Multi-scale analysis of the foaming mechanism in anaerobic digestion of food waste: From physicochemical parameter, microbial community to metabolite response

Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge

Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.

Changes in bacterial diversity of full-scale anaerobic digesters treating secondary sludge

Anaerobic digestion (AD) of secondary sludge (2S) presents challenges because of its high microbial content and complex cell wall structures. The purpose of this study was to investigate the effects of spatiotemporally-variable factors such as water temperature and dietary habits on the 2S bacterial community and its migration into digesters. Bacterial communities and functions were analyzed using high-throughput pyrosequencing. Spatiotemporal variations in bacterial populations were identified, with genera such as Zoogloea and Dechloromonas migrating into digesters and influencing organic degradation. Notably, Zoogloea was negatively correlated with VS removal, potentially due to cell floc formation, whereas Dechloromonas was positively correlated, suggesting its role in acetate metabolism anaerobically. This study emphasizes the importance of microbial migration from 2S to digesters, highlighting the need to monitor microbial communities along with conventional parameters to increase AD performance. These findings provide practical insights into optimizing sludge management and improving biogas production in AD plants.

Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis

Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.

Multi-omics analysis of nitrifying sludge under carbon disulfide stress: Nitrification performance and molecular mechanisms

Carbon disulfide (CS2) is a widely used enzyme inhibitor with cytotoxic properties, commonly employed in viscose fibers and cellophane production due to its non-polar characteristics. In industry, CS2 is often removed by aeration, however, residual CS2 may enter the wastewater treatment plants, impacting the performance of nitrifying sludge. Currently, there is a notable dearth of research on the response of nitrifying sludge to CS2-induced stress. This study delves into the alterations in the performance of nitrifying sludge under short-term and long-term CS2 stress, scrutinizes the toxic effects of CS2 on microbial cells, elucidates the succession of microbial community structure, and delineates changes in microbial metabolic products. The findings from short-term CS2 stress revealed that low concentrations of CS2 induced oxidative stress damage, which was subsequently repaired in cells. However, at concentrations of 100-200 mg/L, CS2 inhibited reactive oxygen species, superoxide dismutase, and catalase, which are associated with metabolic and antioxidant activities. The inhibition of nitrite oxidoreductase activity by high concentrations of CS2 was attributed to its impact on the enzyme's conformation. Prolonged CS2 stress resulted in an increase in the secretion of soluble extracellular polymeric substances in sludge, while CS2 was assimilated into sulfate. The analysis of sludge microbial community structure revealed a decline in the relative abundance of Rhodanobacter, which is associated with nitrification, and an increase in Sinomonas, involved in sulfur oxidation. Metabolite analysis results demonstrated that high concentrations of CS2 affect pantothenate and CoA biosynthesis, purine metabolism, and glutathione metabolism. This study elucidated the microbial response mechanism of nitrifying sludge under short-term and long-term CS2 stress. It also clarified the composition and function of microbial ecosystems, and identified key bacterial species and metabolites. It provides a basis for future research to reduce CS2 inhibition through approaches such as the addition of metal ions, the selection of efficient CS2-degrading strains, and the modification of strain metabolic pathways.

Revealing the comprehensive impact of organic compounds on the partial nitrification-anammox system during incineration leachate treatment: metabolic hierarchy and adaptation

Organics, as widespread pollutants in high-strength ammonia wastewater, typically exert adverse effects on the performance of partial nitrification-anammox (PNA) systems. However, the in-depth knowledge on how microbial consortia respond to these disturbances remains limited. In this study, we unveiled the evolution of complex organic matter flow and its impact on the metabolic hierarchy and adaptation of microbial consortia, employing multi-omics approaches, i.e., 16S amplicon sequencing, metagenomics, and metabolomics. In a two-stage PNA system sequentially treating synthetic wastewater and incineration leachate over 230 days, partial nitrification stayed stable (nitrite accumulation > 97%) while anammox efficiency dropped (nitrogen removal decreased from 86% to 78%). The phenomenon was revealed to be correlated with the evolution of dissolved organic matter (DOM) and xenobiotic organic compounds (XOCs). In the PN stage, ammonia-oxidizing bacteria (AOB) exhibited excellent adaptability through active metabolic regulation after treating leachate. Numerous heterotrophs proliferated to utilize DOM and XOCs, triggering a "boom" state evident in the glycerophospholipid metabolism. However, in the anammox stage, the competition between carbon fixation and central carbon metabolism within autotrophs and heterotrophs became evident. Increased biosynthesis costs inhibited the central metabolism (specific anammox activity decreased by 66%) and the Wood-Ljungdahl pathway of anammox bacteria (AnAOB) in the presence of recalcitrant organics. Additionally, the degradation of organics was limited, exhibiting a "bust" state. This study revealed the metabolic adaption and susceptibility of AOB and AnAOB in response to organics from the leachate, demonstrating the applicability of the two-stage configuration for treating high-strength wastewater containing abundant and diverse organics.

Review in anaerobic digestion of food waste

Due to the special property of food waste (FW), anaerobic digestion of food waste is facing many challenges like foaming, acidification, ammonia nitrogen and (NH4+-N) inhibition which resulted in a low biogas yield. A better understanding on the problems exiting in the FW anaerobic digestion would enhance the bio-energy recovery and increase the stable operation. Meanwhile, to overcome the bottle necks, pretreatment, co-digestion and additives is proposed as well as the solutions to improve biogas yield in FW digestion system. At last, future research directions regarding FW anaerobic digestion were proposed.

Microbiome-functionality in anaerobic digesters: A critical review

Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.

Regulation methods and enhanced mechanism on the efficient degradation of aromatics in biochemical treatment system of coal chemical wastewater

In order to address the problems of poor treatment effect of coal chemical wastewater (CCW) biochemical treatment system resulting in non-compliance with effluent standards and unstable operation, a combination regulation method of co-substrate metabolism and predominant flora enhancement was constructed, and the performance and mechanism of enhanced degradation of aromatics in CCW was also investigated in this study. The results showed that when the influent concentration of chemical oxygen demand (COD) and aromatics was less than 600 mg/L and 180 mg/L respectively, there was no significant effect of the combined regulation method on the enhanced treatment of aromatics, the removal rate of total organic carbon (TOC) in the system could all more than 73%; while when the influent concentration of COD increased to 800 mg/L and the aromatics concentration increased to more than 240 mg/L, the ordinary activated sludge system had collapsed. Compared with the regulation method of co-substrate metabolism alone, the combination regulation method increased the removal rate of TOC by 21%. The analysis of antioxidant enzyme activity showed that under the combination regulation method, the antioxidant enzyme activity of microorganisms was higher and their resistance to adverse environments was stronger. EPS and dehydrogenase analysis indicated that the combination regulation method was more conducive to microbial degradation of aromatics. Meanwhile, the analysis of microbial community structure showed that the aromatics degradation bacteria genera Rhodococcus, Luteococcus, etc. were enriched under the combination regulation method. The study provides a theoretical basis and technical guidance for solving the problems of unstable operation of CCW biochemical treatment systems and non-compliance with effluent standards.

Removal of nitrate nitrogen by Pseudomonas JI-2 under strong alkaline conditions: Performance and mechanism

The nitrate nitrogen removal characteristics of Pseudomonas JI-2 under strong alkaline conditions and the composition and functional groups of extracellular polymeric substance were analyzed. Furthermore, nontargeted metabonomics and bioinformatics technology were used to investigate the alkaline tolerance mechanism. JI-2 removed 11.05 mg N/(L·h) of nitrate with the initial pH, carbon to nitrogen ratio and temperature were 11.0, 8 and 25 °C respectively. Even when the pH was maintained at 11.0, JI-2 could still effectively remove nitrate. JI-2 contains a large number of Na+/H+ antiporters, such as Mrp, Mnh (mnhACDEFG) and Pha (phaACDEFG), which can stabilize the intracellular acid-base environment, and SlpA can enable quick adaptation to alkaline conditions. Moreover, JI-2 responds to the strong alkaline environment by secreting more polysaccharides, acidic functional groups and compatible solutes and regulating key metabolic processes such as pantothenate and CoA biosynthesis and carbapenem biosynthesis. Therefore, JI-2 can survive in strong alkaline environments and remove nitrate efficiently.

Integrated genome-centric metagenomic and metaproteomic analyses unravel the responses of the microbial community to ammonia stress

Ammonia is a major inhibitor in anaerobic digestion of nitrogen-rich organic wastes. In this study, integrated genome-centric metagenomic and metaproteomic analyses were used to identify the key microorganisms and metabolic links causing instability by characterizing the process performance, microbial community, and metabolic responses of key microorganisms during endogenous ammonia accumulation. The identification of 89 metagenome-assembled genomes and analysis of their abundance profile in different operational phases permitted the identification of key taxa (Firmicutes and Proteobacteria) causing poor performance. Metabolic reconstruction indicated that the key taxa had the genetic potential to participate in the metabolism of C2C5 volatile fatty acids (VFAs). Further investigation suggested that during Phase I, the total ammonia nitrogen (TAN) level was maintained below 2000 mg N/L, and the reactor showed a high methane yield (478.30 ± 33.35 mL/g VS) and low VFAs concentration. When the TAN accumulated to > 2000 mg N/L, acid accumulation, mainly of acetate, began to occur, and the methane yield gradually decreased to 330.44 mL/g VS (Phase II). During this phase, the VFA degradation functions of the community were mainly mediated by Firmicutes. Approximately 61.54% of significant differentially expressed proteins (DEPs) related to acetate metabolism in Firmicutes were down-regulated, which led to an increase in acetate concentration to 4897.91 ± 1558.96 mg/L. However, the reactor performance showed spontaneous recovery without any interference (Phase III), during which Firmicutes gradually adapted to the high ammonia conditions. Approximately 75% of the significant DEPs related to acetate metabolism of Proteobacteria were also up-regulated in Phase III compared with Phase II; thus, VFA-related metabolic functions of the community were enhanced, which resulted in a decrease in the total VFA concentration to 195.39 mg/L. When the TAN increased above 4000 mg N/L, the system gradually showed acid accumulation dominated by propionate, accompanied by a second decrease in methane yield (Phase IV). During this phase, the number of up-regulated and down-regulated proteins related to acetate metabolism of Firmicutes and butyrate/valerate metabolism of Proteobacteria was comparable with that of Phase III, indicating that the metabolic functions related to acetate, butyrate, and valerate of the microbial community were not significantly affected. However, for propionate metabolism, the expression activity of fumarate hydratase from Firmicutes and Proteobacteria was severely inhibited by ammonia, as shown by down-regulation ratios of 63.64% and 85.71%, respectively. No protein with the same function that was not inhibited by ammonia could be detected, and the fumarate degradation function of the microbial community was severely damaged, leading to blocked propionate metabolism and irreversible deterioration of reactor performance. This study has provided a new perspective on the microecological mechanisms of ammonia inhibition.

Effects of different concentrations of butyrate on microbial community construction and metabolic pathways in anaerobic digestion

Investigating the effect of butyric acid concentration on anaerobic digestion systems in complex systems is important for the efficient degradation of butyric acid and improving the efficiency of anaerobic digestion. In this study, different loadings of butyric acid with 2.8, 3.2, and 3.6 g/(L·d) were added to the anaerobic reactor. At a high organic loading rate of 3.6 g/(L·d), methane was efficiently produced with VBP (Volumetric Biogas Production) of 1.50 L/(L·d) and biogas content between 65% and 75%. VFAs concentration remained below 2000 mg/L. Metagenome sequencing revealed changes in the functional flora within different stages. Methanosarcina, Syntrophomonas, and Lentimicrobium were the main and functional microorganisms. That the relative abundance of methanogens exceeded 35% and methanogenic metabolic pathways were increased indicated the methanogenic capacity of the system significantly improved. The presence of a large number of hydrolytic acid-producing bacteria also indicated the importance of the hydrolytic acid-producing stage in the system.

Physiological Responses of Methanosarcina barkeri under Ammonia Stress at the Molecular Level: The Unignorable Lipid Reprogramming

Acetotrophic methanogens' dysfunction in anaerobic digestion under ammonia pressure has been widely concerned. Lipids, the main cytomembrane structural biomolecules, normally play indispensable roles in guaranteeing cell functionality. However, no studies explored the effects of high ammonia on acetotrophic methanogens' lipids. Here, a high-throughput lipidomic interrogation deciphered lipid reprogramming in representative acetoclastic methanogen (Methanosarcina barkeri) upon high ammonia exposure. The results showed that high ammonia conspicuously reduced polyunsaturated lipids and longer-chain lipids, while accumulating lipids with shorter chains and/or more saturation. Also, the correlation network analysis visualized some sphingolipids as the most active participant in lipid-lipid communications, implying that the ammonia-induced enrichment in these sphingolipids triggered other lipid changes. In addition, we discovered the decreased integrity, elevated permeability, depolarization, and diminished fluidity of lipid-supported membranes under ammonia restraint, verifying the noxious ramifications of lipid abnormalities. Additional analysis revealed that high ammonia destabilized the structure of extracellular polymeric substances (EPSs) capable of protecting lipids, e.g., declining α-helix/(β-sheet + random coil) and 3-turn helix ratios. Furthermore, the abiotic impairment of critical EPS bonds, including C-OH, C═O-NH-, and S-S, and the biotic downregulation of functional proteins involved in transcription, translation, and EPS building blocks' supply were unraveled under ammonia stress and implied as the crucial mechanisms for EPS reshaping.

Effects of initial volatile fatty acid concentrations on process characteristics, microbial communities, and metabolic pathways on solid-state anaerobic digestion

Solid-state anaerobic digestion (SSAD) is vulnerable to excess volatile fatty acids (VFA), mainly acetate and propionate. The co-effects of VFAs and microbial dynamics under VFA accumulation were investigated in SSAD of pig manure and corn straw. Adding 2 and 4 mg/g acetate or propionate caused initial increases in total VFAs, followed by decreases after day 6, resulting in 'mild' VFA accumulation, while adding 6 mg/g caused similarly increased VFAs, but with no subsequent decrease, causing 'severe' VFA accumulation and poor methanation performance. Mild propionate accumulation promoted acetate consumption, whereas acetate accumulation inhibited propionate degradation by affecting crucial redox reactions. Under severe VFA accumulation, hydrolysis and acidification mainly conducted by acid-tolerant Clostridium sp. exacerbated VFA inhibition, causing a competition between Methanosarcina and Methanosaeta, and impairments of acetoclastic and hydrogenotrophic methanogenesis and interspecies formate transfer. This study provides new insights into mechanisms of VFA accumulation in SSAD, and its effects on methanogenesis.

Evaluation of digestate-derived biochar to alleviate ammonia inhibition during long-term anaerobic digestion of food waste

The feasibility of using food waste anaerobic digestate-derived biochar (FWDB) to mitigate ammonia toxicity in an anaerobic digester was evaluated. The optimal conditions for preparing and adding the activated FWDB were explored using response surface experiments, and the long-term effects of adding activated FWDB on digester performance under optimum conditions were verified in semi-continuous experiments. The results showed that the optimal preparation and addition conditions for activated FWDB were pyrolysis temperature of 565 °C, particle size of 0-0.30 mm, and dosage of 15.52 g·L-1. During the long-term operation of the digesters, when the total ammonia nitrogen (TAN) concentration was higher than 2000 mg·L-1, the control and experimental digesters showed deteriorated reactor performance. Volatile fatty acids in the control digester accumulated to 20,306 mg·L-1 after the TAN concentration increased to 3391 mg·L-1, the methane yield decreased to 31 mL·g VS-1, and the digester experienced process failure. In contrast, the experimental digester with added activated FWDB only suffered a slight short-term accumulation of acetate and a slight decline in methane yield. This may be attributed to the adsorption of NH4+/NH3 by activated FWDB, which reduced the TAN concentration in the anaerobic digestion (AD) system and mitigated ammonia toxicity. Microbial analysis and metagenome predictions demonstrated that the community richness, diversity, and evenness, as well as the abundance of acetogens and related key genes (ACSM1, paaF, and acdA) were higher in the experimental digester than in the control digester. This study provides a closed-loop AD enhancement strategy by pyrolysis of digestate and in-situ supplementation into the digester.