1

People and ecosystems

Understanding of the links between coral reef ecosystems, the goods and services they provide to people, and the wellbeing of human societies.

2

Ecosystem dynamics: past, present and future

Examining the multi-scale dynamics of reefs, from population dynamics to macroevolution

3

Responding to a changing world

Advancing the fundamental understanding of the key processes underpinning reef resilience.

Coral Bleaching

Coral Bleaching

Coral Reef Studies

ARC Centre of Excellence for Coral Reef Studies
James Cook University Townsville
Queensland 4811 Australia

Phone: 61 7 4781 4000
Email: info@coralcoe.org.au

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Pim Bongaerts

Pim Bongaerts


ARC DECRA Research Fellow


Post-doctoral Researcher – Global Change Institute (UQ) (2012-2017)
Post-doctoral Researcher – School of Biological Sciences (UQ) (2011-2012)


University of Queensland



+61 (0)7 4978 1253



Post-doctoral Researcher – Global Change Institute (UQ) (2012-2017)
Post-doctoral Researcher – School of Biological Sciences (UQ) (2011-2012)

Pim is originally from the Netherlands where he completed a BSc in Biology at Utrecht University and a MSc in Limnology and Oceanography at the University of Amsterdam. After completing a PhD at The University of Queensland in 2011, he completed a one-year post-doctoral fellowship (2011-2012) at the School of Biological Sciences (UQ) based out at the Heron Island Research Station. Currently, he holds a position at the Global Change Institute (UQ) as lead scientist on the Deep Reef component of the Catlin Seaview Survey, and is a research fellow on the DSITIA Accelerate Partnership Grant “Coral genomes along environmental gradients”. He uses next-generation sequencing approaches to study the biodiversity and connectivity of mesophotic reefs across the globe, with a major focus on the Great Barrier Reef, the Coral Sea and the Southern Caribbean.

Pim is the lead scientist for the “Deep Reef” component of the Catlin Seaview Survey (www.catlinseaviewsurvey.com) and is a post-doctoral researcher on the DSITIA Accelerate Partnership Grant “Coral genomes along environmental gradients”. He uses next-generation sequencing approaches to study the biodiversity and connectivity of mesophotic reefs across the globe, with a major focus on the Great Barrier Reef, the Coral Sea and the Southern Caribbean.

Selected Publications

Lower mesophotic coral communities (60-125 m depth) of the northern great barrier reef and coral sea

Englebert, Norbert, Bongaerts, Pim, Muir, Paul R., Hay, Kyra B., Pichon, Michel and Hoegh-Guldberg, Ove (2017) Lower mesophotic coral communities (60-125 m depth) of the northern great barrier reef and coral sea.PLoS One12 2: . doi:10.1371/journal.pone.0170336

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m)

Glasl, Bettina, Bongaerts, Pim, Elisabeth, Nathalie H., Hoegh-Guldberg, Ove , Herndl, Gerhard J. and Frade, Pedro R. (2017) Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m).Coral Reefs, 1-6. doi:10.1007/s00338-016-1517-x

To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest?

Laverick, Jack H., Andradi-Brown, Dominic A., Exton, Dan A., Bongaerts, Pim, Bridge, Tom C. L., Lesser, Michael P., Pyle, Richard L., Slattery, Marc, Wagner, Daniel and Rogers, Alex D. (2016) To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest?.Environmental Evidence5 1: . doi:10.1186/s13750-016-0068-5

The microbial signature provides insight into the mechanistic basis of coral success across reef habitats

Hernandez-Agreda, Alejandra, Leggat, William, Bongaerts, Pim and Ainsworth, Tracy D. (2016) The microbial signature provides insight into the mechanistic basis of coral success across reef habitats.mBio7 4: . doi:10.1128/mBio.00560-16

Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies

Riginos, Cynthia, Crandall, Eric D., Liggins, Libby, Bongaerts, Pim and Treml, Eric A. (2016) Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies.Current Zoology62 6: 581-601. doi:10.1093/cz/zow067

High coral cover at lower mesophotic depths: a dense Agaricia community at the leeward side of Curaçao, Dutch Caribbean

Hoeksema, Bert W., Bongaerts, Pim and Baldwin, Carole C. (2016) High coral cover at lower mesophotic depths: a dense Agaricia community at the leeward side of Curaçao, Dutch Caribbean.Marine Biodiversity, 1-4. doi:10.1007/s12526-015-0431-8

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

Ainsworth, Tracy D., Krause, Lutz, Bridge, Thomas, Torda, Gergely, Raina, Jean-Baptise, Zakrzewski, Martha, Gates, Ruth D., Padilla-Gamino, Jacqueline L., Spalding, Heather L., Smith, Celia, Woolsey, Erika S., Bourne, David G., Bongaerts, Pim, Hoegh-Guldberg, Ove and Leggat, William (2015) The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts.The ISME Journal9 10: 2261-2274. doi:10.1038/ismej.2015.39

The effect of seasonal temperature extremes on sediment rejection in three scleractinian coral species

Ganase, A., Bongaerts, P., Visser, P.M. and Dove, S.G. (2015) The effect of seasonal temperature extremes on sediment rejection in three scleractinian coral species.Coral Reefs35 1: 187-191. doi:10.1007/s00338-015-1359-y

Mobility and self-righting by a free-living mushroom coral through pulsed inflation

Hoeksema, Bert W. and Bongaerts, Pim. (2015) Mobility and self-righting by a free-living mushroom coral through pulsed inflation.Marine Biodiversity46 2: 521-524. doi:10.1007/s12526-015-0384-y

Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea

Englebert, N., Bongaerts, P., Muir, P., Hay, K. B. and Hoegh-Guldberg, O. (2015) Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea.Marine Biodiversity45 1: 1-2. doi:10.1007/s12526-014-0221-8

Diverse staghorn coral fauna on the mesophotic reefs of north-east Australia

Muir, Paul, Wallace, Carden, Bridge, Tom C. L. and Bongaerts, Pim (2015) Diverse staghorn coral fauna on the mesophotic reefs of north-east Australia.PLoS One10 2: . doi:10.1371/journal.pone.0117933

Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species

Bongaerts, Pim, Carmichael, Margaux, Hay, Kyra B., Tonk, Linda, Frade, Pedro R. and High-Guldberg, Ove (2015) Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species.Royal Society Open Science2 140297: 1-11. doi:10.1098/rsos.140297

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

Pantos, Olga, Bongaerts, Pim, Dennis, Paul G., Tyson, Gene W. and Hoegh-Guldberg, OVe (2015) Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix.The ISME Journal9 9: 1916-1927. doi:10.1038/ismej.2015.3

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community

Bongaerts, Pim, Frade, Pedro R., Hay, Kyra B., Englebert, Norbert, Latijnhouwers, Kelly R. W., Bak, Rolf P. M., Vermeij, Mark J. A. and Hoegh-Guldberg, Ove (2015) Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community.Scientific Reports5 Art No.: 7652: . doi:10.1038/srep07652

The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems

Gonzalez-Rivero, Manuel, Bongaerts, Pim, Beijbom, Oscar, Pizarro, Oscar, Friedman, Ariell, Rodriguez-Ramirez, Alberto, Upcroft, Ben, Laffoley, Dan, Kline, David, Bailhache, Christophe, Vevers, Richard and Hoegh-Guldberg, Ove (2014) The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems.Aquatic Conservation: Marine and Freshwater Ecosystems24 S2: 184-198. doi:10.1002/aqc.2505

Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef

Bongaerts, Pim, Frade, Pedro R., Ogier, Julie J., Hay, Kyra B., van Bleijswijk, Judith, Englebert, Norbert, Vermeij, Mark J. A., Bak, Rolf P. M., Visser, Petra M. and Hoegh-Guldberg, Ove (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 Biology13 1: 205.1-205.14. doi:10.1186/1471-2148-13-205

Call to protect all coral reefs

Bridge, Tom C. L., Hughes, Terry P., Guinotte, John M. and Bongaerts, Pim (2013) Call to protect all coral reefs.Nature Climate Change3 6: 528-530. doi:10.1038/nclimate1879

SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef

Tonk, Linda, Bongaerts, Pim, Sampayo, Eugenia M. and Hoegh-Guldberg, Ove (2013) SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.Bmc Ecology13 1-7.9. doi:10.1186/1472-6785-13-7

Cyclone damage at mesophotic depths on Myrmidon Reef (GBR)

Bongaerts, P., Muir, P., Englebert, N., Bridge, T.C.L. and Hoegh-Guldberg, O. (2013) Cyclone damage at mesophotic depths on Myrmidon Reef (GBR).Coral Reefs32 4: 935-935. doi:10.1007/s00338-013-1052-y

Mushroom corals overcome live burial through pulsed inflation

Bongaerts, P., Hay, K., Hoegh-Guldberg, O. and Hoeksema, B. W. (2012) Mushroom corals overcome live burial through pulsed inflation.Coral Reefs31 2: 399-399. doi:10.1007/s00338-011-0862-z

Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia

Bridge, T. C. L., Fabricius, K. E., Bongaerts, P., Wallace, C. C., Muir, P. R., Done, T. J. and Webster, J. M. (2012) Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia.Coral Reefs31 1: 179-189. doi:10.1007/s00338-011-0828-1

The first record of Hippocampus denise (Syngnathidae) from Australia

Foster, Ralph, Bridge, Thomas C. L. and Bongaerts, Pim (2012) The first record of Hippocampus denise (Syngnathidae) from Australia.Aqua international Journal of Ichthyology18 1: 55-57.

Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats

Bongaerts, Pim, Riginos, Cynthia, Hay, Kyra B., van Oppen, Madeleine J.H., Hoegh-Guldberg, Ove and Dove, Sophie (2011) Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats.BMC Evolutionary Biology11 1: 1-46. doi:10.1186/1471-2148-11-303

Symbiodinium diversity in mesophotic coral communities on the Great Barrier Reef: a first assessment

Bongaerts, Pim, Sampayo, Eugenia M., Bridge, Thomas C. L., Ridgway, Tyrone, Vermeulen, Francisca, Englebert, Norbert, Webster, Jody M. and Hoegh-Guldberg, Ove (2011) Symbiodinium diversity in mesophotic coral communities on the Great Barrier Reef: a first assessment.Marine Ecology-Progress Series439 117-126. doi:10.3354/meps09315

Mesophotic coral ecosystems on the walls of Coral Sea atolls

Bongaerts, P., Bridge, T.C.L., Kline, D.I., Muir, P.R., Wallace, C.C., Beaman, R.J. and Hoegh-Guldberg, O. (2011) Mesophotic coral ecosystems on the walls of Coral Sea atolls.Coral Reefs30 2: 335-335. doi:10.1007/s00338-011-0725-7

The role of deep reefs in shallow reef recovery: An assessment of vertical connectivity in a brooding coral from west and east Australia

van Oppen, Madeleine J. H., Bongaerts, Pim, Underwood, Jim N., Peplow, Lesa M. and Cooper, Timothy F. (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 Ecology20 8: 1647-1660. doi:10.1111/j.1365-294X.2011.05050.x

Assessing the ‘deep reef refugia’ hypothesis: Focus on Caribbean reefs

Bongaerts, P., Ridgway, T., Sampayo, E. M. and Hoegh-Guldberg, O. (2010) Assessing the ‘deep reef refugia’ hypothesis: Focus on Caribbean reefs.Coral Reefs29 2: 309-327. doi:10.1007/s00338-009-0581-x

Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium

Bongaerts, Pim, Riginos, Cynthia, Ridgway, Tyrone, Sampayo, Eugenia M., van Oppen, Madeleine J. H., Englebert, Norbert, Vermeulen, Francisca and Hoegh-Guldberg, Ove (2010) Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium.PLoS One5 5: e001087:1-e001087:11. doi:10.1371/journal.pone.0010871

In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, and algal symbiont

Frade, P. R., Bongaerts, P., Winkelhagen, A. J. S., Tonk, L. and Bak, R. P. M. (2008) In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, and algal symbiont.Limnology and Oceanography53 6: 2711-2723. doi:10.4319/lo.2008.53.6.2711

Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type

Sampayo, E. M., Ridgway, T., Bongaerts, P. and Hoegh-Guldberg, O. (2008) Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type.Proceedings of the National Academy of Sciences of the United States of America105 30: 10444-10449. doi:10.1073/pnas.0708049105

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Coral Reef Studies

ARC Centre of Excellence for Coral Reef Studies
James Cook University Townsville
Queensland 4811 Australia

Phone: 61 7 4781 4000
Email: info@coralcoe.org.au