Pim Bongaerts

Assistant Curator of Invertebrate Zoology
McCosker Chair of Aquatic Biology
@ California Academy of Sciences

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.

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.
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.

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.
  • scireports2015c
  • plosone2015b
  • roysocopen2015
  • isme2015
  • aquatic_cons2015
  • coralreefs2015
  • 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. – in press
  • 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. – in press
  • Glasl B, Bongaerts P, Elisabeth NH, Hoegh-Guldberg O, Herndl GJ and Frade PR (2017) Microbiome variation in corals with distinct depth distribution ranges across a shallow-mesophotic gradient (15-85 m). Coral Reefs – in press
  • Hernandez A, Ainsworth TD, Bongaerts P, Leggatt W (2016) The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. mBio – in press
  • Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA (2016) Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Current Zoology – in press
  • Hoeksema BW, Bongaerts P, Baldwin CC (2016) High coral cover at lower mesophotic depths: a dense Agaricia community at the leeward side of Curaçao, Dutch Caribbean. Marine Biodiversity – in press
  • Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015) Symbiont zonation plays a crucial role in the vertical distribution of coral species. Royal Society Open Science 2:140297
  • Bongaerts P, Frade PR, Englebert N, Hay KB, Vermeij MJH, Hoegh-Guldberg O (2015) Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community. Scientific Reports 5:7652
  • Hoeksema BW, Bongaerts P (2015) Mobility and self-righting by a free-living mushroom coral through pulsed inflation. Marine Biodiversity – in press
  • Ganase A, Bongaerts P, Visser PM,Dove S (2015) The effect of seasonal temperature extremes on sediment rejection in three scleractinian coral species. Coral Reefs – on-line first
  • Ainsworth TD, Bridge T, Torda G, Raina JB, Gates R, Padilla-Gamino J, Spalding HL, Smith C, Woosley E, Krause L, Zakrzewski M, Bongaerts P, Spalding H, Bourne D, Hoegh-Guldberg O, Leggat W (2015) The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME Journal 9:2261-2274
  • Pantos O, Bongaerts P, Dove S, Hoegh-Guldberg O (2015) Microbial associations in the scleractinian coral Seriatopora hystrix across depths, locations and host/symbiont genotypes. ISME Journal 9:1916-1927
  • Muir P, Wallace C, Bridge TCL, Bongaerts P (2015) Diverse Staghorn Coral Fauna on the Mesophotic Reefs of North-East Australia. PLoS One 10:e0117933
  • González-Rivero M, Bongaerts P, Beijbom O, Pizarro O, Friedman A, Rodriguez-Ramirez A, Upcroft B, Laffoley D, Kline DI, Vevers R, Hoegh-Guldberg O (2014) The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems. Aquatic Conservation 24:184-198
  • Englebert N* & Bongaerts P*, Muir P, Hay KB, Hoegh-Guldberg O (2014) Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea. Marine Biodiversity 45:1-2
  • Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJH, Bak RPM, Visser PM, Hoegh-Guldberg O (2013) Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evolutionary Biology 13:205
  • Bongaerts P, Muir PR, Bridge TCL, Englebert N, Hoegh-Guldberg O (2013) Cyclone damage at mesophotic depths on Myrmidon Reef (GBR). Coral Reefs 32:935
  • Bridge TCL, Hughes TP, Guinotte JM, Bongaerts P (2013) Call to protect all coral reefs. Nature Climate Change 3:528-530
  • Tonk L* & Bongaerts P*, Sampayo EM, Hoegh-Guldberg (2013) SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef. BMC Ecology 13:7
  • Foster R, Bridge T, Bongaerts P (2012) The first record of Hippocampus denise from Australia. Aqua – International Journal of Ichthyology 18:55-57
  • Bongaerts P, Hoeksema B, Hay K, Hoegh-Guldberg O (2012) Mushroom corals overcome live burial through pulsed inflation. Coral Reefs 2:399
  • Bongaerts P, Riginos C, Hay K, van Oppen MJH, Hoegh-Guldberg O, Dove S (2011) Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evolutionary Biology 11:303 (cover article)
  • Bridge TCL, Fabricius KE, Bongaerts P, Wallace CC, Muir P, Done TJ, Webster JM (2011) Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia. Coral Reefs 31:179-189
  • Bongaerts P, Sampayo EM, Bridge TLC, Ridgway T, Vermeulen F, Englebert N, Webster JM, Hoegh-Guldberg O (2011) Symbiodinium diversity of mesophotic coral communities on the GBR: a first assessment. Marine Ecology Progress Series 439:117-126
  • Bongaerts P* & Bridge T*, Kline DI, Muir PR, Wallace CC, Beaman RJ, Hoegh-Guldberg O (2011) Mesophotic coral ecosystems on the walls of Coral Sea atolls. Coral Reefs 30:335
  • Van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF (2011) The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Molecular Ecology 20:1647-1660
  • Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O (2010) Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and its Associated Symbiodinium. PLoS One 5(5):e10871
  • Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010) Assessing the ‘deep reef refugia’ hypothesis: focus on Caribbean reefs. Coral Reefs 29:309–327

Current affiliations

Deep reefs are difficult to access due to the greater depth at which they occur. We are therefore dependent on specialised underwater technologies and innovative approaches to explore and document these habitats.

Recent developments in massively parallel sequencing (e.g. Illumina) and reduced-representation genome-sequencing methods (e.g. RAD-seq) now allow us to obtain genomic data for large numbers of individuals and populations. These methods provide us with an unprecedented resolution to assess the biodiversity of corals and their endosymbionts, and assess the underlying ecological and evolutionary processes structuring this diversity.

For scripts see:

On-line resources

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)