Urbanization drives the succession of antibiotic resistome and microbiome in a river watershed

Ions and nanoparticles of Ag and/or Cd metals in a model aquatic microcosm: Effects on the abundance, diversity and functionality of the sediment bacteriome

Metals can be adsorbed on particulate matter, settle in sediments and cause alterations in aquatic environments. This study assesses the effect of Ag and/or Cd, both in ionic and nanoparticle (NP) forms, on the microbiome of sediments. For that purpose, aquatic controlled-microcosm experiments were exposed to an environmentally relevant and at tenfold higher doses of each form of the metals. Changes in the bacteriome were inferred by 16S rDNA sequencing. Ionic Ag caused a significant decrease of several bacterial families, whereas the effect was opposite when mixed with Cd, e.g., Desulfuromonadaceae family; in both cases, the bacteriome functionalities were greatly affected, particularly the nitrogen and sulfur metabolism. Compared to ionic forms, metallic NPs produced hardly any change in the abundance of microbial families, although the α-biodiversity of the bacteriome was reduced, and the functionality altered, when exposed to the NPs´ mixture. Our goal is to understand how metals, in different forms and combinations, released into the environment may endanger the health of aquatic ecosystems. This work may help to understand how aquatic metal pollution alters the structure and functionality of the microbiome and biogeochemical cycles, and how these changes can be addressed.

Key environmental exposure pathways to antimicrobial resistant bacteria in southern Malawi: A SaniPath approach

Antimicrobial resistance (AMR) poses a severe global health threat, yet the transmission pathways of AMR within communal public environments, where humans and animals interact, remain poorly explored. This study investigated AMR risk pathways, prevalence, and seasonality of extended-spectrum β-lactamase (ESBL) producing E. coli and K. pneumoniae, and observed practices contributing to environmental contamination within urban, peri-urban, and rural Malawi. Using the SaniPath tool, in August 2020, transect walks across three Malawian study sites identified potential AMR exposure pathways, including drains, standing water, soil, and areas of communal hand contact. Subsequently, from September-2020 to August-2021, 1440 environmental samples were collected at critical points along exposure routes (n = 40/month from each site). These underwent microbiological analysis using chromogenic agar techniques to detect the presence of ESBL E. coli and ESBL K. pneumoniae. Results showed the highest ESBL prevalence in urban environments (68.1 %, 95%CI = 0.64-0.72, p < 0.001) with a higher ESBL presence seen in drains (58.8 %, 95%CI = 055-0.62, p < 0.001) and soil (54.1 %, 95%CI = 0.46-0.62, p < 0.001) compared to other pathways. Environmental contamination was attributed to unavailability and poor condition of sanitation and hygiene infrastructure based on key informant interviews with community leaders (n = 9) and confirmed by independent observation. ESBL prevalence varied between seasons (χ2 (2,N = 1440) = 10.89, p = 0.004), with the highest in the hot-dry period (55.8 % (n = 201)). Prevalence also increased with increased rainfall (for ESBL E.coli). We highlight that community environments are likely to be a crucial component in AMR transmission, evident in the abundance of ESBL bacteria in identified exposure pathways. Additionally, poor sanitation infrastructure and practices coupled with seasonal dynamics further affect the presence of ESBLs in communal environments. Therefore, a context appropriate whole system approach that tackles infrastructure and behavioural factors, supported by effective surveillance is required to impact AMR and a range of aligned development challenges in these settings.

Mapping the profiles and underlying driving mechanisms of the antibiotic resistome and microbiome within a subtropical complex river watershed

Antibiotic resistance is an escalating global concern, leading to millions of annual deaths worldwide. Human activities can impact antibiotic resistance gene (ARG) prevalence in aquatic ecosystems, but the intricate interplay between anthropogenic disturbances and river system resilience, and their respective contributions to the dynamics of different river segments, remains poorly understood. In this study, we investigate the antibiotic resistome and microbiome in water and sediment samples from two distinct sub-watersheds within a specific watershed. Results show a decrease in the number of core ARGs downstream in water, while sediments near densely populated areas exhibit an increase. PCoA ordination reveals clear geographic clustering of resistome and microbiome among samples from strong anthropogenic disturbed areas, reservoir areas, and estuary area. Co-occurrence networks highlight a higher connectivity of mobile genetic elements (MGEs) in disturbed areas compared to reservoir areas, presenting a threat to densely populated areas. Water quality parameters and antibiotics concentration were the key factors shaping the ARG profiles in sediment samples from urban regions. Overall, our study reveals distinct patterns of ARGs in sediment and water samples, emphasizing the importance of considering both anthropogenic and natural factors in comprehending and managing ARG distribution in river systems.

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge

Background

Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability.

Methods

In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis.

Results

The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments.

Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes

Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.

Occurrence and prevalence of antimicrobial resistance in urban karst groundwater systems based on targeted resistome analysis

Antimicrobial resistance (AMR) is a global crisis threatening human, animal, and environmental health. The natural environment, specifically water resources, has been recognized as a reservoir and dissemination pathway for AMR; however, urban karst aquifer systems have been overlooked. This is a concern as these aquifer systems provide drinking water to about 10 % of the global population; yet, the urban influence on the resistome in these vulnerable aquifers is sparingly explored. This study used high-throughput qPCR to determine the occurrence and relative abundance of antimicrobial resistant genes (ARG) in a developing urban karst groundwater system in Bowling Green, KY. Ten sites throughout the city were sampled weekly and analyzed for 85 ARGs, as well as seven microbial source tracking (MST) genes for human and animal sources, providing a spatiotemporal understanding of the resistome in urban karst groundwater. To further understand ARGs in this environment, potential drivers (landuse, karst feature type, season, source of fecal pollution) were considered in relation to the resistome relative abundance. The MST markers highlighted a prominent human influence to the resistome in this karst setting. The concentration of targeted genes varied between the sample weeks, but all targeted ARGs were prevalent throughout the aquifer regardless of karst feature type or season, with high concentrations captured for sulfonamide (sul1), quaternary ammonium compound (qacE), and aminoglycoside (strB) antimicrobial classes. Higher prevalence and relative abundance were detected during the summer and fall seasons, as well as at the spring features. Linear discriminant analysis suggested that karst feature type had higher influence on ARGs in the aquifer compared to season and the source of fecal pollution had the least influence. These findings can contribute to the development of effective management and mitigation strategies for AMR.

Linking pharmaceutical residues to dissolved organic matter and aquatic bacterial communities in a highly urbanized bay

Pharmaceuticals are causing environmental concerns associated with their widespread distribution in aquatic ecosystems. The environmental fate and behavior of pharmaceutical residues are related to dissolved organic matter and bacterial communities, both of which are strongly influenced by human activities. However, the relationships among pharmaceutical pollution, dissolved organic matter pool, and bacterial community structure under the pressure of human activities are still unclear, especially in highly urbanized bay areas. In this study, we investigated the occurrence and distribution of 35 pharmaceuticals in a typical urbanized bay (Hangzhou Bay) in Eastern China, and analyzed their relationships with dissolved organic matter and aquatic bacterial community structure. The target pharmaceuticals were ubiquitously detected in surface water samples, with their concentrations ranging from undetectable to 263 ng/L. The detected pharmaceuticals were mostly sulfonamides, macrolides, antidepressants, and metabolites of stimulants. Significant positive correlations were observed between the concentrations of pharmaceuticals and the intensity of human activities. Strong correlations also emerged between the concentration of antidepressants and the speed of urban expansion, as well as between the concentration of cardiovascular drugs and the population density or nightlight index. Three fluorescent components (protein-like C1, terrestrial humic-like C2, protein tryptophan-like C3) were significantly positively correlated with the total concentration of pharmaceuticals. Pharmaceutical pollution reshaped aquatic bacterial communities, based on the close correlation observed between pharmaceutical concentration and bacterial community structure. The results elucidate the potential dynamics of dissolved organic matter pool and aquatic bacterial communities in response to pharmaceutical pollution in urbanized bay ecosystems.

Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens

Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sediments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urbanization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.