title: Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.
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.
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, PragueCzech Republic; Department of Philosophy and History of Science, Faculty of Science, Charles University in Prague, PragueCzech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Ridl
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Kolar
authors.affiliation: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Prague Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Strejcek
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague Czech Republic.
authors.forename: Hynek
authors.initials: H
authors.lastname: Strnad
authors.affiliation: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Prague Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Stursa
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Paces
authors.affiliation: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Prague Czech Republic.
authors.forename: Tomas
authors.initials: T
authors.lastname: Macek
authors.affiliation: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Prague Czech Republic.
authors.forename: Ondrej
authors.initials: O
authors.lastname: Uhlik
keywords: contaminated soil; fertilization; functional potential; microbial community structure; plants