Microbial expression profiles in the rhizosphere of willows depend on soil contamination

Abstract

The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.

Exploring interactions of plant microbiomes

“…In contrast to these observations, differences in the composition of microbial communities in the rhizosphere of Arabidopsis thaliana are likely to be determined by soil type, rather than a unique selection by plant genotype (Lundberg et al, 2012). Along the same lines, Yergeau et al (2014) demonstrated that soil contamination that leads to shifts in community composition ultimately influences the composition of assembled communities in the rhizosphere of willows. In the phyllosphere, which is a niche less subjected to the high density of organism inoculum from soil, the plant genotype seems to exert a stronger selective influence, as observed in specific microbial communities in the phyllosphere of plants living in mangroves Rigonato et al, 2012).…”

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada)

“…Partial 16S ribosomal (rRNA) gene amplicons were produced using the universal primers F343 (5'-TAC GGR AGG CAG CAG-3') and R534 (5'-ATT ACC GCG GCT GCT GGC-3') as in Yergeau et al (2014). The primers contained 10-bp multiplex identifiers (MIDs) and adaptor sequences for Ion Torrent sequencing (Yergeau et al 2012;Bell et al 2013).…”

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

“…Apart from DGGE, thermal gradient gel electrophoresis, and fluorescence in situ hybridization, clone library construction of microbial community-amplified products and sequencing emerged as other supporting techniques for better understanding of microbial ecology (Muyzer, 1999). Furthermore, there are many newer techniques used to understand the microbiome, from metagenomics to metaproteomics (Friedrich, 2006;Mendes et al, 2011;Knief et al, 2012;Rincon-Florez et al, 2013;Schlaeppi et al, 2014;Yergeau et al, 2014). These techniques cover the whole microbiome, instead of selecting particular species, unlike conventional microbial analysis.…”