Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion

Nitrogen-doped activated carbon-based steel slag composite material as an accelerant for enhancing the resilience of flexible biogas production process against shock loads: Performance, mechanism and modified ADM1 modeling

Anaerobic digestion for flexible biogas production can lead to digestion inhibition under high shock loads. While steel slag addition has shown promise in enhancing system buffering, its limitations necessitate innovation. This study synthesized the nitrogen-doped activated carbon composite from steel slag to mitigate intermediate product accumulation during flexible biogas production. Material characterization preceded experiments introducing the composite into anaerobic digestion systems, evaluating its impact on methane production efficiency under hydraulic and concentration sudden shocks. Mechanistic insights were derived from microbial community and metagenomic analyses, facilitating the construction of the modified Anaerobic Digestion Model No. 1 (ADM1) to quantitatively assess the material's effects. Results indicate superior resistance to concentration shocks with substantial increment of methane production rate up to 33.45% compared with control group, which is mediated by direct interspecies electron transfer, though diminishing with increasing shock intensity. This study contributes theoretical foundations for stable flexible biogas production and offers an effective predictive tool for conductor material reinforcement processes.

Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios

Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0%-46.0%) surpassed Methanothrix (3.7%-22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.

New insights on ecological roles of waste activated sludge in nutrient-stressed co-digestion

There have been extensive applications of waste activated sludge (WAS) in anaerobic co-digestion (AcoD). Nonetheless, mechanisms through which AcoD systems maintain stability, particularly under nutrient-stressed conditions, are under-appreciated. In this study, the role of WAS in a nutrient-stressed WAS-food waste AcoD system was re-evaluated. Our findings demonstrated that WAS-based co-digestion increased methane production (by 20-60%) as WAS bolsters such systems' resilience via establishing a core niche-based microbial balance. The carbon utilization investigation suggested a microbial niche balance is attainable if two conditions are satisfied: 1) hydrolysis efficiency is greater than 50%; and 2) both the acidogenesis-to-hydrolysis and acetogenesis-to-hydrolysis efficiencies surpass 0.5. Metagenomic assembly genome (MAG) analysis indicated that the versatile metabolic characteristics strengthened the microbial niche balance, rendering the system resilient and efficient through a syntrophic mode, contributing to both acidogenesis and acetogenesis. The findings of this study provide new insights into the ecological effects of WAS on AcoD.

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.

Comprehensive ADM1 Extensions to Tackle Some Operational and Metabolic Aspects in Anaerobic Digestion

Modelling in anaerobic digestion will play a crucial role as a tool for smart monitoring and supervision of the process performance and stability. By far, the Anaerobic Digestion Model No. 1 (ADM1) has been the most recognized and exploited model to represent this process. This study aims to propose simple extensions for the ADM1 model to tackle some overlooked operational and metabolic aspects. Extensions for the discontinuous feeding process, the reduction of the active working volume, the transport of the soluble compound from the bulk to the cell interior, and biomass acclimation are presented in this study. The model extensions are included by a change in the mass balance of the process in batch and continuous operation, the incorporation of a transfer equation governed by the gradient between the extra- and intra- cellular concentration, and a saturation-type function where the time has an explicit influence on the kinetic parameters, respectively. By adding minimal complexity to the existing ADM1, the incorporation of these phenomena may help to understand some underlying process issues that remain unexplained by the current model structure, broadening the scope of the model for control and monitoring industrial applications.

Tracking microbial community shifts during recovery process in overloaded anaerobic digesters under biological and non-biological supplementation strategies

Anaerobic digestion encounters operational instability due to fluctuations in organic loading. Propionic acid (HPr) is frequently accumulated due to its unfavorable reaction thermodynamics. Here, 'specific' bioaugmentation using HPr enrichment cultures (three different injection regimes of quantity and frequency) was compared with 'non-specific' bioaugmentation using anaerobic sludge, and with non-biological supplementation of magnetite or coenzyme M. The specific bioaugmentation treatments showed superior recovery responses during continuous feeding after a peak overload. A 'one-shot' bioaugmentation with enrichment showed the best remediation, with ~25% recovery time and >10% CH₄ conversion efficiency compared to the control. Consecutive bioaugmentation showed evidence of increased stability of the introduced community. Families Synergistaceae, Syntrophobacteraceae, and Kosmotogaceae were likely responsible for HPr-oxidation, in potential syntrophy with Methanoculleus and Methanobacterium. The different supplementation strategies can be considered to reduce the effect of start-up or overload in anaerobic digesters based on the availability of supplementation resources.

Effect of a variable organic loading rate on process kinetics and volatile solids destruction in synthetic food waste-fed anaerobic digesters

With the increasing installation of weather-dependent renewable sources such as solar and wind power, the ability to produce electricity on demand to balance any shortfall in supply is becoming more important. Anaerobic digestion is a low-carbon energy source with the potential to be flexible to meet this need. An investigation was conducted into the response of two laboratory-scale anaerobic digesters at loading rate of 2.5 gVS L^-1 day^-1 over five months using a synthetic food waste as a substrate. One digester was consistently fed at the same rate, whereas the other digester was fed with periods of varying organic loading rate, from 0.1 to 7 gVS L^-1 day^-1, using a feed pattern derived from a record of restaurant food waste. The digester that had been fed at a variable rate showed a pronounced increase in biogas production after feed events and a 9.6% higher VS breakdown than the steady-feed digester (81% compared to 74%), with no effect on digester stability, volatile fatty acid concentration, overall biogas output or biogas quality. These findings support and encourage the use of variable-rate feeding to balance the electricity demand.

A pig slurry feast/famine feeding regime strategy to improve mesophilic anaerobic digestion efficiency and digestate hygienisation

The increasing concentration of livestock farms results in large amounts of waste production and the need for their management. The study of anaerobic digestion (AD) technology, under mesophilic conditions, applied to pig slurry is of the upmost importance for biogas recovery and sanitised digestate, contributing to a circular economy. The assessment of the effects of a feast/famine regime on biogas and biomethane (bio-CH₄) yield with different feeding frequencies was performed. The evaluation was made in regards to three scenarios: the first is based on daily feeding (FR1); in the second, the feeding occurs once every two days (FR2); and in the third, the feeding happens once every three days (FR3). The results demonstrate that the biogas and methane yield increased by 34% and 37% between FR1 and FR3. The stability inside the reactor was maintained since specific loading energetic rate values did not exceed the recommended limit (0.4 d^-1). It was also possible to conclude that the AD technology was efficient to sanitise the pig slurry, with the count of Escherichia coli going from 1 × 10⁵ colony-forming units (CFU) g^-1 to less than 100 CFU g^-1, meeting the legal requirements for agricultural valorisation. The total anaerobic mesophile plate counts were significantly (p < 0.1) reduced from feeding to digestate, and the plate counts of Clostridia were significantly (p < 0.05) increased, reflecting the changes in the composition of the microbiota. The increasing yield in bio-CH₄ in accordance with Clostridium counts suggests this genus as a positive microbiological key indicator of the AD performance.

Rapid recovery of methane yield in organic overloaded-failed anaerobic digesters through bioaugmentation with acclimatized microbial consortium

Acidification during anaerobic digestion (AD) due to organic overloading is one of the major reasons for process failures and decreased methane productivity in anaerobic digesters. Process failures can cause the anaerobic digesters to stall completely, prolong the digester recovery period, and inflict an increased operational cost on wastewater treatment plants and adverse impacts on the environment. This study investigated the efficacy of bioaugmentation by using acclimatized microbial consortium (AC) in recovering anaerobic digesters stalled due to acidosis. Overloading of digesters with food waste leachate (FWL) led to the accumulation of volatile fatty acids (11.30 g L^-1) and a drop in pH (4.67), which resulted in process failure and a 22-fold decline in cumulative methane production compared to that in the initial phase. In the failure phase, the syntrophic and methanogenic activities of the anaerobic digester microbiota were disrupted by a significant decrease in the abundance of syntrophic populations such as Syntrophomonas, Syntrophorhabdus, Sedimentibacter, and Levilinea, and the phylum Euryarchaeota. Bioaugmentation of the failed digesters by adding AC along with the adjustment of pH resulted in the prompt recovery of methane productivity with a 15.7-fold higher yield than that in unaugmented control. The abundance of syntrophic bacteria Syntrophomonas and phylum Euryarchaeota significantly increased by 29- and 17-fold in the recovered digesters, respectively, which showed significant positive correlations with methane productivity. Methanosarcina and acetoclastic Methanosaeta played a major role in the recovery of the digesters; they were later replaced by hydrogenotrophic Methanoculleus. The increase in the abundance of genes associated with biomethanation contributed to digester recovery, according to the functional annotation of 16S rDNA amplicon data. Thus, bioaugmentation with AC could be a viable solution to recover digesters experiencing process failure due to organic overloading.

Microbial invasions in sludge anaerobic digesters

Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.

Soil-Derived Inocula Enhance Methane Production and Counteract Common Process Failures During Anaerobic Digestion

Although soil-borne methanogens are known to be highly diverse and adapted to extreme environments, their application as potential (anaerobic) inocula to improve anaerobic digestion has not been investigated until now. The present study aimed at evaluating if soil-derived communities can be beneficial for biogas (methane, CH₄) production and endure unfavorable conditions commonly associated with digestion failure. Nine study sites were chosen and tested for suitability as inoculation sources to improve biogas production via in situ measurements (CH₄ fluxes, physical and chemical soil properties, and abundance of methanogens) and during a series of anaerobic digestions with (a) combinations of both sterile or unsterile soil and diluted fermenter sludge, and (b) pH-, acetate-, propionate-, and ammonium-induced disturbance. Amplicon sequencing was performed to assess key microbial communities pivotal for successful biogas production. Four out of nine tested soil inocula exerted sufficient methanogenic activity and repeatedly allowed satisfactory CH₄/biogas production even under deteriorated conditions. Remarkably, the significantly highest CH₄ production was observed using unsterile soil combined with sterile sludge, which coincided with both a higher relative abundance of methanogens and predicted genes involved in CH₄ metabolism in these variants. Different bacterial and archaeal community patterns depending on the soil/sludge combinations and disturbance variations were established and these patterns significantly impacted CH₄ production. Methanosarcina spp. seemed to play a key role in CH₄ formation and prevailed even under stressed conditions. Overall, the results provided evidence that soil-borne methanogens can be effective in enhancing digestion performance and stability and, thus, harbor vast potential for further exploitation.

Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants

Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L^-1 and 193 mg L^-1 or volatile fatty acid concentrations of 0.75 g L^-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.

Competition Between Butyrate Fermenters and Chain-Elongating Bacteria Limits the Efficiency of Medium-Chain Carboxylate Production

Medium-chain carboxylates such as n-caproate and n-caprylate are valuable chemicals, which can be produced from renewable feedstock by anaerobic fermentation and lactate-based microbial chain elongation. Acidogenic microbiota involved in lactate-based chain elongation and their interplay with lactic acid bacteria have not been characterized in detail yet. Here, the metabolic and community dynamics were studied in a continuous bioreactor with xylan and lactate as sole carbon sources. Four succession stages were observed during 148 days of operation. After an adaptation period of 36 days, a relatively stable period of 28 days (stage I) was reached with n-butyrate, n-caproate and n-caprylate productivities of 7.2, 8.2 and 1.8 gCOD L-1 d-1, respectively. After a transition period, the process changed to another period (stage II), during which 46% more n-butyrate, 51% less n-caproate and 67% less n-caprylate were produced. Co-occurrence networks of species based on 16S rRNA amplicon sequences and correlations with process parameters were analyzed to infer ecological interactions and potential metabolic functions. Diverse functions including hydrolysis of xylan, primary fermentation of xylose to acids (e.g., to acetate by Syntrophococcus, to n-butyrate by Lachnospiraceae, and to lactate by Lactobacillus) and chain-elongation with lactate (by Ruminiclostridium 5 and Pseudoramibacter) were inferred from the metabolic network. In stage I, the sub-network characterized by strongest positive correlations was mainly related to the production of n-caproate and n-caprylate. Lactic acid bacteria of the genus Olsenella co-occurred with potentially chain-elongating bacteria of the genus Pseudoramibacter, and their abundance was positively correlated with n-caproate and n-caprylate concentrations. A new sub-network appeared in stage II, which was mainly related to n-butyrate production and revealed a network of different lactic acid bacteria (Bifidobacterium) and potential n-butyrate producers (Clostridium sensu stricto 12). The synergy effects between lactate-producing and lactate-consuming bacteria constitute a division of labor cooperation of mutual benefit. Besides cooperation, competition between different taxa determined the bacterial community assembly over the four succession stages in this resource-limited system. During long-term reactor operation under constant conditions, chain-elongating bacteria were outcompeted by butyrate-producing bacteria, leading to the increase of n-butyrate yield at the cost of medium-chain carboxylate yields in this closed model system.

A compilation and bioenergetic evaluation of syntrophic microbial growth yields in anaerobic digestion

A compilation and analysis of experimentally determined microbial growth yields for syntrophic volatile fatty acid (VFA), lactate oxidisers and methanogens in anaerobic digestion (AD) systems is presented. Only studies based on experimental determinations or sound model-to-data fitting that specifically address parameter identifiability, have been considered. The experimentally determined values are compared and discussed with estimations based on bioenergetic correlations. Only for acetoclastic methanogens the experimentally determined microbial yields appear in good consistency with bioenergetic estimations. For syntrophic microbial groups, the experimetal yield values reported appear much higher than those expected from the low amount of metabolic energy available. These large deviations imply either inaccuracy on the microbial biomass quantification methods or that the syntrophic interspecies electron transfer occurs under mechanisms, or hydrogen equivalent intermediate activities, much below those ever observed in methanogenic environments. In addition, the microbial growth yield values most widely adopted in AD model applications (those reported in the IWA Anaerobic Digestion Model No. 1 (ADM1)) are even higher than the experimental determinations from literature. It is therefore proposed that microbial growth yield values should be restricted by the maximum harvestable ATP calculated through a detailed bioenergetic pathway analysis. Model simulations with different parameter configurations for different yield sources (default ADM1, experimentally determined and bioenergetically estimated values) displayed low sensitivity of the simulations with respect to the yield values as long as the maximum specific microbial growth rate (μ_max) remain the same. This suggests that model calibrations could target the accuracy of μ_max maintaining the bioenergetic upper limit for microbial growth yields.

Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity

The process of anaerobic digestion in which waste biomass is transformed to methane by complex microbial communities has been modeled for more than 16 years by parametric gray box approaches that simplify process biology and do not resolve intracellular microbial activity. Information on such activity, however, has become available in unprecedented detail by recent experimental advances in metatranscriptomics and metaproteomics. The inclusion of such data could lead to more powerful process models of anaerobic digestion that more faithfully represent the activity of microbial communities. We augmented the Anaerobic Digestion Model No. 1 (ADM1) as the standard kinetic model of anaerobic digestion by coupling it to Flux-Balance-Analysis (FBA) models of methanogenic species. Steady-state results of coupled models are comparable to standard ADM1 simulations if the energy demand for non-growth associated maintenance (NGAM) is chosen adequately. When changing a constant feed of maize silage from continuous to pulsed feeding, the final average methane production remains very similar for both standard and coupled models, while both the initial response of the methanogenic population at the onset of pulsed feeding as well as its dynamics between pulses deviates considerably. In contrast to ADM1, the coupled models deliver predictions of up to 1,000s of intracellular metabolic fluxes per species, describing intracellular metabolic pathway activity in much higher detail. Furthermore, yield coefficients which need to be specified in ADM1 are no longer required as they are implicitly encoded in the topology of the species’ metabolic network. We show the feasibility of augmenting ADM1, an ordinary differential equation-based model for simulating biogas production, by FBA models implementing individual steps of anaerobic digestion. While cellular maintenance is introduced as a new parameter, the total number of parameters is reduced as yield coefficients no longer need to be specified. The coupled models provide detailed predictions on intracellular activity of microbial species which are compatible with experimental data on enzyme synthesis activity or abundance as obtained by metatranscriptomics or metaproteomics. By providing predictions of intracellular fluxes of individual community members, the presented approach advances the simulation of microbial community driven processes and provides a direct link to validation by state-of-the-art experimental techniques.

The Future Agricultural Biogas Plant in Germany: A Vision

After nearly two decades of subsidized and energy crop-oriented development, agricultural biogas production in Germany is standing at a crossroads. Fundamental challenges need to be met. In this article we sketch a vision of a future agricultural biogas plant that is an integral part of the circular bioeconomy and works mainly on the base of residues. It is flexible with regard to feedstocks, digester operation, microbial communities and biogas output. It is modular in design and its operation is knowledge-based, information-driven and largely automated. It will be competitive with fossil energies and other renewable energies, profitable for farmers and plant operators and favorable for the national economy. In this paper we discuss the required contribution of research to achieve these aims.

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.