Impact of sulfamethoxazole on a riverine microbiome

The phototoxicity of sulfamethoxazole stress on pakchoi cabbage (Brassica rapa var. chinensis) seedlings: From the perspective of photoreaction and omics analysis

The increasing use of antibiotics has attracted widespread attention to their environmental risks. However, the phototoxicity of sulfonamide antibiotics to plants remain unclear. In this study, the mechanism of the effect of sulfamethoxazole on photosynthesis of pakchoi cabbage (Brassica rapa var. chinensis) was investigated. The results showed that sulfamethoxazole inhibited the growth of pakchoi cabbage and produced photosynthetic toxicity. The growth inhibition rates increased with concentration, the root and shoot weight were 76.02 % and 47.04 % of the control, respectively, with stay-greens phenomenon in 4 mg·L-1 sulfamethoxazole treatment. Chlorophyll precursors (protoporphyrin IX (Proto IX), Mg-proto IX, and protochlorophyllide (Pchlide), 5-aminolevulinic acid (ALA), and porphobilinogen (PBG)) were 1.38-, 1.26-, 1.12-, 1.71-, and 0.96-fold of the control, respectively; photosynthetic pigments (chlorophyll a, chlorophyll b, and carotenoids) were 1.26-, 1.39-, and 1.03-fold of the control, respectively. Respiration rate was 271.42 % of the control, whereas the net photosynthetic rate was 50.50 % of the control. The maximum photochemical quantum yield of PSII (Fv/Fm), the actual photosynthetic efficiency (Y(II)), the quantum yield of non-regulated energy dissipation (Y(NO)), the apparent electron transfer efficiency of PSII (ETR) under actual light intensity were affected, and chloroplast swelling was observed. Proteomic analysis showed that photosynthesis-related pathways were significantly up-regulated, biological processes such as light response, carbohydrates, and reactive oxygen species were activated. Metabolomic analysis revealed that the tricarboxylic acid cycle (TCA cycle) and carbohydrate catabolism were stimulated significantly (p < 0.05), sugars and amino acids were increased to regulate and enhance the resilience of photosynthesis. While folate biosynthesis and ribosomal pathways were significantly down-regulated, the synthesis and translation processes of amino acids and nucleotides were inhibited.

The fate of sulfamethoxazole in microcosms of the macrophyte Schoenoplectus californicus and its impact on microbial communities

Sulfamethoxazole is a widely used antibiotic frequently found as an environmental pollutant. It can alter microbial communities and increase antibiotic resistance, becoming a public health risk. Constructed wetlands have the potential for removing sulfamethoxazole from polluted waters, but the role of different macrophytes in this process is not well understood. We investigated the fate of sulfamethoxazole and its effect on bacterial communities in microcosms containing Schoenoplectus californicus, an altitude-tolerant macrophyte. Within the first ten hours after introducing sulfamethoxazole (initial concentration 5 mg/L) to the microcosms, the concentration in the liquid phase significantly differed between microcosms with and without S. californicus. However, over the long term (15 and 30 days post-addition), the removal percentage (around 75%) in the liquid phase was not significantly influenced by S. californicus, indicating that sediments might be primarily responsible for removing the antibiotic. The presence of S. californicus promoted algae growth in the microcosms, and we determined that algae contributed to sulfamethoxazole removal from the liquid phase, likely through adsorption. Additionally, we characterized bacterial communities in the microcosm sediments via nanopore sequencing to identify changes following sulfamethoxazole addition. The relative abundance of Proteobacteria increased from 37-46% to 48-99% with the addition of the antibiotic. Conversely, the relative abundance of cyanobacteria decreased significantly after sulfamethoxazole was added (from 17-35% to less than 2%), suggesting it may serve as a biological marker for sulfamethoxazole pollution. In addition, the functional profile of the community was estimated from taxonomic diversity using PICRUST.

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.

Metabolic response of bacterial community to sodium hypochlorite and ammonia nitrogen affected the antibiotic resistance genes in pipelines biofilm

The biofilm is important for the antibiotic resistance genes (ARGs) propagation in drinking water pipelines. This study investigated the influence of chlorine disinfection and ammonia nitrogen on the ARGs in pipelines biofilm using metagenomic and metabolomics analysis. Chlorine disinfection reduced the relative abundance of unclassified_c_Actinobacteria, Acidimicrobium, and Candidatus_Pelagibacter to 394-430 TPM, 114-123 TPM, and 49-54 TPM, respectively. Correspondingly, the ARGs Saur_rpoC_DAP, macB, and mfd was reduced to 8-12 TPM, 81-92 TPM and 30-35 TPM, respectively. The results of metabolomics suggested that chlorine disinfection suppressed the pathways of ABC transporters, fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and biosynthesis of amino acids. These pathways were related to the cell membrane integrality and extracellular polymeric substances (EPS) secretion. Chlorine disinfection induced the decrease of EPS-related genes, resulting in the lower relative abundance of bacterial community and their antibiotic resistance. However, added approximately 0.5 mg/L NH3-N induced up-regulation of these metabolic pathways. In addition, NH3-N addition increased the relative abundance of enzymes related to inorganic and organic nitrogen metabolic pathway significantly, such as ammonia monooxygenase, glutamine synthetase, and glutamate synthase. Due to the EPS protection and nitrogen metabolism, the relative abundance of the main bacterial genera and the related ARGs increased to the level equal to that in pipelines biofilm with no disinfection. Therefore, NH3-N reduced the ARGs removal efficiency of chlorine disinfection. It is necessary to take measures to improve the removal rate of NH3-N and ARGs for preventing their risks in drinking water.

Revealing the response characteristics of periphyton biomass and community structure to sulfamethoxazole exposure in aquaculture water: The perspective of microbial network relationships

The widespread application of sulfonamide antibiotics in aquaculture has raised concerns about their adverse environmental impacts. Periphyton plays a crucial role in the aquatic ecosystem. In this study, we examined sulfamethoxazole (SMX) effects on the community structure and interactions of periphyton in simulated aquaculture water. Our findings indicated that the total biomass of periphyton decreased, while the biomass of periphytic algae and the secretion of extracellular polymeric substances (EPS) increased at 0.7 × 10-3 mg/L. Under higher SMX concentrations (5 mg/L and 10 mg/L), periphyton growth was severely inhibited, the microbial community structure of periphyton were sharply altered, characterized by the cyanobacteria growth suppression and decrease in the diversity index of community. Furthermore, elevated SMX concentrations (5 mg/L and 10 mg/L) increased the ratio of negative relationships from 45.4% to 49.4%, which suggested that high SMX concentrations promoted potential competition among microbes and disrupted the microbial food webs in periphyton. The absolute abundance of sul1 and sul2 genes in T2 and T3 groups were 2-3 orders of magnitude higher than those in control group after 30 days of SMX exposure, which elevated the risk of resistance gene enrichment and dissemination in the natural environment. The study contributes to our understanding of the detrimental effects of antibiotic pollution, which can induce changes in the structure and interaction relationship of microbial communities in aquaculture water.

Chronic toxicity of pharmaceuticals to the benthic green alga Closterium ehrenbergii

Pharmaceuticals in the environment have emerged to a topic of global concern. Since these substances are designed to be biologically active, hazardous effects on non-target organisms are frequently reported. Here, the effects of five pharmaceuticals, one radiocontrast agent, and one degradation product on the freshwater green alga Closterium ehrenbergii were evaluated after chronic exposure of 168 h. Growth and maximum quantum yield (FV/FM) were used as endpoints and complemented by the assessment of morphology and chlorophyll fluorescence. We found that the tested antibiotics Ciprofloxacin and Ofloxacin impaired chloroplast integrity, resulting in a reduction of FV/FM from 0.1 mg/L. The disintegration of chloroplasts at higher concentrations (c = 0.3 and 0.8 mg/L, respectively) was visualized by brightfield and fluorescence microscopy. In contrast, Sulfamethoxazole interfered with cell division, leading to malformation of cells from 0.8 mg/L. Furthermore, the antibiotics exhibited a latency period of 72 h after which they started to reveal their true effects. Therefore, the importance of long-term toxicity testing is outlined in order to avoid underestimation of toxic effects of pharmaceuticals. Based on the EC10 values obtained, the antibiotics were considered to meet the criteria for classification as toxic to aquatic life with long lasting effects. The other test substances were found to exert no effects on C. ehrenbergii or only at very high concentrations and were classified as nontoxic.

Mapping the spread and mobility of antibiotic resistance in wastewater due to COVID-19 surge

Large amounts of antibiotics have been discharged into wastewater during the COVID-19 pandemic due to overuse and misuse of antibiotics to treat patients. Wastewater-based surveillance can be used as an early warning for antibiotic resistance (AR) emergence. The present study analyzed municipal wastewater corresponding to the major pandemic waves (WW1, WW2, and WW3) in India along with hospital wastewater (Ho) taken as a benchmark for AR. Commonly prescribed antibiotics during a pandemic, azithromycin and cefixime residues, were found in the range of 2.1-2.6 μg/L in Ho and WW2. Total residual antibiotic concentration was less in WW2; however, the total antibiotic resistance gene (ARG) count was 1065.6 ppm compared to 85.2 ppm in Ho. Metagenome and RT-qPCR analysis indicated a positive correlation between antibiotics and non-corresponding ARGs (blaOXA, aadA, cat, aph3, and ere), where 7.2-7.5% was carried by plasmid in the bacterial community of WW1 and WW2. Moreover, as the abundance of the dfrA and int1 genes varied most among municipal wastewater, they can be suggested as AR markers for the pandemic. The common pathogens Streptococcus, Escherichia, Shigella, and Aeromonas were putative ARG hosts in metagenome-assembled genomes. The ARG profile and antibiotic levels varied between municipal wastewaters but were fairly similar for WW2 and Ho, suggesting the impact of the pandemic in shaping the resistome pattern. The study provides insights into the resistome dynamic, AR markers, and host-ARG association in wastewater during the COVID-19 surge. Continued surveillance and identification of intervention points for AR beyond the pandemic are essential to curbing the environmental spread of ARGs in the near future.

The interaction between extracellular polymeric substances and corrosion products in pipes shaped different bacterial communities and the effects of micropollutants

There are growing concerns over the effects of micropollutants on biofilms formation and antibiotic resistance gene (ARGs) transmission in drinking water distribution pipes. However, there was no reports about the influence of the interaction between extracellular polymeric substances (EPS) and corrosion products on biofilms formation. Our results indicated that the abundance of quorum sensing (QS)-related genes, polysaccharide and amino acids biosynthesis genes of EPS was 6747-8055 TPM, 2221-2619 TPM, and 1461-1535 TPM in biofilms of cast iron pipes, respectively, which were higher than that of stainless steel pipes. The two-dimensional correlation spectroscopy (2D-COS) analysis of attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR) results indicated that polysaccharide of EPS was more easily adsorbed onto the corrosion products of cast iron pipes. Therefore, more human pathogenic bacteria (HPB) carrying ARGs were formed in biofilms of cast iron pipes. The amide I and amide II components and phosphate moieties of EPS were more susceptible to the corrosion products of stainless steel pipes. Thus, more bacteria genera carrying mobile genetic elements (MGE)-ARG were formed in biofilms of stainless steel pipes due to more abundance of QS-related genes, amino acids biosynthesis genes of EPS and the functional genes related to lipid metabolism. The enrichment of dimethyl phthalate (DMP), perfluorooctanoic acid (PFOA) and sulfadiazine (SUL) in corrosion products induced upregulation of QS and EPS-related genes, which promoted bacteria carrying different ARGs growth in biofilms, inducing more microbial risks.

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere

BACKGROUND

The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicrobial Resistance Genes (ARG). In- and ex-situ incubations were used to characterise the riverine plastisphere taxonomically and functionally in order to determine whether antibiotics within the water influenced the ARG profiles in these microbiomes and how these compared to those on natural surfaces such as wood and their planktonic counterparts.

RESULTS

We show that plastics support a taxonomically distinct microbiome containing potential pathogens and ARGs. While the plastisphere was similar to those biofilms that grew on wood, they were distinct from the surrounding water microbiome. Hence, whilst potential opportunistic pathogens (i.e. Pseudomonas aeruginosa, Acinetobacter and Aeromonas) and ARG subtypes (i.e. those that confer resistance to macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents and glycopeptides) were predominant in all surface-related microbiomes, especially on weathered plastics, a completely different set of potential pathogens (i.e. Escherichia, Salmonella, Klebsiella and Streptococcus) and ARGs (i.e. aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone and fosfomycin) dominated in the planktonic compartment. Our genome-centric analysis allowed the assembly of 215 Metagenome Assembled Genomes (MAGs), linking ARGs and other virulence-related genes to their host. Interestingly, a MAG belonging to Escherichia -that clearly predominated in water- harboured more ARGs and virulence factors than any other MAG, emphasising the potential virulent nature of these pathogenic-related groups. Finally, ex-situ incubations using environmentally-relevant concentrations of antibiotics increased the prevalence of their corresponding ARGs, but different riverine compartments -including plastispheres- were affected differently by each antibiotic.

CONCLUSIONS

Our results provide insights into the capacity of the riverine plastisphere to harbour a distinct set of potentially pathogenic bacteria and function as a reservoir of ARGs. The environmental impact that plastics pose if they act as a reservoir for either pathogenic bacteria or ARGs is aggravated by the persistence of plastics in the environment due to their recalcitrance and buoyancy. Nevertheless, the high similarities with microbiomes growing on natural co-occurring materials and even more worrisome microbiome observed in the surrounding water highlights the urgent need to integrate the analysis of all environmental compartments when assessing risks and exposure to pathogens and ARGs in anthropogenically-impacted ecosystems. Video Abstract.

Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment

Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China

The antibiotic concentrations spanned from 11.2 to 173.8 ng/g, with quinolones and tetracyclines being observed to be prevalent. The amount of microbial biomass as determined by Phospholipid fatty acid (PLFA) ranged from 2.92 to 10.99 mg kg-1, with G- bacteria dominating. A total of 254 distinct ARGs and 10 MEGs were identified, with multidrug ARGs having the highest relative abundance (1.18 × 10-2 to 3.00 × 10-1 copies/16S rRNA gene copies), while vancomycin and sulfonamide resistance genes were the least abundant. Results from canonical-correlation analyses combined with redundancy analysis indicated that macrolides were significantly related to the shifts of microbial community structure in sediments, particularly in G+ bacteria that were more sensitive to antibiotic residues. It was observed that sulfonamide ARGs had a greater correlation with residual antibiotics than other ARGs. This study provided a field evidence that multiple residual antibiotics from coastal sites could cause fundamental shifts in microbial community and their associated ARGs.

Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge

The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.

The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream

Introduction

Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2.

Methods

Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene amplicon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ).

Results

Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1, sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and diversity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication.

Discussion

We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.

Selective Oxygen Activation to Reactive Oxygen Species on a Carbon Layer-Encapsulated CuxO Electrocatalyst for Water Purification

In situ synthesis of reactive oxygen species (ROS) on demand via oxygen activation (OA) is significant in biological, chemical, and environmental fields. Thus, the design of OA catalysts with adequate reactivity, durability, and selectivity is critical but challenging. Here, we report a Cu_xO@C core@shell photoelectrode prepared by encapsulating Cu/Cu₂O/CuO into a carbon layer through anodic electropolymerization (electrophoresis-coupled self-assembly of carbon quantum dots). Theoretical prediction and experiments indicate that the carbon layer can effectively facilitate optical trapping and charge transfer, thus promoting photoelectric conversion and anti-photocorrosion performance of Cu_xO@C. The inner Cu_xO core acts as an electron reservoir and continuously injects electrons into the outer carbon layer shell, and the carbon atoms adjacent to oxygen-enriched functional groups (C-O-C and -COOH) in the electron-rich carbon layer work as the reactive sites to adsorb O₂ and donate electrons to the antibonding orbital [lowest unoccupied molecular orbital (π*)] of dioxygen. Optimized adsorption and hydrogenation of the critical intermediates (*O₂, *OOH, and *H₂O₂) and thermodynamically tunable O-O bond cleavage enable O₂ being selectively reduced to the superoxide anion and hydroxyl radical via the mixed multielectron processes consisting of one- and three-electron pathways. Sulfamethoxazole, an emerging refractory organic contaminant widely present in the environment, can be effectively degraded (∼100% removal) in such an electrochemical platform, benefiting from the abundant ROS generated in situ. Our findings demonstrate an innovative strategy to develop highly efficient and selective OA catalysts for practical water purification.

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient

The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of 'ecosurveillance', especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.