Sludge digestibility and functionally active microorganisms in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking

Tris (2-chloroethyl) phosphate presence inhibits methane production from anaerobic digestion: Alterations in organic matter transformation, cell physiological status, and microbial community

Organophosphate flame retardants (OPFRs) are widely used in consumer products, leading to their unavoidable release into the environment, especially accumulation in anaerobic environments and posing potential risks. This study focused on Tris(2-chloroethyl) phosphate (TCEP), a representative OPFR, to investigate its effects on carbon transformation and methane production in anaerobic digestion. Increasing TCEP concentrations from control to 16 mg/L resulted in decreased cumulative methane yield (from 235.4 to 196.3 mL/g COD) and maximum daily methane yield (from 40.8 to 16.17 mL/(g COD·d)), along with an extended optimal anaerobic digestion time (from 15 to 20 days). Mechanistic analysis revealed TCEP binding to tyrosine-like proteins in extracellular polymeric substances, causing cell membrane integrity impairment. The TCEP-caused alteration of the physiological status of cells was demonstrated to be a significant contribution to the inhibited bioprocesses including acidogenesis, acetogenesis, and methanogenesis. Illumina Miseq sequencing showed TCEP decreasing the relative abundance of acidogens (58.8 % to 46.0 %) and acetogens (7.1 % to 5.0 %), partly shifting the methanogenesis pathway from acetoclastic to hydrogenotrophic methanogenesis. These findings enhance understanding of TCEP's impact on anaerobic digestion, emphasizing the environmental risk associated with its continued accumulation.

Combatting multiple aromatic organohalide pollutants in sediments by bioaugmentation with a single Dehalococcoides

Dehalococcoides are capable of dehalogenating various organohalide pollutants under anaerobic conditions, and they have been applied in bioremediation. However, the presence of multiple aromatic organohalides, including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and tetrabromobisphenol A (TBBPA), at contaminated sites may pose challenges to Dehalococcoides-mediated bioremediation due to the lack of knowledge about the influence of co-contamination on bioremediation. In this study, we investigated the bioremediation of aromatic organohalides present as individual and co-contaminants in sediments by bioaugmentation with a single population of Dehalococcoides. Bioaugmentation with Dehalococcoides significantly increased the dehalogenation rate of PCBs, PBDEs, and TBBPA in sediments contaminated with individual pollutants, being up to 19.7, 27.4 and 2.1 times as that in the controls not receiving bioinoculants. For sediments containing all the three classes of pollutants, bioaugmentation with Dehalococcoides also effectively enhanced dehalogenation, and the extent of enhancement depended on the bioinoculants and types of pollutants. Interestingly, in many cases co-contaminated sediments bioaugmented with Dehalococcoides mccartyi strain CG1 displayed a greater enhancement in dehalogenation rates compared to the sediments polluted with individual pollutant. For instance, when augmented with a low quantity of strain CG1, the dehalogenation rates of Aroclor1260 and PBDEs in co-contaminated sediments were approximately two times as that in sediments containing individual pollutants (0.428 and 9.03 vs. 0.195 and 4.20 × 10-3d-1). Additionally, D. mccartyi CG1 grew to higher abundances in co-contaminated sediments. These findings demonstrate that a single Dehalococcoides population can sustain dehalogenation of multiple aromatic organohalides in contaminated sediments, suggesting that co-contamination does not necessarily impede the use of Dehalococcoides for bioremediation. The study also underscores the significance of anaerobic organohalide respiration for effective bioremediation.

Metabolic Synergy of Dehalococcoides Populations Leading to Greater Reductive Dechlorination of Polychlorinated Biphenyls

Polychlorinated biphenyls (PCBs) are dioxin-like pollutants that cause persistent harm to life. Organohalide-respiring bacteria (OHRB) can detoxify PCBs via reductive dechlorination, but individual OHRB are potent in dechlorinating only specific PCB congeners, restricting the extent of PCB dechlorination. Moreover, the low biomass of OHRB frequently leads to the slow natural attenuation of PCBs at contaminated sites. Here we constructed defined microbial consortia comprising various combinations of PCB-dechlorinating Dehalococcoides strains (CG1, CG4, and CG5) to successfully enhance PCB dechlorination. Specifically, the defined consortia consisting of strains CG1 and CG4 removed 0.28-0.44 and 0.23-0.25 more chlorine per PCB from Aroclor1260 and Aroclor1254, respectively, compared to individual strains, which was attributed to the emergence of new PCB dechlorination pathways in defined consortia. Notably, different Dehalococcoides populations exhibited similar growth when cocultivated, but temporal differences in the expression of PCB reductive dehalogenase genes indicated their metabolic synergy. Bioaugmentation with individual strains (CG1, CG4, and CG5) or defined consortia led to greater PCB dechlorination in wetland sediments, and augmentation with the consortium comprising strains CG1 and CG4 resulted in the greatest PCB dechlorination. These findings collectively suggest that simultaneous application of multiple Dehalococcoides strains, which catalyze complementary dechlorination pathways, is an effective strategy to accelerate PCB dechlorination.

Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics

Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste-activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long-term operation. In this study, we found that short-term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%-9.0%, whereas higher levels (30-200 particles/g sludge) suppressed methanogenesis by 15.2%-30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long-term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long-term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.

Identifying local associations in biological time series: algorithms, statistical significance, and applications

Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.

Insights into the Occurrence, Fate, Impacts, and Control of Food Additives in Food Waste Anaerobic Digestion: A Review

The recovery of biomass energy from food waste through anaerobic digestion as an alternative to fossil energy is of great significance for the development of environmental sustainability and the circular economy. However, a substantial number of food additives (e.g., salt, allicin, capsaicin, allyl isothiocyanate, monosodium glutamate, and nonnutritive sweeteners) are present in food waste, and their interactions with anaerobic digestion might affect energy recovery, which is typically overlooked. This work describes the current understanding of the occurrence and fate of food additives in anaerobic digestion of food waste. The biotransformation pathways of food additives during anaerobic digestion are well discussed. In addition, important discoveries in the effects and underlying mechanisms of food additives on anaerobic digestion are reviewed. The results showed that most of the food additives had negative effects on anaerobic digestion by deactivating functional enzymes, thus inhibiting methane production. By reviewing the response of microbial communities to food additives, we can further improve our understanding of the impact of food additives on anaerobic digestion. Intriguingly, the possibility that food additives may promote the spread of antibiotic resistance genes, and thus threaten ecology and public health, is highlighted. Furthermore, strategies for mitigating the effects of food additives on anaerobic digestion are outlined in terms of optimal operation conditions, effectiveness, and reaction mechanisms, among which chemical methods have been widely used and are effective in promoting the degradation of food additives and increasing methane production. This review aims to advance our understanding of the fate and impact of food additives in anaerobic digestion and to spark novel research ideas for optimizing anaerobic digestion of organic solid waste.

Novel electro-assisted micro-aerobic cathode biological technology induces oxidative demethylation of N, N-dimethylformamide for efficient ammonification of refractory membrane-making wastewater

Recalcitrant and toxicological membrane-making wastewater displays negative impacts on environment, and this is difficult to treat efficiently using conventional hydrolytic acidification. In this study, a novel electro-assisted biological reactor with micro-aerobic cathode (EABR-MAC) was developed to improve the biodegradation and ammonification of N, N-dimethylformamide (DMF) in membrane-making wastewater, and the metabolic mechanism using metagenomic sequencing as comprehensively illustrated. The results showed that EABR-MAC significantly improved the ammonification of refractory organonitrogen and promoted DMF oxidative degradation by driving the electron transferred to the cathode. Additionally, the inhibition rates of oxygen uptake rate and nitrification in EABR-MAC were both lower under different cathode aeration frequency conditions. Microbial community analysis indicated that the functional fermentation bacteria and exoelectrogens, which were correlated with COD removal, ammonification, and detoxification, were significantly enriched upon electrostimulation, and the positive biological connections increased to form highly connected communities instead of competition. The functional genes revealed that EABR-MAC forcefully intervened with the metabolic pathway, so that DMF converted to formamide and ammonia by oxidative demethylation and formamide hydrolysis. The results of this study provide a promising strategy for efficient conversion of organonitrogen into ammonia nitrogen, and offer a new insight into the effects of electrostimulation on microbial metabolism.

Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge

Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.

Understanding the mechanism of polybrominated diphenyl ethers reducing the anaerobic co-digestion efficiency of excess sludge and kitchen waste

Polybrominated diphenyl ethers (PBDEs) widely existing in the environment can pose a serious threat to the ecological safety. However, the influence of PBDEs on methane production by excess sludge (ES) and kitchen waste (KW) anaerobic co-digestion and its mechanism is not clear. To fill this gap, in this work, the co-digestion characteristics of ES and KW exposed to different levels of PBDEs at medium temperature were investigated in sequencing batch reactor, and the related mechanisms were also revealed. The results showed that PBDEs reduced methane production and the proportion of methane in the biogas. Methane yield decreased from 215.3 mL/g· volatile suspended solids (VSS) to 161.5 mL/(g·VSS), accompanied by the increase of PBDE content from 0 to 8.0 mg/Kg. Volatile fatty acid (VFA) yield was also inhibited by PBDEs; especially when PBDEs were 8.0 mg/Kg, VFA production was only 215.6 mg/g VSS, accounting for 75.7% of that in the control. Mechanism investigation revealed PBDEs significantly inhibited the processes of hydrolysis, acidogenesis, acetogenesis, and methanogenesis. Further study showed that PBDEs could inhibit the degradation and bioavailability of ES and KW, but it had a greater inhibition on the utilization of KW. Enzyme activity investigation revealed that all the key enzyme activities related to methane production were suppressed by PBDEs.

Impact of substrate digestibility on microbial community stability in methanogenic digestors: The mechanism and solution

This study investigated the temporal dynamics of digestion efficiency and community stability in digesters fed with waste activated sludge (WAS), straw (STR-AD), food waste (FW-AD) and mixture of straw-and-food waste (STR-FW-AD). Results showed that carbon removals of recalcitrant substrates (i.e., 48.2 ± 3.9% in WAS-AD and 57.8 ± 4.9% in STR-AD) were lower than that of labile substrates (i.e., 70.7 ± 4.0% in FW-AD). Nonetheless, carbon removal of recalcitrant substrates was largely improved through co-digestion (70.3 ± 3.2% in STR-FW-AD). In contrast to monopoly communities (e.g., the highly enriched Paludibacter) fed with the labile substrates, recalcitrant substrates supported highly diverse communities. Accordingly, the medians of negative/positive cohesions of communities in WAS-AD, STR-AD, STR-FW-AD and FW-AD decreased from 0.86 to 0.63, suggesting their decreasing community stability. Microbial source tracking analyses showed the major contribution of the STR-AD community to the co-digestion community. This study provided unprecedented mechanistic insight into stability improvement of substrate co-digestion on the methanogenic digestion microbiome.

One-step synthesis of carbonaceous adsorbent from soybean bio-residue by microwave heating: Adsorptive, antimicrobial and antifungal behavior

In this work, the transformation of soybean industrial bio-residue with limited practical applications, into a multifunctional carbonaceous adsorbent (SBAC) via one-step microwave-irradiation has been succeeded. The surface porosity, chemical compositions, functionalities and surface chemistry were featured by microscopic pore-textural analysis, elemental constitution analysis, morphological characterization and Fourier transform infra-red spectroscopy. The adsorptive performance of SBAC was evaluated in a batch experiment by adopting different classes of water pollutants, specifically methylene blue (MB), acetaminophen and 2,4-dichlorophenoxyacetic acid (2,4-D). The equilibrium uptakes were analyzed with respect to the non-linearized Langmuir, Freundlich and Temkin isotherm equations. The unique features of SBAC, specifically the antimicrobial and antifungal efficacies were examined against gram-positive/negative bacteria and fungi species. An ordered microporous-mesoporous structure of SBAC, with the BET surface area and total pore volume of 1696 m2/g and 0.94 m3/g, respectively, has been achieved. The equilibrium data of MB and acetaminophen were found to be in good agreement with the Langmuir isotherm model, with the monolayer adsorption capacities (Qo) of 434.57 mg/g and 393.31 mg/g, respectively. The adsorptive experiment of 2,4-D was best fitted to the Freundlich isotherm equation, with the Qo of 253.17 mg/g. The regeneration performance of the spent SBAC under microwave-irradiation could maintain at 69.42-79.31%, even after five (5) adsorption-regeneration cycles. SBAC exhibited excellent inhibition efficiencies against gram-positive/negative bacteria and fungi species, with the inhibition zones at 14.0-28.0 mm. This newly developed SBAC appears to be a new powerful candidate for the remediation of different classes of water contaminants, and novel antibacterial and antifungal agents against biological contaminations. The novel concept of "turn waste into wealth" in a cost-effective and energy saving manner for environmental preservation has been successfully accomplished.

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

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

Acceleration of polychlorinated biphenyls remediation in soil via sewage sludge amendment

Bioremediation of polychlorinated biphenyls (PCBs) is impeded by difficulties in massively cultivating bioinoculant. Meanwhile, sewage sludge is rich in pollutant-degrading microorganisms and nutrients, drawing our attention to investigate their potential to be used as a supplement for bioremediation of PCBs. Here we reported extensive microbial reductive dechlorination of PCBs by waste activated sludge (WAS) and digestion sludge (DS), which were identified to harbor multiple putative organohalide-respiring bacteria (i.e., Dehalococcoides, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia) and PCB reductive dehalogenase genes (i.e., pcbA4 and pcbA5). Consequently, amendment of 1-20% (w/w) fresh WAS/DS enhanced the attenuation of PCBs by 126-544% in a soil microcosm compared with the control soil, with the fastest dechlorination of PCBs being achieved when spiked with 20% fresh WAS. Notably, dechlorination pathways of PCBs were also changed by sludge amendment. Microbial and physicochemical analyses revealed that the enhanced dechlorination of PCBs by sludge amendment was largely attributed to the synergistic effects of sludge-derived nutrients, PCB-dechlorinating bacteria, and stimulated growth of beneficial microorganisms (e.g., fermenters). Finally, risk assessment of heavy metals suggests low potential ecological risks of sludge amendment in soil. Collectively, our study demonstrates that sewage sludge amendment could be an efficient, cost-effective and environment-friendly approach for in situ bioremediation of PCBs.