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

土壤污染是一个全球性问题，主要是由各种农业、采矿和工业活动引起的。能够在污染土壤中生长的植物面临着由有毒无机和有机分子引起的许多压力，包括细胞膜损伤、DNA修饰和酶失活。虽然农业和采矿业通常是数量有限的污染化合物的来源，但受影响最严重的工业场所含有数千种有毒化学品的混合物，如多环芳烃、多氯联苯、各种石油副产品、杀虫剂、溶剂和微量元素。某些污染物在土壤中的积累对植物、动物、人类和生态系统的健康构成严重威胁。许多微生物和植物能够分解和/或隔离土壤污染物。污染物对植物健康的影响一直是许多研究的主题，但对微生物群落和植物-微生物相互作用的影响不太清楚，因为土壤微生物群落极其复杂。尽管最近我们对形成根际土壤细菌和真菌群落的环境因素的理解取得了进展，但这些群落与它们对污染的反应之间的联系仍然知之甚少。根际是一个紧密相连的元生物，至少包括植物、细菌和真菌的专性连接。许多研究表明植物特性与根际微生物群落结构和活性之间存在联系，但由于其他因素的强烈影响，植物对根际微生物的影响可能因土壤而异。植物如何在受干扰的环境中促进有益微生物的聚集，以及在微生物群落改造上的投入是否会随着植物的胁迫状态而变化，这些都是未知的。在根际内，微生物解毒的程度可能受到微生物间竞争与合作的影响，而这些相互作用可能被植物所改变。根际是质粒转移的热点，因此植物可能促进这种合作遗传交换。本研究计划的总体目标是了解根际微生物组合如何对土壤污染做出反应，以及它们如何促进目标植物和微生物耐受、积累、隔离或降解有毒分子的能力。具体目标是：1)分析石油和金属微量元素污染土壤中功能基因多样性和表达与根相关微生物群落解毒之间的联系；2)分析污染土壤根际共轭移动元件基因编码代谢功能的多样性和丰度；3)评价微生物竞争与合作对烃类生物降解的影响；4)根际群落选择对胁迫的响应特征。将结合各种分子、生化和微生物方法来测试有机和无机土壤污染物对植物生长和根际微生物群落结构和活动的影响，以及植物和微生物参数的变化如何与土壤污染物的命运相关。该研究项目将为指导植物和微生物在根际，特别是在恶劣和受干扰的环境中的多方相互作用的机制提供新的见解。从应用的角度来看，这些知识对于优化根际生物修复至关重要，并将显著提高我们可持续管理污染场地的能力。

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.