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Abstract River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7–1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas , Pseudoxanthomonas , Arenimonas , Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area. Graphical abstract Image 1 Highlights • A metagenomic framework was proposed to identify antibiotic resistomes in river. • Multiple categories were jointly considered to characterize antibiotic resistomes. • Antibiotic resistomes in sediments of Chaobai River were systematically investigated. • Correlations between ARGs and associated genes were revealed via ARG-like contigs. A metagenomic analysis framework was proposed to characterize the antibiotic resistomes and their associations in the river environment. [ABSTRACT FROM AUTHOR]

Increasing anthropogenic contamination poses a significant threat to groundwater security. Identifying potential contamination sources and apportioning their corresponding contributions are of vital importance for the prevention of contamination and management of groundwater resources. In this study, principal component analysis (PCA), modified grey relational analysis (MGRA), absolute principal component score-multiple linear regression (APCS-MLR), and positive matrix factorization (PMF) receptor modeling technologies were employed to evaluate the groundwater quality and apportion the potential contamination sources in the Lalin river basin, a main grain production district in the northeast of China. The contamination assessment with PCA and MGRA suggested that the groundwater in Lalin river basin was polluted due to human activities. The PCA method identified five and four potential contamination sources in wet and dry seasons, respectively, and the main sources were basically same. The APCS-MLR and PMF methods apportioned the source contributions to each groundwater quality variable. The final results showed that agricultural sources including waste water, agrochemicals and fertilizers were identified as the main sources of groundwater contamination both in wet and dry seasons. In addition, groundwater management strategies learned from the advanced experiences were discussed to protect the groundwater system in that region. Unlabelled Image • Groundwater contamination, risk and sources in Lain River Basin were studied in wet and dry seasons. • Agricultural activities was recognized as the significant pollution sources in the groundwater of Lalin River Basin. • The contributions of potential contamination sources of groundwater were comparative studied by APCS-MLR and PMF. • Some suggestions are presented to promote groundwater management. [ABSTRACT FROM AUTHOR]

Heavy metals (HMs) in lake sediments have aroused long-term attention due to their persistent threat to the lake ecosystems. Study into the pollution characteristics and potential sources of HMs in lakes, especially those heavily influenced by human activities, can give some insights to prevent and control the environmental risks of HMs. Lake Tai is the China's third largest freshwater lake but has been a drastic example of water pollution in recent decades. Here, we systematically investigated the characterization of pollution, risk and sources of HMs in the sediments of Lake Tai and its surrounding soils using several methods and tools. Specifically, a total of 46 sediments and 578 soils were collected from the study area, and geochemical approaches (geo-accumulation index and enrichment factor) and pollution indexes were jointly used to reveal the contamination characteristics of HMs. Meanwhile, the potential ecological risk index and probabilistic model of health risk assessment were employed to understand the environmental risk of HMs. Further, absolute principle component score-multiple linear regression and positive matrix factorization models were comparatively applied to apportion the sources of HMs. Results showed that various metals including Cd, Cr, As, Hg, Pb, and Cu appeared contamination level in varying degrees both in the sediments and soils. In particular, Cd, As and Hg were identified as the significant contaminants and presented moderate ecological risk. As a whole, the health risk levels of metals were acceptable. Source apportionment suggested that industrial discharge, agricultural activities, atmospheric deposition and natural source were the potential origins of HMs in this area. Among them, anthropogenic activities were the largest dominator of HMs with contribution of >75%. The study will advance our knowledge on HMs in lake and its surrounding soils and provide reference for policy maker to design migration strategies for protecting the lake ecosystems. Unlabelled Image • Contamination risk and sources of HMs in the sediments of Lake Tai were studied. • Cd, As and Hg were recognized as the significant contaminants. • Contamination risk of HMs in the sediments of Lake Tai was higher than surrounding soils. • Anthropogenic activities were the largest dominator of HMs with contributions of >75%. [ABSTRACT FROM AUTHOR]

The peri-urban rivers are one of the critical interfaces between urban-rural symbiotic ecosystems and appear to be a reservoir of antibiotic resistance genes (ARGs) in the environment. To prevent the transmission risks of ARGs between peri-urban river and human, it is essential to explore the prevalence and source of ARGs in the environment for designing potential mitigation strategies. In this study, we focused on the characterization and source-tracking of ARGs in the sediments of a typical peri-urban river in Beijing, Chaobai River. Twenty-seven ARGs frequently reported in the environment, and two integrons (intI1 and intI2) were detected using high-throughput quantitative PCR. The profile of bacterial community was determined by performing 16S rRNA gene sequencing. Meanwhile, crAssphage , a novel recently-discovered DNA bacteriophage, was employed for tracking the contribution of human fecal pollution to the prevalence of ARGs. Results showed that the targeted ARGs were detected widely in the sediments of Chaobai River. Relatively, the abundances of ARGs in downstream were higher than those in the upstream, likely suggesting a gradient impact of anthropogenic activities along the river. Remarkably, the int1 gene was correlated significantly with most of the ARGs and might be the key factor influencing the shaping of ARGs in the river sediments. However, no significant correlations were observed between the ARGs and selective pressure factors, including antibiotics and metals. Of the identified 1039 genera, Escherichia - Shigella , Bacteroides , Arcobacter , Dechloromonas and Pseudomonas were the top most abundant organisms. Microbial source tracking based on the crAssphage annotation suggested that human sewage might be one of the potential sources of resistance bacteria in the river sediments. The study can advance our knowledge about ARGs in the peri-urban river and provides a management reference for ARG pollution control. Unlabelled Image • A variety of ARGs were widely detected in the sediments of a peri-urban river. • Class 1 integron potentially affected the shaping of ARGs in the river. • A gradient in anthropogenic impacts on ARGs was observed along the river. • CrAssphage-based metagenomics approach was used for microbial source tracking. • Human fecal pollution was identified as potential source of ARGs in the river. [ABSTRACT FROM AUTHOR]

Abstract The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments). In total, 442 ARG subtypes belonging to 22 ARG types were detected in the human-impacted river sediments with an abundance range of 1.1 × 10−1–8.1 × 10−1 copy of ARG per copy of 16S-rRNA gene. The most abundant and diverse ARGs were commonly associated with antibiotics that have been extensively used in that area, likely indicating the spread of ARGs in river environments because of the selective pressure resulting from antibiotic use. As a whole, anthropogenic activities were the dominant contributor of major ARG types, for example, occupying 100% for sulfonamide-ARGs, 97% for beta-lactam-ARGs, 94% for aminoglycoside-ARGs and 64% for tetracycline-ARGs. This study provides insights into the role of human activities in accelerating the dissemination and proliferation of ARGs in urban river environment and draws attention to controlling the use and discharge of antibiotics for protection of public health. Graphical abstract Unlabelled Image Highlights • Characterization of ARGs in Chaobai River was investigated using metagenomics. • 442 ARG subtypes belonging to 22 ARG types were detected in the river sediments. • Bacitracin- and sulfonamide-ARGs were the most abundant types. • 95 ARG subtypes were shared by the river sediments and pristine environments. • Anthropogenic activities contributed >95% for sulfonamide and beta-lactam ARGs. [ABSTRACT FROM AUTHOR]

Colon cancer is one of the most common types of cancer and more than 80% of colon cancer cases are associated with Wnt-β-catenin signaling activation. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a multi-functional long non-coding RNA that is overexpressed in many types of cancers, including colon cancer. In this study, MALAT1 and β-catenin were found to be overexpressed in tumor samples from 62 patients with colon cancer. A positive correlation was identified between MALAT1 levels and β-catenin protein levels in tumors. MALAT1 was found to upregulate β-catenin protein levels in HCT116 and LOVO cells without changing the mRNA expression levels. β-catenin degradation was confirmed to be upregulated in MALAT1 -knockdown cells and inhibited in cells overexpressing MALAT1 overexpressing. MALAT1 was then identified as a negative regulator of GSK-3β; it did so via promotion of H3K27 trimethylation of the promoter region. In conclusion, MALAT1 is an oncogene in colon cancer, which inhibits β-catenin degradation by upregulating H3K27 trimethylation and repressing GSK-3β expression. • MALAT1 is overexpressed in colon cancer. • MALAT1 is positively correlated with β-catenin protein levels. • MALAT1 inhibits β-catenin protein degradation by repressing GSK-3β expression. • MALAT1 inhibits GSK-3β expression by upregulating H3K27 trimethylation. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance is a growing public health concern, and environment is regarded as an important reservoir and dissemination route for antibiotic resistance genes (ARGs). To prevent and control ARG pollution, it is essential to correctly disentangle source-sink relationship of ARGs in the environment. However, accurately apportioning sources of ARGs is still a big challenge due to the complex interaction of multiple sources and contaminants in the environment with changing dynamics. In this study, we addressed this problem and focused on identifying the potential sources of ARGs in a peri-urban river by jointly utilizing two novel microbial source tracking methods. To attain the objective, sediment/water samples were collected from the peri-urban river and four ARG-associated ecotypes including effluents of sewage treatment plants (STPs), STP influent, chicken manures and pig manures. The high-throughput profilings of ARGs and microbial taxa in the river sediments and the four ecotypes were comprehensively characterized in combination of shotgun sequencing and metagenomic assembly analysis. CrAssphage , a recently-discovered DNA bacteriophage, was employed to track the impact of human fecal pollution on ARGs in the river sediments. Further, SourceTracker, a machine-learning classification tool, was used for quantifying the contributions of potential sources to ARGs in the river sediments based on the metagenomic signatures of ARGs and microbial taxa. In total, 888 ARG subtypes belonging to 29 ARG types were detected across all samples, including mcr-1 and a range of carbapenemases types. Statistical analyses suggested different ecotypes generally had distinct profiles of both ARGs and microbial taxa, while the ARG compositions were significantly correlated with the microbial community. Source tracking with crAssphage showed the presence of ARGs in the river sediments might be largely impacted by the extent of human fecal pollution, which was also confirmed by the analyses of SourceTracker that the discharge from STPs was the largest contributor of ARGs (81.6–92.1%) and microbes (49.3–68.1%) in the river sediments. Results of the study can help us to better understand the characterization of ARGs in the peri-urban ecosystem and to design effective prevention and control strategies for reducing ARG dissemination. • 888 ARG subtypes belonging to 29 ARG types were detected in the study. • CrAssphage was a good marker for tracking human fecal pollution in the study area. • Effluent of STPs was the largest contributor of ARGs in the river sediments. [ABSTRACT FROM AUTHOR]