Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

Resilience towards organic load and activated sludge variations in co-fermentation for carboxylic acid production

Two perturbations were investigated in acidogenic co-fermentation of waste activated sludge (WAS) and food waste in continuous mesophilic fermenters: increasing the organic loading rate (OLR) and changing the WAS. A control reactor maintained an OLR of 11 gVS/(L·d), while a test reactor had a prolonged OLR change to 18 gVS/(L·d). For each OLR, two WAS were studied. The change in OLR led to differentiated fermentation product profile without compromising the fermentation yields (∼300 mgCOD/gVS). At 11 gVS/(L·d), the product profile was dominated by acetic, butyric, and propionic acids while at 18 gVS/(L·d) it shifted to acetic acid, ethanol, and caproic acid. Reverting the OLR also reverted the fermentation profile. The biomass immigration with the WAS changed the fermentation microbial structure and introduced acetic acid-consuming methanogens, which growth was only delayed by the OLR increase. Microbial monitoring and post-fermentation tests can be used for early detection of acetic acid-consuming events.

Insights into the response mechanisms of activated sludge system under long-term dexamethasone stress

Dexamethasone (DEX) is a hormone drug that is often detected in wastewater treatment plants, but its impact on activated sludge systems is unknown. This study explored the long-term effects of DEX on nutrient removal, microbial activities, microbial assembly, and microbial interactions in the activated sludge system. During the 90-day DEX exposure experiment, both chemical oxygen demand and total nitrogen removal efficiencies were initially inhibited and then recovered. Microbial activities, i.e., specific oxygen uptake rate and denitrification, did not differ significantly from that of the control reactor (p > 0.05), possibly due to the secretion of extracellular polymers that act as a protective barrier against excess reactive oxygen species induced by DEX. This barrier protects cell membrane integrity and ensures stable treatment performance. Analysis of microbial assembly identified the drift of stochastic processes (from 92.7 % to 51.8 %) and homogeneous selection of deterministic processes (from 1.6 % to 38.7 %) as the main driving forces of microbial community structure succession under long-term DEX stress. Although long-term exposure to 1000 μg/L DEX did not significantly increase the abundance levels of functional bacteria (Nitrosomonas and 996-1) and key genes (AmoCAB and Hao), the ammonia oxidation capacity of the activated sludge system was enhanced. Analysis of microbial interactions indicated that streamlining of functional subnetworks and increased cooperation were the primary reasons. This is the first study to explore the long-term effects of DEX on activated sludge and provide insights into microbial interaction and assembly. Moreover, the findings of this study broaden our knowledge and lay an experimental foundation for reducing risks associated with hormone drugs.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Comprehensive comparison of integrated fixed-film activated sludge (IFAS) and AAO activated sludge methods: Influence of different operational parameters

Due to limited land availability in municipal wastewater treatment plants, integrated fixed-film activated sludge (IFAS) technology offers significant advantages in improving nitrogen removal performance and treatment capacity. In this study, two systems, IFAS and Anaerobic-Anoxic-Oxic Activated sludge process (AAO), were compared by adjusting parameters such as hydraulic retention time (HRT), nitrifying solution recycle ratio, sludge recycle ratio, and dissolved oxygen (DO). The objective was to investigate pollutant removal capacity and differences in microbial community composition between the two systems. The study showed that, at an HRT of 12 h, the IFAS system exhibited an average increase of 5.76%, 8.85%, and 12.79% in COD, NH4+-N, and TN removal efficiency respectively, compared to the AAO system at an HRT of 16 h. The TP concentration in the IFAS system reached 0.82 mg/L without the use of additives. The IFAS system demonstrated superior effluent results under lower operating conditions of HRT, nitrification solution recycle ratio, and DO. The 16S rDNA analysis revealed higher abundance of denitrification-related associated flora, including Proteobacteria, Bacteroidetes, and Planctomycetota, in the IFAS system compared to the AAO system. Similarities were observed between microorganisms attached to the media and activated sludge in the anaerobic, anoxic, and oxic tanks. q-PCR analysis indicated that the incorporation of filler material in the IFAS system resulted in similar abundance of nitrifying bacteria genes on the biofilm as in the oxic tank. Additionally, denitrifying genes showed higher levels due to aeration scouring and the presence of alternating aerobic-anaerobic environments on the biofilm surface, enhancing nitrogen removal efficiency.

Biomineralization of phosphorus during anaerobic treatment of distillery wastewaters

This study addresses the pressing environmental concerns associated with the rapidly growing distillery industry, which is a significant contributor to wastewater generation. By focusing on the treatment of distillery wastewater using anaerobic digestion, this research explores the potential to convert organic materials into biofuels (methane). Moreover, the study aims to recover both methane and phosphorus from distillery wastewater in a single anaerobic reactor, which represents a novel and unexplored approach. Laboratory-scale experiments were conducted using mesophilic and thermophilic upflow anaerobic sludge blanket reactors. A key aspect of the study involved the implementation of a unique strategy: the mixing of centrate and spent caustic wastewater streams. This approach was intended to enhance treatment performance, manipulate the microbial community structure, and thereby optimizing the overall treatment performance. The integration of the centrate and spent caustic streams yielded remarkable co-benefits, resulting in significant biomethane production and efficient phosphorus precipitation. The study demonstrated a phosphorus removal efficiency of ∼60 % throughout the 130-140 days operation period. The recovery of phosphorus via the reactor sludge offers exciting opportunities for its utilization as a fertilizer or as a raw material within the phosphorus refinery industry. The biomethane produced during the treatment exhibits significant energy potential, estimated at 0.5 GJ/(m3 distillery wastewater).

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions

Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.

Temperature-driven carboxylic acid production from waste activated sludge and food waste: Co-fermentation performance and microbial dynamics

This work aims to improve the continuous co-fermentation of waste activated sludge (WAS) and food waste (FW) by investigating the long-term impact of temperature on fermentation performance and the underpinning microbial community. Acidogenic co-fermentation of WAS and FW (70:30 % VS-basis) to produce volatile fatty acids (VFA) was studied in continuous fermenters at different temperatures (25, 35, 45, 55 °C) at an organic loading rate of 11 gVS/(L·d) and a hydraulic retention time of 3.5 days. Two batches of WAS (A and B) were collected from the same wastewater treatment plant at different periods to understand the impact of the WAS microbioota on the fermenters' microbial communities. Solubilisation yield was higher at 45 °C (575 ± 68 mgCOD/gVS) followed by 55 °C (508 ± 45 mgCOD/gVS). Fermentation yield was higher at 55 °C (425 ± 28 mgCOD/gVS) followed by 35 °C (327 ± 17 mgCOD/gVS). Temperature also had a noticeable impact on the VFA profile. At 55 °C, acetic (40 %) and butyric (40 %) acid dominated, while acetic (37 %), butyric acid (31 %), and propionic acid (17 %) dominated at 35 °C. At 45 °C, an accumulation of caproic acid was detected which did not occur at other temperatures. Each temperature had a distinct microbial community, where the WAS microbiota played an important role. The biomass mass-balance showed the highest growth of microorganisms (51 %) at 35 °C and WAS_B, where a consumption of acetic acid was observed. Therefore, at 35 °C, there is a higher risk of acetic acid consumption probably due to the proliferation of methanogens imported from WAS.

Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring

DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

BACKGROUND

Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning.

RESULTS

Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter.

CONCLUSIONS

Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.

Enterobacteria in anaerobic digestion of dairy cattle wastewater: Assessing virulence and resistance for one health security

Samples from a dairy cattle waste-fed anaerobic digester were collected across seasons to assess sanitary safety for biofertilizer use. Isolated enterobacteria (suggestive of Escherichia coli) were tested for susceptibility to biocides, antimicrobials, and biofilm-forming capability. Results revealed a decrease in total bacteria, coliforms, and enterobacteria in biofertilizer compared to the effluent. Among 488 isolates, 98.12 % exhibited high biofilm formation. Biofertilizer isolates exhibited a similar biofilm formation capability as effluent isolates in summer, but greater propensity in winter. Resistance to biocides and antimicrobials varied, with tetracycline resistance reaching 19 %. Of the isolates, 25 were multidrug-resistant (MDR), with 64 % resistant to three drugs. Positive correlations were observed between MDR and increased biofilm formation capacity in both samples, while there was negative correlation between MDR and increased biocide resistance. A higher number of MDR bacteria were found in biofertilizer compared to the effluent, revealing the persistence of E. coli resistance, posing challenges to food safety and public health.

Microbial volatile organic compounds as novel indicators of anaerobic digestion instability: Potential and challenges

The wide application of anaerobic digestion (AD) technology is limited by process fluctuations. Thus, process monitoring based on screening state parameters as early warning indicators (EWI) is a top priority for AD facilities. However, predicting anaerobic digester stability based on such indicators is difficult, and their threshold values are uncertain, case-specific, and sometimes produce conflicting results. Thus, new EWI should be proposed to integrate microbial and metabolic information. These microbial volatile organic compounds (mVOCs) including alkanes, alkenes, alkynes, aromatic compounds are produced by microorganisms (bacteria, archaea and fungi), which might serve as a promising diagnostic tool for environmental monitoring. Moreover, mVOCs diffuse in both gas and liquid phases and are considered the language of intra kingdom microbial interactions. Herein, we highlight the potential of mVOCs as EWI for AD process instability, including discussions regarding characteristics and sources of mVOCs as well as sampling and determination methods. Furthermore, existing challenges must be addressed, before mVOCs profiling can be used as an early warning system for diagnosing AD process instability, such as mVOCs sampling, analysis and identification. Finally, we discuss the potential biotechnology applications of mVOCs and approaches to overcome the challenges regarding their application.

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.

Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment

Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H₂/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Hydrothermal liquefaction of sewage sludge anaerobic digestate for bio-oil production: Screening the effects of temperature, residence time and KOH catalyst

Due to sewage sludge being an abundant biobased resource, and with the number of biogas plants utilizing sewage sludge increasing, digested sewage sludge (DSS) is a promising feedstock for producing bio-oil. This study uses DSS from a biogas plant to produce bio-oil in a hydrothermal liquefaction process adjusting time from 2 to 6 hours, temperature from 280 to 380°C and the presence of a base as a depolymerization agent and potential catalyst. High conversion yields are obtained, with the maximum of 58 wt% on a dry, ash free basis and an energy recovery of up to 94%. The oils contain compounds with a potential for utilization as biofuels and building blocks, especially fatty acids as biodiesel feedstock and biobased phenols, glycols and aliphatic alcohols.

Hydrodynamic disintegration of thickened excess sludge and maize silage to intensify methane production: Energy effect and impact on microbial communities

The aim of this project was to study the combination of two methods to increase methane production: feedstock pretreatment by hydrodynamic disintegration and co-digestion of maize silage (MS) with thickened excess sludge (TES). Disintegration of TES alone resulted in a 15% increase in specific methane production from 0.192 Nml/gVS (TES + MS) to 0.220 Nml/gVS (pretreated TES + MS). The energy balance revealed additional energy (0.14 Wh) would cover only the energy expenditure for the mechanical pretreatment and would not allow for net energy profit. Identification of the methanogenic consortia by 16S rRNA gene amplicon sequencing revealed that Chloroflexi, Bacteroidota, Firmicutes, Proteobacteria and Actinobacteriota were five most abundant bacteria phyla, with Methanothrix and Methanolinea as the dominant methanogens. Principal component analysis did not show any effect of feedstock pretreatment on methanogenic consortia. Instead, the composition of inoculum was the decisive factor in shaping the microbial community structure.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Comparative study of the effect of loading increments on the mesophilic codigestion of waste activated sludge and food waste: Reactor performance, stability analysis, and microbial community

The performance and stability of mesophilic codigestion of waste activated sludge (WAS) and food waste (FW) were compared in two parallel, continuously stirred tank reactors using high- and low-magnitude loading increments for the loading regimes. The results indicated that a high methane (CH₄) production of 6.98 L L^-1·d^-1 was realized without volatile fatty acid accumulation via low-magnitude loading increments at a high loading of 26.5 g-COD·L^-1·d^-1, and this system was more stable and achieved a higher efficiency than the codigestion system that used high-magnitude loading increments at similar loading and operating conditions. Furthermore, higher CH₄ yields of 258-334 mL-CH₄·g-COD^-1, TCOD removal efficiencies of 64-79%, conversion ratios of 62-88%, and methanogenic activities of 0.37-0.40 g-CH₄-COD·g-VS^-1·d^-1 were consistently maintained via the low-magnitude loading increments during the high-rate period. High abundances of the phyla Firmicutes (63.3%) and genus Methanosarcina (94.5%) contributed to the high rates and stable operating conditions of the mesophilic system for WAS and FW codigestion using low-magnitude loading increments.

Structure and core taxa of bacterial communities involved in extracellular electron transfer in paddy soils across China

Microbial communities with extracellular electron transfer (EET) activity are capable of driving geochemical changes and cycles, but a comprehensive understanding of the key microbiota responsible for EET in complex soil matrices is still lacking. Herein, the EET activities, in terms of maximum current density (j_max) and accumulated charge output (C_out), of 41 paddy soils across China were evaluated from the exoelectrogenic properties with a conventional bioelectrochemical system (BES). The j_max with a range of 8.85 × 10^-4 to 0.41 A/m² and C_out with a range of 0.27 to 172.21C were obtained from these soil-based BESs. The bacterial community analyses revealed that the most abundant phylum, order, and genus were Firmicutes, Clostridiales, and Clostridum-sensus-stricto 10, respectively. Bacterial network analysis displayed the positive correlations between the majority of electroactive bacteria-containing genera and multiple other genera, indicating their underlying cooperation for the EET. Partial least squares regression (PLSR) model showed remarkable performance in describing the EET activity with 75 most abundant genera as input variables, identified that 32 genera were very important for governing the EET activities. Multiple linear regression (MLR) analyses further prioritized that the genera norank-c-Berkelbacteria and Fonticella were the key contributors, while the genus Paenibacillus was the key competitor against bacterial exoelectrogenesis in paddy soils. Moreover, the spearman analysis showed that the abundance of these keystone taxa was mainly influenced by the carbon content and pH. This approach provides a promising avenue to monitor the microbial activities in paddy soils as well as the links between microbial community composition and ecological function.

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.

Microorganisms as New Sources of Energy

The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

Economically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.

Responses of mesophilic anaerobic sludge microbiota to thermophilic conditions: Implications for start-up and operation of thermophilic THP-AD systems

Anaerobic digestion (AD) has been widely employed for wastewater and organic waste treatment, in which methanogenesis is highly driven by close microbial interactions among intricate microbial communities. However, the ecological processes underpinning the community assembly that support methanogenesis in such engineered ecosystems remain largely unknown, especially when exposed to challenging circumstances (e.g., high temperature, ammonium content). Here, eight AD bioreactors were seeded with four different inocula (two from full-scale mesophilic AD systems and the other two from lab-scale mesophilic AD systems), and were operated under thermophilic conditions (55 °C) for treating thermal hydrolysis process (THP) pre-treated waste activated sludge to investigate how mesophilic community responds to thermophilic conditions during the long-term cultivation. Results showed that the inocula collected from the full-scale systems were more resilient than that from the lab-scale systems, which may be primarily attributed to indigenous robust methanogens. As a result, the former efficiently generated methane which was predominantly contributed by Methanothermobacter and Methanosarcina (healthy AD ecosystem), while methanogenic activity was remarkably prohibited in the latter (dysfunctional AD ecosystem). Thermophilic environment was a strong selection force, resulting in the convergence of microbial communities in both the healthy and dysfunctional AD ecosystems. Deterministic processes predominated the community assembly regardless of AD ecosystem function, but stronger influences of stochastic processes were observed in dysfunctional AD ecosystems, which was likely attributable from the stronger effect of immigrants from the feedstock. As indicated by molecular ecological network analysis, the microbial network structures in the healthy AD ecosystems were more stable than those in the dysfunctional AD ecosystems. Although keystone taxa were different among the bioreactors, most of which played vital roles in organic hydrolysis/fermentation. To sum up, this study greatly improved our understanding of the relationships between microbiological traits and AD ecosystem function under thermophilic conditions, which could provide useful information to guide thermophilic AD (e.g., THP-AD) start-up and health diagnosis during operation.

Effect of Pretreatment by Freeze Vacuum Drying on Solid-State Anaerobic Digestion of Corn Straw

As a common agricultural waste, corn straw (CS) has a refractory structure, which is not conducive to anaerobic digestion (AD). Appropriate pretreatment is crucial for addressing this problem. Thus, freeze vacuum drying (FVD) was proposed. In this study, fresh CS (F-CS) pretreated (5 h, −40 °C) by FVD and naturally dried CS (D-CS) were compared. Differences in substrate surface structure and nutrient composition were first investigated. Results show that a loose and porous structure, crystallinity, and broken chemical bonds, as well as higher proportions of VS, C, N, cellulose, hemicellulose, and crude proteins in F-CS show a potential for methane production. Besides, process performance and stability were also examined in both high (4, VS basis) and low (1, VS basis) S/I ratio AD. A higher degradation ratio of hemicellulose as well as richer dissolved microbial metabolites, coenzymes, tyrosine-like proteins, and hydrolysis rate of particulate organic matter in the F-CS system enhanced the efficiency of methane conversion. The cumulative methane yield increased from 169.66 (D-CS) to 209.97 (F-CS) mL/gVS in the high S/I ratio system (p = 0.02 < 0.05), and 156.97 to 171.89 mL/gVS in the low S/I ratio system. Additionally, 16S-rRNA-gene-based analysis was performed. Interestingly, the coordination of key bacteria (Clostridium_sensu_stricto_1, Bacillus, Terrisporobacter. Clostridium_sensu_stricto_7, Thermoclostrium, UCG-012, and HN-HF0106) was more active. Poorer Methanosarcina and Methanomassiliicoccus as well as richer Methanobrevibacter and Methanoculleus stimulated the co-relationship of key archaea with diverse methanogenesis pathways. This study aims to verify the positive effect of FVD pretreatment on AD of CS, so as to provide a reference for applications in waste management.

Monitor process state of batch anaerobic digestion in reliance on volatile and semi-volatile metabolome

It has been a challenge to recognize appropriate compounds as indicators for monitoring and early-warning of the anaerobic digestion process. A strategy was initiated to explore the evolution of the panorama profile of volatile and semi-volatile metabolites. Non-target analysis using high-resolution gas chromatography coupled with Orbitrap mass spectrometry was applied to construct a time-series molecular fingerprint of 218 metabolites classified in 14 categories. Alkanes accounted for the main part in early and late stages of methanization and aromatic compounds were the major in middle stage. Spearman correlation analysis and partial least squares analysis unwind that Trichococcus (1.49%-83.96%) was positively related to most of metabolites at early and middle stages, while Brevundimonas (0%-24.04%) was positively related to acylamide at late stage. This indicated that microbial volatile organic compounds were possible to serve as biochemical indicators for anaerobic digestion performance and to build nexus of "what" (metabolites), "who" (microorganism), and "how" (kinetics).

A waste to energy technology for Enrichment of biomethane generation: A review on operating parameters, types of biodigesters, solar assisted heating systems, socio economic benefits and challenges

Anaerobic Digestion (AD) is one of the promising wastestoenergy (WtE) technologies that convert organic wastes to useful gaseous fuel (biogas). In this process methane is produced in the presence of methanogens (bacteria). The survival and activities of methanogens are based on several parameters such as pH, temperature, organic loading rate, types of biodigester. Moreover, these parameters influence the production of biogas in terms of yield and composition. Maintaining an appropriate temperaturefor AD is highly critical and energy intensive. This study reviews the various hybrid technologies assistedbio gas production schemes particularly from renewable energy sources. Also discuss the direct and indirect solar assisted bio-digester impacts and recommendation to improve its performance. In addition, the performance analysis Solar Photovoltaic (PV) and thermal collector assisted bio gas plants; besides their impact on the performance of anaerobic digesters. Since opportunities of solar energy are attractive, the effective utilization of the same is selected for the discussion. Besides, the various constraints that affect the yield and composition of biogas are also evaluated along with the current biogas technologies and the biodigesters. The environmental benefits, challenges and socio-economic factors are also discussed for the successful implementation of various technologies.

Potential of anaerobic co-fermentation in wastewater treatments plants: A review

Fermentation (not anaerobic digestion) is an emerging biotechnology to transform waste into easily assimilable organic compounds such as volatile fatty acids, lactic acid and alcohols. Co-fermentation, the simultaneous fermentation of two or more waste, is an opportunity for wastewater treatment plants (WWTPs) to increase the yields of sludge mono-fermentation. Most publications have studied waste activated sludge co-fermentation with food waste or agri-industrial waste. Mixing ratio, pH and temperature are the most studied variables. The highest fermentation yields have been generally achieved in mixtures dominated by the most biodegradable substrate at circumneutral pH and mesophilic conditions. Nonetheless, most experiments have been performed in batch assays which results are driven by the capabilities of the starting microbial community and do not allow evaluating the microbial acclimation that occurs under continuous conditions. Temperature, pH, hydraulic retention time and organic load are variables that can be controlled to optimise the performance of continuous co-fermenters (i.e., favour waste hydrolysis and fermentation and limit the proliferation of methanogens). This review also discusses the integration of co-fermentation with other biotechnologies in WWTPs. Overall, this review presents a comprehensive and critical review of the achievements on co-fermentation research and lays the foundation for future research.

Effect of sludge retention time on microbial succession and assembly in thermal hydrolysis pretreated sludge digesters: Deterministic versus stochastic processes

Thermal hydrolysis process (THP) assisted anaerobic digestion (AD) has been demonstrated to be an efficient approach to improve biogas production and solids reduction. Given the faster reaction kinetics in the THP-AD system, reduction of sludge retention time (SRT) is possible. However, a comprehensive understanding of the effects of sludge retention time (SRT) on microbial dynamics and community assemblages is still lacking in THP-AD systems. Thus, twelve THP-AD reactors were operated at different SRTs (10-30 d) to fulfill the knowledge gap. Results showed that, although all the bioreactors displayed good performance, shorter SRT reactors (SRT 10 d) took a longer time to reach the stable state. The total biogas production at SRT of 10 d was lower than that at other longer SRTs, attributing to the limited hydrolytic/fermentative capacities of AD microbiomes. Different SRTs resulted in distinct succession patterns of AD microbiomes. THP sludge reduced the microbial diversity in all the bioreactors over time, but longer SRTs maintained higher biodiversity. Null model analysis suggested that THP-AD microbial community assembly was predominately driven by deterministic selection at the tested SRT range, but stochasticity increased with elevated SRTs, likely attributing to the immigrants from the feedstock. Phylogenetic molecular ecological networks (pMENs) analysis revealed more stable network structures at longer SRTs, evidenced by the lower modularity, shorter harmonic geodesic distance, and higher connectivity. The potential keystone taxa under varied SRTs were identified, some of which were hydrolytic/fermentative bacteria (e.g., Peptostreptococcus, Lutispora, Synergistaceae), suggesting that these species related to organic hydrolysis/fermentation even with low-abundance could still play pivotal ecological roles in maintaining the THP-AD microbial community structure and functions. Collectively, this study provides comprehensive and in-depth insights into the mechanisms underlying community assembly in THP-AD reactors, which could aid in diagnosing system stability.

The challenges of monitoring and manipulating anaerobic microbial communities

Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.

Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures

Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg²⁺ and Ca²⁺ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world.

Mass-immigration determines the assembly of activated sludge microbial communities

Wastewater treatment plants are engineering technologies used worldwide to protect the environment and human health. Microbial communities sustain these plants, so it is crucial to know the key factors responsible for the community assembly. We show, in contrast to existing understanding, that microbial immigration largely controls the community structure in these plants and that the fate (growth or death) of immigrating species in the plants is controlled by local factors. The community structure was quantitatively predicted by the immigrating microbial community, highlighting the need to revise the way we today understand, design, and manage microbial communities in wastewater treatment plants.

The assembly of bacterial communities in wastewater treatment plants (WWTPs) is affected by immigration via wastewater streams, but the impact and extent of bacterial immigrants are still unknown. Here, we quantify the effect of immigration at the species level in 11 Danish full-scale activated sludge (AS) plants. All plants have different source communities but have very similar process design, defining the same overall environmental growth conditions. The AS community composition in each plant was strongly reflected by the corresponding influent wastewater (IWW) microbial composition. Most species in AS across the plants were detected and quantified in the corresponding IWW, allowing us to identify their fate in the AS: growing, disappearing, or surviving. Most of the abundant species in IWW disappeared in AS, so their presence in the AS biomass was only due to continuous mass-immigration. In AS, most of the abundant growing species were present in the IWW at very low abundances. We predicted the AS species abundances from their abundance in IWW by using a partial least square regression model. Some species in AS were predicted by their own abundance in IWW, while others by multiple species abundances. Detailed analyses of functional guilds revealed different prediction patterns for different species. We show, in contrast to the present understanding, that the AS microbial communities were strongly controlled by the IWW source community and could be quantitatively predicted by taking into account immigration. This highlights a need to revise the way we understand, design, and manage the microbial communities in WWTPs.