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•109 ARGs were detected in manure and compost from chicken, bovine and pig farms.•Chicken and pig manure had higher ARG diversity and abundance than bovine manure.•Composting was ...better at reducing ARGs in chicken manure than pig and bovine manure.•There was widespread co-occurrence of ARGs and MGEs in animal manure.•MGEs, heavy metal, and total nitrogen may explain differences among various manure.
Aerobic composting is used widely for animal manure recycling, and it may reduce the amount of antibiotic resistance genes (ARGs) that enter the environment. We sampled three types of animal (bovine, chicken, and pig) manure and the corresponding composts from 12 large-scale farms, and tested multiple ARGs and mobile genetic elements (MGEs) by high-throughput qPCR. A total of 109 ARGs were detected in the manure and compost samples, thereby demonstrating that both are important ARG reservoirs. The diversity and abundance of ARGs were significantly higher in chicken and pig manure than bovine manure, but industrial composting was more efficient at reducing the ARGs in chicken manure than pig and bovine manure. Composting universally reduced some ARGs, but inconsistently influenced other ARGs from different types of animal manures. Network analysis detected the widespread co-occurrence of ARGs and MGEs. floR, ermF, catB3, aac(6′)-lb(akaaacA4), and aadA were identified as suitable indicator genes for estimating the total abundance of ARGs. Our results suggest that different animal species had significant effects on the diversity, abundance, and persistence of ARGs, where the abundance of transposons, heavy metal concentration, total nitrogen level, and the dosage and duration of exposure to antibiotics may explain these differences.
Antibiotic residues could promote the dissemination of antibiotic resistance genes (ARGs) in the environments, and biodegradation represent a major route for antibiotic removal. Previous studies have ...showed that earthworm could enhance the degradation of certain organic contaminants, however, its effectiveness in ciprofloxacin removal and ARG reduction in soil remains unclear. In the present study, high-performance liquid chromatography, 16S rRNA gene sequencing and high-throughput quantitative PCR were employed to explore the effects of earthworm addition on ciprofloxacin removal and ARG abundance in ciprofloxacin-amended soil. Ciprofloxacin removal was significantly higher in earthworm cast as compare to control soil, and ARG abundance in earthworm cast was significantly lower than that of control soil. Procrustes analysis together with Mantel test showed that the ARG profiles were strongly associated with bacterial communities, indicating that the lower abundance of ARGs in cast samples could be attributed to changes in bacterial community compositions by earthworm activity. Flavobacterium and Turicibacter were enriched in cast samples, which were negatively correlated with ciprofloxacin concentration (p < 0.05), implying their potential roles in ciprofloxacin removal. These results suggested that earthworm gut is a hotspot for ciprofloxacin removal, and could be an option for mitigation of antibiotic pollution in soil.
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•Ciprofloxacin removal is significantly enhanced by earthworm activities.•Earthworm gut is a hotspot for ciprofloxacin removal.•ARG abundance significantly decreased in earthworm cast compared to soil.•Earthworm can be a cost-effective option for antibiotic removal and ARG reduction.
Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased ...environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms. We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls. Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases—the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure—as well as the high correlation (r ² = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes. Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.
In many practical problems, multiple alternatives are ranked with respect to related criteria, and the criteria's weights are usually unknown. In order to solve this kind of multicriteria decision ...making (MCDM) problem, this paper proposes an interactive MCDM approach based on an acronym in Portuguese of interactive and multicriteria decision‐making (TODIM) method and nonlinear programming (NLP) with intuitionistic linguistic numbers (ILNs). First, by comparing the existing operations and comparison methods for ILNs, new operations and a new comparison method are defined based on linguistic scale functions to obtain rational results. Second, considering their linguistic terms, membership degrees, and nonmembership degrees as a whole, the generalized distance between ILNs is defined with an adjustable parameter. Third, the total ranking of alternatives is obtained using the proposed NLP‐based TODIM approach based on the generalized ILN distance. Finally, an example of selecting hotels from a tourism website is presented to verify the validity and feasibility of the proposed approach. A comparison with existing methods is also conducted and analyzed.
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•Numerous online reviews of hotels are described by linguistic distribution assessments that can retain original information effectively.•New comparison method is defined based on ...linguistic scale functions to break through the restriction of previous comparison method for linguistic distribution assessments.•New distance measurement between linguistic distribution assessments is defined based on the linguistic scale functions to calculate the distance between any two linguistic distribution assessments that have different numbers of linguistic terms.•In order to deal with the conflicting criteria and the preferences for criteria in different groups, a mathematical model is designed based on an extended VIKOR approach and the idea of PA operator to select hotels on tourism websites.•A case study of TripAdvisor.com is conducted to select suitable hotels using online reviews of these hotels.
The effect of online reviews on resulting decisions attracted the interests of merchants and researchers in different fields. According to existing studies, the decisions of tourists are highly likely modified after browsing online reviews from other travelers on a tourism website. The manner in which online reviews on tourism websites are utilized to select hotels and support tourists is a noteworthy research problem. Online reviews of a hotel are provided by various tourists with respect to different criteria; thus, each tourist is regarded as a decision-maker. In this instance, the problem of hotel selection is based on online reviews in a tourism website and is expressed as a multi-criteria decision-making problem. In this study, a mathematical model was designed to select appropriate hotels on websites. First, a new comparison method for linguistic distribution assessments was proposed based on linguistic scale functions. Second, a novel distance measurement between linguistic distribution assessments with different numbers of linguistic terms was defined with an adjustable parameter. Third, a model for calculating weights and a mathematical model were constructed according to the idea of prioritized aggregation operator and distance measurement. Finally, a case study of TripAdvisor.com was conducted to select suitable hotels using online reviews of hotels. Data analysis was completed to prove the viability of the designed model.
The rapid construction of reservoir in river basin generates a river-reservoir system containing an environmental gradient from river system to reservoir system in modern aquatic environment ...worldwide. Profiles of antibiotic resistance genes (ARGs) in river-reservoir system is essential to better understand their dynamic mechanisms in aquatic eco-environment. In this study, we investigated the diversity, abundance, distribution of ARGs and mobile genetic elements (MGEs) in a representative river-reservoir system using high-throughput quantitative PCR, as well as ranked the factors (e.g. antibiotics, bacterial biomass, bacteria communities, and MGEs) influencing the patterns of ARGs based on structural equation models (SEMs). Seasonal variations in absolute abundance of ARGs and MGEs exhibited similar trends with local rainfall, suggesting that seasonal runoff induced by the rainfall potentially promote the absolute abundance of ARGs and MGEs. In contrast, environmental gradient played more important roles in the detected number, relative abundance, distribution pattern of ARGs and MGEs in the river-reservoir system. Moreover, environmental gradient also made the co-occurrence patterns associated with ARGs subtypes, MGEs and bacteria genera in river system different from those in reservoir system. The SEMs revealed that MGEs contributed the most to shape the ARG profiles. Overall, our findings provide novel insights into the mechanisms of environmental gradient on ARGs dynamics in river-reservoir system, probably via influencing the MGEs, antibiotics, pathogenic bacteria community and nonpathogenic bacteria community.
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•Seasonal rainfall potentially promoted the absolute abundance of ARGs and MGEs.•Environmental gradient played important roles in the distribution pattern of ARGs and MGEs.•MGEs contributed the most to shape the ARG profiles both in river and reservoir systems.
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•ARG absolute abundance was 12-fold enriched in manure fertilized GVP soil.•Significance effect of different types of manure on ARGs in soil was not observed.•Introduction of ARGs ...from manure explained most to the increased diversity of ARGs.•A baseline level of ARG abundance was provided to assess ARG contamination.
A large quantity of manure is applied in greenhouse vegetable production (GVP) soils, while manure fertilization often leads to the proliferation of antibiotic resistance genes (ARGs) in soils. However, comprehensive study on the effects of different types of manure on ARGs in GVP soils remains unknown, and the baseline level of ARGs in GVP soil is poorly quantified. This study conducted a comprehensive survey of ARGs in GVP soils using high-throughput quantitative PCR. We found elevated ARG diversity and absolute abundance in fertilized soil, whereas no significant difference in soil ARGs amended with different types of manure. Redundancy analysis indicated that the change of bacterial community compositions and environmental factors contributed partially to the shift in ARG profiles. Bipartite network analysis indicated that one ARG was detected in non-manured soils, while 50 ARGs and 4 mobile gene elements were exclusively detected in fertilized soils, suggesting introduction of ARGs from manure into soils largely explained the increased ARG diversity in fertilized soil. By comparison of ARG absolute abundance between manured and non-manured soil, we estimated the typical level of ARG absolute abundance in non-manured soil, which provided the first rough baseline level of ARGs to assess ARG contamination in GVP soils.
Antibiotic Resistomes in Plant Microbiomes Chen, Qing-Lin; Cui, Hui-Ling; Su, Jian-Qiang ...
Trends in plant science,
June 2019, 2019-06-00, 20190601, Volume:
24, Issue:
6
Journal Article
Peer reviewed
Open access
Antibiotic resistance is increasing in the biosphere, but the antibiotic resistome in the plant microbiome is overlooked compared to its presence in soil and water environments.
The plant microbiome ...can act as the interface between human and natural microbiomes, representing a crucial pathway for human exposure to environmental antibiotic resistance.
Microorganisms associated with plants may exacerbate the dissemination of antibiotic resistance via the food chain, direct contact, and globalization.
Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.
Anaerobic ammonium oxidation coupled to iron(III) reduction, termed Feammox, is a newly discovered nitrogen cycling process. However, little is known about the roles of electron shuttles in the ...Feammox reactions. In this study, two forms of Fe(III) (oxyhydr)oxide ferrihydrite (ex situ ferrihydrite and in situ ferrihydrite) were used in dissimilatory Fe(III) reduction (DIR) enrichments from paddy soil. Evidence for Feammox in DIR enrichments was demonstrated using the 15N-isotope tracing technique. The extent and rate of both the 30N2–29N2 and Fe(II) formation were enhanced when amended with electron shuttles (either 9,10-anthraquinone-2,6-disulfonate (AQDS) or biochar) and further simulated when these two shuttling compounds were combined. Although the Feammox-associated Fe(III) reduction accounted for only a minor proportion of total Fe(II) formation compared to DIR, it was estimated that the potentially Feammox-mediated N loss (0.13–0.48 mg N L–1 day–1) was increased by 17–340% in the enrichments by the addition of electron shuttles. The addition of electron shuttles led to an increase in the abundance of unclassified Pelobacteraceae, Desulfovibrio, and denitrifiers but a decrease in Geobacter. Overall, we demonstrated a stimulatory effect of electron shuttles on Feammox that led to higher N loss, suggesting that electron shuttles might play a crucial role in Feammox-mediated N loss from soils.
The rapid global urbanization and other extensive anthropogenic activities exacerbated the worldwide human health risks induced by antibiotic resistance genes (ARGs). Knowledge of the origins and ...dissemination of ARGs is essential for understanding modern resistome, while little information is known regarding the overall resistance levels in urban river. In this study, the abundance of multi-resistant bacteria (MRB) and ARGs was investigated using culture-based method and high-throughput qPCR in water samples collected from urban stream and source of Jiulongjiang River, China, respectively. The abundance of MRB (conferring resistance to three combinations of antibiotics and vancomycin) was significantly higher in urban samples. A total of 212 ARGs were detected among all the water samples, which encoded resistance to almost all major classes of antibiotics and encompassed major resistant mechanisms. The total abundance of ARGs in urban samples (ranging from 9.72 × 10¹⁰ to 1.03 × 10¹¹ copies L⁻¹) was over two orders of magnitude higher than that in pristine samples (7.18 × 10⁸ copies L⁻¹), accompanied with distinct ARGs structures, significantly higher diversity, and enrichment of ARGs. Significant correlations between the abundance of ARGs and mobile genetic elements (MGEs) were observed, implicating the potential of horizontal transfer of ARGs. High abundance and enrichment of diverse ARGs and MGEs detected in urban river provide evidence that anthropogenic activities are responsible for the emergence and dissemination of ARGs to the urban river and management options should be taken into account for minimizing the spread of ARGs.
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