Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

Jakub Ridl,Ondrej Uhlik,Jan Paces,Petr Stursa,Michal Strejcek,Michal Kolar,Michal Kolar,Hynek Strnad,Tomas Macek,Hynek Strnad

doi:10.3389/fmicb.2016.00995

Abstract

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Highlights

Soil as a microbial habitat contains numerous microsites and gradients which harbor enormous microbial diversity
The shotgun metagenomic data indicated that sequenced metagenomes were almost entirely composed of bacterial genomes, with 96.79 ± 0.46% of reads being classified as derived from bacterial DNA
In the horseradish- and nightshade-vegetated soils, the majority of reads clustered with Acidobacteria, with the difference being more pronounced in the horseradishvegetated samples

Summary

Introduction

Soil as a microbial habitat contains numerous microsites and gradients which harbor enormous microbial diversity. In a single gram of soil there are billions of microbial cells spanning thousands of microbial species. Rhizosphere, the thin layer of soil directly influenced by the roots, is a active spot for microbial-plant interactions (Chaudhry et al, 2005; Philippot et al, 2013) due to the organic compounds present here that are often lacking in the bulk soil (Hartmann et al, 2009). The main source of plant organic carbon in soil is rhizodeposition, which is the release of compounds from roots into the surrounding soil (Jones et al, 2009; Lambers et al, 2009). The activity of roots impacts the physical and chemical conditions of the rhizosphere compartment which, in turn, influences microbial populations. A greater density of microorganisms develops in the rhizosphere than bulk soil (Dennis et al, 2010)

Methods

Results

Discussion

Conclusion