Xenobiotic Degradation Research Articles

Draft genome of hydrocarbon-degrader Burkholderia cepacia BCTT, isolated from soil chronically polluted with crude oil in Trinidad.

Burkholderia cepacia BCTT, isolated from chronically polluted soil in Trinidad, shows a capacity to survive in crude oil as a sole carbon source. Here, we report its high-quality draft genome sequence and highlight those pathways and genes involved in xenobiotic degradation. These data give a clearer insight into this organism's biotechnological potential.

Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus-host interactions.

Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype. We analyzed metagenomes from cheek skin swabs collected from 124 Chinese women in our previous study and found that the viruses associated with the two microbiome cutotypes had distinct diversities, compositions, functions, and lifestyles following PAH exposure. Moreover, exposure to high concentrations of PAHs substantially increased interactions between viruses and certain biodegrading bacteria. Under high-PAH exposure, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Under low-PAH exposure conditions, the interactions followed the "Piggyback-the-Winner" model, with Cutibacterium acnes being "winners," whereas under high-PAH exposure, they followed the "Piggyback-the-Persistent" model, with biodegradation bacteria being "persistent." These findings highlight the impact of air pollutants on skin bacteria and viruses, their interactions, and their modulation of skin health. Understanding these intricate relationships could provide insights for developing targeted strategies to maintain skin health in polluted environments, emphasizing the importance of mitigating pollutant exposure and harnessing the potential of viruses to help counteract the adverse effects.

Insights into the community structure and environmental functions of water hyacinth rhizobiome in urban river ecosystem.

Water hyacinth (WH) is a widespread floating invasive aquatic plant with a prolific reproductive and dispersion rate. With the aid of its root-associated microbes, WH significantly modulates the ecosystem's functioning. Despite their irrevocable importance, the WH microbiome remains unexplored in detail. Here, we present a shotgun sequencing analysis of WH rhizobiome predominant in urban rivers and their surrounding water to unveil the diversity drivers and functional relationship. The core microbiome of the WH mainly consisted of the methane-metabolizing archaebacteria and sulfate-reducing bacteria, which are probably driving the methane and sulfur metabolic flux along the vegetative zone in the water. The beta diversity analysis revealed temporal variations (River WH_2020 vs. WH_2022) (R of 0.8 to 1 and R2 of 0.17 to 0.41), which probably could be attributed to the transient taxa as there was a higher sharing of core bacteria (48%). Also, the WH microbiome significantly differed (R = 0.46 to 1.0 and R2 of 0.18 to 0.52) from its surrounding water. Further, the functional analysis predicted 140 pollutant-degrading enzymes (PDEs) well-implicated in various xenobiotic pollutant degradation, including hydrocarbons, plastics, and aromatic dyes. These PDEs were mapped to bacterial genera such as Hydrogenophaga, Ideonella, Rubrivivax, Dechloromonas, and Thauera, which are well-reported for facilitating the metabolism of xenobiotic compounds. The higher prevalence of metal and biocide resistance genes further highlighted the persistence of resistant microbes assisting WH in bioremediation applications.

Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach

Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%–16%), aminoglycosides (7%–9%), multi-drug (5%–9%), and rifampin (3%–9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.

Polystyrene nanoplastics alter intestinal toxicity of 2,4-DTBP in a sex-dependent manner in zebrafish (Danio rerio)

Nanoplastics (NPs) and 2,4-di-tert-butylphenol (2,4-DTBP) are ubiquitous emerging environmental contaminants detected in aquatic environment. While the intestinal toxicity of 2,4-DTBP alone has been studied, its combined effects with NPs remain unclear. Herein, adult zebrafish were exposed to 80 nm polystyrene nanoplastics (PS-NPs) or/ and 2,4-DTBP for 28 days. With co-exposure of PS-NPs, impact of 2,4-DTBP on feeding capacity and intestinal histopathology was enhanced in males while attenuated in females. Addition of PS-NPs significantly decreased the uptake of 2,4-DTBP in females, while the intestinal concentrations of 2,4-DTBP were not different between the sexes in co-exposure groups. Furthermore, lower intestinal pH and higher contents of digestive enzymes were detected in male fish, while bile acid was significantly increased in co-exposed females. In addition, co-exposure of PS-NPs stimulated female fish to remodel microbial composition to potentially enhance xenobiotics degradation, while negative Aeromonas aggravated inflammation in males. These results indicated that in the presence of PS-NPs, the gut microenvironment in females can facilitate the detoxification of 2,4-DTBP, while exaggerating toxiciy in males. Overall, this study demonstrates that toxicological outcomes of NPs-chemical mixtures may be modified by sex-specific physiology and microbiota composition, furthering understanding for environmental risk assessment and management of aquatic environments.

Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi.

Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these 4 genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in esca symptoms and host resistance.

Remediation Strategies of Xenobiotics in Urban Soils and Water: A Review

Xenobiotic substances are synthetic chemicals that are not native to a specificecological system yet have biological activity. Drugs, industrial chemicals, naturally occurring toxins, and environmental contaminants are all examples of xenobiotics. By disrupting or interfering with many cellular communication routes that control growth, development, and normal physiological function, xenobiotics can have a negative impact on human health. These chemicals are extremely poisonous in nature and can harm both lower and higher eukaryotes. These substances are persistent, allowing for bioaccumulation or biomagnification in the environment over time. They also find their way into food chains, where their concentrations are found to be high even in creatures that do not come into direct contact with xenobiotics. Industries regularly release xenobiotics into the environment, increasing the danger of human and other biota exposure. Despite the use of a variety of traditional and modern environment remediation technologies, some of them are unsuccessful at eliminating xenobiotics, while others are too expensive to use on a wide scale. Maize Stover and Rice Husk are abundantly generated across the world, making them attractive and cost-effective feedstocks for large scale biochar synthesis for environmental clean-up. Because virgin Maize Stover and Rice Husk biochar may not be successful in removing some xenobiotics, adding modifiers to MS/RH biochar can help to generate composite MS/RH biochar, which can aid to disinfect water and soil more effectively. Some microbes have the ability to partially or completely break down xenobiotic substances. The most dependable ways for degrading these chemicals are biological and non-biological remediation procedures. Bacterial biodegradation is a cost-effective approach for land filling and composting that employs both wild type and genetically engineered bacterial strains. Many non-biological approaches that are suited for xenobiotic degradation have been categorised under thermal and non-thermal procedures.

Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis

BackgroundThe genus Geobacillus and its associated taxa have been the focal point of numerous thermophilic biotechnological investigations, both at the whole cell and enzyme level. By contrast, comparatively little research has been done on its recently delineated sister genus, Parageobacillus. Here we performed pan-genomic analyses on a subset of publicly available Parageobacillus and Saccharococcus genomes to elucidate their biotechnological potential.ResultsPhylogenomic analysis delineated the compared taxa into two distinct genera, Parageobacillus and Saccharococcus, with P. caldoxylosilyticus isolates clustering with S. thermophilus in the latter genus. Both genera present open pan-genomes, with the species P. toebii being characterized with the highest novel gene accrual. Diversification of the two genera is driven through the variable presence of plasmids, bacteriophages and transposable elements. Both genera present a range of potentially biotechnologically relevant features, including a source of novel antimicrobials, thermostable enzymes including DNA-active enzymes, carbohydrate active enzymes, proteases, lipases and carboxylesterases. Furthermore, they present a number of metabolic pathways pertinent to degradation of complex hydrocarbons and xenobiotics and for green energy production.ConclusionsComparative genomic analyses of Parageobacillus and Saccharococcus suggest that taxa in both of these genera can serve as a rich source of biotechnologically and industrially relevant secondary metabolites, thermostable enzymes and metabolic pathways that warrant further investigation.

Total RNA analysis of the active microbiome on moving bed biofilm reactor carriers under incrementally increasing micropollutant concentrations.

Micropollutants are increasingly prevalent in the aquatic environment. A major part of these originates from wastewater treatment plants since traditional treatment technologies do not remove micropollutants sufficiently. Moving bed biofilm reactors (MBBRs), however, have been shown to aid in micropollutant removal when applied to conventional wastewater treatment as a polishing step. Here, we used Total RNA sequencing to investigate both the active microbial community and functional dynamics of MBBR biofilms when these were exposed to increasing micropollutant concentrations over time. Concurrently, we conducted batch culture experiments using biofilm carriers from the MBBRs to assess micropollutant degradation potential. Our study showed that biofilm eukaryotes, in particular protozoa, were negatively influenced by micropollutant exposure, in contrast to prokaryotes that increased in relative abundance. Further, we found several functional genes that were differentially expressed between the MBBR with added micropollutants and the control. These include genes involved in aromatic and xenobiotic compound degradation. Moreover, the biofilm carrier batch experiment showed vastly different alterations in benzotriazole and diclofenac degradation following the increased micropollutant concentrations in the MBBR. Ultimately, this study provides essential insights into the microbial community and functional dynamics of MBBRs and how an increased load of micropollutants influences these dynamics.

Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications

The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.

Assembly and comparative analyses of the Geosiphon pyriformis metagenome.

Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.

Optimizing microbial strain selection for pyrethroid biodegradation in contaminated environments through a TOPSIS-based decision-making system

Improved and contemporary agriculture relies heavily on pesticides, yet some can be quite persistent and have a stable chemical composition, posing a significant threat to the ecology. Removing harmful effects is upon their degradability. Biodegradation must be emphasized to lower pesticide degradation costs, especially in the soil. Here, a decision-making system was used to determine the best microbial strain for the biodegradation of the pyrethroid-contaminated soil. In this system, the criteria chosen as: pH (C1), Temp (C2), RPM (C3), Conc. (C4), Degradation (%) (C5) and Time required for degradation(hrs) (C6); and five alternatives were Bacillus (A1), Acinetobacter (A2), Escherichia (A3), Pseudomonas (A4), and Fusarium (A5). The best alternative was selected by applying the TOPSIS (technique for order performance by similarity to ideal solution) method, which evaluates based on their closeness to the ideal solution and how well they meet specific requirements. Among all the specified criteria, Acinetobacter (A2) was the best and optimal based on the relative closeness value ((Ri∗\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${R}_{i}^{*}$$\\end{document}) = 0.740 (A2) > 0.544 (A5) > 0.480 (A1) > 0.403 (A4) > 0.296 (A3)). However, the ranking of the other alternatives is also obtained in the order Fusarium (A5), Bacillus (A1), Pseudomonas (A4), Escherichia (A3). Hence this study suggests Acinetobacter is the best microbial strain for biodegradation of pyrethroids; while least preference should be given to Escherichia. Acinetobacter, versatile metabolic nature with various xenobiotic compounds' degradation ability, is gram-negative, aerobic, coccobacilli, nonmotile, and nonspore forming bacteria. Due to less study about Acinetobacter it is not in that much frame as the other microorganisms. Hence, considering the Acinetobacter strain for the biodegradation study will give more optimal results than the other microbial strains. Novelty of this study, the TOPSIS method is applied first time in selecting the best microbial strain for the biodegradation of pyrethroid-contaminated soil, considering this selection process as multi-criteria decision-making (MCDM) problem.

The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef

Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Bacillus velezensis is a member of the genus Bacillus, which harbours useful, novel, and efficient secondary metabolites that can be utilized in the disruption of xenobiotics. Although a few strains of B. velezensis and related species are reported every year as having xenobiotic metabolism potential, several novel gene clusters are still unexplored, which could be more potent than those already discovered. The current B. velezensis strain was isolated from gills of healthy Oreochromis niloticus and the novelty of the strain was assessed through whole genome sequence analysis. Prokka, DFAST, BAKTA, and RASTtk were computational tools utilized for genome elucidation following the genome assembly. Protein and protein pathway prediction was achieved through the PATRIC database. Additionally, the resistance genes against microorganisms were examined through CARD (via Proksee), bacteriocin, and RiPPs using BAGEL4, and forecast of virulence factors using VFDB in PATRIC. The analysis led to identification of indicator genes for xenobiotic breakdown. The results were compared to pre-existing strains of B. velezensis and it was compelling to conclude the high biotechnological potential and the candidacy of the strain in xenobiotic degradation.

PGPg_finder: A comprehensive and user-friendly pipeline for identifying plant growth-promoting genes in genomic and metagenomic data

Identifying and comparing plant growth-promoting traits (PGPT) within whole-genome and metagenomic sequencing data can significantly advance agricultural research and promote sustainable crop production. This study introduces PGPg_finder, a comprehensive pipeline designed to annotate and compare PGPT from both whole-genome and metagenome sequencing datasets. This pipeline utilizes direct sequence annotation alongside de novo assembly methods to accurately detect PGPT. By cross-referencing sequences from the PLaBAse database, it identifies and quantifies the presence of these genes within the original datasets, facilitating an intuitive comparison of the abundance and distribution of PGPT across various samples. We evaluated the performance of PGPg_finder by analyzing genomes from five rhizobacterial strains: Paenibacillus vini, Paenibacillus polymyxa, Fictibacillus sp., Brevibacillus agri, and Bacillus cereus, and also metagenomic samples from bulk soils subjected to forest-to-pasture conversion in the Amazon rainforest. The genomic workflow revealed several genes associated with substrate utilization, abiotic stress neutralization, phosphate solubilization, and iron acquisition. It also identified genes unique to specific lineages, including those associated with colonization and plant-derived substrate usage in P. polymyxa, quorum sensing response and biofilm formation in P. vini, heavy metal detoxification and nitrogen acquisition in B. agri, and spore production and neutralizing biotic stress in B. cereus. The strain Fictibacillus sp. presented several unique genes related to surface attachment, stress response, xenobiotic degradation, phosphate solubilization, and phytohormone production. The use of PGPg_finder highlights its potential to uncover novel inoculants and strains. The metagenomic workflow distinguished plant-growth promotion gene profiles between soils from the Amazon rainforest and pasture, with the latter showing a profile more aligned with simple carbohydrate consumption, abiotic stress tolerance, motility and chemotaxis, and phosphorus mineralization. Native forests exhibited a profile associated with the degradation of complex organic matter, oxidative stress tolerance, xenobiotic degradation, bactericidal activity, iron acquisition, and volatile pathways. These findings underscore the effectiveness and sensitivity of PGPg_finder in accurately identifying and comparing PGPT genes, highlighting both commonalities and variations across samples. The application of this pipeline has the potential to significantly facilitate the identification of plant growth-promoting microbes.

Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca)

Soil contains a great diversity of microorganisms, including bacteria which are known to be drivers of soil ecosystem functions. This study was aimed at investigating the bacterial communities in bulk and rhizosphere soil of Fusarium wilt-infected plantain (Musa paradisiaca). Physicochemical analysis revealed that electrical conductivity (312 µS/cm), cation exchange capacity (15.62 meq/100g), phosphate (0.16 mg/kg), nitrogen (1.53 mg/kg), moisture (19.45 mg/kg), potassium (1.39 mg/kg), magnesium (0.61 mg/kg), clay (60 %), and silt (35%) were higher in bulk soil than rhizosphere soil. The 16S rRNA metagenomic sequences quantified a total of 89341 bacterial taxonomic units from bulk soil which consist of 10 phyla, 13 classes, 16 orders, 18 families, 21 genera, and 19 species. A total of 88034 bacterial taxonomic units which comprised of 9 phyla, 13 classes, 23 orders, 22 families, 26 genera, and 25 species, were found in rhizosphere soil. The most abundant phyla in bulk soil are Actinobacteria (31%), Proteobacteria (26%), and Gemmatimonadetes (17%) Acidobacteria (17%) and Planctomycetes (3%) while the prominent phyla in rhizosphere soil are Actinobacteria (63%) Proteobacteria (24%), Acidobacteria (7%) and Planctomycetes (3%). The major functional profiles of bacterial communities in both bulk and rhizosphere soils are metabolism of amino acids, carbohydrates, terpenoids, polyketides, cofactors, and xenobiotic degradation. Alpha diversities among the bacterial community were higher in Simpson’s reciprocal index for both bulk and rhizosphere soils. This study opens up new frontiers in expanding metagenomics studies on environmental samples which would capture and contribute to the identification of soil bacteria useful to ecosystem functions.

Metagenome-assembled genomes from enrichment cultures grown on xenobiotic solvents.

Microbes play a significant role in the cleanup of xenobiotic contaminants. Based on metagenomes derived from long-term enrichment cultures grown on xenobiotic solvents, we report 166 metagenome-assembled genomes, of which 137 are predicted to be more than 90% complete. These genomes broaden the representation of xenobiotic degraders.

Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes

The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8–3.7 ppm), COD (23–29.2 ppm) and organic carbon (0.18–0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.

Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing

The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.

Bacterial diversity and functional characteristics of natural rainwater lakes in Saihanba artificial forest farm as revealed by 16S rRNA sequencing

The Saihanba Mechanical Forest is an artificial national forest park with a forest-steppe landscape. The flora and fauna have been extensively studied, but a comprehensive understanding of the bacterial community composition and structure of the natural rainwater lakes present in the area has rarely been reported. In this study, the structure and functional characteristics of bacterial communities in lake sediments and water samples in the Saihanba artificial forest were investigated using 16s rRNA high-throughput sequencing. Microbial diversity analyses revealed that Proteobacteria, Acidobacteria, Bacteroidota and Verrucomicrobiota microbiota dominated. The abundance of Proteobacteria and Actinobacteriota was significantly higher (p < .05) in water samples compared to sediment samples. PICRUSt2 functional analysis predicted genes associated with the degradation of xenobiotics and the execution of essential metabolic processes. Here, we report differences in the composition of native bacterial communities in sediments and water under the Saihanba artificial forest and make functional gene predictions. This study provides a reference for further exploring the structure and functional characteristics of microbial communities in water samples and sediment environments of lakes under planted forests.