CAREER: Holobionts Unfiltered: integrated comparative and experimental examination of the role of cnidarian innate immunity on microbiome structure and stability

热带珊瑚礁是生物多样性的热点。对于许多沿海社区来说，它们是收入的来源，是抵御风暴破坏的盾牌，也是文化的象征。在2.4亿多年的时间里，石珊瑚的生长造就了这些生态系统。在那段时间里，石珊瑚分成了两大类，超过1500种。但珊瑚并不是个例；分子工具的使用确定了微观尺度上的共生。在每个珊瑚虫的内部是由甲藻、细菌和古菌组成的群落，这些群落一起被称为珊瑚微生物群。珊瑚微生物群可以帮助或损害压力较大的珊瑚。这可能会影响珊瑚礁因珊瑚疾病和大规模珊瑚白化而导致的珊瑚礁衰退。据认为，具有更多天然免疫基因的珊瑚物种的微生物群多样性较差。然而，这一点还没有得到检验。该项目将使用一种经济高效的“基因组浏览”方法来测试这一想法，以比较128个珊瑚物种的珊瑚微生物和免疫基因。这种比较将表明不同的先天免疫基因如何塑造珊瑚微生物群。该项目将使用卡列尼娜，一种新的统计学方法，来测试关于免疫如何在压力期间改变微生物群动态的想法。最后，该项目将在实验室实验中检验这些预测。这些研究目标与一项教育计划相结合，该计划将在本科课堂上使用项目数据，开发一种新的在线互动生物信息学教科书，并制作珊瑚礁场景，这是一种学习产品，让高中生和本科生在课堂练习中模拟珊瑚礁生态。从大型藻类竞争到漂白等多种生态压力，硬珊瑚的生存能力被认为取决于珊瑚、微生物和环境相互作用的结果。因此，了解珊瑚如何调节它们的微生物群对于了解珊瑚对环境压力的反应是很重要的。珊瑚的先天免疫被认为在调节微生物群方面起着关键作用。然而，珊瑚先天免疫与微生物群落的丰富度、组成和稳定性之间的关系还没有得到很好的理解。该项目实施了一项综合研究和教育计划，以研究哺乳动物先天免疫的进化如何影响微生物群的结构，以及微生物群中细菌和古生菌部分的变化如何影响热应激的生存。这一方法将结合一项全球跨物种调查，该调查涉及不同珊瑚基因组中的天然免疫基因库及其微生物组的丰富性和组成，并将结合实验室实验，在一个模式珊瑚中可以证实或证伪调查中提出的免疫-微生物组相互作用。一种新的建模方法将被用来仔细区分先天免疫和热应激对微生物组动态的影响的相互竞争的时间序列模型。通过将测序方法与易于处理的线虫模型系统相结合，该项目将检验线虫寄主-微生物共生、生态学和进化的关键假说。这些研究目标与教育和推广计划相结合，包括在本科课堂上使用项目数据，开发新的交互式在线生物信息学文本，以及制作珊瑚礁场景，这是一个模拟珊瑚礁生态的课堂产品。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Tropical coral reefs are biodiversity hotspots. For many coastal communities, they are a source of income, a shield against storm damage, and a cultural icon. For more than 240 million years, the growth of stony corals engineered these ecosystems. Over that time, stony corals split into two main groups with more than 1500 species. But corals are not alone; the use of molecular tools identified symbiosis on microscopic scale. Inside each coral polyp are communities of dinoflagellates, bacteria, and archaea that are together called the coral microbiome. Coral microbiomes can help or harm stressed corals. This can affect reef decline due to coral disease and mass coral bleaching. It is thought that coral species with more innate immunity genes have less diverse microbiomes. However, this has not yet been tested. This project will test this idea using a cost-effective ‘genome skimming’ approach to compare coral microbes and immunity genes across 128 coral species. This comparison will suggest how different innate immunity genes shape coral microbiomes. The project will use Karenina, a new statistical method, to test ideas about how immunity changes microbiome dynamics during stress. Finally, the project will test those predictions in laboratory experiments. These research aims are paired with an education plan that will use project data in undergraduate classes, develop a new online interactive bioinformatics textbook, and produce Reef Scenarios, a learning product that will let high school and undergraduate students simulate reef ecology in engaging classroom exercises.The ability of scleractinian (‘stony’) corals to survive many ecological stressors – from macroalgal competition to bleaching – is thought to depend on the outcome of coral x microbe x environment interactions. Therefore, understanding how corals regulate their microbiome is important for understanding coral’s response to environmental stress. Coral innate immunity is thought to play a critical role in regulating the microbiome. Yet the relationship between coral innate immunity and microbiome richness, composition, and stability is not yet well understood. This project implements an integrated research and education plan to study how the evolution of cnidarian innate immunity has influenced microbiome structure, and how changes in the bacterial and archaeal portion of the microbiome may influence survival of thermal stress. This approach will combine a global cross-species survey relating innate immune gene repertoires in diverse coral genomes with their microbiome richness and composition and laboratory experiments in a model cnidarian that can confirm or falsify proposed immunity-microbiome interactions from the survey. A new modeling approach will be used to carefully distinguish competing time-series models of the effects of innate immunity and thermal stress on microbiome dynamics. By uniting sequencing approaches with a tractable cnidarian model system, this project will test key hypotheses in cnidarian host-microbe symbiosis, ecology and evolution. These research objectives are integrated with an education and outreach plan that includes use of project data in undergraduate classes, development of a new interactive online bioinformatics text, and production of Reef Scenarios, a classroom product for simulating reef ecology.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.