Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation

Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage

A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.

Disentangling microbial niche balance and intermediates' trade-offs for anaerobic digestion stability and regulation

Anaerobic digestion (AD) is a key technology for converting organic matters to methane-rich biogas. However, nutrient imbalance can destabilize the whole digestion. To realize stable operation of AD and improve its efficiency, this work considers a new strategy to control the intermediate concentrations of poor AD under nutrient stress. For this purpose, long-term digestion under different nutrient conditions was investigated. Results showed that the feedstock with a low C/N ratio (= 6) caused VFA accumulation (2072 ± 632 mg/L), leading to the inhibition of methane production. Employing a substrate with a higher C/N ratio (= 11) and/or adding NH4HCO3 (200 mg NH4+-N/Ladd) could alleviate the VFA inhibition, but excessive dosage of NH4HCO3 would induce ammonia inhibition. Through the established digestion balance between free ammonia nitrogen (FAN) between 0 and 25 mg/L, volatile fatty acid (VFA) 510-2100 mg/L, and alkalinity (ALK) 3300-7800 mg/L, an efficient methane yield of 150-250 mL/g VS was achieved and stable operation of AD under nutrient stress (low C/N ratio) was realized. Metabolic reconstruction between Euryarchaeota sp. MAG162, Methanosarcina mazei MAG53 and Mesotoga infera MAG119 highlighted that microbial niche balance was developed as a result of digestion balance, which is beneficial for stable operation of AD. These findings improved our understanding of the interaction mechanism between intermediates and microbial niches for stability control in AD.

Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction

Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as n-caproate (C6) and n-caprylate (C8), from organic substrates such as wastes. Even though the production of n-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for n-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed. n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2 and O2 between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the Clostridia class. Several Oscillibacter spp., including Oscillibacter valericigenes, were positively correlated with n-caprylate production rates, while Clostridium kluyveri was positively correlated with n-caproate production. Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of n-caprylate production rates. This study provides insight into microbiota that are associated with n-caprylate production in open-culture reactors and provides ideas for further work.IMPORTANCEMicrobial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including n-caproate (C6) and n-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for n-caproate or n-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from n-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.

Bacillus subtilis Feed Supplementation Combined with Oral E. coli Immunization in Sows as a Tool to Reduce Neonatal Diarrhea in Piglets

To investigate the effects of B. subtilis on the specific immune response of lactating sows to E. coli and the diarrhea rate in suckling piglets, thirty large white sows with similar farrowing dates were randomly divided into two groups: a feedback feeding (i.e., feeding a homogenate of intestinal contents and tissues from E. coli-infected piglets to sows; FB) group and a feedback feeding with B. subtilis (FB + BS) group. Serum, colostrum, and intestinal tissues from sows and piglets were collected to assess the immune response and intestinal barrier function at weaning. T and B cells from Peyer's patches (PPs) and mesenteric lymph nodes (MLNs) in lactating mice (with treatments consistent with the sows') were isolated to explore the underlying mechanism. The results showed that, compared with the FB group, the reproductive performance of sows and the growth performance of their offspring were effectively improved in the FB + BS group. Moreover, the levels of IgG/IgA and those of IgG/IgA against E. coli in the serum and colostrum of sows in the FB+BS group were increased (p < 0.05). Meanwhile, the ratio of CD4+/CD8+, CD4+CXCR5+PD1+, and B220+IgA+ cells in MLNs and PPs, and the IgA levels in the mammary glands of mice, were also increased in the FB + BS group (p < 0.05). Notably, in suckling piglets in the FB + BS group, the diarrhea rate was decreased (p < 0.05), and the intestinal barrier function and intestinal flora composition at weaning were significantly improved. Overall, these results indicated that B. subtilis feed supplementation combined with feedback feeding in pregnant and lactating sows can reduce diarrhea in suckling piglets by enhancing the maternal immune response against E. coli and intestinal barrier function in their offspring, improving survival rates and pre-weaning growth.

DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities

There have been a growing number of computational strategies to aid in the design of synthetic microbial consortia. A framework to identify regions in parametric space to maximize two essential properties, evenness and stability, is critical. In this study, we introduce DyMMM-LEAPS (dynamic multispecies metabolic modeling-locating evenness and stability in large parametric space), an extension of the DyMMM framework. Our method explores the large parametric space of genetic circuits in synthetic microbial communities to identify regions of evenness and stability. Due to the high computational costs of exhaustive sampling, we utilize adaptive sampling and surrogate modeling to reduce the number of simulations required to map the vast space. Our framework predicts engineering targets and computes their operating ranges to maximize the probability of the engineered community to have high evenness and stability. We demonstrate our approach by simulating five cocultures and one three-strain culture with different social interactions (cooperation, competition, and predation) employing quorum-sensing-based genetic circuits. In addition to guiding circuit tuning, our pipeline gives an opportunity for a detailed analysis of pockets of evenness and stability for the circuit under investigation, which can further help dissect the relationship between the two properties. DyMMM-LEAPS is easily customizable and can be expanded to a larger community with more complex interactions.

Metabolism of novel potential syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats

Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH4. In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics. In addition to the reported SAOB classified in the genera Tepidanaerobacter, Desulfotomaculum, and Thermodesulfovibrio, we identified a number of potential SAOB that are affiliated with Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. The potential SAOB possessing the glycine-mediated acetate oxidation pathway dominates SAOB communities. Moreover, formate appeared to be the main product of the acetate degradation by the most active potential SAOB. We identified the methanogen partner of these potential SAOB in the acetate-fed chemostat as Methanosarcina thermophila. The dominated potential SAOB in each chemostat had similar metabolic characteristics, even though they were in different fatty-acid-fed chemostats. These novel syntrophic lineages are prevalent and may play critical roles in thermophilic methanogenic reactors. This study expands our understanding of the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders and presents novel insights into how they interact with methanogens.IMPORTANCECombining reactor operation with omics provides insights into novel uncultured syntrophic acetate degraders and how they perform in thermophilic anaerobic digesters. This improves our understanding of syntrophic acetate degradation and contributes to the background knowledge necessary to better control and optimize anaerobic digestion processes.

Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics

Ammonia release from proteinaceous feedstocks represents the main inhibitor of the anaerobic digestion (AD) process, which can result in a decreased biomethane yield or even complete failure of the process. The present study focused on the adaptation of mesophilic AD communities to a stepwise increase in the concentration of ammonium chloride in synthetic medium with casein used as the carbon source. An adaptation process occurring over more than 20 months allowed batch reactors to reach up to 20 g of NH4+ N/L without collapsing in acidification nor ceasing methane production. To decipher the microbial dynamics occurring during the adaptation and determine the genes mostly exposed to selective pressure, a combination of biochemical and metagenomics analyses was performed, reconstructing the strains of key species and tracking them over time. Subsequently, the adaptive metabolic mechanisms were delineated by following the single nucleotide variants (SNVs) characterizing the strains and prioritizing the associated genes according to their function. An in-depth exploration of the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacteria Acetomicrobium sp. ma133 identified positively selected SNVs on genes involved in stress adaptation. The intraspecies diversity with multiple coexisting strains in a temporal succession pattern allows us to detect the presence of an additional level of diversity within the microbial community beyond the species level.

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

Direct interspecies electron transfer enables anaerobic oxidation of sulfide to elemental sulfur coupled with CO2-reducing methanogenesis

Electric syntrophy between fatty acid oxidizers and methanogens through direct interspecies electron transfer (DIET) is essential for balancing acidogenesis and methanogenesis in anaerobic digestion. Promoting DIET using electrically conductive additives proved effective in enhancing methanogenesis; however, its possibility to affect other microbial redox reactions in methanogenic systems has been little studied. This study provides the first confirmation of the electro-syntrophic coupling of sulfide oxidation to S0 with CO2-reducing methanogenesis in sulfur-rich methanogenic cultures supplemented with conductive magnetite (100-700-nm particle size). The H2S content in biogas, initially exceeding 5000 ppmv, decreased to below 1 ppmv along with an accumulation of extracellular S0 (60-70 mg/L; initially <1 mg/L) at a magnetite dose of 20 mM Fe, while there were no significant changes in methane yield. A comprehensive polyphasic approach demonstrated that the S0 formation occurs through electro-syntrophic oxidation of sulfide coupled with CO2-reducing methanogenesis, involving Methanothrix as the dominant methanogen.

Biomethane production and microbial strategies corresponding to high organic loading treatment for molasses wastewater in an upflow anaerobic filter reactor

Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. In this study, an upflow anaerobic filter (UAF) reactor was employed to establish a high organic loading treatment system for molasses wastewater and further investigated the microbial community dynamics in response to this stressful operation. The biogas production increased with an increase in total organic carbon (TOC) loading rate from 1.0 to 14 g/L/day, and then it decreased with further TOC loading rate addition until 16 g/L/day. The UAF reactor achieved a maximum biogas production of 6800 mL/L/day with a TOC removal efficiency of 66.5% at a TOC loading rate of 14 g/L/day. Further microbial analyses revealed that both the bacterial and archaeal communities developed multiple strategies to maintain stable operation of the reactor at high organic loading (e.g., Proteiniphilum and Defluviitoga maintained high abundances throughout the operation; Tissierella temporarily dominated the bacterial community at TOC loading rates of 8.0 to 14 g/L/day; and multi-trophic Methanosarcina shifted as the dominant methanogen at the TOC loading rates of 8.0 to 16 g/L/day). This study presents insights into a high organic loading molasses wastewater treatment system and the microbial flexibility in methane fermentation in response to process disturbances.

Comparison of mesophilic and thermophilic anaerobic digestions of thermal hydrolysis pretreated swine manure: Process performance, microbial communities and energy balance

Anaerobic digestion (AD) of swine manure (SM) commonly shows low biogas output and unsatisfactory economic performance. In this study, thermophilic AD (TAD, 50 ± 1 °C) was combined with thermal hydrolysis pretreatment (THP, 170 °C/10 bar), to investigate its potential for maximizing biogas yield, securing successful digestion and microbial diversity, as well as improving energy balance. Four lab-scale continuously stirred tank reactors were operated for 300 days and compared with each other, i.e., reactor 1 (raw SM fed in mesophilic AD: RSM-MAD), reactor 2 (THP-treated SM fed in MAD: TSM-MAD), reactor 3 (RSM-TAD), and reactor 4 (TSM-TAD). The results showed that THP was efficient to increase methane production of SM, TSM-TAD mode led to the highest methane yield (129.8 ± 40.5 mL-CH₄/g-VS/day) among the tests (p < 0.05). Although TAD was more likely to induce free ammonia (> 700 mg/L) or volatile fatty acids (> 6000 mg/L) accumulation compared with MAD in start-up phase, TSM-TAD treatment mode behaved a sustainable digestion process in a long-term operation. For TSM-TAD scenario, higher Shannon-Weaver (3.873) and lower Simpson index (0.061) indicated this mode ensured and enlarged the diversity of bacteria communities. Phylum Bathyarchaeota was dominant (59.3%-90.0%) in archaea community, followed by Euryarchaeota in the four reactors. RSM-MAD treatment mode achieved the highest energy output (4.65 GJ/day), TSM-TAD was less effective (-17.38 GJ/day) due to increased energy demands. Thus improving the energetic efficiency of THP units is recommended for the development of TSM-TAD treatment mode.

Magnetite-based nanoparticles and nanocomposites for recovery of overloaded anaerobic digesters

The effect of magnetite nanoparticles and nanocomposites (magnetite nanoparticles impregnated into graphene oxide) supplement on the recovery of overloaded laboratory batch anaerobic reactors was assessed using two types of starting inoculum: anaerobic granular sludge (GS) and flocculent sludge (FS). Both nanomaterials recovered methane production at a dose of 0.27 g/L within 40 days in GS. Four doses of magnetite nanoparticles from 0.075 to 1 g/L recovered the process in FS systems between 30 and 50 days relaying on the dose. The presence of nanomaterials helped to reverse the effect of volatile fatty acids inhibition and enabled microbial communities to recover but also favoured the development of certain microorganisms over others. In GS reactors, the methanogenic population changed from being mostly acetoclastic (Methanothrix soehngenii) to being dominated by hydrogenotrophic species (Methanobacterium beijingense). Nanomaterial amendment may serve as a preventative measure or provide an effective remedial solution for system recovery following overloading.

Osmoprotectants boost adaptation and protect methanogenic microbiome during ammonia toxicity events in continuous processes

Different osmoprotectants were used to counteract ammonia toxicity in continuous anaerobic reactors. The anaerobic microbiome osmoadaptation process and its role to the methanogenic recovery are also assessed. Three osmoprotectants (i.e., glycine betaine, MgCl2 and KCl) were respectively introduced in continuous reactors at high ammonia levels, namely RGB, RMg, RK, while a control reactor (RCtrl) was also used. After ammonia was introduced, the RGB, RMg, RK and RCtrl suffered 39.0%, 36.6%, 39.9% and 36.2% methane production loss, respectively. Osmoprotectants addition recovered significantly methane production by up to 68.9%, 54.3% and 32.2% for RGB, RMg and RK, respectively contrary to RCtrl, where production increased only by 13.6%. The recovered methane production was maintained in RGB and RMg for at least four HRTs, even after the addition of osmoprotectants was stopped, due to the formed methanogenic microbiota by osmoadaptation process, with Methanoculleus sp. as the dominant species.

Distinguishing responses of acetoclastic and hydrogenotrophic methanogens to ammonia stress in mesophilic mixed cultures

A shift from the acetoclastic to the hydrogenotrophic pathway in methanogenesis under ammonia inhibition is a common observation in anaerobic digestion. However, there are still considerable knowledge gaps concerning the differential ammonia tolerance of acetoclastic and hydrogenotrophic methanogens (AMs and HMs), their responses to different ammonia species (NH₄⁺, NH₃), and their recoverability after ammonia inhibition. With the successful enrichment of mesophilic AMs and HMs cultures, this study aimed at addressing the above knowledge gaps through batch inhibition/recovery tests and kinetic modeling under varying total ammonia (TAN, 0.2-10 g N/L) and pH (7.0-8.5) conditions. The results showed that the tolerance level of HMs to free ammonia (FAN, IC₅₀=1345 mg N/L) and NH₄⁺ (IC₅₀=6050 mg N/L) was nearly 11 times and 3 times those of AMs (NH₃, IC₅₀=123 mg N/L; NH₄⁺, IC₅₀=2133 mg N/L), respectively. Consistent with general belief, the AMs were more impacted by FAN. However, the HMs were more adversely affected by NH₄⁺ when the pH was ≤8.0. A low TAN (1.0-4.0 g N/L) could cause irreversible inhibition of the AMs due to significant cell death, whereas the activity of HMs could be fully or even over recovered from severe ammonia stress (FAN≤ 0.9 g N/L or TAN≤10 g N/L; pH ≤8.0). The different tolerance responses of AMs and HMs might be associated with the cell morphology, multiple energy-converting systems, and Gibbs free energy from substrate-level phosphorylation.

Anaerobic digester microbiome dynamics in response to moderate and failure-inducing shock loads of fats, oils and greases

Accidental organic overloading (shock loading) is common during the anaerobic co-digestion of fats, oils and greases (FOG) and may lead to decreased performance or reactor failure due to the effects on the microbiome. Here, adapted and non-adapted lab-scale anaerobic digesters were exposed to FOG shocks of varying organic strengths. The microbiome was sequenced during the recovery periods employed between each shock event. Non-failure-inducing shocks resulted in enrichment of fermentative bacteria, and acetoclastic and methylotrophic methanogens. However, sub-dominant bacterial populations were largely responsible for increased biogas production observed after adaptation. Following failure events, early recovery communities were dominated by Pseudomonas and Methanosaeta while late recovery communities shifted toward sub-dominant bacterial taxa and Methanosarcina. Generally, the recovered microbiome structure diverged from that of both the initial and optimized microbiomes. Thus, while non-failure-inducing FOG shocks can be beneficial, the adaptations gained are lost after a failure event and adaptation must begin again.

Novel bioaugmentation strategy boosted with biochar to alleviate ammonia toxicity in continuous biomethanation

This study investigated for the first time if ammonia tolerant methanogenic consortia can be stored in gel (biogel) and used in a later time on-demand as bioaugmentation inocula, to efficiently relieve ammonia inhibition in continuous biomethanation systems. Moreover, wood biochar was assessed as a potential enhancer of the novel biogel bioaugmentation process. Three thermophilic (55 °C), continuous stirred-tank reactors (R_Bgel, R_Char and R_Mix), operated at 4.5 g NH₄⁺-N L^-1 were exposed to biogel, biochar and mixture of biogel and biochar, respectively, while a fourth reactor (R_Ctrl) was used as control. The results showed that the methane production yields of R_Mix, R_Char and R_Bgel increased by 28.6%, 20.2% and 10.7%, respectively compared to R_Ctrl. The highest methane yield was achieved by the synergistic interaction between biogel and biochar. Additionally, biogel stimulated a rapid recovery of Methanoculleus thermophilus sp. and syntrophic acetate oxidising bacteria populations.

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.

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

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

Gradual development of ammonia-induced syntrophic acetate-oxidizing activities under mesophilic and thermophilic conditions quantitatively tracked using multiple isotopic approaches

Insights into microbiota adaptation to increased ammonia stress, and identification of indicator microorganisms can help to optimize the operation of anaerobic digesters. To identify microbial indicators and investigate their metabolic contribution to acetoclastic methanogenesis (AM), syntrophic acetate oxidation (SAO) or hydrogenotrophic methanogenesis (HM), 40 anaerobic batch reactors fed with acetate of 110 mmol/L were set up at NH₄⁺-N concentrations of 0.14 g/L, 5.00 g/L or 7.00 g/L, inoculated with thermophilic or mesophilic microbiota with or without pre-exposure to ammonia stress. Four stable carbon isotope probing approaches were applied in parallel, with [1,2-¹³C]-CH₃COOH, [2-¹³C]-CH₃COOH, [¹³C]NaHCO₃ or non-labeled CH₃COOH used individually. The last three approaches were used to quantify the methanogenic pathways by tracking labeled ¹³C or natural ¹³C signatures in the resulting CH₄ and CO₂, and consistently detected the dynamic transition of dominant pathways from AM to SAO-HM under ammonia stress. Results of quantitative PCR and fluorescence in-situ hybridization illustrated the procedure, acetotrophic methanogens being outcompeted by acetate-oxidizing syntrophs. The first and last isotope-labeling approaches were designed to probe the active acetate-mineralizing microbes with DNA-SIP. Known acetate-oxidizing bacteria like Syntrophaceticus and Tepidanaerobacter, as well as novel members of Pseudomonas, Bacillus and Symbiobacteraceae were detected, with Methanoculleus as the predominant H₂/CO₂-utilizing partner. Using NanoSIMS, some bacterial cells were observed to be fixing CO₂ from [¹³C]NaHCO₃. In this study, Methanosaeta was only active with ammonia < 200 mg-N/L; the syntrophs catalyzing SAO-HM started to compete with AM-conducting Methanosarcina at intermediate concentrations of ammonia, i.e. 200-500 mg-N/L, and outcompeted the acetotrophic methanogens with ammonia > 500 mg-N/L. Under ammonia stress, diverse known and novel microbial taxa were involved in acetate mineralization, comparable with those identified in previous studies.

Understanding methane emission from stored animal manure: A review to guide model development

National inventories of methane (CH₄ ) emission from manure management are based on guidelines from the Intergovernmental Panel on Climate Change using country-specific emission factors. These calculations must be simple and, consequently, the effects of management practices and environmental conditions are only crudely represented in the calculations. The intention of this review is to develop a detailed understanding necessary for developing accurate models for calculating CH₄ emission from liquid manure, with particular focus on the microbiological conversion of organic matter to CH₄ . Themes discussed are (a) the liquid manure environment; (b) methane production processes from a modeling perspective; (c) development and adaptation of methanogenic communities; (d) mass and electron conservation; (e) steps limiting CH₄ production; (f) inhibition of methanogens; (g) temperature effects on CH₄ production; and (h) limits of existing estimation approaches. We conclude that a model must include calculation of microbial response to variations in manure temperature, substrate availability and age, and management system, because these variables substantially affect CH₄ production. Methane production can be reduced by manipulating key variables through management procedures, and the effects may be taken into account by including a microbial component in the model. When developing new calculation procedures, it is important to include reasonably accurate algorithms of microbial adaptation. This review presents concepts for these calculations and ideas for how these may be carried out. A need for better quantification of hydrolysis kinetics is identified, and the importance of short- and long-term microbial adaptation is highlighted.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Investigation of Fats, Oils, and Grease Co-digestion With Food Waste in Anaerobic Membrane Bioreactors and the Associated Microbial Community Using MinION Sequencing

Co-digestion of fats, oils, and grease (FOG) with food waste (FW) can improve the energy recovery in anaerobic membrane bioreactors (AnMBRs). Here, we investigated the effect of co-digestion of FW and FOG in AnMBRs at fat mass loading of 0.5, 0.75, and 1.0 kg m^–3 day^–1 with a constant organic loading rate of 5.0 gCOD L^–1 day^–1 in both a single-phase (SP) and two-phase (TP) configuration. A separate mono-digestion of FW at an identical organic loading rate was used as the benchmark. During co-digestion, higher daily biogas production, ranging from 4.0 to 12.0%, was observed in the two-phase methane phase (TP-MP) reactor compared to the SP reactor, but the difference was statistically insignificant (p > 0.05) due to the high variability in daily biogas production. However, the co-digestion of FW with FOG at 1.0 kg m^–3 day^–1 fat loading rate significantly (p < 0.05) improved daily biogas production in both the SP (11.0%) and TP (13.0%) reactors compared to the mono-digestion of FW. Microbial community analyses using cDNA-based MinION sequencing of weekly biomass samples from the AnMBRs revealed the prevalence of Lactobacillus (92.2–95.7% relative activity) and Anaerolineaceae (13.3–57.5% relative activity), which are known as fermenters and fatty acid degraders. Syntrophic fatty acid oxidizers were mostly present in the SP and TP-MP reactors, possibly because of the low pH and short solid retention time (SRT) in the acid phase digesters. A greater abundance of the mcrA gene copies (and methanogens) was observed in the SP and MP reactors compared to the acid-phase (AP) reactors. This study demonstrates that FW and FOG can be effectively co-digested in AnMBRs and is expected to inform full-scale decisions on the optimum fat loading rate.

Comparison of microbial community structures between mesophilic and thermophilic anaerobic digestion of vegetable waste

The anaerobic digestion performance correlates with the functional microbial community. Mesophilic and thermophilic digestions of vegetable waste were conducted, and dynamics of the microbial community were investigated. The mesophilic and thermophilic collapsed stages occurred at organic loading rates of 1.5 and 2.0 g VS/(L d) due to the accumulation of volatile fatty acids with final concentrations of 2276 and 6476 mg/L, respectively. A high concentration of volatile fatty acids caused the severe inhibition of methanogens, which finally led to the imbalance between acetogenesis and methanogenesis. The mesophilic digestion exhibited a higher microbial diversity and richness than the thermophilic digestion. Syntrophic acetate-oxidizing coupled with hydrogenotrophic methanogenesis was the dominant pathway in the thermophilic stable system, and acetoclastic methanogenesis in the mesophilic stable system. The dominant acidogens, syntrophus, and methanogens were unclassified_f__Anaerolineaceae (8.68%), Candidatus_Cloacamonas (19.70%), Methanosaeta (6.10%), and Methanosarcina (4.08%) in the mesophilic stable stage, and Anaerobaculum (12.59%), Syntrophaceticus (4.84%), Methanosarcina (30.58%), and Methanothermobacter (3.17%) in thermophilic stable stage. Spirochaetae and Thermotogae phyla were the characteristic microorganisms in the mesophilic and thermophilic collapsed stages, respectively. These findings provided valuable information for the deep understanding of the difference of the microbial community and methane-producing mechanism between mesophilic and thermophilic digestion of vegetable waste.

Stress induced by crude glycerol in a thermophilic digester: microbial community divergence and resilience, but slow process recovery

Recovery from stress is an important property for anaerobic digestion (AD). Although AD is quite adaptable with regard to waste composition, new substrates added to stable systems may cause process decline. We tested whether crude glycerol would cause stress to a thermophilic AD microbiome previously stabilized long-term on a low C/N ratio feedstock. Three-percent (v/v) crude glycerol was added to the basal substrate (poultry litter) for two hydraulic retention time (HRT) periods. This caused stress where biogas volume and methane percentage dramatically decreased and VFA levels increased. When the basal substrate was resumed, secondary inhibition occurred, resulting in even greater stress (biogas production ceased, methane 3.6%). Unassisted recovery of system processes required eight HRT periods. In contrast, crude glycerol applied at a lower organic loading rate did not cause inhibition. Crude glycerol caused changes in dominance in the microbial community (16S rRNA pyrotags). Although process resilience was slow, the recovery of digester functions occurred in conjunction with the recovery of community structure, particularly putative syntrophic acetate-oxidizing bacteria. KEY POINTS: • Crude glycerol caused stress in thermophilic co-digestion with poultry litter. • Unassisted resilience of digester functions (methane) required 8 HRT. • Syntrophic acetate-oxidizing bacteria implicated for keystone resilience functions. Graphical abstract.

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste

BACKGROUND

Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited.

RESULTS

A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected.

CONCLUSIONS

Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.

Dynamic shifts within volatile fatty acid-degrading microbial communities indicate process imbalance in anaerobic digesters

Buildup of volatile fatty acids (VFAs) in anaerobic digesters (ADs) often results in acidification and process failure. Understanding the dynamics of microbial communities involved in VFA degradation under stable and overload conditions may help optimize anaerobic digestion processes. In this study, five triplicate mesophilic completely mixed AD sets were operated at different organic loading rates (OLRs; 1-6 g chemical oxygen demand [COD] L_R^-1day^-1), and changes in the composition and abundance of VFA-degrading microbial communities were monitored using amplicon sequencing and taxon-specific quantitative PCRs, respectively. AD sets operated at OLRs of 1-4 g COD L_R^-1day^-1 were functionally stable throughout the operational period (120 days) whereas process instability (characterized by VFA buildup, pH decline, and decreased methane production rate) occurred in digesters operated at ≥ 5 g COD L_R^-1day^-1. Though microbial taxa involved in propionate (Syntrophobacter and Pelotomaculum) and butyrate (Syntrophomonas) degradation were detected across all ADs, their abundance decreased with increasing OLR. The overload conditions also inhibited the proliferation of the acetoclastic methanogen, Methanosaeta, and caused a microbial community shift to acetate oxidizers (Tepidanaerobacter acetatoxydans) and hydrogenotrophic methanogens (Methanoculleus). This study's results highlight the importance of operating ADs with conditions that promote the maintenance of microbial communities involved in VFA degradation.

Detection of early imbalances in semi-continuous anaerobic co-digestion process based on instantaneous biogas production rate

The aim of this study was to investigate the use of biogas production rate kinetics for the monitoring of anaerobic co-digestion. Recent extensive studies of degradation pathways showed that acetoclastic methanogenesis is not always the main pathway. Hydrogenotrophic methanogenesis and syntrophic acetate oxidation can also dominate, mostly for operating conditions with high concentrations of ammonia or volatile fatty acids … These conditions are also known to cause instability in the digester's operation especially in co-digestion due to substrate variability. Therefore, co-digestion experiments were conducted with several co-substrates using a continuously stirred 35-L tank reactor. Degradation pathways and their potential shifts were identified by monitoring variations in biogas production rate kinetics using a principal component analysis model. The shifts in the degradation pathways were used to monitor the process. These shift points were found to provide early warnings of instabilities in the anaerobic co-digestion process.

New insights of enhanced anaerobic degradation of refractory pollutants in coking wastewater: Role of zero-valent iron in metagenomic functions

Coking wastewater (CWW) has long been a serious challenge for anaerobic treatment due to its high concentrations of phenolics and nitrogen-containing heterocyclic compounds (NHCs). Herein, we proposed and validated a new strategy of using zero-valent iron (ZVI) to strengthen the anaerobic treatment of CWW. Results showed that COD removal efficiencies was increased by 9.5-13.7% with the assistance of ZVI. GC-MS analysis indicated that the removal of phenolics and NHCs was improved, and the intermediate 2(1H)-Quinolinone of quinoline degradation was further removed by ZVI addition. High-throughput sequencing showed that phenolics and NHCs degraders, such as Levilinea and Sedimentibacter were significantly enriched, and the predicted gene abundance of xenobiotic degradation and its downstream metabolic pathways was also increased by ZVI. Network and redundancy analysis indicated that the decreased oxidation-reduction potential (ORP) by ZVI was the main driver for microbial community succession. This study provided an alternative strategy for strengthening CWW anaerobic treatment.

Increased loading stress leads to convergence of microbial communities and high methane yields in adapted anaerobic co-digesters

Enhancing biogas production, while avoiding inhibition of methanogenesis during co-digestion of grease interceptor waste (GIW), can help water resource recovery facilities reduce their carbon footprint. Here we used pre-adapted and non-adapted digesters to link microbial community structure to digester function. Before disturbance, the pre-adapted and non-adapted digesters showed similar methane production and microbial community diversity but dissimilar community composition. When exposed to an identical disturbance, the pre-adapted digester achieved better performance, while the non-adapted digester was inhibited. When re-exposed to disturbance after recovery, communities and performance of both digesters converged, regardless of the temporal variations. Co-digestion of up to 75% GIW added on a volatile solids (VS) basis was achieved, increasing methane yield by 336% from 0.180 to 0.785 l-methane/g-VS-added, the highest methane yield reported to date for lipid-rich waste. Progressive perturbation substantially enriched fatty acid-degrading Syntrophomonas from less than 1% to 24.6% of total 16S rRNA gene sequences, acetoclastic Methanosaeta from 2.3% to 11.9%, and hydrogenotrophic Methanospirillum from less than 1% to 6.6% in the pre-adapted digester. Specific hydrolytic and fermentative populations also increased. These ecological insights demonstrated how progressive perturbation can be strategically used to influence methanogenic microbiomes and improve co-digestion of GIW.

Different inhibitory mechanisms of chlortetracycline and enrofloxacin on mesophilic anaerobic degradation of propionate

In anaerobic digestion, propionate is a key intermediate whose degradation is thermodynamically challenging and accumulation is detrimental to the process. Many wastewater streams contain antibiotics due to its globally increasing use, and these compounds can inhibit methane production. However, the effect of antibiotics on propionate degradation in anaerobic digestion remains unclear. In this study, the influence of two antibiotics (chlortetracycline [CTC] and enrofloxacin [EFX]) on biogas production and mesophilic propionate-degrading microbial community was investigated. CTC strongly repressed propionate oxidation, acetate utilization, and methane production, while EFX only inhibited propionate oxidation and methane production to a lesser extent. Microbial community analyses showed that syntrophic propionate-oxidizing bacteria (SPOB) Syntrophobacter had strong tolerance to both CTC and EFX. CTC inhibition mainly acted on the activity of acetate-oxidizing bacteria (Mesotoga, Geovibrio, Tepidanaerobacter, unclassified Bacteroidetes, and unclassified Clostridia) and acetoclastic methanogen, while EFX inhibition applied to the SPOB Smithella and acetoclastic methanogen. Network analysis further indicated that more complicated correlation among bacterial genera occurred in CTC treatments. These results suggested that CTC and EFX inhibited propionate degradation via different mechanisms, which was the result of joint action by antibiotics and microbial interactions.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Hydrogenotrophic methanogens are the key for a successful bioaugmentation to alleviate ammonia inhibition in thermophilic anaerobic digesters

Bioaugmentation to alleviate ammonia inhibition under thermophilic anaerobic digestion has never been reported, as well as the working mechanism that allows a fast and successful bioaugmentation. Thus two bioaugmentation inocula (an enriched culture, and a mixed culture composed 50/50 by Methanoculleus thermophilus and the enriched culture) on the recovery of ammonia-inhibited thermophilic continuous reactors was assessed. The results showed that bioaugmentation improved methane yield by 11-13% and decreased the volatile fatty acids (VFA) by 45-52% compared to the control reactor (abiotic augmentation). Moreover, the importance of hydrogenotrophic methanogens to a fast and successful bioaugmentation was recognized. Specifically, the instant hydrogen partial pressure reduction by the bioaugmented hydrogenotroph created thermodynamically favourable conditions for the acetate oxidation process and consequently, the catabolism of other VFA. High-throughput sequencing results strengthened this explanation by showing that the bioaugmented M. thermophilus stimulated the growth of syntrophic acetate oxidising bacterium Thermacetogenium phaeum, immediately after bioaugmentation.

Air-side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome

Air-side stripping without a prior solid-liquid phase separation step is a feasible and promising process to control ammonia concentration in thermophilic digesters. During the process, part of the anaerobic biomass is exposed to high temperature, high pH and aerobic conditions. However, there are no studies assessing the effects of those harsh conditions on the microbial communities of thermophilic digesters. To fill this knowledge gap, the microbiomes of two thermophilic digesters (55°C), fed with a mixture of pig manure and nitrogen-rich co-substrates, were investigated under different organic loading rates (OLR: 1.1-5.2 g COD l-1  day-1 ), ammonia concentrations (0.2-1.5 g free ammonia nitrogen l-1 ) and stripping frequencies (3-5 times per week). The bacterial communities were dominated by Firmicutes and Bacteroidetes phyla, while the predominant methanogens were Methanosarcina sp archaea. Increasing co-substrate fraction, OLR and free ammonia nitrogen (FAN) favoured the presence of genera Ruminiclostridium, Clostridium and Tepidimicrobium and of hydrogenotrophic methanogens, mainly Methanoculleus archaea. The data indicated that the use of air-side stripping did not adversely affect thermophilic microbial communities, but indirectly modulated them by controlling FAN concentrations in the digester. These results demonstrate the viability at microbial community level of air side-stream stripping process as an adequate technology for the ammonia control during anaerobic co-digestion of nitrogen-rich substrates.

Microbial community dynamics in anaerobic digesters treating conventional and vacuum toilet flushed blackwater

Decentralized wastewater treatment represents a promising sustainable option for future wastewater management. Blackwater collected from toilets contains high concentrations of organic matter, ideal for energy recovery using anaerobic digestion. Up-flow anaerobic sludge blanket (UASB) reactors treating conventional toilet (CT, 9 L water per flush) and vacuum toilet (VT, 1 L water per flush) blackwater with increments of loadings were successfully operated to steady state in three phases. The organic loading rates were maintained at comparable levels between the two reactors. The methanisation rates were 0.23-0.29 and 0.41-0.48 gCH₄-COD/gfeedCOD in the CT and VT reactors, and the COD removal rates were 72% and 89%, respectively. The enriched microbial consortia and the community dynamics under different loading phases were compared. The rank abundance distributions and alpha-diversity showed that archaeal communities were predominated by mono-enrichments in both CT and VT reactors, while bacterial communities showed lower diversity in the VT reactor. Through principal coordinates analysis (beta-diversity), clear divergences of archaeal and bacterial communities between the CT and VT reactors were revealed, and the archaeal community developed at a slower rate than the bacterial community. The enriched archaea were hydrogenotrophic methanogens, Methanolinea in the CT reactor (56.6%), and Methanogenium in the VT reactor (62.3%). The enriched bacteria were Porphyromonadaceae in both CT (15.9%) and VT (13.4%) reactors, sulfate-reducing bacteria in the CT reactor, and Fibrobacteraceae in the VT reactor (13.8%). Links between enriched consortia and ammonia stress were discussed. Isotope fraction analysis of the biogas showed a slight shift from acetoclastic methanogenesis to hydrogenotrophic methanogenesis. A closer look into the predicted metagenomic functional profiles showed agreeing results, where hydrogenotrophic methanogenesis and fhs gene abundances were higher in the VT reactor. We demonstrated that different blackwater types enriched different microbial consortia, probably due to ammonia concentrations and sulfate loadings, which should be taken into consideration for practical applications.

Bioaugmentation strategy for overcoming ammonia inhibition during biomethanation of a protein-rich substrate

High ammonia levels inhibit anaerobic digestion (AD) process and bioaugmentation with ammonia tolerant methanogenic culture is proposed to alleviate ammonia inhibition. In the current study, hydrogenotrophic Methanoculleus bourgensis was bioaugmented in an ammonia-inhibited continuous reactor fed mainly with microalgae (a protein-rich biomass), at extreme ammonia levels (i.e. 11 g NH₄⁺-N L^-1). The results showed 28% increase in methane production immediately after bioaugmentation. Moreover, volatile fatty acids decreased rapidly from more than 5 g L^-1 to around 1 g L^-1, with a fast reduction in propionate concentration. High throughput 16s rRNA gene sequencing demonstrated that the bioaugmented M. bourgensis doubled its relative abundance after bioaugmentation. "Microbiological domino effect", triggered by the bioaugmented M. bourgensis establishing a newly efficient community, was proposed as the working mechanism of the successful bioaugmentation. Additionally, a strong aceticlastic methanogenesis was found at the end of the experiment evidenced by the dominant presence of Methanosarcina soligelidi and the low abundance of syntrophic acetate oxidising bacteria at the final period. Overall, for the first time, this study proved the positive effect of bioaugmentation on ammonia inhibition alleviation of the microalgae-dominating fed reactor, paving the way of efficient utilization of other protein-rich substrates in the future.

Two-Phase Improves Performance of Anaerobic Membrane Bioreactor Treatment of Food Waste at High Organic Loading Rates

Anaerobic membrane bioreactors (AnMBRs) are in use at the full-scale for energy recovery from food waste (FW). In this study, the potential for two-phase (acid/gas) AnMBR treatment of FW was investigated as a strategy to increase microbial diversity, thereby improving performance. Two bench-scale AnMBRs were operated in single-phase (SP) and two-phase (TP) mode across incremental increases in organic loading rate (OLR) from 2.5 to 15 g total chemical oxygen demand (COD) L·d^-1. The TP acid-phase (TP-AP) enriched total VFAs by 3-fold compared to influent FW and harbored a distinct microbial community enriched in fermenters that thrived in the low pH environment. The TP methane phase (TP-MP) showed increased methane production and resilience relative to SP as OLR increased from 3.5 to 10 g COD L·d^-1. SP showed signs of inhibition (i.e., rapid decrease in methane production per OLR) at 10 g COD L·d^-1, whereas both systems were inhibited at 15 g COD L·d^-1. At 10 g COD L·d^-1, where the highest difference in performance was observed (20.3% increase in methane production), activity of syntrophic bacteria in TP-MP was double that of SP. Our results indicate that AnMBRs in TP mode could effectively treat FW at OLRs up to 10 g COD·L day^-1 by improving hydrolysis rates, microbial diversity, and syntroph activity, and enriching resistant communities to high OLRs relative to AnMBRs in SP mode.

Influence of Traditional vs Alternative Dietary Carbohydrates Sources on the Large Intestinal Microbiota in Post-Weaning Piglets

Simple Summary

Nutritional and environmental changes result in significant physiological changes in pigs at the weaning stage. The post-weaning period is mainly characterized by low feed intake and feed efficiency, together with intestinal disturbances. Maximizing the energy intake is known to be critical for promoting growth in weaned piglets, and it is essential to formulate diets with highly digestible and absorbable nutrients/ingredients, as the degree of intestinal maturation is limited. The current challenge is to find new sustainable, effective, and simple carbohydrate sources to satisfy these conditions without producing detrimental effects on the gut ecosystem. In this research, processed and ready-to-eat food products that are no longer suitable for humans were tested, which have high potential as an alternative energy source for pig nutrition. The results demonstrated that replacing conventional ingredients with highly digestible and simple carbohydrate-rich ingredients in the diets of post-weaning piglets did not affect their growth. However, both the abundance and composition of the bacterial community in the large intestine changed. Thus, the results should be interpreted with caution, as they are case-specific, and when these alternative feed ingredients are used in the post-weaning period, their inclusion rate and their effect on microbiota must be carefully considered.

Abstract

In this study, common cereal grains were partially replaced by former foodstuffs products (FFPs) in post-weaning piglets’ diets, to investigate how these alternative ingredients influence the faecal microbiota in the post-weaning period. Twelve post-weaning piglets were housed for 16 days in individual pens and were then fed two diets: a standard wheat-barley-corn meal diet and a diet containing 30% FFPs, thus partially substituting conventional cereals. The growth performance was monitored and faecal microbiota was characterized by the next generation sequencing of the 16S rRNA gene. The results showed no detrimental effects on growth performance when FFPs were used. However, the FFP diet decreased the bacterial richness and evenness in the large intestine, while minor differences were observed in the taxa composition. The core microbiota composition was only slightly affected, and no differences between the two groups in the gut microbiota composition at the phylum level over time were observed. Thus, although these results should be interpreted with caution, as they are case-specific, FFPs can be potentially used as alternative carbohydrate sources in post-weaning piglets, but further investigations are necessary to clarify their impact on gut health when used for a longer period.

Impacts of feed dilution and lower solids retention time on performance of thermal hydrolysis/anaerobic digestion

The goal of this study was to evaluate using feed dilution/solids retention time (SRT) control to manage potential ammonia inhibition in highly loaded anaerobic digesters after thermal hydrolysis. The study compared three digesters operated at the same target volatile solids (VS) loading rate of 5.5 kg VS/d-m³ , but at different feed concentrations resulting in SRTs of 10, 15, and 18 days. Lowering the feed concentration decreased the digester total ammonia nitrogen concentrations which averaged 1,580, 2,610, and 3,080 mg NH 4 + -N/L for the 10-, 15-, and 18-day digesters. The VS reduction and methane yields were equivalent for the 15- and 18-day digesters and about 4% lower for the 10-day digester. Ammonia inhibition of the 18-day digester occurred early in the study, but the system acclimated over time. Feed dilution reduced the viscosity and the potential for volume expansion due to gas holdup and foaming. PRACTIONER POINTS: Feed dilution reduces digester ammonia concentrations and inhibition potential without sacrificing digester performance at lower SRTs. Feed dilution greatly reduces digester viscosity and associated issues with digester volume expansion due to gas holdup and foaming. Operating at the lower SRT does not impact cake solids after dewatering and substantially decreases polymer demand for conditioning.

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis

Ammonia caused disturbance of biogas production is one of the most frequent incidents in regular operation of biogas reactors. This study provides a detailed insight into the microbial community of a mesophilic, full-scale biogas reactor (477 kWh h-1 ) fed with maize silage, dried poultry manure and cow manure undergoing initial process disturbance by increased ammonia concentration. Over a time period of 587 days, the microbial community of the reactor was regularly monitored on a monthly basis by high-throughput amplicon sequencing of the archaeal and bacterial 16S rRNA genes. During this sampling period, the total ammonia concentrations varied between 2.7 and 5.8 g l-1 [NH4 + -N]. To gain further inside into the active metabolic pathways, for selected time points metatranscriptomic shotgun analysis was performed allowing the quantification of marker genes for methanogenesis, hydrolysis and syntrophic interactions. The results obtained demonstrated a microbial community typical for a mesophilic biogas plant. However in response to the observed changing process conditions (e.g. increasing NH4 + levels, changing feedstock composition), the microbial community reacted highly flexible by changing and adapting the community composition. The Methanosarcina-dominated archaeal community was shifted to a Methanomicrobiales-dominated archaeal community in the presence of increased ammonia conditions. A similar trend as in the phylogenetic composition was observed in the transcription activity of genes coding for enzymes involved in acetoclastic methanogenesis and syntrophic acetate oxidations (Codh/Acs and Fthfs). In accordance, Clostridia simultaneously increased under elevated ammonia concentrations in abundance and were identified as the primary syntrophic interaction partner with the now Methanomicrobiales-dominated archaeal community. In conclusion, overall stable process performance was maintained during increased ammonia concentration in the studied reactor based on the microbial communities' ability to flexibly respond by reorganizing the community composition while remaining functionally stable.

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

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

Impact of food-to-microorganisms ratio on the stability of aerobic granular sludge treating high-strength organic wastewater

This work investigated the long-term stability of aerobic granular sludge treating high-strength organic wastewater in a semi-pilot scale sequential batch reactor (SBR). The reactor was operated for 316 days under different operational conditions. It was found that the F/M ratio is an important parameter affecting granules formation and stability. Three selection mechanisms were investigated: (1) cultivation and maturation at moderately high influent COD concentration (2500 mg/L) followed by increase in influent COD concentration to 7500 mg/L; (2) stressed cultivation and operation at high influent COD concentration of 4500 mg/L; and (3) alternate feed loading strategy (variable influent COD concentration across the daily schedule of cycles at 50%, 75%, and 100% of the peak concentration of 5000 mg/L). It was found that adopting high OLR at the reactor start-up accelerated the formation of granules. However, the overgrowth of biomass under high organics concentration negatively affected the stability of granules and led to disintegration due to the presence of methanogens in the granule core. Cultivation at high organics concentration resulted in a rapid loss of microbial diversity and reactor failure. Under alternate feed loading, adequate selection of microbial community was maintained and resulted in stable reactor performance. Moreover, a strong correlation between F/M ratio and the granules settling ability was observed. When F/M ratio exceeded 1.5 gCOD/gSS.d, granules showed poor settleability and under very high sludge loading rates (above 2.5), sludge bulking occurred and led to washout of sludge due to the strong selection pressure of short settling time. Operating the reactor at F/M ratio of 0.5-1.4 gCOD/gSS.d appears to favor stable long-term granule stability.

Controlled experiment contradicts the apparent benefits of the Fenton reaction during anaerobic digestion at a municipal wastewater treatment plant

A previous study had reported that the Fenton reaction at full scale increased the digestibility of thickened sludge in a digester. The authors of the study had observed a positive effect on biogas productivity, but without a control. Here, we evaluated this result by investigating the anaerobic treatment characteristics of fresh, thickened sludge in an experimental design with a control. To accomplish this, two identical continuously stirred anaerobic digesters (CSADs) were operated in parallel at mesophilic conditions. We also included anaerobic settlers to mimic the full-scale plant and to accomplish sludge recycling. We fed fresh, thickened sludge to both setups once every other day, but performed the Fenton reaction with only the experimental system by adding H₂O₂ to the recycled biosolids from the anaerobic settler. We observed very large fluctuations in biogas production due to ever-changing characteristics of the thickened sludge both on a daily and seasonal basis. Regardless, the two setups performed almost identically with: 1) chemical oxygen demand removal efficiencies of 63.8 ± 2.9% and 62.1 ± 3.2%; and 2) biogas productivities of 0.280 and 0.279 L CH₄·g^-1 volatile solids for the experimental (with Fenton) and control (without Fenton) CSADs, respectively. These results indicate that the use of a Fenton reaction did not affect biogas productivities.

Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities

Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens.

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

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

Organic loading rate and hydraulic retention time shape distinct ecological networks of anaerobic digestion related microbiome

Understanding of how anaerobic digestion (AD)-related microbiomes are constructed by operational parameters or their interactions within the biochemical process is limited. Using high-throughput sequencing and molecular ecological network analysis, this study shows the succession of AD-related microbiome hosting diverse members of the phylum Actinobacteria, Bacteroidetes, Euryarchaeota, and Firmicutes, which were affected by organic loading rate (OLR) and hydraulic retention time (HRT). OLR formed finer microbial network modules than HRT (12 vs. 6), suggesting the further subdivision of functional components. Biomarkers were also identified in OLR or HRT groups (e.g. the family Actinomycetaceae, Methanosaetaceae and Aminiphilaceae). The most pair-wise link between Firmicutes and biogas production indicates the keystone members based on network features can be considered as markers in the regulation of AD. A set of 40% species ("core microbiome") were similar across different digesters. Such noteworthy overlap of microbiomes indicates they are generalists in maintaining the ecological stability of digesters.

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.

Comprehensive analysis of microbial communities in full-scale mesophilic and thermophilic anaerobic digesters treating food waste-recycling wastewater

Microbes were sampled for a year in a full-scale mesophilic anaerobic digester (MD) and a thermophilic anaerobic digester (TD) treating food waste-recycling wastewater (FRW), then microbial community structure, dynamics and diversity were quantified. In the MD, Fastidiosipila, Petrimonas, vadinBC27, Syntrophomonas, and Proteiniphilum were dominant bacterial genera; they may contribute to hydrolysis and fermentation. In the TD, Defluviitoga, Gelria and Tepidimicrobium were dominant bacteria; they may be responsible for hydrolysis and acid production. In the MD, dominant methanogens changed from Methanobacterium (17.1 ± 16.9%) to Methanoculleus (67.7 ± 17.8%) due to the increase in ammonium concentration. In the TD, dominant methanogens changed from Methanoculleus (42.8 ± 13.6%) to Methanothermobacter (49.6 ± 11.0%) due to the increase of pH. Bacteria and archaea were more diverse in the MD than in the TD. These results will guide development of microbial management methods to improve the process stability of MD and TD treating FRW.