Benthic survey protocol to determine coral cover, abundance, and growth form diversity

Corals and the reefs they built are being decimated by anthropogenic impact, hastening the need to develop strategies that can mitigate the effects of local stressors and global climate change. To this end, short-term acute heat stress assays provide a standardized thermal stress diagnostic to identify colonies, populations, and species with superior thermotolerance at scale, e.g. for restoration purposes or to study their genetic/genomic underpinnings.. Such data is greatly enhanced through the collection of environmental data to contextualize measured thermal tolerance differences, as thermal resilience is likely a product of genetic and environmental differences. Thus, when assessing thermal tolerance of coral colonies, it is vital to assess the status of the coral reef as a whole. Important parameters for instance are live coral cover or species richness (biodiversity). These parameters can be collected during a benthic survey, and there are many different methods for conducting benthic surveys, with some widely used methods being line intercept transects (LITs), point intercept transects (PITs) [16], and photoquadrats. Here we present a standardized photoquadrat protocol with subsequent analysis using CoralNet to contextualize measured thermotolerance differences with overall reef condition [18]. Photoquadrats have the advantage that data can be collected in the form of an underwater image while being analyzed later, allowing for flexibility and time-saving in the field. Further, it provides the possibility to work with divers with limited taxonomic experience/expertise. Importantly, desk-based digital analysis allows for standardized exploration with the ability to upload raw and processed data into databases for cross-study comparison.