Novel Syntrophic Isovalerate-Degrading Bacteria and Their Energetic Cooperation with Methanogens in Methanogenic Chemostats

Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors

Anaerobic digestion (AD) of organic wastes relies on the interaction and cooperation of various microorganisms. Phages are crucial components of the microbial community in AD systems, but their diversity and interactions with the prokaryotic populations are still inadequately comprehended. In this study, 2121 viral operational taxonomic units (vOTUs) were recovered from 12 anaerobic fatty acid-fed reactors. Notably, 63.1% of these vOTUs could not be assigned to any known family, revealing a substantial presence of uncharted phages specifically associated with AD environments. Over half of the vOTUs associated with hosts had the capability to infect multiple hosts, ranging from 2 to 49, with a prevalent tendency to infect 2-5 hosts. In silico predictions of phage-host linkages uncovered that only a small fraction of vOTUs were shared across different functional groups, including fermentative bacteria, syntrophic fatty acid-oxidising bacteria (SFOB) and methanogens. Phages linked to hosts in all three groups primarily consisted of generalists and temperate species, especially those linked to SFOB. Additionally, metabolic reconstruction identified auxiliary metabolic genes participating in fatty acid degradation, methanogenesis and energy conservation. The present study provides insights into phage characteristics and their in situ interactions with prokaryotic hosts, highlighting their ecological role in AD systems.

Characteristics of stachyose-induced effects on gut microbiota and microbial metabolites in vitro associated with obesity in children

Childhood obesity presents a serious health concern associated with gut microbiota alterations. Dietary interventions targeting the gut microbiota have emerged as promising strategies for managing obesity in children. This study aimed to elucidate the impact of stachyose (STS) supplementation on the gut microbiota composition and metabolic processes in obese children. Fecal samples were collected from 40 obese children (20 boys and 20 girls) aged between 6 and 15 and in vitro fermentation was conducted with or without the addition of STS, respectively, followed by 16S rRNA amplicon sequencing and analysis of short-chain fatty acids (SCFAs) and gases. Notably, our results revealed that STS supplementation led to significant alterations in gut microbiota composition, including an increase in the abundance of beneficial bacteria such as Bifidobacterium and Faecalibacterium, and a decrease in harmful bacteria including Escherichia-Shigella, Parabacteroides, Eggerthella, and Flavonifractor. Moreover, STS supplementation resulted in changes in SCFAs production, with significant increases in acetate levels and reductions in propionate and propionate, while simultaneously reducing the generation of gases such as H2S, H2, and NH3. The Area Under the Curve (AUC)-Random Forest algorithm and PICRUSt 2 were employed to identify valuable biomarkers and predict associations between the gut microbiota, metabolites, and metabolic pathways. The results not only contribute to the elucidation of STS's modulatory effects on gut microbiota but also underscore its potential in shaping metabolic activities within the gastrointestinal environment. Furthermore, our study underscores the significance of personalized nutrition interventions, particularly utilizing STS supplementation, in the management of childhood obesity through targeted modulation of gut microbial ecology and metabolic function.

Sulfate-reducing bacteria decreases fractional pressure of H2 to accelerate short-chain fatty acids production from waste activated sludge fermentation assisted with zero-valent iron activated sulfite pretreatment

The production of short-chain fatty acids (SCFAs) is constrained by substrate availability and the increased fractional pressure of H2 emitted by acidogenic/fermentative bacteria during anaerobic fermentation of waste activated sludge (WAS). This study introduced a novel approach employing zero-valent iron (ZVI)-activated sulfite pretreatment combined with H2-consuming sulfate-reducing bacteria (SRB) mediation to improve SCFAs, especially acetate production from WAS fermentation. Experimental results showed that the combined ZVI-activated sulfite and incomplete-oxidative SRB (io-SRB) process achieved a peak SCFAs production of 868.11 mg COD/L, with acetate accounting for 80.55 %, which was 7.90- and 2.18-fold higher than that obtained from raw WAS fermentation, respectively. This could be firstly attributed to the SO4- and OH generated by ZVI-activated sulfite, which significantly promoted WAS decomposition, e.g., soluble proteins and carbohydrates increased 14.3- and 10.8-fold, respectively, over those in raw WAS. The biodegradation of dissolved organic matter was subsequently enhanced by the synergistic interaction and H2 transfer between anaerobic fermentation bacteria (AFB) and io-SRB. The positive and negative correlations among AFB, nitrate-reducing bacteria (NRB) and the io-SRB consortia were revealed by molecular ecological network (MEN) and Mantel test. Moreover, the expression of functional genes was also improved, for instance, in relation to acetate formation, the relative abundances of phosphate acetyltransferase and acetate kinase was 0.002 % and 0.005 % higher than that in the control test, respectively. These findings emphasized the importance of sulfate radicals-based oxidation pretreatment and the collaborative relationships of multifunctional microbes on the value-added chemicals and energy recovery from sludge fermentation.

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.

Tailored short-chain fatty acids conversion from waste activated sludge fermentation via persulfate oxidation and C3-C5 io-SRB metabolizers

Boosting acetate production from waste activated sludge (WAS) fermentation is often hindered by the inefficient solubilization in the hydrolysis step and the high hydrogen pressure ( [Formula: see text] ) during the acidogenesis of C3-C5 short-chain fatty acid (SCFAs), i.e., propionate (HPr), butyrate (HBu) and valerate (HVa). Therefore, this study employed persulfate (PS) oxidation and C3-C5 incomplete-oxidative sulfate reducing bacteria (io-SRB) metabolizers to tailor SCFAs conversion from WAS fermentation. The decomposition efficiency, performance of SCFAs production was investigated. Results showed that the PS significantly promoted WAS decomposition, with a dissolution rate of 39.4%, which is 26.0% higher than the un-treated test. Furthermore, SCFAs yields were increased to 462.7 ± 42 mg COD/g VSS in PS-HBu-SRB, which was 7.4 and 2.2 times higher than that of un-treated and sole PS tests, respectively. In particular, the sum of acetate and HPr reached the peak value of 85%, indicating that HBu-SRB mediation promoted the biotransformation of HBu and macromolecular organics by reducing the [Formula: see text] restriction. Meanwhile, sulfate radical (SO4∙-)-based oxidation (SR-AOPs) was effective in the decomposition of WAS, the oxidative product, i.e., sulfate served the necessary electron acceptor for the metabolism of io-SRB. Further analysis of Mantel test revealed the cluster of the functional genus and their interaction with environmental variables. Additionally, molecular ecological network analysis explored the potential synergistic and competitive relationships between critical genera. Additionally, the potential synergistic and competitive relationships between critical genera was explored by molecular ecological network analysis. This study provides new insights into the integration of SR-AOPs with microbial mediation in accelerating SCFAs production from WAS fermentation.

Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti

Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.

Evaluating effects of biochar on anaerobic digestion of dewatered waste activated sludge: Digester performance, microbial co-metabolism and underlying mechanism

Biochar has been proven to be capable of improving the performance of anaerobic digestion (AD). However, the effect of biochar on microbial communities remains ambiguous. In this study, the influence of pH was excluded in a semi-continuous anaerobic digestor for the treatment of dewatered waste activated sludge (WAS) to determine the effect of biochar on microbes. Compared with the control group, the average methane production increased by 24.5% and 23.2% at the organic loading rates (OLRs) of 1.56 and 3.00 gTS/L/d, respectively, in the presence of biochar. This study innovatively found biochar accelerated the enrichment of Methanofastidiosaceae, which competed with Methanobacteriaceae for H2, and its abundance increased from 0.99% at the OLR of 1.56 g TS/L/d to 16.57% and 38.11% at the OLR of 3.00 and 5.60 gTS/L/d, respectively. The efficient metabolic network of f__norank_o__Aminicenantales, syntrophic bacteria, Methanofastidiosaceae and Methanosaetaceae promoted the conversion of WAS to CH4 in the biochar group. In addition, metagenome analysis revealed that biochar optimized the metabolites related to energy conservation and electron transfer, particularly for hydrogenase (frhABG, mbhLHK and hndA-D), confirming that biochar changed the way H2 was involved in methanogenesis. These findings provide novel insights into the direct effect of biochar on microbial evolution and facilitate the reduction of WAS to achieve higher economic benefits in biogas production.

Using heat-activated persulfate to accelerate short-chain fatty acids production from waste activated sludge fermentation triggered by sulfate-reducing microbial consortium

Persulfate has been applied extensively for waste activated sludge (WAS) decomposition due to the strong oxidizing sulfate radical generated as a product. However, the efficiency is not improved without activation to produce free radicals. In this study, a novel coupling strategy of heat-activated persulfate (Heat_PS) pretreatment and sulfate-reducing bacteria (SRB) triggering was explored to enhance short-chain fatty acids (SCFAs) produced by WAS fermentation. The remaining sulfate acts as an essential acceptor of electrons for the metabolism of synergistic SRB, thereby boosting WAS acidification by energetic cooperation with anaerobic fermenters. The results showed that SCFAs yield in the Heat_PS + SRB group peaked at 431.89 mg COD/gVSS, with the proportion of acetate reaching 57.8 %. This was 6.33 and 1.75 times higher than that in raw and single Heat_PS treated WAS, respectively. Carbon balance revealed a conversion rate of 26.1 % of carbon content in WAS to SCFAs, with 4.5 % lower CO₂ equivalents emitted than that in raw WAS fermentation by the assessments of environmental impacts. This was partially attributed to the strong decomposition of WAS by SO₄^•- and ^•OH oxidation from heat-activated PS and the SRB trigger. In addition, the synergistic relationship among acidogenic/fermentative bacteria and SRB consortia was further verified by the positive correlation among Desulfovibrio, the hydrolytic Escherichia-Shigella, Morganella and the fermetative Macellibacteroides and Bacteroides, as revealed by molecular ecological networks (MENs) analysis. The results of this study may highlight the cooperation of the synergistic micribial consortia as an additional perspective for the recovery of value-added biological metabolites from complex biotransformation.

Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress

Microorganisms in anaerobic digestion (AD) are easily affected by ammonia, especially acetoclastic methanogens. Thus, in ammonia-suppressed AD systems, acetate degradation is reported to be carried out mainly by the cooperation of syntrophic acetate oxidizers and hydrogenotrophic methanogens. Previous studies have revealed ammonia inhibition on microbial flora by AD performance, but the effect mechanism of ammonia on microbial metabolism remains poorly understood. In this study, we constructed a mesophilic chemostat fed with acetate as the sole carbon source, gradually increased the total ammonia nitrogen (TAN) concentration from 1 g L^-1 to 6 g L^-1, and employed the 16S rRNA gene, metagenomics, and metatranscriptomics analysis to characterize the microbial community structure and metabolic behavior. The results showed that even at the TAN of 6 g L^-1 (pH 7.5), the methanogenesis kept normal, the biogas production was approximately 92% of that at TAN of 1 g L^-1 and the acetate degradation ratio reached 99%, suggesting the strong TAN tolerance of the microbial community enriched. 16S rRNA gene analysis suggested that the microbial community structure changed along with the TAN concentration. Methanothrix predominated in methanogens all the time, in which the dominant species was gradually replaced from M. soehngenii to M. harundinacea with the increased TAN. Dominant bacterial species also changed and Proteiniphilum showed a significant positive correlation with increased TAN. Meta-omics analysis showed that the absolute dominant microorganisms at TAN of 6 g L^-1 were M. harundinacea and Proteiniphilum, both of which highly expressed genes for anti-oxidative stress. M. harundinacea and the second dominant methanogen Methanosarcina highly expressed both acetate cleavage and CO₂ reduction pathways, suggesting the possibility that these two pathways contributed to methanogenesis together. Proteiniphilum and some other species in Firmicutes and Synergistetes were likely acetate oxidizers in the community as they highly expressed genes for syntrophic acetate oxidization, H₂ generation, and electron transfer. These results suggested that Proteiniphilum as well as M. harundinacea have strong ammonia tolerance and played critical roles in acetate degradation under ammonia-suppressed conditions. The achievements of the study would contribute to the regulation and management of the AD process.

Biodegradation of phenol by Candida tropicalis sp.: Kinetics, identification of putative genes and reconstruction of catabolic pathways by genomic and transcriptomic characteristics

Candida tropicalis sp. was isolated with predominant biodegradation capability to phenol compounds, even with high concentration or in acid environment. The biodegradation of phenol was evaluated at the following concentrations 10-1750 mg L^-1, the strain exhibited well biodegradation efficiency. The maximum specific growth rate was 0.660 h^-1 and the specific biodegradation rates was 0.47 mg (phenol) [(mg (VSS) h]^-1. Differentially expressed genes were screened out, and results revealed a complete process of energy and carbon metabolism. The genes' arrangements and phylogenetic information showed the unique genetic characteristics of the strain. Catabolic pathways were reconstructed and some key phenol-degrading genes were obviously upregulated, including pheA, catA, OXCT and fadA. A notable detail that CMBL encoding carboxymethylenebutenolidase was speculated to be involved in a shortened pathway of phenol biodegradation, thereby contributing to the reconstruction of the novel phenol catabolic pathway through the hydrolases of dienelactone. Finally, key enzymes were verified by the analysis of specific activity.

Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis

Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (∼130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner-Doudoroff pathway of alginate via 5-dehydro-4-deoxy-d-glucuronate (DDG) and 3-deoxy-d-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.

Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats

In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.

Effects of a Postbiotic and Prebiotic Mixture on Suckling Rats' Microbiota and Immunity

Human milk serves as a model for infant formula providing nutritional solutions for infants not able to receive enough mother's milk. Infant formulas aim to mimic the composition and functionality of human milk by providing ingredients reflecting those of the latest human milk insights, such as prebiotics, probiotics and postbiotics. The aim of this study was to examine the effects of the supplementation with a postbiotic (LactofidusTM) and its combination with the prebiotics short-chain galactooligosaccharides (scGOS) and long-chain fructooligosaccharides (lcFOS) in a preclinical model of healthy suckling rats. Pups were supplemented daily with LactofidusTM (POST group) and/or scGOS/lcFOS (P+P and PRE groups, respectively). Body weight and fecal consistency were analyzed. At the end of the study, immunoglobulin (Ig) profile, intestinal gene expression, microbiota composition and short chain fatty acid (SCFA) proportion were quantified. The supplementation with all nutritional interventions modulated the Ig profile, but the prebiotic mixture and the postbiotic induced differential effects: whereas scGOS/lcFOS induced softer feces and modulated microbiota composition and SCFA profile, Lactofidus™ upregulated Toll-like receptors gene expression. The use of the combination of scGOS/lcFOS and Lactofidus™ showed the effects observed for the oligosaccharides separately, as well as showing a synergistic impact on animal growth. Thus, the combined use of both products seems to be a good strategy to modulate immune and microbial features in early life.

Effects of inhibitions by sodium ion and ammonia and different inocula on acetate-utilizing methanogenesis: Methanogenic activity and succession of methanogens

Acetate-fed anaerobic sequential batch experiments with four different inhibitory conditions (non-inhibitory (Lo), sodium-ion inhibitory (Na), ammonia inhibitory (Am), combined inhibitory (Hi)) were conducted using thirteen different inocula to investigate the inhibition effects by sodium-ion and ammonia and different inocula on acetate-utilizing methanogenesis and succession of methanogens. Sodium-ion and ammonia significantly extended lag-time λ and reduced specific-methanogenic-activity RCH4, and caused synergistic inhibition. The inhibition differed according to the initial methanogen community structures: the inhibition effects on λ and RCH4 were strongest ininocula with Methanosaeta concilii dominant and weakest in inocula with Methanoculleus bourgensis dominant. These inhibitory conditions determined the succession of methanogens: the most competitive methanogens were Methanosaeta concilii in Lo, Methanosarcina sp. in Na, Methanosarcina sp. and Methanoculleus bourgensis in Am, Methanoculleus bourgensis in Hi. This study provides valuable information for microbial management and optimization for AD processes treating wastewater that is rich in protein and/or salt.