Reactor performances and microbial communities of biogas reactors: effects of inoculum sources

Evaluation of the optimal sewage sludge pre-treatment technology through continuous reactor operation: Process performance and microbial community insights

This study investigated the impact of two low-temperature thermal pre-treatments on continuous anaerobic reactors' performance, sequentially fed with sludge of different total solids content (∼3 % and ∼6 %) and subjected to progressively increasing Organic Loading Rates (OLR) from 1.0 to 2.5 g volatile solids/(LReactor⋅day). Assessing pre-treatments' influence on influent sludge characteristics revealed enhanced organic matter hydrolysis, facilitating sludge solubilization and methanogenesis; volatile fatty acids concentration also increased, particularly in pre-treated sludge of ∼6 % total solids, indicating improved heating efficiency under increased solids content. The reactor fed with sludge pre-treated at 45 °C for 48 h and 55 °C for an extra 48 h exhibited the highest methane yield under all applied OLRs, peaking at 240 ± 3.0 mL/g volatile solids at the OLR of 2.5 g volatile solids/(LReactor⋅day). 16S rRNA gene sequencing demonstrated differences in the reactors' microbiomes as evidence of sludge thickening and the different pre-treatments applied, which promoted the release of organic matter in diverse concentrations and compositions. Finally, the microbial analysis revealed that specific foam-related genera increased in abundance in the foam layer of reactors' effluent bottles, dictating their association with the sludge foaming incidents that occurred inside the reactors during their operation at 2.0 g volatile solids/(LReactor⋅day).

Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions

Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.

Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production

Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.

Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics

The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4+/LR and 5 g NH4+/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for control of natural and engineered systems. Discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28 d microcosm incubations to examine microbial community compositional and functional stability during plant-litter decomposition. Using DOC abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a "low DOC" phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as 1 solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. Importance Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

IMPORTANCE

Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

Investigating Variability in Microbial Fuel Cells

In scientific studies, replicas should replicate, and identical conditions should produce very similar results which enable parameters to be tested. However, in microbial experiments which use real world mixed inocula to generate a new "adapted" community, this replication is very hard to achieve. The diversity within real-world microbial systems is huge, and when a subsample of this diversity is placed into a reactor vessel or onto a surface to create a biofilm, stochastic processes occur, meaning there is heterogeneity within these new communities. The smaller the subsample, the greater this heterogeneity is likely to be. Microbial fuel cells are typically operated at a very small laboratory scale and rely on specific communities which must include electrogenic bacteria, known to be of low abundance in most natural inocula. Microbial fuel cells (MFCs) offer a unique opportunity to investigate and quantify variability as they produce current when they metabolize, which can be measured in real time as the community develops. In this research, we built and tested 28 replica MFCs and ran them under identical conditions. The results showed high variability in terms of the rate and amount of current production. This variability perpetuated into subsequent feeding rounds, both with and without the presence of new inoculate. In an attempt to control this variability, reactors were reseeded using established "good" and "bad" reactors. However, this did not result in replica biofilms, suggesting there is a spatial as well as a compositional control over biofilm formation. IMPORTANCE The research presented, although carried out in the area of microbial fuel cells, reaches an important and broadly impacting conclusion that when using mixed inoculate in replica reactors under replicated conditions, different communities emerge capable of different levels of metabolism. To date there has been very little research focusing on this, or even reporting it, with most studies using duplicate or triplicate reactors, in which this phenomenon is not fully observed. Publishing data in which replicas do not replicate will be an important and brave first step in the research into understanding this fundamental microbial process.

Bioaugmentation with well-constructed consortia can effectively alleviate ammonia inhibition of practical manure anaerobic digestion

Bioaugmentation is an attractive method to improve methane production (MP) in the anaerobic digestion (AD) process. In this study, to tackle the ammonia inhibition problem, a long-term (operating over 6 months) acclimatized consortia and a well-constructed consortia were selected as the bioaugmentation consortia for sequencing batch AD reactors fed with dairy manure and pig manure under mesophilic condition. Similar responses, in terms of the reactor performance and microorganisms structure to the different consortia, were observed with both manure kinds indicating that the effectiveness of bioaugmentation was mainly decided by the composition of the added consortia, not the feedstock. 39 - 49% increment in MP was obtained in the reactors bioaugmented with well-constructed consortia, which was higher than the acclimatized consortia (about 25% increment in MP). Both acetogenesis and methanogenesis (advantageous) steps were stimulated with well-constructed consortia bioaugmentation. According to key functional enzyme analysis, the increment of glycine hydroxymethyltransferase and phosphoglycerate mutase might be the critical point in the bioaugmented AD system. Based on the higher functional contribution rate of the well-constructed consortia bioaugmentation reactors, Methanosarcina could have expressed more comprehensive functions or performed stronger activities in different functions than Methanosaeta.

Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste

Future manned space travel will require efficient recycling of nutrients from organic waste back into food production. Microbial systems are a low-energy, efficient means of nutrient recycling, but their use in a life support system requires predictability and reproducibility in community formation and reactor performance. To assess the reproducibility of microbial community formation in fixed-film reactors, we inoculated replicate anaerobic reactors from two methanogenic inocula: a lab-scale fixed-film, plug-flow anaerobic reactor and an acidic transitional fen. Reactors were operated under identical conditions, and we assessed reactor performance and used 16s rDNA amplicon sequencing to determine microbial community formation. Reactor microbial communities were dominated by similar groups, but differences in community membership persisted in reactors inoculated from different sources. Reactor performance overlapped, suggesting a convergence of both reactor communities and organic matter mineralization. The results of this study suggest an optimized microbial community could be preserved and used to start new, or restart failed, anaerobic reactors in a life support system with predictable reactor performance.

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions

Anaerobic digestion is a promising method for energy recovery through conversion of organic waste to biogas and other industrial valuables. However, to tap the full potential of anaerobic digestion, deciphering the microbial metabolic pathway activities and their underlying bioenergetics is required. In addition, the behavior of organisms in consortia along with the analytical abilities to kinetically measure their metabolic interactions will allow rational optimization of the process. This review aims to explore the metabolic bottlenecks of the microbial communities adopting latest advances of profiling and ¹³C tracer-based analysis using state of the art analytical platforms (GC, GC-MS, LC-MS, NMR). The review summarizes the phases of anaerobic digestion, the role of microbial communities, key process parameters of significance, syntrophic microbial interactions and the bottlenecks that are critical for optimal bioenergetics and enhanced production of valuables. Considerations into the designing of efficient synthetic microbial communities as well as the latest advances in capturing their metabolic cross talk will be highlighted. The review further explores how the presence of additives and inhibiting factors affect the metabolic pathways. The critical insight into the reaction mechanism covered in this review may be helpful to optimize and upgrade the anaerobic digestion system.

Effect of microbial community structure in inoculum on the stimulation of direct interspecies electron transfer for methanogenesis

To investigate how the seed microbial community structure affects the improvement of methanogenesis efficiency through direct interspecies electron transfer (DIET), a biomethane potential (BMP) test was conducted using sludge collected from a total of six anaerobic digesters. DIET-stimulating microbial populations were investigated by 16S rRNA gene sequence analysis. Correlations between microbial community composition and methane production performance by DIET were analyzed. The methane production rate increased under all conditions when granular activated carbon (GAC) was injected regardless of the inoculum type. However, redundancy analysis indicated a significant correlation between the inoculum microbial community and lag time. In a network analysis, Methanolinea species distributed in the inocula formed a single modularity with lag time, suggesting that the methanogens in the inocula might reduce the lag time of methanogenesis through DIET. Overall, this study revealed that the inoculum microbial community composition is an important factor affecting methane production efficiency by DIET.

Evolution of the microbial community structure in biogas reactors inoculated with seeds from different origin

The aim of this work was to provide solid proofs regarding the achievement of "steady-state conditions", which means that the performance of the anaerobic digester is representative of the applied environmental conditions. For this reason, we investigated how, starting from different inoculum sources (i.e., municipal wastewater treatment, bio-waste treatment, and agricultural waste biogas plant), the microbial community adapted to the operational parameters and led to stable biogas production in thermophilic digesters treating the same influent feedstock. The results revealed that the different system achieved similar process performance and microbial community structure after a period that was equal to four hydraulic retention times, approved by a constant pH of 7.89 ± 0.08, 7.92 ± 0.05 and 7.85 ± 0.08, respectively, and stable TAN concentration of 1500 mg/L. Moreover, it was found that the microbial composition of the inocula was a key factor for the speed of achieving stable process performance; thus, a pre-adapted to the influent feedstock inoculum can shorten the stabilization process. On the contrary, after long term reactor operation, the microbial structure was shaped according to the chemical composition of the influent feedstock. The results of the study can also be used as a guide in future researches on anaerobic degradation, particularly in determining the time interval of an experiment to reflect changes in the microbial community of anaerobic digester.

Perspectives on microbial community in anaerobic digestion with emphasis on environmental parameters: A systematic review

This paper review is aiming to comprehensively identify and appraise the current available knowledge on microbial composition and microbial dynamics in anaerobic digestion with focus on the interconnections between operational parameters and microbial community. We systematically searched Scopus, Web of Science, pubmed and Embase (up to August 2019) with relative keywords to identify English-language studies published in peer-reviewed journals. The data and information on anaerobic reactor configurations, operational parameters such as pretreatment methods, temperature, trace elements, ammonia, organic loading rate, and feedstock composition and their association with the microbial community and microbial dynamics were extracted from eligible articles. Of 306 potential articles, 112 studies met the present review objectives and inclusion criteria. The results indicated that both aceticlastic and hydrogenotrophic methanogenesis are dominant in anaerobic digesters and their relative composition is depending on environmental conditions. However, hydrogenotrophic methanogens are more often observed in extreme conditions due to their higher robustness compared to aceticlastic methangoens. Firmicutes and Bacteroidetes phyla are most common fermentative bacteria of the acidogenic phase. These bacteria secrete lytic enzymes to degrade organic matters and are able to survive in extreme conditions and environments due to their spores. In addition, among archaea Methanosaeta, Methanobacterium, and Methanosarcinaceae are found at high relative abundance in anaerobic digesters operated with different operational parameters. Overall, understanding the shifts in microbial composition and diversity as results of operational parameters variation in anaerobic digestion process would improve the stability and process performance.

A spiking neural network-based long-term prediction system for biogas production

Efficient energy production from biomass is a central issue in the context of clean alternative energy resource. In this work we propose a novel model based on spiking neural networks cubes in order to model the chemical processes that goes on in a digestor for the production of usable biogas. For the implementation of the predictive structure, we have used the NeuCube computational framework. The goals of the proposed model were: develop a tool for real applications (low-cost and efficient), generalize the data when the system presents high sensitivity to small differences on the initial conditions, take in account the "multi-scale" temporal dynamics of the chemical processes occurring in the digestor, since the variations present in the early stages of the processes are very quick, whereas in the later stages are slower. By using the first ten days of observation the implemented system has been proven able to predict the evolution of the chemical process up to the 100th day obtaining a high degree of accuracy with respect to the experimental data measured in laboratory. This is due to the fact that the spiking neural networks have shown to be able to modeling complex information processes and then it has been shown that spiking neurons are able to handle patterns of activity that spans different time scales. Thanks to such properties, our system is able to capture the multi-scale trend of the time series associated to the early-stage evolutions, as well as their interaction, which are crucial in the point of view of the information content to obtain a good long-term prediction.

Exploration and enrichment of methane-oxidizing bacteria derived from a rice paddy field emitting highly concentrated methane

Methane-oxidizing bacteria (MOB) possess the metabolic potential to assimilate the highly potent greenhouse gas, CH₄, and can also synthesize valuable products. Depending on their distinct and fastidious metabolic pathways, MOB are mainly divided into Type I and Type II; the latter are known as producers of polyhydroxyalkanoate (PHA). Despite the metabolic potential of MOB to synthesize PHA, the ecophysiology of MOB, especially under high CH₄ flux conditions, is yet to be understood. Therefore, in this study, a rice paddy soil receiving a high CH₄ flux from underground was used as an inoculum to enrich MOB using fed-batch operation, then the enriched Type II MOB were characterized. The transitions in the microbial community composition and CH₄ oxidation rates were monitored by 16S rRNA gene amplicon sequencing and degree of CH₄ consumption. With increasing incubation time, the initially dominant Methylomonas sp., affiliated with Type I MOB, was gradually replaced with Methylocystis sp., Type II MOB, resulting in a maximum CH₄ oxidation rate of 1.40 g-CH₄/g-biomass/day. The quantification of functional genes encoding methane monooxygenase, pmoA and PHA synthase, phaC, by quantitative PCR revealed concomitant increases in accordance with the Type II MOB enrichment. These increases in the functional genes underscore the significance of Type II MOB to mitigate greenhouse gas emission and produce PHA.

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.

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

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

Combined Deterministic and Stochastic Processes Control Microbial Succession in Replicate Granular Biofilm Reactors

Granular sludge is an efficient and compact biofilm process for wastewater treatment. However, the ecological factors involved in microbial community assembly during the granular biofilm formation are poorly understood, and little is known about the reproducibility of the process. Here, three replicate bioreactors were used to investigate microbial succession during the formation of granular biofilms. We identified three successional phases. During the initial phase, the successional turnover was high and α-diversity decreased as a result of the selection of taxa adapted to grow on acetate and form aggregates. Despite these dynamic changes, the microbial communities in the replicate reactors were similar. The second successional phase occurred when the settling time was rapidly decreased to selectively retain granules in the reactors. The influence of stochasticity on succession increased and new niches were created as granules emerged, resulting in temporarily increased α-diversity. The third successional phase occurred when the settling time was kept stable and granules dominated the biomass. Turnover was low, and selection resulted in the same abundant taxa in the reactors, but drift, which mostly affected low-abundant community members, caused the community in one reactor to diverge from the other two. Even so, performance was stable and similar between reactors.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L_r^-1 d^-1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions.

The effect of substrate/inoculum ratio on the kinetics of methane production in swine wastewater anaerobic digestion

Methane production from swine wastewater was evaluated by using sewage sludge as inoculum in three substrate to inoculum ratios (SIRs) named A (1:1), B (3:1) and C (6:1), with the objective to identify the proportion that optimizes the performance of the process. Duplicated batch bioreactors of 1 L capacity under mesophilic conditions were used to carry out the experiment. The highest biogas yield was observed in A treatment (554 ± 75 mL/g volatile solid (VS)). Cumulative methane production decreased from 382 ± 22 to 232 ± 5 mL/g VS when SIR increased from 1:1 to 6:1. The first-order model and the modified Gompertz equation were used to model the experimental cumulative methane yield giving adjustments with coefficients of determination of 96 and 99% respectively. The effect of the SIR was analysed based on the kinetic parameters of the Gompertz equation, which are methane production potential, maximum methane production rate and lag-phase time. The best performance in terms of the kinetic parameters was obtained for treatment A; however, treatment B could still ensure a stable process. The use of higher inoculum concentration generated 463.1% higher methane production rate and required 77.3% shorter adaptation time (lag phase) in the SIR range studied. When higher SIR was used (e.g. 14:1, previous work), it could be observed that the Gompertz equation also adjusted adequately the experimental data (R ² > 0.99) although the lag-phase time did not remain in a linear relationship with SIR but exponentially above SIR = 6:1. These results demonstrated that when a low amount of inoculum was used, the adaptation time of microorganisms resulted much higher than expected delaying the methane production and extending the time needed to achieve adequate performance of the process.

Bioaugmentation strategy for enhancing anaerobic digestion of high C/N ratio feedstock with methanogenic enrichment culture

To investigate whether bioaugmentation could improve the digestion performance of high C/N ratio feedstock without co-digestion with nitrogen-rich substrate, different forms of enriched methanogenic culture were introduced to the continuous feed digesters. The performance efficiency of bioaugmentation on digestion improvement was compared. The effect of bioaugmentation on microbial community composition was revealed as well. Results demonstrated that routine bioaugmentation with liquid culture (containing the microbes and the medium remains) showed the best performance, with the organic loading rate (OLR), methane percentage, volumetric methane production (VMP) and volatile solid methane production (VSMP) higher at 1.0 g L^-1 d^-1, 24%, 0.22 L L^-1 d^-1 and 0.23 L g^-1 VS d^-1 respectively, compared to the non-bioaugmentation control. Whole genome pyrosequencing analysis suggested that consecutive microbial consortium addition could reconstruct the methanogens community by increasing the populations of acetoclastic methanogens Methanothrix, which could accelerate the degradation of acetate and methane production.

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

BACKGROUND

Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.

RESULTS

A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.

CONCLUSIONS

In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.

Importance of inoculum source and initial community structure for biogas production from agricultural substrates

This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.

Acclimatization of a mixed-animal manure inoculum to the anaerobic digestion of Axonopus compressus reveals the putative importance of Mesotoga infera and Methanosaeta concilii as elucidated by DGGE and Illumina MiSeq

In this study, a multifarious microbial mix from different sources is acclimatized over a period of three months to digesting cowgrass, and the changes in the community structure are examined with both a traditional denaturing gradient gel electrophoresis method as well as a next generation sequencing MiSeq method. It is shown that the much more in depth analysis by Illumina gives more information about the relative abundance and thus putative importance of the role of various microbes, in particular the bacterium Mesotoga infera and the archaeon Methanosaeta concilii.

Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD) consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin) on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i) an agricultural biogas plant (ABP) which utilizes maize silage as a main substrate, (ii) cattle slurry (CS), which contain elevated levels of lignocelluloses materials, and (iii) raw sewage sludge (RSS) with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS) and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS) prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic Methanosarcinaceae was observed by the end of the experiment. As a result, three independent, functional communities that syntrophically produced methane from acetate (primarily) and H₂/CO₂, methanol and methylamines were adapted. This study provides new insights into the specific process by which different inocula sampled from typical methanogenic environments that are commonly used to initiate industrial installations gradually adapted to allow biogas production from maize silage.

Effects of co-inoculating rice straw with ruminal microbiota and anaerobic sludge: digestion performance and spatial distribution of microbial communities

Ruminal microbiota (RM) were co-inoculated with anaerobic sludge (AS) at different ratios to study the digestion of rice straw in batch experiments. The CH₄ yield reached 273.64 mL/g volatile solid (VS) at a co-inoculum ratio of 1:1. The xylanase and cellulase activities were 198.88-212.88 and 24.51-29.08 U/mL in co-inoculated samples, respectively, and were significantly different compared to the results for single inoculum (p < 0.05). Higher ratios of AS enhanced acetoclastic methanogenesis, and propionate accumulation could be the main reason for the longer lag phase observed in samples with a higher RM ratio. The microbial compositions were clearly altered after digestion. Fibrobacter, Ruminococcus and Butyrivibrio from the rumen did not settle in the co-inoculated system, whereas Clostridiales members became the main polysaccharide degraders. Microbial interactions involving hydrolytic bacteria and acetoclastic methanogens in the residue were considered to be significant for hydrolysis activities and methane production. Syntrophy involving propionate oxidizers with associated methanogens occurred in the liquid phase. Our findings provide a better understanding of the anaerobic digestion of rice straw that is driven by specific microbial populations.

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.

Incubation of innovative methanogenic communities to seed anaerobic digesters

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

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes

This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production.

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

BACKGROUND

The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.

RESULTS

The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation.

CONCLUSIONS

This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.