Organization of microbial community and fate of pollutants in the rhizosphere

Informations

Funding country

France

Acronym

RHIZORG

URL

-

Start date

1/1/2013

End date

-

Budget

227,000 EUR

Fundings

Abstract

Rhizoremediation (i.e. soil bioremediation assisted by plants) could be an interesting strategy for long-term management of industrial wasteland soils harbouring high organic pollutant concentrations, among which polycyclic aromatic hydrocarbons (PAH). However, studies on PAH-biodegradation in the plant rhizospheres showed contrasted results, with activation as well as inhibition or even no effect of plants on the fate of pollutants. To better understand the processes, we hypothesized that spatial heterogeneities and temporal fluctuations of the plant-soil system would explain the previously observed contrasted results. A soil is heterogeneous due to its intrinsic characteristics, to the pollution and the microorganisms presenting hotspots and plants creating spatial variations around roots (rhizosphere effect). It’s thus important to start taking into account the spatial heterogeneity to better understand the fate of pollutants in planted soils. In the RHIZORG project, all the experiments will be performed on a well-known aged PAH-contaminated soil largely studied in the GISFI consortium (www.gisfi.fr; Neuves-Maisons coking plant wasteland soil, 54, France). The soil will be spiked with a complex pollutant mixture (organic extract from the same soil) to increase pollutant bioavailability and biodegradation. Due to its ability to grow on highly contaminated soils and because it was previously used in phytoremediation studies, ryegrass will be the reference plant used all along the project. The project will focus on chemical analyses of pollutants (PAH and polar aromatic compounds PACs) in parallel with analyses of microbial community diversity and organization within the rhizosphere. The 3 main objectives of the RHIZORG project are to: 1) Determine the spatial and temporal variations of the microbial community and the fate of pollutant during plant growth and root development at a cm-scale, 2) Identify the pollutant-degraders and their metabolic pathways in rhizospheric and bulk soils, and 3) Observe the µm-scale organization and localization of microorganisms and pollutants in the root vicinity. The RHIZORG project will focus on taxonomic and functional bacterial diversity using complementary tools: culture-dependent method (Biolog® MT plates to be develop for organic pollutant degradation metabolic profiles), molecular tools (DNA extraction, fingerprinting TTGE, qPCR, 16S rDNA amplicon pyrosequencing and metagenomic), and microspectroscopic methods (fluorescence, confocal laser scanning and micro-Raman). To meet our objectives new experimental devices need to be designed. The first scientific task aims to study the spatio-temporal variations in the rhizosphere. To do it an original rhizotron will be designed with independent openings for sampling at different times. A regionalized multiple sampling strategy will be used to estimate and map changes in regionalized variables (root biomass, pollutant concentration, bacterial diversity indexes, abundance of functional genes) using geostatistics. The second scientific task is dedicated to the identification of PAH-degrading bacteria and PAH-degradation pathways. Pot devices will be developed to perform Stable Isotope Probing (SIP) on rhizospheric soil and combine the difficulties of using 13C-labeled PAH compound during plant growth. Active functional PAH-degrading populations in plant rhizosphere and bulk soils will be identified, as well as their metagenome, that will tell about specific metabolic pathways involved. The third scientific task has the objective to investigate statistically the spatial organization of the microorganisms and pollutants in the root vicinity using microscopic observation of undisturbed soil thin sections and aims to extrapolate µm-scale organization to the whole root system. Fluorescent in situ Hybridization (FISH) technique will be adapted to undisturbed soil samples and root system will be described using X-Ray tomography.