Molecular ecology of the coral holobiont

Installation of an acoustic current Doppler profiler to characterize near shore currents in Pago Bay (left) and temperature, salinity, and light logger data retrieval around Porites corals in Fouha Bay near Humåtak in the south of Guam (right).

Called the coral holobiont, corals represent complex organisms comprised of a host, photosynthetic symbiont’s, and a complex community of bacterial, fungal, and viral micro-organisms that all interact with each other. The combination of these organisms determine the coral holobiont’s response to environmental change. Understanding these interactions involves characterizing the diversity of this symbiotic community and understanding their physiological responses to environmental stimuli. Our students rely on field, common garden, and tank experiments to investigate how the coral-host and their microbial community is affected by environmental change, which ultimately determines reef resilience. See our recent paper on photosystem damage in response to temperature stress (Berg et al. 2021)

Metabarcoding, genomics, and gene expression studies are used to generate datasets that are analyzed using data intensive bio-informatics approaches. We have recently revealed the transcriptomic response of some dominant, reef-building corals to high flow environments (Fifer et al. 2021) and colony fragmentation (Lock et al. 2022). We are also in the final stages of revealing sedimentation-associated patterns in microbial diversity and coral physiology (e.g. Fifer et al. 2022).

Coral holobionts demonstrate high phenotypic plasticity and variance. The maintenance of diverse traits suggests differences in function between phenotypes, which may allow us to better predict a holobionts’ response to climate change. To identify functional variance between coral phenotypes, we have surveyed coral communities (in collaboration with the Raymundo Laboratory), outplanted experimental common gardens, and completed multiple tank experiments to reveal phenotype-associated functional variance through differences in distribution, gene expression, or microbial biodiversity.

Cnidarian phylogeny and evolution

Work in the genetics lab (left). Specimens are collected in the field and preserved (right) prior to DNA or RNA extraction. A variety of molecular genetic techniques are used to generate data, including transcriptome and target-enrichment sequencing.

Using molecular genetic data for phylogenetic analyses, members of our lab infer the evolutionary relationships of cnidarians (jellyfish, hydroids, anemones, corals and their kin). By doing so, we lay the foundation for understanding the diversity of cnidarians observed today. Using genetic information in conjunction with phylogenetic analyses has allowed our collaborators and us revision of the classification of cnidarians, delimitation and description of new species. Phylogenies based on expanding molecular genetic datasets allows for discerning between competing hypotheses of evolutionary relationships and revision of the characters defining taxonomic units using a reverse taxonomic approach – the phylogenetic tree informs us on how to interpret the morphology and anatomy of species.

Cnidarian relationships proposed by Kayal et al. 2018.

Recent contributions have included a phylogenetic analysis using Bayesian hypothesis testing frameworks to resolve the conflicting topologies present in Hydroidolina (Bentlage and Collins. 2021), phylogenetic analysis based on genome-scale data that clarified several long-standing debates on broad cnidarian relationships (Kayal et al. 2018), the revision of a genus of deep-sea jellyfish (Lindsay et al. 2017), and a phylogeographic study that established the box jellyfish Alatina alata as circumtropically distributed (Lawley et al. 2016). Taxonomic revisions and keys are natural byproducts of this research (e.g., Bentlage & Lewis 2012).

Using the information on historical relationships encoded in phylogenies allows for testing evolutionary scenarios. We have used this approach to infer the patterns of life cycle evolution in hydrozoan jellyfish (Bentlage et al. 2018), and intend on continuing this work to understand the evolution of colonial polymorphism. More recently, we are working toward understanding the history of the symbiosis between corals and their photosynthetic symbionts (zooxanthellae). This work shed light on the last common ancestor of photosymbiotic corals, when photosymbiosis evolved in corals, and how reef-expansion coincided with the acquisition of zooxanthellae (Gault et al. 2021). We have also proposed the use of ancient endosymbionts as a vessel for mediating horizontal gene transfer between viruses and animals (Shimpi and Bentlage 2022).


Our work is currently funded through the National Science Foundation’s Guam EPSCoR grant OIA-14577769. Any opinions, findings, and conclusions or recommendations expressed on this website are those of the authors and do not necessarily reflect the views of the National Science Foundation.


%d bloggers like this: