Mesophotic coral ecosystems (MCEs) are light-dependent coral communities that occur at depths beyond regular diving limits (~30-150 m). Although these communities can occupy areas equivalent to that of shallow reefs, they remain largely undocumented and are often not considered in conservation planning. I am interested in characterising the ecology and biodiversity of these ecosystems, and evaluating their vulnerability in the context of a rapidly changing environment.

Tropical scleractinian corals can be found across a broad depth range, spanning a wide range of different underwater habitats. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however the underlying mechanisms remain poorly understood. By studying patterns of genetic and phenotypic divergence across distinct reef habitats, I aim to identify the ecological drivers and genomic mechanisms underlying the diversification of scleractinian corals and their associated endosymbionts on tropical reefs.
Deep reefs can provide a critical refuge to common shallow reef disturbances, and have therefore been hypothesized to act as a reproductive source for recovering shallow reefs. This potential ability to aid in shallow reef recovery is strongly dependent on the connectivity between shallow and deep reefs. I use molecular ecological approaches to infer the extent of such “vertical connectivity”, and ultimately assess the broader role of deep reefs in shallow reef recovery.

Our understanding of coral biodiversity on tropical reefs has been greatly hampered by the difficulty of accurate in situ taxonomic identification (namely in the Indo-Pacific) and the fact that species within many genera remain unresolved. In addition, there has been a traditional lack of informative genetic markers for corals to assist in this process using phylogenetic approaches. Now, with the emergence of massively parallel sequencing approaches, we have the ability to tackle these resolution issues and assist in taxonomic classification.


Pim Bongaerts
Principal Investigator

Alejandra Hernandez
Hope for Reefs – Postdoctoral Fellow

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Hope for Reefs – Postdoctoral Fellow

Caroline Dubé
NSERC Postdoctoral Fellow (Ulaval)

Katharine Prata
PhD Candidate (UQ)

Joel Huckeba
MSc student (UvA)

Livia Sinigaglia
MSc student (UvA)

Johanna Gijsbers
MSc student (UvA)

BBC News – Coral time-lapse

BBC News item on “the secret life of corals” showing coral time-lapse footage from Heron Island (2014)

Qantas – Great Barrier Reef

Part of a short film series by Qantas featuring one story from each state of Australia (2013)

ARC CoE Symposium – Seminar

Seminar during the “Future of Marine Ecosystems” symposium of the ARC Centre of Excellence for Coral Reef Studies (2015)

Lens of Time: Corals in Motion

Video from bioGraphic / Lens of Time on coral timelapse footage and deep reef work (2016)

Recent publications


Muir P, Wallace C, Pichon M, Bongaerts P (2018) High species richness and lineage diversity of reef corals in the mesophotic zone. Proc Roy Soc B

Frade PR, Bongaerts P, Englebert N, Rogers A, Gonzalez-Rivero M, Hoegh-Guldberg O (2018) Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nature Communications

Rocha LA, Pinheiro HT, Shepherd B, Papastamatiou YP, Luiz OJ, Pyle RL, Bongaerts P (2018) Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361:281-284

Hernandez-Agreda A, Leggat W, Bongaerts P, Herrera C, Ainsworth TD (2018) Rethinking the Coral Microbiome. Simplicity exists in a diverse microbial biosphere. mBio

van Oppen MJH, Bongaerts P, Frade P, Peplow LM, Boyd SE, Nim HT, Bay LK (2018) Adaptation to reef habitats through selection on the coral animal and its associated microbiome. Molecular Ecology

Benzoni F, Arrigoni R, Berumen ML, Taviani M, Bongaerts P, Frade PR (2018) Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): too much for one species? Zootaxa

Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA and Chan CX (2018) Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology

Laverick JH, Piango S, Andradi-Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slattery M, Wagner D, Rogers AD (2018) To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic review. Environmental Evidence 7:15

Gonzalez-Zapata FL, Bongaerts P, Ramirez-Portilla C, Adu-Oppong B, Walljasper G, Reyes A, Sanchez JA (2018) Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone. Frontiers in Marine Science

Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2017) Deep reefs are not universal refuges: reseeding potential varies among coral species. Science Advances 3: e1602373

Sinniger F, Prasetia R, Yorifuji M, Bongaerts P, Harii S (2017) Seriatopora diversity preserved in upper mesophotic coral ecosystems in Southern Japan. Frontiers in Marine Science 4:155

Englebert N, Bongaerts P, Muir PR, Hay KB, Pichon M, Hoegh-Guldberg O (2017) Lower mesophotic coral communities (60-125 m depth) of the northern Great Barrier Reef and Coral Sea. PLoS One

Glasl B, Bongaerts P, Elisabeth NH, Hoegh-Guldberg O, Herndl GJ, Frade PR (2017) Microbiome variation in corals with distinct depth distribution ranges across a shallow-mesophotic gradient (15-85 m). Coral Reefs

On-line resources