Gene expression
Genetic biomarkers are emerging as powerful tools to identify sources of stress and measure stress responses in corals (Edge et al. 2005; Morgan et al. 2005) and their symbionts (Leggat et al. 2007 and see reviews by van Oppen and Gates 2006; Foret et al. 2007). Regulation of stress-specific genes is determined by comparing gene expression in populations exposed to environmental stressors with those at reference conditions. For example, the development of a complimentary DNA (cDNA) array containing 32 stress genes allowed the profiling of gene expression in corals exposed to changes in seawater temperature, salinity and ultraviolet light in the laboratory (Edge et al. 2005) and with increasing distance from leachate associated with a municipal dump (Morgan et al. 2005; Table 2). Other studies have investigated changes in the expression of large numbers of genes with DNA microarrays for stressors, such as changing seawater temperatures (Foret et al. 2007), suggesting potential for similar applications to detect changes in water quality. Gene expression ranked a medium-priority bioindicator for use in long- and short-term monitoring programmes (Table 3). Whilst it has been shown to be highly specific, the methods to detect changes in water quality require testing under field conditions and the patterns of temporal variability are not well understood.