Integrated responses of plants and associated rhizosphere microbial communities to abiotic disturbances caused by organic and inorganic soil contamination

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Soil contamination is a global problem that is caused primarily by various agricultural, mining and industrial activities. Plants that are able to grow in contaminated soils face a number of stresses caused by toxic inorganic and organic molecules, which include damage to cellular membranes, DNA modification, and inactivation of enzymes. While agriculture and mining are generally the source of a limited number of contaminating compounds, the most affected industrial sites contain mixtures of thousands of toxic chemicals, such as polycyclic aromatic hydrocarbons, polychlorinated biphenyls, various oil by-products, pesticides, solvents and trace elements. The accumulation of certain contaminants in the soil poses serious threats to the health of plants, animals, humans and ecosystems. Many microorganisms and plants are capable of breaking down and/or sequestering soil pollutants. The effects of pollutants on plant health have been the subject of many studies, but the effects on microbial communities and plant-microbe interactions are less clear, since soil microbial communities are extremely complex. Despite recent advances in our understanding of the environmental factors that shape soil bacterial and fungal communities in the rhizosphere, the link between these communities and their response to contamination is still poorly understood. The rhizosphere is an intimately connected metaorganism, involving obligate connections of at least plants, bacteria and fungi. A number of studies have shown a link between plant identity and rhizosphere microbial community structure and activity, but the effect of plants on rhizosphere microbes can vary between soils due to the strong influence of other factors. Still unknown is how plants facilitate the assembly of beneficial microbes in disturbed environments, and whether investment in microbial community modification varies with the stress state of the plant. Within the rhizosphere, the extent of detoxification by microbes is likely influenced by intermicrobial competition and cooperation, and these interactions may be modified by the plant. The rhizosphere is a hotspot of plasmid transfer and so plants may facilitate this cooperative genetic exchange. The general goal of this research program is to understand how rhizosphere microbial assemblages respond to soil contamination, and how they contribute to the ability of target plants and microorganisms to tolerate, accumulate, sequester, or degrade toxic molecules. Specific goals are to: 1) analyze the links between functional gene diversity and expression, and detoxification within root-associated microbial communities in soils contaminated with petroleum and metal trace elements; 2) analyze the diversity and abundance of metabolic functions encoded by genes located on conjugative mobile elements in the rhizosphere of contaminated soils; 3) assess the effect of microbial competition and cooperation on hydrocarbon biodegradation; and 4) characterize rhizosphere community selection in response to stress. Various molecular, biochemical and microbiological approaches will be combined to test the effects of organic and inorganic soil contaminants on plant growth and the structure and activity of rhizosphere microbial communities, as well as how variations in plant and microbial parameters correlate with the fate of soil contaminants. This research program will provide novel insight into the mechanisms that guide multipartite interactions between plants and microorganisms within the rhizosphere, specifically in harsh and disturbed environments. From an applied perspective, this knowledge will be crucial to optimizing bioremediation within the rhizosphere, and will significantly enhance our ability to sustainably manage polluted sites.