Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches

Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular

The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.

Metagenomic analysis reveals metabolic mechanism of enhancing lignocellulosic anaerobic digestion mediated by CO2/O2-nanobubble water

Nanobubble water (NW) has been reported to enhance anaerobic digestion (AD), but its influence on the metabolic pathways of microorganisms remains unclear. In this study, the specific methane yields of rice straw in the CO2NW and O2NW treatments increased by 6.9% and 18.3%, respectively. The electron transport system (ETS) and coenzyme F420 activities were enhanced by the addition of NW. Metagenomic analysis showed that the abundances of most enzymes in the acidification were significantly increased by both CO2NW and O2NW. Regarding methanogenesis, CO2NW promoted the expression of genes encoding enzymes of hydrogenotrophic methanogenesis, while O2NW stimulated both the acetoclastic and hydrogenotrophic methanogenesis. With the addition of O2NW, the expressions of modules related to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation were enhanced, resulting in increased ATP production. This study provided fundamental evidence of the metabolic pathways of microorganisms mediated by NW at each stage of AD.

A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review

The increasing reliance on fossil fuels and the growing accumulation of organic waste necessitates the exploration of sustainable energy alternatives. Anaerobic digestion (AD) presents one such solution by utilizing secondary biomass to produce biogas while reducing greenhouse gas emissions. Given the crucial role of microbial activity in anaerobic digestion, a deeper understanding of the microbial community is essential for optimizing biogas production. While metagenomics has emerged as a valuable tool for unravelling microbial composition and providing insights into the functional potential in biodigestion, it falls short of interpreting the functional and metabolic interactions, limiting a comprehensive understanding of individual roles in the community. This emphasizes the significance of expanding the scope of metagenomics through innovative tools that highlight the often-overlooked, yet crucial, role of microbiota in biomass digestion. These tools can more accurately elucidate microbial ecological fitness, shared metabolic pathways, and interspecies interactions. By addressing current limitations and integrating metagenomics with other omics approaches, more accurate predictive techniques can be developed, facilitating informed decision-making to optimize AD processes and enhance biogas yields, thereby contributing to a more sustainable future.

Utilization strategy for algal bloom waste through co-digestion with kitchen waste: Comprehensive kinetic and metagenomic analysis

Anaerobic co-digestion (AcoD) with kitchen waste (KW) is an alternative utilization strategy for algal bloom waste (AW). However, the kinetic characteristic and metabolic pathway during this process need to be explored further. This study conducted a comprehensive kinetic and metagenomic analysis for AcoD of AW and KW. A maximum co-digestion performance index (CPI) of 1.13 was achieved under the 12% AW addition. Co-digestion improved the total volatile fatty acids generation and the organic matter transformation efficiency. Kinetic analysis showed that the Superimposed model fit optimally (R2Adj = 0.9988-0.9995). The improvement of the kinetic process by co-digestion was mainly reflected in the increase of the methane production from slowly biodegradable components. Co-digestion enriched the cellulolytic bacterium Clostridium and the hydrogenotrophic methanogenic archaea Methanobacterium. Furthermore, for metagenome analysis, the abundance of key genes concerned in cellulose and lipid hydrolysis, pyruvate and methane metabolism were both increased in co-digestion process. This study provided a feasible process for the utilization of AW produced seasonally and a deeper understanding of the AcoD synergistic mechanism from kinetic and metagenomic perspectives.

Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales

Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.

Distinctive effects of graphene oxide and reduced graphene oxide on methane production kinetics and pharmaceuticals removal in anaerobic reactors

Graphene oxide (GO) addition to anaerobic digestion has been suggested to enhance direct electron transfer. The impact of GO (0.075 g GO g-1 VS) and biologically and hydrothermally reduced GO (bio-rGO and h-rGO, respectively) on the methane production kinetics and removal of 12 pharmaceuticals was assessed in Fed-batch reactors. A decrease of 15 % in methane production was observed in the tests with GO addition compared with the control and the h-rGO. However, bio-rGO and h-rGO substantially increased the methane production rate compared to the control tests (+40 %), in the third fed-batch test. Removal of pharmaceuticals was enhanced only during the bio-reduction of GO (1st fed-batch test), whereas once the GO was bio-reduced, it followed a similar trend in the control and h-rGO tests. The addition of GO can enhance the methane production rate and, therefore, reduce the anaerobic treatment time.

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

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

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective

Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.

Metagenomic analysis of ethylene glycol contamination in anaerobic digestion

Anaerobic digestion is an established method for the biological conversion of waste feedstocks to biogas and biomethane. While anaerobic digestion is an excellent waste management technique, it can be susceptible to toxins and pollutants from contaminated feedstocks, which may have a detrimental impact on a digester's efficiency and productivity. Ethylene glycol (EG) is readily used in the heat-transfer loops of anaerobic digestion facilities to maintain reactor temperature. Failure of the structural integrity of these heat transfer loops can cause EG to leak into the digester, potentially causing a decrease in the resultant gas yields. Batch fermentations were incubated with 0, 10, 100 and 500 ppm (parts per million) of EG, and analysis showed that the EG was completely metabolised by the digester microbiome. The concentrations of EG tested showed significant increases in gas yields, however there were no significant changes to the digester microbiome.

An ecological explanation for carbon source-associated denitrification performance in wastewater treatment plants

The underlying mechanism associated with the roles of dosed carbon source in denitrification performance remains largely unknown. In this study, three denitrifying consortia (DNC) were constructed via evolutionary top-down enrichment method with well-defined conditions and specific carbon sources (acetate, glucose and their mixture). The reactor operation shows that nearly complete nitrate removal was achieved; however, the glucose feeding resulted in much higher concentrations of biomass and non-settable flocs. The 16S rRNA sequencing suggests that the bacterial diversity of the acetate-fed DNC was significantly higher than those of acetate/glucose-fed and glucose-fed DNCs. The dentrifying population in the acetate-fed DNC was dominated by Propionivibrio (16.1 %) and Thauera (3.4 %); whereas those of acetate/glucose- and glucose-fed DNCs were dominated by Pleomorphomonas (21.5 % and 26.3 %, respectively). Interestingly, the supernatant of acetate-fed DNC contained a high abundance of genera Thauera (averaged at 85.1 %), indicating the free-living nature of Thauera. Both PICURSt2 analysis of 16S rRNA sequencing and metagenomic analysis indicate that the acetate-fed DNC contained higher abundances of denitrifying genes; the acetate/glucose-fed and glucose-fed DNCs, in comparison, enriched genes related to glucose transportation and metabolism. Additionally, the acetate-fed DNC had better network stability than other two groups. This study adds important knowledge regarding the ecological traits of DNC, providing important clues for rational addition of carbon sources in wastewater treatment plants.

Biofilm Formation and Genetic Diversity of Microbial Communities in Anaerobic Batch Reactor with Polylactide (PLA) Addition

In this paper, an anaerobic digestion (AD) study was conducted on confectionery waste with granular polylactide (PLA) as a cell carrier. Digested sewage sludge (SS) served as the inoculum and buffering agent of systems. This article shows the results of the analyses of the key experimental properties of PLA, i.e., morphological characteristics of the microstructure, chemical composition and thermal stability of the biopolymer. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, performed using the state-of-the-art next generation sequencing (NGS) technique, revealed that the material significantly enhanced bacterial proliferation; however, it does not change microbiome biodiversity, as also confirmed via statistical analysis. More intense microbial proliferation (compared to the control sample, without PLA and not digested, CW-control, CW-confectionery waste) may be indicative of the dual role of the biopolymer-support and medium. Actinobacteria (34.87%) were the most abundant cluster in the CW-control, while the most dominant cluster in digested samples was firmicutes: in the sample without the addition of the carrier (CW-dig.) it was 68.27%, and in the sample with the addition of the carrier (CW + PLA) it was only 26.45%, comparable to the control sample (CW-control)-19.45%. Interestingly, the number of proteobacteria decreased in the CW-dig. sample (17.47%), but increased in the CW + PLA sample (39.82%) compared to the CW-control sample (32.70%). The analysis of biofilm formation dynamics using the BioFlux microfluidic system shows a significantly faster growth of the biofilm surface area for the CW + PLA sample. This information was complemented by observations of the morphological characteristics of the microorganisms using fluorescence microscopy. The images of the CW + PLA sample showed carrier sections covered with microbial consortia.

Molecular characterization of microorganisms with industrial potential for methane production in sludge from Kangemi sewage treatment plant, Nyeri county-Kenya

Microbial consortia under anaerobic conditions are involved in oxidizing organic matter in the sludge to produce methane gas. However, in developing countries like Kenya, these microbes have not been fully identified to target them for the efficient harnessing of biofuel. This study collected wet sludge from two anaerobic digestion lagoons 1 and 2 that were operational during sampling at Kangemi Sewage Treatment Plant, in Nyeri County, Kenya. DNA was extracted from samples using commercially available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for identifying microorganisms directly involved in various stages of methanogenesis pathways. The study found hydrogenotrophic methanogens, such as Methanospirillum (32%), Methanobacterium (27%), Methanobrevibacter (27%), and Methanosarcina (32%), being predominant in the lagoon communities, whereas acetoclastic microorganisms such as the Methanoregula (22%) and the acetate oxidazing bacteria such as Clostridia (68%) were the key microbes for that pathway in the sewage digester sludge. Furthermore, Methanothermobacter (18%), Methanosarcina (21%), Methanosaeta (15%), and Methanospirillum (13%) carried out the methylotrophic pathway. In contrast, Methanosarcina (23%),Methanoregula (14%), methanosaeta (13%), and methnanoprevibacter (13%) seemed to play an important role in the final step of methane release. This study concluded that the sludge produced from the Nyeri-Kangemi WWTP harbors microbes with significant potential for biogas production. The study recommends a pilot study to investigate the efficiency of the identified microbes for biogas production.

Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw

High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Effects of ferroferric oxide on propionate methanogenesis in sequencing batch reactors: Microbial community structure and metagenomic analysis

This study investigated the effects of ferroferric oxide (Fe₃O₄) on propionate methanogenesis in anaerobic sequencing batch reactor (ASBR). Compared to ASBR_C (without Fe₃O₄ addition), the addition of 10 g/L Fe₃O₄ (ASBR_Fe) decreased the maximum methane production rate by 69.6 % when propionate was used as the sole substrate. The addition of Fe₃O₄ reduced the contents of humic substances, riboflavin and nicotinamide adenine dinucleotide in extracellular polymeric substances. Therefore, Fe₃O₄ inhibited interspecies electron transfer of microorganisms through electronic mediators. Microbial community analysis revealed that Fe₃O₄ addition increased the relative abundance of acetate oxidizing bacterium (Mesotoga), but decreased the abundance of hydrogenotrophic methanogen (Methanobacterium). Further metagenomics analysis indicated that Fe₃O₄ increased the abundance of acetate oxidation genes and decreased that of hydrogenotrophic methanogenesis, quorum sensing and V/A-type ATPase genes. Thus, Fe₃O₄ reduced propionate methanogenesis during anaerobic digestion. The overall results indicate that Fe₃O₄ addition inhibits methanogenesis for treatment of propionate-contaminated wastewater in ASBR.

Microbial shifts in anaerobic digestion towards phenol inhibition with and without hydrochar as revealed by metagenomic binning

The inhibition of anaerobic digestion (AD) by phenolic compounds is an obstacle to the efficient treatment of organic wastes. Besides, hydrochar produced from hydrothermal liquefaction of biomass has been previously reported to enhance AD. The present study aimed to provide deep insights into the microbial shifts at the species level to phenol (0-1.5 g/L) inhibition in AD of glucose with and without hydrochar by metagenomic analysis. Phenol higher than 1 g/L had severe inhibition on both the amount and rate of methane production in control experiments, while hydrochar significantly enhanced methane production, especially at phenol 1 g/L and 1.5 g/L. From metagenomic analysis, 78 High-quality metagenome-assembled genomes (MAGs) were obtained. Principal components analysis showed that the microbial communities were shifted when phenol concentration was increased to 0.25 g/L in control experiments and 1 g/L in hydrochar experiments. In control experiments, no MAGs involved in acetogenesis were found at phenol 1.5 g/L and Methanothrix sp.FDU243 was also inhibited. However, hydrochar resulted in the maintenance of several MAGs involved in acetogenesis and Methanothrix sp.FDU243 even at phenol 1.5 g/L, ensuring a persistent methane production. Furthermore, 6 phenol-degrading MAGs were identified, shifting dependent on the concentrations of phenol and the presence of hydrochar.

Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation

In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.

Genome-centric metagenomics analysis revealed the metabolic function of abundant microbial communities in thermal hydrolysis-assisted thermophilic anaerobic digesters under propionate stress

The ecological roles of microbial communities and how they interact with each other in thermal hydrolysis process (THP) assisted thermophilic anaerobic digestion (THP-AD) reactors remain largely unknown, especially under propionate stress. Two thermophilic THP-AD reactors had methane yield of 240-248 mL/g VS_added, but accumulated approximately 2000 mg/L propionate. Genome-centric metagenomics analysis showed that 68 metagenome-assembled genomes (MAGs) were recovered, 32 MAGs of which were substantially enriched. Firmicutes spp. dominated the enriched microbial community, including hydrolytic/fermentative bacteria and syntrophs. Methanogenic activities were mainly mediated by Methanosarcina sp. and Methanothermobacter spp. In addition to hydrogenotrophic methanogens, Thermodesulfovibrio sp. could also be a vital H₂ scavenger, contributing to maintaining low H₂ partial pressure in the bioreactors. The remarkable accumulation of propionate could be likely attributed to the weak syntrophic propionate-oxidizing activity or its absence. These findings advanced our knowledge about the mutualistic symbiosis of carbon metabolism in thermophilic THP-AD reactors.

Distribution of extracellular amino acids and their potential functions in microbial cross-feeding in anaerobic digestion systems

Anaerobic digestion is a prevalent bioenergy production process relying on a complex network of symbiotic interactions, where the nutrient based cross-feeding is an essential microbial mechanism. Here, the cross-feeding function was assessed by analyzing extracellular polymeric substances-associated amino acids in microbial aggregates collected from 14 lab-scale anaerobic digesters, as well as deciphering their genetically biosynthetic potential by syntrophic bacteria and methanogens. The total concentration of essential amino acids ranged from 1.2 mg/g VSS to 174.0 mg/g VSS. The percentages of glutamic acid (8.5 ∼ 37.6%), lysine (2.7 ∼ 22.6%), alanine (5.6 ∼ 13.2%), and valine (3.0 ∼ 10.4%) to the total amount of detected amino acids were the highest in most samples. Through metagenomics analysis, several investigated syntrophs (i.e., Smithella, Syntrophobacter, Syntrophomonas, and Mesotoga) and methanogens (i.e., Methanothrix and Methanosarcina) were auxotrophies, but the genetic ability of syntrophs and methanogens to synthesize some essential amino acids could be complementary, implying potential cross-feeding partnership.

Alleviating "inhibited steady-state" in anaerobic digestion of poultry manure by bentonite amendment: Performance evaluation and microbial mechanism

This study systematically evaluated the effects of bentonite as a possible additive to alleviate the "inhibited steady-state" induced by ammonia and acid accumulation during anaerobic digestion. Continuous stirred tank reactors fed with poultry manure were operated at 35 ± 1 °C either with bentonite or not. The results demonstrate that bentonite amendment increased average specific methane production by 35% as suffered from steady-state at an organic loading rate of 6.25 g VS/L·d. 16S rRNA gene amplicon sequencing revealed that the relative abundance of electron-donating Sedimentibacter and Syntrophomonas, and electrophilic Methanosarcina was increased by 110%, 91%, and 49%, respectively. The genera were identified as crucial for alleviating "inhibited steady-state", through establishment of a more robust syntrophic pathway of methanogenic acetate degradation. The enhancement might result from the accelerated electron transfer by bentonite, which is qualified for serving as an exogenetic electron mediator due to containing abundant redox-active metal elements.

Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review

Acidogenic fermentation of food waste using mixed microbial cultures can produce carboxylates [or volatile fatty acids (VFA)] as high-valued bioproducts via a complex interplay of microorganisms during different stages of this process. However, the present fermentation systems are incapable of reaching the industrially relevant VFA production yields of ≥50 g/L primarly due to the complex process operation, competitive metabolic pathways, and limited understanding of microbial interplays. Recent reports have demonstrated the significant roles played by microbial communities from different phyla, which work together to control the process kinetics of various stages underlying acidogenic fermentation. In order to fully delineate the abundance, structure, and functionality of these microbial communities, next-generation high-throughput meta-omics technologies are required. In this article, we review the potential of metagenomics and metatranscriptomics approaches to enable microbial community engineering. Specifically, a deeper analysis of taxonomic relationships, shifts in microbial communities, and differences in the genetic expression of key pathway enzymes under varying operational and environmental parameters of acidogenic fermentation could lead to the identification of species-level functionalities for both cultivable and non-cultivable microbial fractions. Furthermore, it could also be used for successful gene sequence-guided microbial isolation and consortium development for bioaugmentation to allow VFA production with high concentrations and purity. Such highly controlled and engineered microbial systems could pave the way for tailored and high-yielding VFA synthesis, thereby creating a petrochemically competitive waste-to-value chain and promoting the circular bioeconomy.Research HighlightsMixed microbial mediated acidogenic fermentation of food waste.Metagenomics and metatranscriptomics based microbial community analysis.Omics derived function-associated microbial isolation and consortium engineering.High-valued sustainable carboxylate bio-products, i.e. volatile fatty acids.

Performance and metagenomics analysis of anaerobic digestion of food waste with adding biochar supported nano zero-valent iron under mesophilic and thermophilic condition

A large amount of food waste (FW) brings environmental pollution and sanitation problems. Anaerobic digestion (AD) is an effective technology to treat FW and generate biogas energy. This study investigated the effect of biochar supported nano zero-valent iron (BC-nZVI) on AD performance of FW. Results showed that the cumulative methane yield (CMY) increased by 21.52%-54.90% and the lag time decreased significantly with BC-nZVI. Under mesophilic and thermophilic condition, the peak of CMY was achieved at 178.82 ± 5.27 mL/g VS and 193.01 ± 6.81 mL/g VS with 5 g/L BC-nZVI, respectively. Besides, BC-nZVI stimulated hydrolysis process and reduced the inhibition of NH₄⁺-N and volatile fatty acids accumulation, and it could improve the system stability. Structural equation model analysis indicated that digestion time, BC-nZVI, NH₄⁺-N, temperature and total volatile fatty acid had significant effects on CMY, explaining 92.20% of its total variation. The metagenomic analysis of key microorganisms and related metabolism pathways involved in AD system was further investigated. The results suggested that BC-nZVI contributed to strengthen methanogenesis through enriching the various predominant methanogenic pathways and activating most enzymes related to methane metabolism. BC-nZVI could improve the AD system function and provided a better AD performance by shifting the microbial communities and altering functional genes. This study provided a theoretical basis for BC-nZVI applications and improvements in AD process of FW.