Organic loading rate and hydraulic retention time shape distinct ecological networks of anaerobic digestion related microbiome

Long-term evaluating the strengthening effects of iron-carbon mediator for coking wastewater treatment in EGSB reactor

Coking wastewater (CWW) treatment is difficult due to its complex composition and high biological toxicity. Iron-carbon mediators was used to enhance the treatment of CWW through iron-carbon microelectrolysis (ICME). The results indicated that the removal rate of COD and phenolic compounds were enhanced by 24.1 % and 23.5 %, while biogas production and methane content were promoted by 50 % and 7 %. Microbial community analysis indicated that iron-carbon mediators had a transformative impact on the reactor's performance and dependability by enriching microorganisms involved in direct and indirect electron transfer, such as Anaerolineae and Methanothrix. The mediator also produced noteworthy gains in LB-EPS and TB-EPS, increasing by roughly 109.3 % and 211.6 %, respectively. PICRISt analysis demonstrated that iron-carbon mediators effectively augment the abundance of functional genes associated with metabolism, Citrate cycle, and EET pathway. This study provides a new approach for CWW treatment.

In-situ methane enrichment in anaerobic digestion of food waste slurry by nano zero-valent iron: Long-term performance and microbial community succession

In this work, nano zero-valent iron (nZVI) was added to a lab-scale continuous stirring tank reactor (CSTR) for food waste slurry treatment, and the effect of dosing rate and dosage of nZVI were attempted to be changed. The results showed that anaerobic digestion (AD) efficiency and biomethanation stability were optimum under the daily dosing and dosage of 0.48 g/gTCOD. The average daily methane (CH4) yield reached 495.38 mL/gTCOD, which was 43.65% higher than that at control stage, and the maximum CH4 content reached 95%. However, under single dosing rate conditions, high nZVI concentrations caused microbial cell rupture and loosely bound extracellular polymeric substances (LB-EPS) precipitation degradation. The daily dosing rate promoted the hydrogenotrophic methanogenesis pathway, and the activity of coenzyme F420 increased by 400.29%. The microbial analysis indicated that daily addition of nZVI could promote the growth of acid-producing bacteria (Firmicutes and Bacteroidetes) and methanogens (Methanothrix).

Bisphenol A affects microbial interactions and metabolic responses in sludge anaerobic digestion

The widespread use of bisphenol A (BPA) has resulted in the emergence of new pollutants in various environments, particularly concentrated in sewage sludge. This study investigated the effects of BPA on sludge anaerobic digestion, focusing specifically on the interaction of microbial communities and their metabolic responses. While the influence of BPA on methane accumulation is not significant, BPA still enhanced the conversion of soluble COD, protein, and polysaccharides. BPA also positively influenced the hydrolysis-acidogenesis process, leading to 17% higher concentrations of volatile fatty acids (VFAs). Lower BPA levels (0.2-0.5 mg/kg dw) led to decreased hydrolysis and acidogenesis gene abundance, indicating metabolic inhibition; conversely, higher concentrations (1-5 mg/kg dw) increased gene abundance, signifying metabolic enhancement. Diverse methane metabolism was observed and exhibited alterations under BPA exposure. The presence of BPA impacted both the diversity and composition of microbial populations. Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi dominated in BPA-treated groups and varied in abundance among different treatments. Changes of specific genera Sedimentibacter, Fervikobacterium, Blvii28, and Coprothermobacter in response to BPA, affecting hydrolysis and acetogenesis. Archaeal diversity declined while the hydrogenotrophic methanogen Methanospirillum thrived under BPA exposure. BPA exposure enabled microorganisms to form structured community interaction networks and boost their metabolic activities during anaerobic digestion. The study also observed the enrichment of BPA biodegradation pathways at high BPA concentrations, which could interact and overlap to ensure efficient BPA degradation. The study provides insights into the digestion performance and interactions of microbial communities to BPA stress and sheds light on the potential effect of BPA during anaerobic digestion.

Innovative approach for predicting biogas production from large-scale anaerobic digester using long-short term memory (LSTM) coupled with genetic algorithm (GA)

An artificial neural network (ANN) model called long-short term memory (LSTM), coupled with a genetic algorithm (GA) for feature selection, was used to predict biogas production of large-scale anaerobic digesters (ADs) of Tehran South Wastewater Treatment Plant (Iran), with a biogas production of approximately 30,000 Nm3/d. In order to employ the real conditions, the hydraulic retention time (HRT) of the ADs (21 days) was considered as the LSTM look-back window. To evaluate the model predictions, three different scenarios were defined. In the first scenario, the model predicted the produced biogas by using raw wastewater characteristics and reached the coefficient of determination of R2 = 0.84. The GA selected four out of eleven parameters of raw wastewater, including loads of BOD5, COD, TSS, and TN (kg/d), as the most informative data for the model. In the second scenario, the model predicted the produced biogas by employing the data of the thickened sludge streams entering the ADs and yielded a higher accuracy (R2 = 0.89). In this scenario, GA selected two out of six parameters of the sludge streams, including total flow rate (m3/d) and average solids content (w/w%). Finally, in the third scenario, by putting the parameters of the two previous scenarios together, the model's prediction accuracy increased slightly (R2 = 0.90). The results demonstrated that the GA-LSTM modeling technique could achieve reliable performance in predicting biogas production of large-scale ADs by including HRT in modeling procedure. It was also found that the raw wastewater characteristics severely affect AD behavior and can be successfully used as the input data of the AD models.

Enhancing methane production and organic loading capacity from high solid-content wastewater in modified granular activated carbon (GAC)-amended up-flow anaerobic sludge blanket (UASB)

Anaerobic digestion of high solid-content wastewater is hindered by high organic loading rates (OLRs). Granular activated carbon (GAC) was reported to promote direct interspecies electron transfer (DIET) and enhance reactor performance. In this study, three up-flow anaerobic sludge blanket (UASB) reactors were supplied with GAC in different locations: bottom (R1), top (R2), and bottom+top (R3). The performances of three reactors at different OLRs treating high solid-content wastewater were evaluated. At a low OLR, the highest methane yield (74 ± 4 %, g CH4-COD/g TCOD) was detected when GAC was supplied at top of the UASB (R2). When a high OLR was applied, the UASB supplemented with GAC at both bottom and top (R3) achieved the highest methane yield (66 ± 2 %, g CH4-COD/g TCOD), whereas the UASB supplemented with GAC at the top (R2) failed. Further studies on spatial distributions of sludge stability, specific methanogenic activities (SMAs), and microbial communities demonstrated the different impacts of GAC location on reactor performance and sludge characteristics under different OLRs. This study highlights the significance of considering organic loading capacity treating high solid-content wastewater when choosing GAC-based UASB systems.

Insights into the recent advances of agro-industrial waste valorization for sustainable biogas production

Recent years have seen a transition to a sustainable circular economy model that uses agro-industrial waste biomass waste to produce energy while reducing trash and greenhouse gas emissions. Biogas production from lignocellulosic biomass (LCB) is an alternative option in the hunt for clean and renewable fuels. Different approaches are employed to transform the LCB to biogas, including pretreatment, anaerobic digestion (AD), and biogas upgradation to biomethane. To maintain process stability and improve AD performance, machine learning (ML) tools are being applied in real-time monitoring, predicting, and optimizing the biogas production process. An environmental life cycle assessment approach for biogas production systems is essential to calculate greenhouse gas emissions. The current review presents a detailed overview of the utilization of agro-waste for sustainable biogas production. Different methods of waste biomass processing and valorization are discussed that contribute towards developing an efficient agro-waste to biogas-based circular economy.

Molecular insights informing factors affecting low temperature anaerobic applications: Diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems

Fats, oil and grease, and their hydrolyzed counterparts-long chain fatty acids (LCFA) make up a large fraction of numerous wastewaters and are challenging to degrade anaerobically, more so, in low temperature anaerobic digestion (LtAD) systems. Herein, we perform a comparative analysis of publicly available Illumina 16S rRNA datasets generated from LCFA-degrading anaerobic microbiomes at low temperatures (10 and 20 °C) to comprehend the factors affecting microbial community dynamics. The various factors considered were the inoculum, substrate and operational characteristics, the reactor operation mode and reactor configuration, and the type of nucleic acid sequenced. We found that LCFA-degrading anaerobic microbiomes were differentiated primarily by inoculum characteristics (inoculum source and morphology) in comparison to the other factors tested. Inoculum characteristics prominently shaped the species richness, species evenness and beta-diversity patterns in the microbiomes even after long term operation of continuous reactors up to 150 days, implying the choice of inoculum needs careful consideration. The generalised additive models represented through beta diversity contour plots revealed that psychrophilic bacteria RBG-13-54-9 from family Anaerolineae, and taxa WCHB1-41 and Williamwhitmania were highly abundant in LCFA-fed microbial niches, suggesting their role in anaerobic treatment of LCFAs at low temperatures of 10-20 °C. Overall, we showed that the following bacterial genera: uncultured Propionibacteriaceae, Longilinea, Christensenellaceae R7 group, Lactivibrio, candidatus Caldatribacterium, Aminicenantales, Syntrophus, Syntrophomonas, Smithella, RBG-13-54-9, WCHB1-41, Trichococcus, Proteiniclasticum, SBR1031, Lutibacter and Lentimicrobium have prominent roles in LtAD of LCFA-rich wastewaters at 10-20 °C. This study provides molecular insights of anaerobic LCFA degradation under low temperatures from collated datasets and will aid in improving LtAD systems for treating LCFA-rich wastewaters.

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

The role of pretreatments in handling antibiotic resistance genes in anaerobic sludge digestion - A review

Sludge is among the most important reservoirs of antibiotic resistance genes (ARGs), which would cause potential environmental risks with the sludge utilization. Currently, anaerobic digestion (AD) is effective to simultaneously realize the resource recovery and pollutants removal, including antibiotic resistance genes (ARGs), and various pretreatments are used to enhance the performance. Recently, plentiful publications have focused on the effects of pretreatment on ARGs removal, but the contradictory results are often obtained, and a comprehensive understanding of the research progress and mechanisms is essential. This study summarizes various pretreatment techniques for improving AD efficiency and ARGs reduction, investigates promising performance in ARGs removal when pretreatments combined with AD, and analyzes the potential mechanisms accounting for ARGs fates. The results showed that although thermal hydrolysis pretreatment showed the best performance in ARGs reduction during the pretreatment process, the significant rebound of ARGs would occur in the subsequent AD process. Conversely, ozone pretreatment and alkali pretreatment had no significant effect on ARGs abundance in the pretreatment stage, but could enhance ARGs removal by 15.6-24.3 % in the subsequent AD. Considering the efficiency and economic effectiveness, free nitrous acid pretreatment would be a promising and feasible option, which could enhance methane yield and ARGs removal by up to 27 % and 74.5 %, respectively. Currently, the factors determining ARGs fates during pretreatment and AD processes included the shift of microbial community, mobile genetic elements (MGEs), and environmental factors. A comprehensive understanding of the relationship between the fate of ARGs and pretreatment technologies could be helpful for systematically evaluating various pretreatments and facilitating the development of emerging and effective pretreatment techniques. Moreover, given the effectiveness, economic efficiency and environmental safety, we called for the applications of modern analysis approaches such as metagenomic and machine learning on the optimization of pretreatment conditions and revealing underlying mechanisms.

Effects of Magnetic Biochar Addition on Mesophilic Anaerobic Digestion of Sewage Sludge

As a low-cost additive to anaerobic digestion (AD), magnetic biochar (MBC) can act as an electron conductor to promote electron transfer to enhance biogas production performance in the AD process of sewage sludge and has thus attracted much attention in research and industrial applications. In the present work, Camellia oleifera shell (COS) was used to produce MBC as an additive for mesophilic AD of sewage sludge, in order to explore the effect of MBC on the mesophilic AD process and its enhancement mechanism. Analysis by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), Fourier-transform infrared spectrometry (FTIR), and X-ray diffraction (XRD) further confirmed that biochar was successfully magnetized. The yield of biogas from sewage sludge was enhanced by 14.68-39.24% with the addition of MBC, and the removal efficiency of total solid (TS), volatile solids (VS), and soluble chemical oxygen demand (sCOD) were 28.99-46.13%, 32.22-48.62%, and 84.18-86.71%, respectively. According to the Modified Gompertz Model and Cone Model, the optimum dosage of MBC was 20 mg/g TS. The maximum methane production rate (R_m) was 15.58% higher than that of the control reactor, while the lag-phase (λ) was 43.78% shorter than the control group. The concentration of soluble Fe²⁺ and Fe³⁺ were also detected in this study to analyze the function of MBC for improving biogas production performance from sewage sludge. The biogas production was increased when soluble Fe³⁺ was reduced to soluble Fe²⁺. Overall, the MBC was beneficial to the resource utilization of COS and showed a good prospect for improving mesophilic AD performance.

Effect of Temperature on Anaerobic Fermentation of Poplar Ethanol Wastewater: Performance and Microbial Communities

Temperature plays an important role in anaerobic digestion (AD), and different substrates have different optimum temperatures in AD. However, the effect of temperature on the performance of AD when cellulosic ethanol wastewater was used as a substrate was rarely reported. Therefore, the digestion characteristics of cellulosic ethanol wastewater at 25, 35, 45, and 55 °C were investigated, and the microbial communities of the sludge sample were analyzed after fermentation. The results showed that the cumulative methane production was the highest at 55 °C, 906.40 ± 50.67 mL/g VS, which was 81.06, 72.42, and 13.33% higher than that at 25, 35, and 45 °C, respectively. The content of methane was 68.13, 49.26, 70.46, and 85.84% at the terminal period of fermentation at temperatures of 25, 35, 45, and 55 °C, respectively. The testing of volatile fatty acids (VFAs) indicated that the accumulation of VFAs did not occur when the fermentation was carried out at 25, 35, and 45 °C; however, the VFA content at 55 °C was much larger than that in the three groups (25, 35, and 45 °C), and the ratio of propionic acid to acetic acid was larger than 1.4 at the late stage of fermentation, so it inhibited the fermentation. The diversity of the microbial community indicated that the floral structure and metabolic pathway of fermentation were alike at 25 and 35 °C. Firmicutes and Proteobacteria were the main flora covering the 25-55 °C-based phylum or below it. The relative abundance of Methanosaeta was the highest when fermentation temperatures were 25 and 35 °C; however, its relative abundance decreased sharply and the relative abundance of Methanosarcina increased substantially when the temperature increased from 35 to 45 °C, which indicated that Methanosarcina can exist in higher temperatures. At the same time, hydrogenotrophic methanogens such as Methanoculleus and Methanothermobacter were dominant when fermentation temperatures were 45 and 55 °C, which indicated that the metabolic pathway changed from acetoclastic methanogenesis to hydrogenotrophic methanogenesis.

Elucidation of microbial interactions, dynamics, and keystone microbes in high pressure anaerobic digestion

High-pressure anaerobic digestion (HPAD) is a promising technology for producing biogas enriched with high methane content in a single-step process. To enhance HPAD performance, a comprehensive understanding of microbial community dynamics and their interactions is essential. For this, mesophilic batch high-pressurized anaerobic reactors were operated under 3 bars (H3) and 6 bars (H6). The experimental results showed that the effect of high-pressure (up to 6 bar) on acidification was negligible while methanogenesis was significantly delayed. Microbial analysis showed the predominance of Defluviitoga affiliated with the phylum Thermotogae and the reduction of Thiopseudomonas under high-pressure conditions. In addition, the microbial cluster pattern in H3 and H6 was significantly different compared to the CR, indicating a clear shift in microbial community structure. Moreover, Methanobacterium, Methanomicrobiaceae, Alkaliphilus, and Petrimonas were strongly correlated in network analysis, and they could be identified as keystone microbes in the HPAD reactor.

The responses of mesophilic and thermophilic anaerobic digestion of municipal sludge to periodic fluctuation disturbance of organic loading rate

Fluctuation disturbance of organic loading rate (OLR) is common in actual anaerobic digestion (AD), but its effects on AD of municipal sludge gets little attention. This study investigated the responses of reactor performance and active microbial community in mesophilic and thermophilic AD of municipal sludge before, during and after OLR periodic fluctuation disturbance. The performance of both reactors were similar before and after disturbance although some parameter values changed during the disturbance, which indicated their enough buffer capacity to OLR periodic fluctuation. Different microbial community at RNA level was observed in the two reactors. When the OLR disturbance commenced, the microbial community changed greatly in thermophilic AD. Error and attack tolerance of the microbial network was analyzed in order to learn the response mechanisms to OLR disturbance. The results assisted that the thermophilic microbial community was more vulnerable, but the reactor performance of which could be maintained using the functional redundancy strategy under OLR fluctuation disturbance.

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

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

Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks

This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. LactobacillalesandCloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.

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.

Determination of methanogenesis by nutrient availability via regulating the relative fitness of methanogens in anaerobic digestion

Response of microbial community to nutrient availability in anaerobic digestion (AD) remains elusive. Prokaryotic communities in AD batch cultures with 0, 1, 3, 5, 7, 11, 15, 20, and 25 g/L peptone were monitored using massive parallel sequencing and quantitative PCR over a 34-day experimental period. Methane production displayed a hump-shaped response to the nutrient gradient (peaking at 15 g/L peptone). Moreover, total and acetoclastic methanogens showed hump-shaped responses (both peaking at 11 g/L peptone). However, prokaryotic population increased with nutrient concentration (linear regression, R² = 0.86) while diversity decreased (R² = 0.94), and ordination analysis showed a gradual succession of community structure along the first axis. Network analysis revealed that extent of interspecific interactions (e.g., edge number and clustering coefficient) exhibited a hump-shaped response. The combined results indicate that abundant species became more dominated with increasing nutrient, which can result in a gain or loss of interspecific interaction within the community. Network module analysis showed that one module dominated the network at each nutrient level (comprising 41%-65% of the nodes), indicating that AD community formed a core microbial guild. The most abundant phylotypes, Macellibacteroides and Butyricicoccaceae, were consistently negative with acetoclastic methanogens in the dominant modules. Their predominance at ≥15 g/L peptone can explain the hump-shaped responses of methanogenesis and methanogens. Collectively, methanogenesis and microbial network exhibited hump-shaped responses, although microbial community exhibited monotonic responses. Therefore, nutrient availability can determine the methanogenesis through regulating the relative fitness of methanogens within the community.

Syntrophic bacteria- and Methanosarcina-rich acclimatized microbiota with better carbohydrate metabolism enhances biomethanation of fractionated lignocellulosic biocomponents

An inadequate lignocellulolytic capacity of a conventional anaerobic digester sludge (ADS) microbiota is the bottleneck for the maximal utilization of lignocellulose in anaerobic digestion. A well-constructed microbial consortium acclimatized to lignocellulose outperformed the ADS in terms of biogas productivity when fractionated biocomponents of rice straw were used to achieve a high methane bioconversion rate. A 33.3 % higher methane yield was obtained with the acclimatized consortium (AC) compared to that of ADS control. The dominant pair-wise link between Firmicutes (18.99-40.03 %), Bacteroidota (10.94-28.75 %), and archaeal Halobacteriota (3.59-20.57 %) phyla in the AC seed digesters indicated that the keystone members of these phyla were responsible for higher methane yield. A high abundance of syntrophic bacteria such as Proteiniphilum (1.22-5.19 %), Fermentimonas (0.71-5.31 %), Syntrophomonas (0.87-3.59 %), and their syntrophic partner Methanosarcina (4.26-18.80 %) maintained the digester stability and facilitated higher substrate-to-methane conversion in the AC seed digesters. The present combined strategy will help in boosting the 'biomass-to-methane" conversion.

Valorization of Brewery Waste through Polyhydroxyalkanoates Production Supported by a Metabolic Specialized Microbiome

Simple Summary

Raw brewers’ spent grain, a by-product of beer production, is produced at a large scale and is usually used as animal feed or is landfilled. However, its composition shows that this feedstock has the potential for other applications, such as bioplastics production (e.g., polyhydroxyalkanoates). In this way, the aim of this work was to assess the use of raw brewers’ spent grain for polyhydroxyalkanoates production, adding new value to this feedstock. The results confirm the potential of raw brewers’ spent grain to produce polyhydroxyalkanoates, as the population was enriched in the microorganisms able to accumulate these biopolymers. These results will contribute to society’s knowledge and competence via the development of a treatment process for brewery waste of both environmental (productive waste treatment) and economic interest (production of biopolymers), which will certainly attract its application to the brewery industry worldwide.

Abstract

Raw brewers’ spent grain (BSG), a by-product of beer production and produced at a large scale, presents a composition that has been shown to have potential as feedstock for several biological processes, such as polyhydroxyalkanoates (PHAs) production. Although the high interest in the PHA production from waste, the bioconversion of BSG into PHA using microbial mixed cultures (MMC) has not yet been explored. This study explored the feasibility to produce PHA from BSG through the enrichment of a mixed microbial culture in PHA-storing organisms. The increase in organic loading rate (OLR) was shown to have only a slight influence on the process performance, although a high selectivity in PHA-storing microorganisms accumulation was reached. The culture was enriched on various PHA-storing microorganisms, such as bacteria belonging to the Meganema, Carnobacterium, Leucobacter, and Paracocccus genera. The enrichment process led to specialization of the microbiome, but the high diversity in PHA-storing microorganisms could have contributed to the process stability and efficiency, allowing for achieving a maximum PHA content of 35.2 ± 5.5 wt.% (VSS basis) and a yield of 0.61 ± 0.09 Cmmol_PHA/Cmmol_VFA in the accumulation assays. Overall, the production of PHA from fermented BSG is a feasible process confirming the valorization potential of the feedstock through the production of added-value products.

Co-occurrence network analysis reveals loss of microbial interactions in anaerobic digester subjected to repeated organic load shocks

Fluctuations in the anaerobic digestion (AD) organic loading rate (OLR) cause shocks to the AD microbiome, which lead to unstable methane productivity. Managing these fluctuations requires a larger digester, which is impractical for community-scale applications, limiting the potential of AD in advancing a circular economy. To allow operation of small-scale AD while managing OLR fluctuations, we need to tackle the issue through elucidation of the microbial community dynamics via 16S rRNA gene sequencing. This study elucidated the interrelation of the AD performance and the dynamics of the microbial interactions within its microbiome in response to repeated high OLR shocks at different frequencies. The OLR shocks were equivalent to 4 times the baseline OLR of 2 g VS/L/d. We found that less frequent organic load shocks result to deterioration of methane productivity. Co-occurrence network analysis shows that this coincides with the breakdown of the microbiome network structure. This suggests loss of microbial interactions necessary in maintaining stable AD. Identification of species influencing the network structure revealed that a species under the genus Anaerovorax has the greatest influence, while orders Spirochaetales and Synergistales represent the greatest number of the influential species. We inferred that the impact imposed by the OLR shocks shifted the microbiome activity towards biochemical pathways that are not contributing to methane production. Establishing a small-scale AD system that permits OLR fluctuations would require developing an AD microbiome resilient to infrequent organic loading shocks.

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.

Quorum quenching of autoinducer 2 increases methane production in anaerobic digestion of waste activated sludge

The ubiquitous signaling molecule autoinducer 2 (AI-2) is involved in intra- and interspecies communication, most notably between Gram-negative and Gram-positive bacteria. AI-2 accumulates during the exponential phase of the Escherichia coli (E. coli) monoculture and then rapidly decreases upon entry into the stationary phase. However, deleting both the genes encoding AI-2 synthase (LuxS) and the lsr operon regulator (LsrR) in the E. coli genome causes impaired AI-2 production and continuous AI-2 scavenging from the environment. This genetically-engineered E. coli mutant capable of quenching AI-2 quorum sensing (QS) system was utilized to evaluate the effect of AI-2 quenching on the anaerobic digestion of waste activated sludge (WAS) because the role of QS system via AI-2 in the process remains obscure. In this study, E. coli ∆luxS lsrR mutant cells were microencapsulated in sodium alginate beads and incubated with WAS anaerobically. After 15 days of anaerobic fermentation, the WAS containing double mutant cells produced significantly more methane than that of the parent E. coli cells. AI-2 quenching occurred concurrently with a shift of microbial communities that contribute to increasing acetate consumption by the Methanosarcina spp. resulting in an increase in methane production. KEY POINTS: • Impact of autoinducer 2 quenching in complex bacterial populations were determined. • Key microorganisms contributing to the increase of methane in WAS anaerobic digestion were found. • The AI-2 quenching is a potential regulatory in wastewater treatment and bioenergy research.

Effects of organic loading rate and pretreatments on digestion performance of corn stover and chicken manure in completely stirred tank reactor (CSTR)

The performance, system stability, and microbial community response in anaerobic co-digestion (AcoD) of corn stover (CS) and chicken manure (CM) were investigated by running completely stirred tank reactor (CSTR) under controlled organic loading rate (OLR). Prior to anaerobic digestion (AD), potassium hydroxide (KOH) or liquid fraction of digestate (LFD) was applied to pretreat CS, respectively. The results showed that the daily biogas production (DBP) in co-digestion showed a gradual increasing trend with an increase in the OLR from 65 g TS·L^-1 to 100 g TS·L^-1. The daily methane production per g volatile solids (DMP-VS) in co-digestion increased by 23.0%-27.1%, 18.7%-18.8%, and 17.5%-18.0% at the OLRs of 65, 80, and 100 g TS·L^-1, respectively, upon pretreatment with KOH or LFD, as compared to that in co-digestion CSTR without any pretreatment. In addition, all co-digestion CSTRs were operated in stable state. Approximately half of the total carbon in the substrates was recovered in the form of a biogas product, with the carbon mass balance being impacted by the OLR as well as pretreatment. The diversity as well as function of the microbial community varied in response to different OLRs and pretreatment methods. The majority of bacterial genera were strongly correlated with operational parameters. The study indicates that management of OLR and selection of proper pretreatment method could enhance the efficiency and productivity of CS and CM co-digestion in CSTR.

Short-term changes in the anaerobic digestion microbiome and biochemical pathways with changes in organic load

Fluctuations in organic loading rate are frequently experienced in practical-scale anaerobic digestion systems. These impose shocks to the microbiome leading to process instability and failure. This study elucidated the short-term changes in biochemical pathways and the contributions of microbial groups involved in anaerobic digestion with varying organic load shocks. A mixture of starch and hipolypeptone corresponding to a carbon-to‑nitrogen ratio of 25 was used as substrate. Batch vial reactors were run using acclimatized sludge fed with organic load varying from 0 to 5 g VS/L. Methane yield decreased with increasing organic load. The microbiome alpha diversity represented as the number of operational taxonomic units (OTUs) and the Shannon index both decreased with organic load indicating microbiome specialization. The biochemical pathways predicted using PICRUSt2 were analyzed along with the corresponding contributions of microbial groups leading to a proposed pathway of substrate utilization. Genus Trichococcus (order Lactobacillales) increased in contribution to starch degradation pathways with increase in organic load while genus Macellibacteroides (order Bacteroidales) was prominent in contribution to bacterial anaerobic digestion pathways. Strictly acetoclastic Methanosaeta increased in prominence over hydrogenotrophic Methanolinea with increase in organic load. Results from this study provide better understanding of how anaerobic digesters respond to organic load shocks.

Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera

Operational factors and microbial interactions affect the ecology in anaerobic digestion systems. From 12 lab-scale reactors operated under distinct engineering conditions, bacterial communities were found driven by temperature, while archaeal communities by both temperature and substrate properties. Combining the bacterial and archaeal community clustering patterns led to five sample groups (ambient, mesophilic low-solid-substrate, mesophilic, mesophilic co-digestion and thermophilic) for co-occurrence network analysis. Network topological properties were associated with substrate characteristics and hydrolysis-methanogenesis balance. The hydrolysis efficiency correlated (p < 0.05) with clustering coefficient positively and with normalized betweenness negatively. The influent particulate COD ratio and the relative differential hydrolysis-methanogenesis efficiency (D_efficiency) correlated negatively with the average path length (p < 0.05). Individual genera’s topological properties showed more connector genera in thermophilic network, representing stronger inter-module communication. Individual genera’s normalized degree and betweenness revealed that lower-abundance genera (as low as 0.1%) could perform central hub roles and communication roles, maintaining the stability and functionality of the microbial community.

Response of soil protozoa to acid mine drainage in a contaminated terrace

Acid mine drainage (AMD) system represents one of the most unfavorable habitats for microorganisms due to its low pH and high concentrations of metals. Compared to bacteria and fungi, our understanding regarding the response of soil protozoa to such extremely acidic environments remains limited. This study characterized the structures of protozoan communities inhabiting a terrace heavily contaminated by AMD. The sharp environmental gradient of this terrace was generated by annual flooding from an AMD lake located below, which provided a natural setting to unravel the environment-protozoa interactions. Previously unrecognized protozoa, such as Apicomplexa and Euglenozoa, dominated the extremely acidic soils, rather than the commonly recognized members (e.g., Ciliophora and Cercozoa). pH was the most important factor regulating the abundance of protozoan taxa. Metagenomic analysis of protozoan metabolic potential showed that many functional genes encoding for the alleviation of acid stress and various metabolic pathways were enriched, which may facilitate the survival and adaptation of protozoa to acidic environments. In addition, numerous co-occurrences between protozoa and bacterial or fungal taxa were observed, suggesting shared environmental preferences or potential bio-interactions among them. Future studies are required to confirm the ecological roles of these previously unrecognized protozoa as being important soil microorganisms.

Carboxylic acids production via anaerobic fermentation: Microbial communities' responses to stepwise and direct hydraulic retention time decrease

Carboxylic acids, traditionally produced from fossil fuels, might be generated from renewable biomass resources via anaerobic fermentation. Considering that the microbial activity of this bioprocess is ruled by the imposed hydraulic retention time (HRT), this investigation explored the relationship between process stability and microbial community. Stepwise and direct HRT reduction strategies were assessed in terms of waste bioconversion into volatile fatty acids (VFAs). Microbial community dynamics revealed a microbial specialization along the HRT decrease. The direct implementation of low HRT resulted in drastic microbial fluctuations, leading to process failure at HRT below 6 days. Stepwise strategy for HRT reduction favored microbial adaptation, supporting maximum bioconversions efficiencies (32 % VFA_COD/tCOD_in) at low HRT values (HRT 4 days). Microbial similarity analysis revealed Clostridiales, Lactobacillales and Bacteroidales orders as keystone microorganisms involved in VFAs production, being responsible for protein degradation and propionic acid accumulation.

Diversity and Metabolic Potentials of As(III)-Oxidizing Bacteria in Activated Sludge

Biological arsenite [As(III)] oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOB) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOB in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOB, while bacteria associated with Hydrogenophaga were identified as aerobic AOB in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOB. Functional genes encoding As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOB in activated sludge and enhance their capacity for As(III) oxidation. IMPORTANCE AOB play an important role in the removal of toxic arsenic from wastewater. Most of the AOB have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities is not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOB community inhabiting the activated sludges. In this study, the putative AOB responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials, including As(III) oxidation, denitrification, carbon fixation, secondary metabolite biosynthesis, and extracellular polymeric substance metabolism, were investigated. This observation provides an understanding of anoxic and/or oxic AOB during the As(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.

Pushing the organic loading rate in electrochemically assisted anaerobic digestion of blackwater at ambient temperature: Insights into microbial community dynamics

Decentralized blackwater treatment by anaerobic digestion is being considered as a sustainable sanitation concept. However, the low biodegradability and complex composition restrictedly limited the treatability of blackwater, resulting in requirements of low operational organic loading rates (OLRs). In this study, a microbial electrolysis cell assisted anaerobic digester (MEC-AD) treating vacuum toilet blackwater was successfully operated for 420 days at OLRs ranging from 0.77 to 3.03 g COD/L-d in 6 stages (including an open-circuit Stage 5) at ambient temperature. Based on the steady-state results from different stages, the highest methane yield (42.4% out of 45% biochemical methane potential value) was achieved in Stage 1 with an OLR of 0.77 g COD/L-d. At the same OLR of ~3.0 g COD/L-d, Stage 4 (32.4%) and Stage 6 (35.2%) showed significantly higher methane yield (p < 0.01) than open-circuit Stage 5 (24.1%). The lowest COD removal efficiency of 31.8% was observed in Stage 5 with short-chain volatile fatty acids (SCVFAs) accumulated to ~1000 mg/L, which was more than double the values of Stage 4 and 6. The microbial community analysis revealed that the applied potential did not significantly affect archaeal diversity but largely increased the archaeal abundance on the cathode, and led the bacterial community shift with the enrichment of specific electroactive bacteria. Microbial co-occurrence network analysis further confirmed the positive correlations between known electroactive bacteria and electrotrophic methanogens. Moreover, electric energy consumed by the MEC-AD system was fully recovered as biomethane.

Insights into organic loading rates of anaerobic digestion for biogas production: a review

Anaerobic digestion (AD) for biogas production is affected by many factors that includes organic loading rate (OLR). This OLR appears to be closely linked to various other factors and understanding these linkages would therefore allow the sole use of OLR for process performance monitoring, control, as well as reactor design. This review's objective is to collate the various AD factor specific studies, then relate these factors' role in OLR fluctuations. By further analyzing the influence of OLR on the AD performance, it would then be possible, once all the other factors have been determined and fixed, to manage an AD plant by monitoring and controlling OLR only. Decisions on reactor design, process kinetics, biogas yield and process stability can then be made much more quickly and with minimal troubleshooting steps.

Anaerobic co-digester microbiome during food waste valorization reveals Methanosaeta mediated methanogenesis with improved carbohydrate and lipid metabolism

This study determines the optimum food waste (FW) loading in an anaerobic digester for methane production. Interrelation between the degradation mechanism and microbial community composition was assessed through in-depth metabolic pathway analysis and gene quantification. Higher methane production and short lag phase were observed in the FW reactors with low substrate loadings (<4% v/v) while extended lag phase and incomplete substrate utilization were observed in the reactors fed with higher substrates (>6% v/v). The long-chain fatty acids (LCFAs) degradation was influenced by initial FW loading, and up to 99% LCFA degradation occurred at 4% FW reactor. The addition of 8 to 10% FW substrate inhibited methanogenesis due to the accumulation of volatile fatty acids (VFA) and low LCFA degradation. Under optimal conditions of substrate loading, Methanosaeta and Methanosarcina were abundant, indicating their role in methanogenesis and syntrophic acetogenesis, along with enhanced metabolic pathways specific for carbohydrate and lipid metabolism.

Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis

The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.

Insight into the performance and microbial community profiles of magnetite-amended anaerobic digestion: Varying promotion effects at increased loads

In current study, the enhancement effect of magnetite on anaerobic digestion was evaluated at increased organic loading rate (OLR) from 1.6 to 25.6 kg COD·m^-3·d^-1. The supplement of magnetite enhanced the methane yield by 7-483% accompanied with faster VFAs conversion. Microbial analysis suggested the varied enhancing effect achieved at different OLRs was attributed to different syntrophic interactions triggered by magnetite. More specially, an electroactive syntropy was established between Trichococcus with Methanobacterium at OLR lower than 6.4 kg COD·m^-3·d^-1, while with the OLR increase, more acid fermentative bacteria (Propionimicrobium, Syner-01) were enriched and further enhanced methanogenesis in a syntrophic way with Methanosaeta. Overall, the incorporation of magnetite was a promising approach to achieve efficient anaerobic digestion, OLR was also critical factor affecting the methanogenesis and should be carefully regulated in future application.

Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review

Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.

Effects of higher temperature on antibiotic resistance genes for in-situ biogas upgrading reactors with H2 addition

In-situ biogas upgrading by H₂ injection is a promising method for bio-natural gas production, yet the effect of H₂ addition on antibiotic resistance genes during the in-situ biogas upgrading process remains unknown. We analyzed mesophilic and thermophilic in-situ biogas upgrading digesters with intermittent or continuous mixing models using metagenomic and metatranscriptomic methods to evaluate the effects of H₂ addition on antibiotic resistance profiles. We found that H₂ addition had less impact in the mesophilic reactor. In the thermophilic reactor, the influenced antibiotic resistance ontology (AROs) was mostly bound to the integral membrane transporters of the ATP-binding cassette and major facilitator superfamily. The annotated gene numbers of four drug classes, including macrolide, glycopeptide, lincosamide, and fluoroquinolone, increased distinctly after H₂ addition. Acetate concentration is a vital indicator for distinguishing the abundance of different antibiotic efflux pumps. Most of the AROs influenced by Ruminiclostridium replaced the original dominant species Clostridium, and the versatile genus Methanosarcina was the sole methanogen correlated with the altered AROs of efflux pumps conferring antibiotic resistance. The introduced H₂ was synthesized to CH₄via the hydrogenotrophic pathway of Methanosarcina flavescens, and part of the consumed H₂ was used for cell growth.

Rapid recovery of methane yield in organic overloaded-failed anaerobic digesters through bioaugmentation with acclimatized microbial consortium

Acidification during anaerobic digestion (AD) due to organic overloading is one of the major reasons for process failures and decreased methane productivity in anaerobic digesters. Process failures can cause the anaerobic digesters to stall completely, prolong the digester recovery period, and inflict an increased operational cost on wastewater treatment plants and adverse impacts on the environment. This study investigated the efficacy of bioaugmentation by using acclimatized microbial consortium (AC) in recovering anaerobic digesters stalled due to acidosis. Overloading of digesters with food waste leachate (FWL) led to the accumulation of volatile fatty acids (11.30 g L^-1) and a drop in pH (4.67), which resulted in process failure and a 22-fold decline in cumulative methane production compared to that in the initial phase. In the failure phase, the syntrophic and methanogenic activities of the anaerobic digester microbiota were disrupted by a significant decrease in the abundance of syntrophic populations such as Syntrophomonas, Syntrophorhabdus, Sedimentibacter, and Levilinea, and the phylum Euryarchaeota. Bioaugmentation of the failed digesters by adding AC along with the adjustment of pH resulted in the prompt recovery of methane productivity with a 15.7-fold higher yield than that in unaugmented control. The abundance of syntrophic bacteria Syntrophomonas and phylum Euryarchaeota significantly increased by 29- and 17-fold in the recovered digesters, respectively, which showed significant positive correlations with methane productivity. Methanosarcina and acetoclastic Methanosaeta played a major role in the recovery of the digesters; they were later replaced by hydrogenotrophic Methanoculleus. The increase in the abundance of genes associated with biomethanation contributed to digester recovery, according to the functional annotation of 16S rDNA amplicon data. Thus, bioaugmentation with AC could be a viable solution to recover digesters experiencing process failure due to organic overloading.

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

Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.

Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?

The dissemination of antibiotic resistance genes (ARGs) in food waste (FW) disposal can pose severe threats to public health. Lipid is a primary composition in FW, while whether lipid stress can affect ARGs dynamics during anaerobic digestion (AD) process of FW is uncertain. This study focused on the impacts of lipid stress on methane production, fate of ARGs and its microbial mechanisms during AD of FW. Results showed that high lipid content increased methane yield but prolonged hydrolysis and lag time of methane production compared to AD of FW without oil. Moreover, variations of ARGs were more susceptible to lipid stress. Lipid stress could facilitate the reduction of total ARGs abundances compared to the group without oil, particularly restraining the proliferation of sul1, aadA1 and mefA in AD systems (P < 0.05). Mantel test suggested that integrons (intl1 and intl2) were significantly correlated with all detected ARGs (r: 0.33, P < 0.05), indicating that horizontal gene transfer mediated by integrons could be the driving force on ARGs dissemination. Network analysis suggested that Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria were the main potential hosts of ARGs. In addition, under the lipid stress, the reduction of host bacteria was responsible for the elimination of several specific ARGs, thereby affecting ARGs profiles. These findings firstly deciphered ARGs dynamics and their driving factors responding to lipid stress during anaerobic biological treatment of FW.

Microbiome-environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination

Mining activities of antimony (Sb) and arsenic (As) typically result in severe environmental contamination. These contaminants accumulate in rice and thus threaten the health of local residents, who consume Sb- and As-enriched rice grains. Microorganisms play a critical role in the transformation and transportation of Sb and As in paddy soil. Thus, an understanding of the microbiology of contaminated sites would promote the production of safe agricultural products. In this study, six Sb- and As-contaminated rice fields near an active Sb-mining area were investigated. The Sb and As concentrations of all samples were elevated compared to the background level in China. Nitrate, total As, total Sb, and Fe(III) were the major determinants of the microbial community structure. Seven bacterial taxa (i.e. Bradyrhizobium, Bryobacter, Candidatus Solibacter, Geobacter, Gemmatimonas, Halingium, and Sphingomonas) were identified as the core microbiome. These taxa were strongly correlated with the As and Sb contaminant fractions and likely to metabolize As and Sb. Results imply that many soil microbes can survival in the Sb/As contaminated sites.

Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

Critical evidence for direct interspecies electron transfer with tungsten-based accelerants: An experimental and theoretical investigation

Accelerants can significantly enhance the biodegradability in anaerobic digestion (AD), which can be attributed to the direct interspecies electron transfer (DIET) mechanism. However, critical evidence for DIET mechanism is absent. In this work, nano-scale tungsten (W)-based compounds (WC, W₂N, and W₁₈O₄₉) are employed to clarify the roles of W-based accelerants in AD systems. A DIET mechanism based on the W-based accelerants is proposed, and three critical pieces of evidence are provided: (i) First-principle density functional theory calculations provide theoretical evidence, illustrating that W-based accelerants are of zero band gap. (ii) Electrical conductivity evaluation further elucidates that W-based accelerants have superior electronic transport. (iii) Pyrosequencing of 16S rRNA gene confirms the existence of acetogens and methanogens in AD systems, which can act as electron-donor bacteria and electron-acceptor archaea, respectively. Combining theoretical with experimental results, the critical evidence provides a general strategy for understanding the DIET mechanism of accelerant in AD systems.

Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure

In this work, fate of antibiotic resistance genes (ARGs), heavy metal resistance genes (MRGs) and intI1 were investigated during mesophilic (mAD) and thermophilic anaerobic digestion (tAD) of swine manure with presence of Cu and Zn. Results showed that metal reduced the lag phase time. Cu showed stronger inhibition than Zn on archaea community and metals inhibited the growth of acetoclastic methanogens during mAD. Although total concentration of metals increased after AD, they were transformed into stable state. The abundance of qnrS, sul1, sul2 and drfA7 increased 1.2-5.7 times after mAD, while reduced after tAD, showed that tAD was effective in ARGs removal. Structural equation model analysis suggested that intI1 had the most standardized direct effects on ARGs variation in mAD (R = 0.85, p < 0.01), while the co-occurrence of MRGs with ARGs showed significantly positive influences on ARGs variation in tAD (R = 0.82, p < 0.01).

Transition of microbial communities and degradation pathways in anaerobic digestion at decreasing retention time

Tuning of operational variables is a common practice to control the anaerobic digestion process and, in advanced applications, to promote the accumulation of fermentation products. However, process variables are interrelated. In this study, the hydraulic retention time (HRT) was decoupled from the organic loading rate (OLR) in order to isolate the effect of HRT as a selective pressure on: process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and the microbial community. Four mesophilic anaerobic digesters were subjected to a sequential decrease in HRT from 15 to 8, 4 and 2 days while keeping the OLR constant at chemical oxygen demand of 1 gCOD L _r^-1 d^-1. The results showed that HRT alone was insufficient to washout methanogens from the digesters, which in turn prevented the accumulation of volatile fatty acids (VFA). Methanosaeta was the dominant genus in the four digesters at all HRTs. Metabolic rates showed that process performance was controlled by hydrolysis, with a clear shift in acetogenic rates, from butyrate and propionate degradation to ethanol degradation at 4 and 2d HRT. The change in acetogenic pathways was attributed to a shift in the fermentation pathways co-current with changes in fermentative bacteria. At 2d HRT, biofilm was formed on the walls and paddles of the digesters, probably as a survival strategy. Most of the taxa in the biofilm were also present in the digester media. Overall, it is the combination of HRT with other operational parameters which promotes the washout of methanogens and the accumulation of VFA.

Simultaneous evaluation of bioactivity and settleability of activated sludge using fractal dimension as an intermediate variable

Bioactivity and settleability of activated sludge are essential for the operation of activated sludge systems in wastewater treatment. In this work, the fractal dimension of sludge image is proposed as a tool to evaluate these two factors. The specific endogenous respiration rate (SOUR_e) and the specific quasi-endogenous respiration rate (SOUR_q) are found to be more dependent on the 3D structure of sludge than the specific total respiration rate (SOUR_t). The relationship between the fractal structure and bioactivity suggests that the bioactivity governs the acceptable upper bound of the fractal dimension (D_f), as at its theoretical maximum of 2.0, the non-porous compact flocs are predominant. The settleability or the biomass concentration determines the acceptable lower bound of D_f, as at its theoretical minimum of 1.0, the free-swimming microbes are predominant. Our data reveal that the activated sludge has an acceptable fractal dimension D_f in a range of 1.07-1.68. In practice, the fractal dimension should be controlled at a reasonable value as there is a trade-off between the bioactivity and physical structure to achieve better performance. A decrease or increase in the fractal dimension can serve as a signal for the change of the operational status, and this is further elucidated from the perspective of settling tanks using state point analysis. Compared with respirogram measurement, measuring fractal dimension is a complex process and its online implementation is challenging. Also, the measured value varies with the methods used. In addition, the difference in their theoretical values depends on the homogeneity of the sludge structure. Since the fractal dimension D_f reflects both bioactivity and settleability of the sludge but is difficult to measure, in this work a relationship between D_f and the easily measurable respirogram is established, and a method using the respirogram as a proxy of D_f is proposed to control the bioactivity and settleability simultaneously. This respiration-based method is able to simultaneously control aeration and settling tanks, and could serve as an efficient tool for the management of wastewater treatment plants.

Evolutions of antibiotic resistance genes (ARGs), class 1 integron-integrase (intI1) and potential hosts of ARGs during sludge anaerobic digestion with the iron nanoparticles addition

In this work, we investigated the impact of iron nanoparticle, including magnetite nanoparticles (Fe₃O₄ NPs) and nanoscale zero-valent iron (nZVI), on the anaerobic digestion (AD) performance. Moreover, the evolutions of antibiotic resistance genes (ARGs), class 1 integrons-integrase (intI1) and potential hosts of ARGs were also investigated. The optimal addition of Fe₃O₄ NPs and nZVI to promote methane production was 0.5 g/L and 1 g/L, which led to 22.07% and 23.02% increase in methane yield, respectively. The degradation rate of organic matter was also enhanced with the addition of Fe₃O₄ NPs or nZVI. The results of high-throughput sequencing showed that the reactors with iron NPs exhibited significant differences in microbial community structure, compared to the reactors with the non‑iron NPs. Iron NPs have caused the relative abundance of the dominant bacteria (Proteobacteria, Firmicutes and Actinobacteria) generally decreased, while the dominant archaea (Euryarchaeota) increased in AD sludge. Quantitative PCR results revealed that iron NPs accelerated the reductions in total absolute abundance of ARGs, especially a beta-lactamase resistance encoded gene (blaOXA). Network analysis displayed that the attenuation of ARGs was mainly attributed to the decline of potential hosts (Proteobacteria, Firmicutes and Actinobacteria). Meanwhile, environmental factors (such as pH, soluble chemical oxygen demand and heavy metals) were also strongly correlated with ARGs.

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage

Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.

Effects of different conductive nanomaterials on anaerobic digestion process and microbial community of sludge

The effects of four conductive nanomaterials (nano-carbon powder, nano-Al₂O₃, nano-ZnO, nano-CuO) on sludge anaerobic digestion (AD) performance and microbial community were investigated through a 36-day fermentation experiment. Results showed that biogas production enhanced by 16.9% and 23.4% with nano-carbon powder and nano-Al₂O₃ added but decreased by 90.2% and 17.3% with nano-ZnO and nano-CuO. Total solids (TS) removal efficiency was increased by 38.73% and 27.11% with nano-carbon powder and nano-Al₂O₃ added but decreased by 70.67% and 43.70% with nano-ZnO and nano-CuO. Kinetic analysis indicated four conductive nanomaterials could shorten the lag phase of AD sludge with an average rate of 51.75%. 16S rRNA amplicon sequencing results demonstrated microbes such as Syntrophomonas and Methanosaeta were enriched in nano-carbon powder and nano-Al₂O₃ reactors. However, microbial community diversity and richness were both inhibited by adding nano-ZnO and nano-CuO. Redundancy analysis (RDA) revealed that genera belong to Firmicutes and Chloroflexi could conduce to methanogenesis process.

Impacts of antimony and arsenic co-contamination on the river sedimentary microbial community in an antimony-contaminated river

Antimony (Sb) and arsenic (As) are toxic elements that occur widely in trace soil concentrations. Expansion of mining activities has increased Sb and As pollution, thus posing a severe threat to human welfare and ecological systems worldwide. Knowledge regarding the composition and adaptation of the microbial communities in these metal(loid) contaminated sites is still limited. In the current study, samples along a river flowing through the world's largest Sb mining area (Xikuangshan) were selected to investigate the microbial response to different Sb or As species. A comprehensive analysis of geochemical parameters, high-throughput sequencing, and statistical methods were applied to reveal the different effects of Sb and As on sedimentary microorganisms. Results suggested that the majority of the Sb and As fractions were not bioavailable. The Sb extractable fraction had a stronger effect on the microbial community compared with its As counterpart. Random forest analyses indicated that the easily exchangeable Sb fraction and specifically sorbed surface-bound fraction were the two most selective variables shaping microbial community diversity. A total of 11 potential keystone phyla, such as bacteria associated with the Bacteroidetes, Proteobacteria, and Firmicutes, were identified according to a molecular ecological network analysis. Strong correlations (|R| > 0.7, P < 0.05) were identified among the indigenous microbial community and pH (negative), sulfate (negative), and exchangeable Sb fraction (positive). Bacteria associated with the genera Geobacter, Phormidium, Ignavibacterium, Desulfobulbus, Ferruginibacter, Fluviicola, Methylotenera, and Scytonema, were predicted to tolerate or metabolize the Sb extractable fraction.