Temporal variation in methanogen communities of four different full-scale anaerobic digesters treating food waste-recycling wastewater

Enhanced digestion of sludge via co-digestion with food waste in a high-solid anaerobic membrane bioreactor: Performance evaluation and microbial response

A 15 L high-solid mesophilic AnMBR was operated for the digestion of food waste, primary sludge and excess sludge. The digestion performance was evaluated from the perspective of methane generation, permeate quality and organic reduction. Furthermore, the change in the microbial community was investigated by 16S rRNA gene analysis. The results showed that the introduction of sludge decreased the H2S levels in biogas compared with the mono-digestion of food waste and the co-digestion with food waste increased biogas and methane production compared with the mono-digestion of sludge. A substitution ratio of 25 % became a turning point of permeate composition and reaction rates. The energy recovery ratios of the mesophilic AnMBR were over 75 % based on stoichiometric analysis. In reaction kinetics analysis, hydrolysis as the first step of anaerobic digestion was found to be most influenced by the composition of the substrate. Finally, the microbial community structures were stable under tested conditions while the evolutionary relationships within the dominant phyla were observed. In the archaea community, Methanosaeta was the dominant methanogen regardless sludge ratio in the substrate.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste

While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.

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.

Comparative study of industrial-scale high-solid biogas production from food waste: Process operation and microbiology

Anaerobic high-solid treatment (HST) for processing food waste and biogas production is a viable technology with considerable commercial potential. In this study, we examined and compared mesophilic and thermophilic industrial-scale plug-flow digesters. The HSTs demonstrated reasonable biogas yields from food waste (0.4-0.6 Nm³ CH₄/kg volatile solids). However, during operation at thermophilic conditions ammonia inhibition (~2 g NH₃-N/L) and acid accumulation (6-14 g/L) caused severe process disturbance. Microbial community structures diverged between the processes, with temperature appearing to be a strong driver. A unique feature of the thermophilic HSTs was high abundance of the uncultivated Clostridia group MBA03 and temperature fluctuations in one mesophilic HST were linked to drastically decreased abundance of methanogens and relative abundance of Cloacimonetes. The process data obtained in this study clearly demonstrate both potential and challenges in HST of food waste but also possibilities for management approaches to tackle process imbalance and restore process function.

A snapshot of microbial community structures in 20 different field-scale anaerobic bioreactors treating food waste

This study aimed to identify significant factors shaping the microbial populations in biogas plants treating food waste (FW). Twenty full-scale anaerobic acidogenic/methanogenic bioreactors, located at 11 FW treatment facilities, were compared to find patterns in their microbial community structures and potential interactions with the process parameters. Temperature, hydraulic retention time, and organic loading rate were design parameters that systematically influenced the microbial communities. The latter two clearly separated the acidogenic and methanogenic bioreactors. Lactobacillus was the dominant (69.7 ± 19.8%) bacteria in the acidogenic reactors, while hydrogen-utilizing methanogens, such as Methanoculleus (65.1 ± 33.5%), were the dominant archaea in most methanogenic digesters. Defluiviitoga was the dominant (82.7 ± 1.4%) bacteria in the thermophilic digesters, but was also the most abundant (33.1-33.6%) bacteria in dry mesophilic digesters. The two bioreactor categories had lower bacterial diversities, and also higher propionate concentrations (>5 g/L in 4 out of 5 cases), which may impose potential risks for the management of such digesters. The current 'snapshot' of the microbial communities suggests several bacterial and archaeal taxa as potential indicators of bioreactor categories and/or process variables.

Effects of ZnO nanoparticles on the performance of anaerobic membrane bioreactor: An attention to the characteristics of supernatant, effluent and biomass community

Two laboratory-scale anaerobic membrane bioreactor (AnMBRs) were built to investigate the effect of zinc oxide nanoparticles (ZnO-NPs) on their performance, and the recovery phase was also examined. Results showed that the addition of ZnO-NPs with 0.4 mg/L caused significant deteriorations of AnMBR performance, including decrements of chemical oxygen demand (COD) removal efficiency from 96.4% to 81.5% and biogas production from 0.36 to 0 L/g COD removal within 40 days. A significant increment from 13.2 to 52.1 mg/L in soluble microbial products (SMP) was obtained, while no obvious effect on colloids was observed except an increased fluctuation of colloid concentration. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis revealed remarkable changes of compounds in effluent with exposure to ZnO-NPs, and some new alkanes and esters were produced, such as Cyclobutane, 1,2-diethyl-, trans-, Tetradecane, Cyclopropane, octyl-, and Butanoic acid, methyl ester. The microbial community was compared using high-throughput sequencing, clearly showing the changes in both bacteria and archaea communities. Furthermore, results for recovery phase indicated that the AnMBR performance can be recovered within around 60 days after stopping ZnO-NPs addition, accompanied by the decrement of zinc concentration mainly adsorbed by sludge.

A comparative study of single- and two-phase anaerobic digestion of food waste under uncontrolled pH conditions

This study compared single- versus two-phase systems for semi-continuous anaerobic digestion of food waste without pH control at varying organic loading rates (OLRs). The methanogenic reactors of both systems required trace element supplementation for stable operation at 3.0 g VS (volatile solids)/L∙d or higher OLRs. Under trace-element supplemented conditions, both systems achieved stable and efficient performance at OLRs up to 4.0 g VS/L∙d. The two-phase system outperformed the single-phase system at 1.0-4.0 g VS/L∙d OLRs, but it failed at an OLR of 5.0 g VS/L∙d. Meanwhile, the single-phase system maintained the stable performance and reached its maximum methane production at this OLR. These results suggest that a single-phase configuration is more advantageous for robust treatment of food waste without pH control at high organic and hydraulic loads. Hydrogenotrophic methanogens dominated the methanogen community throughout the experiment in both systems. Microbial community structure shifts correlated with reactor operation and performance characteristics.

Comprehensive analysis of microbial communities in full-scale mesophilic and thermophilic anaerobic digesters treating food waste-recycling wastewater

Microbes were sampled for a year in a full-scale mesophilic anaerobic digester (MD) and a thermophilic anaerobic digester (TD) treating food waste-recycling wastewater (FRW), then microbial community structure, dynamics and diversity were quantified. In the MD, Fastidiosipila, Petrimonas, vadinBC27, Syntrophomonas, and Proteiniphilum were dominant bacterial genera; they may contribute to hydrolysis and fermentation. In the TD, Defluviitoga, Gelria and Tepidimicrobium were dominant bacteria; they may be responsible for hydrolysis and acid production. In the MD, dominant methanogens changed from Methanobacterium (17.1 ± 16.9%) to Methanoculleus (67.7 ± 17.8%) due to the increase in ammonium concentration. In the TD, dominant methanogens changed from Methanoculleus (42.8 ± 13.6%) to Methanothermobacter (49.6 ± 11.0%) due to the increase of pH. Bacteria and archaea were more diverse in the MD than in the TD. These results will guide development of microbial management methods to improve the process stability of MD and TD treating FRW.

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: A full-scale study

Ten mesophilic full-scale anaerobic digesters treating food wastewater (FW-digesters) or sewage sludge (SL-digesters) were monitored for 1 year to investigate: (1) microbial communities underpinning FW-digesters and SL-digesters, (2) the effects of total ammonia-nitrogen concentration [TAN] and Na⁺ concentration [Na⁺] on variations of these communities. [TAN] and [Na⁺] in the digester varied among digesters: 1.7-6.5 g TAN/L and 1.0-3.6 g Na⁺/L for the FW-digesters, and 0.1-2.2 g TAN/L and 0.1-1.2 g Na⁺/L for the SL-digesters; [TAN] negatively correlated with the process efficiency of the FW-digesters. Microbial communities were less diverse in the FW-digesters than in the SL-digesters. The FW- and SL-digesters formed very distinct microbial community structures; [TAN] and [Na⁺] in the digester were the critical factors shaping these structures. Immigrant bacteria from influent sludge significantly influence the bacterial communities of the SL-digesters. Methanoculleus might be tolerant to high ammonia in AD of such organic wastewater.

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.

Effect of Fe0 addition on volatile fatty acids evolution on anaerobic digestion at high organic loading rates

Excessive acidification frequently occurs in the anaerobic digestion of the organic fraction of municipal solid waste (OFMSW) at high organic loading rates (OLR), due to the accumulation of non-acetic volatile fatty acids (VFA). In this study, the performance of Fe⁰ in enhancing various VFA production and metabolism was investigated. The butyric acid concentration in a high OLR reactor with Fe⁰ addition decreased from 7200 to 0mg/L after a short lag phase, and the total VFA (TVFA) concentration also decreased substantially. The corresponding dominant acidogenesis type also changed from butyric type to propionic type fermentation. Furthermore, the CH₄ yield of the reactor with added Fe⁰ was approximately 595ml CH₄/g VS_added, which was an increase of 41.7% compared with the biochemical methane potential (BMP) test results in controls without added ZVI. A microbial diversity analysis, using high throughput sequencing, showed that Methanofollis and Methanosarcina were dominant in terms of the archaeal structures of the Fe⁰ reactor at the butyric converting stage; however, Methanosaeta was predominant in the reactor during the control BMP test. These results suggested that Fe⁰ can convert non-acetic VFA to acetic VFA and improve the CH₄ yield by enhancing the activity of methanogens.

Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions

Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H₂ producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH₄⁺-N] (p<0.1); this relationship suggests that ammonia was a significant parameter for bacterial selection. The bacterial niche information reported in this study can be useful to understand the ecophysiology of anaerobic digesters treating swine manure that contains high ammonia content.

Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability

In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na⁺, and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW.

Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes

A novel anaerobic digestion configuration, the upflow multi-layer anaerobic reactor (UMAR), was developed to treat high-solids organic wastes. The UMAR was hypothesized to form multi-layer along depth due to the upflow plug flow; use of a recirculation system and a rotating distributor and baffles aimed to assist treating high-solids influent. The chemical oxygen demand (COD) removal efficiency and methane (CH₄ ) production rate were 89% and 2.10 L CH₄ /L/d, respectively, at the peak influent COD concentration (110.4 g/L) and organic loading rate (7.5 g COD/L/d). The 454 pyrosequencing results clearly indicated heterogeneous distribution of bacterial communities at different vertical locations (upper, middle, and bottom) of the UMAR. Firmicutes was the dominant (>70%) phylum at the middle and bottom parts, while Deltaproteobacteria and Chloroflexi were only found in the upper part. Potential functions of the bacteria were discussed to speculate on their roles in the anaerobic performance of the UMAR system. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1226-1234, 2017.

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer

Food processing facilities often use antimicrobial quaternary ammonium compound (QAC) sanitizers to maintain cleanliness. These QACs can end up in wastewaters used as feedstock for anaerobic digestion. The aim of this study was to measure the effect of QAC contamination on biogas production and structure of microbial communities in thermophilic digester sludge. Methane production and biogas quality data were analyzed in batch anaerobic digesters containing QAC at 0, 15, 50, 100 and 150mg/L. Increasing sanitizer concentration in the bioreactors negatively impacted methane production rate and biogas quality. Microbial community composition data was obtained through 16S rRNA gene sequencing from the QAC-contaminated sludges. Sequencing data showed no significant restructuring of the bacterial communities. However, significant restructuring was observed within the archaeal communities as QAC concentration increased. Further studies to confirm these effects on a larger scale and with a longer retention time are necessary.

Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions

Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m³ m^-3 d^-1). Restoring the recirculation loop led to a methane production of 0.55 m³ m^-3 d^-1 concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass.

Adaption of microbial community during the start-up stage of a thermophilic anaerobic digester treating food waste

A successful start-up enables acceleration of anaerobic digestion (AD) into steady state. The microbial community influences the AD performance during the start-up. To investigate how microbial communities changed during the start-up, microbial dynamics was analyzed via high-throughput sequencing in this study. The results confirmed that the AD was started up within 25 d. Thermophilic methanogens and bacterial members functioning in hydrolysis, acidogenesis, and syntrophic oxidation became predominant during the start-up stage, reflecting a quick adaption of microorganisms to operating conditions. Such predominance also indicated the great contribution of these members to the fast start-up of AD. Redundancy analysis confirmed that the bacterial abundance significantly correlated with AD conditions. The stable ratio of hydrogenotrophic methanogens to aceticlastic methanogens is also important to maintain the stability of the AD process. This work will be helpful to understand the contribution of microbial community to the start-up of AD.