RUI: Collaborative Research: Genetic and ecological drivers of microbial adaptation to high-nickel serpentine soils

由于地球上的地质情况在景观上各不相同，土壤微生物群落的性质也各不相同。这些微生物群落之间的差异反映了一种适应过程，在这种过程中，在特定土壤栖息地中提供有益基因的微生物在该土壤栖息地中更为常见。加州的草原景观自然地被不寻常的有毒富镍土壤所点缀。几千年来，这些斑块一直是微生物适应有毒金属的场所。该项目的主要目标是发现允许固氮土壤细菌（中根菌）耐受有毒金属的基因，了解这些基因如何在斑块状景观中的细菌中分布，并测试当有毒金属不存在时，这些耐受基因是否会施加不利影响。这项研究的见解将有助于制定基于生物的人类污染土壤修复策略，并为微生物对有毒环境的适应提供见解。由于根瘤菌，其中包括中根瘤菌，负责大约一半的生物固氮，这项研究具有农业意义。该项目将整合一个以本科生为重点的培训计划，为学生提供真实的研究经验。在这个项目中，学生将分离出对有毒金属具有极高耐受性的细菌菌株，并研究它们的基因组是否包含已知提供重金属耐受性的基因。因此，这项受资助的工作有助于理解生物体如何适应极端环境，并利用了处于培训关键阶段的年轻科学家的努力。该项目探索了微生物进化生态学的一个关键前沿：微生物在自然界中的局部适应，以及适应权衡在确定异质环境中基因型分布中的作用。在本项目中，将从蛇形和非蛇形土壤中分离出易从共生寄主植物中分离出的固氮细菌——中根菌。这些中根菌菌株将在不同的镍水平下进行简单的实验室生理学和适应性分析。全基因组测序，转录谱分析，以及分子遗传操作，也将用于表征这些菌株。这个高度易于处理的系统将使镍适应的基因和机制的识别，以及适应性权衡的直接测量。该项目还将把权衡与蛇形斑块中不同大小和镍富集水平的特定适应性分布联系起来，从而测试关于专业化和适应性权衡之间关系的一般进化生态学理论。本科生将参与生理学，分类学，遗传学和基因组学的表征过程中，以课程为基础的研究经验。此外，还将在K-12学校开展外展活动，让这些学生接触STEM研究。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

As Earth's geology varies across the landscape, so do the properties of soil microbial communities. Variation among these microbial communities reflect an adaptive process in which genes providing benefits in a particular soil habitat are more common in the microbes dwelling there. Grassland landscapes in California are naturally punctuated by unusual patches of toxic, nickel-rich soil. For thousands of years, these patches have been sites of microbial adaptation to toxic metals. The primary goal of this project is to discover genes that allow the nitrogen fixing soil bacteria, Mesorhizobium, to tolerate toxic metals, to understand how these genes are distributed among bacteria across a patchy landscape, and to test whether these tolerance genes impose disadvantages when toxic metals are not present. Insights from this study will assist in developing strategies for biologically based remediation of human-contaminated soils and provide insight into adaptation of microbes to toxic environments. Since rhizobial bacteria, which include the Mesorhizobium, are responsible for approximately half of the biological nitrogen fixation, this research has agricultural implications. The project will integrate an undergraduate-focused training program that provides students with authentic research experiences. In this program, students will isolate bacterial strains with extremely high tolerance to toxic metals, and investigate whether their genomes include genes known to provide heavy metal tolerance. The funded work therefore contributes to understanding how organisms adapt to extreme environments and employs the efforts of young scientists at a critical stage of their training.This project explores a critical frontier in microbial evolutionary ecology: microbial local adaptation in nature, and the role of fitness trade-offs in determining genotype distributions across heterogeneous environments. In this project, mesorhizobia, nitrogen-fixing bacteria that are easily isolated from symbiotic host plants, will be isolated from serpentine and non-serpentine soils. These Mesorhizobium strains will be subjected to straightforward laboratory physiology and fitness assays under varying nickel levels. Whole genome sequencing, transcriptional profiling, as well as molecular genetic manipulations, will also be used to characterize these strains. This highly tractable system will enable the identification of genes and mechanisms of nickel adaptation, along with direct measurement of fitness trade-offs. The project will additionally link trade-offs to the distribution of specific adaptations across a landscape of serpentine patches that vary in size and level of nickel enrichment, thereby testing general evolutionary-ecological theories about the relationship between specialization and fitness trade-offs. Undergraduates will be involved in characterization of the physiology, taxonomy, genetics, and genomics of Mesorhizobia during a course based research experience. Additionally, outreach will be performed to K-12 schools to expose these students to STEM research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.