Fungicides enhanced the abundance of antibiotic resistance genes in greenhouse soil

Zhang, Houpu; Chen, Shiyu; Zhang, Qianke; Long, Zhengnan; Yu, Yunlong; Fang, Hua

doi:10.1016/j.envpol.2019.113877

Cited by 57 publications

(21 citation statements)

References 60 publications

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“…CBD residues in the soil were determined according to the modified methods [ 16 ]. Before CBD extraction from the earthworms, the gut content of earthworms was empty overnight.…”

Section: Methodsmentioning

confidence: 99%

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Song

Zheng

et al. 2022

Microbiome

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Background It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods. Results CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments. Conclusions It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Graphical Abstract

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“…CBD residues in the soil were determined according to the modified methods [ 16 ]. Before CBD extraction from the earthworms, the gut content of earthworms was empty overnight.…”

Section: Methodsmentioning

confidence: 99%

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Song

Zheng

et al. 2022

Microbiome

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“…Of particular concern is the enrichment of conjugation, plasmid mobility and plasmid propagation‐related genes, implying that biobed environmental conditions favour mobilizable plasmids, which reflects what has been seen in other pesticide‐exposure studies exploring single pesticide types (Zhang et al . 2020), and incompatibility group quantification after pesticide exposure (Anjum et al . 2011; Jechalke et al .…”

Section: Resultsmentioning

confidence: 99%

“…However, their enrichment may be of clinical relevance as HGT mechanisms allow for more rapid dissemination of ARGs than is observed from mutation-based evolution (Sun et al 2019). Of particular concern is the enrichment of conjugation, plasmid mobility and plasmid propagationrelated genes, implying that biobed environmental conditions favour mobilizable plasmids, which reflects what has been seen in other pesticide-exposure studies exploring single pesticide types (Zhang et al 2020), and incompatibility group quantification after pesticide exposure (Anjum et al 2011;Jechalke et al 2013;Holmsgaard et al 2017). However, as the sequencing platform selected for this study did not allow for reliable reassembly of genomes or plasmids, we are unable to establish the genetic composition of these plasmids, and we are further unable to determine specific bacterial hosts.…”

Section: Enrichment Of Genes Related To Gene Mobilitymentioning

confidence: 94%

“…However, the extent to which pesticides could enrich for ARGs in these bioremediation systems remains unclear. Recent studies have identified ABR-plasmids and ARGs in pesticide-polluted soils (Anjum et al 2011;Martini et al 2016;Jørgensen et al 2020;Zhang et al 2020), and research suggests that certain herbicides can select for kanamycin and chloramphenicol resistance in Escherichia coli at sublethal concentrations (Kurenbach et al 2015), and that biobeds have increased incidence of mobile genetic elements (MGEs) (Jechalke et al 2013;Holmsgaard et al 2017). However, most studies are restricted to examining these environments postpesticide exposure, which makes it difficult to directly link pesticide application with ARG enrichment.…”

Section: Introductionmentioning

confidence: 99%

“…2020; Zhang et al . 2020), and research suggests that certain herbicides can select for kanamycin and chloramphenicol resistance in Escherichia coli at sublethal concentrations (Kurenbach et al . 2015), and that biobeds have increased incidence of mobile genetic elements (MGEs) (Jechalke et al .…”

Section: Introductionmentioning

confidence: 99%

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Metagenomic and metatranscriptomic analyses reveal that biobed systems can enrich for antibiotic resistance and genetic mobility genes

Russell

Yost

2022

Letters in Applied Microbiology

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Antibiotic resistance gene pollution in the environment has been identified as a potential contributor to the global issue of antibiotic resistance prevalence, creating a need to identify and characterize environmental reservoirs for antibiotic resistance genes. Because many polluted environments have been shown to contain elevated levels of antibiotic resistance genes, agriculturally based pesticide bioremediation systems called ‘biobeds’ could serve as environmental reservoirs for antibiotic resistance genes, although this has never been extensively explored. Metagenomic and metatranscriptomic analyses of an on‐farm biobed system sampled before and after a season of pesticide use demonstrated that in situ pesticide applications applied to biobeds can enrich for multidrug, sulphonamide, aminoglycoside and beta‐lactam resistance genes. Additionally, this study demonstrated an enrichment for genes associated with gene mobilization, such as genes involved in horizontal gene transfer and plasmid mobility, as well as transposons and integrases.

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Linking soil fungi to bacterial community assembly in arid ecosystems

Jiao

Chu

Zhang

et al. 2022

iMeta

142

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Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.

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Fungicides enhanced the abundance of antibiotic resistance genes in greenhouse soil

Cited by 57 publications

References 60 publications

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Metagenomic and metatranscriptomic analyses reveal that biobed systems can enrich for antibiotic resistance and genetic mobility genes

Linking soil fungi to bacterial community assembly in arid ecosystems

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