Metagenomic analysis of drinking water samples collected from treatment plants of Hyderabad City and Mehran University Employees Cooperative Housing Society

Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India

Yamuna River water in Agra city of India is contaminated with toxic pollutants, including heavy metals that cause damage to the environment and human health. At present, the direct use of river water for drinking purposes and household activities lead to the direct exposure of society to the contaminants. In this study, Yamuna River water samples were collected from three different sites in Agra city during the monsoon, summer, and winter seasons. The physico-chemical parameters were estimated along with heavy metals. In physico-chemical parameter, the values found were mostly above the permissible limits. The results water samples contain high levels of cadmium, chromium, lead, and nickel above the desirable levels in most cases. The metagenomic analysis revealed that Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctobacteria were the most abundant phyla with a relative abundance of 61%, 9.34%, 5.23%, 4.64%, and 4.3%, respectively. The Comamonadaceae, the most abundant family consists of the genera involved in hydrogen oxidation, iron reduction, degraders of polycyclic aromatic hydrocarbons, and fermentation. The presence of Pseudomonas, Nitrosomonas sp., Thauera humireducens and Dechloromonas denitrificans (decomposition of sewage and organic matter) and Pseudomonas aeruginosa indicates the presence of heavy metal degrading bacteria in water sample. Functional prediction showed the presence of genes responsible for different metabolic pathways that could help developing new bioremediation strategies. The study concludes the status of water contamination, the presence of complex microbial community and suggests the futuristic use and their role in bioremediation.

Phthalate acid esters promoted the enrichment of chlorine dioxide-resistant bacteria and their functions related to human diseases in rural polyvinyl chloride distribution pipes

Polyvinyl chloride (PVC) pipes are widely used as drinking water distribution pipes in rural areas of China. However, whether phthalate acid esters (PAEs) released from PVC pipes will affect tap water quality is still unknown. The influence of released PAEs on the water quality was analysed in this study, especially after ClO2 disinfection. The results indicated that ClO2 disinfection could control the growth of total coliforms and heterotrophic bacteria (HPC). However, when the ClO2 residual decreased to below 0.10 mg/L, HPC and opportunistic pathogens, including Mycobacterium avium and Pseudomonas aeruginosa, increased significantly. In addition, after ClO2 disinfection, PAEs concentrations increased from 10.6-22.2 μg/L to 21.2-58.8 μg/L in different sampling cites. Linear discriminant analysis (LDA) effect size (LEfSe) and statistical analysis of metagenomic profiles (Stamp) showed that ClO2 disinfection induced the enrichment of Pseudomonas, Bradyrhizobium, and Mycobacterium and functions related to human diseases, such as pathogenic Escherichia coli infection, shigellosis, Staphylococcus aureus infection, and Vibrio cholerae infection. The released PAEs not only promoted the growth of these ClO2-resistant bacterial genera but also enhanced their functions related to human diseases. Moreover, these PAEs also induced the enrichment of other bacterial genera, such as Blastomonas, Dechloromonas, and Kocuria, and their functions, such as chronic myeloid leukaemia, African trypanosomiasis, leishmaniasis, hepatitis C and human T-cell leukaemia virus 1 infection. The released PAEs enhanced the microbial risk of the drinking water. These results are meaningful for guaranteeing water quality in rural areas of China.

Spatiotemporal distribution of opportunistic pathogens and microbial community in centralized rural drinking water: One year survey in China

Centralized water supply in rural areas, supported by small waterworks (small-central mode) and by municipal water treatment plants (urban-extension mode), is an important guarantee to implement the Rural Revitalization Strategy Plan (2018-2022) in China. Opportunistic pathogens (OPs) could not be evaluated by the national drinking water sanitation standards in China (GB 5749-2022), posing potential microbial risks in rural drinking water. In this study, the spatiotemporal distribution of OPs, microbial community and the associated functional composition under two central water supply modes were investigated by molecular approaches. The results indicated that OPs were widely presented in the rural drinking water regardless of water supply modes, and were more abundant than those in the urban tap water. The insufficient residual chlorine and higher turbidity triggered more microbial proliferation, posing a seasonal variation of OPs gene copy numbers and bacterial community compositions. In warm seasons of summer and autumn, the gene copies of E. coli, M. avium, Pseudomonas spp. and the amoeba host Acanthamoeba spp. achieved up to 4.92, 3.94, 6.75 and 3.74 log₁₀ (gene copies/mL), respectively. Potential functional prediction indicated higher relative abundance of pathogenic genes and infectious risks associated with the rural drinking water under small-central water supply mode. This one-year survey of the spatiotemporal distribution of OPs and microbial community provided scientific insights into microbial safety of rural drinking water, prompting attention on small-central water supply mode against OPs risks.

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.

A road map on synthetic strategies and applications of biodegradable polymers

Biodegradable polymers have emerged as fascinating materials due to their non-toxicity, environmentally benign nature and good mechanical strength. The toxic effects of non-biodegradable plastics paved way for the development of sustainable and biodegradable polymers. The engineering of biodegradable polymers employing various strategies like radical ring opening polymerization, enzymatic ring opening polymerization, anionic ring opening polymerization, photo-initiated radical polymerization, chemoenzymatic method, enzymatic polymerization, ring opening polymerization and coordinative ring opening polymerization have been discussed in this review. The application of biodegradable polymeric nanoparticles in the biomedical field and cosmetic industry is considered to be an emerging field of interest. However, this review mainly highlights the applications of selected biodegradable polymers like polylactic acid, poly(ε-caprolactone), polyethylene glycol, polyhydroxyalkanoates, poly(lactide-co-glycolide) and polytrimethyl carbonate in various fields like agriculture, biomedical, biosensing, food packaging, automobiles, wastewater treatment, textile and hygiene, cosmetics and electronic devices.

Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.

Clean and Safe Drinking Water Systems via Metagenomics Data and Artificial Intelligence: State-of-the-Art and Future Perspective

The use of next-generation sequencing technologies in drinking water distribution systems (DWDS) has shed insight into the microbial communities' composition, and interaction in the drinking water microbiome. For the past two decades, various studies have been conducted in which metagenomics data have been collected over extended periods and analyzed spatially and temporally to understand the dynamics of microbial communities in DWDS. In this literature review, we outline the findings which were reported in the literature on what kind of occupancy-abundance patterns are exhibited in the drinking water microbiome, how the drinking water microbiome dynamically evolves spatially and temporally in the distribution networks, how different microbial communities co-exist, and what kind of clusters exist in the drinking water ecosystem. While data analysis in the current literature concerns mainly with confirmatory and exploratory questions pertaining to the use of metagenomics data for the analysis of DWDS microbiome, we present also future perspectives and the potential role of artificial intelligence (AI) and mechanistic models to address the predictive and mechanistic questions. The integration of meta-omics, AI, and mechanistic models transcends metagenomics into functional metagenomics, enabling deterministic understanding and control of DWDS for clean and safe drinking water systems of the future.

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.

Emerging priorities for microbial metagenome research

Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.

Super Effective Removal of Toxic Metals Water Pollutants Using Multi Functionalized Polyacrylonitrile and Arabic Gum Grafts

Super adsorbent polymers can be considered to be a very efficient solution for wastewater treatment. In general, their adsorption capacities depend on the type and amount of the functional groups present on the surface of the polymers, while their economic value is affected by their cost. Therefore, this study aims to understand the effect of multi-functionalization of cheap Arabic gum on the adsorption capability toward heavy metals. Graft copolymers of polyacrylonitrile (PAN) onto Arabic gum (AG) were prepared in aqueous solution using (KMnO₄/HNO₃) as a redox initiator. Chemical modification of the graft copolymer was carried out by reaction with hydrazine hydrochloride followed by hydrolysis in the basic medium. The modified graft product was characterized by various techniques, such as Fourier transform infrared spectroscopy (FTIR), elemental analysis, scanning electron microscope (SEM), and X-ray powder diffraction (XRD). The modified graft copolymer was used to adsorb Pb²⁺, Cd²⁺ and Cu²⁺ from their aqueous solutions using batch extraction. Different parameters influence the uptake behavior, including contact time, pH, and the initial concentration of the metal ions; all of these were investigated. The kinetics were investigated using the pseudo first order and pseudo second order, and the equilibrium data were analyzed using the Langmuir and Freundlich model. The modified graft product showed the superadsorbent capacity to obtain maximum values (Qmax) 1017, 413 and 396 mg/g for Pb²⁺, Cd²⁺ and Cu²⁺, respectively. Acid treatment with 0.2 M HNO₃ resulted in 96%, 99% and 99% metal recovery for the Pb²⁺, Cd²⁺ and Cu²⁺, respectively. This indicates the recyclability of product for further usage upon drying between treatments.