Genomic analysis of adaptation to an extreme terrestrial environment

生物已经适应了地球上惊人的栖息地多样性。最极端的陆地栖息地之一是蛇纹岩地质暴露的结果，蛇纹岩是地球地幔物质化学和水文变化的产物。蛇形岩（以及从这些岩石中提取的土壤）含有极其有限的一些必需的矿物质营养物质，包括氮、磷、钾和钙。此外，它们天然含有高水平的有毒“重金属”，如镍和铬。由于这些多重化学挑战，蛇纹石环境的特点是土壤发育不良，有机质含量低，易受干旱影响。只有少数植物、动物和微生物的生命形式已经适应了恶劣的蛇形环境。圣巴巴拉宝石花，C. amplexicaulis变种巴巴拉是芥菜科的一种野生植物，适应（实际上仅限于）蛇形地质。为了研究该植物适应蛇形石生境的遗传、生理和分子机制，将其与生长在花岗岩土壤上且对蛇形石死亡率为100%的近亲C. amplexicauis变种. amplexicaulis杂交。这个杂交的后代被用来创造一个实验群体，该群体显示出几个耐蛇纹石性状的遗传分离，包括在低钙、低氮、低磷和高镍浓度下的生长。这些遗传资源将与所有表达基因的下一代测序（转录组学）和全基因组重测序一起使用，以确定对蛇形环境适应的基因和遗传相互作用。蛇形类C. amplexicaulis var. barbarae在低氮低磷条件下的生长优于非蛇形类C. amplexicaulis var. amplexicaulis。了解这些遗传差异背后的分子机制，将激发开发作物的新方法，减少氮肥和磷肥的施用，以达到最佳生产力，从而有助于解决人类面临的一些最紧迫的农业环境问题：平衡全球粮食生产与过量施用氮肥和磷肥造成的污染（导致富营养化、沿海“死亡区”、珊瑚礁破坏和其他生态退化）。此外，在实验室实验中，C. amplexicaulis var. barbarae对有毒镍表现出优异的耐受性，实际上镍的超积累达到了非常高的水平（~1%干重）。了解重金属耐受和积累的遗传机制将为促进金属污染场地有效植物修复系统的发展提供基础科学。通过与一所教育创新高中的合作，该项目将探索一种新的模式，让学生和教师参与到真正的合作研究中，并与数学、空间科学、地球科学和生物学的教学相结合。

Organisms have adapted to an astonishing diversity of habitats on our planet. One of the most extreme terrestrial habitats is the result of geological exposures of serpentine rocks, which are the product of chemical and hydrological modification of materials from the Earth's mantle. Serpentine rocks (and soils derived from these rocks) have extremely limited amounts of a number of essential mineral nutrients, including nitrogen, phosphorous, potassium, and calcium. In addition, they have naturally high levels of toxic 'heavy' metals such as nickel and chromium. As a result of these multiple chemical challenges, serpentine environments are characterized by poor soil development, low levels of organic matter, and susceptibility to drought. Only a small number of plant, animal and microbial life forms have adapted to the harsh serpentine environment. The Santa Barbara Jewelflower, C. amplexicaulis var. barbarae is a wild plant in the mustard family that is adapted to (and in fact restricted to) serpentine geology. To study the genetic, physiological and molecular mechanisms that underlie adaptation to serpentine habitats, this plant was crossed to its close relative C. amplexicauis var. amplexicaulis, which grows on granite soils and shows 100% mortality on serpentine. Progeny from this cross were used to create an experimental population that showed genetic segregation for several serpentine-tolerance traits, including growth on low calcium, low nitrogen, and low phosphorous, as well as high nickel concentrations. These genetic resources will be used along with next-generation sequencing of all expressed genes (transcriptomics) and whole-genome resequencing to identify the genes and genetic interactions that underlie adaptation to the serpentine environment. The serpentine taxon C. amplexicaulis var. barbarae shows superior growth in low nitrogen and low phosphorous conditions, compared to the non-serpentine C. amplexicaulis var. amplexicaulis. Knowledge of the molecular mechanisms underlying these genetic differences will stimulate new approaches to the development of crops that require smaller applications of nitrogen and phosphorous fertilizers to achieve optimum productivity, and thus help address some of the most pressing agro-environmental issues facing humankind: balancing global food production against pollution by excess application of nitrogen and phosphorous fertilizers (leading to eutrophication, coastal 'dead zones', coral reef destruction, and other ecological degradation). Further, in laboratory experiments, C. amplexicaulis var. barbarae shows superior tolerance to toxic nickel, and actually hyper-accumulates nickel to extraordinary levels (~1% dry weight). Understanding the genetic mechanisms of heavy metal tolerance and accumulation will provide the foundational science that will foster the development of efficient phytoremediation systems for metal contaminated sites. In collaboration with an educationally innovative high school that encompasses a natural serpentine outcrop with a native population of Caulanthus amplexicaulis var. barbarae, this project will explore a new paradigm for involving students and faculty in authentic collaborative research that is integrated with teaching in mathematics, spatial sciences, earth sciences, and biology.