Complementary sampling methods for coral histology, metabolomics and microbiome

Abstract

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). 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. 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. 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.

Does Predation Exacerbate the Risk of Endosymbiont Loss in Heat Stressed Hermatypic Corals? Molecular Cues Provide Insights Into Species-Specific Health Outcomes in a Multi-Stressor Ocean

“…This suggests that these organisms display considerable molecular flexibility and can quickly acclimatize to changing conditions, which explains their overall tolerance to stress. In future studies, histological analysis of coral samples would be useful to anchor molecular results at higher biological complexity levels and identify tissue changes and pathological processes contributing to thermosensitivity (for a detailed review of histological methods in aquatic organisms, see Costa, 2017 ; for coral sampling techniques for histological analysis, see Greene et al, 2020 ).…”

A review of coral bleaching specimen collection, preservation, and laboratory processing methods

“…For instance, if the primary goal of a study is to collect coral specimens for Symbiodiniaceae density enumeration, but the researchers were able to use sterile handling and collection techniques, then specimens collected would also be suitable for downstream analysis of the microbiome. A recent seminal paper by Greene et al (2020) outlined an optimized and standardized protocol for collecting coral specimens such that researchers could maximize their potential and be used for microbial, metabolomic, and histological analyses simultaneously. Additional highly detailed papers such as this are needed to further guide future researchers along methodological pathways that maximize the utility and comparability of coral specimens for multiple downstream analyses.…”

Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution

“…Repeated through time, these measures will provide unique insights into how microbiome-mediated phenotypic plasticity may allow hosts to rapidly accommodate to novel environments or resources (e.g., microbes allow some host individuals to obtain nutrients from novel foods) through periodic (e.g., seasonal fluctuations) and transient environmental changes (e.g., heat waves). For foundational, long-lived, and large colonial host species, noninvasive methods exist for repetitive sampling of tagged individuals (e.g., for corals [ 60 ]). The focus should also expand beyond foundation species to include small, ecologically important host organisms and those with life history strategies that make them particularly tractable for transgenerational studies.…”