapid identification of living microbes would be indispensable for process management, a commercial method was tested that detects them by measuring the rRNA of selected microbial groups. Small-scale testing indicated that the method gives results comparable with plate counts and microscopic counting, especially for bacterial quantification. The applicability of the method was verified in an industrial bioethanol plant, inspecting the clean-in-place process quality and detecting viability during yeast separation. The results supported it as a fast and promising tool for monitoring microbes throughout industrial bioethanol processes.

System Performance Corresponding to Bacterial Community Succession after a Disturbance in an Autotrophic Nitrogen Removal Bioreactor

Performance of a bioreactor is affected by complex microbial consortia that regulate system functional processes. Studies so far, however, have mainly emphasized the selective pressures imposed by operational conditions (i.e., deterministic external physicochemical variables) on the microbial community as well as system performance, but have overlooked direct effects of the microbial community on system functioning. Here, using a bioreactor with ammonium as the sole substrate under controlled operational settings as a model system, we investigated succession of the bacterial community after a disturbance and its impact on nitrification and anammox (anaerobic ammonium oxidation) processes with fine-resolution time series data. System performance was quantified as the ratio of the fed ammonium converted to anammox-derived nitrogen gas (N₂) versus nitrification-derived nitrate (npNO₃ ^-). After the disturbance, the N₂/npNO₃ ^- ratio first decreased, then recovered, and finally stabilized until the end. Importantly, the dynamics of N₂/npNO₃ ^- could not be fully explained by physicochemical variables of the system. In comparison, the proportion of variation that could be explained substantially increased (tripled) when the changes in bacterial composition were taken into account. Specifically, distinct bacterial taxa tended to dominate at different successional stages, and their relative abundances could explain up to 46% of the variation in nitrogen removal efficiency. These findings add baseline knowledge of microbial succession and emphasize the importance of monitoring the dynamics of microbial consortia for understanding the variability of system performance.IMPORTANCE Dynamics of microbial communities are believed to be associated with system functional processes in bioreactors. However, few studies have provided quantitative evidence. The difficulty of evaluating direct microbe-system relationships arises from the fact that system performance is affected by convolved effects of microbiota and bioreactor operational parameters (i.e., deterministic external physicochemical forcing). Here, using fine-resolution time series data (daily sampling for 2 months) under controlled operational settings, we performed an in-depth analysis of system performance as a function of the microbial community in the context of bioreactor physicochemical conditions. We obtained statistically evaluated results supporting the idea that monitoring microbial community dynamics could improve the ability to predict system functioning, beyond what could be explained by operational physicochemical variables. Moreover, our results suggested that considering the succession of multiple bacterial taxa would account for more system variation than focusing on any particular taxon, highlighting the need to integrate microbial community ecology for understanding system functioning.

Optimizing the production of short and medium chain fatty acids (SCFAs and MCFAs) from waste activated sludge using different alkyl polyglucose surfactants, through bacterial metabolic analysis

Alkyl polyglucose is an environmentally-friendly biosurfactant, which is able to enhance short-chain fatty acids production with different carbon chain lengths and concentrations, during sludge anaerobic fermentation. This presents a promising strategy for sludge re-utilization by effectively converting hazardous sludge into value-added compounds. The maximum yield of short-chain fatty acids produced from sludge was 479.3 and 462.2 mg COD/g VSS, following pretreatment with APG06 and APG1214, respectively. To the best of our knowledge, the short-chain fatty acid production performance by sludge fermentation reported here, achieved a higher level than reported in previous studies. Additionally, these findings indicate that the production of medium-chain fatty acids from sludge can be induced by alkyl polyglucoses. Finally, the microbial community and enzyme activity were also assessed to reveal the mechanism of short-/medium-chain fatty acids biosynthesis under alkyl polyglucose pretreatment. This study demonstrates that alkyl polyglucose provides an environmentally-friendly and effective strategy for enhancing the production of short-/medium-chain fatty acids from waste activated sludge. These findings are useful for the assessment of alkyl polyglucose-assisted production of short-/medium-chain fatty acids, as well as for understanding the interactions between short-/medium-chain fatty acids and microbial communities with key enzymes, to establish short-/medium-chain fatty acids metabolic pathways during sludge fermentation.

Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters

This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.

Exploring the performance limits of a sulfidogenic UASB during the long-term use of crude glycerol as electron donor

SOx contained in flue gases and S-rich liquid effluents can be valorized to recover elemental sulfur in a two-stage bioscrubbing process. The reduction of sulfate to sulfide is the most crucial stage to be optimized. In this study, the long-term performance of an up-flow anaerobic sludge blanket (UASB) reactor using crude glycerol as electron donor was assessed. The UASB was operated for 400 days with different sulfate and organic loading rates (SLR and OLR, respectively) and a COD/S-SO₄^2- ratio ranging from 3.8 g O₂ g^-1 S to 5.4 g O₂ g^-1 S. After inoculation with methanogenic, granular biomass, the competition between sulfate-reducing and methanogenic microorganisms determined to what extent dissolved sulfide and methane were produced. After the complete washout of methanogens, which was revealed by next-generation sequencing analysis, the highest S-EC was reached in the system. The highest average sulfate elimination capacity (S-EC = 4.3 kg S m^-3d^-1) was obtained at a COD/S-SO₄^2- ratio of 5.4 g O₂ g^-1 S and an OLR of 24.4 kg O₂ m^-3d^-1 with a sulfate removal efficiency of 94%. The conversion of influent COD to methane decreased from 12% to 2.5% as the SLR increased while a large fraction of acetate (35% of the initial COD) was accumulated. Our data indicate that crude glycerol can promote sulfidogenesis. However, the disappearance of methanogens in the long-term due to the out competition by sulfate reducing bacteria, lead to such large accumulation of acetate.

The study of structure of anaerobic granules and methane producing pathways of pilot-scale UASB reactors treating municipal wastewater under sub-mesophilic conditions

This study was carried out to investigate the relationship between the methane producing pathways and the characteristics of anaerobic granules treating municipal wastewater. For this purpose, two pilot scale upflow anaerobic sludge blanket reactors with different granule size distribution (1-2 mm and 3-4 mm) were investigated at operating temperatures of 20 °C and 28 °C for 239 days. There was an increased and stable biogas production when temperature was elevated to 28 °C likely due to reduction in methane solubility. Larger granules had multi-layered internal microstructures with higher acetoclastic methanogenic activities (250-437 mL CH₄ g^-1 VS d^-1) than smaller granules (150-260 mL CH₄ g^-1 VS d^-1). The relative abundance of acetoclastic methanogens of larger granules was higher, confirming acetoclastic methane producing pathway was more prominent. However, there was no significant difference in the performance of the two reactors because they were operating below their capacities in terms of organic loading rate to volatile solids ratio.

Synthetic Effect of EDTA and Ni2+ on Methane Production and Microbial Communities in Anaerobic Digestion Process of Kitchen Wastes

Batch tests were carried out to study the effect of simultaneous addition of ethylenediaminetetraacetic acid and Ni2+ (EDTA-Ni) on anaerobic digestion (AD) performances of kitchen wastes (KWs). The results indicated that the cumulative biogas yield and methane content were enhanced to 563.82 mL/gVS and 63.7% by adding EDTA-Ni, respectively, which were almost 1.15 and 1.07-fold of that in the R2 with Ni2+ addition alone. At the same time, an obvious decrease of propionic acid was observed after EDTA-Ni addition. The speciation analysis of Ni showed that the percentages of water-soluble and exchangeable Ni were increased to 38.8% and 36.3% due to EDTA-Ni addition, respectively. Also, the high-throughput sequencing analysis revealed that the EDTA-Ni promoted the growth and metabolism of Methanosarcina and Methanobacterium, which might be the major reason for propionic acid degradation and methane production.

Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters

Knowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.

Stepwise pH control to promote synergy of chemical and biological processes for augmenting short-chain fatty acid production from anaerobic sludge fermentation

Although sludge-converted short-chain fatty acids (SCFAs) are promising feedstocks for biorefineries, it remains challenging to maximise SCFA production by enhancing synergies between chemical/biological hydrolysis and acidogenesis processes while employing a balanced composition of microbial communities to counteract methanogenesis. Herein, stepwise control of fermentation pH and chemical/microbiological composition analysis of fermented sludge were used to probe the underlying mechanisms of SCFA production. Fermentation at pH 11 during the first three days promoted both chemical and microbial hydrolysis of sludge proteins and provided a niche for Anaerobrancaceae sp. to transform soluble protein into SCFAs. When pH was decreased from 11 to 9, Acinetobacter, Proteiniborus, Proteiniclasticum, and other acetogens became predominant and stayed significantly more active than during first-stage fermentation at pH 11, which benefited the acidification of hydrolysed substrates. Further assays indicated that early-stage sludge fermentation at pH 11 decreased the total amount of methanogenic archaea and hence reduced the amount of SCFAs consumed for methane production. Thus, the use of stepwise pH control for sludge fermentation allowed one to establish process synergies, facilitate chemical and biological hydrolysis, inhibit methanogens, and promote the growth of acidifying bacterial communities, which resulted in efficient SCFA production from sludge.

A Review on Anaerobic Co-Digestion with a Focus on the Microbial Populations and the Effect of Multi-Stage Digester Configuration

Recent studies have shown that anaerobic co-digestion (AnCoD) is superior to conventional anaerobic digestion (AD). The benefits of enhanced bioenergy production and solids reduction using co-substrates have attracted researchers to study the co-digestion technology and to better understand the effect of multi substrates on digester performance. This review will discuss the results of such studies with the main focus on: (1) generally the advantages of co-digestion over mono-digestion in terms of system stability, bioenergy, and solids reduction; (2) microbial consortia diversity and their synergistic impact on biogas improvement; (3) the effect of digester mode, i.e., multi-stage versus single stage digestion on AnCoD. It is essential to note that the studies reported improvement in the synergy and diverse microbial consortia when using co-digestion technologies, in addition to higher biomethane yield when using two-stage mode. A good example would be the co-digestion of biodiesel waste and glycerin with municipal waste sludge in a two-stage reactor resulting in 100% increase of biogas and 120% increase in the methane content of the produced biogas with microbial population dominated by Methanosaeta and Methanomicrobium.

Active prokaryotic population dynamics exhibit high correlation to reactor performance during methane production from acid hydrolysates of Agave tequilana var. azul bagasse

AIMS

The purpose of this study was to apply cDNA approach for the characterization of active prokaryotic community to understand microbial scenarios and performance of an AnSBR digester fed with acid hydrolysates of Agave tequilana var. azul bagasse (ATAB).

METHODS AND RESULTS

The digester was implemented for methane production under organic loading rate (OLR) disturbances to correlate physicochemical variables with changes in abundance, diversity and population dynamics of active Bacteria and Archaea by principal components analysis (PCA). Results indicated that methane yield increased as well as active syntrophic relationships for interspecies hydrogen/formate (Anaerolinaceae-Methanobacterium beijingense) and acetate (Anaerolinaceae-Methanosaeta concilii) transfers at 8 g-COD l^-1  day^-1 . However, methane yield was negatively affected at 16 g-COD l^-1  day^-1 due to the competition for acetate by active Desulfovibrio marrakechensis and volatile fatty acids inhibition.

CONCLUSIONS

Microbial scenarios obtained by PCA correlations indicated that methane production from acid hydrolysates of ATAB was feasible at 8 g-COD l^-1  day^-1 . The digester operation at higher OLR only favoured methanogenesis by the hydrogenotrophic pathway.

SIGNIFICANCE AND IMPACT OF THE STUDY

Only cDNA analysis showed Archaea population dynamics, exhibiting high correlation with physicochemical variables towards the understanding of the methanogenic digester performance during OLR disturbances.

Biochar Modulates Methanogenesis through Electron Syntrophy of Microorganisms with Ethanol as a Substrate

Biochar has the potential to influence methanogenesis which is a key component of global carbon cycling. However, the mechanisms governing biochar's influence on methanogenesis is not well understood, especially its effects on interspecies relationships between methanogens and anaerobic bacteria (e.g., Geobacteraceae). To understand how different types of biochar influence methanogenesis, biochars derived from rice straw (RB), wood chips (WB), and manure (MB) were added to the methanogenic enrichment culture system of a paddy soil. Compared to the nonbiochar control, RB and MB additions accelerated methanogenesis remarkably, showing 10.7 and 12.3-folds higher methane production rate, respectively; while WB had little effect on methanogenesis. Using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electrochemical methods, RB and MB also had higher redox-active properties or charging and discharging capacities than WB, and the functional groups, mainly quinones, on the biochar surface played an important role in facilitating methanogenesis. Quantitative polymerase chain reaction results demonstrated that electronic syntrophy did exist between methanogens and Geobacteraceae. RB and MB stimulate methanogenesis by facilitating direct interspecies electron transfer between methanogens and Geobacteraceae. Our findings contribute to a better understanding of the effects of biochars from different feedstocks on methanogenesis and provide new evidence to the mechanisms of stimulating methanogenesis via biochar.

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.

Control of VOCs from printing press air emissions by anaerobic bioscrubber: Performance and microbial community of an on-site pilot unit

A novel process consisted of an anaerobic bioscrubber was studied at the field scale for the removal of volatile organic compounds (VOCs) emitted from a printing press facility. The pilot unit worked under high fluctuating waste gas emissions containing ethanol, ethyl acetate, and 1-ethoxy-2-propanol as main pollutants, with airflows ranging between 184 and 1253 m³ h^-1 and an average concentration of 1126 ± 470 mg-C Nm^-3. Three scrubber configurations (cross-flow and vertical-flow packings and spray tower) were tested, and cross-flow packing was found to be the best one. For this packing, daily average values of VOC removal efficiency ranged between 83% and 93% for liquid to air volume ratios between 3.5·10^-3 and 9.1·10^-3. Biomass growth was prevented by periodical chemical cleaning; the average pressure drop was 165 Pa m^-1. Rapid initiation of anaerobic degradation was achieved by using granular sludge from a brewery wastewater treatment plant. Despite the intermittent and fluctuating organic load, the expanded granular sludge bed reactor showed an excellent level of performance, reaching removal efficiencies of 93 ± 5% at 25.1 ± 3.2 °C, with biogas methane content of 94 ± 3% in volume. Volatile fatty acid concentration was as low as 200 mg acetic acid L^-1 by treating daily average organic loads up to 3.0 kg COD h^-1, equivalent to 24 kg COD m^-3 bed d^-1. The denaturing gradient gel electrophoresis (DGGE) results revealed the initial shift of the domains Archaea and Bacteria associated with the limitation of the carbon source to a few organic solvents. The Archaea domain was more sensitive, resulting in a drop of the Shannon index from 1.07 to 0.41 in the first 123 days. Among Archaea, the predominance of Methanosaeta persisted throughout the experimental period. The increase in the proportion of Methanospirillum and Methanobacterium sp. was linked to the spontaneous variations of operating temperature and load, respectively. Among Bacteria, high levels of ethanol degraders (Geobacter and Pelobacter sp.) were observed during the trial.

Incubation of innovative methanogenic communities to seed anaerobic digesters

The methanogenic communities in alternative inocula and their potential to increase CH₄ production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH₄ produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH₄ production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH₄ than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.

Metabolic adaptation of microbial communities to ammonium stress in a high solid anaerobic digester with dewatered sludge

A high solid digester with dewatered sludge was operated for 110 days to ascertain the interactions between bacterial and archaeal communities under ammonium stress, as well as the corresponding changes in bio-degradation mechanisms. The volatile solids reduction (95% confidence intervals in mean) changed from 31.6 ± 0.9% in the stable period (day 40-55) to 21.3 ± 1.5% in the last period (day 71-110) when ammonium concentration was elevated to be within 5,000-6,000 mgN/L. Biogas yield dropped accordingly from 11.9 ± 0.3 to 10.4 ± 0.2 L/d and carbon dioxide increased simultaneously from 35.2% to 44.8%. Anaerobranca better adapted to the ammonium stress, while the initially dominant protein-degrading microbes-Tepidimicrobium and Proteiniborus were suppressed, probably responsible for the increase of protein content in digestate. Meanwhile, Methanosarcina, as the dominant Archaea, was resistant to ammonium stress with the constant relative abundance of more than 92% during the whole operation. Nonmetric Multidimensional Scaling (NMDS) analysis was thus conducted which indicated that the gradually increased TAN dictated the bacterial clusters. The dominant Methanosarcina and the increased carbon dioxide content under ammonium stress suggested that, rather than the commonly acknowledged syntrophic acetate oxidation (SAO) with hydrogenotrophic methanogenesis, only SAO pathway was enhanced during the initial 'ammonium inhibition'.

Relating Anaerobic Digestion Microbial Community and Process Function

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Microbial community analysis in a combined anaerobic and aerobic digestion system for treatment of cellulosic ethanol production wastewater

This study investigated the microbial diversity established in a combined system composed of a continuous stirred tank reactor (CSTR), expanded granular sludge bed (EGSB) reactor, and sequencing batch reactor (SBR) for treatment of cellulosic ethanol production wastewater. Excellent wastewater treatment performance was obtained in the combined system, which showed a high chemical oxygen demand removal efficiency of 95.8% and completely eliminated most complex organics revealed by gas chromatography-mass spectrometry (GC-MS). Denaturing gradient gel electrophoresis (DGGE) analysis revealed differences in the microbial community structures of the three reactors. Further identification of the microbial populations suggested that the presence of Lactobacillus and Prevotella in CSTR played an active role in the production of volatile fatty acids (VFAs). The most diverse microorganisms with analogous distribution patterns of different layers were observed in the EGSB reactor, and bacteria affiliated with Firmicutes, Synergistetes, and Thermotogae were associated with production of acetate and carbon dioxide/hydrogen, while all acetoclastic methanogens identified belonged to Methanosaetaceae. Overall, microorganisms associated with the ability to degrade cellulose, hemicellulose, and other biomass-derived organic carbons were observed in the combined system. The results presented herein will facilitate the development of an improved cellulosic ethanol production wastewater treatment system.

Evaluation of functional microbial community's difference in full-scale and lab-scale anaerobic digesters feeding with different organic solid waste: Effects of substrate and operation factors

Samples taken from the full-scale and lab-scale anaerobic digesters feeding with different organic solid waste were investigated with assessment of the substrate effects. To understand the substrate effects on the microbial community diversity, heterogeneity, and functional structure, twelve samples were analyzed by constructing 16S rRNA gene clone libraries and statistical analysis. Microbial diversity varied according to substrate types and operating parameters. With acetoclastic methanogen of genus Methanosaeta predominated in full scale and Methanosarcina predominated in the lab-scale digesters, a significant difference archaeal communities were found. Principal component analysis clearly indicates that both bacterial and archaeal communities create independent clusters according to substrate types. However, the relationship between acetogenic bacteria and the acetoclastic methanogens had a similar variation tends in most of full-scale and lab-scale reactors. Canonical correlation analysis and variance partitioning analysis implied that bacterial and archaeal community variations were significantly affected by substrate and the operation conditions.

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.

Anaerobic co-digestion of biodiesel waste glycerin with municipal wastewater sludge: microbial community structure dynamics and reactor performance

Two 10 L completely mixed reactors operating at 37°C and 20 days SRT were used to evaluate the relationships between reactor performance and microbial community dynamics during anaerobic co-digestion of biodiesel waste glycerin (BWG) with municipal wastewater sludge (MWS). The addition of up to 1.35% (v/v) BWG to reactor feeds yielded increased VS and COD removal together with enhanced the biogas production and methane yield. This represented 50% of the MWS feed COD. Pyrosequencing analysis showed Methanosaeta (acetoclastic) and Methanomicrobium (hydrogenotrophic) to be the methanogenic genera present in greatest diversity during stable reactor operation. Methanosaeta sequences predominated at the lowest BWG loading while those of Methanomicrobium were present in greatest abundance at the higher BWG loadings. Genus Candidatus cloacamonas was present in the greatest number of bacterial sequences at all loadings. Alkalinity, pH, biogas production and methane yield declined and VFA concentrations (especially propionate) increased during the highest BWG loading.

Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester

A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.

Comparison of droplet digital PCR and quantitative real-time PCR in mcrA-based methanogen community analysis

Two different quantitative PCR platforms, droplet digital PCR (dd-PCR) and quantitative real-time PCR (qPCR), were compared in a mcrA-based methanogen community assay that quantifies ten methanogen sub-groups. Both technologies exhibited similar PCR efficiencies over at least four orders of magnitude and the same lower limits of detection (8 copies μL-DNA extract-1). The mcrA-based methanogen communities in three full-scale anaerobic digesters were examined using the two technologies. dd-PCR detected seven groups from the digesters, while qPCR did five groups, indicating that dd-PCR is more sensitive for DNA quantification. Linear regression showed quantitative agreements between both of the technologies (R2 = 0.59-0.98) in the five groups that were concurrently detected. Principal component analysis from the two datasets consistently indicated a substantial difference in the community composition among the digesters and revealed similar levels of differentiation among the communities. The combined results suggest that dd-PCR is more promising for examining methanogenic archaeal communities in biotechnological processes.

Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages

Linkage between reactor performance and microbial community dynamics was investigated during mesophilic anaerobic co-digestion of restaurant grease waste (GTW) with municipal wastewater sludge (MWS) using 10L completely mixed reactors and a 20day SRT. Test reactors received a mixture of GTW and MWS while control reactors received only MWS. Addition of GTW to the test reactors enhanced the biogas production and methane yield by up to 65% and 120%, respectively. Pyrosequencing revealed that Methanosaeta and Methanomicrobium were the dominant acetoclastic and hydrogenotrophic methanogen genera, respectively, during stable reactor operation. The number of Methanosarcina and Methanomicrobium sequences increased and that of Methanosaeta declined when the proportion of GTW in the feed was increased to cause an overload condition. Under this overload condition, the pH, alkalinity and methane production decreased and VFA concentrations increased dramatically. Candidatus cloacamonas, affiliated within phylum Spirochaetes, were the dominant bacterial genus at all reactor loadings.

Stratified microbial structure and activity in sulfide- and methane-producing anaerobic sewer biofilms

Simultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescence in situ hybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera, Desulfobulbus, Desulfomicrobium, Desulfovibrio, Desulfatiferula, and Desulforegula, while about 90% of the MA population belonged to the genus Methanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates.

Microaerobic digestion of sewage sludge on an industrial-pilot scale: the efficiency of biogas desulphurisation under different configurations and the impact of O2 on the microbial communities

Biogas produced in an industrial-pilot scale sewage sludge reactor (5m(3)) was desulphurised by imposing microaerobic conditions. The H2S concentration removal efficiency was evaluated under various configurations: different mixing methods and O2 injection points. Biogas was entirely desulphurised under all the configurations set, while the O2 demand of the digester decreased over time. Although the H2S removal seemed to occur in the headspace, S(0) (which was found to be the main oxidation product) was scarcely deposited there in the headspace. O2 did not have a significant impact on the digestion performance; the VS removal remained around 47%. Conversely, DGGE revealed that the higher O2 transfer rate to the sludge maintained by biogas recirculation increased the microbial richness and evenness, and caused an important shift in the structure of the bacterial and the archaeal communities in the long term. All the archaeal genera identified (Methanosaeta, Methanospirillum and Methanoculleus) were present under both anaerobic and microaerobic conditions.

Characterization of persistent virus-like particles in two acetate-fed methanogenic reactors

The objective of this study was to characterize the morphology, size-distribution, concentration and genome size of virus-like particles (VLPs) in two acetate-fed Methanosaeta-dominated reactors to better understand the possible correlation between viruses and archaeal hosts. The study reactors were dominated by a single genus of acetoclastic methanogen, Methanosaeta, which was present at 6 to 13 times higher than the combined bacterial populations consisting of Proteobacteria, Firmicutes, and Bacteroidetes. Epifluorescent microscopy showed VLPs concentration of 7.1 ± 1.5×10⁷ VLPs/ml and 8.4 ± 4.3×10⁷ VLPs/ml in the two laboratory reactors. Observations of no detectable import of VLPs with the reactor feed combined long operational time since the last inocula were introduced suggests that the VLP populations were actively propagating in the reactors. Transmission electron microscopy images showed VLPs with morphology consistent with Siphoviridae in both reactors, and VLPs with morphologies consistent with Myoviridae in one of the reactors. The morphology, size-distribution and genome size of VLPs were distinct between reactors suggesting that unique viral populations inhabited each reactor, though the hosts of these VLPs remain unclear.

Microbial community shifts and biogas conversion computation during steady, inhibited and recovered stages of thermophilic methane fermentation on chicken manure with a wide variation of ammonia

The thermophilic methane fermentation of chicken manure (10% TS) was investigated within a wide range of ammonia. Microbiological analysis showed significant shifts in Archaeal and Bacterial proportions with VFA accmulation and CH4 formation before and after inhibition. VFA accumulated sharply with lower methane production, 0.29 L/g VS, than during the steady stage, 0.32 L/g VS. Biogas production almost ceased with the synergy inhibition of TAN (8000 mg/L) and VFA (25,000 mg/L). Hydrogenotrophic Methanothermobacter thermautotrophicus str. was the dominate archaea with 95% in the inhibition stage and 100% after 40 days recovery compared to 9.3% in the steady stage. Aceticlastic Methanosarcina was not encountered with coincided phenomenal of high VFA in the inhibition stage as well as recovery stage. Evaluation of the microbial diversity and functional bacteria indicated the dominate phylum of Firmicutes were 94.74% and 84.4% with and without inhibition. The microbial community shifted significantly with elevated ammonia concentration affecting the performance.