Changes in bacterial community structure and antibiotic resistance genes in soil in the vicinity of a pharmaceutical factory

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Airborne antibiotic resistome and microbiome in pharmaceutical factories

Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.

Effects of tidal action on the stability of microbiota, antibiotic resistance genes, and microplastics in the Pearl River Estuary, Guangzhou, China

In this study, the 16S rRNA gene amplicon sequencing technique was used to explore the microbial diversity and differences in the water environment of the Pearl River Estuary in Nansha District with various land use types such as the aquaculture area, industrial area, tourist area, agricultural plantation, and residential area. At the same time, the quantity, type, abundance, and distribution of two types of emerging environmental pollutants, antibiotic resistance genes (ARGs) and microplastics (MPs), are explored in the water samples from different functional areas. The results show that the dominant phyla in the five functional regions are Proteobacteria, Actinobacteria and Bacteroidetes, and the dominant genera are Hydrogenophaga, Synechococcus, Limnohabitans and Polynucleobacter. A total of 248 ARG subtypes were detected in the five regions, belonging to nine classes of ARGs (Aminoglycoside, Beta_Lactamase, Chlor, MGEs, MLSB, Multidrug, Sul, Tet, Van). Blue and white were the dominant MP colors in the five regions; 0.5-2 mm was the dominant MP size, and cellulose, rayon, and polyester comprised the highest proportion of the plastic polymers. This study provides the basis for understanding the environmental microbial distribution in estuaries and the prevention of environmental health risks from ARGs and microplastics.

Metatranscriptome deciphers the effects of non-antibiotic antimicrobial agents on antibiotic resistance and virulence factors in freshwater microcosms

The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Seasonal dissemination of antibiotic resistome from livestock farms to surrounding soil and air: Bacterial hosts and risks for human exposure

Feces in livestock farms is a reservoir of antibiotic resistance genes (ARGs), which can disseminate into surrounding soil and air, bringing risks to human health. In this study, seasonal dissemination of ARGs in a livestock farm and implications for human exposure was explored. The experimental results showed that ARGs abundance basically ranked as feces > soil > air, and significant seasonal dependence was observed. The total ARGs in pig feces was relatively higher in autumn (10^9.7 copies g^-1) and winter (10^10.0 copies g^-1), and lower in summer (10^5.0 copies g^-1). Similarly, the lowest total ARGs in soil and air were also observed in summer. There were correlations among ARGs, integron intI1, and bacterial community. Total organic carbon was an important factor affecting ARGs distribution in the feces, and pH and moisture content significantly affected soil ARGs. The daily intakes of integron intI1 and ARGs from air were 10°^.5 copies h^-1 and 10^2.3 copies h^-1 for human exposure, respectively. Pseudomonas was a potential pathogenic host of bla_TEM-1 in feces, Pseudomonas and Acinetobacter were potential pathogenic hosts of multiple ARGs in soil, while ARGs in air did not migrate into pathogens.

Antibiotic resistance development and human health risks during wastewater reuse and biosolids application in agriculture

The reuse of treated wastewater (TWW) and sewage sludge are considered as solutions to the limited water resource and sludge disposal issues, respectively. The associated environmental and human health risks need to be analyzed to assess whether they are safe solutions or not. This paper discusses issues that relate to the accumulation of antibiotics and antibiotic resistance (AR) determinants in agricultural lands and crops, following TWW irrigation and biosolid amendment. Exposure assessment and dose-response assessment are the two important aspects of risk assessment discussed in this paper. Finally, research gaps in current knowledge that are relevant to a comprehensive and quantitative AR risk assessment were identified which includes: 1.) Studies on soil conditions that increase the frequency of horizontal gene transfer (HGT) between native soil resistome and pathogenic microbes in biosolids and TWW 2.) Holistic studies that examine the accumulation or dissipation of antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from the irrigation/biosolids application stage to crop consumption stage 3.) The influences of soil environmental conditions (e.g. salinity, nutrients) on the fate of ARB and ARGs in soil and translocation in edible plants 4.) The development of dose-response models that explicitly incorporate the potential for ARGs transfer between microbes when quantifying the risks of infection due to ARB.

Occurrence and distribution of antimicrobial resistance genes in the soil of an industrial park in China: A metagenomics survey

As zoned areas of industries, industrial parks have great impacts on the environment. Several studies have demonstrated that chemical compounds and heavy metals released from industrial parks can contaminate soil, water, and air. However, as an emerging pollutant, antimicrobial resistance genes (ARGs) in industrial parks have not yet been investigated. Here, we collected soil samples from 35 sites in an industrial park in China and applied a metagenomics strategy to profile the ARGs and virulence factors (VFs). We further compared the relative abundance of ARGs between the sites (TZ_31-35) located in a beta-lactam antimicrobial-producing factory and other sites (TZ_1-30) in this industrial park. Metagenomic sequencing and assembly generated 14, 383, 065 contigs and 17, 631, 051 open reading frames (ORFs). Taxonomy annotation revealed Proteobacteria and Actinobacteria as the most abundant phylum and class, respectively. The 32 pathogenic bacterial genera listed in the virulence factor database (VFDB) were all identified from the soil metagenomes in this industrial park. In total, 685,354 ARGs (3.89% of the ORFs) and 272,694 virulence factors (VFs) (1.55% of the ORFs) were annotated. These ARGs exhibited resistance to several critically important antimicrobials, such as rifampins, fluroquinolones, and beta-lactams. In addition, no significant difference in the relative abundance of ARGs was observed between sites TZ_31-35 and TZ_1-30, indicating that ARGs have already disseminated widely in this industrial park. The present study gave us a better understanding of the whole picture of the resistome and virulome in the soil of the industrial park and suggested that we should treat the industrial park as a whole in the surveillance and maintenance of ARGs.

Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery

In order to effectively use microbial-based strategies to manage anaerobic digesters, it is necessary to distinguish between community shifts that are part of the natural dynamic of the system and shifts caused by environmental or operational disturbances. The objective of this research study was to evaluate the significance of changes in the microbial community of anaerobic digesters during failure in correlation to operational parameters such as an organic acid overload. Five continuously stirred 0.5 L reactors were set-up as semi-continuously-fed, mesophilic dairy manure digesters with a 30-day hydraulic retention time. After a 120-day stabilization period, two digesters were kept as controls, while the organic loading rates in the triplicate set were increased step-wise to ultimately provide a shock-load leading to failure using propionic acid spikes. Acidosis resulting in near cessation of biogas and termination of methane production occurred between 4 and 7 weeks, after which all the digesters continued to be fed only dairy manure. The shock loading of propionic acid led to an accumulation of mainly acetate and propionate, with low levels of iso-butyrate, butyrate, iso-valerate, and valerate. High-throughput Illumina sequencing of the V4 region of the bacterial and archaeal 16S rRNA gene in digester samples showed a significant change in the microbial community composition during propionic acid overload, followed by a return to the original composition with regular feedstock. Bacterial genera whose relative abundance decreased during the inhibition stage included Sedimentibacter, Syntrophomonas, TSCOR003.O20, and Marinilabiaceae, while the relative abundance of Lachnospiraceae, Ruminococcus, Mogibacteriaceae, Pyramidobacter, and Bacteroides increased. The relative abundance of dominant methanogens, Methanosarcina and Methanobacterium, although initially resistant, were decreased (from 91.71 to 12.14% and from 2.98 to 0.73%, respectively) during inhibition, while Methanobrevibacter and Methanosphaera that were prominent in the manure feedstock increased from 17.36 to 79.45% and from 0.14 to 1.12%, respectively. Shifts in bacterial and archaeal compositions, back to their pre-shock steady state after failure, highlight the digester's microbial resilience and recovery potential.

Phytoremediation of pharmaceutical-contaminated wastewater: Insights into rhizobacterial dynamics related to pollutant degradation mechanisms during plant life cycle

Rhizobacterial dynamics, relating to pollutant degradation mechanisms, over the course of plant lifespan have rarely been reported when using phytoremediation technologies for pharmaceutical-contaminated wastewater treatment. This study investigated the rhizobacterial dynamics of Typha angustifolia in constructed wetlands to treat ibuprofen (IBP)-polluted wastewater throughout plant development from seedling, vegetative, bolting, mature, to senescent stages. It was found that conventional pollutant and IBP removals increased with plant development, reaching to the best performance at bolting or mature stage (removal efficiencies: 92% organics, 52% ammonia, 60% phosphorus and 76% IBP). In the IBP-stressed wetlands, the rhizobacterial diversity during plant development was adversely affected by IBP accompanied with a reduced evenness. The bacterial communities changed dynamically at different developmental stages and showed significant differences compared to the control wetlands (free of IBP). The dominant bacteria colonized in the rhizosphere was the phylum Actinobacteria, having a final relative abundance of 0.79 and containing a large amount of genus norank_o__PeM15. Positive interactions were evident among the rhizobacteria in IBP-stressed wetlands and the predicted functions of 16S rRNA genes revealed the potential co-metabolism and metabolism of IBP. The co-metabolism of IBP might be related to root exudates such as amino acid, lipid, fatty acid and organic acid. In addition, positive correlations between the organic compounds of interstitial water (bulk environment) and the rhizobacterial communities were observed in IBP-stressed wetlands, which suggests that the influence of IBP on bulk microbiome might be able to modulate rhizosphere microbiome to achieve the degradation of IBP via co-metabolism or metabolism.

The fungicide azoxystrobin perturbs the gut microbiota community and enriches antibiotic resistance genes in Enchytraeus crypticus

The use of pesticides to ensure global food security is the most important pest control strategy in modern agriculture but causes extensive soil pollution. This pollution involves potential risks to human health and ecosystems. In addition to soil animal growth, the adverse impact of pesticides on the gut microbiomes of nontarget soil fauna remains largely unknown. Here, the effect of the fungicide azoxystrobin (AZ) on soil and the gut microbiota of soil animals (Enchytraeus crypticus) was studied. The tested concentrations of AZ altered the bacterial community in the soil and E. crypticus gut and were slightly toxic with respect to E. crypticus adult mortality and reproduction. The most abundant bacterial phylum, Proteobacteria, significantly increased in response to the 2 and 5 mg/kg AZ treatments, which implied a disordered unhealthy gut bacterial community. Furthermore, bacterial community analysis between the soil and gut showed that the main effect of AZ on the gut microbiota was directly through AZ, not soil microbiota. In addition, AZ exposure significantly enhanced the number and total abundance of antibiotic resistance genes (ARGs) in the E. crypticus gut; these genes may enter the soil food web to affect higher trophic levels and cause a more serious ecological risk. Our study reported the effect of pesticides on the gut of soil animals and on the enrichment of ARGs as global emerging contaminants, revealing unknown potential impacts of fungicides on ecosystem services and sustainable food production.

Association of colistin residues and manure treatment with the abundance of mcr-1 gene in swine feedlots

BACKGROUND

The extensive use of colistin in swine production may have contributed to the recent emergence of corresponding mobile resistance gene mcr-1. The use of colistin as a feed additive was banned in China in April 2017.

OBJECTIVES

To examine the occurrence of colistin and dissemination of mcr-1 in swine feedlots before and after the colistin ban and effects of different manure treatments.

METHODS

Environmental samples were collected from swine feedlots before (December 2016) and after (December 2017) the colistin ban. Colistin concentrations were determined by ultra-high performance liquid chromatography coupled to tandem mass spectrometry. The prevalence of mcr-1 were determined by quantitative PCR analysis, while bacterial community composition was investigated by 16S rRNA sequencing.

RESULTS

In 2016, colistin was detected in feed and fresh manure samples at 67 mg/kg and 17 mg/kg, respectively, but was absent from all samples in 2017. In 2016, the relative abundance of mcr-1 in fresh manure was lower than that in solid samples after natural drying, while a higher relative abundance was detected in fresh manure samples compared with biogas slurry samples. A strong correlation between colistin concentration and relative abundance of mcr-1 was observed in fresh manure. The samples collected in 2017 showed a lower relative abundance of mcr-1 compared with those collected in 2016. Bacterial community analysis showed that the abundance of Enterobacteriaceae, which act as a vehicle and reservoir of mcr-1, increased with natural dying but decreased with anaerobic digestion.

CONCLUSIONS

The presence of colistin exerts direct selection pressure for the accumulation of mcr-1 in manure, while the ban on colistin likely halted the dissemination of mcr-1 on pig farms. Anaerobic digestion is an effective waste treatment process for removing mcr-1, which might be mainly driven by the shift in bacterial community structure.

Soil contamination with antibiotics in a typical peri-urban area in eastern China: Seasonal variation, risk assessment, and microbial responses

The prevalence and persistence of antibiotics in soils has become an emerging environmental issue and an increasing threat to soil security and global public health. The problem is more severe in areas undergoing rapid urbanization; however, the ecological risks of antibiotics, seasonal variability, and associated soil microbial responses in peri-urban soils have not been well-explored. The seasonal soil sampling campaigns were conducted in a typical peri-urban watershed in eastern China to investigate distribution of antibiotics. The results demonstrated higher mean concentrations of most antibiotic compounds in winter than in summer in peri-urban soils. The seasonal variations of norfloxacin, enrofloxacin, and ciprofloxacin were more significant than those of other antibiotics, due to their higher migration ability and bioavailability. An ecological risk assessment demonstrated that chlortetracycline, ciprofloxacin, doxycycline, and ofloxacin can pose high risks to soil microorganisms. Furthermore, the coexistence of multiple antibiotics obviously poses higher risks than individual compounds. A redundancy analysis demonstrated that tetracyclines mainly showed negative correlations with Firmicutes and Chloroflexi, and quinolones showed obviously negative correlations with Acidobacteria, Gemmatimonadetes, and Nitrospirae, suggesting potential inhibition from antibiotics on biological activities or biodegradation processes. However, the persistence of antibiotics in soil results in a significant decrease in bacterial diversity and a change in dominant species. Our results provide an overview of the seasonal variability of antibiotics and the associated effects on bacterial communities in peri-urban soils. The results can provide scientific guidance on decreasing soil contamination with antibiotics to enhance soil security in similar areas.

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities

Sertraline hydrochloride (Ser-HCl), a widely used antidepressant, becomes an aquatic contaminant via metabolic excretion and improper disposal; however, it is unknown how Ser-HCl affects aquatic microbial communities. The present study investigated the effects of Ser on the structures of aquatic microbial communities via high-throughput sequencing analyses. Ser-HCl treatment inhibited the growth of two model algae (the green alga, Chlorella vulgaris, and the cyanobacterium, Microcystis aeruginosa) and decreased the chlorophyll a (Chl-a) concentration in the microcosm to reduce the photosynthetic efficiency. High-throughput sequencing analyses showed that exposure to Ser-HCl disturbed the balance of cyanobacteria species by stimulating the growth of specific cyanobacteria. Among eukaryotes, the richness as well as the diversity indices were significantly enhanced after 5 days of Ser-HCl treatment but sharply decreased with exposure time. Nucleariida occupied an absolute majority (97.83%) within the eukaryotes, implicating that Ser-HCl disturbed the ecological equilibrium in microcosms. Ser-HCl will continue to be an environmental contaminant due to its wide usage and production. Our current study clarified the potential ecological risk of Ser-HCl to aquatic microorganisms. These findings suggest that more attention should be given to the negative effects of these bioactive pollutants on aquatic environments.

Fate of microbial pollutants and evolution of antibiotic resistance in three types of soil amended with swine slurry

Swine waste is a reservoir of microbial pollutants, including pathogens, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB); therefore, soil fertilized with swine waste is an essential pathway for the dissemination of microbial pollutants from concentrated swine farms to the public. To rationalize the intervals of swine wastes application and investigate the effects of soil type on the occurrences of microbial pollutants and antibiotic resistance, pot experiments were conducted with three typical soils, humic acrisol, calcaric cambisols and histosols, being collected from south, northwest and northeast China (soil-R, soil-Y and soil-B, respectively). The soils were amended with swine slurry, digestate and chemical fertilizers and then conducted for 172 days. The influence of microbial pollutants and antibiotic resistance in soil posed by digestate application was similar to that of the chemical fertilizers, while swine slurry posed high risks to the soil. Soil-B which had the highest organic matter and neutral pH was least influenced by the swine slurry amendment. tetG, tetM and ermF were persistent ARGs in the slurry treated soil, and their decay rates fitted to first-order kinetics in the order soil-B> soil-Y > soil-R. Putative pathogens showed strong correlations with ARGs, suggesting a risk of dissemination. The initial 43-82 days was the active phase of microbial pollution in slurry treated soil, during which time heavy metals, moisture content, total organic carbon and the microbial community were key factors contributing to changes in antibiotic resistance. Fertilization intervals of livestock wastes should be lengthened over the ARG active phase.