Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils

Gou, Min; Hu, Hang‐Wei; Zhang, Yu Jing; Wang, Jun‐Tao; Hayden, Helen L.; Tang, Yue‐Qin

doi:10.1016/j.scitotenv.2017.09.028

Cited by 211 publications

(73 citation statements)

References 52 publications

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“…A key finding of this study is that more than 160 ARGs (encoding resistance to eight major classes of antibiotics) were detected from the 300 forest soils with minimal anthropogenic disturbance. In line with previous screening of ARGs in polluted estuaries , urban environments (Xiang et al, 2018), agricultural soils (Hu et al, 2016a,b;Chen et al, 2017;Gou et al, 2018) and Chinese swine farms (Zhu et al, 2013), genes conferring resistance to multidrug, b-lactam, aminoglycoside, MLSB, tetracycline and vancomycin were the most dominant ARG types in these forest soils. Our findings contribute to the growing body of evidence that ARGs are widespread in relatively pristine habitats with less contact with commercial sources of antibiotics (Chen et al, 2013;Segawa et al, 2013;Pawlowski et al, 2016), and highlight that the natural forest ecosystem is a significant reservoir of ARGs and needs to be considered in the risk assessment frameworks of antibiotic resistance.…”

Section: Ubiquitous Args In Forest Biomessupporting

confidence: 84%

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Wang

Singh

et al. 2018

Environmental Microbiology

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Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.

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Section: Ubiquitous Args In Forest Biomessupporting

confidence: 84%

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Wang

Singh

et al. 2018

Environmental Microbiology

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“…Outside of the multidrug ARG type, the relative abundance of the predominant ARGs in this study differed from several others on soils in which ARGs such as β‐lactamases, macrolide‐lincosamide‐steptogramin, aminoglycoside were also frequently occurring (Forsberg et al , 2014; Hu et al , 2016, 2017; Gou et al , 2018). Notably, our results were particularly interesting with respect to vancomycin, a ‘last resort’ broad‐spectrum antibiotic rarely used in hospital settings.…”

Section: Discussioncontrasting

confidence: 60%

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Thomas

Oladeinde

Kieran

et al. 2020

Microbial Biotechnology

109

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Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.

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“…In addition to domains, one could also easily imagine splitting datasets for mSourceTracker analysis by phylogenetic groups at a lower taxonomic level (e.g., methanogens or the proteobacteria) or even using non-organismal datasets (e.g., untargeted chemical or metabolic datasets). This is similar in principle to the approach taken by previous research studying the origins of antibiotic resistance markers (Gou et al, 2018;Baral et al, 2018;Li, Yin & Zhang, 2018). The identification of distinct source origins for different taxonomic groups in the same ''sink'' samples is not without precedent in the literature.…”

Section: Discussionmentioning

confidence: 63%

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics

McGhee

Rawson

Bailey

et al. 2020

PeerJ

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Background Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. Methods Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS). Results SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.

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Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils

Cited by 211 publications

References 52 publications

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics

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