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

Unveiling the mechanisms of Fe(III)-loaded chitosan composite (CTS-Fe) in enhancing anaerobic digestion of waste activated sludge

Anaerobic digestion (AD) of waste activated sludge (WAS) is usually limited by the low generation efficiency of methane. Fe(III)-loaded chitosan composite (CTS-Fe) have been reported to effectively enhanced the digestion of WAS, but its role in promoting anaerobic sludge digestion remains unclear. In present study, the effects of CTS-Fe on the hydrolysis and methanogenesis stages of WAS anaerobic digestion were investigated. The addition of CTS-Fe increased methane production potential by 8%-23% under the tested conditions with the addition of 5-20 g/L CTS-Fe. Besides, the results demonstrate that the addition of CTS-Fe could effectively promote the hydrolysis of WAS, evidenced by lower protein or polysaccharides concentration, higher soluble organic carbon in rector adding CTS-Fe, as well as the increased activity of extracellular hydrolase with higher CTS-Fe concentration. Meanwhile, the enrichment of Clostridia abundance (iron-reducing bacteria (IRBs)) was observed in CTS-Fe adding reactor (8.9%-13.8%), which was higher than that in the control reactor (7.9%). The observation further suggesting the acceleration of hydrolysis through dissimilatory iron reduction (DIR) process, thus providing abundant substrates for methanogenesis. However, the presence of CTS-Fe was inhibited the acetoclastic and hydrogenotrophic methanogenesis process, which could be ascribed to the Fe(III) act as electron acceptor coupled to methane for anaerobic oxidation. Furthermore, coenzyme F420 activity in the CTS-Fe added reactor was 34.9% lower than in the blank, also abundance of microorganisms involved in hydrogenotrophic methanogenesis was decreased. Results from this study could provide theoretical support for the practical applications of CTS-Fe.

Sodium butyrate reduces ammonia emissions through glutamate metabolic pathways in cecal microorganisms of laying hens

Ammonia emission is an important problem that needs to be solved in laying hen industries. Sodium butyrate (SB) is considered to have potential for reducing ammonia production because of its ability to improve nitrogen metabolism. In this in vitro fermentation study, we presented a correlation analysis of the metatranscriptome and metaproteome of lay hen cecal microorganisms, in order to identify important proteins and pathways involved in ammonia production reduction due to sodium butyrate supplementation. The results showed that sodium butyrate supplement decreased the production of ammonia by 26.22% as compared with the non-sodium butyrate supplementation (CK) group. The SB group exhibited a lower concentration of ammonium nitrogen (NH₄⁺-N) and a decreased pH. Sodium butyrate promoted the uric acid concentration and lowered the uricase activity in the fermentation broth of laying hens cecal content. Notably, the 'alanine, aspartate and glutamate metabolism' category was more abundant in the SB group. The addition of sodium butyrate increased the expression of glutamate dehydrogenase (GDH) gene in cecal microbiota (e.g., Ruminococcus sp. and Bacteroides sp.) in vitro. The metaproteome analysis results showed that the expression of GDH with NADPH as coenzyme (NADPH-GDH) was up-regulated in cecal microbiota by sodium butyrate supplement. Our results indicate that sodium butyrate can affect glutamate metabolism through regulating the expression of glutamate dehydrogenase in cecal microorganisms, thereby reducing ammonia production. This study reveals that glutamate dehydrogenase-mediated glutamate metabolism play a key role in ammonia emission reduction in laying hen and provide theoretical basis for further developing ammonia production reduction approach.

Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes

Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.

Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies

Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.

Archaeal community dynamics in biogas fermentation at various temperatures assessed by mcrA amplicon sequencing using different primer pairs

In this study, the taxonomic and functional diversity of methanogenic archaea in two parallel 120 l fermenters operated at different temperatures and fed with maize silage was estimated by mcrA metabarcoding analysis using two typical primer pairs (ML and MLA) amplifying part of the functional methyl coenzyme M reductase (mcrA) gene. The alpha diversity indices showed that the ML primer pair detected a higher Operational Taxonomic Unit (OTU) abundance compared to the MLA primer pair and methanogen diversity was significantly lower in the 60 °C fermenters. The beta diversity analysis showed the methanogenic community clustered together at 50 °C and 40° and was statistically different from the 60 °C community. Similar, to alpha diversity, beta diversity was also significantly different between primer pairs. At all temperatures analysed, the primer pairs showed a different abundance of the different methanogenic OTUs, e.g. more OTUs relative to Methanoculleus sp. with the ML primer pair, and more OTUs corresponding to Methanobacterium sp. with the MLA primer pair. Moreover, OTUs corresponding to Methanosphaera sp. and Methanobrevibacter sp. were found only by using ML primer pair, while the MLA primer pair detected sequences corresponding to Methanothrix sp.

Microbiome signature and diversity regulates the level of energy production under anaerobic condition

The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH₄%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH₄, respectively. The physicochemical analysis revealed that level of energy production (CH₄%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O₂ level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH₄ concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH₄ producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH₄ concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.

Microbial adaptation and response to high ammonia concentrations and precipitates during anaerobic digestion under psychrophilic and mesophilic conditions

This study explored microbial adaptation to high ammonia concentrations (<1000 mg/L to 4000 mg/L) during anaerobic digestion (AD) under psychrophilic and mesophilic conditions, the latter of which yielded precipitates facilitating investigation of microbial response. The experimental setup was performed at bench-scale using microbial consortia from four different operating anaerobic digesters treating different organic wastes (WW-wastewater sludge, MN-manure, FW- food waste and CO-co-digestion (FW & MN)). Adaptation experiments were conducted with semi-continuous flow mode to resemble large-scale operation. Metagenome and 16S RNA analysis were performed for the first time in a psychrophilic reactor during an ammonia acclimation process. These analyses were also performed in mesophilic reactor exposed to precipitates and high ammonia levels. Diversity reduced when adaptation occurred successfully from 1.1 to 4 g/L of total ammonia nitrogen (TAN) under psychrophilic conditions, while the microbial community became more diverse under mesophilic conditions with ammonia inhibition. We report for the first time Methanocorposculum as a robust hydrogenotrophic methanogen at high ammoniacal concentrations under psychrophilic conditions. Additionally, Methanosarcina was present in low and high ammoniacal concentrations in mesophilic conditions, but there was a shift in species dominance. Methanosarcina barkeri stands out as a more resilient methanogen compared to Methanosarcina mazei, which initially dominated at <1.1 g/L TAN. We also explored the effects of sudden precipitates on methanogenic communities and methane production when they occurred under mesophilic conditions in two reactors. Methane production declined by more than 50% when precipitates occurred and was accompanied by pH reduction and VFA accumulation. Diversity data corroborated that methanogens were severely reduced. These two reactors were not able to recover with 50 days of added operation, demonstrating potential for long-term negative impacts of precipitate formation on AD performance stemming from negative impact to methanogenic communities.

Effects of organic loading rate and hydraulic retention time on bioaugmentation performance to tackle ammonia inhibition in anaerobic digestion

Three continuously stirred-tank reactors fed with manure operating under high ammonia levels (5.0 g NH3-N L-1) and with increased organic loading rate (OLR), (2.09 R1, 3.02 R2 and 4.0 R3 g VS L-1 d-1), achieved through glucose amendment in R2 and R3, were inoculated with an ammonia-acclimatized microbial culture. Successful bioaugmentation was endured only in R2 and R3, both reactors characterized by high OLR, resulting in 19.6 and 24.5% increase in methane production, respectively. The high OLRs in these reactors favored the co-occurrence of the hydrogenotrophic (Methanobacteriaceae), methylotrophic (Methanomethylophilaceae) and aceticlastic methanogenic pathways. The latter was supported by the successful establishment of ammonium-tolerant Methanosarcina, prevailing in the inoculum. Oppositely in R1, the low OLR prevented the establishment of Methanosarcina, leading to an exclusive hydrogenotrophic methanogenesis and reduced methane production. HRT shortening resulted in limited effect on biomethane performance, indicating a well establishment of the introduced bioaugmentation culture in the reactors.

Effects of inhibitions by sodium ion and ammonia and different inocula on acetate-utilizing methanogenesis: Methanogenic activity and succession of methanogens

Acetate-fed anaerobic sequential batch experiments with four different inhibitory conditions (non-inhibitory (Lo), sodium-ion inhibitory (Na), ammonia inhibitory (Am), combined inhibitory (Hi)) were conducted using thirteen different inocula to investigate the inhibition effects by sodium-ion and ammonia and different inocula on acetate-utilizing methanogenesis and succession of methanogens. Sodium-ion and ammonia significantly extended lag-time λ and reduced specific-methanogenic-activity RCH4, and caused synergistic inhibition. The inhibition differed according to the initial methanogen community structures: the inhibition effects on λ and RCH4 were strongest ininocula with Methanosaeta concilii dominant and weakest in inocula with Methanoculleus bourgensis dominant. These inhibitory conditions determined the succession of methanogens: the most competitive methanogens were Methanosaeta concilii in Lo, Methanosarcina sp. in Na, Methanosarcina sp. and Methanoculleus bourgensis in Am, Methanoculleus bourgensis in Hi. This study provides valuable information for microbial management and optimization for AD processes treating wastewater that is rich in protein and/or salt.

High-rate blackwater anaerobic digestion under septic tank conditions with the amendment of biosolids-derived biochar synthesized at different temperatures

Septic tanks have been widely used for blackwater treatment in developing countries, while high-rate septic tanks with improved methane recovery are yet to be achieved. This study investigated biosolids-derived biochar (synthesized at 300℃, 425℃, and 550℃) as an additive for developing high-rate septic tanks. The experiments were conducted with anaerobic bioreactors operated with synthetic blackwater under septic tank conditions. All biochar amended reactors demonstrated a steady increase in daily methane production for increasing OLR from 0.08 to 3 g COD/L/d. The control reactor showed significant process disturbances at OLRs ≥ 2 g COD/L/d with an accumulation of volatile fatty acids followed by pH drop. At OLR of 3 g COD/L/d, the daily methane production from biochar amended reactors was ~ 4.3 times higher than the control (300 vs. 70 mL per day). Biochar addition established a robust microbiome consisted of a higher abundance of hydrogenotrophic and acetoclastic methanogens and hydrogen-producing fermentative bacteria.

Effect of mixing duration on biogas production and methanogen distribution in an anaerobic digester

Mixing has been shown to have effect on biogas production in anaerobic digestion systems. To further examine this impact, a study was designed to evaluate nearly continuous mixing (mixing for 15 min followed by no mixing for 15 min, CON), intermediate mixing (mixing for 15 min followed by no mixing for 45 min, INT) and no mixing (unmixed, NO) on biogas production in three 208 L pilot-scale tank reactors. The experiments were conducted in triplicates at a controlled temperature of 37 ± 1°C, with a total solids percentage of 5%, a hydraulic retention time (HRT) of 21 days, and an organic loading rate (OLR) of 2 kg VS m^-3 d^{- 1}. Digesters with NO mixing had greater solids build up in the bottom quarter of the digester after four weeks' retention time. The methane percentage in biogas produced from digesters with INT and CON mixing were 63% and 62%, respectively, which were 4% and 5% higher than that from digesters with NO mixing (58%). The specific methane yield for digesters with NO, INT and CON mixing was 1.15, 1.15, and 1.49 m³-methane per kg-VS destroyed, however, those differences were not statistically significant (p > 0.05). Digesters had the least amount of Methanosarcinales of the methanogens measured under all treatments. However, the Methanosarcinales, Methanosarcinaceae, Methanomicrobiales, and the total amount of methanogens were less in digesters with INT mixing compared to NO and CON mixing treatments.

Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Direct interspecies electron transfer (DIET) can be suppressed under ammonia-stressed condition - Reevaluate the role of conductive materials

Thermal hydrolysis pretreatment (THP) and anaerobic digestion (AD) integrated (THP-AD) process is a promising process for sludge management. However, the high ammonia production during the THP-AD process severely affects system's stability and performance. Conductive materials are widely reported to stimulate AD, thus they are potentially helpful in alleviating ammonia inhibition. This study investigated the effects of three widely studied conductive materials, i.e. zero-valent iron (ZVI), magnetite nanoparticles (Mag.) and powder activated carbon (PAC), on THP-AD process. Results showed that all the tested materials could effectively stimulate methanogenesis process under non-ammonia inhibition conditions. However, upon ammonia stress, these materials behaved distinctively with the best methanogenic performance in ZVI group followed by Mag. Group, and even worsened inhibition occurred in PAC group. The mechanisms behind were investigated from two levels-the reaction kinetics of each anaerobic digestion step and the responses of intracellular metabolism. It is revealed that ZVI effectively promoted all AD reactions, especially the energy unfavorable propanoate and butanoate metabolism and overall methanogenesis. In addition, ZVI likely acted as intracellular electron shuttles, and the conjunction point of ZVI to electron transfer system was identified as EtfAB: quinone oxidoreductase. On the contrary, the declined methanogenic performance in PAC group was attributed to selectively stimulated the growth of acetoclastic methanogen - Methanosaeta, which is sensitive to ammonia toxicity. The proteomic information further revealed that ammonia stress was unfavorable to the formation of direct interspecies electron transfer between syntrophic anaerobes. Overall, the present study provides fundamental knowledge about the role of different conductive materials in AD systems from intracellular proteomic level.

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.

Effect of a Profound Feedstock Change on the Structure and Performance of Biogas Microbiomes

In this study the response of biogas-producing microbiomes to a profound feedstock change was investigated. The microbiomes were adapted to the digestion of either 100% sugar beet, maize silage, or of the silages with elevated amounts of total ammonium nitrogen (TAN) by adding ammonium carbonate or animal manure. The feedstock exchange resulted in a short-range decrease or increase in the biogas yields according to the level of chemical feedstock complexity. Fifteen taxa were found in all reactors and can be considered as generalists. Thirteen taxa were detected in the reactors operated with low TAN and six in the reactors with high TAN concentration. Taxa assigned to the phylum Bacteroidetes and to the order Spirochaetales increased with the exchange to sugar beet silage, indicating an affinity to easily degradable compounds. The recorded TAN-sensitive taxa (phylum Cloacimonetes) showed no specific affinity to maize or sugar beet silage. The archaeal community remained unchanged. The reported findings showed a smooth adaptation of the microbial communities, without a profound negative impact on the overall biogas production indicating that the two feedstocks, sugar beet and maize silage, potentially do not contain chemical compounds that are difficult to handle during anaerobic digestion.

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

BACKGROUND

Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.

RESULTS

Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain.

CONCLUSIONS

The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

Microbiome digital signature of MCR genes - an in silico approach to study the diversity of methanogenic population in laboratory-developed and pilot-scale anaerobic digesters

The production of biogas by anaerobic digestion (AD) of organic/biological wastes has a firm place in sustainable energy production. A simple and cost-effective anaerobic jar at a laboratory scale is a prerequisite to study the microbial community involved in biomass conversion and releasing of methane gas. In this study, a simulation was carried out using a laboratory-modified anaerobic-jar-converted digester (AD1) with that of a commercial/pilot-scale anaerobic digester (AD2). Taxonomic profiling of biogas-producing communities by means of high-throughput methyl coenzyme-M reductase α-subunit (mcrA) 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 Euryarchaeota, Chordata, Firmicutes and Proteobacteria appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Key micro-organisms identified from AD were Methanocorpusculum labreanum and Methanobacterium formicicum. Specific biogas production was found to be significantly correlating to Methanosarcinaceae. It can be implied from this study that the metagenomic sequencing data was able to dissect the microbial community structure in the digesters. The data gathered indicates that the anaerobic-jar system could throw light on the population dynamics of the methanogens at laboratory scale and its effectiveness at large-scale production of bio-methane. The genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies will be highly valuable in determining the efficacy of an anaerobic digester.

Effects of H2:CO2 ratio and H2 supply fluctuation on methane content and microbial community composition during in-situ biological biogas upgrading

BACKGROUND

Commercial biogas upgrading facilities are expensive and consume energy. Biological biogas upgrading may serve as a low-cost approach because it can be easily integrated with existing facilities at biogas plants. The microbial communities found in anaerobic digesters typically contain hydrogenotrophic methanogens, which can use hydrogen (H₂) as a reducing agent for conversion of carbon dioxide (CO₂) into methane (CH₄). Thus, biological biogas upgrading through the exogenous addition of H₂ into biogas digesters for the conversion of CO₂ into CH₄ can increase CH₄ yield and lower CO₂ emission.

RESULTS

The addition of 4 mol of H₂ per mol of CO₂ was optimal for batch biogas reactors and increased the CH₄ content of the biogas from 67 to 94%. The CO₂ content of the biogas was reduced from 33 to 3% and the average residual H₂ content was 3%. At molar H₂:CO₂ ratios > 4:1, all CO₂ was converted into CH₄, but the pH increased above 8 due to depletion of CO₂, which negatively influenced the process stability. Additionally, high residual H₂ content in these reactors was unfavourable, causing volatile fatty acid accumulation and reduced CH₄ yields. The reactor microbial communities shifted in composition over time, which corresponded to changes in the reactor variables. Numerous taxa responded to the H₂ inputs, and in particular the hydrogenotrophic methanogen Methanobacterium increased in abundance with addition of H₂. In addition, the apparent rapid response of hydrogenotrophic methanogens to intermittent H₂ feeding indicates the suitability of biological methanation for variable H₂ inputs, aligning well with fluctuations in renewable electricity production that may be used to produce H₂.

CONCLUSIONS

Our research demonstrates that the H₂:CO₂ ratio has a significant effect on reactor performance during in situ biological methanation. Consequently, the H₂:CO₂ molar ratio should be kept at 4:1 to avoid process instability. A shift toward hydrogenotrophic methanogenesis was indicated by an increase in the abundance of the obligate hydrogenotrophic methanogen Methanobacterium.

Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors

The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H₂. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.

Ammonia stress on a resilient mesophilic anaerobic inoculum: Methane production, microbial community, and putative metabolic pathways

Short term inhibition tests, 16S rRNA tag sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), were employed to visualise the effects of increasing total ammoniacal nitrogen (TAN) concentration (3400-10166 ppm TAN) on microbial community structure and metabolic pathways for acetate degradation. The rate of methane production on acetate was significantly reduced by TAN concentrations above 6133 ppm; however, methane continued to be produced, even at 10166 ppm TAN (0.026 ± 0.0003 gCOD.gVS^-1_inoculum.day^-1). Hydrogenotrophic methanogenesis with syntrophic acetate oxidation (SAO) was identified as the dominant pathway for methane production. A shift towards SAO pathways at higher TAN concentrations and a decrease in the number of 'gene hits' for key genes in specific methanogenesis pathways was observed. Overall, the results highlighted potential for inhibition activity testing to be used together with PICRUSt, to estimate changes in microbial metabolism and to better understand microbial resilience in industrial AD facilities.

Functional biodiversity and plasticity of methanogenic biomass from a full-scale mesophilic anaerobic digester treating nitrogen-rich agricultural wastes

The effect of ammonia on methanogenic biomass from a full-scale agricultural digester treating nitrogen-rich materials was characterized in batch activity assays subjected to increasing concentrations of total ammonia N. Acetotrophic and methanogenic profiles displayed prolonged lag phases and reduced specific activity rates at 6.0 gN-TAN L^-1, though identical methane yields were ultimately reached. These results agreed with the expression levels of selected genes from bacteria and methanogenic archaea (qPCR of 16S rRNA and mrcA cDNA transcripts). Compound-specific isotope analysis of biogas indicated that ammonia exposure was associated to a transition in methanogenic activity from acetotrophy at 1.0 gN-TAN L^-1 to intermediate and complete hydrogenotrophy at 3.5 and 6.0 gN-TAN L^-1. Such pattern matched the results of 16S-Illumina sequencing of genes and transcripts in that predominant methanogens shifted, along with increasing ammonia, from the obligate acetotroph Methanosaeta to the hydrogenotrophic Methanoculleus and the poorly understood methylotrophic Methanomassiliicoccus. The underlying bacterial community structure remained rather stable but, at 6.0 gN-TAN L^-1, the expression level increased considerably for a number of ribotypes that are related to potentially syntrophic genera (e.g. Clostridium, Bellilinea, Longilinea, and Bacteroides). The predominance of hydrogenotrophy at high ammonia levels clearly points to the occurrence of the syntrophic acetate oxidation (SAO), but known SAO bacteria were only found in very low numbers. The potential role of the identified bacterial and archaeal taxa with a view on SAO and on stability of the anaerobic digestion process under ammonia stress has been discussed.

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.

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.

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.

A New Combination of Substrates: Biogas Production and Diversity of the Methanogenic Microorganisms

Agriculture, food industry, and manufacturing are just some of the areas where anaerobic technology can be used. Currently, anaerobic technologies are mainly used for wastewater treatment, solid waste treatment, or for the production of electrical and thermal energy from energy crops processing. However, a clear trend is towards more intensive use of this technology in biomass and biodegradable waste processing and hydrogen or biomethane production. An enormous number of anaerobic digesters are operating worldwide but there is very little information about the effect of different substrate combinations on the methanogens community. This is due to the fact that each of the anaerobic digesters has its own unique microbial community. For the most effective management of anaerobic processes it would be important to know the composition of a consortium of anaerobic microorganisms present in anaerobic digesters processing different input combinations of raw material. This paper characterizes the effect of the input raw materials on the diversity of the methanogen community. Two predominant microorganisms in anaerobic digesters were found to be 99% identity by the sequences of the 16S rRNA gene to the Methanoculleus and Thermogymnomonas genera deposited in GenBank.

Effects of graphene oxide on the performance, microbial community dynamics and antibiotic resistance genes reduction during anaerobic digestion of swine manure

The role of graphene oxide (GO) on anaerobic digestion (AD) of swine manure concerning the performance, microbial community and antibiotic resistance genes (ARGs) reduction was investigated. Results showed that methane production was reduced by 13.1%, 10.6%, 2.7% and 17.1% at GO concentration of 5mg/L, 50mg/L, 100mg/L and 500mg/L, respectively, but propionate degradation was enhanced along with GO addition. Both bacterial and archaeal community changed little after GO addition. AD could well reduce ARGs abundance, but it was deteriorated at the GO concentration of 50mg/L and 100mg/L and enhanced at 500mg/L, while no obvious changes at 5mg/L. Network and SEM analysis indicated that changes of each ARG was closely associated with variation of microbial community composition, environmental variables contributed most to the dynamics of ARGs indirectly, GO influenced the ARGs dynamics negatively and (heavy metal resistance genes (MRGs)) influenced the most directly.

Assessing the performance and microbial structure of biofilms adhering on aerated membranes for domestic saline sewage treatment

MABR for effective treatment of domestic saline sewage and its microbial community.

Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment

Activated sludge is essential for the biological wastewater treatment process and the identification of active microbes enlarges awareness of their ecological functions in this system.