Abstract
Soil is one of the biggest reservoirs of microbial diversity, yet the processes that define the community dynamics are not fully understood. Apart from soil management being vital for agricultural purposes, it is also considered a favorable environment for the evolution and development of antimicrobial resistance, which is due to its high complexity and ongoing competition between the microorganisms. Different approaches to agricultural production might have specific outcomes for soil microbial community composition and antibiotic resistance phenotype. Therefore in this study we aimed to compare the soil microbiota and its resistome in conventional and organic farming systems that are continually influenced by the different treatment (inorganic fertilizers and pesticides vs. organic manure and no chemical pest management). The comparison of the soil microbial communities revealed no major differences among the main phyla of bacteria between the two farming styles with similar soil structure and pH. Only small differences between the lower taxa could be observed indicating that the soil community is stable, with minor shifts in composition being able to handle the different styles of treatment and fertilization. It is still unclear what level of intensity can change microbial composition but current conventional farming in Central Europe demonstrates acceptable level of intensity for soil bacterial communities. When the resistome of the soils was assessed by screening the total soil DNA for clinically relevant and soil-derived antibiotic resistance genes, a low variety of resistance determinants was detected (resistance to β-lactams, aminoglycosides, tetracycline, erythromycin, and rifampicin) with no clear preference for the soil farming type. The same soil samples were also used to isolate antibiotic resistant cultivable bacteria, which were predominated by highly resistant isolates of Pseudomonas, Stenotrophomonas, Sphingobacterium and Chryseobacterium genera. The resistance of these isolates was largely dependent on the efflux mechanisms, the soil Pseudomonas spp. relying mostly on RND, while Stenotrophomonas spp. and Chryseobacterium spp. on RND and ABC transporters.
Highlights
Microbiota of the soil is greatly important for life on our planet, including its role in the cycling of carbon, nitrogen and other nutrients (Jansson and Hofmockel, 2018)
Total DNA was extracted from both soils and used for 16S rRNA gene sequencing in order to analyze the microbial community composition
Recent study demonstrates that high abundances of beneficial bacteria are related with soil quality, which is indicated by better plant growth, lower outbreaks of diseases, higher soil pH and better nutrient activities (Wang et al, 2017)
Summary
Microbiota of the soil is greatly important for life on our planet, including its role in the cycling of carbon, nitrogen and other nutrients (Jansson and Hofmockel, 2018). Bacteria and other soil microorganisms are the agents of biotransformation of soil organic matter and nutrients and of most key soil processes. Their activities are influenced by both soil physicochemical processes and ecological interactions (Powlson et al, 2001). Culture-based methods suggest that a gram of soil contains for about one hundred species of microorganisms (Dunbar et al, 1999), but such data are underestimated because multiple lines of evidence indicate that fewer than 1% of the species in soil are presently cultivable (Amann et al, 1995). DNA based methods revealed that soils typically contain 109 to 1010 microorganisms per gram, which may represent thousands of bacterial species (Gans et al, 2005). Metagenomic and other next-generation sequencing based studies might be very useful for the studying the soil microbiome for understanding soil microbial functioning (Baveye, 2009; Raynaud and Nunan, 2014; Mandal et al, 2015)
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