Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste

Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits

Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.

Synergetic anaerobic digestion of food waste for enhanced production of biogas and value-added products: strategies, challenges, and techno-economic analysis

The generation of food waste (FW) is increasing at an alarming rate, contributing to a total of 32% of all the waste produced globally. Anaerobic digestion (AD) is an effective method for dealing with organic wastes of various compositions, like FW. Waste valorization into value-added products has increased due to the conversion of FW into biogas using AD technology. A variety of pathways are adopted by microbes to avoid unfavorable conditions in AD, including competition between sulfate-reducing bacteria and methane (CH4)-forming bacteria. Anaerobic bacteria decompose organic matter to produce biogas, a digester gas. The composition depends on the type of raw material and the method by which the digestion process is conducted. Studies have shown that the biogas produced by AD contains 65-75% CH4 and 35-45% carbon dioxide (CO2). Methanothrix soehngenii and Methanosaeta concilii are examples of species that convert acetate to CH4 and CO2. Methanobacterium bryantii, Methanobacterium thermoautotrophicum, and Methanobrevibacter arboriphilus are examples of species that produce CH4 from hydrogen and CO2. Methanobacterium formicicum, Methanobrevibacter smithii, and Methanococcus voltae are examples of species that consume formate, hydrogen, and CO2 and produce CH4. The popularity of AD has increased for the development of biorefinery because it is seen as a more environmentally acceptable alternative in comparison to physico-chemical techniques for resource and energy recovery. The review examines the possibility of using accessible FW to produce important value-added products such as organic acids (acetate/butyrate), biopolymers, and other essential value-added products.

MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques

BACKGROUND

In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning and single-cell sequencing. However, our ability to functionally characterize these genomes by experimental assays is orders of magnitude less efficient. Consequently, there is a pressing need for the development of swift and automated strategies for the functional classification of microbial genomes.

RESULTS

The present work leverages a suite of supervised machine learning algorithms to establish a range of 86 metabolic and other ecological functions, such as methanotrophy and plastic degradation, starting from widely obtainable microbial genome annotations. Tests performed on independent datasets demonstrated robust performance across complete, fragmented, and incomplete genomes above a 70% completeness level for most of the considered functions. Application of the algorithms to the Biogas Microbiome database yielded predictions broadly consistent with current biological knowledge and correctly detecting functionally-related nuances of archaeal genomes. Finally, a case study focused on acetoclastic methanogenesis demonstrated how the developed machine learning models can be refined or expanded with models describing novel functions of interest.

CONCLUSIONS

The resulting tool, MICROPHERRET, incorporates a total of 86 models, one for each tested functional class, and can be applied to high-quality microbial genomes as well as to low-quality genomes derived from metagenomics and single-cell sequencing. MICROPHERRET can thus aid in understanding the functional role of newly generated genomes within their micro-ecological context.

Food waste impact on dry anaerobic digestion of straw in a novel reactor: Biogas yield, stability, and hydrolysis-methanogenesis processes

Gradient anaerobic digestion reactor (GADR) can improve substrate utilization efficiency by solving the problem of the "short circuit" of materials. However, the substrate's composition significantly affects the reactor's performance. This study investigated the impact of food waste (FW) levels on corn straw's dry anaerobic digestion (AD) in a novel GADR. The results show that biomethane production can be improved by coupling urban and agricultural solid waste recycling. The mechanism is to increase the hydrolysis and acid production efficiency, and the abundance of enzymes related to methanogenesis. The maximum methane yield (494.2 mL CH4/g VS) and the highest anaerobic biodegradability (85.7 %) were obtained when the FW was added at 60 %. The co-digestion of FW and straw can improve the hydrolysis and acid production efficiency and methane yield, which improves the buffering capacity and stability of the system compared with the single digestion of FW.

Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant

Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.

Biochar inoculated with Rhodococcus biphenylivorans altered microecological regulation by promoting quorum sensing and electron transfer: Up-regulation of related genes and enhancement of phenol and ammonia degradation

Bioaugmentation is an efficient method for improving the efficiency of coking wastewater removal. Nevertheless, how different immobilization approaches affect the efficiency of bioaugmentation remains unclear, as does the corresponding mechanism. With the assistance of immobilized bioaugmentation strain Rhodococcus biphenylivorans B403, the removal of synthetic coking wastewater was investigated (drying agent, alginate agent, and absorption agent). The reactor containing the absorption agent exhibited the highest average removal efficiency of phenol (99.74 %), chemical oxygen demand (93.09 %), and NH4+-N (98.18 %). Compared to other agents, the covered extracellular polymeric substance on the absorption agent surface enhanced electron transfer and quorum sensing, and the promoted quorum sensing benefited the activated sludge stability and microbial regulation. The phytotoxicity test revealed that the wastewater's toxicity was greatly decreased in the reactor with the absorption agent, especially under high phenol concentrations. These findings showed that the absorption agent was the most suitable for wastewater treatment bioaugmentation.

Evaluating the potential of different bioaugmented strains to enhance methane production during thermophilic anaerobic digestion of food waste

Bioaugmentation technology for improving the performance of thermophilic anaerobic digestion (TAD) of food waste (FW) treatment is gaining more attention. In this study, four thermophilic strains (Ureibacillus suwonensis E11, Clostridium thermopalmarium HK1, Bacillus thermoamylovorans Y25 and Caldibacillus thermoamylovorans QK5) were inoculated in the TAD of FW system, and the biochemical methane potential (BMP) batch study was conducted to assess the potential of different bioaugmented strains to enhance methane production. The results showed that the cumulative methane production in groups inoculated with E11, HK1, Y25 and QK5 improved by 2.05%, 14.54%, 19.79% and 9.17%, respectively, compared with the control group with no inoculation. Moreover, microbial community composition analysis indicated that the relative abundance of the main hydrolytic bacteria and/or methanogenic archaea was increased after bioaugmentation, and the four strains successfully became representative bacterial biomarkers in each group. The four strains enhanced methane production by strengthening starch, sucrose, galactose, pyruvate and methane metabolism functions. Further, the correlation networks demonstrated that the representative bacterial genera had positive correlations with the differential metabolic functions in each bioaugmentation group. This study provides new insights into the TAD of FW with bioaugmented strains.

Optimization of semi-continuous dry anaerobic digestion process and biogas yield of dry yellow corn straw: Based on "gradient anaerobic digestion reactor"

In China, the problem of low biogas yield of traditional biogas projects has become increasingly prominent. This study investigated the effects of different hydraulic retention times (HRTs) on the biogas production efficiency and microbial community under pilot conditions. The results show that the "Gradient anaerobic digestion reactor" can stably carry out semi-continuous dry anaerobic digestion and improve biogas yield. The highest volatile solids (VS) biogas yield (413.73 L/kg VS and 221.61 L CH4/kg VS) and VS degradation rate (48.41%) were observed at an HRT of 25 days. When the HRT was 15 days, the volumetric biogas yield was the highest (2.73 L/L/d, 1.43 L CH4/L/d), but the VS biogas yield and degradation rate were significantly decreased. Microbial analysis showed that HRT significantly affected microbial community. It provides basic data support for the development of a new anaerobic digestion process and the practical application of the straw biogas project in China.

Lactic acid production from food waste at an anaerobic digestion biorefinery: effect of digestate recirculation and sucrose supplementation

Low lactic acid (LA) yields from direct food waste (FW) fermentation restrict this production pathway. However, nitrogen and other nutrients within FW digestate, in combination with sucrose supplementation, may enhance LA production and improve feasibility of fermentation. Therefore, this work aimed to improve LA fermentation from FWs by supplementing nitrogen (0-400 mgN·L^-1) as NH₄Cl or digestate and dosing sucrose (0-150 g·L^-1) as a low-cost carbohydrate. Overall, NH₄Cl and digestate led to similar improvements in the rate of LA formation (0.03 ± 0.02 and 0.04 ± 0.02 h^-1 for NH₄Cl and digestate, respectively), but NH₄Cl also improved the final concentration, though effects varied between treatments (5.2 ± 4.6 g·L^-1). While digestate altered the community composition and increased diversity, sucrose minimised community diversion from LA, promoted Lactobacillus growth at all dosages, and enhanced the final LA concentration from 25 to 30 g·L^-1 to 59-68 g·L^-1, depending on nitrogen dosage and source. Overall, the results highlighted the value of digestate as a nutrient source and sucrose as both community controller and means to enhance the LA concentration in future LA biorefinery concepts.

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.

Impacts of organic loading rate and hydraulic retention time on organics degradation, interspecies interactions and functional traits in thermophilic anaerobic co-digestion of food waste and sewage sludge

This study provided novel insights into the effects of organic loading rate (OLR) and hydraulic retention time (HRT) on thermophilic anaerobic co-digestion of food waste and sewage sludge. The obtained maximum methane (CH₄) yield of 328 ± 4 mL CH₄/g COD_fed at HRT of 15 days (OLR = 5.8 g VS/L/d) was partly attributable to the enhanced acidogenesis, acetogenesis, and methanogenesis phases. The increased key enzyme activities, particularly acetate kinase (improved by 5.2-fold), providing substantial methanogenic substrates for efficient CH₄ production. The functional syntrophs that were related to syntrophic decarboxylation, novel acetate oxidation & reductive acetyl-CoA, and β-oxidation pathways could drive trophic interactions with methanogens. This markedly stimulated hydrogenotrophic Methanoculleus thermophilus metabolism and concomitantly enriched mixotrophic Methanosarcina thermophila. The distinctive cross-feeding interspecies interactions significantly affected the assembly and dynamics of thermophilic consortia. These findings shed light on the physicochemical and microbial mechanisms of HRT- and OLR-dependent enhancement of methanogenesis.

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.

Recent advances in conductive materials amended anaerobic co-digestion of food waste and municipal organic solid waste: Roles, mechanisms, and potential application

Recently, conductive materials (i.e., carbon-based and iron-based materials) as a feasible and attractive approach have been introduced to anaerobic co-digestion (ACoD) system for promoting its performance and stability through direct interspecies electron transfer. Owing to the key roles of conductive materials in ACoD process, it is imperative to gain a profound understanding of their specific functions and mechanisms. Here, this review critically examined the state of the art of conductive materials assisted ACoD of food waste and common municipal organic solid waste. Then, the fundamental roles of conductive materials on ACoD enhancement and the relevant mechanisms were discussed. Last, the perspectives for co-digestate treatment, reutilization, and disposal were summarized. Moreover, the main challenges to conductive materials amended ACoD in on-site application were proposed and the future remarks were put forward. Collectively, this review poses a scientific basis for the potential application of conductive materials in ACoD process in the future.

Effective utilization of refractory dissolved organic matters in domestic sewage allows to enhanced nitrogen removal by integrated fermentation, nitrification, denitratation and anammox process

To take full advantage of refractory dissolved organic matters (rDOMs) and generate sufficient nitrate for domestic sewage treatment, this study presented a novel integrated fermentation, nitrification, denitratation and anammox (IFNDA) process in a combined ABR-CSTR reactor. The results showed that an advanced total nitrogen (TN) removal efficiency of 94.1% was obtained after over 190 days operation, resulting in effluent TN concentration as low as 3.6 mg/L. The system nitrogen removal was dominated by anammox with a high proportion of 88.6%. The high conversion rate of acetic acid (54.0%) and volatile fatty acids (64.5%) from rDOMs in domestic sewage by in-situ fermentation drove efficient denitratation. Microflora analysis indicated that the enriched Commamonas (3.5%) and Longilinea (3.3%) dominated hydrolysis and acidogenesis of organics, and Methanosaeta (9.0%) obligated acetoclastic methanogenesis in two-stage fermentation process. Thauera (8.4%) and Candidatus Brocadia (2.5%) were the core bacteria for nitrogen metabolism in the IFNDA system.