Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments

Distribution, sources, ecological risk and microbial response of polycyclic aromatic hydrocarbons in Qingdao bays, China

Bay ecosystem has garnered significant attention due to the severe threat posed by organic pollutants, particularly polycyclic aromatic hydrocarbons (PAHs). However, there is a dearth of information regarding the extent of PAHs pollutant risk and its impact on microbial communities and metabolism within this environment. In this study, the distribution, sources, ecological risk, and microbial community and metabolic response of PAHs in Jiaozhou Bay, Aoshan Bay, and Lingshan Bay in Qingdao, China were investigated. The results showed that the average concentration of ∑PAHs ranged from 120 to 614 ng/L across three bays, with Jiaozhou and Aoshan Bay exhibiting a higher risk than Lingshan Bay due to an increased concentration of high-molecular-weight PAHs. Further analysis revealed a negative correlation between dissolved organic carbon concentration and ∑PAHs concentration in water. Metagenomic analysis demonstrated that higher levels of PAHs can lead to decreased microbial diversity, while the abundance of PAHs-degrading bacteria is enhanced. Additionally, the Erythrobacter, Jannaschia and Ruegeria genera were found to have a significant correlation with low-molecular-weight PAH concentrations. In terms of microbial metabolism, higher PAH concentrations were beneficial for carbohydrate metabolic pathway but unfavorable for amino acid metabolic pathways and membrane transport pathways in natural bay environments. These findings provide a foundation for controlling PAHs pollution and offer insights into the impact of PAHs on bacterial communities and metabolism in natural bay environments.

Exploring microbial diversity responses in agricultural fields: a comparative analysis under pesticide stress and non-stress conditions

Exposure to pesticides changes the microbial community structure in contaminated agricultural fields. To analyze the changes in the native microbial composition qRT-PCR, a metagenomic study was conducted. The qRT-PCR results exhibited that the uncontaminated soil has a higher copy number of 16S rDNA relative to the soil contaminated with pesticide. Metagenome analysis interprets that uncontaminated soil is enriched with proteobacteria in comparison with pesticide-contaminated soil. However, the presence of Actinobacteria, Firmicutes, and Bacteroides was found to be dominant in the pesticide-spiked soil. Additionally, the presence of new phyla such as Chloroflexi, Planctomycetes, and Verrucomicrobia was noted in the pesticide-spiked soil, while Acidobacteria and Crenarchaeota were observed to be extinct. These findings highlight that exposure to pesticides on soil significantly impacts the biological composition of the soil. The abundance of microbial composition under pesticide stress could be of better use for the treatment of biodegradation and bioremediation of pesticides in contaminated environments.

Dynamics of Bacterioplankton Communities during Wet and Dry Seasons in the Danjiangkou Reservoir in Hubei, China

Water quality is directly linked to drinking water safety for millions of people receiving the water. The Danjiangkou Reservoir is the main water source for the Middle Route of the South-to-North Water Diversion Project (MR-SNWDP), located in the vicinity of Henan and Hubei provinces in China. Aquatic microorganisms are key indicators of biologically assessing and monitoring the water quality of the reservoir as they are sensitive to environmental and water quality changes. This study aimed to investigate the spatiotemporal variations in bacterioplankton communities during wet (April) and dry (October) seasons at eight monitoring points in Hanku reservoir and five monitoring points in Danku reservoir. Each time point had three replicates, labeled as wet season Hanku (WH), wet season Danku (WD), dry season Hanku (DH), and dry season Danku (DD) of Danjiangkou Reservoir in 2021. High-throughput sequencing (Illumina PE250) of the 16S rRNA gene was performed, and alpha (ACE and Shannon) and beta (PCoA and NDMS) diversity indices were analyzed. The results showed that the dry season (DH and DD) had more diverse bacterioplankton communities compared to the wet season (WH and WD). Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phyla, and Acinetobacter, Exiguobacterium, and Planomicrobium were abundant in the wet season, while polynucleobacter was abundant in the dry season. The functional prediction of metabolic pathways revealed six major functions including carbohydrate metabolism, membrane transport, amino acid metabolism, signal transduction, and energy metabolism. Redundancy analysis showed that environmental parameters greatly affected bacterioplankton diversity during the dry season compared to the wet season. The findings suggest that seasonality has a significant impact on bacterioplankton communities, and the dry season has more diverse communities influenced by environmental parameters. Further, the relatively high abundance of certain bacteria such as Acinetobacter deteriorated the water quality during the wet season compared to the dry season. Our findings have significant implications for water resource management in China, and other countries facing similar challenges. However, further investigations are required to elucidate the role of environmental parameters in influencing bacterioplankton diversity in order to devise potential strategies for improving water quality management in the reservoir.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

Enhanced phytoremediation of atrazine-contaminated soil by vetiver (Chrysopogon zizanioides L.) and associated bacteria

The intensive and long-term use of atrazine (ATZ) has led to the contamination of agricultural soils and non-target organisms, posing a series of threats to human health through the transmission of the food chain. In this study, a 60-day greenhouse pot experiment was carried out to explore the phytoremediation by Chrysopogon zizanioides L. (vetiver). The uptake, accumulation, distribution, and removal of ATZ were investigated, and the degradation mechanisms were elucidated. The results showed that the growth of vetiver was inhibited in the first 10 days of the incubation; subsequently, the plant recovered rapidly with time going. Vetiver grass was capable of taking up ATZ from the soil, with root concentration factor ranging from 2.36 to 15.55, and translocating to the shoots, with shoot concentration factor ranging from 7.51 to 17.52. The dissipation of ATZ in the rhizosphere soil (97.51%) was significantly higher than that in the vetiver-unplanted soil (85.14%) at day 60. Metabolites were identified as hydroxyatrazine (HA), deethylatrazine (DEA), deisopropylatrazine (DIA), and didealkylatrazine (DDA) in the samples of the shoots and roots of vetiver as well as the soils treated with ATZ. HA, DEA, DIA, and DDA were reported first time as metabolites of ATZ in shoots and roots of vetiver grown in soil. The presence of vetiver changed the formation and distribution of the dealkylated products in the rhizosphere soil, which remarkably enhanced the occurrence of DEA, DIA, and DDA. Arthrobacter, Bradyrhizobium, Nocardioides, and Rhodococcus were the major atrazine-degrading bacterial genera, which might be responsible for ATZ degradation in the rhizosphere soil. Our findings suggested that vetiver grass can significantly promote ATZ degradation in the soil, and it could be a strategy for remediation of the atrazine-contaminated agricultural soil.

Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.

Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil

Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.

Zero-valent iron-induced successive chemical transformation and biodegradation of lindane in historically contaminated soil: An isotope-informed metagenomic study

Zero-valent iron (ZVI) is widely used to mitigate environmental pollutants such as chlorinated pesticides through reductive reactions accompanied by extensive impacts on the soil microbial community. However, whether and how ZVI changes the biodegradation of target compounds remain poorly understood. Here, we monitor the fate of lindane using a ¹⁴C-labled tracer and evaluate the growth and functions of the bacterial community in ZVI-stressed conditions in a historically γ-hexachlorocyclohexane (lindane)-contaminated soil using a combination of isotopic (¹⁸O-H₂O) and metagenomic methods. ZVI promoted the biomineralization of lindane in a dose-dependent manner. Soil bacteria were inhibited by amendment with ZVI during the initial stages of incubation (first three days) but recovered during the subsequent six weeks. Metagenomic study indicates that the todC1/bedC1 genes involved in the oxidation of dechlorinated lindane intermediates were upregulated in the ¹⁸O-labeled bacterial community but the presence of the lin genes responsible for lindane dechlorination was not confirmed. In addition, the benzoate biodegradation pathway that links to downstream catabolism of lindane was enhanced. These findings indicate successive chemical and biological degradation mechanisms underlying ZVI-enhanced lindane mineralization and provide a scientific basis for the inclusion of an extended bioremediation stage in the environmental application of ZVI materials.

Metagenomic Approaches to Explore the Quorum Sensing-Mediated Interactions Between Algae and Bacteria in Sequence Membrane Photo-Bioreactors

Algal–bacterial water treatment is more effective for better harvesting and promotes energy savings than other traditional treatments, while the relationships between them are multifarious. Among all the interactions, quorum sensing plays an essential ecological role. However, the relative contributions of signaling in the interaction between algae and bacteria are not clear. To elucidate the role of quorum sensing by indole-3-acetic acid (IAA) in terms of the algal–bacterial interaction during the nitrogen removal process, the bioreactors, respectively, inoculated with Chlorella, Phormidium, and both of them were started. We manifest the existence of multiple signaling-related proteins by alignment with the constructed database, and the signaling was analyzed using metagenomic sequence data obtained during bioreactor operation. We found that IAA was mainly synthetized depending on indole-3-acetamide (IAM) and indole-3-pyruvic acid (IPA) pathways by calculating the gene abundance of IAA synthetase. Both Chlorella and the co-culture reactor possessed higher nitrogen removal rate (NRR) than the Phormidium reactor, and the abundance profile of the signaling-related gene is similar with the NRR. The signaling-related gene abundance increased in Chlorella and co-culture reactors but decreased in the Phormidium reactor. Pseudomonas, Hydrogenophaga, and Zoogloea are the dominant signaled bacteria. Chlorella is the dominant signaled algae. The relative abundance of total signaled bacteria in the whole bacterial community increased during the start-up in Chlorella and co-culture reactors. According to the network analysis, phytoplankton prefers to positively correlate with signaled bacteria than non-signaled bacteria, which indicated that the signaling influences the algal–bacterial interaction. These findings hint at the significance of algal–bacterial signaling in this interkingdom interaction during nitrogen removal.

Profiling microbial removal of micropollutants in sand filters: Biotransformation pathways and associated bacteria

Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full-scale DWTPs to explore the biotransformation of eight micropollutants. Under seven different empty bed contact times (EBCTs), the column experiments showed that caffeine and atenolol were easily removed (up to 92.1% and 97.6%, respectively) with adsorption and microbial biotransformation of the filters. In contrast, the removal of other six micropollutants (i.e., naproxen, carbamazepine, atrazine, trimethoprim, sulfamethoxazole, and sulfadiazine) in the filters were less than 27.1% at shorter EBCTs, but significantly increased at EBCT = 4 h, indicating the dominant role of microbial biotransformation in these micropollutants removal. Integrated analysis of metagenomic reads and transformation products of micropollutants showed a shift in caffeine oxidation and demethylation pathways at different EBCTs, simultaneous occurrence of atrazine hydrolysis and oxidation pathways, and sulfadiazine and sulfamethoxazole oxidation in the filters. Furthermore, using genome-centric analysis, we observed previously unidentified degrading strains, e.g., Piscinibacter, Hydrogenophaga, and Rubrivivax for caffeine transformation, and Methylophilus and Methyloversatilis for atenolol transformation.

Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey

Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.

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.

Plants exert beneficial influence on soil microbiome in a HCH contaminated soil revealing advantage of microbe-assisted plant-based HCH remediation of a dumpsite

Persistence of hexachlorocyclohexane (HCH) pesticide is a major problem for its disposal. Soil microflora plays an important role in remediating contaminated sites. Keeping concepts of microbial- and phyto-remediation together, the difference between soil microflora with and without association of HCH accumulating plant species was studied. Metagenomic analysis among the non-plant soil (BS) (∑HCH 434.19 mg/g), rhizospheric soil of shrubs (RSS) (∑HCH 157.31 mg/g), and rhizospheric soil of trees (RSD) (∑HCH 105.39 mg/g) revealed significant differences in microbial communities. Shrubs and trees occurred at a long-term dumpsite accumulated α- and β- HCH residues. Plant rhizospheric soils exhibited high richness and evenness with higher diversity indices compared to the non-plant soil. Order Rhizobiales was most abundant in all soils and Streptomycetales was absent in the BS soil. Proteobacteria and Ascomycota were highest in BS soil, while Actinobacteria was enriched in both the plant rhizospheric soil samples. In BS soil, Pseudomonas, Sordaria, Caulobacter, Magnetospirillum, Rhodospirillum were abundant. While, genera Actinoplanes, Streptomyces, Bradyrhizobium, Rhizobium, Azospirillum, Agrobacterium are abundant in RSD soil. Selected plants have accumulated HCH residues from soil and exerted positive impacts on soil microbial communities in HCH contaminated site. This study advocates microbe-assisted plant-based bioremediation strategy to remediate HCH contamination.

Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

Marine Actinomycetes, New Sources of Biotechnological Products

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Do dissipation and transformation of γ-HCH and p,p'-DDT in soil respond to a proxy for climate change? Insights from a field study on the eastern Tibetan Plateau

While the influence of climate change on the fate of persistent organic pollutants (POPs) is becoming a topic of global concern, it has yet to be demonstrated how POPs and their transformation products in soil respond to a changing climate at the local scale. We conducted a year-long field experiment with spiked soils to investigate the impact of climate on the dissipation of γ-hexachlorocyclohexane (γ-HCH) and p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT) as well as the formation of their products. Four sites along an elevational gradient on the eastern Tibetan Plateau were selected to represent four scenarios ranging from a dry and cold to a warm and humid climate. Based on the measured concentrations of the two pesticides and their transformation products, we calculated the dissipation rates of γ-HCH and p,p'-DDT in soil using two biphasic kinetic models, and the formation rates of transformation products using a mid-point rectangular approximation method. The spiked γ-HCH generally showed the expected decrease in dissipation from soils with increasing altitudes, and therefore decreasing temperature and precipitation, whereas dissipation of p,p'-DDT was influenced more by photolysis and sequestration in soil. The formation rates of the primary products of γ-HCH (i.e. γ-HCH→PeCCH and γ-HCH→TeCCH) and p,p'-DDT (i.e. p,p'-DDT→p,p'-DDE and p,p'-DDT→p,p'-DDD) indicate that a warmer and wetter climate favors dechloroelimination (anaerobic biodegradation) over dehydrochlorination (aerobic biodegradation). The significantly longer dissipation half-lives of γ-HCH at the coldest site suggests that the fate of POPs in frozen regions (e.g. polar regions) needs more attention. Overall, the fate of more volatile chemicals (e.g. γ-HCH) might be more responsive to the climate change.

Changes in soil and rat gut microbial diversity after long-term exposure to the chiral fungicide epoxiconazole

In previous articles, it was found that epoxiconazole enantiomers can persist for a long time in the environment, causing severe environmental damage. Herein, we investigated alterations in the soil microbial community and rat gut microbiota after six weeks of treatment with rac-epoxiconazole or one of its enantiomers. The selected concentrations were 1, 2, and 6 times greater than the maximum residue limits (MRLs). The rat gut microbiota relative abundance in the feces significantly changed following exposure to rac-epoxiconazole or one of its enantiomers. At the phylum level, in the R,S-, S,R-epoxiconazole, and rac-treated groups, Firmicutes presented the greatest decrease in abundance; however, Spirochaetes presented the greatest increase in abundance in the rac- and S,R-epoxiconazole-treated groups. In response to R,S-epoxiconazole, Epsilonbacteraeota presented the greatest increase in abundance. In soil samples treated with epoxiconazole, the relative abundance of the soil bacterial community also changed. Proteobacteria presented the greatest decrease in abundance in the S,R- and rac-treated samples. However, Firmicutes presented the greatest increase in abundance. In the R,S-treated soil samples, the situation was the opposite. In general, prolonged exposure to epoxiconazole at high concentrations could initiate noticeable alterations in rat gut microbiota and soil microbial diversity. R,S-epoxiconazole had improved bioactivity and less toxic effects at relatively low concentrations. Therefore, we recommend using R,S-epoxiconazole at a relatively low concentration, which is better for environmental safety.

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.

Effects of the insecticide fipronil in freshwater model organisms and microbial and periphyton communities

Fipronil is a broad-spectrum insecticide whose release in the environment damages many non-target organisms. This study evaluated the toxicity of fipronil at two biological levels using in vivo conditions and environmentally relevant concentrations: the first based on two model organisms (aquatic invertebrate Daphnia magna and the unicellular freshwater alga Chlamydomonas reinhardtii) and a second based on three natural communities (river periphyton and freshwater and soil microbial communities). The physicochemical properties of fipronil make it apparently unstable in the environment, so its behaviour was followed with high performance liquid chromatography (HPLC) under the different test conditions. The most sensitive organism to fipronil was D. magna, with median lethal dose (LC₅₀) values from 0.07 to 0.38 mg/L (immobilisation test). Toxicity was not affected by the media used (MOPS or river water), but it increased with temperature. Fipronil produced effects on the photosynthetic activity of C. reinhardtii at 20 °C in MOPS (EC₅₀ = 2.44 mg/L). The freshwater periphyton presented higher sensitivity to fipronil (photosynthetic yield EC₅₀ of 0.74 mg/L) in MOPS and there was a time-dependent effect (toxicity increased with time). Toxicity was less evident when periphyton and C. reinhardtii tests were performed in river water, where the solubility of fipronil is poor. Finally, the assessment of the metabolic profiles using Biolog EcoPlates showed that bacteria communities were minimally affected by fipronil. The genetic identification of these communities based on 16S rRNA gene sequencing revealed that many of the taxa are specialists in degrading high molecular weight compounds, including pesticides. This work allows us to better understand the impact of fipronil on the environment at different levels of the food chain and in different environmental conditions, a necessary point given its presence in the environment and the complex behaviour of this compound.

Influence of the neonicotinoid insecticide thiamethoxam on soil bacterial community composition and metabolic function

Understanding of neonicotinoid insecticides toxicity on non-target organisms, such as bees, has indirectly promoted their soil treatment use. However, their effect on soil ecosystems haven't fully understood. Here, based on 16S rRNA high-throughput sequencing and metagenomics, the effects of neonicotinoid insecticide thiamethoxam on bacterial communities and metabolic functions in two types of soils were studied. Thiamethoxam treatment significantly affected soil bacterial abundance, reduced microbial diversity, and changed the bacterial community structure in the short term, and the structure soon returned to a stable state. Soil type and time were important factors affecting bacterial community structure. Some plant growth-promoting rhizosphere bacteria (PGPR) including Actinobacteria were found, and their populations were reduced, while pollutant-degrading bacteria including Firmicutes were also found, and their populations were increased. Based on metagenomics analysis, thiamethoxam treatment insignificantly promoted or inhibited multiple metabolic processes, but gene abundance of some key processes significantly changed. Subtypes of 18 biodegradation genes (BDGs) and 5 pesticide degradation genes (PDGs) were identified. Thiamethoxam treatment significantly increased the abundance of BDGs and PDGs, including cytochrome P450. Potential hosts of P450 degradation genes, including the genus Rhodococcus, were discovered. Conclusions of this study will promote safety evaluation and degradation-related research on neonicotinoid insecticides in soil.

Characterization of a novel carbendazim-degrading strain Rhodococcus sp. CX-1 revealed by genome and transcriptome analyses

The persistence and ecotoxicity of carbendazim residues pose a potential risk to environmental ecology and human health. Here, a novel and highly efficient carbendazim-degrading bacterium Rhodococcus sp. CX-1, capable of utilizing carbendazim as its sole source of carbon and energy, was isolated from contaminated soil. The biodegradation characteristics and metabolic pathways were studied by mass spectrometry, genomic annotation, and transcriptome analysis. The degradation rate of carbendazim by strain CX-1 was 3.98-9.90 mg/L/h under different conditions, and the optimum degradation conditions were 40 °C and pH 7.0. The addition of carbon sources (glucose, fructose, and sucrose, 100 mg/L) could accelerate carbendazim degradation. HPLC-MS/MS identification suggested that carbendazim is first hydrolyzed into 2-aminobenzimidazole and then to 2-hydroxybenzimidazole, and is ultimately mineralized to carbon dioxide. The genome of strain CX-1 contained 6,511,628 bp nucleotides, 2 linear plasmids, 2 circular plasmids, and 6437 protein coding genes. Genome annotation and transcriptome analysis indicated that carbendazim degradation may be regulated by the degradation genes harbored in the chromosome and in plasmid 2, and two different degradation pathways of carbendazim by imidazole ring cleavage or benzene ring cleavage were predicted. This study provided new insight to reveal the biodegradation mechanism of carbendazim; furthermore, strain CX-1 is a promising bioresource for carbendazim bioremediation.

Metagenomic analysis reveals mechanisms of atrazine biodegradation promoted by tree species

Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus-Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

Do pyrene and Kandelia obovata improve removal of BDE-209 in mangrove soils?

Combined pollution caused by polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs) in mangrove wetlands is serious, with their remediation to be been paid more and more attention. However, little is known about the combined impact of PAHs and mangrove species on removal of PBDEs in contaminated soils. In this study, BDE-209 and pyrene were selected and a 9 months experiment was conducted to explore how BDE-209 removal in contaminated soil varied with pyrene addition and Kandelia obovata planting, and to clarify corresponding microbial responses. Results showed that BDE-209 removals in soil induced by pyrene addition or K. obovata planting were significant and stable after 6 months, with the lowest levels of BDE-209 in combined pyrene addition with K. obovata planting. Unexpected, root uptake of BDE-209 in K. obovata was limited for BDE-209 removal in soil, which was verified by lower total amount of BDE-209 bioaccumulated in K. obovata's root. In soil without K. obovata planting, BDE-209 removal caused by pyrene addition coexisted with changed bacterial abundance at phylum Planctomycetes and Chloroflexi, class Planctomycetacia, and genus Blastopirellula. K. obovata-induced removal of BDE-209 in soil may be related to bacterial enrichment in phylum Proteobacteria, class Gammaproteobacteria and genus Ilumatobacter, Gaiella. Thus, in BDE-209 contaminated soil, microbial community responses induced by pyrene addition and K. obovata planting were different at phylum, class and genus levels. This is the first study demonstrating that pyrene addition and K. obovata planting could improve BDE-209 removal, and differently affected the corresponding responses of microbial communities.

Heavy metal spill influences bacterial communities in freshwater sediments

Bacteria are highly abundant in freshwater sediments and play a crucial role in biogeochemical cycling. Bacterial assemblage is known to be sensitive to heavy metal pollution. However, the shift in freshwater sediment bacterial community after a sudden exposure to heavy metal spill remains unknown. The present study explored the impact of metal (metalloid) spill on sediment bacterial community in a freshwater reservoir. Although sediment bacterial abundance was relatively insensitive to metal (metalloid) spill, bacterial richness, diversity and community structure displayed considerable temporal variations. In addition, the proportions of Proteobacteria Chloroflexi, Nitrospirae, Acidobacteria and Bacteroidetes drastically declined, while a significant enrichment of Firmicutes was observed.

Evidence of non-DDD pathway in the anaerobic degradation of DDT in tropical soil

DDT transformation to DDD in soil is the most commonly reported pathway under anaerobic conditions. A few instances of DDT conversion to products other than DDD/DDE have been reported under aerobic conditions and hardly any under anaerobic conditions. In particular, few reports exist on the anaerobic degradation of DDT in African tropical soils, despite DDT contamination arising from obsolete pesticide stockpiles in the continent as well as new contamination from DDT use for mosquito and tsetse fly control. Moreover, the development of possible remediation strategies for contaminated sites demands adequate understanding of different soil processes and their effect on DDT persistence, hence necessitating the study. The aim of this work was to study the effect of simulated anaerobic conditions and slow-release carbon sources (compost) on the dissipation of DDT in two tropical clay soils (paddy soil and field soil) amenable to periodic flooding. The results showed faster DDT dissipation in the field soil but higher metabolite formation in the paddy soil. To explain this paradox, the levels of dissolved organic carbon and carbon mineralization (CH₄ and CO₂) were correlated with p,p-DDT and p,p-DDD concentrations. It was concluded that DDT underwent reductive degradation (DDD pathway) in the paddy soil and both reductive (DDD pathway) and oxidative degradation (non-DDD pathway) in the field soil.

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

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.

Metagenomic approaches to understanding bacterial communication during the anammox reactor start-up

Increasing attention has been paid to the anammox community for its significant function in high-efficiency wastewater treatment. However, bacterial interaction in terms of bacterial communication is still elusive. This study firstly explored the intra- and interspecific communication of bacteria in the anammox community using metagenomic sequence data obtained during bioreactor operation. We verified the existence of multiple bacterial communication gene (BCG) subtypes by alignment with the constructed BCG database containing 11 identified gene subtypes. Bacterial communication was more active at the initial start-up than in the high loading-rate phase, and was correlated with the gradually decreasing bacterial diversity. Hdts, one of the key genes that produced the intraspecific signaling molecule AHL, and RpfF, the key gene that produced the intra- and interspecific signaling molecule DSF, were the primary communication engines in the anammox community because of their high abundance. Anammox bacteria mainly used Hdts genes to communicate with others, while RpfF gene played a core role characterized by their multiple correlations with other BCG subtypes. Interestingly, bacteria with abundant BCGs were more inclined to interact with the bacteria with the same functional traits, indicating the potential communication-related interaction among these bacteria in addition to the frequently reported substrate co-utilization. This highlights the primary importance of AHL and DSF for the anammox community, and thereby hints at a potential strategy for the target regulation of the signals to improve anammox viability and competitive capacity in wastewater treatment.

Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio

Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.

Metagenomics profiling for assessing microbial diversity in both active and closed landfills

The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×10⁷ and 1.50×10⁷, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.

Changes in microbial community during removal of BDE-153 in four types of aquatic sediments

Indigenous microorganisms in sediments could degrade polybrominated diphenyl ethers (PBDEs), but how the microbial communities respond to PBDEs was seldom reported. The effect of BDE-153, a common congener in aquatic environments, on the microbial communities in four types of aquatic sediments was evaluated during the 150days' incubation under an anaerobic condition. The intrinsic potential to remove BDE-153 varied significantly among four sediment types, and the removal rates of mangrove, mudflat, marine and freshwater sediments were 0.013, 0.013, 0.011, and 0.009day^-1, respectively. The observed microbial species, Simpson, Shannon, and Chao1 indices in all sediments were rather stable and were not changed significantly by BDE-153 amendment. However, BDE-153 amendment altered the microbial community compositions in three saline sediments at the end of the incubation period. Distance-based multivariate multiple regression analysis revealed that salinity, total organic carbon (TOC) and BDE-52, the major debromination product of BDE-153, were the three main factors explaining the variations in microbial community compositions in BDE-treated sediments; whereas salinity, TOC and pH were the main contributing factors in control sediments without BDE-153. The daughter congeners generated during anaerobic debromination process need more attention, especially their effect on the microbial communities in aquatic sediments.

Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season

A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.

Characterization and genome functional analysis of the DDT-degrading bacterium Ochrobactrum sp. DDT-2

A strain of Ochrobactrum sp. DDT-2 that was capable of degrading DDT as the sole carbon and energy source was isolated and sequenced, and its biodegradation characteristics and metabolism mechanism were examined. The genome sequence of the isolate DDT-2 was composed of 4,630,303bp with a GC content of 55.99% and 4454 coding genes. The degradation rate of DDT by the isolate DDT-2 increased with the increasing substrate concentration (0.1-10mg/l) and temperature (20-40°C). The degradation half-life of DDT in the presence of the isolate DDT-2 at pH7.0 was obviously shorter than those at pH5.0 and 9.0. Potential DDT degradation genes were found in the isolate DDT-2 genome by a BLASTx search against a DDT degradation genes (DDGs) database. A common biodegradation pathway of DDT was proposed based on the combined analysis of genome annotation and mass spectrometry. DDT was initially dechlorinated to form DDD and DDE. Then, it was transformed into DDMU and DDA via dechlorination and carboxylation, and it may ultimately be mineralized to carbon dioxide. The results suggested that the isolate DDT-2 could be useful for the bioremediation of DDT and its metabolite residues.

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods

Microcosms for enrichment of DDT degrading microorganisms were monitored using culture-dependent and -independent methods. Culture dependent methods isolated several strains with DDT degradation potential, Pseudomonas species being the most frequent. One isolate, Streptomyces sp. strain D3, had a degradation rate of 77% with 20mgL^-1 of DDT after 7days incubation, D3 also had degradation rates of 75% and 30% for PCB77 (3,3',4,4'-tetrachloro biphenyl) and PCNB (pentachloronitrobenzene) respectively. Culture-independent high-throughput sequencing identified a different subset of the microbial community within the enrichment microcosms to the culture dependent method. Pseudomonas, the most frequently isolated strain, only represented the 12th most abundant operational taxonomic unit in the sequencing dataset (relative abundance 0.9%). The most frequently observed bacterial genus in the culture-independent analysis did not correspond with those recovered by culture-dependent methods. These results suggested that deep sequencing followed by a targeted isolation approach might provide an advantageous route to bioremediation studies.

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation

The aim of the present review is to highlight the potential use of marine biocatalysts (whole cells or enzymes) as an alternative bioprocess for the degradation of aromatic pollutants. Firstly, information about the characteristics of the still underexplored marine environment and the available scientific tools used to access novel marine-derived biocatalysts is provided. Marine-derived enzymes, such as dioxygenases and dehalogenases, and the involved catalytic mechanisms for the degradation of aromatic and halogenated compounds, are presented, with the purpose of underpinning their potential use in bioremediation. Emphasis is given on persistent organic pollutants (POPs) that are organic compounds with significant impact on health and environment due to their resistance in degradation. POPs bioaccumulate mainly in the fatty tissue of living organisms, therefore current efforts are mostly focused on the restriction of their use and production, since their removal is still unclear. A brief description of the guidelines and criteria that render a pollutant POP is given, as well as their potential biodegradation by marine microorganisms by surveying recent developments in this rather unexplored field.

Scientific Opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms

Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science behind the risk assessment of plant protection products for in-soil organisms. The current risk assessment scheme is reviewed, taking into account new regulatory frameworks and scientific developments. Proposals are made for specific protection goals for in-soil organisms being key drivers for relevant ecosystem services in agricultural landscapes such as nutrient cycling, soil structure, pest control and biodiversity. Considering the time-scales and biological processes related to the dispersal of the majority of in-soil organisms compared to terrestrial non-target arthropods living above soil, the Panel proposes that in-soil environmental risk assessments are made at in- and off-field scale considering field boundary levels. A new testing strategy which takes into account the relevant exposure routes for in-soil organisms and the potential direct and indirect effects is proposed. In order to address species recovery and long-term impacts of PPPs, the use of population models is also proposed.

Insight into the long-term effect of mangrove species on removal of polybrominated diphenyl ethers (PBDEs) from BDE-47 contaminated sediments

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous environmental contaminants, particularly in mangrove wetlands. However, little is known about the long-term effect of mangrove plants on PBDE removal from contaminated sediments. A 12-month microcosm experiment was conducted to understand the effect of two mangrove species, namely Avicennia marina (Am) and Aegiceras corniculatum (Ac), on PBDE removal from the sediments spiked with 2000ngg^-1 dry weight of BDE-47, and to explore the microbial mechanism responsible for the planting-induced effects on BDE-47 removal. Results showed that planting of mangrove species, either Am or Ac, could accelerate BDE-47 removal from contaminated sediments during the 12months experiment, mainly through enhancing microbial degradation process. In particular, Am sediment had significantly higher BDE-47 degradation efficiency compared with Ac sediment, which may be mainly attributed to higher activities of urease and dehydrogenase, as well as higher 16S rRNA gene copies of total bacteria and organohalide-respiring bacteria (OHRB) in Am sediment. Moreover, planting could shift sediment bacterial community composition and selectively enrich some bacterial genera responsible for PBDE degradation. Such selective enrichment effect of Am on the potential PBDE-degrading bacteria differed distinctly from that of Ac. These results indicated that long-term planting of mangrove species, especially Am, could significantly promote BDE-47 removal from the contaminated sediments by enhancing microbial activity, increasing total bacterial and OHRB abundances and altering bacterial community composition.

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.

The Environmental Issues of DDT Pollution and Bioremediation: a Multidisciplinary Review

DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane) is probably the best known and most useful organochlorine insecticide in the world which was used since 1945 for agricultural purposes and also for vector-borne disease control such as malaria since 1955, until its banishment in most countries by the Stockholm convention for ecologic considerations. However, the World Health Organization allowed its reintroduction only for control of vector-borne diseases in some tropical countries in 2006. Due to its physicochemical properties and specially its persistence related with a half-life up to 30 years, DDT linked to several health and social problems which are due to its accumulation in the environment and its biomagnification properties in living organisms. This manuscript compiles a multidisciplinary review to evaluate primarily (i) the worldwide contamination of DDT and (ii) its (eco) toxicological impact onto living organisms. Secondly, several ways for DDT bioremediation from contaminated environment are discussed. For this, reports on DDT biodegradation capabilities by microorganisms and ways to enhance bioremediation strategies to remove DDT are presented. The different existing strategies for DDT bioremediation are evaluated with their efficiencies and limitations to struggle efficiently this contaminant. Finally, rising new approaches and technological bottlenecks to promote DDT bioremediation are discussed.

Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.