1. Underwater visual surveys of coral reefs are the primary method managers use to monitor coral health. However, these surveys are limited to visual signs, such as bleaching and tissue loss lesions, which occur only after significant stress has accumulated. More holistic characterization of coral health can allow for better monitoring of reef changes across natural environmental gradients, in response to anthropogenic stress and after disturbance events (e.g. disease outbreaks, mass bleaching, dredging, run‐off events).
2. Various methods exist to evaluate the health of the coral holobiont that do not depend on visual signs, including histological assessment, microbiome dysbiosis and metabolic profiles, yet these tools are rarely deployed concurrently. We present a clear, readily deployable protocol for sampling and preserving coral fragments, including (a) extraction of coral metabolites for analysis, (b) preservation of microbiome DNA for sequencing and (c) preservation of coral tissues for histopathology. Combined with visual surveys, these methods provide an unparalleled, holistic characterization of coral health.
3. We provide a field‐tested, optimized protocol for conducting coral sampling. This protocol guides the user through concurrent assessments of coral tissue structure and the holobiont microbiome and metabolome, and directs the user to useful resources for downstream data analysis.
4. This protocol facilitates quantitative characterization of coral health beyond visual surveys alone, which is a valuable step forward in reef research and management and will improve our ability to describe, model and mediate impacts to coral reefs.

中文翻译：

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珊瑚组织学，代谢组学和微生物组的补充采样方法

1. 水下目视珊瑚礁调查是管理人员用来监测珊瑚健康的主要方法。但是，这些调查仅限于视觉迹象，例如漂白和组织丢失病变，这些迹象仅在累积大量压力后才会发生。更加全面的珊瑚健康特征可以更好地监测自然环境梯度下的珊瑚礁变化，以应对人为压力和干扰事件（例如，疾病暴发，大规模漂白，疏dr，径流事件）。
2. 存在多种不依赖视觉迹象的方法来评估珊瑚虹鳟的健康状况，包括组织学评估，微生物组营养不良和代谢状况，但是很少同时使用这些工具。我们提出了一个清晰，易于部署的协议，用于采样和保存珊瑚碎片，包括（a）提取珊瑚代谢产物进行分析，（b）保留微生物组DNA进行测序和（c）保留珊瑚组织用于组织病理学。结合视觉调查，这些方法提供了珊瑚健康无与伦比的整体特征。
3. 我们提供了经过现场测试的优化协议来进行珊瑚采样。该协议指导用户通过同时评估珊瑚组织结构和全生命微生物组和代谢组，并指导用户找到有用的资源进行下游数据分析。
4. 该协议不仅可以通过视觉调查促进珊瑚健康的定量表征，这是珊瑚礁研究和管理迈出的重要一步，并将提高我们描述，建模和调解对珊瑚礁影响的能力。