Collaborative Research: Dissolved organic matter feedbacks in coral reef resilience: The genomic & geochemical basis for microbial modulation of algal phase shifts

珊瑚礁的退化，无论是由过度捕捞、营养污染、水质下降或其他人为因素造成的，都与珊瑚礁向以肉质藻类为主的珊瑚礁的阶段转变有关。在许多情况下，管理和改善这些应激源并不会导致珊瑚恢复主导地位，珊瑚礁会在以藻类为主的状态下枯萎多年。近十年的研究表明，藻类优势度上升的轨迹是重组微生物群落组成和新陈代谢；研究人员假设，微生物过程通过代谢藻类释放的有机化合物来促进藻类优势的维持，从而通过缺氧和疾病对珊瑚造成压力。珊瑚礁对这些阶段变化的适应能力是珊瑚礁生态学中的一个关键问题，管理经历这些群落变化的珊瑚礁需要了解微生物相互作用在促进藻类过度生长和改变珊瑚礁生态系统功能方面的作用。这里提出的研究将调查藻类产生的有机物，代谢有机物的微生物，以及这些过程对珊瑚健康和生长的影响。这项研究通过测试珊瑚相关微生物群落对藻类的不同抵抗力，并确定改变生态系统生物地球化学的藻类物种复盖率阈值，对管理珊瑚礁对藻类相变的适应能力具有重要意义。该项目提供跨越多个职业层次的指导，将未被充分代表的本科生、两名研究生、一名博士后研究员以及一名初级和成熟的研究人员联系起来。该项目将在与生态相关的空间和时间尺度上整合溶解有机质(DOM)地球化学、微生物基因组学和生态系统过程测量，以测试微生物介导的反馈可能促进肉质藻类在太平洋珊瑚礁生态系统中传播的假想机制。这项研究的一个关键成果将是了解珊瑚礁上珊瑚和藻类的组成如何与复杂的微生物群落协同作用，以影响珊瑚礁生态系统对藻类相变的适应能力。新兴的分子和生物地球化学方法将被用来在多个空间和时间尺度上研究微生物-DOM相互作用的机制。该项目将利用法属波利尼西亚莫奥里亚珊瑚礁长期生态研究项目的背景环境数据、实验室设施和现场后勤资源，并为该项目调查面对全球变化的珊瑚礁弹性的任务做出贡献。研究人员将量化DOM生产的散装Diel模式，并表征发色成分的组成，以及来自不同底栖藻来源的游离和可酸解的中性单糖和氨基酸的组成。该小组还将利用系统发育学和生物转录组学，包括跟踪特定微生物谱系对藻类渗出物的利用，在现场受控的环境舱中表征浮游和珊瑚相关微生物群落分类组成和基因表达的变化。现场部署的100升帐篷生态系统将用于研究包括藻类和珊瑚物种组合在内的典型底栖生物群落的DOM生产和消费、微生物群落基因组学和生态系统新陈代谢的现场动态模式。总之，这些实验结果将指导对珊瑚-藻类相互作用区浮游和珊瑚相关微生物基因组和新陈代谢的厘米级空间动力学的现场调查的解释，包括使用平面光谱仪、高通量流式细胞术和荧光光谱分析的氧、细菌和DOM的边界层动力学。

Coral reef degradation, whether driven by overfishing, nutrient pollution, declining water quality, or other anthropogenic factors, is associated with a phase shift towards a reefs dominated by fleshy algae. In many cases managing and ameliorating these stressors does not lead to a return to coral dominance, and reefs languish in an algal-dominated state for years. Nearly a decade of research has demonstrated that trajectories toward increasing algal dominance are restructuring microbial community composition and metabolism; the investigators hypothesize that microbial processes facilitate the maintenance of algal dominance by metabolizing organic compounds released by algae thereby stressing corals through hypoxia and disease. The resilience of reefs to these phase shifts is a critical question in coral reef ecology, and managing reefs undergoing these community shifts requires developing an understanding of the role of microbial interactions in facilitating algal overgrowth and altering reef ecosystem function. The research proposed here will investigate the organics produced by algae, the microbes that metabolize the organics, and the impacts of these processes on coral health and growth. This research has implications for managing reef resilience to algal phase shifts by testing the differential resistance of coral-associated microbial communities to algae and defining thresholds of algal species cover which alter ecosystem biogeochemistry. This project provides mentoring across multiple career levels, linking underrepresented undergraduates, two graduate students, a postdoctoral researcher, and a beginning and established investigators. This project will integrate dissolved organic matter (DOM) geochemistry, microbial genomics and ecosystem process measurements at ecologically-relevant spatial and temporal scales to test hypothetical mechanisms by which microbially-mediated feedbacks may facilitate the spread of fleshy algae on Pacific reef ecosystems. A key product of this research will be understanding how the composition of corals and algae on reefs interact synergistically with complex microbial communities to influence reef ecosystem resilience to algal phase shifts. Emerging molecular and biogeochemical methods will be use to investigate mechanisms of microbial-DOM interactions at multiple spatial and temporal scales. This project will leverage the background environmental data, laboratory facilities and field logistical resources of the Mo'orea Coral Reef Long Term Ecological Research Project in French Polynesia and contribute to the mission of that program of investigating coral reef resilience in the face of global change. The investigators will quantify bulk diel patterns of DOM production and characterize the composition of chromophoric components and both free and acid-hydrolyzable neutral monosaccharides and amino acids from varying benthic algae sources. The team will also characterize planktonic and coral-associated microbial community changes in taxonomic composition and gene expression caused by algal DOM amendments in on-site controlled environmental chambers using phylogenetics and metatranscriptomics, including tracking algal exudate utilization by specific microbial lineages. Field-deployed 100 liter tent mesocosms will be used to examine in situ diel patterns of coupled DOM production and consumption, microbial community genomics and ecosystem metabolism over representative benthic communities comprising combinations of algal and coral species. Together these experimental results will guide interpretation of field surveys of centimeter-scale spatial dynamics of planktonic and coral-associated microbial genomics and metabolism at zones of coral-algal interaction, including boundary layer dynamics of oxygen, bacteria and DOM using planar optodes, high-throughput flow cytometry and fluorescence spectroscopy.