High variations of methanogenic microorganisms drive full-scale anaerobic digestion process

Organic molecular network analysis reveals transformation signatures of dissolved organic matter during anaerobic digestion process

Identifying the transformation types, i.e., syntheses or decompositions, of organic molecules in complex environmental systems remains a significant challenge. To address this, we propose a new analytical framework, Transformation-based Organic Molecular Ecological Network Analysis (TOMENA) for the systematic recognition and analysis of molecular transformations according to the measurement of high-resolution mass spectrometry (FT-ICR MS) through time-series data. Applying the TOMENA framework, we systematically investigated transformation signatures of dissolved organic matter (DOM) during anaerobic digestion processes. We found a close relationship between molecular transformation and molecular weight in the biodegradation system. A total of 129 transformations were identified, involving carbon numbers ranging from 0 to 24, with 59 of these transformations concentrated in small molecular weight changes involving 1-3 carbons. As the molecular weight corresponding to transformations increased, the proportion of bio-transformations used for decomposition decreased linearly. Simultaneously, large molecules were decomposed and small molecules synthesized, indicating a system tendency to transform molecules towards a medium mass range. Topological analysis of the transformation network further expanded our understanding. We discovered that molecular transformations did not follow the shortest path, as the path distance was significantly longer than in random networks (2.558 vs. 2.383). We identified that N-containing transformations were centrally located in the system through edge analysis. However, the transformations' position did not coincide with functional importance. A comprehensive indicator of irreplaceability and usage frequency revealed that C(+1)H(+3)O(+2)N(-1), C(+1)H(+2), O(+1), C(+3)H(+4)O(+2), and H(-2)O(+1) are critical transformation pathways in the system, showing the top 5 efficiency contributions. Our developed TOMENA workflow provides novel insights and robust methodological support for future research, advancing our understanding of molecular transformations in complex biodegradation system.

New insights into the factors influencing methanogenic pathways in anaerobic digesters

INTRODUCTION

Anaerobic digestion integrates waste treatment, energy generation, and nutrient recycling, producing methane mainly through acetoclastic (AM) and hydrogenotrophic methanogenesis (HM). Methanogenic pathway management can improve biogas productivity and quality. The balance between pathways is influenced by environmental and physicochemical conditions, with conflicting results on the effect of different factors often reported. This systematic review aims to clarify the influence of various parameters on methanogenic pathways in anaerobic digesters.

METHODS

Literature search was conducted in the Web of Science and Scopus databases. The effects of different parameters on the predominant methanogenic pathway were evaluated using Kruskal-Wallis tests and Spearman's rank correlation.

RESULTS

Thermophilic temperatures and high free ammonia nitrogen concentrations (>300 mg L-1) increase HM, with a strong combined effect of these variables. Conversely, under moderate temperature and ammonia concentrations, the primary feedstock influences the methanogenic pathway, with algae biomass, pig manure, and food industry wastewater showing the lowest contribution of hydrogenotrophic methanogens. pH effect varied with temperature, with acidic and alkaline pH favoring HM in mesophilic and thermophilic digesters, respectively. Furthermore, higher levels of volatile fatty acids (>2000 mg L-1), carbohydrates (>10 g/L) and lipids (>10 g/L) also appeared to favor HM over AM, while most metals - especially Cr, Se and W - promoted AM.

CONCLUSION

This study emphasizes the role of various factors in methanogenic pathway selection, highlighting the impact of previously overlooked parameters, such as inorganic elements and organic matter composition. These insights are essential for understanding the methanogenic pathway balance and optimizing biogas processes.

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.

Insight into response mechanism of short-chain fatty acids to refined microbial transformation order of dissolved organic matter ranked by molecular weight during dry anaerobic digestion

Dynamic transformation of dissolved organic matter (DOM) contributes to short-chain fatty acids (SCFAs) production during anaerobic digestion. However, the impact of refined transformation of DOM ranked by molecular weight (MW) on SCFAs has never been investigated. Results indicated that DOM conversion order was 3500-7000 Da>(MW>14000 Da) > 7000-4000 Da during hydrolysis stage, while it was independent of their MW in acidogenesis phase and followed a low to high MW order during methanogenesis stage. Proteins-like DOMs with different MW were closely related to SCFAs. Eight groups of microorganisms (e.g., Bacillus and Caldicoprobacter) responsible for the conversion of proteins-like DOMs to SCFAs. The possible routes linking environmental properties to microorganisms-proteins-like DOMs-SCFAs connections were constructed. Microbial activity modifications by regulating moisture, pH, NO3--N and NH4+-N can expedite the conversion of proteins-like DOMs to SCFAs. The study emphasizes the importance of MW-classification-based biotransformation of organic waste, offering a potential strategy to enhance anaerobic digestion performance.

Rare biosphere drives deterministic community assembly, co-occurrence network stability, and system performance in industrial wastewater treatment system

Bacterial community is strongly associated with activated sludge performance, but there still remains a knowledge gap regarding the rare bacterial community assembly and their influence on the system performance in industrial wastewater treatment plants (IWWTPs). Here, we investigated bacterial communities in 11 full-scale IWWTPs with similar process designs, aiming to uncover ecological processes and functional traits regulating abundant and rare communities. Our findings indicated that abundant bacterial community assembly was governed by stochastic processes; thereby, abundant taxa are generally present in wastewater treatment compartments across different industrial types. On the contrary, rare bacterial taxa were primarily driven by deterministic processes (homogeneous selection 61.9%-79.7%), thus they only exited in specific IWWTPs compartments and wastewater types. The co-occurrence networks analysis showed that the majority of keystone taxa were rare bacterial taxa, with rare taxa contributing more to network stability. Furthermore, rare bacteria rather than abundant bacteria in the oxic compartment contributed more to the degradation of xenobiotics compounds, and they were main potential drivers of pollutant removal. This study demonstrated the irreplaceable roles of rare bacterial taxa in maintaining system performance of IWWTPs, and called for environmental engineers and microbial ecologists to increase their attention on rare biosphere.

Occurrence, characteristics, and microbial community of microplastics in anaerobic sludge of wastewater treatment plants

Wastewater treatment plants (WWTPs) usually contain microplastics (MPs) due to daily influents of domestic and municipal wastewater. Thus, the WWTPs act as a point source of MPs distribution in the environment due to their incapability to remove MPs completely. In this study, MPs occurrence and distribution in anaerobic sludge from WWTPs in different regions (Kaifeng "KHP", Jinan "JSP", and Lanzhou "LGP") were studied. Followed by MPs identification by microscopy and Fourier transform infrared (FTIR) spectrum. The microbial communities associated with anaerobic sludge and MPs were also explored. The results showed that MPs concentrations were 16.5, 38.5, and 17.2 particles/g of total solids (TS) and transparent MPs accounted for 49.1%, 58.5%, and 48.3% in KHP, JSP, and LGP samples, respectively. Fibers represented the most common shape of MPs in KHP (49.1%), JSP (56.0%), and LGP (69.0%). The FTIR spectroscopy indicated the predominance of polyethylene polymer in 1-5 mm MPs. The Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes were the abundant phyla in all anaerobic sludge. The bacterial genera in KHP and LGP were similar, in which Caldilinea (>23%), Terrimonas (>10%), and Ferruginibacter (>7%) formed the core bacterial genera. While Rhodococcus (15.3%) and Rhodoplanes (10.9%) were dominating in JSP. The archaeal genera Methanosaeta (>69%) and Methanobrevibacter (>10%) were abundant in KHP and LGP sludge. While Methanomethylovorans accounted for 90% of JSP. Acetyltransferase and hydratase were the major bacterial enzymes, while reductase was the key archaeal enzyme in all anaerobic sludge. This study provided the baseline for MPs distribution, characterization, and MPs associated microbes in WWTPs.

Mechanistic insights into synergistic facilitation of copper/zinc ions and dewatered swine manure-derived biochar on anaerobic digestion of swine wastewater

Biochar-assisted anaerobic digestion (AD) has been proposed an advanced system for swine wastewater (SW) management. However, the effects of metallic nutrients in SW, such as copper/zinc ions (Cu2+/Zn2+), on the biochar-assisted AD of SW are not well understood. This study investigated the influences of individual Cu2+/Zn2+ or dewatered swine manure-derived biochar, as well as their combined additions, on the AD of SW. The results showed that exposure to 50 mg/L Cu2+/Zn2+ temporary inhibited methane production, but the addition of 20 g/L biochar alleviated this inhibition by shortening the methanogenic lag time and increasing methane yield. Following a period of acclimation, both Cu2+/Zn2+ and biochar promoted methane production, although metagenomic analysis revealed distinct mechanisms underlying their promotion. Cu2+/Zn2+ enhanced ATP processing, including electron exchange between NADH/NAD+ and succinate/fumarate transformation, by 26.0-35.8%. Additionally, the gene encoding Coenzyme M methylation was upregulated by 36.2% along with enrichments of Methanocullus and Methanosarcina, contributing to accelerated hydrolysis and methanogenesis rates by 54.7% and 44.8%, respectively. On the other hand, biochar mainly stimulated bacterial F-type ATPase activities by 28.4%, likely facilitating direct interspecies electron transfer between Geobacter and Methanosarcina for syntrophic methanogenesis. The combined addition of Cu2+/Zn2+ and biochar resulted in "win-win" benefits, significantly increasing the maximum methane production rate from 40.3 mL CH4/d to 53.7 mL CH4/d. Moreover, the introduction of biochar into AD of SW facilitated the transformation of more Cu2+/Zn2+ from a reducible Fe-Mn oxides form to a residual form, which potentially reduced the metallic toxicity of the digestate for soil amendment. The findings of this study provide novel insights into understanding the synergistic impacts of heavy metals and biochar in regulating SW during AD, as well as the management of associated digestate.

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.

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.

Anaerobic digestion of hydrothermally pretreated dewatered sewage sludge: effects of process conditions on methane production and the fate of phosphorus

The hydrothermal pretreatment (HTP) characteristics and the fate of phosphorus (P) and anaerobic digestion (AD) performance of dewatered sewage sludge (DSS) were investigated at different hydrothermal conditions. The maximum methane yield reached 241 mL CH₄/g COD when the hydrothermal conditions were 200 °C-2 h-10% (A4), and the yield was 78.28% higher than that without pretreatment (A0) and 29.62% higher than that of the initial hydrothermal conditions (A1, 140 °C-1 h-5%). Proteins, polysaccharides, and volatile fatty acids (VFAs) were the main hydrothermal products of DSS. 3D-EEM analysis revealed that tyrosine, tryptophan proteins, and fulvic acids decreased after HTP, but the content of humic acid-like substances increased, and this phenomenon was more noticeable after AD. Solid-organic P was converted into liquid-P during the hydrothermal process, and nonapatite inorganic P was converted into organic P during AD. All samples achieved positive energy balance, and the energy balance of A4 was 10.50 kJ/g VS. Microbial analysis showed that the composition of the anaerobic microbial degradation community changed as the sludge organic composition was altered. Results showed that the HTP improved the anaerobic digestion of DSS.

Biomethane Production from Sugarcane Vinasse in a Circular Economy: Developments and Innovations

Sugarcane ethanol production generates about 360 billion liters of vinasse, a liquid effluent with an average chemical oxygen demand of 46,000 mg/L. Vinasse still contains about 11% of the original energy from sugarcane juice, but this chemical energy is diluted. This residue, usually discarded or applied in fertigation, is a suitable substrate for anaerobic digestion (AD). Although the technology is not yet widespread—only 3% of bioethanol plants used it in Brazil in the past, most discontinuing the process—the research continues. With a biomethane potential ranging from 215 to 324 L of methane produced by kilogram of organic matter in vinasse, AD could improve the energy output of sugarcane biorefineries. At the same time, the residual digestate could still be used as an agricultural amendment or for microalgal production for further stream valorization. This review presents the current technology for ethanol production from sugarcane and describes the state of the art in vinasse AD, including technological trends, through a recent patent evaluation. It also appraises the integration of vinasse AD in an ideal sugarcane biorefinery approach. It finally discusses bottlenecks and presents possible directions for technology development and widespread adoption of this simple yet powerful approach for bioresource recovery.

Biomethane recovery through co-digestion of cheese whey and glycerol in a two-stage anaerobic fluidized bed reactor: Effect of temperature and organic loading rate on methanogenesis

Anaerobic digestion for CH₄ recovery in wastewater treatment has been carried out with different strategies to increase process efficiency, among which co-digestion and the two-stage process can be highlighted. In this context, this study aimed at evaluating the co-digestion of cheese whey and glycerol in a two-stage process using fluidized bed reactors, verifying the effect of increasing the organic loading rate (OLR) (2-20 g-COD.L^-1.d^-1) and temperature (thermophilic and mesophilic) in the second stage methanogenic reactor. The mesophilic methanogenic reactor (R-Meso) (mean temperature of 22 °C) was more tolerant to high OLR and its best performance was at 20 g-COD.L^-1.d^-1, resulting in methane yield (MY) and methane production (MPR) of 273 mL-CH₄.g-COD^-1 and 5.8 L-CH₄.L^-1.d^-1 (with 67% of CH₄), respectively. Through 16S rRNA gene massive sequencing analysis, a greater diversity of microorganisms was identified in R-Meso than in R-Thermo (second stage methanogenic reactor, 55 °C). Firmicutes was the phyla with higher relative abundance in R-Thermo, while in R-Meso the most abundant ones were Proteobacteria and Bacteroidetes. Regarding the Archaea domain, a predominance of hydrogenotrophic microorganisms could be observed, being the genera Methanothermobacter and Methanobacterium the most abundant in R-Thermo and R-Meso, respectively. The two-stage system composed with a thermophilic acidogenic reactor + R-Meso was more adequate for the co-digestion of cheese whey and glycerol than the single-stage process, promoting increases of up to 47% in the energetic yield (10.3 kJ.kg-COD^-1) and 14% in organic matter removal (90.5%).

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.

Chronic effects of benzalkonium chlorides on short chain fatty acids and methane production in semi-continuous anaerobic digestion of waste activated sludge

As an emerging pollutant, benzalkonium chlorides (BACs) potentially enriched in waste activated sludge (WAS). However, the microbial response mechanism under chronic effects of BACs on acidogenesis and methanogenesis in anaerobic digestion (AD) has not been clearly disclosed. This study investigated the AD (by-)products and microbial evolution under low to high BACs concentrations from bioreactor startup to steady running. It was found that BACs can lead to an increase of WAS hydrolysis and fermentation, but a disturbance to acidogenic bacteria also occurred at low BACs concentration. A noticeable inhibition to methanogenesis occurred when BAC concentration was up to 15 mg/g TSS. Metagenomic analysis revealed the key genes involved in acetic acid (HAc) biosynthesis (i.e. phosphate acetyltransferase, PTA), β-oxidation pathway (acetyl-CoA C-acetyltransferase) and propionic acid (HPr) conversion was slightly promoted compared with control. Furthermore, BACs inhibited the acetotrophic methanogenesis (i.e. acetyl-CoA synthetase), especially BAC concentration was up to 15 mg/g TSS, thereby enhanced short chain fatty acids (SCFAs) accumulation. Overall, chronic stimulation of functional microorganisms with increasing concentrations of BACs impact WAS fermentation.

Salinity impact on the metabolic and taxonomic profiles of acid and alkali treated inoculum for hydrogen production from food waste

This study evaluated the combined impact of salinity (2.5, 13, and 19.3 g NaCl/L) and inoculum pretreatment (acid/alkali) on the genomic and metabolic profiles of mesophilic fermentative bacteria for hydrogen (H₂) production from food waste. Experimental results revealed that acid-treated inoculum showed the highest H₂ yield (201.12 ± 13.84 mL H₂/g of volatile solids added) under medium salinity levels compared to other experimental conditions. A 7-56% increase in H₂ yield was observed for pretreated inoculum than untreated inoculum. Genomic analysis and metabolic pattern revealed that the H₂ production was mainly through Clostridial-type fermentation under medium to high salinity levels, whereas Enterococcus-type fermentation under low salinity levels. Further, the genomic analysis uncovered that phyla Firmicutes (69.71-96.81%) and genus Clostridium sensu stricto 1 (33.28-94.04%) dominated during the exponential gas production phase. Overall, this study showed the significance of inoculum pretreatment for the bioconversion of food waste at different salinity levels.

Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment

Pit latrines provide essential onsite sanitation services to over a billion people, but there are concerns about their role in infectious disease transmission, and impacts on groundwater resources. We conducted fieldwork in an informal settlement in Dar es Salaam, where cholera is endemic. We combined plate counting with portable MinION sequencing and quantitative polymerase chain reaction (qPCR) methods for characterization of bacteria in pit latrine sludge, leachate, shallow and deep groundwater resources. Pit latrine sludge was characterized by log₁₀ marker gene concentrations per 100 mL of 11.2 ± 0.2, 9.9 ± 0.9, 6.0 ± 0.3, and 4.4 ± 0.8, for total bacteria (16S rRNA), E. coli (rodA), human-host-associated Bacteroides (HF183), and Vibrio cholerae (ompW), respectively. The ompW gene observations suggested 5 % asymptomatic Vibrio cholerae carriers amongst pit latrine users. Pit leachate percolation through one-meter-thick sand beds attenuated bacterial hazard indicators by 1 to 4 log₁₀ units. But first-order removal rates derived from these data substantially overestimated the longer-range hazard attenuation in the sand aquifers. Cooccurrence of human sewage marker gene HF183 in all shallow groundwater samples testing positive for ompW genes demonstrated the human origin of Vibrio cholerae hazards in the subsurface. All borehole water samples tested negative for ompW and HF183 genes, but 16S rRNA gene sequencing data suggested ingress of faecal pollution into boreholes at the peak of the "long rainy season". Quantitative microbial risk assessment (QMRA) predicted a gastrointestinal disease burden of 0.05 DALY per person per year for the community, well above WHO targets of 10^-4-10^-6 DALY for disease related to drinking water.

Interaction and spatio-taxonomic patterns of the soil microbiome around oil production wells impacted by petroleum hydrocarbons

Numerous onshore oil production wells currently exist, and the petroleum hydrocarbon contamination of the surrounding soil caused by oil production wells is not well understood. Moreover, the impact of the distribution of the total petroleum hydrocarbons (TPH) in the soil on the microbiota requires further investigation. Accordingly, in this study, the distribution of petroleum hydrocarbons in the soils around oil production wells was investigated, and their alteration of the microbiota was revealed. The results revealed that in the horizontal direction, the heavily TPH-contaminated soils were mainly distributed within a circle with a radius of 200 cm centered on the oil production well; and in the vertical direction, the heavily TPH-contaminated soils were distributed within the 0-50 cm soil layer. A significant positive correlation was found between the microbial abundance and the TPH concentration in the soil with relatively low total carbon contents. Heavy TPH contamination (TPH concentration of >3000 mg/kg) significantly reduced the microbial diversity and altered the microbiota compared with the light TPH contamination (TPH concentration of around 1000 mg/kg). In the heavily TPH-contaminated soils, the relative abundances of the Proteobacteria and Bacteroides increased significantly; the network complexity among the soil microorganisms decreased; and the co-occurrence patterns were altered. In summary, the results of this study have reference value in the remediation of soils around oil production wells and provide guidance for the construction of microbial remediation systems for petroleum contamination.

Application of dry olive residue-based biochar in combination with arbuscular mycorrhizal fungi enhances the microbial status of metal contaminated soils

Biochar made-up of dry olive residue (DOR), a biomass resulting from the olive oil extraction industry, has been proposed to be used as a reclamation agent for the recovery of metal contaminated soils. The aim of the present study was to investigate whether the soil application of DOR-based biochar alone or in combination with arbuscular mycorrhizal fungi (AMF) leads to an enhancement in the functionality and abundance of microbial communities inhabiting metal contaminated soils. To study that, a greenhouse microcosm experiment was carried out, where the effect of the factors (i) soil application of DOR-based biochar, (ii) biochar pyrolysis temperature (considering the variants 350 and 500 °C), (iii) soil application dose of biochar (2 and 5%), (iv) soil contamination level (slightly, moderately and highly polluted), (v) soil treatment time (30, 60 and 90 days) and (vi) soil inoculation with Funneliformis mosseae (AM fungus) on β-glucosidase and dehydrogenase activities, FA (fatty acid)-based abundance of soil microbial communities, soil glomalin content and AMF root colonization rates of the wheat plants growing in each microcosm were evaluated. Biochar soil amendment did not stimulate enzyme activities but increased microbial abundances. Dehydrogenase activity and microbial abundances were found to be higher in less contaminated soils and at shorter treatment times. Biochar pyrolysis temperature and application dose differently affected enzyme activities, but while the first factor did not have a significant effect on glucosidase and dehydrogenase, a higher biochar dose resulted in boosted microbial abundances. Soil inoculation with F. mosseae favored the proliferation of soil AMF community and increased soil glomalin content as well as rates of AMF root colonization. This factor also interacted with many of the others evaluated to significantly affect soil enzyme activities, microbial abundances and AMF community. Our results indicate that the application of DOR-based biochar along with AMF fungi is an appropriate approach to improve the status of microbial communities in soils with a moderate metal contamination at short-term.

Metagenomic Analysis of the Long-Term Synergistic Effects of Antibiotics on the Anaerobic Digestion of Cattle Manure

The conversion of cattle manure into biogas in anaerobic digestion (AD) processes has been gaining attention in recent years. However, antibiotic consumption continues to increase worldwide, which is why antimicrobial concentrations can be expected to rise in cattle manure and in digestate. This study examined the long-term synergistic effects of antimicrobials on the anaerobic digestion of cattle manure. The prevalence of antibiotic resistance genes (ARGs) and changes in microbial biodiversity under exposure to the tested drugs was investigated using a metagenomic approach. Methane production was analyzed in lab-scale anaerobic bioreactors. Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant bacteria in the samples. The domain Archaea was represented mainly by methanogenic genera Methanothrix and Methanosarcina and the order Methanomassiliicoccales. Exposure to antibiotics inhibited the growth and development of methanogenic microorganisms in the substrate. Antibiotics also influenced the abundance and prevalence of ARGs in samples. Seventeen types of ARGs were identified and classified. Genes encoding resistance to tetracyclines, macrolide–lincosamide–streptogramin antibiotics, and aminoglycosides, as well as multi-drug resistance genes, were most abundant. Antibiotics affected homoacetogenic bacteria and methanogens, and decreased the production of CH4. However, the antibiotic-induced decrease in CH4 production was minimized in the presence of highly drug-resistant microorganisms in AD bioreactors.

Solid state anaerobic digestion of food waste and sewage sludge: Impact of mixing ratios and temperature on microbial diversity, reactor stability and methane yield

Food waste (FW) and sewage sludge (SS) were anaerobically co digested under solid state conditions (Total solids >15%) and observed that mixing ratio of 3:1 and 2:1 is optimum for mesophilic and thermophilic conditions respectively. The VS reduction and methane yield at optimized ratio was 76% and 0.35 L CH₄/(g VS reduced) respectively at mesophilic temperature whereas it was 88% and 0.42 L CH₄/(g VS reduced) at thermophilic temperature. The metagenomic analysis for these cases were done and high throughput DNA sequencing revealed that diversified bacterial groups that participate in the different metabolisms (hydrolysis, acidogenesis and acetogenesis) were mainly dominated by the phylum Firmicutes and Bacteriodetes. Genus Methanothrix is found to be dominant which is capable of generating methane by any methanogenic pathway among all the archaeal communities in the reactors followed by Methanolinea and Methanoculleus. However, it was understood through metagenomic studies that acetotrophic pathway is observed to be the major metabolic pathway in the reactors.

Microbiome signature and diversity regulates the level of energy production under anaerobic condition

The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH₄%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH₄, respectively. The physicochemical analysis revealed that level of energy production (CH₄%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O₂ level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH₄ concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH₄ producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH₄ concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.

Microbiota profile in mesophilic biodigestion of sugarcane vinasse in batch reactors

The vinasse is a residue of ethanol production with the potential for methane production, requiring an allochthonous inoculum. Several microorganisms act in the different phases of anaerobic digestion, and the identification of these microbial communities is essential to optimize the process. The characterization of the microbiota involved in the biodigestion of vinasse was observed in the initial stage (IS), at the peak of methane production (MS) and the end of the process (FS) of the best performance assay by high-throughput sequencing. The highest methane production was 0.78 mmolCH₄.gVS.h^-1 at 243.7 h in the substrate/inoculum ratio of 1.7, with consumption partial of acetic, propionic and isobutyric acids and an 82% reduction of chemical oxygen demand. High microbial diversity was found. The genera Clostridium, Acinetobacter, Candidatus Cloacamonas, Bacteroides, Syntrophomonas, Kosmotoga, the family Porphyromonadaceae and the class Bacteroidia were the most abundant in the maximum methane production. Methane production was driven by Methanobacterium and Methanosaeta, suggesting the metabolic pathways used were hydrogenotrophic and acetoclastic.

Waste to energy: valorization of spent tea waste by anaerobic digestion

The conversion of renewable resources into value-added products such as bioenergy is one of the growing concerns of bioeconomy strategy. Within this concept, assessing the proper combination of local wastes has major importance. This study set out to assess the feasibility of using spent tea waste as a single and co-substrate on anaerobic digestion and to explore the influence of the amount of microorganisms on the digester performance. For this purpose, biomethane potentials tests were conducted for seven different mixing ratios of spent tea waste and cow manure on a mass basis. The reactors operated under mesophilic conditions for 20 days with two inoculum/substrate ratios. The results revealed that using spent tea waste as a co-substrate did not reveal a significant effect on biomethane production in the reactors. Contrarily, the amount of inoculum had a remarkable effect on biomethane production, resulted in an increase in methane production between 28 and 32%. While the biomethane yields were in the range of 129-138 mL_N CH₄ g_VS^-1 for the co-digesters operated with inoculum/substrate ratio of 1, the range was 165-181 mL_N CH₄ g_VS^-1 for the co-digesters operated with inoculum/substrate ratio of 2. These findings represent the potential usage of the spent tea waste as a co-substrate within the sustainable waste management approach and are relevant to plant operators.

The Effect of Antibiotics on Mesophilic Anaerobic Digestion Process of Cattle Manure

This study explored the effect of eight antimicrobials on the efficiency of biogas production in the anaerobic digestion (AD) process of cattle manure. The microbiome involved in AD, presence and number of genes mcrA, MSC and MST specific for Archaea, and antibiotic resistance genes (ARGs) concentration in digestate (D) were examined. Supplementation of antibiotics to substrate significantly lowered biogas production. Amoxicillin caused a 75% decrease in CH4 production in comparison with the control samples. Enrofloxacin, tetracycline, oxytetracycline, and chlortetracycline reduced the amount of biogas produced by 36, 39, 45 and 53%, respectively. High-throughput sequencing of 16S rRNA results revealed that bacteria dominated the Archaea microorganisms in all samples. Moreover, antibiotics led to a decrease in the abundance of the genes mcrA, MSC, MST, and induced an increase in the number of tetracyclines resistance genes. Antibiotics decreased the efficiency of the AD process and lowered the quantity of CH4 obtained, while stimulating an increase in the number of ARGs in D. This work reveals how antimicrobials affect the cattle manure AD process and changes in microbial biodiversity, number of functional genes and ARGs in the digestate due to drugs exposure. It also, provides useful, practical information about the AD process.

Microbiome of Seven Full-Scale Anaerobic Digestion Plants in South Korea: Effect of Feedstock and Operational Parameters

In this study, the microbiomes linked with the operational parameters in seven mesophilic full-scale AD plants mainly treating food waste (four plants) and sewage sludge (three plants) were analyzed. The results obtained indicated lower diversity and evenness of the microbial population in sludge digestion (SD) plants compared to food digestion (FD) plants. Candidatus Accumulibacter dominated (up to 42.1%) in SD plants due to microbial immigration from fed secondary sludge (up to 89%). Its potential activity in SD plants was correlated to H2 production, which was related to the dominance of hydrogenotrophic methanogens (Methanococcus). In FD plants, a balance between the hydrogenotrophic and methylotrophic pathways was found, while Flavobacterium and Levilinea played an important role during acidogenesis. Levilinea also expressed sensitivity to ammonia in FD plants. The substantial differences in hydraulic retention time (HRT), organic loading rate (OLR), and total ammonium nitrogen (TAN) among the studied FD plants did not influence the archaeal methane production pathway. In addition, the bacterial genera responsible for acetate production through syntrophy and homoacetogenesis (Smithella, Treponema) were present in all the plants studied.

Bacterial community composition and function succession under aerobic and anaerobic conditions impacts the biodegradation of 17β-estradiol and its environmental risk

The widespread detection of 17β-estradiol (E2) in the environment has become an emerging concern worldwide due to its endocrine disrupting effects. This work focuses on the aerobic and anaerobic biodegradations of E2 in various sedimentary environments with different availabilities of electron acceptors, including O₂, NO₃^-, Fe³⁺, SO₄^2-, or HCO₃^-. The highest removal efficiency (98.9%) and shortest degradation half-life of E2 (t_1/2 = 5.0 d) were achieved under aerobic condition, followed by nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions. We propose four different degradation pathways of E2 based on the metabolites identified under various redox conditions. Although most of E2 was effectively removed under aerobic condition, the potential environmental risk still needs to be considered due to the residual estrogenic activity induced by estrone (E1) formation. The endocrine-disrupting activities, as indicated by estradiol equivalent (EEQ) values, were related to E2 degradation rate and metabolite formation. We further analyzed the succession of bacterial community compositions and functions using Illumina HiSeq sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The findings herein evidenced that bacterial community compositions and metabolic functions associated with different redox conditions impact the biodegradation of E2 and its endocrine-disrupting activity. This knowledge will be useful in predicting the environmental fates of estrogenic hormones in various sedimentary environments and aid in establishing appropriate strategies for eliminating potential environmental risks.

Microbiome taxonomic and functional profiles of two domestic sewage treatment systems

Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.

Annual microbial community dynamics in a full-scale anaerobic sludge digester from a wastewater treatment plant in Colombia

Anaerobic digestion is a microbe-driven process widely applied to treat activated sludge from municipal wastewater treatment plants. It is one of the most efficient solutions for sludge reduction along with biogas production. However, the knowledge of the microbial consortium involved in this process is still unknown in full-scale anaerobic digesters from Latin America. This study aimed to elucidate the dynamics of the microbial community of a full-scale anaerobic digester for a year using 16S rDNA amplicon sequencing with the Illumina Miseq platform. The results showed fluctuations in the frequencies of dominant phyla with a decrease of Proteobacteria and Bacteroidetes after a temporary suspension of anaerobic digester. The core community was affiliated with bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Chloroflexi. The core community was represented by 154 OTUs that accounted for 74% of all the processed reads. The Anaerolineaceae family, within Chloroflexi phylum, was the most frequently observed taxonomic group in all samples analyzed. Despite the microbial fluctuations, the biogas production was stable over the studied year (average 66% methane production), which might indicate a functional redundancy in the microbial consortium.

Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses

An understanding of microbial communities present in anaerobic bioreactors can strongly facilitate the development of approaches to control undesirable microorganisms, such as sulfate-reducing bacteria (SRB), in the system. In this study, overall microbial communities present in anaerobic bioreactors from seven industrial wastewater treatment plants (including food, pulp and paper industries) were investigated using 16S rRNA gene amplicon sequencing (MiSeq, Illumina). The dominant methanogens identified in the anaerobic bioreactors treating industrial wastewater were Methanobacterium and Methanosaeta; Methanospirillum was a predominant methanogen in the anaerobic sludge digester. Hydrogenotrophic and acetoclastic methanogens were detected at similar relative abundances in the anaerobic covered lagoons treating starch wastewater, whereas hydrogenotrophic methanogens were the predominant methanogens present in the sludge digester. SRB communities were further investigated using dsrB gene clone libraries. The results indicated the presence of SRB, such as uncultured Desulfobulbus sp., Syntrophobacter fumaroxidans, Syntrophorhabdus sp. PtaB.Bin027, and Desulfovibrio fructosivarans JJ. Incomplete-oxidizing SRB were the predominant SRB in all of the anaerobic bioreactors treating wastewater. In contrast, similar relative abundances of complete and incomplete-oxidizing SRB were observed in the sludge digester. The results of this study can further facilitate the development of SRB-controlling strategies to improve the efficiency of wastewater treatment.

Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland

Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.

A novel acetogenic bacteria isolated from waste activated sludge and its potential application for enhancing anaerobic digestion performance

The development of anaerobic digestion (AD) for volatile fatty acids (VFAs) production from waste activated sludge (WAS) is arrested due to low hydrolysis and acidification efficiency. This study proposed to enhance WAS reduction and VFAs accumulation during AD process via bioaugmentation of acetate-producing bacteria. Four acetogens were firstly isolated from a temperature-phased anaerobic digestion (TPAD) system. The acetate production efficiency of different isolates ranged from 15.8 to 73.7 mg acetate/g TOC, in which the bacterial strain NJUST19 was found to be the most effective strain. The results of morphological, biochemical characteristics as well as phylogenetic analysis showed that the isolate NJUST19 was Gram-positive and rod-shaped, catalase-negative, nitrate reduction-positive, methyl red-negative and capable of starch and gelatin hydrolysis, for which the name of Clostridium sp. NJUST19 was proposed. The optimal culture conditions (i.e. initial pH and temperature) were evaluated for their effects on microbe growth of selected NJUST19, and the maximum acetate production was observed at pH 9.0 and temperature of 40 °C. In the case of modified TPAD system inoculated with Clostridium sp. NJUST19, total suspended solids (TSS) removal rate and maximum VFAs accumulation increasing to 35.3% and 4200 mg/L, respectively, which was much higher than that of control (21.9% and 2894 mg/L). These results indicated that Clostridium sp. NJUST 19 is capable of enhancing digestion efficiency with a great benefit for VFAs production, offering potential prospects for bioaugmentation of WAS anaerobic digestion.

The microbiome driving anaerobic digestion and microbial analysis

The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.