Decoupling the Dynamics of Bacterial Taxonomy and Antibiotic Resistance Function in a Subtropical Urban Reservoir as Revealed by High-Frequency Sampling

A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions

Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.

Hydraulic conditions control the abundance of antibiotic resistance genes and their potential host microorganisms in a frequently regulated river-lake system

Antibiotic resistance genes (ARGs) are a growing problem that is widespread in river-lake ecosystems, where they pose a threat to the aquatic environment's health and public safety. These systems serve as critical nodes in water management, as they facilitate the equitable allocation of water resources through long-term and frequent water diversions. However, hydrological disturbances associated with water-regulation practices can influence the dynamics of their potential host microorganisms and associated resistance genes. Consequently, identifying the key ARGs and their resistance mechanisms in heavily regulated waters is vital for safeguarding human health and that of river-lake ecosystems. In this study, we examined the impact of water-regulation factors on ARGs and their hosts within a river-lake continuum using 16S rRNA and metagenomic sequencing. We found that a significant increase in ARG abundance during regulation periods (p < 0.05), especially in the aquatic environment. Key resistance genes were macB, tetA, evgS, novA, and msbA, with increased efflux pinpointed as their principal resistance mechanism. Network analysis identified Flavobacteriales, Acinetobacter, Pseudomonas, Burkholderiaceae, and Erythrobacter as key potential host microorganisms, which showed increased abundance within the water column during regulation periods (p < 0.05). Flow velocity and water depth both drove the host microorganisms and critical ARGs. Our findings underscore the importance of monitoring and mitigating the antibiotic resistance risk during water transfers in river-lake systems, thereby supporting informed management and conservation strategies.

Characterization of the soil resistome and mobilome in Namib Desert soils

The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.

Mass-immigration shapes the antibiotic resistome of wastewater treatment plants

Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily (inter-day) variations of ARG profiles in the whole process (influent-INF, activated sludge-AS and effluent-EF) of WWTPs is still lacking. Here, 285 ARGs and ten mobile gene elements were monitored in seven WWTPs in Xiamen for seven days via high-throughput qPCR. The average daily load of ARGs to WWTPs was about 1.32 × 1020 copies/d, and a total of 1.56 × 1018 copies/d was discharged to the environment across the entire city. Stochastic processes were the main force determining the assembly of ARG communities during sampling campaign, with their relative importance ranked in the order of INF > EFF > AS. There're little daily variations in ARG richness, abundance, β-diversity composition as well as assembly mechanisms. The results of SourceTracker, variation partitioning analysis, and hierarchical partitioning analysis indicated that bacteria and ARGs from upstream treatment processes played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment processes. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems

Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.

Ecological insight into antibiotic resistome of ion-adsorption rare earth mining soils from south China by metagenomic analysis

Antibiotic resistome has led to growing global threat to public health. Rare earth elements play important roles in modern society and mining activity for them has caused serious impact on soil ecosystems. However, antibiotic resistome in, especially, ion-adsorption rare earth-related soils is still poorly understood. In this work, soils were collected from ion-adsorption rare earth mining areas and adjacent regions of south China and metagenomic analysis was employed for profile, driving factors and ecological assembly of antibiotic resistome in the soils. Results show prevalence of antibiotic resistance genes conferring resistance to tetracycline/fluoroquinolone (adeF), peptide (bcrA), aminoglycoside (rpsL), tetracycline (tet(A)) and mupirocin (mupB) in ion-adsorption rare earth mining soils. Profile of antibiotic resistome is accompanied by its driving factors, i.e., physicochemical properties (La, Ce, Pr, Nd and Y of rare earth elements in 12.50-487.90 mg kg^-1), taxonomy (Proteobacteria, Actinobacteria) and mobile genetic elements (MGEs, plasmid pYP1, Transposase_20). Variation partitioning analysis and partial least-squares-path modeling demonstrate that taxonomy is the most important individual contributor and pose most direct/indirect effect to antibiotic resistome. Further, null model analysis reveals stochastic processes as dominant ecological assembly of antibiotic resistome. This work advances our knowledge on antibiotic resistome with emphasis on ecological assembly in ion-adsorption rare earth-related soils for ARGs mitigation, mining management and mine restoration.

Usage of antibiotics in aquaculture and the impact on coastal waters

For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria

Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10⁶ cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.

Storm promotes the dissemination of antibiotic resistome in an urban lagoon through enhancing bio-interactions

Antibiotic-resistance genes (ARGs) and resistant bacteria (ARB) are abundant in stormwater that could cause serious infections, posing a potential threat to public health. However, there is no inference about how stormwater contributes to ARG profiles as well as the dynamic interplay between ARGs and bacteria via vertical gene transfer (VGT) or horizontal gene transfer (HGT) in urban water ecosystems. In this study, the distribution of ARGs, their host communities, and the source and community assembly process of ARGs were investigated in Yundang Lagoon (China) via high-throughput quantitative PCR, 16S rRNA gene amplicon sequencing, and application of SourceTracker before, after and recovering from an extreme precipitation event (132.1 mm). The abundance of ARGs and mobile genetic elements (MGEs) was the highest one day after precipitation and then decreased 2 days after precipitation and so on. Based on SourceTracker and NMDS analysis, the ARG and bacterial communities in lagoon surface water from one day after precipitation were mainly contributed by the wastewater treatment plant (WWTP) influent and effluent. However, the contribution of WWTP to ARG communities was minor 11 days after the precipitation, suggesting that the storm promoted the ARG levels by introducing the input of ARGs, MGEs, and ARB from point and non-point sources, such as sewer overflow and land-applied manure. Based on a novel microbial network analysis framework, the contribution of positive biological interactions between ARGs and MGEs or bacteria was the highest one day after precipitation, indicating a promoted VGT and HGT for ARG dissemination. The microbial networks deconstructed 11 days after precipitation, suggesting the stormwater practices (e.g., tide gate opening, diversion channels, and pumping) alleviated the spread of ARGs. These results advanced our understanding of the distribution and transport of ARGs associated with their source in urban stormwater runoff.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

Controlling AMR in the Pig Industry: Is It Enough to Restrict Heavy Metals?

Heavy metals have the potential to influence the transmission of antimicrobial resistance (AMR). However, the effect on AMR caused by heavy metals has not been clearly revealed. In this study, we used a microcosm experiment and metagenomics to examine whether common levels of Cu and Zn in pig manure influence AMR transmission in manured soil. We found that the abundance of 204 ARGs significantly increased after manure application, even though the manure did not contain antibiotic residuals. However, the combined addition of low Cu and Zn (500 and 1000 mg/kg, respectively) only caused 14 ARGs to significantly increase, and high Cu and Zn (1000 and 3000 mg/kg, respectively) caused 27 ARGs to significantly increase. The disparity of these numbers suggested that factors within the manure were the primary driving reasons for AMR transmission, rather than metal amendments. A similar trend was found for biocide and metal resistance genes (BMRGs) and mobile genetic elements (MGEs). This study offers deeper insights into AMR transmission in relation to the effects of manure application and heavy metals at commonly reported levels. Our findings recommend that more comprehensive measures in controlling AMR in the pig industry are needed apart from restricting heavy metal additions.

Biogeographical Patterns of Bacterial Communities and Their Antibiotic Resistomes in the Inland Waters of Southeast China

Freshwater ecosystems are important sources of drinking water and provide natural settings for the proliferation and dissemination of bacteria and antibiotic resistance genes (ARGs). However, the biogeographical patterns of ARGs in natural freshwaters and their relationships with the bacterial community at large scales are largely understudied. This is of specific importance because data on ARGs in environments with low anthropogenic impact is still very limited. We characterized the biogeographical patterns of bacterial communities and their ARG profiles in 24 reservoirs across southeast China using 16S rRNA gene high-throughput sequencing and high-throughput-quantitative PCR, respectively. We found that the composition of both bacterial communities and ARG profiles exhibited a significant distance-decay pattern. However, ARG profiles displayed larger differences among different water bodies than bacterial communities, and the relationship between bacterial communities and ARG profiles was weak. The biogeographical patterns of bacterial communities were simultaneously driven by stochastic and deterministic processes, while ARG profiles were not explained by stochastic processes, indicating a decoupling of bacterial community composition and ARG profiles in inland waters under relatively low-human-impact at a large scale. Overall, this study provides an overview of the biogeographical patterns and driving mechanisms of bacterial community and ARG profiles and could offer guidance and reference for the control of ARGs in drinking water sources. IMPORTANCE Antibiotic resistance has been a serious global threat to environmental and human health. The "One Health" concept further emphasizes the importance of monitoring the large-scale dissemination of ARGs. However, knowledge about the geographical patterns and driving mechanisms of bacterial communities and ARGs in natural freshwater environments is limited. This study uncovered the distinct biogeographical patterns of bacterial communities and ARG profiles in inland waters of southeast China under low-anthropogenic impact at a large scale. This study improved our understanding of ARG distribution in inland waters with emphasis on drinking water supply reservoirs, therefore providing the much-needed baseline information for future monitoring and risk assessment of ARGs in drinking water resources.

Linkage and driving mechanisms of antibiotic resistome in surface and ground water: Their responses to land use and seasonal variation

Antibiotic resistance in the environment, mostly mediated by antibiotic resistance genes (ARGs), has posed a threat to ecological and human health. Contamination of surface water and groundwater with ARGs has become a serious environmental concern. However, the distinctions and similarities across ARG profiles, the various ecological processes associated with ARGs, the driving mechanisms for ARG profiles in surface water and groundwater, and how they respond to land use and seasonal variation remain unknown. To tackle these issues, the contamination of ARGs in surface water and groundwater in central China was investigated using metagenomic technology. The results indicated that seasonal changes in ARG abundance and diversity were inconsistent across surface water and groundwater, and that the relationship between ARGs in surface water and groundwater was stronger during the rainy season. Land use had a greater effect on ARGs in surface water than in groundwater and was stronger during the dry season than during the rainy season. More interestingly, the ideal buffer zones with the greatest impact of land use on the ARGs of surface water and groundwater had distinct radii: 1500 m for both dry and rainy seasons in surface water, and 1000 m for dry season and 500 m for rainy season in groundwater. Furthermore, stochastic mechanisms mediated by mobile gene elements (MGEs) contribute significantly more to ARG assemblages than deterministic processes, particularly in groundwater. Furthermore, our results also showed that ARG enrichment in microbial communities was host- dependent, and the risk of ARGs in groundwater was greater both during the rainy season and dry season. In conclusion, the findings have improved our understanding of the relationship and driving mechanisms of ARGs in surface and ground water, as well as their responses to land use and seasonal variation, which may be beneficial for limiting ARG pollution in a watershed with high levels of anthropogenic activity.

KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds

Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: bla_KPC (n = 20), bla_GES-5 (n = 6), and bla_VIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that bla_KPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, bla_GES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE.

Precision early detection of invasive and toxic cyanobacteria: A case study of Raphidiopsis raciborskii

Blooms of the toxic cyanobacterium, Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii), are becoming a major environmental issue in freshwater ecosystems globally. Our precision prevention and early detection of R. raciborskii blooms rely upon the accuracy and speed of the monitoring method. A duplex digital PCR (dPCR) monitoring approach was developed and validated to detect the abundance and toxin-producing potential of R. raciborskii simultaneously in both laboratory spiked and environmental samples. Results of dPCR were strongly correlated with traditional real time quantitative PCR (qPCR) and microscopy for both laboratory and environmental samples. However, discrepancies between methods were observed when measuring R. raciborskii at low abundance (1 - 10⁵ cells L ^- 1), with dPCR showing a higher precision compared to qPCR at low cell concentration. Furthermore, the dPCR assay had the highest detection rate for over two hundred environmental samples especially under low abundance conditions, followed by microscopy and qPCR. dPCR assay had the advantages of simple operation, time-saving, high sensitivity and excellent reproducibility. Therefore, dPCR would be a fast and precise monitoring method for the early warning of toxic bloom-forming cyanobacterial species and assessment of water quality risks, which can improve prediction and prevention of the impacts of harmful cyanobacterial bloom events in inland waters.

Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China

Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.

Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens

Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

BACKGROUND

Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.

RESULTS

Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.

CONCLUSIONS

Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.

Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir

Investigation of bacterial community dynamics across different time scales is important for understanding how environmental conditions drive community change over time. Bacterioplankton from the surface waters of a subtropical urban reservoir in southeast China were analyzed through high-frequency sampling over 13 months to compare patterns and ecological processes between short (0‒8 weeks), medium (9‒24 weeks) and long (25‒53 weeks) time intervals. We classified the bacterial community into different subcommunities: abundant taxa (AT); conditionally rare taxa (CRT); rare taxa (RT). CRT contributed > 65% of the alpha-diversity, and temporal change of beta-diversities was more pronounced for AT and CRT than RT. The bacterial community exhibited a directional change in the short- and medium-time intervals and a convergent dynamic during the long-time interval due to a seasonal cycle. Cyanobacteria exhibited a strong succession pattern than other phyla. CRT accounted for > 76% of the network nodes in three stations. The bacteria-environment relationship and deterministic processes were stronger for large sample size at station G (n = 116) than small sample size at stations C (n = 12) and L (n = 22). These findings suggest that a high-frequency sampling approach can provide a better understanding on the time scales at which bacterioplankton can change fast between being abundant or rare, thus providing the facts about environmental factors driving microbial community dynamics. Patterns and processes in alpha- and beta-diversities and community assembly of bacterioplankton differ among different time intervals (short-, medium- and long-time intervals) and different subcommunities (abundant, conditionally rare and rare taxa) in a subtropical urban reservoir, demonstrating the importance of temporal scale and high-frequency sampling in microbial community ecology.

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes (ARGs) in urban aquatic ecosystems. However, limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems. Here, we employed high-throughput quantitative PCR (HT-qPCR) to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon, China. The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments, highlighting the role of anthropogenic activities in ARG pollution. Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-, Deltaproteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Synergistetes were the potential hosts of ARGs. The partial least squares-path modeling (PLS-PM) analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles, via biotic factors, respectively. The horizontal (mediated by mobile genetic elements) and vertical (mediated by prokaryotic communities) gene transfer may directly contribute the most to drive the abundance and composition of ARGs, respectively. Furthermore, the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes. Overall, this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Urban ponds as hotspots of antibiotic resistome in the urban environment

The occurrence, dissemination and assembly processes of antibiotic resistance genes (ARGs) in urban water ecosystems are far from being understood. Here, we examined the diversity and abundance of ARGs in urban water ecosystems including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city, China through high-throughput quantitative PCR. A total of 237 ARGs were identified, where multidrug, aminoglycoside and beta-lactamase resistance genes were the most abundant. Urban ponds had a comparatively high diversity and large numbers of shared ARGs with IFs and EFs. The average absolute abundance of ARGs (1.38 × 10⁷ copies/mL) and mobile genetic elements (MGEs) (4.19 × 10⁶ copies/mL) in ponds were only one order of magnitude lower than those of IFs, but higher than those of EFs and reservoirs. Stochastic processes dominated the ARG community assembly in IFs and ponds due to the random horizontal gene transfer caused by MGEs. These results imply that urban ponds are hotspots of ARGs. We further identified 25, 3, and 11 indicator ARGs for tracing the ARG contamination from IFs, EFs and ponds, respectively. Our study represents the first to highlight the role of urban ponds in the dissemination of ARGs.

Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

Occurrence and distribution of antibiotic resistance genes in various rural environmental media

Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.

Urbanization drives riverine bacterial antibiotic resistome more than taxonomic community at watershed scale

Although the occurrence and distribution of antibiotic resistance genes (ARGs) in various aquatic ecosystems are well explored, understanding of the ecological processes and mechanisms governing the composition and dynamics of bacterial ARGs still remains limited across space and time. Here, we used high-throughput approaches to detect spatial patterns of bacterial ARGs and operational taxonomic units (OTUs) in an urbanizing subtropical watershed, Xiamen, southeast China over a five-year period. At watershed scale, the OTU profiles were undergoing a directional change, but the ARG profiles showed a high stability or stochastic change over time. Compared with the upstream and midstream, the richness, absolute abundance, normalized abundance and diversity of ARGs were significantly higher in the downstream waters. Our results revealed a clear rural-urban disparity in ARG and OTU profiles which were mainly governed by deterministic and stochastic assembly processes, respectively. With the increase of urban building area along the river, the ecological processes of ARG profiles shifted from stochastic to deterministic. In downstream waters, the bacterial ARG profiles were much more stable than bacterial OTUs. Further, our results indicated that both human-dominated environment (e.g., land use) and mobile genetic elements (MGEs) played an important role in shaping the ARG profiles and dynamics. Overall, this was a response to spatially extensive human-landscape interactions that included urban development in the river downstream region, which were common across subtropical coastal cities of China and can alter the ARG profile dynamics along rural-urban gradient. Therefore, watershed management actions aiming at reducing threats posed by ARGs in urbanizing watershed should first consider the surrounding urbanization level and the mode and intensity of human activity. Our findings also imply that due to the decoupling of bacterial function and taxonomy, both aspects should be studied separately.