NSF PRFB FY 2023: Multi-omics Assessment of Translocation Impacts on Sonoran Pronghorn

该行动资助了美国国家科学基金会2023财年生物学博士后研究奖学金，研究基因组，环境和表型之间相互作用的生命规则的综合研究。该奖学金支持将以创新方式对生活规则领域作出贡献的研究员的研究和培训。个体对环境变化的生物反应并不完全是由于个体的遗传因素。相反，一个有机体代表了一个复杂的生态系统，而反应的产生部分是由于该有机体内存在的种群或群落微生物之间的相互作用。此外，这些微生物群落的组成和功能是动态的，反映了宿主更广泛的环境背景。本研究旨在阐明野生动物及其肠道相关细菌、病毒和寄生虫群落如何应对不断变化的环境并相互作用。具体来说，这位研究员将研究索诺兰叉角羚（Antilocapra americana sonoriensis）之间的这些关系，索诺兰叉角羚是一种只在亚利桑那州和墨西哥索诺兰沙漠地区发现的濒危有蹄类哺乳动物。索诺兰叉角羚是这项研究的理想物种，因为圈养的叉角羚每年都会被放归野生栖息地，这是它们恢复工作的一部分，而且计划将叉角羚引入加州的新栖息地。研究野生动物对这种迁移的反应对于提高其他需要这些保护措施的物种的成功和长期健康至关重要。该项目还将通过为传统上代表性不足的群体（从高中到研究生）整合身临其境的实地、实验室和计算研究经验，扩大科学参与。该研究员将使用多组学方法来解决以下目标：1)研究肠道微生物组和病毒组组成的基因组和环境驱动因素；2)评估宿主和微生物对易位的反应。基因组、病毒组和微生物组扩增子测序将使用圈养索诺兰叉角羚的成对血液和粪便样本进行。叉角羚将在亚利桑那州和加利福尼亚州进行微生物组/病毒组鉴定和亚转录组测序，以评估宿主和微生物的转录反应。该研究员将研究宿主基因组变异、环境和免疫因素以及微生物群落多样性之间的关系，并将数据集结合起来开发对索诺兰叉角羚易位影响和生态系统健康的预测模型。该项目将扩展该研究员在微生物组表征和将不同数据集集成为预测建模与机器学习方法方面的研究技能，并提供指导机会（每年四名学生实习生，以及一名来自墨西哥的博士生），利用项目生成的数据解决独立研究问题。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。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2023, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment, and Phenotypes. The fellowship supports research and training of the fellow that will contribute to the area of Rules of Life in innovative ways. Biological responses of individuals to changing environments are not due exclusively to individual genetic factors. Rather, an organism represents a complex ecosystem, and responses arise partly due to interactions among populations or communities microorganisms that exist within that organism. Furthermore, composition and function of these microorganism communities are dynamic and reflect the broader environmental context of hosts. This research seeks to clarify how wildlife and their gut-associated bacterial, viral, and parasite communities respond to changing environments and interact with each other. Specifically, the fellow will study these relationships within Sonoran pronghorn (Antilocapra americana sonoriensis), an endangered hoofed-mammal found only in the Sonoran Desert region of Arizona and Mexico. The Sonoran pronghorn is an ideal species for this study because captive individuals undergo annual releases to their wild habitat as part of their recovery efforts, and additional translocations are planned to introduce pronghorn to new habitats in California. Studying how wildlife respond to such translocations is crucial to improving success and long-term health of other species in need of these conservation measures. The project will also broaden participation in science through incorporating immersive field, laboratory, and computational research experiences for traditionally underrepresented groups, from high school to graduate students. The fellow will use a multi-omics approach to address the following objectives: 1) investigate the genomic and environmental drivers of gut microbiome and virome composition, and 2) assess host and microbial responses to translocation. Genome, virome, and microbiome amplicon sequencing will be conducted using paired blood and fecal samples from captive Sonoran pronghorn. Pronghorn will be sampled pre- and post-release in Arizona and California for microbiome/virome characterization and metatranscriptomic sequencing to assess host and microbial transcriptional responses. The fellow will examine relationships among host genomic variation, environmental and immunological factors, and diversity of microbial communities, and datasets will be combined to develop predictive models for translocation impacts on Sonoran pronghorn and ecosystem health. The project will expand the fellow’s research skillset in microbiome characterization and integration of diverse datasets for predictive modeling with machine learning approaches, providing mentorship opportunities (four student interns per year, as well as a PhD student from Mexico) in addressing independent research questions using data generated by the project.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.