Heatwave-driven persistent microbes threaten the resilience of Mediterranean coral holobionts

Abstract

Background: The climate crisis poses a serious threat to octocorals in the Mediterranean Sea as marine heatwaves (MHWs) not only impair coral metabolism but also disrupt the complex symbiosis between the coral host and its microbiome. Since octocorals are the foundation species of the Mediterranean animal forests, understanding their resilience, i.e. ability to recover and survive to MHWs, is crucial to predict their viability under future climatic conditions. Using amplification of 16 S and 18 S rRNA genes for metabarcoding and qPCR analyses to follow the changes in bacterial microbiome and eukaryome as well as host response under stress and recovery conditions, this study provides the first comprehensive assessment of the resilience of an iconic Mediterranean octocoral (the red coral Corallium rubrum) to a mild (19 °C) and more severe (23 °C) heat stress.

Results: The results of this work indicate a stress response of the host to elevated temperatures, even under mild temperature. The eukaryome was highly sensitive to heat stress and underwent rapid structural changes among the dominant microeukaryotes. In contrast, the relative and absolute abundance of the major bacterial symbionts remained stable throughout the stress. However, heat stress led to a significant increase in the abundance of some taxa such as Vibrionaceae that persisted after a week of recovery.

Conclusions: While the host recovered from the stress, and the microbiome largely returned to its original composition during recovery, the results highlight the persistent presence of some taxa that might compromise the short-term resilience of octocoral holobionts. This study provides new information on how octocoral holobionts respond to MHWs in the Mediterranean Sea. This knowledge is crucial for the development of effective, science-based strategies for coral protection and restauration.

Keywords: Bacteria; Climate change; Marine animal forests; Mass mortality events; Metabarcoding; Microbial communities; Microbiome; Microeukaryotes; Octocorals; Resilience; Temperate corals.

Fig. 1

Schematic representation of the experimental design. (A) Experimental temperature regimes applied to the corals, with the three sample collection time points. (B) Nine colonies were cut in nine nubbins randomly allocated into groups of three in the aquaria. One nubbin per colony and thermal treatment was removed at each sampling time point

Fig. 2

Relative abundance of the bacterial and microeukaryotic families associated with C. rubrum colonies depending on the sampling time and thermal treatment. Taxa with an average relative abundance below 3% are grouped

Fig. 3

Bacteria and microeukaryote ASVs differentially abundant (ANCOM-BC results) between the sampling times and thermal treatments. Differences in relative abundance are calculated as log fold change (natural log)

Fig. 4

Network representation of significant microbial associations inferred from 16 S (prokaryotic) and 18 S (microeukaryotic) rRNA genes metabarcoding datasets. Nodes represent ASVs, with colors distinguishing bacterial (blue) and microeukaryotic (green) taxa. Edges indicate associations: red edges denote positive correlations, and blue edges denote negative correlations. Edge thickness corresponds to the strength of the association. Families of the ASVs of the 6 higher positive correlations for each group (intra-kingdom and inter-kingdom) as well as the first 3 higher negative correlations are labeled next to the nodes

Fig. 5

Relative expression ratio of stress response genes in fold change (TNFR1 and HSP70) between control and thermally treated colonies (C + 4 and C + 8) at the different sampling times. Graphs are presented in logarithmic scale. Statistical significance levels of differences compared to the controls are indicated by stars (* for p < 0.05 and ** for p < 0.01)

Fig. 6

Relative expression ratio (fold change) between control and thermally treated colonies (C + 4 and C + 8) at the different sampling times of the different targeted genes. Concentration per host cell of the total bacteria, Vibrio and Spirochaetaceae bacteria. Graphs are presented in logarithmic scale. Statistical significance levels of differences compared to the controls are indicated by stars (* for p < 0.05, ** for p < 0.01 and *** for p < 0.001)

Fig. 7

Microbiome dynamics of the red coral observed in this study during and after the heat stress. Under control conditions, the coral microbiome remained stable and was primarily composed of Spirochaetaceae bacteria and Labyrinthulaceae microeukaryotes. Exposure to elevated temperatures induced compositional changes in the microbiome: first in the eukaryome then in the bacterial communities. We observed an increase in opportunistic taxa and a decline in the relative abundance of microbial taxa consistently associated with healthy corals. As conditions normalize post-stress (2-weeks recovery period), the abundance of most original community members returned to baseline levels while the relative abundance of most opportunistic taxa declined. However, the coral microbiome did not fully recovered as some heat stress-associated microorganisms persisted at elevated relative abundances