Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge

Study on the synergistic mechanism of proline in the treatment of high-salt phenolic wastewater by short-time aerobic digestion process

High salt concentrations pose a significant challenge to the efficiency of activated sludge (AS) in phenolic wastewater treatment. As a cellular osmoprotectant, proline (Pro) has the capacity to increase the salt tolerance of microbes in AS, hence improving the efficiency of phenolic wastewater degradation. Nevertheless, the precise mechanism behind this enhancement remains ambiguous. This study utilized short-time aerobic digestion (STAD) to examine the kinetics of phenol degradation (250-750 mg/L) by AS under high-salinity stress (2-8%), with the inclusion of Pro (115-575 mg/L) as an auxiliary agent. The process was optimized via response surface methodology (RSM), and the mitigating effect of Pro on microorganisms in AS subjected to salt stress was evaluated. The results demonstrated that the addition of 468 mg/L Pro substantially improved the ability of AS to withstand high-salinity wastewater with high phenol concentrations, which had a salinity of 5.1% and a phenol concentration of 531 mg/L. The addition led to a mitigation rate of the phenol degradation constant k0 of 38.59 ± 1.54%, resulting in enhanced degradation of chemical oxygen demand (COD), NH4+-N, and NO3--N. In addition, the prolonged presence of Pro increased AS dehydrogenase activity (DHA) by 24.82% after 30 days. Microbial community analysis demonstrated that Pro promoted the proliferation of functional microorganisms such as Proteobacteria, Firmicutes, Acinetobacter, and Comamonas. These bacteria have essential functions in the elimination of phenol and organic matter, as well as the absorption of nitrogen. This study emphasizes the impact of Pro as a compatible solute in the treatment of high-salinity and high-phenol wastewater in the STAD process.

Asymmetries among soil fungicide residues, nitrous oxide emissions and microbiomes regulated by nitrification inhibitor at different moistures

Carbendazim residue has been widely concerned, and nitrous oxide (N2O) is one of the dominant greenhouse gases. Microbial metabolisms are fundamental processes of removing organic pollutant and producing N2O. Nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) can change soil abiotic properties and microbial communities and simultaneously affect carbendazim degradation and N2O emission. In this study, the comprehensive linkages among carbendazim residue, N2O emission and microbial community after the DMPP application were quantified under different soil moistures. Under 90% WHC, the DMPP application significantly reduced carbendazim residue by 54.82% and reduced soil N2O emission by 98.68%. The carbendazim residue was negatively related to soil ammonium nitrogen (NH4+-N), urease activity, and ratios of Bacteroidetes, Thaumarchaeota and Nitrospirae under 90% WHC, and the N2O emission was negatively related to NH4+-N content and relative abundance of Acidobacteria under the 60% WHC condition. In the whole (60% and 90% WHC together), the carbendazim residue was negatively related to the abundances of nrfA (correlation coefficient = -0.623) and nrfH (correlation coefficient = -0.468) genes. The hao gene was negatively related to the carbendazim residue but was positively related to the N2O emission rate. The DMPP application had the promising potential to simultaneously reduce ecological risks of fungicide residue and N2O emission via altering soil abiotic properties, microbial activities and communities and functional genes. ENVIRONMENTAL IMPLICATION: Carbendazim was a high-efficiency fungicide that was widely used in agricultural production. Nitrous oxide (N2O) is the third most important greenhouse gas responsible for global warming. The 3, 4-dimethylpyrazole phosphate (DMPP) is an effective nitrification inhibitor widely used in agricultural production. This study indicated that the DMPP application reduced soil carbendazim residues and N2O emission. The asymmetric linkages among the carbendazim residue, N2O emission, microbial community and functional gene abundance were regulated by the DMPP application and soil moisture. The results could broaden our horizons on the utilizations DMPP in decreasing fungicide risks and N2O emission.

Effectiveness of wastewater treatment plant at the removal of nutrients, pathogenic bacteria, and antibiotic-resistant bacteria in wastewater from hospital source

This study is aimed at assessing the effectiveness of hospital's wastewater treatment plant (WWTP) in removing nutrients, pathogenic bacteria, and addressing antibiotic resistance using a case study of a tertiary hospital in Ibadan, Nigeria. During the dry and wet seasons in the month of July and December, respectively, samples were collected, and analyzed using standard guidelines to examine significant physicochemical parameters of the WTTP; to evaluate the removal efficiency of biological oxygen demand (BOD) and chemical oxygen demand (COD), and to examine the prevalence of pathogenic and antibiotic-resistant bacteria. The results of this study showed that during the dry season, certain parameters exceeded acceptable limits, including temperature, total suspended solids (TSS), total dissolved solids (TDS), phosphate, and nitrate. Although there were reductions in BOD (1555 mg/L to 482 mg/L) and COD levels (3160 mg/L to 972 mg/L), they remained above acceptable limits by World Health Organization. In the wet season, the level of COD (20 mg/L) in the effluent was within acceptable limit, while the BOD (160 mg/L) was above the acceptable limit. The WWTP effectively removed nutrients and reduced the microbial load, as evident from the absence of fecal coliforms in the effluent in both seasons. In respect to BOD removal efficiency, the level of purification of wastewater by the WWTP was 69% during the dry season, while the removal efficiency of COD was 83.54% which showed the efficiency of the WWTP at the removal of COD. However, antibiotic resistance was still present. The study concludes that while the WWTP effectively addressed nutrients and microbial load, additional measures such as tertiary treatment methods like chlorination and UV radiation are necessary to tackle antibiotic resistance. This is crucial to prevent the release of antibiotic-resistant bacteria into the environment, safeguarding human health, animals, plants, and overall environmental well-being.

Metagenomic analysis reveals the distribution, function, and bacterial hosts of degradation genes in activated sludge from industrial wastewater treatment plants

For comprehensive insights into the bacterial community and its functions during industrial wastewater treatment, with a particular emphasis on its pivotal role in the bioremediation of organic pollutants, this study utilized municipal samples as a control group for metagenomic analysis. This approach allowed us to investigate the distribution, function, and bacterial hosts of biodegradation genes (BDGs) and organic degradation genes (ODGs), as well as the dynamics of bacterial communities during the industrial wastewater bioprocess. The results revealed that BDGs and ODGs associated with the degradation of benzoates, biphenyls, triazines, nitrotoluenes, and chlorinated aromatics were notably more abundant in the industrial samples. Specially, genes like clcD, linC, catE, pcaD, hbaB, hcrC, and badK, involved in the peripheral pathways for the catabolism of aromatic compounds, benzoate transport, and central aromatic intermediates, showed a significantly higher abundance of industrial activated sludge (AS) than municipal AS. Additionally, the BDG/ODG co-occurrence contigs in industrial samples exhibited a higher diversity in terms of degradation gene carrying capacity. Functional analysis of Clusters of Orthologous Groups (COGs) indicated that the primary function of bacterial communities in industrial AS was associated with the category of "metabolism". Furthermore, the presence of organic pollutants in industrial wastewater induced alterations in the bacterial community, particularly impacting the abundance of key hosts harboring BDGs and ODGs (e.g. Bradyrhizobium, Hydrogenophaga, and Mesorhizobium). The specific hosts of BDG/ODG could explain the distribution characteristics of degradation genes. For example, the prevalence of the Adh1 gene, primarily associated with Mesorhizobium, was notably more prevalent in the industrial AS. Overall, this study provides valuable insights into the development of more effective strategies for the industrial wastewater treatment and the mitigation of organic pollutant contamination.

Linking Carbendazim Accumulation with Soil and Endophytic Microbial Community Diversities, Compositions, Functions, and Assemblies: Effects of Urea-hydrogen Peroxide and Nitrification Inhibitors

Fungicide carbendazim accumulation in soils and plants is a wide concern. Nitrogen (N) is a substantial nutrient limiting crop growth and affecting soil microbial activity and the community in degrading fungicides. We investigated the effects of urea-hydrogen peroxide (UHP) and nitrification inhibitors Dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) on carbendazim accumulation and soil and endophytic microbial communities. The UHP application had negligible influences on soil and plant carbendazim accumulation, but the combined UHP and DCD decreased soil carbendazim accumulation by 5.31% and the combined UHP and DMPP decreased plant carbendazim accumulation by 44.36%. The combined UHP and nitrification inhibitor significantly decreased the ratios of soil Firmicutes and endophytic Ascomycota. Soil microbial community assembly was governed by the stochastic process, while the stochastic and deterministic processes governed the endophyte. Our findings could provide considerable methods to reduce fungicide accumulation in soil-plant systems with agricultural N management strategies.

Anaerobic biodegradation of pyrene and benzo[a]pyrene by a new sulfate-reducing Desulforamulus aquiferis strain DSA

The study of anaerobic high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) biodegradation under sulfate-reducing conditions by microorganisms, including microbial species responsible for biodegradation and relative metabolic processes, remains in its infancy. Here, we found that a new sulfate-reducer, designated as Desulforamulus aquiferis strain DSA, could biodegrade pyrene and benzo[a]pyrene (two kinds of HMW-PAHs) coupled with the reduction of sulfate to sulfide. Interestingly, strain DSA could simultaneously biodegrade pyrene and benzo[a]pyrene when they co-existed in culture. Additionally, the metabolic processes for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA were newly proposed in this study based on the detection of intermediates, quantum chemical calculations and analyses of the genome and RTqPCR. The initial activation step for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA was identified as the formation of pyrene-2-carboxylic acid and benzo[a]pyrene-11-carboxylic acid by carboxylation Thereafter, CoA ligase, ring reduction through hydrogenation, and ring cracking occurred, and short-chain fatty acids and carbon dioxide were identified as the final products. Additionally, DSA could also utilize benzene, naphthalene, anthracene, phenanthrene, and benz[a]anthracene as carbon sources. Our study can provide new guidance for the anaerobic HMW-PAHs biodegradation under sulfate-reducing conditions.

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks

BACKGROUND

Activated sludge (AS) of wastewater treatment plants (WWTPs) is one of the world's largest artificial microbial ecosystems and the microbial community of the AS system is closely related to WWTPs' performance. However, how to predict its community structure is still unclear.

RESULTS

Here, we used artificial neural networks (ANN) to predict the microbial compositions of AS systems collected from WWTPs located worldwide. The predictive accuracy R²_1:1 of the Shannon-Wiener index reached 60.42%, and the average R²_1:1 of amplicon sequence variants (ASVs) appearing in at least 10% of samples and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs), glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using ANN models, with R²_1:1 ranging from 32.62% to 56.81%. Furthermore, we found that whether industry wastewater source contained in inflow (IndConInf) had good predictive abilities, although its correlation with ASVs in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlighted by the ANN model.

CONCLUSIONS

We demonstrated that the microbial compositions and major functional groups of AS systems are predictable using our approach, and IndConInf has a significant impact on the prediction. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure. Video Abstract.

Occurrence of OCPs & PCBs and their effects on multitrophic biological communities in riparian groundwater of the Beiluo River, China

Persistent Organic Pollutants (POPs) may exert adverse effects on human and ecosystem health. However, as an ecologically fragile zone with strong interaction between river and groundwater, the POPs pollution in the riparian zone has received little attention. The goal of this research is to examine the concentrations, spatial distribution, potential ecological risks, and biological effects of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in the riparian groundwater of the Beiluo River, China. The results showed that the pollution level and ecological risk of OCPs in riparian groundwater of the Beiluo River were higher than PCBs. The presence of PCBs (Penta-CBs, Hexa-CBs) and CHLs, respectively, may have reduced the richness of bacteria (Firmicutes) and fungi (Ascomycota). Furthermore, the richness and Shannon's diversity index of algae (Chrysophyceae and Bacillariophyta) decreased, which could be linked to the presence of OCPs (DDTs, CHLs, DRINs), and PCBs (Penta-CBs, Hepta-CBs), while for metazoans (Arthropoda) the tendency was reversed, presumably as a result of SULPHs pollution. In the network analysis, core species belonging to bacteria (Proteobacteria), fungi (Ascomycota), and algae (Bacillariophyta) played essential roles in maintaining community function. Burkholderiaceae and Bradyrhizobium can be considered biological indicators of PCBs pollution in the Beiluo River. Note that the core species of interaction network, playing a fundamental role in community interactions, are strongly affected by POPs pollutants. This work provides insights into the functions of multitrophic biological communities in maintaining the stability of riparian ecosystems through the response of core species to riparian groundwater POPs contamination.

Recovery trajectories of the bacterial community at distances in the receiving river under wastewater treatment plant discharge

Microbes in rivers are an important part of the biogeochemical cycle in aquatic ecosystems, and understanding the major factors that influence the composition of microbial communities has an important role in assessing and improving ecosystem functioning. A high-throughput 16 S rRNA gene sequencing technique was employed to sequence bacterial communities in 21 sediment samples and 21 water samples from an urban river WWTP (wastewater treatment plant) discharge. A systematic study of changes in bacterial community composition in downstream river sediment and water was conducted. The study found that compared with the bacterial diversity in the natural upstream area of the wastewater outfall, the bacterial diversity in the sediment lower reaches decreased significantly, while the bacterial abundance and diversity in the water increased significantly. The Mantel test and redundancy analysis showed that the downstream distance and physicochemical properties were significantly related to the succession of bacterial communities in the sediment downstream of the WWTP discharge. Among them, TOC (total organic carbon) was the most important factor affecting the change in the bacterial community in the downstream sediment. The physicochemical properties were significantly correlated with the succession of bacterial communities in the water downstream of the WWTP discharge. Among them, TN (total nitrogen), PO₄^3--P (phosphorus phosphate) and TP (total phosphorus) were the main factors that affected the change in the bacterial community in the downstream water. Key taxa in the co-occurrence network at different distances downstream reflected the depth of the effect of the WWTP effluent on the bacterial community. The bacterial community in the lower reaches of the river sediment showed a strong recovery ability under the influence of pollutants, while the bacterial community in the lower reaches of the river water was difficult to recover under the influence of pollutants. In general, pollutants contained in effluent are the key to changing the composition of bacterial communities in the lower reaches of the river, but exogenous bacteria in effluent are not. This study provides a basis for further improving the effluent discharge standards of WWTPs in the future.

Designing Knowledge-Based Bioremediation Strategies Using Metagenomics

Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.

Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo

Purpose

Urban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes.

Methods

Metagenomic DNA-seq analysis of water samples and resistome analysis were performed.

Results

The most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. bla _OXA and bla _GES were frequently detected, whereas the bla _CTX-M cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6')-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs.

Conclusion

We characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.

Synthetic physical contact-remodeled rhizosphere microbiome for enhanced phytoremediation

Phytoremediation is a prevalent strategy to treat environmental pollution caused by heavy metals and eutrophication-related pollutants. Although rhizosphere microbiome is critical for phytoremediation, it remains a great challenge to artificially remodel rhizosphere microbiome for enhancing multiple pollutant treatment. In this study, we designed a synthetic bacterium to strengthen physical contact between natural microbes and plant roots for remodeling the Eichhornia crassipes rhizosphere microbiome during phytoremediation. The synthetic bacterium EcCMC was constructed by introducing a surface-displayed synthetic protein CMC composed of two glucan-binding domains separated by the sequence of the fluorescent protein mCherry. This synthetic bacterium strongly bound glucans and recruited natural glucan-producing bacterial and fungal cells. Microbiome and metabolomic analysis revealed that EcCMC remarkably remodeled rhizosphere microbiome and increased stress response-related metabolites, leading to the increased activity of antioxidant enzymes involved in stress resistance. The remodeled microbiome further promoted plant growth, and enhanced accumulation of multiple pollutants into the plants, with the removal efficiency of the heavy metal cadmium, total organic matters, total nitrogen, total potassium, and total phosphorus reaching up to 98%, 80%, 97%, 93%, and 90%, respectively. This study sheds a novel light on remodeling of rhizosphere microbiome for enhanced phytoremediation of water and soil systems.

Novel intertidal wetland sediment-inoculated moving bed biofilm reactor treating high-salinity wastewater: Metagenomic sequencing revealing key functional microorganisms

In this study, two lab-scale moving bed biofilm reactors (MBBR), seeded with intertidal wetland sediment (IWS) and activated sludge (AS), were constructed to compare their performances in treating high-salinity (3%) wastewater. Under a wide range of influent TOC (178-620 mg/L) and NH₄⁺-N (25-100 mg/L), both the MBBRs (R_iws and R_as) exhibited excellent TOC removal efficiencies of >95%. Regarding nitrogen reduction, R_iws exhibited a significantly superior TN removal efficiency of 90.2 ± 1.8% than that of R_as (76.8 ± 2.9%). A correlation analysis was innovatively conducted comparing the results between metagenomic sequencing and DNA pyrosequencing, and positive linear relationships were found with R² values of 0.763-0.945. Meanwhile, for illustration of different TN removal performance, nitrogen metabolic pathways were also assessed. Moreover, a list of functional oxidases (EC: 1.13.11.1, EC: 1.13.11.2, EC: 1.13.11.24, EC: 1.13.12.16, EC: 1.4.3.4, EC: 1.16.3.3, EC: 1.14.14.28) was found in IWS, revealing its potential in degradation of recalcitrant organics.

Lipid degrading microbe consortium driving micro-ecological evolvement of activated sludge for cooking wastewater treatment

In this study, a lipid degrading microbe consortium (LDMC) was assembled to improve the performance of activated sludge (AS) on cooking wastewater purification. LDMC can rapidly degrade high-level oil (efficiency beyond 93.0% at 5.0 g/L) as sole carbon source under various environmental conditions (10.0-45.0 °C, pH 2.0-12.0). With LDMC inoculation, AS' water treatment performance was significantly enhanced, which removed 36.10 and 48.93% more chemical oxygen demand (COD) and ammonia nitrogen from wastewater than control. A better settling property and smaller bulking risk were found with LDMC inoculation, indicated by a lower SV₃₀ and SVI index but a higher MLSS. By GC/MS analysis, a gradual degradation on the end of the fatty acid chain was suggested. LDMC inoculation significantly changed AS's microbial community structure, improved its stability, decreased the microbial community diversity, facilitated the enrichment of lipid degraders and functional genes related to lipid bio-degradation. Lipid degraders including Nakamurella sp. and Stenotrophomona sp., etc. played a crucial role during oil degradation. Sludge structure maintainers such as Kineosphaera sp. contributed largely to the stability of AS under exogenous stress. This study provided an efficient approach for cooking wastewater treatment along with the underlying mechanism exploration, which should give insights into oil-containing environmental remediation.

Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family

The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.

Coupled biodegradation of p-nitrophenol and p-aminophenol in bioelectrochemical system: Mechanism and microbial functional diversity

Biodegradation mechanisms and microbial functional diversity during coupled p-nitrophenol (PNP) and p-aminophenol (PAP) degradation were studied in a bioelectrochemical system. PNP in the biocathode and PAP in the bioanode were almost completely removed within 28hr and 68hr respectively. The degradation followed the steps including hydrating hydroxyalkylation, dehydrogenating carbonylation, and hydrolating ring cleavage, etc. Metagemomic analysis based on the KEGG and eggNOG database annotations revealed the microbial composition and functional genes/enzymes related to phenol degradation in the system. The predominant bacteria genera were Lautropia, Pandoraea, Thiobacillus, Ignavibacterium, Truepera and Hyphomicrobium. The recognized biodegradation genes/enzymes related to pollutant degradation were as follows: pmo, hbd, & ppo for phenol degradation, nzba, amie, & badh for aromatic degradation, and CYP & p450 for xenobiotics degradation, etc. The co-occurrence of ARGs (antibiotic resistant genes), such as adeF, MexJ, ErmF, PDC-93 and Escherichia_coli_mdfA, etc., were annotated in CARD database during the biodegradation process. The Proteobacteria & Actinobacteria phylum was the primary host of both the biodegradation genes & ARGs in this system. The microbial functional diversity ensured the effective biodegradation of the phenol pollutants in the bioelectrochemical system.

Microbiome degrading linear alkylbenzene sulfonate in activated sludge

As the most widely used anionic surfactant, linear alkylbenzene sulfonate (LAS) requires biological alkane degradation when it is treated using an activated sludge (AS) process in a wastewater treatment plant because of its structural carboxylic unavailability. As consumption of LAS is gradually increasing, LAS loading into the WWTP is accordingly increasing. However, fewer studies have examined the involvement of the AS microbial community in the LAS degradation. In this study, metagenomic approaches were used to define microbiomes involved in LAS degradation in AS, with a particular focus on ω-hydroxylation. The abundance and diversity of alkane-degrading genes were investigated, and these genes were integrated with reconstructed metagenome-assembled genomes (MAGs). Additionally, the association of functional genes and MAGs with respect to LAS degradation was investigated. The results showed that alkB and cytochrome P450 genes were only shared within specific MAGs. Unique sets of genes with diverse abundances were detected in each sample. The MAGs with the alkB and cytochrome P450 genes were strongly associated with the other MAGs and involved in positive commensal interactions. The findings provided significant insights into how the AS microbiomes, which have continuously treated anionic surfactants for decades, potentially metabolize LAS and interact with commensal bacteria.

Research on microbial structures, functions and metabolic pathways in an advanced denitrification system coupled with aerobic methane oxidation based on metagenomics

Methanotrophs can oxidize methane as the sole carbon and energy, and the resulting intermediate products can be simultaneously utilized by coexistent denitrifying bacteria to remove the nitrogen, which named Aerobic Methane Oxidation Coupled to Denitrification (AME-D). In this paper, an AME-D system was built in an improved denitrification bio-filter, to analyze the nitrogen removal efficiency and mechanism. The maximum TN removal rate reached 95.05%. As shown in Raman spectroscopy, in the effluent wave crests generated by the symmetric expansion and contraction of NO₃^- disappeared, and the distortion of olefin CH₂ and C-OH stretching of alcohols appeared. Metagenomics revealed Methylotenera and Methylobacter were the dominated methanotrophs. There was a completed methane and nitrogen metabolism pathway with the synergism of nxrAB, narGHI, nasAB, pmo-amoABC and mmo genes. Dissimilatory reduction pathway was the primary nitrate removal pathway. Moreover, Bradyrhizobium could participate in methane and nitrogen metabolism simultaneously.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Wastewater treatment alters microbial colonization of microplastics

Microplastics are ubiquitous contaminants in aquatic habitats globally, and wastewater treatment plants (WWTPs) are point sources of microplastics. Within aquatic habitats microplastics are colonized by microbial biofilms, which can include pathogenic taxa and taxa associated with plastic breakdown. Microplastics enter WWTPs in sewage and exit in sludge or effluent, but the role that WWTPs play in establishing or modifying microplastic bacterial assemblages is unknown. We analyzed microplastics and associated biofilms in raw sewage, effluent water, and sludge from two WWTPs. Both plants retained >99% of influent microplastics in sludge, and sludge microplastics showed higher bacterial species richness and higher abundance of taxa associated with bioflocculation (e.g. Xanthomonas) than influent microplastics, suggesting that colonization of microplastics within the WWTP may play a role in retention. Microplastics in WWTP effluent included significantly lower abundances of some potentially pathogenic bacterial taxa (e.g. Campylobacteraceae) compared to influent microplastics; however, other potentially pathogenic taxa (e.g. Acinetobacter) remained abundant on effluent microplastics, and several taxa linked to plastic breakdown (e.g. Klebsiella, Pseudomonas, and Sphingomonas) were significantly more abundant on effluent compared to influent microplastics. These results indicate that diverse bacterial assemblages colonize microplastics within sewage and that WWTPs can play a significant role in modifying the microplastic-associated assemblages, which may affect the fate of microplastics within the WWTPs and the environment.

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

Metagenomic insights into Chinese northeast suancai: Predominance and diversity of genes associated with nitrogen metabolism in traditional household suancai fermentation

Chinese northeast suancai represents a typical and valuable food product that has been handed down by traditional household procedures over centuries. Nitrite is formed and accumulated during the suancai fermentation process and commonly causes food safety problems. The biogeochemical cycle of nitrite may provide a reference and guidance for the enzymatic degradation of nitrite in fermented food. The potential nitrogen metabolic pathways in the microbially driven suancai fermentation were reasonably inferred through monitoring nitrogen conversions and detecting the genes of different functional enzymes. Complex microbial metabolism is responsible for the unique nitrogen conversions during suancai fermentation. The metagenomic results showed that Pseudomonas with nitrate reductase genes (narG, narH, narI) and nitrite reductase genes (nirB, nirD) contributed the most to both nitrite reduction and nitrate reduction. The majority of the sequences of nitrate reductase and nitrite reductase were derived from the families of Pseudomonadaceae, Erwiniaceae and Yersiniaceae. According to the physicochemical analysis, the nitrite concentration of the fermentation broth reached the peak value (0.48 mM) and gradually decreased to the minimum (0.02 mM). The downward trend of the pH and nitrite concentration were closely associated with the nitrite enzymatic degradation period before the acid degradation period. Our results indicated that nitrite removal in suancai fermentation involved the reduction of nitrite to ammonia and denitrification, which were mainly contributed by the reduction of nitrite to ammonia mediated by the nirB/nirD enzyme (Indentified ECs: 1.7.1.15). This research offers new insights into the metagenome-based bioinformatic roles of the previously unstudied microorganisms in spontaneous suancai fermentation for the enzymatic degradation of nitrite. It provides helpful basis for the detection and even elimination of nitrite in suancai and for improving the safety level of suancai.

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN3-H, and COD removal activities of activated sludge were improved as temperature elevated from 20 °C to 35 °C. While, the TN, HN3-H, COD and total phosphorus removal activities of activated sludge were inhibited as temperature declined from 20 °C to 5 °C. Both the extracellular polymer substances (EPS) composition (e.g., total amount, PS, PN and DNA) and sludge index of activated sludge were altered by simulated seasonal temperature variation. The variation of microbial community structures and the functional potentials of activated sludge were further explored by metagenomics. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla for each activated sludge sample under different temperatures. However, the predominant genera of activated sludge were significantly modulated by simulated temperature variation. The functional genes encoding enzymes for nitrogen metabolism in microorganisms were analyzed. The enzyme genes related to ammonification had the highest abundance despite the changing temperature, especially for gene encoding glutamine synthetase. With the temperature raising from 20 °C to 35 °C. The abundance of amoCAB genes encoding ammonia monooxygenase (EC:1.14.99.39) increased by 305.8%. Meanwhile, all the enzyme genes associate with denitrification were reduced. As the temperature declined from 20 °C to 5 °C, the abundance of enzyme genes related to nitrogen metabolism were raised except for carbamate kinase (EC:2.7.2.2), glutamate dehydrogenase (EC:1.4.1.3), glutamine synthetase (EC:6.3.1.2). Metagenomic data indicate that succession of the dominant genera in microbial community structure is, to some extent, beneficial to maintain the functional stability of activated sludge under the temperature variation within a certain temperature range. This study provides novel insights into the effects of seasonal temperature variation on the activities of activated sludge.

Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology

In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH₄⁺-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO₃^--N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO₃^--N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.

Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater

Biological treatment of table olive processing wastewater (TOPW) may be problematic due to its high organic and polyphenolic compound content. Biomass acclimatization is a necessary, yet sensitive, stage for efficient TOPW biological treatment. Next-generation sequencing technologies can provide valuable insights into this critical process step. An aerobic membrane bioreactor (MBR) system, initially inoculated with municipal activated sludge, was acclimatized to treat TOPW. Operational stability and bioremediation efficiency were monitored for approx. three months, whereas microbial community dynamics and metabolic adaptation were assessed through metagenomic and metatranscriptomic analysis. A swift change was identified in both the prokaryotic and eukaryotic bio-community after introduction of TOPW in the MBR, and a new diverse bio-community was established. Thauera and Paracoccus spp. are dominant contributors to the metabolic activity of the stable bio-community, which resulted in over 90% and 85% removal efficiency of total organic carbon and total polyphenols, respectively. This is the first study assessing the microbial community dynamics in a well-defined MBR process treating TOPW, offering guidance in the start-up of large-scale applications.

Removal of anti-inflammatory/analgesic pharmaceuticals from urban wastewater in a pilot-scale A2O system: Linking performance and microbial population dynamics to operating variables

In this study, the removal rates of eight anti-inflammatory and/or analgesic pharmaceuticals, AIAPs (acetaminophen, ibuprofen, naproxen, ketoprofen, diclofenac, codeine, indomethacin and propyphenazone) were assessed in a pilot-scale A²O system (including anaerobic/anoxic/aerobic zones), long term operated during two experimental phases using different sets of environmental conditions and operating parameters. qPCR was used to quantify the absolute abundances of total Bacteria, total Archaea, mycolic-acid containing filamentous Actinobacteria (Mycolata) and Fungi within the activated sludge microbial community developed in the system. Multivariate analyses and Spearman correlation coefficients were used in search of significant links among the removal rates of the AIAPs, the abundances of the targeted microbial groups in the activated sludge, and the changes of environmental/operating variables in the A²O system. Improved removal efficiencies of several of the AIAPs analyzed (acetaminophen, ibuprofen, naproxen, ketoprofen) were correlated to higher organic load in the influent water, higher concentration of mixed liquor suspended solids (MLSS), lower temperature and lower food-to-microorganisms ratio (F/M). Removal efficiencies of several pharmaceuticals correlated with increased abundances of Mycolata in the A²O system, pointing at this group of bacteria as candidate key players for AIAPs removal in activated sludge.

Exploring bacterial communities and biodegradation genes in activated sludge from pesticide wastewater treatment plants via metagenomic analysis

Activated sludge (AS) has been regarded as the main driver in the removal of organic pollutants such as pesticides due to a high diversity and abundance of microorganisms. However, little is known about the biodegradation genes (BDGs) and pesticide degradation genes (PDGs) harbored in the AS from wastewater treatment plants (WWTPs). In this study, we explored the bacterial communities and BDGs/PDGs in the AS from five WWTPs affiliated with pesticide factories across four consecutive seasons based on high-throughput sequencing. The AS in pesticide WWTPs exhibited unique bacterial taxa at the genus level. Furthermore, a total of 17 BDGs and 68 PDGs were explored with a corresponding average relative abundance of 0.002-0.046% and 2.078-7.143% in each AS sample, respectively, and some BDGs/PDGs clusters were also identified in the AS. The bacterial communities and BDGs/PDGs were season-dependent, and the total variations of 50.4% and 76.8% were jointly explained by environmental variables (pesticide types, wastewater characteristics, and temperature). In addition, network analysis and distribution patterns suggested that the potential hosts of BDGs/PDGs were Thauera, Stenotrophomonas, Mycobacterium, Hyphomicrobium, Allochromatium, Ralstonia, and Dechloromonas. Our findings demonstrated the linkages of bacterial communities and BDGs/PDGs in the AS, and depended on the seasons and the pesticide wastewater characteristics.

Metagenomics-Based Discovery of Malachite Green-Degradation Gene Families and Enzymes From Mangrove Sediment

Malachite green (MG) is an organic contaminant and the effluents with MG negatively influence the health and balance of the coastal and marine ecosystem. The diverse and abundant microbial communities inhabiting in mangroves participate actively in various ecological processes. Metagenomic sequencing from mangrove sediments was applied to excavate the resources MG-degradation genes (MDGs) and to assess the potential of their corresponding enzymes. A data set of 10 GB was assembled into 33,756 contigs and 44,743 ORFs were predicted. In the data set, 666 bacterial genera and 13 pollutant degradation pathways were found. Proteobacteria and Actinobacteria were the most dominate phyla in taxonomic assignment. A total of 44 putative MDGs were revealed and possibly derived from 30 bacterial genera, most of which belonged to the phyla of Proteobacteria and Bacteroidetes. The MDGs belonged to three gene families, including peroxidase genes (up to 93.54% of total MDGs), laccase (3.40%), and p450 (3.06%). Of the three gene families, three representatives (Mgv-rLACC, Mgv-rPOD, and Mgv-rCYP) which had lower similarities to the closest sequences in GenBank were prokaryotic expressed and their enzymes were characterized. Three recombinant proteins showed different MG-degrading activities. Mgv-rPOD had the strongest activity which decolorized 97.3% of MG (300 mg/L) within 40 min. In addition, Mgv-rPOD showed a more complete process of MG degradation compared with other two recombinant proteins according to the intermediates detected by LC-MS. Furthermore, the high MG-degrading activity was maintained at low temperature (20°C), wider pH range, and the existence of metal ions and chelating agent. Mgv-rLACC and Mgv-rCYP also removed 63.7% and 54.1% of MG (20 mg/L) within 24 h, respectively. The results could provide a broad insight into discovering abundant genetic resources and an effective strategy to access the eco-friendly way for preventing coastal pollution.

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.

Aerobic degradation of crude oil by microorganisms in soils from four geographic regions of China

A microcosm experiment was conducted for 112 d by spiking petroleum hydrocarbons into soils from four regions of China. Molecular analyses of soils from microcosms revealed changes in taxonomic diversity and oil catabolic genes of microbial communities. Degradation of total petroleum hydrocarbons (TPHs) in Sand from the Bohai Sea (SS) and Northeast China (NE) exhibited greater microbial mineralization than those of the Dagang Oilfield (DG) and Xiamen (XM). High-throughput sequencing and denaturing gradient gel electrophoresis (DGGE) profiles demonstrated an obvious reconstruction of the bacterial community in all soils. The dominant phylum of the XM with clay soil texture was Firmicutes instead of Proteobacteria in others (DG, SS, and NE) with silty or sandy soil texture. Abundances of alkane monooxygenase gene AlkB increased by 10- to 1000-fold, relative to initial values, and were positively correlated with rates of degradation of TPHs and n-alkanes C13-C30. Abundances of naphthalene dioxygenase gene Nah were positively correlated with degradation of naphthalene and total tricyclic PAHs. Redundancy analysis (RDA) showed that abiotic process derived from geographical heterogeneity was the primary effect on bioremediation of soils contaminated with oil. The optimization of abiotic and biotic factors should be the focus of future bioremediation of oil contaminated soil.

Effect of static magnetic field on trichloroethylene removal in a biotrickling filter

A laboratory-scale biotrickling filter combined with a magnetic field (MF-BTF) and a single BTF (S-BTF) were set up to treat trichloroethylene (TCE) gas. The influences of phenol alone and NaAc-phenol as co-substrates and different MF intensities were investigated. At low MF intensity, MF-BTF displayed better performance with 0.20g/L of phenol, 53.6-337.1mg/m³ of TCE, and empty bed residence times of 202.5s. The performances followed the order MF-BTF (60.0mT)>MF-BTF (30.0mT)>S-BTF (0mT)>MF-BTF (130.0mT), and the removal efficiencies (REs) and maximum elimination capacities (ECs) corresponded to: 92.2%-45.5%, 2656.8mg/m³h; 89.8%-37.2%, 2169.1mg/m³h; 89.8%-29.8%, 1967.7mg/m³h; 76.0%-20.8%, 1697.1mg/m³h, respectively. High-throughput sequencing indicated that the bacterial diversity was lower, whereas the relative abundances of Acinetobacter, Chryseobacterium, and Acidovorax were higher in MF-BTF. Results confirmed that a proper MF could improve TCE removal performance in BTF.

Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol

In order to predict the fate of chemicals in the environment, a range of regulatory tests are performed with microbial inocula collected from environmental compartments to investigate the potential for biodegradation. The abundance and distribution of microbes in the environment is affected by a range of variables, hence diversity and biomass of inocula used in biodegradation tests can be highly variable in space and time. The use of artificial or natural biofilms in regulatory tests could enable more consistent microbial communities be used as inocula, in order to increase test consistency. We investigated spatial and temporal variation in composition, biomass and chemical biodegradation potential of bacterial biofilms formed in river water. Sampling time and sampling location impacted the capacity of biofilms to degrade p-nitrophenol (PNP). Biofilm bacterial community structure varied across sampling times, but was not affected by sampling location. Degradation of PNP was associated with increased relative abundance of Pseudomonas syringae. Partitioning of the bacterial metacommunity into core and satellite taxa revealed that the P. syringae could be either a satellite or core member of the community across sampling times, but this had no impact on PNP degradation. Quantitative PCR analysis of the pnpA gene showed that it was present in all samples irrespective of their ability to degrade PNP. River biofilms showed seasonal variation in biomass, microbial community composition and PNP biodegradation potential, which resulted in inconsistent biodegradation test results. We discuss the results in the context of the mechanisms underlying variation in regulatory chemical degradation tests.

Organic micropollutants in aerobic and anaerobic membrane bioreactors: Changes in microbial communities and gene expression

Organic micro-pollutants (OMPs) are contaminants of emerging concern in wastewater treatment due to the risk of their proliferation into the environment, but their impact on the biological treatment process is not well understood. The purpose of this study is to examine the effects of the presence of OMPs on the core microbial populations of wastewater treatment. Two nanofiltration-coupled membrane bioreactors (aerobic and anaerobic) were subjected to the same operating conditions while treating synthetic municipal wastewater spiked with OMPs. Microbial community dynamics, gene expression levels, and antibiotic resistance genes were analyzed using molecular-based approaches. Results showed that presence of OMPs in the wastewater feed had a clear effect on keystone bacterial populations in both the aerobic and anaerobic sludge while also significantly impacting biodegradation-associated gene expression levels. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while associated antibiotic resistance genes were lower.

Removal performance and microbial communities in a sequencing batch reactor treating hypersaline phenol-laden wastewater

Hypersaline phenol-rich wastewater is hard to be treated by traditional biological systems. In this work, a sequencing batch reactor was used to remove phenol from hypersaline wastewater. The removal performance was evaluated in response to the variations of operating parameters and the microbial diversity was investigated by 454 pyrosequencing. The results showed that the bioreactor had high removal efficiency of phenol and was able to keep stable with the increase of initial phenol concentration. DO, pH, and salinity also affected the phenol removal rate. The most abundant bacterial group was phylum Proteobacteria in the two working conditions, and class Gammaproteobacteria as well as Alphaproteobacteria was predominant subgroup. The abundance of bacterial clusters was notably different along with the variation of operation conditions, resulting in changes of phenol degradation rates. The high removal efficiency of phenol suggested that the reactor might be promising in treating phenol-laden industrial wastewater in high-salt condition.

Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols.

IMPORTANCE

This work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis

The compositions of bacterial community in one site contaminated with PCE/TCE after the slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, and surfactants) addition were analyzed. Results show that SPRS caused a rapid enhancement of reductive dechlorination of TCE. The transformation of PCE/TCE into ethene was observed after 20 days of operation. To compare the change of bacterial communities before and after SPRS addition, 16S rRNA amplicon sequencing using the metagenome analysis was performed. Results demonstrated the detection of the increased amounts of Dehalogenimonas by 2.2-fold, Pseudomonas by 3.4-fold and Sulfuricurvum by 4-fold with the analysis of the ribosomal database project (RDP). Metagenomic DNA was extracted from PCE/TCE-contaminated groundwater after SPRS addition, and subjected to sequencing. Results obtained from metagenomic sequencing indicate that genes from Dehalococcoides mccartyi was ranked as the second abundant bacteria among all of the detected bacteria via the analysis of the lowest common ancestor (LCA). Abundance of these bacterial groups, as shown above suggests their role in TCE biodegradation. Functional analysis of the metagenome, with the specific reference to chloroalkane and chloroalkene degradation, revealed the presence of some genes responsible for TCE biodegradation. Overall, results of this study provided new insights for a better understanding of the potential of biostimulation on TCE-contaminated sites.

Why Small Differences Matter: Elucidation of the Mechanisms Underlying the Transformation of 2OH- and 3OH-Carbamazepine in Contact with Sand Filter Material

Carbamazepine (CBZ) is a worldwide used antiepileptic drug, which is metabolized to a large extent in the human body to several metabolites, including 10,11-dihydroxy-10,11-dihydrocarbamazepine (DiOHCBZ), 2-hydroxycarbamazepine (2OHCBZ), and 3-hydroxycarbamazepine (3OHCBZ). 2OHCBZ and 3OHCBZ were previously detected in raw and treated wastewater revealing their widespread emission into the aquatic environment, eventually leading to the contamination of drinking water resources. Sand filtration is frequently applied in drinking water treatment for the removal of inorganic species and suspended particles but has been shown to be capable of removing trace organic contaminants. This study focuses on the elucidation of the (bio)transformation mechanisms of 2OHCBZ and 3OHCBZ in contact with material taken from a rapid sand filter of a German waterworks. Despite their similar structure, which differs only in the position of the phenolic OH moiety, both compounds underwent distinct transformation reactions leading to the formation of a variety of transformation products (TPs). The main biochemical reactions thereby included enzymatic transformation of 2OHCBZ resulting in the formation of a reactive iminoquinone intermediate (2OHCBZ) and nitration via peroxynitrite (2OHCBZ and 3OHCBZ) as well as formation of radicals leading to dimerization (3OHCBZ). Further transformation reactions included hydroxylation, ring cleavage, loss of carbamoyl group, and decarboxylation, as well as O-methylation.

Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

There is increasing interest in using meta-omics association studies to investigate contaminant biotransformations. The general strategy is to characterize the complete set of genes, transcripts, or enzymes from in situ environmental communities and use the abundances of particular genes, transcripts, or enzymes to establish associations with the communities' potential to biotransform one or more contaminants. The associations can then be used to generate hypotheses about the underlying biological causes of particular biotransformations. While meta-omics association studies are undoubtedly powerful, they have a tendency to generate large numbers of non-causal associations, making it potentially difficult to identify the genes, transcripts, or enzymes that cause or promote a particular biotransformation. In this perspective, we describe general scenarios that could lead to pervasive non-causal associations or conceal causal associations. We next explore our own published data for evidence of pervasive non-causal associations. Finally, we evaluate whether causal associations could be identified despite the discussed limitations. Analysis of our own published data suggests that, despite their limitations, meta-omics association studies might still be useful for improving our understanding and predicting the contaminant biotransformation capacities of microbial communities.

Linking operation parameters and environmental variables to population dynamics of Mycolata in a membrane bioreactor

The community structure and population dynamics of Mycolata were monitored in a full-scale membrane bioreactor during four experimental phases under changing operating and environmental conditions, by means of temperature-gradient gel electrophoresis of partial 16S-rRNA genes amplified from community DNA and RNA templates (total and active populations). Non-metric multidimensional scaling and BIO-ENV analyses demonstrated that population dynamics were mostly explained (30-32%) by changes in the input of nutrients in the influent water and the accumulation of biomass in the bioreactors, while the influence of hydraulic and solid retention times, temperature and F/M ratio was minor. Significant correlations were observed between particular Mycolata phylotypes and one or more variables, contributing information for the prediction of their abundance and activity under changing conditions. Fingerprinting and multivariate analyses demonstrated that two foaming episodes, recorded at temperatures <20°C, were connected to the increase of the relative abundance of Mycolata unrelated to Gordonia amarae.

Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants

This study applied Illumina high-throughput sequencing to explore the microbial communities and functions in anaerobic digestion sludge (ADS) from two wastewater treatment plants based on a metagenomic view. Taxonomic analysis using SILVA SSU database indicated that Proteobacteria (9.52-13.50 %), Bacteroidetes (7.18 %-10.65 %) and Firmicutes (7.53 %-9.46 %) were the most abundant phyla in the ADS. Differences of microbial communities between the two types of ADS were identified. Genera of Methanosaeta and Methanosarcina were the major methanogens. Functional analysis by SEED subsystems showed that the basic metabolic functions of metagenomes in the four ADS samples had no significant difference among them, but they were different from other microbial communities from activated sludge, human faeces, ocean and soil. Abundances of genes in methanogenesis pathway were also quantified using a methanogenesis genes database extracted from KEGG. Results showed that acetotrophic was the major methanogenic pathway in the anaerobic sludge digestion.

Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass

Metagenome analysis was used to understand the microbial community in activated sludge treating industrial wastewaters at a Common Effluent Treatment Plant (CETP) in South India. The taxonomic profile mapped onto National Center for Biotechnology Information (NCBI) taxonomy using MEtaGenome ANalyzer (MEGAN), demonstrated that the most abundant domain belonged to prokaryotes, dominated by bacteria. Bacteria representing nine phyla were identified from the sequence data including representatives from two new phyla, Synergistetes and Elusimicrobia. Functional analysis of the metagenome, with specific reference to the metabolism of aromatic compounds, revealed the dominance of genes of the central meta-cleavage pathway. This information was used to improve the degradative efficiency in the wastewater treatment plant. A pilot scale plant was set up with 200L of activated sludge using salicylate induced sludge and results demonstrated 52% removal in chemical oxygen demand (COD) against non-induced biomass.

Biodegradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin in liquid broth by brown-rot fungi

Dioxins are a class of extremely hazardous molecules that might pose a threat to the environment. This work evaluated the microbial degradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TCDD), in liquid broth using three brown-rot fungi and one white-rot fungi as control. A fast and reliable extraction method with recoveries of over 98% together with a validated GC-MS method was developed, and applied to quantify 1,2,3,4-TCDD in liquid broth, mycelia and reaction flask, with detection limits of 10 ppb. Among the four strains tested, brown-rot fungus Aspergillus aculeatus showed best results, removing up to 21% of dioxin after 30-day incubation. The results open both a path for biotechnological interest in bioremediation purposes and environmental behavior studies by using brown-rot fungus.

FunGene: the functional gene pipeline and repository

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

A novel approach to stimulate the biphenyl-degrading potential of bacterial community from PCBs-contaminated soil of e-waste recycling sites

SRpf, culture supernatants from Micrococcus luteus containing the resuscitation-promoting factor (Rpf), was used to enhance the biphenyl-degrading capability of potential microorganisms. The obtained results suggest that the enrichment culture produced by the addition of SRpf (enrichment culture treatment group, ECT) enhanced the biphenyl degradation efficiency, cell growth and bacterial diversity significantly. Biphenyl at concentration of 1500 mg/L was almost completely degraded in 24 h using SRpf at a dosage of 15% (v/v). Six strains unique to the ECT were isolated in pure cultures. This study provides a new insight into bacterial degradation of biphenyl for PCBs-bioremediation, and could be developed as a novel efficient method for obtaining highly desirable pollutant-degrading microorganisms.