Molecular tools for coral reef restoration: beyond biomarker discovery

Abstract

As coral reefs continue to decline due to climate change and other stressors, scientists have proposed adopting genomic tools, such as biomarkers, to aid in the conservation and restoration of these threatened ecosystems. Biomarkers are easily measured indicators of higher-order biological processes that can be used to predict or diagnose health, resilience, and other key performance metrics. The ultimate goal of developing biomarkers is to determine the conservation value and utility of a given coral colony, including the host animal, its algal symbionts, and their microbial partners. However, we remain far from achieving this goal because most efforts have not yet moved beyond the initial discovery phase. Here, we review recent progress in the development of coral molecular biomarkers from a practical standpoint and consider the many challenges that remain as roadblocks to large-scale implementation. We caution practitioners that, while biomarkers are a promising technology, they are unlikely to be available for field application in the near future barring a rapid shift in research focus from discovery to subsequent validation and field trials. To facilitate such a shift, we propose a stepwise framework to guide additional study in this area, with the aim of accelerating practical molecular biomarker development to enhance coral restoration practice.

Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic

“…However, biomarkers are often context‐ and species‐specific (Parkinson et al. ), and therefore multiple markers may be needed depending on the types of information desired. In addition, there are many steps between identifying a potential biomarker and deploying it in the field, and the intermediate steps involved in biomarker development are often overlooked.…”

“…The process involves four major phases: discovery, validation, field trials, and implementation. At present, the majority of basic scientific research has not progressed past the discovery phase (Parkinson et al 2018a). Consequently, the costs associated with developing practical biomarkers as predictive tools for selective restoration may be high.…”

“…This information could then be applied to select colonies for parental stocks in larval propagation, rearing in nurseries, or matching outplants to particular sites in anticipation of future environmental challenges. However, biomarkers are often context-and species-specific (Parkinson et al 2018a), and therefore multiple markers may be needed depending on the types of information desired. In addition, there are many steps between identifying a potential biomarker and deploying it in the field, and the intermediate steps involved in biomarker development are often overlooked.…”

A framework for understanding gene expression plasticity and its influence on stress tolerance

“…While we recognize and discuss the implications of the fact that gene expression, such as many phenotypic traits, is a function‐valued trait (often in a multivariate state), we focus on a reaction norm framework, in which expression is measured at only a few discrete instances, as this remains the predominant experimental design for gene expression studies (e.g., comparing healthy and diseased tissues or individuals across two different conditions). We also leverage reef‐building corals as a case study for non‐model organisms because their ecological importance and susceptibility to climate change (Hughes et al, 2018) has led to a plethora of transcriptomic studies of stress responses (Box 1; Figure 1; Parkinson et al, 2019; Thomas et al, 2018) that provide tangible examples from which we design our conceptual framework. Nevertheless, the framework described herein can be widely used to interpret gene expression plasticity in any species.…”

Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events

“…By focusing on understanding the coral transcriptomic response, we can characterize the disease responses to a wide range of potential pathogens and identify core sets of genes that are activated regardless of pathogen stimulation. This will be particularly important in identifying signatures of disease resistance in coral species for restoration activities, while also providing potential diagnostic tools for coral health [ 27 ]. While different diseases may elicit unique responses in corals, we hypothesize that there will also be a core immune response of corals in response to infectious pathogens which can be measured using transcriptomics.…”