Fig. 1

Overview of the diagnostic value of various coral reef microbiomes. The diagnostic value (indicated as stars) is based on the sum of advantages (+) and disadvantages (−) for key characteristics of optimal microbial indicators: (1) ease of sampling, (2) sensitivity towards environmental fluctuations, (3) uniformity of community assembly, (4) our ability to link microbiome shifts to host health. Based on these criteria, seawater microbial communities collectively have the highest diagnostic potential to be used as microbial indicators of reef health, followed by sediment-associated and host-associated microbial communities, respectively. Free-living microbial communities (seawater and sediment) can be easily collected, without interfering with ecosystem processes and/or the health of reef organisms, consistent with desirable characteristics for environmental monitoring programs. In contrast, the collection of host-associated microbiomes is labour intensive and potentially poses a certain risk for host health when collecting tissue, although collections of the host-biofilm are non-invasive for the host. Seawater also revealed the highest sensitivity to changes in the surrounding environment (e.g., temperature and eutrophication) due to uniform community assembly patterns of the seawater microbiome across replicates, while sediments were primarily influenced by site-specific patterns (e.g. grain size) and host-associated microbiomes predominantly showed a host-genotype modulation. While the diagnostic value is highest for most criteria in the seawater microbiome, it is challenging to link disturbance-induced shifts in marine bacterioplankton to host health. Given the importance of host-associated microbes to the health of reef holobionts, the establishment of microbial baselines for host-associated microbiomes and the search for host health microbial indicators are still warranted