Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie and tropical ecosystems

Abstract

BackgroundSoil is likely the largest reservoir of antibiotic resistance genes (ARGs), but their distribution across soil resistomes of different ecosystems is unknown. We used a metagenomic approach to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. ResultsHigh diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance genes and efflux pump the dominant class and mechanism. We identified 55 "background ARGs" which were shared by all 26 soil metagenomes of all three ecosystems, which accounted for more than 81% of resistome abundance.No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. Conversion of Amazon rainforest to pasture significantly increased soil ARG diversity, with eight ARGs significantly enriched. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. There was also wide cooccurrence among ARGs in all samples. ConclusionsOur results define common background ARGs, quantify resistance classes, provide sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future.

Transmission of tetracycline resistance genes and microbiomes from manure-borne black soldier fly larvae frass to rhizosphere soil and pakchoi endophytes

“…From the correlation analysis of microorganisms and TRGs, Proteobacteria, Spirochaetota, Bacteroidota, and Firmicutes were potential host bacteria (phylum level) of TRGs in BSFL frass and rhizosphere soil. However, reports have been published of Proteobacteria as ARG hosts are common (Wang et al, 2020;Qian et al, 2021;Yanlong et al, 2021;Zhang et al, 2021). We performed network analysis on the relative abundance of microorganisms at the genus level and their corresponding TRGs from different samples and found that rhizosphere soil had the most complex association (Figure 4) and was associated with the highest microbial species (Supplementary Figures S2a,e).…”

Impacts of soybean agriculture on the resistome of the Amazonian soil

“…Natural forest soils are a significant source of antibiotic ARG, and their large-scale distribution is regulated by the diversity of microorganisms and herbaceous plants (Hu et al, 2018;Qian et al, 2021). In this way, native ARGs in different soils can be shared with plants, becoming a potential route for the transfer of these genes to the human microbiome and the potential for transferring pathogens through the food chain (Zhang et al, 2019).…”

“…However, it remains unclear whether traditional agricultural activities affect the soil resistome (Qian et al, 2021), although data on sewage sludge contamination constitutes a vast repository of antibiotic, biocide, and MGE resistance genes that can affect the soil resistome (Markowicz et al, 2021).…”

“…The native antibiotic resistance profile of soil is varied but always presents high gene diversity (Qian et al, 2021;Zheng et al, 2021), as shown in forest soil. As for the profile of the resistome of the crop soils, a strong association was not found; it is possibly affected by the addition of compounds, such as fertilizers, and manure, among others (Martins and Rabinowitz, 2020;Macedo et al, 2021).…”