Comparison of anaerobic digestion strategies of nitrogen-rich substrates: Performance of anaerobic reactors and microbial community diversity

Exploring the Relationships Between Bacterial Community, Taste-Enhancing Peptides and Aroma in Thai Fermented Fish (Pla-ra)

As a traditional Thai condiment, Pla-ra is used to add flavor and richness to dishes. Nine treatment combinations of Pla-ra formulations created from 3 types of fish (Mor fish, Kradee fish, and Mor + Kradee fish) and 4 different carbohydrate sources (none, rice bran, roasted rice, and rice bran─roasted rice mixture) were studied through a 12 month fermentation period (1, 3, 5, 7, 8, 9, 10, 11, and 12 months). 16S rRNA Next Generation Sequencing (NGS) and LC-MS/MS techniques were used to analyze the microbial diversity and identify taste-enhancing peptides. Descriptive sensory analysis was performed on the extracts of the 108 Pla-ra samples mixed in a model broth. Koku perception and saltiness-enhancing attributes were clearly perceived and dominant in all samples, even though glutamyl peptides, including γ-Glu-Val-Gly, were found at subthreshold levels. The samples from mixed fish and Mor fish fermented with roasted ground rice and rice bran for 12 months had the most typical Pla-ra odors and tastes and had high taste-enhancing activities. NGS analysis revealed the presence of bacteria containing a large number of protease and aminopeptidase genes in the samples. Bacillus spp., Gallicola spp., and Proteiniclasticum spp. correlated well with the generation of glutamyl and arginyl peptides and typical odors in the samples. These results confirmed the typical sensory quality of Pla-ra depended on protein sources, carbohydrate sources, and bacteria communities. Further optimization of the microbial composition found could lead to the development of starter cultures to control and promote flavor development in fermented fish products.

Elucidation of microbial interactions, dynamics, and keystone microbes in high pressure anaerobic digestion

High-pressure anaerobic digestion (HPAD) is a promising technology for producing biogas enriched with high methane content in a single-step process. To enhance HPAD performance, a comprehensive understanding of microbial community dynamics and their interactions is essential. For this, mesophilic batch high-pressurized anaerobic reactors were operated under 3 bars (H3) and 6 bars (H6). The experimental results showed that the effect of high-pressure (up to 6 bar) on acidification was negligible while methanogenesis was significantly delayed. Microbial analysis showed the predominance of Defluviitoga affiliated with the phylum Thermotogae and the reduction of Thiopseudomonas under high-pressure conditions. In addition, the microbial cluster pattern in H3 and H6 was significantly different compared to the CR, indicating a clear shift in microbial community structure. Moreover, Methanobacterium, Methanomicrobiaceae, Alkaliphilus, and Petrimonas were strongly correlated in network analysis, and they could be identified as keystone microbes in the HPAD reactor.

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.

Carbon cloth amendment for boosting high-solids anaerobic digestion with percolate recirculation: Spatial patterns of microbial communities

The addition of conductive materials in anaerobic digestion (AD) is a promising method for boosting biomethane recovery from organic waste. However, conductive additives have rarely been investigated for the high-solids anaerobic digestion (HSAD). Here, the impact of adding carbon cloth in the solid phase of an HSAD system with percolate recirculation was investigated. Furthermore, spatial patterns of microbial communities in suspended biomass, percolate, and carbon cloth attached biofilm were assessed. Carbon cloth increased biomethane yield from source-separated organics (SSO) by 20% more than the unamended control by shortening the lag phase (by 15%) and marginally improving the methanogenesis rate constant (by ∼8%) under a batch operation for 50 days. Microbial community analysis demonstrated higher relative abundances of the archaeal population in the carbon cloth amended reactor than in unamended control (12%-21% vs. 5%-15%). Compared to percolate and suspension, carbon cloth attached microbial community showed higher enrichment of known electroactive Pseudomonas species along with Methanosarcina and Methanobacterium species, indicating the possibility of DIET-based syntrophy among these species.

Bioaugmentation with methanogenic culture to improve methane production from chicken manure in batch anaerobic digestion

This study sought to investigate the effect of bioaugmentation on batch anaerobic digestion of chicken manure. The digestion performance with and without bioaugmentation and bioaugmented efficiency under different dosages were compared. The results demonstrated that bioaugmentation increased the methane yield and shortened the methane production time in batch reactors. Compared to the un-bioaugmented control, the methane yield of bioaugmented digesters was increased by 1.2-, 1.7-, 2.2-, 3.4-, and 3.6-fold at addition ratios of 0.07, 0.14, 0.21, 0.27, and 0.34 g VS _{bioaugmentation seed (BS)}/g VS_CM, respectively. However, higher bioaugmentation doses (0.34 g VS_BS/g VS_CM) did not exhibit significantly improved bioaugmentation efficiency, thus, the recommended dose is 0.27 g VS_BS/g VS_CM for biomethane conversion of CM. Moreover, whole genome pyrosequencing revealed that Methanoculleus and Methanobrevibacter predominated the non-bioaugmentation digesters, whereas Methanothrix, Methanobacterium, and Methanomassiliicoccus were the dominant methanogens in bioaugmentation digesters. The increased methane may be explained by an increase in the Methanothrix population, which accelerated acetic acid degradation. With bioaugmentation the mainly methanogenic pathways have become more diverse. From gene function perspective, bioaugmentation enhanced metabolic activities in digestor which function better in metabolism.

Effect of biochar derived from biogas residue on methane production during dry anaerobic fermentation of kitchen waste

Kitchen wastes (KW) dramatically increasing with population and economy enhancing, and dry anaerobic fermentation was used to treat it. However, the large amount of biogas residue severely restricted the application of dry anaerobic fermentation, because the high total solid might lead to the system failure. Therefore, it is urgent to find appropriate way to improve the efficiency of dry anaerobic fermentation and reduce the great amount of biogas residue. In this study, a tentative experiment was conducted to investigate the effect of biochar prepared from biogas residue on the performance of dry anaerobic fermentation system. The results showed that almost half of the biogas residue was reduced and converted into biochar. At the presence of biochar, methane yield was 308.6 mL/gVS, which was 10.5% higher than that of control. Compared to the system without biochar, the highest volatile fatty acid (VFA) concentration was 19.3% higher and the percentage of acetate and valerate was 25.3％ and 12.8％, while it was 16.3% and 22.0% in the control, suggesting that biochar accelerated the degradation of VFA. Bacteria community diversity increased, Fastidiosipila and Proteiniphilum enriched at the presence of biochar, which might accelerate the hydrolysis and acidification of KW. Hydrogenotrophic methanogens was dominated and syntrophic acetate oxidation was the primary pathway to produce methane. This study developed a new recycle route for improving the efficiency of dry anaerobic fermentation while reducing the large amount of biogas residue generated from dry anaerobic fermentation.

Hydrothermal pretreatment contributes to accelerate maturity during the composting of lignocellulosic solid wastes

The aim of this work was to study the optimal conditions and mechanism of lignocellulose degradation in the hydrothermal pretreatment coupled with aerobic fermentation (HTPAF). The optimized process parameters in the hydrothermal pretreatment (HTP) were discussed. The response relationship between enzyme activity and microbial community in HTPAF were explored. The results showed that with the moisture content of 50%-90%, the lignin content decreased by 150 mg/g after treatment at 120 °C for 6 h, and a loose pore structure was formed on the surface of the chestnut shells after HTP. The compost maturity time was shortened to 12 days. The dominant microbial genera in HTPAF were Gallicola, Moheibacter and Atopostipes, which were significant different with that of the traditional composting. HTPAF is beneficial to increase the maximum temperature of aerobic fermentation and quickly degrade lignin to shorten the maturity time.

Effect of sludge retention time on microbial succession and assembly in thermal hydrolysis pretreated sludge digesters: Deterministic versus stochastic processes

Thermal hydrolysis process (THP) assisted anaerobic digestion (AD) has been demonstrated to be an efficient approach to improve biogas production and solids reduction. Given the faster reaction kinetics in the THP-AD system, reduction of sludge retention time (SRT) is possible. However, a comprehensive understanding of the effects of sludge retention time (SRT) on microbial dynamics and community assemblages is still lacking in THP-AD systems. Thus, twelve THP-AD reactors were operated at different SRTs (10-30 d) to fulfill the knowledge gap. Results showed that, although all the bioreactors displayed good performance, shorter SRT reactors (SRT 10 d) took a longer time to reach the stable state. The total biogas production at SRT of 10 d was lower than that at other longer SRTs, attributing to the limited hydrolytic/fermentative capacities of AD microbiomes. Different SRTs resulted in distinct succession patterns of AD microbiomes. THP sludge reduced the microbial diversity in all the bioreactors over time, but longer SRTs maintained higher biodiversity. Null model analysis suggested that THP-AD microbial community assembly was predominately driven by deterministic selection at the tested SRT range, but stochasticity increased with elevated SRTs, likely attributing to the immigrants from the feedstock. Phylogenetic molecular ecological networks (pMENs) analysis revealed more stable network structures at longer SRTs, evidenced by the lower modularity, shorter harmonic geodesic distance, and higher connectivity. The potential keystone taxa under varied SRTs were identified, some of which were hydrolytic/fermentative bacteria (e.g., Peptostreptococcus, Lutispora, Synergistaceae), suggesting that these species related to organic hydrolysis/fermentation even with low-abundance could still play pivotal ecological roles in maintaining the THP-AD microbial community structure and functions. Collectively, this study provides comprehensive and in-depth insights into the mechanisms underlying community assembly in THP-AD reactors, which could aid in diagnosing system stability.

Effect of Mephosphonee on methane generation in organic waste processing

The purpose of the study is to determine an effective technological method for the complete anaerobic processing of agricultural waste. It also aims to create and implement an effective technological method of sufficiently complete anaerobic processing of agricultural waste, including taking into account biologically active additives. A new technology for the disposal of organic agricultural waste and the influence of Mephosphone on the process of methane formation using a biogas unit at a processing facility developed at Kazan State Agrarian University is considered. The results of theoretical and experimental studies are presented, which made it possible to significantly reduce the utilization time, and reduce the cost of electricity and fuel. The experiments were carried out in a low-capacity biogas unit (LCBU) without air access in a heat-insulated reactor filled by 2/3. The results of numerical studies of the products of conversion of cattle manure are presented. Manure was kept in the reactor for 7 days. The use of Mephosphone in ultra-low concentrations (10-4) made it possible to obtain a useful product in the form of high-quality organic biofertilizer and biogas. The results of microbiological analysis of experiments in the test center of the Tatar Interregional Veterinary Laboratory are shown.

Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste

In our study, we used 16SrRNA and ITS to investigate the microbial community composition and the effect of compound bacterial agent on the microbial community composition in the aerobic composting process of food waste (FW). At the bacterial level, the main phyla of Group A (compost naturally) were Proteobacteria and Firmicutes, and the main species were Pseudomonas_sp._GR7, Bacillus licheniformis and Pediococcus acidilactici. The main phyla of Group B (compost with compound bacterial agent) were Proteobacteria, Firmicutes and Streptophyta, and the main species were Klebsiella pneumoniae, Cronobacter sakazakii, Macrococcus caseolyticus, Enterococcus faecalis, Citrobacter freundii and Bacillus velezensis. It is worth noting that M. caseolyticus may be able to improve the effect of odour which is an important sensory index during aerobic composting. At the fungal level, the main phylum of both Groups A and B was Ascomycota, and the main species of Group A were Paecilomyces variotii, Byssochlamys spectabilis and Aspergillus fumigatus. The main species of Group B were Ogataea polymorpha and Millerozyma farinosa. Finally, the degradation rate of Group B was 81% that was about 15% higher than that of Group A, indicating that the compound bacterial agent could effectively improve the degradation rate and the composting process, while the low abundance of the compound bacterial agent in the composting process might be due to the small initial addition or the inhibition of other bacteria or fungi in the composting process.

Exploring the combined effect of total ammonia nitrogen, pH and temperature on anaerobic digestion of chicken manure using response surface methodology and two kinetic models

Ammonia inhibition is the most challenging issue in the anaerobic digestion (AD) of nitrogen-rich substrates. Total ammonia nitrogen (TAN) concentration, temperature and pH are the main operational parameters affecting the chemical equilibrium between free ammonium nitrogen (NH₃; FAN) and ammonium ions (NH₄⁺). However, it is still unclear how these parameters together affect digestion performance by influencing this equilibrium. To determine the effect and linkages of these parameters, a Box-Behnken design-response surface methodology (RSM), correlation analysis and two kinetic models were carried out. The results revealed that the linear effect of TAN, the interaction effect between TAN and temperature, and temperature and pH were significant, however, the quadratic effect of TAN, temperature and pH were also significant. Furthermore, TAN and temperature were positively correlated with M_max, k and R_max. Findings from this study could provide a theoretical basis to develop the way of relieving ammonia inhibition.

Oyster shells improve anaerobic dark fermentation performances of food waste: Hydrogen production, acidification performances, and microbial community characteristics

Anaerobic dark fermentation (DF) performances of food waste (FW) were investigated using oyster shells. The different amount oyster shells(6%-12%(w/w)) were added to the DF system of FW. The result showed that the H₂ production rate and cumulative H₂ production improved after addition oyster shells. The highest H₂ production rate and cumulative H₂ production of 8% oyster shells addition group were 8.4 mL/(gVS·h) and 88.2 mL/gVS, which were 11.7%-30.6% and 17.4%-52.9% higher than those of the other test groups. TVFAs production, especially acetic and butyric acids improved after addition oyster shells. The highest TVFAs production was 19291.4 mg/L for 8% oyster shells added group, which was 90.24% higher than that of the unadded group. For 8% oyster shells added group, Lactobacillales, Gallicola, and Bacteroides were the dominant species at genus levels. Thus, the addition of an appropriate amount oyster shells could improve H₂ production rate, cumulative H₂ production, promote buffering capacity, enhance TVFAs production.

Obstacles faced by methanogenic archaea originating from substrate-driven toxicants in anaerobic digestion

Anaerobic digestion (AD) is used to treat waste and produce bioenergy. However, toxicants, which originate from the substrate, can inhibit or damage the digestion process. Methanogenic archaea (MA), which are the executor in the methanogenesis stage, are more sensitive than bacteria to these toxicants. This review discusses the effects of substrate-driven toxicants, namely, antibiotics, H₂S and sulfate, heavy metals (HMs), long-chain fatty acids (LCFAs), and ammonia nitrogen, on the activity of MAs, methanogenic pathways, and the inter-genus succession of MAs. The adverse effects of these five toxicants on MA include effects on pH, damages to cell membranes, the prevention of protein synthesis, changes in hydrogen partial pressure, a reduction in the bioavailability of trace elements, and hindrance of mass transfer. These effects cause a reduction in MA activity and the succession of MAs and methanogenic pathways, which affect AD performance. Under the stress of these toxicants, succession occurs among HA (hydrogenotrophic methanogen), AA (acetoclastic methanogen), and MM (methylotrophic methanogen), especially HA gradually replaces AA as the dominant MA. Simultaneously, the dominant methanogenic pathway also changes from the aceticlastic pathway to other methanogenic pathways. A comprehensive understanding of the impact of toxicants on MA permits more specific targeting when developing strategies to mitigate or eliminate the effects of these toxicants.

The use of the Mephosphon drug to accelerate the process of biogas output and ripening of organic wastes

This article discusses a new method for the reclamation of organic waste into biogas with the addition of the biologically active additive Mephosphon to the substrate to accelerate the process of obtaining biogas (decomposition) and preserving nutrient elements in the final product. The study object was cow manure from a private farm household. The experiments were carried out for 10 days in a lowvolume biogas unit (LVBU) without airtight in a heat-insulated reactor filled with 2/3 cow manure. The use of the Mephosphon drug in ultra-low concentrations (10-4) allowed us to obtain a useful product in the form of high-quality organic fertilizer and biogas.

Influence of Granular Activated Carbon on Anaerobic Co-Digestion of Sugar Beet Pulp and Distillers Grains with Solubles

Anaerobic digestion is an important technology to receive energy from various types of biomass. In this work, the impact of granular activated carbon (GAC) on the mesophilic anaerobic co-digestion of sugar beet pulp and distillers grains was investigated. After a short period, anaerobic reactors began to produce biomethane and were ready for completion within 19–24 days. The addition of GAC to reactors (5–10 g L−1) significantly enhanced the methane production rate and consumption of produced volatile fatty acids. Thus, the maximum methane production rate increased by 13.7% in the presence of GAC (5 g L−1). Bacterial and archaeal community structure and dynamics were investigated, based on 16S rRNA genes analysis. The abundant classes of bacteria in GAC-free and GAC-containing reactors were Clostridia, Bacteroidia, Actinobacteria, and Synergistia. Methanogenic communities were mainly represented by the genera Methanosarcina, Methanoculleus, Methanothrix, and Methanomassiliicoccus in GAC-free and GAC-containing reactors. Our results indicate that the addition of granular activated carbon at appropriate dosages has a positive effect on anaerobic co-digestion of by-products of the processing of sugar beet and ethanol distillation process.

Effect of Clinoptilolite and Halloysite Addition on Biogas Production and Microbial Community Structure during Anaerobic Digestion

The study presents a comparison of the influence of a clinoptilolite-rich rock-zeolite (commonly used for improving anaerobic digestion processes)-and a highly porous clay mineral, halloysite (mainly used for gas purification), on the biogas production process. Batch experiments showed that the addition of each mineral increased the efficiency of mesophilic anaerobic digestion of both sewage sludge and maize silage. However, halloysite generated 15% higher biogas production during maize silage transformation. Halloysite also contributed to a much higher reduction of chemical oxygen demand for both substrates (by ~8% for maize silage and ~14% for sewage sludge) and a higher reduction of volatile solids and total ammonia for maize silage (by ~8% and ~4%, respectively). Metagenomic analysis of the microbial community structure showed that the addition of both mineral sorbents influenced the presence of key members of archaea and bacteria occurring in a well-operated biogas reactor. The significant difference between zeolite and halloysite is that the latter promoted the immobilization of key methanogenic archaea Methanolinea (belong to Methanomicrobia class). Based on this result, we postulate that halloysite could be useful not only as a sorbent for (bio)gas treatment methodologies but also as an agent for improving biogas production.

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.

Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L⁻¹ d⁻¹ was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L⁻¹ d⁻¹ loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VS_des generation and carbon conversion efficiency (72.56 ± 3.40 mL g⁻¹ and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

Effects of thermal hydrolytic pre-treatment on biogas process efficiency and microbial community structure in industrial- and laboratory-scale digesters

This study examined the impact of thermal hydrolysis process (THP) pre-treatment on anaerobic co-digestion of wastewater sludge and household waste and assessed whether THP was vital to achieve higher process capacity. Performance data were collected for both industrial- and laboratory-scale digesters and response in microbial community structure was evaluated by Illumina sequencing. Implementation of THP at the industrial-scale plant increased methane yield by 15% and enhanced substrate degradability. Possibility to extend the sludge retention time due to a higher solid content of the substrate, sanitisation of the digestate and improved fertiliser quality of the digestate were other industrial-scale benefits of THP installation. Continuously-fed laboratory-scale digesters were fed THP-treated or untreated substrate at an organic loading rate (OLR) of 5 g volatile solid (VS)/L/day, a feeding rate necessary at the corresponding industrial-scale plant to meet the estimated population increase within the municipality. The results indicated that the plant could have increased the capacity with unimpaired stability independently of THP installation, even though the retention time was significantly shortened during operation with untreated substrate. Microbial community analyses revealed increased contribution of the Clostridia class after THP installation in industrial-scale digesters and positive correlation between Firmicutes:Bacteriodetes and methane yield in all digesters. Differentiated profiles in laboratory-scale digesters indicated that a temperature increase from 37 to 42 °C in association with THP installation and altered substrate composition were strong determining factors shaping the microbial community. Overall, these findings can assist industrial-scale plants in choosing management strategies aimed at improving the efficiency of anaerobic digestion processes.

Anaerobic Digestion Technology for Methane Production Using Deer Manure Under Different Experimental Conditions

Anaerobic digestion (AD) is an important technology for the treatment of livestock and poultry manure. The optimal experimental conditions were studied, with deer manure as a fermentation material and mushroom residue as an inoculum. At the same time, methane production was increased by adding zeolite and changing the magnetic field conditions. The results showed that a 6% solid content was the best condition for producing methane. The optimal conditions for methane production were obtained by adding 35 g of mushroom residue to 80 g of deer manure at 35 °C. The addition of organic wastewater (OW) improved methane production. The result of improving the methane production factor showed that adding zeolite during the reaction process could increase the methane production rate. When the amount of zeolite was over 8% total solids (TSes), methane production could improve, but the rate decreased. Setting a different magnetic field strength in the AD environment showed that when the distance between the magnetic field and the reactor was 50 mm and the magnetic field strength was 10–50 mT, the methane production increment and the content of methane in the mixed gases increased.

Draft genome sequence data and analysis of Brachybacterium sp. strain EE-P12 isolated from a laboratory-scale anaerobic reactor

The species of the genus Brachybacterium belonging to the family Dermabacteraceae within the phylum Actinobacteria are gram-positive, facultatively anaerobic or aerobic, nonmotile and nonsporeforming bacteria. Cells of Brachybacterium spp. vary in shape from coccoid forms (stationary phase) to rods (exponential phase). Brachybacterium species can be isolated from numerous sources such as poultry deep litter, human gut, soil, food products. Here we describe the draft genome sequence of Brachybacterium sp. EE-P12 that was isolated from a laboratory-scale anaerobic digester. The genome sequencing generated 3,964,988 bp, with a G+C content of 72.2%. This draft genome data has been deposited at DDBJ/ENA/GenBank under the accession number QXCP00000000 (https://www.ncbi.nlm.nih.gov/nuccore/QXCP00000000).

Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.

Draft genome sequence of Staphylococcus sp. EZ-P03 isolated from a mesophilic anaerobic digester

OBJECTIVES

Staphylococcus species of the family Staphylococcaceae are facultatively anaerobic Gram-positive cocci growing in clusters, pairs and occasionally in short chains. Staphylococci can be detected in different environments. They are common commensals, but some can also cause infections in humans. Hence, their investigation is required to understand ecology and genetics and to create an opportunity for comparative studies.

DATA DESCRIPTION

In this study, we report the determination of a draft genome sequence of Staphylococcus sp. strain EZ-P03 which was isolated from anaerobically digested chicken waste materials. The draft genome of Staphylococcus sp. EZ-P03 constituted a total of 62 contigs (> 500 bp) amounting to 2,689,358 bp with a G+C content of 37.3% and a N50 contig size of 126,562 bp. The whole genome shotgun project of Staphylococcus sp. strain EZ-P03 has been deposited at DDBJ/ENA/GenBank under the accession number QPMO00000000.

Draft genome sequence of Bacillus pumilus strain EZ-C07 isolated from digested agricultural wastes

Objectives

Bacillus species, belonging to the family Bacillaceae, are rod-shaped aerobic or facultative anaerobic Gram-positive bacteria that can be isolated from various environmental niches. Bacillus pumilus strains are resistant to unfavorable conditions such as UV, H₂O₂ and chemical disinfection. Furthermore, B. pumilus strains synthesize multifarious important enzymes and can be used in the production of some fermented foods, bioremediation of wastewater systems and biodegradation of environmental contaminants. Hence, investigation at the genomic level is required to understand their ecology, genetics and potential applications.

Data description

In this research, we provide the genomic insights into one Bacillus species (EZ-C07) isolated from digested agricultural waste materials. The draft genome of the strain EZ-C07 consists of 3,724,869 bp with 3890 coding sequences and 41.5% G + C content. Based on 16S rRNA gene sequence analysis followed by in silico DNA–DNA hybridization studies, the strain EZ-C07 was identified as Bacillus pumilus belonging to the family Bacillaceae within the phylum Firmicutes. The whole genome shotgun project of B. pumilus strain EZ-C07 can be accessed at DDBJ/ENA/GenBank under the Accession QLVI00000000.

Improved process performance of the acidification phase in a two-stage anaerobic digestion of complex organic waste: Effects of an iron oxide-zeolite additive

Improvement of the acidification phase is an attractive alternative to break through the rate-limiting step in the two-phase anaerobic digestion of complex organic wastes. An additive named iron oxide-zeolite was introduced into the acidification phase at mesophilic and room temperature. By virtue of the additive supplemented, significantly improved hydrolysis/fermentation in regard to higher soluble chemical oxygen demand (sCOD) concentration (21.53-27.30%) and better lignocellulosic degradation at both temperatures has been obtained. Furthermore, an optimized volatile fatty acid formation type (more favorable acetate and less undesired propionate) has been achieved. The favorable environment of the acidogenic effluent facilitated the subsequent methanogenesis. The increased microbial community abundances of some hydrolytic, acetogenic and cellulolytic bacteria may provide the explanation on the promoted hydrolysis/acidogenesis. The results in this study suggested that supplementation of the iron oxide-zeolite into the acidification phase is a valuable alternative to improve hydrolysis/acidogenesis of the complex substrates.

Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae)

The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.

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.

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera)

Interpretation of how partnerships between fungi, bacteria, archaea, and insects are maintained through the life of the hosts is a big challenge within the framework of symbiosis research. The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. Thus, larvae with various food preferences, including Amphimallon solstitiale, Oryctes nasicornis, Cucujus cinnaberinus, Schizotus pectinicornis, Rhagium mordax, and Rhagium inquisitor, were thoroughly investigated in this work. We revealed an association of these beetle species mainly with four bacterial phyla, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, as well as with three fungal phyla, Ascomycota, Zygomycota, and Basidiomycota, but microbial communities varied depending on the beetle host, individual organism, and surrounding environment. Moreover, archaea within the phyla Euryarchaeota and Crenarchaeota in the hindgut content of O. nasicornis and A. solstitiale were additionally detected. The identified microbial communities suggest their potential role in the exploitation of various resources, providing nutritional needs for the host organism. These microorganisms can also represent a valuable source of novel metabolic capacities for their application in different biotechnologies.

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

To enrich syntrophic acetate‐oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)‐dominated systems and continuously supplied with acetate (0.4 or 7.5 g l⁻¹) at high‐ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64–69% and effluent acetate level of 0.4–1.0 g l⁻¹ were recorded in chemostats fed high acetate. Low methane production in the low‐acetate chemostats indicated that the substrate supply was below the threshold for methanization of acetate via SAO. Novel representatives within the family Clostridiales and genus Syntrophaceticus (class Clostridia) were identified to represent putative SAOB candidates in mesophilic and thermophilic conditions respectively. Known SAOB persisted at low relative abundance in all chemostats. The hydrogenotrophic methanogens Methanoculleus bourgensis (mesophilic) and Methanothermobacter thermautotrophicus (thermophilic) dominated archaeal communities in the high‐acetate chemostats. In line with the restricted methane production in the low‐acetate chemostats, methanogens persisted at considerably lower abundance in these chemostats. These findings strongly indicate involvement in SAO and tolerance to high ammonia levels of the species identified here, and have implications for understanding community function in stressed anaerobic processes.

Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations (‘low’ at 1.9, ‘high’ at 3.7 g L⁻¹, termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L⁻¹.

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

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

Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.