Host identity determines plant associated resistomes

https://doi.org/10.1016/j.envpol.2019.113709Get rights and content

Highlights

  • Plant phyllosphere microbiome is an important reservoir of ARGs.

  • Host identities significantly affect the profile of plant resistomes.

  • A core plant associated resistomes was identified.

Abstract

Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.

Introduction

Antibiotic resistance is ancient (D’Costa et al., 2011), however, the increasing selection pressures caused by use of synthetic antibiotics and heavy metal contamination have accelerated the evolution and dissemination of antibiotic resistance genes (ARGs) in environmental and clinical settings (Baker-Austin et al., 2006; Martinez, 2008). The occurrence and aggregation of ARGs in pathogenic bacteria have severely compromised the therapeutic efficacy of human and animal antibiotics (WHO, 2014, 2018). The development of bacterial resistance to antibiotics is one of the most intractable clinical challenges and ARGs have been recognized as an emerging environmental pollutant that may threaten public health (UNEP, 2017).

A growing body of studies have identified wastewater treatment plants and livestock wastes generated from confined animal feeding operations as two major ARG reservoirs (Michael et al., 2013; Wichmann et al., 2014; Su et al., 2017b). By using high throughput quantitative PCR and metagenomic techniques, hundreds of ARGs have been detected in wastewaters and animal manures (Zhu et al., 2013; An et al., 2018b). The current technology, however, is incapable of effectively removing ARGs in wastewater and manures before final discharge and most of these ARGs are eventually released into the soil environment and may migrate into the human food chain (Rizzo et al., 2013; Burch et al., 2017; An et al., 2018a).

Plants are generally populated by a vast diversity of microorganisms (known as plant microbiome), which is a key determinant of plant health, fitness and productivity (Bulgarelli et al., 2013; Turner et al., 2013; Vandenkoornhuyse et al., 2015; Agler et al., 2016). An emerging body of studies are beginning to evaluate the importance of plant microbiome for the host immune system, and these studies found that plant microbiome can trigger developmental processes in host for protection against pathogens (Pieterse et al., 2012; Carvalhais et al., 2015; Lebeis et al., 2015). Plant associated microbiota may originate from surrounding environments such as soil and air, and resistomes in the plant microbiome especially the phyllosphere microbiome may disperse to humans via food consumption or direct contact. Therefore, plant microbiome is key interface between human microbiome and natural microbiome (Zarraonaindia et al., 2015; Chen et al., 2017), and represents a potentially important pathway for dissemination of antibiotic resistance from natural resistomes to human microbiome. However, we know astonishingly little about plant resistomes, compared with soil, wastewater and air particulates (Zhu et al., 2013; An et al., 2018a; An et al., 2018b; Li et al., 2018).

To date, only a few studies have examined the profile of plant resistomes, which offer valuable insights into the diversity, composition and potential dissemination of ARGs in the habitats of plant hosts. For instance, over a hundred of ARGs were detected in lettuce phyllosphere and leaf endophyte, and these genes confer resistance to almost all major classes of antibiotics commonly administered to animals and humans (Wang et al., 2015; Zhu et al., 2017a). More importantly, it has been demonstrated that organic fertilization not only increased the abundance of ARG in soil but also in the phyllosphere of plants (Udikovic-Kolic et al., 2014; Wang et al., 2015). A previous study has identified a large number of ARGs detected in phyllosphere are also detectable in soil resistomes, indicating that soil could be a major source for plant resistomes (Chen et al., 2017). In addition, phyllosphere is assumed to be conducive to horizontal gene transfer due to the high possibility of cells to cluster and form biofilms, which accelerates the dissemination of antibiotic resistance (van Elsas et al., 2003). Despite of this progress in plant microbiome studies, however they did not consider the impacts of host identities per se on the plant resistomes, and this knowledge is important for controlling the spread of antibiotic resistance.

In the present study, high-capacity quantitative PCR and 16S rRNA gene amplicon sequencing techniques were applied to analyze the plant resistomes and microbiome in 12 plant species (Zhu et al., 2017b). We aimed to address the following two questions (1) is there a core plant resistome across different plant identities? and (2) does host identities had a major impact on plant resistomes? The results of this study will yield a comprehensive understanding of plant resistomes and improve our knowledge on the role of plant phyllosphere microbiome in the dissemination of antibiotic resistance in the environment.

Section snippets

Sampling

Twelve different plant leaf tissues with three replicates were collected at harvest from a vegetable field in Kunming City located in Southwest of China (25°03′ N, 102°44′E). Based on the position of eating part, the twelve plants are divided into two groups. Group I (above ground) including Foeniculum vulgare, Glycine max, Brassica oleracea var.capitata, Lactuca sativa, Brassica pekinensis, Allium sativum, Vicia faba, Allium fistulosum, Lablab purpureus and Cucurbita moschata. Group II

Comparation between plant and soil resistomes

A total of 162 unique ARGs and 10 MGEs were identified in plant and soil microbiome (Fig. 1A). The detected number of ARGs in plants ranged from 12 to 73, with an average of 43, which was significantly lower than that of soil with an average of 83 (P < 0.0001). Similarly, the abundance of ARGs (normalized) in plant phyllosphere microbiome greatly varied from 0.0003 to 0.0475 copies per 16S rRNA gene, which was significantly lower than that of soil with an average of 0.0585 copies per 16S rRNA

Plant core resistomes

In the present study, by using HT-qPCR with 296 primer sets, a total of 162 ARGs and 10 MGEs were detected in the plant phyllosphere microbiome. Our results revealed that in addition to the agricultural soils (Han et al., 2018), wastewater/groundwater (Su et al., 2017b; An et al., 2018b), and air particulates (Li et al., 2018; Xie et al., 2018), the plant phyllosphere microbiome is another important reservoir of ARGs in the environment (Chen et al., 2019). An emerging body of phylogenetic

Conclusions

Altogether, our results revealed that plant phyllosphere microbiome harbored a broad spectrum of ARGs, and a core set of resistomes accounting for over 64% of total resistance genes was identified. The preference of recruiting environmental microbes caused the dissimilarity of the phylogeny in plant phyllosphere microbiome across host identities was a primary determinant of plant resistome content. The potential role of HGT in decoupling resistomes from phylogeny should not be neglected. These

CRediT authorship contribution statement

Qing-Lin Chen: Investigation, Formal analysis, Writing - original draft. Hang-Wei Hu: Writing - review & editing. Dong Zhu: Writing - review & editing. Jing Ding: Writing - review & editing. Zhen-Zhen Yan: Writing - review & editing. Ji-Zheng He: Writing - review & editing. Yong-Guan Zhu: Funding acquisition, Project administration.

Declaration of competing interest

The authors declare no conflict of interest.

Acknowledgement

This work was supported by the National Key Research and Development Program of China-International collaborative project from Ministry of Science and Technology (2017YFE0107300), National Natural Science Foundation of China (41571130063, 21210008), and Strategic Priority Research Program of Chinese Academy of Sciences (XDB15020402).

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