Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation

Organic matter removal and CH4 production performance recoveries and microbial community changes in upflow anaerobic biofilter after long term starvation

The organic matter in municipal wastewater can be recovered by anaerobic biological treatment, making further resource utilization of municipal wastewater, which meets the requirements of sustainable development. An upflow anaerobic biofilter (UAF) treating municipal wastewater was established. The performances of stable operation and recovery operation of UAF after long-term starvation (234 days) and the changes of microbial community structure were researched. By gradually reducing HRT from 10 h to 4 h, the UAF achieved the treatment performance of pre-starvation after only 50 days recovery operation, in which total COD and soluble COD removal efficiencies reached 66 % and 69 %, respectively, and the CH4 production rate was 0.21 L CH4/g CODremoval. The recovery performance of UAF after long term starvation showed that the recovery sequence of three main anaerobic processes was hydrolytic acidification, hydrogen-acetate production and methanogenesis. High-throughput sequencing results indicated that dominant bacteria associated with hydrolytic acidification process changed from Moduliflexaceae and Trichococcus in stable operation stage to Trichococcus and Romboutsia in recovery stage. Besides, the dominant archaea changed from Methanosaeta (hydrotrophic methanogens) to Methanobacterium (acetotrophic methanogens), showing Methanobacterium was more resistant to starvation environment. Therefore, by using UAF for biological treatment of organic matter, even after a long period of starvation, the system would not be completely destroyed. Once it resumed operation, the treatment performance could be restored in a short period of time.

Graph-based deep learning for predictions on changes in microbiomes and biogas production in anaerobic digestion systems

Anaerobic digestion (AD), which relies on a complex microbial consortium for efficient biogas generation, is a promising avenue for renewable energy production and organic waste treatment. However, understanding and optimising AD processes are challenging because of the intricate interactions within microbial communities and the impact of volatile fatty acids (VFAs) on biogas production. To address these challenges, this study proposes the application of graph convolutional networks (GCNs) to comprehensively model AD processes. GCN models were developed to predict microbial dynamics and biogas production by integrating network analyses of high-throughput sequencing data and VFA inhibition effects. The models were trained based on the responses of anaerobic digesters to organic loading rate shock, starvation, and bioaugmentation for 281 d under various feeding conditions. Shifts in microbial community composition during AD stages and feeding conditions were successfully identified using next-generation sequencing tools. Graph topological features indicated a significant coupling between VFAs and microbial families, and the hydrogenotrophic archaeal families were most frequently connected to other families or residual acids. The GCN accurately predicted microbial abundances and gas production rates, achieving a mean squared error of 0.11 and 0.01 and a coefficient of determination of 0.72 and 0.87 for the testing dataset. These results provide valuable insights into the effects of starvation and bioaugmentation on the microbiome by utilising GCNs to model anaerobic treatment processes, predict microbial dynamics, and assess reactor productivity. Our study suggests a new modelling framework for understanding and improving AD systems by considering microbial interaction networks in relation to chemical parameter information at relevant operating scales.

Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances

Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.

IMPORTANCE

Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.

Resilience and response of anaerobic digestion systems to short-term hydraulic loading shocks: Focusing on total and active microbial community dynamics

Anaerobic digestion is known to be sensitive to operational changes, such as hydraulic loading shock, yet the impact on the microbiome, particularly the active RNA-based community, has not been fully understood. This study aimed to investigate the performance of anaerobic reactors and their microbial communities under short-term hydraulic loading shocks. Using synthetic wastewater, the reactor was subjected to 24-h shocks at three-fold and seven-fold the baseline loading rate, followed by DNA and RNA analyses to assess the system's resiliency and microbial responses. The research focused on shifts in major microbial groups and their functions, paying close attention to the active RNA community during loading shock events to better reflect the system's immediate condition. Findings indicated that although the microbial community structure, particularly among the archaea, was altered, the reactor quickly regained its balance. Differences were observed between DNA and RNA profiles and between regular and shock loadings; however, the alpha diversity and functions of the overall community were sustained. This study offers important insights for the design and operation of wastewater treatment plants, with the goal of achieving stable and efficient anaerobic digestion systems.

Comparing sewage sludge vs. digested sludge for starting-up thermophilic two-stage anaerobic digesters: Operational and economic insights

Despite advances in anaerobic digestion (AD), full-scale implementation faces significant challenges, particularly during the start-up phase, where inoculum selection is crucial. This study examines the impact of inoculum choice on the operational and economic performance of thermophilic digesters during the start-up phase. Methanogenic reactors R3 and R4 were inoculated with digested sludge (DiS) and diluted sewage sludge (DSS), respectively, and fed with hydrolyzed source-sorted organic fraction of municipal solid waste (SS-OFMSW) and thickened sewage sludge, which were processed in R1 and R2, serving as acidogenic reactors. A two-stage AD configuration was employed to mitigate inhibitory effects associated with the undigested inoculum (DSS). This approach enabled the establishment of methanogenic activity in R4 when the AD system is initiated with DSS. However, R3 outperformed R4, achieving 49 % of the feedstock's theoretical methane potential compared to 15 % in R4. Methane production and volatile solids (VS) processing costs in R4 were 18 and 3 times higher than in R3, respectively. R3's superior performance was attributed to DiS's diverse bacterial community, with over 66 % of genera involved in hydrolysis, volatile fatty acid production, and syntrophic methane production. In contrast, DSS was dominated by Trichococcus and Lactococcus (75.4 %), primarily involved in butyrate oxidation and lactate production. This study provides valuable insights into effective inoculum selection for the start-up of full-scale digesters.

Thermally enhanced solid-liquid separation process in food waste biorefinery: modelling the anaerobic digestion of solid residues

The biochemical valorization potential of food waste (FW) could be exploited by extracting decreasing added-value bio-based products and converting the final residues into energy. In this context, multi-purpose and versatile schemes integrating thermal and biochemical conversion processes will play a key role. An upstream thermal pretreatment + solid-liquid separation unit was here proposed to optimize the conversion of the liquid fraction of FW into valuable chemicals through semi-continuous fermentation process, and the conversion of the residual solid fraction into biomethane through anaerobic digestion. The solid residues obtained after thermal pretreatment presented a higher soluble COD fraction, which resulted in higher methane production with respect to the raw residues (0.33 vs. 0.29 Nm3CH4 kg-1VSfed) and higher risk of acidification and failure of methanogenesis when operating at lower HRT (20d). On the contrary, at HRT = 40 d, the pretreatment did not affect the methane conversion rates and both tests evidenced similar methane productions of 0.33 Nm3CH4 kg-1VSfed. In the reactor fed with pretreated residue, the association of hydrogenotrophic methanogens with syntrophic bacteria prevented the acidification of the system. Modelling proved the eligibility of the FW solid residues as substrates for anaerobic digestion, given their small inert fractions that ranged between 0% and 30% of the total COD content.

Long-term in-situ starvation and reactivation of co-digestion with food waste and corn straw in a continuous AnDMBR: Performance, sludge characteristics, and microorganism community

To explore the effects of in-situ starvation and reactivation in a continuous anaerobic dynamic membrane reactor (AnDMBR), the anaerobic co-digestion system of food waste and corn straw was firstly start-up and stability operated, and then stopped feeding substrate approximately 70 days. After long-term in-situ starvation, the continuous AnDMBR was reactivated using the same operation conditions and organic loading rate as the continuous AnDMBR used before in-situ starvation. Results shown that the anaerobic co-digestion of corn straw and food waste in the continuous AnDMBR can resume stable operation within 5 days, and the corresponding methane production of 1.38 ± 0.26 L/L/d was completely returned to the methane production before in-situ starvation (1.32 ± 0.10 L/L/d). Through analysis of the specific methanogenic activity and key enzyme activity of the digestate sludge, only the acetic acid degradation activity of methanogenic archaea can be partially recovered, however, the activities of lignocellulose enzyme (lignin peroxidase, laccase, and endoglucanase), hydrolase (α-glucosidase) and acidogenic enzyme (acetate kinas, butyrate kinase, and CoA-transferase) can be fully recovered. Analysis of microorganism community structure using metagenomic sequencing technology showed that starvation decreased the abundance of hydrolytic bacteria (Bacteroidetes and Firmicutes) and increased the abundance of small molecule-utilizing bacteria (Proteobacteria and Chloroflexi) due to lack of substrate during the long-term in-situ starvation stage. Furthermore, the microbial community structure and key functional microorganism still maintained and similar with that of starvation final stage even after long-term continuous reactivation. The reactor performance and sludge enzymes activity in the continuous AnDMBR co-digestion of food waste and corn straw can be well reactivated after long-term in-situ starvation, even though the microbial community structure can not be recovered to the initiating stage.

Improvement of biogas production and nitrogen recovery in anaerobic digestion of purple phototrophic bacteria by thermal hydrolysis

Purple phototrophic bacteria (PPB) are a novel driver to recover organics and nutrients from wastewater by assimilative growth. Depending on the source, assimilated resources from the PPB biomass can still be recovered after a releasing step. Anaerobic digestion (AD) releases carbonand nutrients, but the release is incomplete. Thermal hydrolysis (TH) as a pretreatment before AD improves the digestibility, release, and subsequent recovery potentials. This work determines the effects of TH in batch and continuous modes regarding methane potential, nutrients' release efficiencies, volatile solids destruction, degradability, and hydrolysis rates. Continuous runs over 165 days (d) confirmed enhanced recovery potentials, achieving up to 380 LCH₄/kgVS (83 % solids destruction) and 73 % N release, respectively. The TH pretreatment is energy-intensive, but with appropriate heat recovery and increased methane production in the AD of the pretreated biomass, a combined configuration is energy positive.

Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks

This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. LactobacillalesandCloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.

Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy

Syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis (HM) plays a vital role in the anaerobic digestion of protein-rich feedstocks such as food wastes. However, current knowledge of the biodiversity and genetic potential of the involved microbial participants, especially syntrophic acetate-oxidizing bacteria (SAOB), is limited due to the low abundance of these microorganisms and challenges in their isolation. The intent of this study was to enrich and identify potential SAOB. Therefore, we conducted continuous acetate feeding under high ammonia concentrations using two separate inoculum consortia of microorganisms that originated from full-scale mesophilic food waste digesters, which lasted for more than 200 days. Using 16S rRNA gene amplicon and metagenomic analyses, we observed a convergence of the experimental microbial communities during the enrichment regarding taxonomic composition and metabolic functional composition. Stable carbon isotope analyses of biogas indicated that SAO-HM was the dominant methanogenic pathway during the enrichment process. The hydrogenotrophic methanogen Methanoculleus dominated the archaeal community. The enriched SAO community featured high biodiversity and metabolic functional redundancy. By analyzing the metagenome-assembled genomes, the known SAOB Syntrophaceticus schinkii and six uncultured populations were identified to have the genetic potential to perform SAO through the conventional reversed Wood-Ljungdahl pathway, while another six bacteria were found to encode the reversed Wood-Ljungdahl pathway combined with a glycine cleavage system as novel SAOB candidates. These results showed that the food waste anaerobic digesters harbor diverse SAOB and highlighted the importance of the glycine cleavage system for acetate oxidation. IMPORTANCE Syntrophic acetate oxidation to CO2 and H2, together with hydrogenotrophic methanogenesis, contributes to much of the carbon flux in the anaerobic digestion of organic wastes, especially at high ammonia concentrations. A deep understanding of the biodiversity, metabolic genetic potential, and ecology of the SAO community can help to improve biomethane production from wastes for clean energy production. Here, we enriched the SAO-HM functional guild obtained from full-scale food waste anaerobic digesters and recorded dynamic changes in community taxonomic composition and functional profiles. By reconstructing the metabolic pathways, diverse known and novel bacterial members were found to have SAO potential via the reversed Wood-Ljungdahl (WL) pathway alone, or via the reversed WL pathway with a glycine cleavage system (WLP-GCS), and those catalyzing WLP-GCS showed higher microbial abundance. This study revealed the biodiversity and metabolic functional redundancy of SAOB in full-scale anaerobic digester systems and provided inspiration for further genome-centric studies.

Short-term changes in the anaerobic digestion microbiome and biochemical pathways with changes in organic load

Fluctuations in organic loading rate are frequently experienced in practical-scale anaerobic digestion systems. These impose shocks to the microbiome leading to process instability and failure. This study elucidated the short-term changes in biochemical pathways and the contributions of microbial groups involved in anaerobic digestion with varying organic load shocks. A mixture of starch and hipolypeptone corresponding to a carbon-to‑nitrogen ratio of 25 was used as substrate. Batch vial reactors were run using acclimatized sludge fed with organic load varying from 0 to 5 g VS/L. Methane yield decreased with increasing organic load. The microbiome alpha diversity represented as the number of operational taxonomic units (OTUs) and the Shannon index both decreased with organic load indicating microbiome specialization. The biochemical pathways predicted using PICRUSt2 were analyzed along with the corresponding contributions of microbial groups leading to a proposed pathway of substrate utilization. Genus Trichococcus (order Lactobacillales) increased in contribution to starch degradation pathways with increase in organic load while genus Macellibacteroides (order Bacteroidales) was prominent in contribution to bacterial anaerobic digestion pathways. Strictly acetoclastic Methanosaeta increased in prominence over hydrogenotrophic Methanolinea with increase in organic load. Results from this study provide better understanding of how anaerobic digesters respond to organic load shocks.

Wood-Ljungdahl pathway utilisation during in situ H2 biomethanation

Biogas production from organic waste is a waste-to-energy technology with the potential to contribute significantly to sustainable energy production. Upgrading of biogas using in situ biomethanation with hydrogen has the potential for surplus electricity storage, and delivery of biogas with a methane content of >90%, allowing for easier integration into the natural gas grid, as well as conversion to other products. Microbial communities in biomethanation reactors undergo changes, however, these changes are largely unexplored. In the present study, metagenome-resolved protein stable isotope probing (Protein-SIP) was applied to laboratory scale batch incubations operating under anaerobic digestion, and (pre-adapted) biomethanation conditions, fed with ¹³C-labelled bicarbonate, in order to gain insight into the microbial activities during CO₂-reduction. The strongest and most microbially diverse isotopic incorporation was observed in the pre-adapted biomethanation incubation. Furthermore, divergent incorporation of ¹³C-labelled bicarbonate was also observed in the Wood-Ljungdahl pathway, with the anaerobic digester incubations primarily showing labelled proteins in the peripheral pathways leading toward production of energy and biomass. The pre-adapted biomethanation incubations consumed H₂ and CO₂, but did not convert it to CH₄, suggesting the production of acetate in these incubations, which was supported by heavy labelling of key enzymes in the Wood-Ljungdahl pathway. Twelve (ten high quality) metagenome-assembled genomes (MAGs) coding for ¹³C-incorporated proteins were extracted from the metagenome, eight of which contained one or more of the key genes in the Wood-Ljungdahl pathway, one of which was affiliated to Methanosarcina. Together, the findings in the present study deepen our knowledge surrounding microbial communities in biomethanation systems, and contribute to the development of better strategies for implementation of biogas upgrading and microbial management.

Microbial community redundance in biomethanation systems lead to faster recovery of methane production rates after starvation

The Power-to-Gas concept corresponds to the use of the electric energy surplus to produce H₂ by water electrolysis, that can be further converted to methane by biomethanation. However, the fluctuant production of renewable energy sources can lead to discontinuous H₂ injections into the reactors, that may interfere with the adaptation of the microbial community to high H₂ partial pressures. In this study, the response of the microbial community to H₂ and organic feed starvation was evaluated in in-situ and ex-situ biomethanation. The fed-batch reactors were fed with acetate or glucose and H₂, and one or four weeks of starvation periods were investigated. Methane productivity was mostly affected by the four-week starvation period. However, both in-situ and ex-situ biomethanation reactors recovered their methane production rate after starvation within approximately one-week of normal operation, while the anaerobic digestion (AD) reactors did not recover their performances even after 3 weeks of normal operation. The recovery failure of the AD reactors was probably related to a slow growth of the syntrophic and methanogen microorganisms, that led to a VFA accumulation. On the contrary, the faster recovery of both biomethanation reactors was related to the replacement of Methanoculleus sp. by Methanobacterium sp., restoring the methane production in the in-situ and ex-situ biomethanation reactors. This study has shown that biomethanation processes can respond favourably to the intermittent H₂ addition without compromising their CH₄ production performance.

Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions

During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.

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.

Cellulolytic and Xylanolytic Microbial Communities Associated With Lignocellulose-Rich Wheat Straw Degradation in Anaerobic Digestion

The enzymatic hydrolysis of lignocellulosic polymers is generally considered the rate-limiting step to methane production in anaerobic digestion of lignocellulosic biomass. The present study aimed to investigate how the hydrolytic microbial communities of three different types of anaerobic digesters adapted to lignocellulose-rich wheat straw in continuous stirred tank reactors operated for 134 days. Cellulase and xylanase activities were monitored weekly using fluorescently-labeled model substrates and the enzymatic profiles were correlated with changes in microbial community compositions based on 16S rRNA gene amplicon sequencing to identify key species involved in lignocellulose degradation. The enzymatic activity profiles and microbial community changes revealed reactor-specific adaption of phylogenetically different hydrolytic communities. The enzymatic activities correlated significantly with changes in specific taxonomic groups, including representatives of Ruminiclostridium, Caldicoprobacter, Ruminofilibacter, Ruminococcaceae, Treponema, and Clostridia order MBA03, all of which have been linked to cellulolytic and xylanolytic activity in the literature. By identifying microorganisms with similar development as the cellulase and xylanase activities, the proposed correlation method constitutes a promising approach for deciphering essential cellulolytic and xylanolytic microbial groups for anaerobic digestion of lignocellulosic biomass.

Mechanism of cell proliferation during starvation in a continuous stirred tank anaerobic reactor treating food waste

Anaerobic digestion is a mature technology; however, the mechanism of cell proliferation during starvation has not yet been clarified. In this study, a continuous stirred tank reactor (CSTR) treating food waste was exposed to deliberate starvation for 12 days. The cell density and the variability of digestate characteristics during starvation were monitored. Starvation increased cell density from 2.8 × 10¹⁰ to 7.9 × 10¹⁰ cells mL^-1 within 2 days and reduced the residual substrate. This increase in cell density was suggested owing to a switch of the anaerobic digester microorganisms' substrate preference to the complex fractions because the easily digestible fractions were exhausted. The prolonged starvation of more than approximately 3-6 days induced an increase in the free ammonia concentration to an inhibitive level of more than 0.10 g-N L^-1 for anaerobic digestion microorganisms due to the excessive ammonification of residual nitrogen, thereby resulting in a drastic decrease in cell density. Our results demonstrated that a deliberate starvation operation in an appropriate timeframe applied to a CSTR treating food waste is beneficial to proliferate cells and, at the same time, reduce residual substrate.

Characterisation of microbial communities for improved management of anaerobic digestion of food waste

Anaerobic digestion of food waste is an attractive and increasingly popular technology within waste management and energy recovery. A better understanding of the microbiology associated with anaerobic digestion of food waste will provide new insight into the operational conditions required for optimizing this process, as well as its potential for utilisation in co-digestion systems. Eighteen full-scale reactors processing varying proportions of food waste under diverse operational configurations were subjected to microbial community analysis by amplicon sequencing of the 16S rRNA and mcrA genes to capture the bacterial and methanogenic populations. Statistical correlations between microbial populations, plant design and operating conditions revealed that the microbial communities were shaped by operational parameters such as the primary substrate type and operational temperature, while the methanogenic communities showed a more reactor specific distribution. The distribution of microbes based on the waste processed in the surveyed digesters was explored, as well as the presence of specialist populations such as syntrophs and methanogens. Food waste digester communities were not associated with a strong microbial fingerprint compared to other waste types (wastewater and manure) but contained greater abundance and unique syntrophic acetate oxidising populations, suggesting that co-digestion with food waste may improve the functional diversity of anaerobic digesters.

Microbial community in an anaerobic membrane bioreactor and its performance in treating organic solid waste under controlled and deteriorated conditions

The adoption of anaerobic membrane bioreactors (AnMBRs) for organic solid waste management is important for the recovery of energy and high-quality treated water. However, few studies have focused on AnMBR treatment of high-strength organic solid waste and the microorganisms involved under deteriorated operating conditions. In the present study, a 15-L bench-scale AnMBR was operated using a model slurry of high-strength organic solid waste with the organic loading rate (OLR) increasing from 2.3 g chemical oxygen demand (COD) L^-1 day^-1 (represented as a controlled condition) to 11.6 g COD L^-1 day^-1 (represented as a deteriorated condition), and microbial community dynamics over 120 days of operation were analyzed. The abundances of methanogens and bacteria that were dominant under the controlled condition decreased as a result of both high organic loading and sludge withdrawal under the deteriorated condition and did not recover thereafter. Instead, numbers of putative volatile fatty acid (VFA)-producing bacterial operational taxonomic units (OTUs) related to the genus Prevotella increased rapidly, reaching a relative abundance of 43.2%, leading to the deterioration of methanogenic AnMBR operation. Considering that the sequences of these OTUs exhibited relatively low sequence identity (91-95%) to those of identified Prevotella species, the results strongly suggest that the accumulation of VFAs by novel VFA-producing bacteria in the digestion sludge promotes the disruption of the methanogen community under deteriorated conditions.

Volatile Fatty Acids Production from Microalgae Biomass: Anaerobic Digester Performance and Population Dynamics during Stable Conditions, Starvation, and Process Recovery

Disturbances in anaerobic digestion (AD) negatively impact the overall reactor performance. These adverse effects have been widely investigated for methane generation. However, AD recently appeared as a potential technology to obtain volatile fatty acids (VFAs) and thus, the impact of process disturbances must be evaluated. In this sense, microbial response towards a starvation period of two weeks was investigated resulting in a conversion of organic matter into VFAs of 0.39 ± 0.03 COD-VFAs/CODin. However, the lack of feeding reduced the yield to 0.30 ± 0.02 COD-VFAs/CODin. Microbial analysis revealed that the starvation period favored the syntrophic acetate-oxidizing bacteria coupled with hydrogenotrophic methanogens. Finally, the system was fed at 9 g COD/Ld resulting in process recovery (0.39 ± 0.04 COD-VFAs/CODin). The different microbiome obtained at the end of the process was proved to be functionally redundant, highlighting the AD robustness for VFAs production.

Performance and bacterial community of moving bed biofilm reactors with various biocarriers treating primary wastewater effluent with a low organic strength and low C/N ratio

A laboratory-scale sequencing batch reactor (SBR) and two moving bed biofilm reactors (MBBRs) with different types of biocarriers were operated to treat the effluent of chemically enhanced primary sedimentation (CEPS). Due to the low organic strength and low carbon/nitrogen ratio of the CEPS effluent, COD and NH₄⁺-N were effectively removed by the MBBRs but not by the SBR. Of the two MBBRs, MBBR2 filled with LEVAPOR biocarrier cubes performed even better than MBBR1 filled with K3 polystyrene biocarriers. The continuous decline of the sludge concentration in the SBR and the high and stable biomass content in MBBR2 contributed to their performances. High-throughput sequencing analysis showed that the reactors had selective effects on the bacterial community structure. Principal coordinate analysis indicated the different dynamic successions in the three reactors. Network analysis showed different community composition and diversity that were highly suggestive of different bacterial interactions among the three bioreactors.

Elucidating the effects of starvation and reactivation on anaerobic sulfidogenic granular sludge: Reactor performance and granular sludge transformation

In biological wastewater treatment, the bacteria starvation always challenges the stability of system operation. Yet, the effects of starvation and possibility of reactivation are less understood for anaerobic sulfidogenic system. Sulfidogenic systems use sulfate as electron acceptor for organic chemical oxygen demand (COD) degradation, so it will encounter two kind of starvations: (i) complete stoppage of wastewater flow (named complete food starvation) and (ii) remaining organic COD but with very low level sulfate in the influent (named sulfate starvation). In this study, the relative long-term starvation (over 30-day) and subsequent reactivation were studied in two lab-scale continuous gas recirculation sulfate-reducing upflow sludge bed (CGR-SRUSB) reactors. It was observed that the complete food starvation and sulfate starvation decreased the COD removal rate (in the similar range of 60-65%) and the specific sulfidogenic activity (about 45% and 61% respectively), as well as increasing the sludge flotation potential (SFP) from <15% to 58% and 35% respectively. Moreover, the following restoration experiments proved that the perturbed systems could be reactivated within 10-15 days for both cases. The results of investigating the mechanisms showed the performance deterioration were highly attributed to the starvation-induced granular sludge transitions, with respect to the changing of sludge physico-chemical properties (permeability, porosity, hydrophobicity and viscocity) and microbial stuctures (sulfate-reducting bacteria and extracellular polymeric substances). The outcomes of this study can provide useful information for dealing with the prolonged starvation problems in sulfidogenesis-based systems in industrial and municipal wastewater treatment.

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.

Responsiveness extracellular electron transfer (EET) enhancement of anaerobic digestion system during start-up and starvation recovery stages via magnetite addition

Two up-flow anaerobic sludge blanket (UASB) reactors (RM with 10 g Fe L^-1 magnetite, RB without magnetite) feeding with synthetic wastewater were built to investigate the effect of magnetite addition on anaerobic digestion (AD) performance during start-up and starvation recovery stages. With the magnetite addition, the COD removal efficiency and biogas production during the two stages were enhanced, and the recovery time of RM was shortened by about 50%. The reduced synthesis of riboflavin and heme c along with enhanced sludge conductivity of RM indicated that magnetite could replace their roles for efficient extracellular electron transfer (EET), which favors the growth of anaerobes. Microbial community analysis showed that potential syntrophic partners like Syntrophaceae and Methanothrix were enriched in RM during the recovery stage, and the performance was improved with quick responsiveness. Results demonstrated that addition of conductive materials like magnetite could improve the stability and restorability of AD process efficiently.

Enhanced anaerobic digestion of ammonia-rich swine manure by zero-valent iron: With special focus on the enhancement effect on hydrogenotrophic methanogenesis activity

Zero-valent iron (ZVI) supplementation for improving anaerobic digestion (AD) of ammonia-rich swine manure (initial ammonia-N ∼5000 mg/L) was tested. The addition of 5 g/L ZVI powder apparently accelerated the acidification process to produce more volatile fatty acids (VFAs) and optimized the fermentation type by contributing to a lower system oxidation-reduction potential (ORP) level of -181.7 to -250.0 mV favorable for ethanol-type and butyric-type fermentation during day 14-30, in comparison with that of -164.3 to -216.3 mV in the control group favorable for propionic-type. Overall, ZVI significantly decreased the proportion of propionic acid from 49.8% to 30.9% while increased the proportion of n-butyric acid from 6.8% to 18.7%. Microbial analysis revealed that fast growing and ammonia-tolerant hydrogenotrophic Methanoculleus species were enriched with ZVI, helping achieve a 54.2% higher CH₄ yield relative to control. Results from this study demonstrated the potential of ZVI addition to enhance AD of ammonia-rich animal manure.

Temperature shapes the microbiota in anaerobic digestion and drives efficiency to a maximum at 45 °C

Throwing longstanding habits over the pile may be necessary to improve biogas production, in particular when it comes to the process temperature. Its effect on biogas production was investigated with lab-scale reactors operated in fed-batch mode (cattle slurry and maize straw) at 10-55 °C over six months. Biochemical and microbial changes were comprehensively investigated. Production was highest and most efficient at 45 °C with an average methane yield of 166 NL kg^-1 VS, and thus 12.8% and 9.6% higher than at 37 and 55 °C. Temperature significantly affected the microbiota and higher temperature provoked a shift from Bacteroidetes/Proteobacteria to Firmicutes. A transition from hydrogenotrophic to acetoclastic methanogenesis was observed from 10 to 45 °C, while the trend was reversed at 55 °C. The results contest the textbook notion of preferred and most efficient temperatures for AD and suggest reconsideration of the temperature range around 45 °C for efficient manure-based co-fermentation.

The time response of anaerobic digestion microbiome during an organic loading rate shock

Knowledge of connections between operational conditions, process stability, and microbial community dynamics is essential to enhance anaerobic digestion (AD) process efficiency and management. In this study, the detailed temporal effects of a sudden glycerol-based organic overloading on the AD microbial community and process imbalance were investigated in two replicate anaerobic digesters by a time-intensive sampling scheme. The microbial community time response to the overloading event was shorter than the shifts of reactor performance parameters. An increase in bacterial community dynamics and in the abundances of several microbial taxa, mainly within the Firmicutes, Tenericutes, and Chloroflexi phyla and Methanoculleus genera, could be detected prior to any shift on the reactor operational parameters. Reactor acidification already started within the first 24 h of the shock and headed the AD process to total inhibition in 72 h alongside with the largest shifts on microbiome, mostly the increase of Anaerosinus sp. and hydrogenotrophic methanogenic Archaea. In sum, this work proved that AD microbial community reacts very quickly to an organic overloading and some shifts occur prior to alterations on the performance parameters. The latter is very interesting as it can be used to improve AD process management protocols.

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.

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor

A lab-scale anaerobic membrane bioreactor (AnMBR) with a side stream tubular membrane was developed to treat synthetic domestic sewage to evaluate its performance and the dynamic shift of bacterial and archaeal communities during the start-up, steady-state, overloading and recovery periods of operation at mesophilic temperatures. During the start-up period, the bacterial and archaeal communities changed drastically, and Proteobacteria and Bacteroidetes predominated. During the steady-state period, the AnMBR exhibited excellent COD removal above 91%, and COD of the effluent was below 50 mg/L. High-throughput sequencing analysis results revealed that bacterial and archaeal communities shifted significantly from the start-up to the steady-state period, and that the Proteobacteria phylum predominated on days 140, 162 and 190, and the archaea community hydrogenotrophic methanogen genus Methanolinea (1.5–6.64%) predominated over the aceticlastic methanogen genus Methanothrix (1.35–3.07%). During the overloading period, significant changes occurred in microbial community on day 210, e.g., the phyla Bacteroidetes (30%), Proteobacteria (23%) and Firmicutes (18%) predominated and the archaeal community was completely suppressed, and Methanobrevibacter (0.7%) was the only methanogen genus that emerged in the overloading period. After a shock loading period, the microbial communities exhibited significant changes within the ranks of methanogens and shifted to dominance of the aceticlastic methanogen pathway. In addition, the TVFAs to alkalinity ratio in this study was suitable as an indicator of monitoring performance in the AnMBR operation.

Inhibition of anaerobic digestion processes: Applications of molecular tools

Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors. More recent molecular methods such as 'omics' tools, substrate mapping, and real-time sequencing are helping to unravel the complexity of AD inhibition by elucidating physiological and ecological significance of key microbial populations. The AD community must strive towards developing predictive abilities to avoid system failure (e.g., real-time tracking of an indicator species) to improve resilience of AD systems.

Metaproteomic analysis of the relationship between microbial community phylogeny, function and metabolic activity during biohydrogen-methane coproduction under short-term hydrothermal pretreatment from food waste

Short-term hydrothermal pretreatment (SHP) is an attractive method for food waste anaerobic digestion, which facilitates the solubilisation of recalcitrant particles. This study employed metaproteomic method to evaluate the relationships among microbial community phylogeny, function, and metabolic activity during two-stage anaerobic digestion under SHP (SHPT) from food waste. The presence of 651 bacterial proteins and 477 archaeal protein has been detected by liquid chromatography online linked to mass spectrometry, revealing a high metabolic heterogeneity during SHPT. The different stages of SHPT highlighted important roles for the bacterial proteins from Gammaproteobacteria, Bacilli, and Clostridia and the archaeal proteins from Methanosarcinales. The identified proteins related to biohydrogen production come from pyruvic acid decarboxylase and formic acid decomposition pathway in carbohydrate metabolism and methanogenesis from acetate, CO₂ and a methylotrophic pathway during energy metabolism. This could provide functional evidence of the metabolic activities and biogas production during SHPT.