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

Abstract

Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen’s investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen’s utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect.

Experimental considerations of acute heat stress assays to quantify coral thermal tolerance

“…There are currently no guidelines on appropriate fragment sizes for experimental examination of coral thermal tolerance 13 and this metric is rarely reported 52 . The coral restoration literature has suggested that larger fragments may result in greater survival 53 although this is not always the case 54 – 56 .…”

Perspective: Opportunities for advancing aquatic invertebrate welfare

“…In cases where invasive sampling cannot be avoided, sharing samples with other researchers can reduce the need for additional specimen collection ( 54 ). If lethal sampling is required, aquatic invertebrates should be euthanized prior to sampling.…”

Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration

“…Between 2014 and 2021 over 20,000 coral specimens and samples were collected for bleaching studies ( McLachlan et al, 2021 ), many of which are suitable for additional analyses that could address new questions concerning various aspects of bleaching. The technology and methods commonly used in coral biology research have quickly progressed in recent decades ( Cziesielski, Schmidt-Roach & Aranda, 2019 ; Grottoli et al, 2021 ).…”

“…Integration of these approaches thus allows individual specimens to be used for multiple downstream applications and expands the potential utility of every coral sample collected. Despite this, scientists and practitioners tend to sample, preserve, and archive specimens in a manner specific to their own specialized applications or aims, and on average only conduct one or two downstream analyses per study ( McLachlan et al, 2021 ). However, it is unclear how many or how often archived samples are utilized.…”

“…A previous literature review identified many methodologies in coral-bleaching studies ( McLachlan et al, 2021 ), broadly categorized into three disciplinary areas: Omics ( e.g ., genomics, epigenomics, transcriptomics, metagenomics, amplicon analysis, proteomics, and metabolomics), Physiology ( e.g ., chlorophyll, lipid/protein/carbohydrate concentrations, biomass, tissue and skeletal stable isotopes), and Microscopy & Imaging-based analyses ( e.g ., Symbiodiniaceae density measures, electron microscopy, histology, Raman spectroscopy). Using 36 defined analytical assessments ( Fig.…”