Prokaryotic diversity and dynamics in a full-scale municipal solid waste anaerobic reactor from start-up to steady-state conditions

Effects of bacterial inoculation on lignocellulose degradation and microbial properties during cow dung composting

Inoculation with exogenous microbial agents is a common method to promote organic waste degradation and improve the quality of compost. However, the biotic effects of different microbial agents are often quite different. To evaluate the potential effects of a complex bacterial agent comprised of three strains (belonging to Bacillus and Geobacillus) on lignocellulose degradation and the underlying microbial mechanisms during cow dung composting, two lab-scale composting experiments, a control and a bacterial inoculation treatment, were established. The results suggest that bacterial inoculation accelerated the rate of temperature increase and extended the thermophilic phase. Compared to those in the negative control group, cellulose, hemicellulose, and lignin degradation rates in the inoculated group increased from 53.3% to 70.0%, 50.2% to 61.3%, and 46.4% to 60.0%, respectively. The microbial community structure and diversity in the compost were clearly changed by the bacterial inoculation. Moreover, stamp analysis showed that inoculation modulated the key compost microbial functional populations linked to the degradation of lignocellulose. Correlation matrix analysis indicated that the expression of bacterial lignocellulolytic enzymes is closely related to key microbial functional populations. Overall, the results confirm the importance of bacterial inoculation, and have important implications for promoting the efficiency and quality of cow dung compost.

Combined effects of liquid digestate recirculation and biochar on methane yield, enzyme activity, and microbial community during semi-continuous anaerobic digestion

The combined effects of liquid digestate recirculation (LDR) and biochar on methanogenesis and microbial communities were studied in semi-continuous anaerobic reactors fed with wheat straw and swine manure. The tolerated organic loading rate (OLR) was expanded from 5 g- volatile solids (VS)∙L-1∙d-1 in the control to higher than 6 g-VS∙L-1∙d-1 in the LDR. At the OLR of 5.0 g-VS∙L-1∙d-1, average special methane yield in LDR with biochar was 0.234 L∙g-VS-1, which was 5.4 % higher than that of the LDR alone. Moreover, enzyme activity and microbial community analysis indicated that LDR with biochar enhanced the processes of hydrolysis and methanogenesis, and balanced the pathway between hydrogenotrophic and acetoclastic methanogenesis. The co-application of LDR and biochar synergistically enhanced the degradation pathways of substrates and the loading shock resistance of anaerobic digestion system. This study could offer strategies for developing sustainable applications of full and continuous LDR in industrial biogas projects.

Low biological phosphorus removal from effluents treated by slow sand filters

The legislation for environment protection requires strict controls of the wastewater releasing in water bodies. The wastewater treatment plants (WWTP) have been used for organic matter degradation; however, the residual total phosphorus (TP) removal has not been efficient. TP and nitrogen present in wastewater are associated to eutrophication of water bodies and algae growth. Therefore, this study discusses the efficiency of phosphorus removal by a slow filter (SF), complementary to a WWTP and the microbial community involved. The results showed that the use of SF, with or without macrophytes, is not suitable to remove TP. Spatial variation in microbial communities distributed in three distinct zones was identified in the SF. Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes covered the hydrolytic and fermentative bacteria. The acetogenesis, nitrification, and denitrification, as well as the removal of phosphorus from the effluent, were performed by representatives affiliated to different groups. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria among these, Dokdonella sp., Frateuria sp., Comamonas sp., Diaphorobacter sp., Nitrosospira sp., Ferruginibacter sp., Flavobacterium sp., and the uncultured OD1 were the most abundant bacteria in the SF. The low efficiency for TP removing from SF effluents can be explained by the low abundance of phosphorus accumulating organisms (PAOs), with the association of the low concentration of biodegradable organic matter in the inlet effluent. Therefore, the alternative to using SF as a complement to WWTPs, as recommended by some Brazilian environmental agencies, did not prove to be viable and new approaches must be evaluated. KEY POINTS: • The phosphorus removal was performed by a slow filter system in a WWTP but obtained a low efficiency. • Microbial spatial variation was distributed into distinct zones from slow filter. • Low abundance of PAOs was observed due to the low availability of organic matter.

Metagenomic Analysis of Bacterial Community Structure and Dynamics of a Digestate and a More Stabilized Digestate-Derived Compost from Agricultural Waste

Recycling of different products and waste materials plays a crucial role in circular economy, where the anaerobic digestion (AD) constitutes an important pillar since it reuses nutrients in the form of organic fertilizers. Knowledge about the digestate and compost microbial community structure and its variations over time is important. The aim of the current study was to investigate the microbiome of a slurry cow digestate produced on a farm (ADG) and of a more stabilized digestate-derived compost (DdC) in order to ascertain their potential uses as organic amendments in agriculture. The results from this study, based on a partial fragment of 16S bacterial rRNA NGS sequencing, showed that there is a greater microbial diversity in the DdC originated from agricultural waste compared to the ADG. Overall, the existence of a higher microbial diversity in the DdC was confirmed by an elevated number (1115) of OTUs identified, compared with the ADG (494 OTUs identified). In the DdC, 74 bacterial orders and 125 families were identified, whereas 27 bacterial orders and 54 families were identified in the ADG. Shannon diversity and Chao1 richness indexes were higher in DdC samples compared to ADG ones (Shannon: 3.014 and 1.573, Chao1: 68 and 24.75; p < 0.001 in both cases). A possible association between the microbiome composition at different stages of composting process and the role that these microorganisms may have on the quality of the compost-like substrate and its future uses is also discussed.

Metataxonomics, metagenomics and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters

Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35 °C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25 °C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.

Microbial community composition and metabolic functions in landfill leachate from different landfills of China

Landfill leachate usually harbors complex microbial communities responsible for the decomposition of municipal solid waste. However, the diversity and metabolic functions of the microbial communities in landfill leachate as well as the factors that influence them are still not well understood. In this study, Illumina MiSeq high-throughput sequencing was used to investigate the microbial community composition and metabolic functions in landfill leachate from 11 cities in China. The microbial diversity and structure of different leachate samples exhibited obvious differences. In general, Bacteroidetes, Firmicutes and Proteobacteria were the three dominant microbial communities among the 26 bacterial phyla identified in landfill leachate, regardless of the geographical locations. Diverse bacterial genera associated with various functions such as cellulolytic bacteria (e.g., Sphaerochaeta and Defluviitoga), acidifying bacteria (e.g., Prevotella and Trichococcus) and sulfate-reducing bacteria (e.g., Desulfuromonas and Desulfobacterium) were detected abundantly in the landfill leachate. Moreover, the archaeal community in all leachate samples was dominated by the orders Methanomicrobiales and Methanosarcinales belonging to the Euryarchaeota phylum. Notably, the archaea-specific primer pair covered more diverse archaeal communities than the universal bacteria-archaea primer pair. Seventeen archaeal genera belonging to acetoclastic, hydrogenotrophic, and methylotrophic methanogens were identified, and the composition of the dominant genera in these samples varied greatly. The canonical correlation analysis indicated that landfill age, electrical conductivity, ammonia nitrogen, and total nitrogen were significantly correlated with the microbial community structure. Based on PICRUSt2, a total of 41 metabolic pathways belonging to six metabolic pathway groups were predicted, and the KEGG pathway Metabolism was the most abundant group across all leachate samples. This study provides an important insight into the composition and functional characteristics of the microbial communities in landfill leachate.

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.

Extracellular enzyme and microbial activity in MSW landfills with different gas collection and leachate management practices

The performance of simulated municipal solid waste (MSW) landfills with two different biogas collection practices - (1) upward and upward-downward biogas flow collection (L_T-TB) in sequence and (2) simultaneous upward-downward biogas flow collection (L_TB) from the beginning of the anaerobic degradation process - was investigated in terms of landfill gas and leachate, enzyme activity, and microbial community structure associated with MSW compression and leachate recirculation. The cumulative methane volume in L_TB was 1.5 times higher than that in L_T-TB. With MSW compression and leachate recirculation, amylase and lipase activity were enhanced in L_TB. In L_T-TB, the activities gradually decreased after reaching a peak with compression. The two biogas collection strategies influenced the community structure and activity of bacteria and archaea. The upward and downward gas collection flow with waste compression and leachate recirculation improved the environment for enriching bacterial phyla Firmicutes, Proteobacteria, and Synergistetes and genus Methanosarcina in Archaea.

Full-scale of composting process of biogas residues from corn stover anaerobic digestion: Physical-chemical, biology parameters and maturity indexes during whole process

Recycling of biogas residues from corn stover anaerobic digestion is crucial for the development of biogas industry. Full-scale composting process is the feasible way to convert biogas residues to fertilizer. The aim of the study was to explore the feasibility of full-scale composting process to dispose biogas residue to fertilizer, and to evaluate the quality of the compost. The results showed the biogas residues could rapidly reach the thermophilic stage and last at least 20 days, NH₄⁺-N, TOC and C/N decreased along with the composting process, while TP, TK and NO₃^--N showed an opposite trend. Germination index(GI) and seedling growth index showed that raw biogas residues was toxic for plant, but the GI and seedling growth index were increased during the composting process, except for the cooling stage sample. Anaerolineaceae and Limnochordaceae were the main bacteria involved in the composting process, and Chaetomium was the most important fungus.

Effects of biochar addition on the anaerobic digestion of carbohydrate-rich, protein-rich, and lipid-rich substrates

Although biochar addition into the anaerobic digestion of food waste (FW) is an efficient means to enhance methane production, the effects of biochar on various FW components remain unclear. Laboratory batch experiments were conducted to investigate the impact of sewage sludge-derived biochar (SSB) supplementation on the anaerobic digestion (AD) of major FW components, including carbohydrate-rich, protein-rich, and lipid-rich substrates. The lag phase of AD with the carbohydrate-rich substrate was 48.6% shorter when SSB was added, and the cumulative methane yield was 4.74 times higher compared to AD without biochar. SSB supplementation also increased the rate of methane production from the lipid-rich substrate. However, the effect of SSB addition on AD of the protein-rich substrate was minor. Analysis of the microbial communities revealed that methanogen growth was enhanced during AD of the carbohydrate-rich and lipid-rich substrates, but not the protein-rich substrate, following SSB supplementation. Also, the most dominant methanogenic genus varied with the substrates. SSB addition promoted the growth of hydrolytic and fermentative bacteria, particularly phylum Bacteroidetes.Implications: Biochar supplementation has been studied to overcome the shortcomings of anaerobic digestion (AD). However, the effects of biochar on different substrates remain unclear. This study compared carbohydrate-rich, protein-rich, and lipid-rich substrates in anaerobic digestion with sewage sludge-derived biochar (SSB). SSB supplementation improved methane generation from all but the protein-rich substrate. The study results imply that the effect of SSB addition on AD varied with the substrate due to the substrates underwent different degradation processes with different microbial communities.

Microbial interactions regulated by the dosage of ferroferric oxide in the co-metabolism of organic carbon and sulfate

Effects of ferroferric oxide (Fe₃O₄) and organic carbon on co-metabolism of sulfate and organic carbon were investigated. With Fe₃O₄, the degradation of acetate and sulfate was inhibited when fed with acetate, while the degradation of acetate and propionate produced from ethanol was promoted when fed with ethanol. The dominant sulfate reducing bacteria (SRB) of acetate-fed reactors were Desulfobacteraceae (complete oxidizing SRB, CO-SRB) and Desulfurmonas (incomplete oxidizing SRB, IO-SRB). IO-SRBs of Desulfobulbus and Desulfomicrobium were dominant in ethanol-fed reactors. CO-SRB had higher competitiveness than methanogens to utilize acetate, while IO-SRBs might cooperate with methanogens to produce methane when dosed with ethanol and Fe₃O₄. The dosage of Fe₃O₄ changed the dominant methanogen from Methanosarcina to Methanosaeta with acetate as the organic carbon, while increased the relative abundance of Methanosaeta with ethanol as the organic carbon.

Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing

Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.

Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach

Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.

Effect of nickel-containing activated carbon on food waste anaerobic digestion

Anaerobic digestion (AD) is frequently restricted with the long lag phase and low methane (CH₄) production rate. Laboratory batch experiments were conducted to investigate the impact of different supplements on the performance of food waste AD, including AC-Ni, AC, and Ni. Results showed that the lag phase of AD was reduced with the addition of those supplementations. Compared with the control group without any supplementation, the AC-Ni could shorten the lag phase by 67% and increase the maximum CH₄ production rate by 50%, respectively. The speciation analysis indicated that the environmental risks of the AC-Ni was reduced by 30% after digestion. Microbial community structure analysis revealed that the AC-Ni promoted the evolution and activity of the hydrolytic-fermentative bacteria (e.g. Firmicutes and Bacteroidetes) and methanogens (e.g. Methanobacterium, Methanoregula and Methanomassiliicoccus). This study suggested that the AC-Ni waste could be feasible to be applied to enhance the performance of AD.

Exogenous acyl-homoserine lactones adjust community structures of bacteria and methanogens to ameliorate the performance of anaerobic granular sludge

Quorum sensing (QS) signalling has been extensively studied in single species populations, activated sludge, biofilm and aerobic granular sludge. However, ecological roles of QS in anaerobic granular sludge, particularly in the content of the relationship between QS signalling and microbial community composition and function, have been rarely reported. Herein, five acyl-homoserine lactones (AHLs) molecules were added in the anaerobic granular sludge system for treating traditional Chinese medicine (TCM) wastewater respectively. The results indicated that the introduction of specific AHLs could enhance the abilities of organic matters removal and methanation in anaerobic granular sludge, and meanwhile, exogenous AHLs played an important role to regulate the concentration of EPS. Sequencing analysis indicated that microbial community structures of bacteria and methanogens changed to varying degrees by adding AHLs. This study suggested that exogenous AHLs could play a role in mediating microbial community structure, thereby enhancing the performance of anaerobic granular sludge. The regulatory mechanism of AHLs on community structure was discussed, and a speculative action model was established. Exogenous regulation by selective enhancement of AHLs-mediated QS in anaerobic granular sludge provided an innovative and attractive strategy for strengthening wastewater treatments.

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor

A lab-scale anaerobic membrane bioreactor (AnMBR) with a side stream tubular membrane was developed to treat synthetic domestic sewage to evaluate its performance and the dynamic shift of bacterial and archaeal communities during the start-up, steady-state, overloading and recovery periods of operation at mesophilic temperatures. During the start-up period, the bacterial and archaeal communities changed drastically, and Proteobacteria and Bacteroidetes predominated. During the steady-state period, the AnMBR exhibited excellent COD removal above 91%, and COD of the effluent was below 50 mg/L. High-throughput sequencing analysis results revealed that bacterial and archaeal communities shifted significantly from the start-up to the steady-state period, and that the Proteobacteria phylum predominated on days 140, 162 and 190, and the archaea community hydrogenotrophic methanogen genus Methanolinea (1.5–6.64%) predominated over the aceticlastic methanogen genus Methanothrix (1.35–3.07%). During the overloading period, significant changes occurred in microbial community on day 210, e.g., the phyla Bacteroidetes (30%), Proteobacteria (23%) and Firmicutes (18%) predominated and the archaeal community was completely suppressed, and Methanobrevibacter (0.7%) was the only methanogen genus that emerged in the overloading period. After a shock loading period, the microbial communities exhibited significant changes within the ranks of methanogens and shifted to dominance of the aceticlastic methanogen pathway. In addition, the TVFAs to alkalinity ratio in this study was suitable as an indicator of monitoring performance in the AnMBR operation.

Hydrocarbon Degradation and Bacterial Community Responses During Remediation of Sediment Artificially Contaminated with Heavy Oil

　Natural biodegradation of heavy oil in the marine environment can be accelerated by the addition of nutrients or seeding of pre-selected microorganisms. In this study, a microcosm experiment was conducted to investigate the effects of inorganic nutrient supplementation (biostimulation) and bacterial consortium amendment (bioaugmentation) on the natural degradative processes of artificially contaminated sediment. Our results revealed that the addition of nutrients had greater effect on remediation than the addition of bacterial cells. Supplementation of inorganic nutrients promoted and sustained the growth of oil-degrading and heterotrophic bacteria throughout the experimental period. Highest reduction in the total petroleum hydrocarbons, and of their components, n-alkanes, polycylic aromatic hydrocarbons (PAHs) and alkyl PAHs, were obtained in the biostimulated microcosms. Changes in the bacterial community were monitored by the PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) method targeting the 16S rDNA gene. Results revealed different responses of the bacterial community to the addition of heavy oil and remediation agents. Shifts in the bacterial communities in the seawater were more dynamic than in the sediment. Results of this study showed that addition of remediation agents significantly enhanced the natural biodegradation of heavy oil in a sediment-seawater microcosm trial.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

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.

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.

Stimulation of the anaerobic digestion of the dry organic fraction of municipal solid waste (OFMSW) with carbon-based conductive materials

Growth of bacterial and archaeal species capable of interspecies electron exchange was stimulated by addition of conductive materials (carbon cloth or granular activated carbon (GAC)) to anaerobic digesters treating dog food (a substitute for the dry-organic fraction of municipal solid waste (OFMSW)). Methane production (772-1428mmol vs <80mmol), volatile solids removal (78%-81% vs 54%-64%) and COD removal efficiencies (∼80% vs 20%-30%) were all significantly higher in reactors amended with GAC or carbon cloth than controls. OFMSW degradation was also significantly accelerated and VFA concentrations were substantially lower in reactors amended with conductive materials. These results suggest that both conductive materials (carbon cloth and GAC) can promote conversion of OFMSW to methane even in the presence of extremely high VFA concentrations (∼500mM).

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance.

Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge

The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the results showed that electrokinetic pre-treatment of WAS increases substrate solubility and biogas production. Changes in bacterial community composition and abundances of dominant bacterial OTUs were observed during anaerobic degradation of pre-treated WAS, whereas the relative abundance of methanogenic community members remained stable.

Anaerobic digestion of food waste - Effect of recirculation and temperature on performance and microbiology

Recirculation of digestate was investigated as a strategy to dilute the food waste before feeding to anaerobic digesters, and its effects on microbial community structure and performance were studied. Two anaerobic digesters with digestate recirculation were operated at 37 °C (MD + R) and 55 °C (TD + R) and compared to two additional digesters without digestate recirculation operated at the same temperatures (MD and TD). The MD + R digester demonstrated quite stable and similar performance to the MD digester in terms of the methane yield (around 480 mL CH4 per gVSadded). In both MD and MD + R Methanosaeta was the dominant archaea. However, the bacterial community structure was significantly different in the two digesters. Firmicutes dominated in the MD + R, while Chloroflexi was the dominant phylum in the MD. Regarding the thermophilic digesters, the TD + R showed the lowest methane yield (401 mL CH4 per gVSadded) and accumulation of VFAs. In contrast to the mesophilic digesters, the microbial communities in the thermophilic digesters were rather similar, consisting mainly of the phyla Firmicutes, Thermotoga, Synergistetes and the hydrogenotrophic methanogen Methanothermobacter. The impact of ammonia inhibition was different depending on the digesters configurations and operating temperatures.

Isolation and Characterization of a New Methanobacterium formicicum KOR-1 from an Anaerobic Digester Using Pig Slurry

A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to 15 μm long and 0.7 μm wide. They stained Gram-positive and produced methane from H₂+CO₂ and formate. Strain KOR-1 grew optimally at 38°C. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR–1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology

Biomethanization entails a good means to reduce the organic fraction (OF) derived from municipal solid wastes (MSW). The bacterial diversity of a full scale MSW anaerobic reactor located in Madrid (Spain) was investigated using high-throughput 454 pyrosequencing. Even though the proteolytic bacteria prevailed throughout all of the process, community shifts were observed from the start-up to the steady-state conditions, with an increasing biodiversity displayed over time. The Bacteroidetes and the Firmicutes were the majority phyla: 55.1 and 40.2% (start-up) and 18.7 and 78.7 (steady-state) of the total reads. The system's lack of evenness remains noteworthy as the sequences affiliated to the proteolytic non-saccharolytic Proteiniphylum, Gallicola and Fastidiosipila genera, together with the saccharolytic Saccharofermentans, were predominant on the system and this predominance appears to correlate with the presence of a high ammonium concentration. The 454 pyrosequencing revealed a great diversity of rare organisms which seemingly do not sustain any metabolic roles in the course of the OF-MSW degradation. However, this scarce and unique microbiota can confer great resilience to the system as a buffer against nutritional and environmental changing conditions, thus opening the door to increase the current knowledge about the bacterial community dynamics taking place during MSW treatment processes.

Ammonia threshold for inhibition of anaerobic digestion of thin stillage and the importance of organic loading rate

Biogas production from nitrogen-rich feedstock results in release of ammonia (NH3), causing inhibition of the microbial process. The reported threshold ammonia value for stable biogas production varies greatly between studies, probably because of differences in operating conditions. Moreover, it is often difficult to separate the effect of ammonia inhibition from that of organic loading rate (OLR), as these two factors are often interrelated. This study attempted to distinguish the effects of ammonia and OLR by analysis of two laboratory-scale biogas reactors operating with thin stillage and subjected to an increase in free ammonia (from 0.30 to 1.1 g L(-1)) either by addition of an external nitrogen source (urea) or by increasing the OLR (3.2-6.0 g volatile solids L(-1) d(-1)). The results showed that ammonia concentration was detrimental for process performance, with the threshold for stability in both processes identified as being about 1 g NH3-N L(-1), irrespective of OLR. Analysis of the methanogenic community showed limited differences between the two reactors on order level and a clear increase in the abundance of Methanomicrobiales, particularly Methanoculleus sp., in response to increasing ammonia concentration. Further comprehensive molecular analysis revealed that diverse Methanoculleus species dominated in the reactors at a given ammonia level at different OLR. The acetogenic community was clearly affected by both ammonia concentration and OLR, suggesting that the volatile fatty acid load in relation to the higher OLR was important for the dynamics of this community.

Microbial community dynamics in an anaerobic biofilm reactor treating heavy oil refinery wastewater

We have established an anaerobic biofilm reactor (AnBR) for treating heavy oil refinery wastewater at the field scale for the first time.

Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing

2-Phase anaerobic digestion (AD), where the acidogenic phase was operated at 2day hydraulic retention time (HRT) and the methanogenic phase at 10days HRT, had been evaluated to determine if it could provide higher organic reduction and methane production than the conventional single-stage AD (also operated at 12days HRT). 454 pyrosequencing was performed to determine and compare the microbial communities. The acidogenic reactor of the 2-phase system yielded a unique bacterial community of the lowest richness and diversity, while bacterial profiles of the methanogenic reactor closely followed the single-stage reactor. All reactors were predominated by hydrogenotrophic methanogens, mainly Methanolinea. Unusually, the acidogenic reactor contributed up to 24% of total methane production in the 2-phase system. This could be explained by the presence of Methanosarcina and Methanobrevibacter, and their activities could also help regulate reactor alkalinity during high loading conditions through carbon dioxide production. The enrichment of hydrolytic and acidogenic Porphyromonadaceae, Prevotellaceae, Ruminococcaceae and unclassified Bacteroidetes in the acidogenic reactor would have contributed to the improved sludge volatile solids degradation, and ultimately the overall 2-phase system's performance. Syntrophic acetogenic microorganisms were absent in the acidogenic reactor but present in the downstream methanogenic reactor, indicating the retention of various metabolic pathways also found in a single-stage system. The determination of key microorganisms further expands our understanding of the complex biological functions in AD process.

Microbial-chemical indicator for anaerobic digester performance assessment in full-scale wastewater treatment plants for biogas production

Anaerobic digestion was introduced into wastewater treatment plants several years ago, but anaerobic digestion performance has not yet been achieved. The variability of the microbial community in digesters is poorly understood, and despite the crucial role of anaerobic digestion reactors, the microbial equilibrium that yields the best performance in these reactors has only recently been hypothesised. In this study, two full-scale continuous anaerobic reactors, placed in Torino's main wastewater treatment plant in northern Italy, were followed to develop a summary indicator for measuring anaerobic digestion performance. A total of 100 sludge samples were collected. The samples were characterised chemically and physically, and microbial groups were quantified by qRT-PCR. A chemical biological performance index strictly correlated to specific biogas production (rho=0.739, p<0.01) is proposed. This approach will produce new management tools for anaerobic digestion in wastewater treatment plants.

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.

Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment

Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world's largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.

Semi-continuous anaerobic digestion for biogas production: influence of ammonium acetate supplement and structure of the microbial community

BACKGROUND

As an efficient disposal method of food waste, anaerobic digestion (AD) for biogas production is widely used. In order to understand the enhanced efficiency and stability of AD by appropriate amounts of ammonia and volatile fatty acids (NH4 (+)/VFAs), the characteristics of the corresponding microbial community with ammonium acetate supplement were investigated by denatured gradient gel electrophoresis (DGGE) and pyrosequencing analyses of samples, with or without supplement of NH4 (+)/VFAs.

RESULTS

In this study, four different supplement strategies of adding ammonium acetate were investigated, including a blank group (without supplement of ammonium acetate), a low group (L group, 0.7 g/L/d), a moderate group (M group, 1.0 g/L/d) and a high group (H group, 1.3 g/L/d), respectively. The average daily gas production was 1,839 mL/d, 1,655 mL/d, 1,448 mL/d and 1,488 mL/d for L, M, H and blank groups, respectively. The results reveal that the absence or overload of NH4 (+)/VFAs leads to the inhibition or failure of the AD operation. The blank and H groups were selected for further investigation of the microbial community by DGGE and pyrosequencing analyses. A significant difference of the microbial communities at different AD stages was observed between the blank and H groups.

CONCLUSIONS

Ammonium acetate, as an efficient supplement, significantly influences the characteristics of a semi-continuous AD operation. The DGGE and pyrosequencing analyses indicated that the different bacterial and archaeal communities occurred in the blank and H groups at different AD stages. Thus, an appropriate ammonium acetate supplement may maintain the balance of the microbial community and could be applied to adjust the AD operation and microbial composition towards optimal biogas production.

Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems

Microbial community profiles in two parallel CSTR biogas reactors fed with whey permeate and cow manure were investigated. The operating conditions for these two reactors were identical, yet only one of them (R1) showed stable performance, whereas the other (R2) showed a decrease in methane production accompanied by accumulation of propionic acid and, later, acetic acid. This gave a unique opportunity to study the dynamics of the microbial communities in two biogas reactors apparently operating close to the edge of stability. The microbial community was dominated by Bacteroidetes and Firmicutes, and the methanogens Methanobacteriales and Methanomicrobiales in both reactors, but with larger fluctuations in R2. Correlation analyses showed that the depletion of propionic acid in R1 and the late increase of acetic acid in R2 was related to several bacterial groups. The biogas production in R1 shows that stable co-digestion of manure and whey can be achieved with reasonable yields.

Development of Methanoculleus-specific real-time quantitative PCR assay for assessing methanogen communities in anaerobic digestion

AIM

To develop a Methanoculleus-specific real-time quantitative PCR (RT-qPCR) assay with high coverage and specificity for the analysis of methanogenic populations in anaerobic digestion.

METHODS AND RESULTS

A Methanoculleus-specific primer/probe set for RT-qPCR was designed in this study based on all Methanoculleus 16S rRNA gene sequences in Ribosomal Database Project (RDP) according to TaqMan chemistry. The newly designed primer/probe set was shown to have high coverage and specificity by both in silico and experimental analyses. Amplification efficiency of the Methanoculleus-specific primer/probe set was determined to be ideal for RT-qPCR applications. Subsequent field testing on anaerobic digesters showed that results from RT-qPCR were consistent with those from clone library analysis, validating the accuracy of the RT-qPCR assay.

CONCLUSIONS

The Methanoculleus-specific RT-qPCR assay designed in this study can serve as a rapid and effective tool for the quantification of Methanoculleus populations in anaerobic digestion.

SIGNIFICANCE AND IMPACT OF THE STUDY

Methanoculleus populations represent important members of archaeal communities in methanogenic processes, necessitating the need to develop effective tools to monitor Methanoculleus population abundance. The RT-qPCR developed in this study provides an essential tool for the quantification of Methanoculleus populations in anaerobic digestion and for the understanding of the functions of these methanogens in anaerobic biotransformation.

Optimisation of the two-phase dry-thermophilic anaerobic digestion process of sulphate-containing municipal solid waste: population dynamics

Microbial population dynamics and anaerobic digestion (AD) process to eight different hydraulic retention times (HRTs) (from 25d to 3.5d) in two-phase dry-thermophilic AD from sulphate-containing solid waste were investigated. Maximum values of gas production (1.9 ± 0.2 l H2/l/d; 5.4 ± 0.3 l CH4/l/d and 82 ± 9 ml H2S/l/d) and microbial activities were obtained at 4.5d HRT; where basically comprised hydrolysis step in the first phase (HRT=1.5d) and acidogenic step finished in the second phase as well as acetogenic-methanogenic steps (HRT=3d). In the first phase, hydrolytic-acidogenic bacteria (HABs) was the main group (44-77%) and Archaea, acetogens and sulphate-reducing bacteria (SRBs) contents were not significant; in the second phase (except to 2d HRT), microbial population was able to adapt to change in substrate and HRTs to ensure the proper functioning of the system and both acetogens and Archaea were dominated over SRBs. Decreasing HRT resulted in an increase in microbial activities.

Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters

While the use of anaerobic digestion to generate methane as a source of bioenergy is increasing worldwide, our knowledge of the microbial communities that perform biomethanation is very limited. Using next-generation sequencing, bacterial population profiles were determined in three full-scale mesophilic anaerobic digesters operated on dairy farms in the state of Vermont (USA). To our knowledge, this is the first report of a metagenomic analysis on the bacterial population of anaerobic digesters using dairy manure as their main substrate. A total of 20,366 non-chimeric sequence reads, covering the V1-V2 hypervariable regions of the bacterial 16S rRNA gene, were assigned to 2,176 operational taxonomic units (OTUs) at a genetic distance cutoff value of 5 %. Based on their limited sequence identity to validly characterized species, the majority of OTUs identified in our study likely represented novel bacterial species. Using a naïve Bayesian classifier, 1,624 anaerobic digester OTUs could be assigned to 16 bacterial phyla, while 552 OTUs could not be classified and may belong to novel bacterial taxonomic groups that have yet to be described. Firmicutes, Bacteroidetes, and Chloroflexi were the most highly represented bacteria overall, with Bacteroidetes and Chloroflexi showing the least and the most variation in abundance between digesters, respectively. All digesters shared 132 OTUs, which as a "core" group represented 65.4 to 70.6 % of sequences in individual digesters. Our results show that bacterial populations from microbial communities of anaerobic manure digesters can display high levels of diversity despite sharing a common core substrate.

Organic loading rate and food-to-microorganism ratio shape prokaryotic diversity in a demo-scale up-flow anaerobic sludge blanket reactor treating domestic wastewater

We investigated the microbial community in an up-flow anaerobic sludge blanket (UASB) reactor treating domestic wastewater (DW) during two different periods of organic loading rate (OLR) and food-to-microorganism (F/M) ratio. 16S rDNA clone libraries were generated, and quantitative real-time PCR (qPCR) analyses were performed. Fluctuations in the OLR and F/M ratio affected the abundance and the composition of the UASB prokaryotic community, mainly at the species level, as well as the performance of the UASB reactor. The qPCR analysis suggested that there was a decrease in the bacterial cell number during the rainy season, when the OLR and F/M ratio were lower. However, the bacterial diversity was higher during this time, suggesting that the community degraded more diversified substrates. The diversity and the abundance of the archaeal community were higher when the F/M ratio was lower. Shifts in the methanogenic community composition might have influenced the route of methane production, with methane produced by acetotrophic methanogens (dry season), and by hydrogenotrophic, methylotrophic and acetotrophic methanogens (rainy season). This study revealed higher levels of bacterial diversity, metabolic specialization and chemical oxygen demand removal efficiency of the DW UASB reactor during the rainy season.

Monitoring methanogenic population dynamics in a full-scale anaerobic digester to facilitate operational management

Microbial populations in a full-scale anaerobic digester fed on food waste were monitored over an 18-month period using qPCR. The digester exhibited a highly dynamic environment in which methanogenic populations changed constantly in response to availability of substrates and inhibitors. The methanogenic population in the digester was dominated by Methanosaetaceae, suggesting that aceticlastic methanogenesis was the main route for the production of methane. Sudden losses (69%) in Methanosaetaceae were followed by a build-up of VFAs which were subsequently consumed when populations recovered. A build up of ammonium inhibited Methanosaetaceae and resulted in shifts from acetate to hydrogen utilization. Addition of trace elements and alkalinity when propionate levels were high stimulated microbial growth. Routine monitoring of microbial populations and VFAs provided valuable insights into the complex processes occurring within the digester and could be used to predict digester stability and facilitate digester optimization.

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

The microbial community of 21 full-scale biogas reactors was examined using 454 pyrosequencing of 16S rRNA gene sequences. These reactors included seven (six mesophilic and one thermophilic) digesting sewage sludge (SS) and 14 (ten mesophilic and four thermophilic) codigesting (CD) various combinations of wastes from slaughterhouses, restaurants, households, etc. The pyrosequencing generated more than 160,000 sequences representing 11 phyla, 23 classes, and 95 genera of Bacteria and Archaea. The bacterial community was always both more abundant and more diverse than the archaeal community. At the phylum level, the foremost populations in the SS reactors included Actinobacteria, Proteobacteria, Chloroflexi, Spirochetes, and Euryarchaeota, while Firmicutes was the most prevalent in the CD reactors. The main bacterial class in all reactors was Clostridia. Acetoclastic methanogens were detected in the SS, but not in the CD reactors. Their absence suggests that methane formation from acetate takes place mainly via syntrophic acetate oxidation in the CD reactors. A principal component analysis of the communities at genus level revealed three clusters: SS reactors, mesophilic CD reactors (including one thermophilic CD and one SS), and thermophilic CD reactors. Thus, the microbial composition was mainly governed by the substrate differences and the process temperature.

Comparative study of changes in reaction profile and microbial community structure in two anaerobic repeated-batch reactors started up with different seed sludges

Microbial community structure and dynamics were examined in two anaerobic reactors run in repeated-batch mode to treat whey permeate. Despite being started up using different seeding sources, the reactors showed generally similar reaction patterns and performances. During the repeated-batch operation for three cycles, the overall reaction rate increased with the increase in the initial population size of both bacteria and methanogens over cycles. Clostridium- and Methanospirillum-related microorganisms were likely the main acidogenic and methanogenic populations, respectively, in both reactors. Bacterial community structure shifted dynamically over cycles, while little change was observed in methanogen community structure throughout the operation. This means that the changes in bacterial community structure changes had little influence on the formation and evolution of methanogen community structure in the reactors. The increased methanogenesis rate with cycles seemed therefore more likely due to the effect of the increase in methanogen abundance rather than the alteration of community structure.