Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef

Abstract

Background: Coral reefs have sustained damage of increasing scale and frequency due to climate change, thereby intensifying the need to elucidate corals' biological characteristics, including their thermal tolerance and microbial symbioses. The sea anemone, Exaiptasia diaphana, has proven an ideal coral model for many studies due to its close phylogenetic relationship and shared traits, such as symbiosis with algae of the family Symbiodiniaceae. However, established E. diaphana clonal lines are not available in Australia thus limiting the ability of Australian scientists to conduct research with this model. To help address this, the bacterial and Symbiodiniaceae associates of four Great Barrier Reef (GBR)-sourced E. diaphana genotypes established in laboratory aquaria and designated AIMS1-4, and from proxies of wild GBR E. diaphana were identified by metabarcoding of the bacterial 16S rRNA gene and eukaryotic rRNA gene ITS2 region. The relationship between AIMS1-4 and their bacterial associates was investigated, as was bacterial community phenotypic potential. Existing data from two existing anemone clonal lines, CC7 and H2, were included for comparison. Results: Overall, 2238 bacterial amplicon sequence variants (ASVs) were observed in the AIMS1-4 bacterial communities, which were dominated by Proteobacteria and Bacteroidetes, together comprising > 90% relative abundance. Although many low abundance bacterial taxa varied between the anemone genotypes, the AIMS1-4 communities did not differ significantly. A significant tank effect was identified, indicating an environmental effect on the microbial communities. Bacterial community richness was lower in all lab-maintained E. diaphana compared to the wild proxies, suggesting a reduction in bacterial diversity and community phenotypic potential due to culturing. Seventeen ASVs were common to every GBR lab-cultured anemone, however five were associated with the Artemia feedstock, making their specific association to E. diaphana uncertain. The dominant Symbiodiniaceae symbiont in all GBR anemones was Breviolum minutum. Conclusion: Despite differences in the presence and abundance of low abundance taxa, the bacterial communities of GBR-sourced lab-cultured E. diaphana are generally uniform and comparable to communities reported for other lab-cultured E. diaphana. The data presented here add to the global E. diaphana knowledge base and make an important contribution to the establishment of a GBR-sourced coral model organism.

Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana

“…While PERMANOVA analysis found host genotype to be a driver of bacterial communities, pairwise comparisons did not detect differences between genotypes, and an analysis of shared ASVs across genotypes showed high consistency between acontia microbiomes across genotypes. This is consistent with a recent paper showing that whole anemone communities from these four same genotypes were not significantly different [ 35 ]. Nonetheless, the four genotypes used in this study are reared in very similar environments.…”

“…Nonetheless, the four genotypes used in this study are reared in very similar environments. It would thus be relevant to sample other genotypes as well as wild populations for comparison of their bacterial community composition with that of the acontia, as whole organism microbiomes have been shown to be more diverse in wild populations [ 35 ].…”

Short-Term Exposure to Sterile Seawater Reduces Bacterial Community Diversity in the Sea Anemone, Exaiptasia diaphana

“…From this study, the average number of ASVs from GBR-sourced E. diaphana was 134, which is substantially lower than >750 ASVs, which was previously reported for these anemones (Hartman et al, 2020). After anemones were maintained for 3 weeks in fRSS, the number of observed bacterial ASVs was significantly reduced in all genotypes while maintaining holobiont health.…”

“…In both conditions, anemones were fed ad libitum with freshly hatched Artemia salina (brine shrimp, Salt Creek, UT, United States) nauplii twice weekly. A. salina feedstock was not sterile prior to feeding (see Hartman et al, 2020 for details on feedstock bacterial community composition). Control and "sterile" anemone tanks were cleaned each week after feeding with complete RSS or fRSS water changes, respectively.…”

“…As an alternative approach to creating the MM, we have explored a community reduction strategy of the E. diaphana microbiome by manipulating the external environment (Clavel et al, 2017), instead of the application of antibiotics. Studies on the microbiome of E. diaphana indicate a similar phylum level diversity to corals (Blackall et al, 2015) for anemones sourced from the Great Barrier Reef (GBR) (Hartman et al, 2019(Hartman et al, , 2020Dungan et al, 2020a), Hawaii (Herrera et al, 2017), Pacific and Caribbean (Brown et al, 2017), Atlantic (Röthig et al, 2016), and Red Sea (Ahmed et al, 2019). We hypothesize that selective forces acting on E. diaphana and its microbiome, when placed in sterile seawater, will reduce the complexity of the microbiome with the loss of some (e.g., transient) members.…”