Past, present and future of turbid reefs in the Coral Triangle

Deliverables

The website for 4D-REEF website is in operation.

Publications

High diversity of benthic cyanobacterial mats on coral reefs of Koh Tao, Gulf of Thailand

Author(s): Stuij, T. M., Cleary, D. F., Gomes, N. C.M., Mehrotra, R., Visser, P. M., Speksnijder, A. G., and Hoeksema, B. W.
Published in: Coral Reefs, 2023, ISSN 0722-4028
Publisher: Springer Verlag
DOI: 10.1007/s00338-022-02304-0

Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

Author(s): Macher, J.-N., Coots, N.L., Poh, Y.-P., Girard, E.B., Langerak, A., Muñoz-Gómez, S.A., Sinha, S.D., Jirsová, D., Vos, R., Wissels, R., Gile, G.H., Renema, W., Wideman, J.G.
Published in: MBio, Issue 14, 2023, Page(s) e0030223, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.00302-23

Is the Coral Triangle’s future shown in a Pliocene reef gap?

Author(s): Harrison, G.W.M., Santodomingo, N., Johnson, K.G. Renema, W.
Published in: Coral Reefs, Issue 42, 2023, Page(s) 1219–1225, ISSN 1432-0975
Publisher: Springer
DOI: 10.1007/s00338-023-02412-5

Exploring Prokaryotic Communities in the Guts and Mucus of Nudibranchs, and Their Similarity to Sediment and Seawater Microbiomes

Author(s): Tamara Stuij, Daniel F. R. Cleary, Ana R. M. Polónia, Sumaitt Putchakarn, Ana C. C. Pires, Newton C. M. Gomes & Nicole J. de Voogd
Published in: Current Microbiology, Issue 80, 2023, ISSN 0343-8651
Publisher: Springer Verlag
DOI: 10.1007/s00284-023-03397-8

Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp

Author(s): Tamara M Stuij, Daniel F R Cleary, Rui J M Rocha, Ana R M Polónia, Davide A M Silva, Antonio Louvado, Nicole J de Voogd, Newton C M Gomes
Published in: FEMS Microbiology Ecology, Issue 100/3, 2024, ISSN 0168-6496
Publisher: Blackwell
DOI: 10.1093/femsec/fiae022

The hydrological cycle and ocean circulation of the Maritime Continent in the Pliocene: results from PlioMIP2

Author(s): Ren, X., Lunt, D. J., Hendy, E., von der Heydt, A., Abe-Ouchi, A., Otto-Bliesner, B., Williams, C. J. R., Stepanek, C., Guo, C., Chandan, D., Lohmann, G., Tindall, J. C., Sohl, L. E., Chandler, M. A., Kageyama, M., Baatsen, M. L. J., Tan, N., Zhang, Q., Feng, R., Hunter, S., Chan, W.-L., Peltier, W. R., Li, X., Kamae, Y., Zhang, Z., and Haywood, A. M.
Published in: Climate of the Past, Issue 19, 2023, Page(s) 2053-2077, ISSN 1814-9332
Publisher: Gottingen Copernicus Publishers
DOI: 10.5194/cp-19-2053-2023,2023

Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?

Author(s): Girard, E.B., Estradivari, Ferse, S., Ambo-Rappe, R., Jompa, J., Renema, W.
Published in: Science of the Total Environment, Issue 811, 2022, Page(s) 151396, ISSN 1879-1026
Publisher: Elsevier
DOI: 10.1016/j.scitotenv.2021.151396

Limited Progress in Improving Gender and Geographic Representation in Coral Reef Science

Author(s): Gabby N. Ahmadia, Samantha H. Cheng, Dominic A. Andradi-Brown, Stacy K. Baez, Megan D. Barnes, Nathan J. Bennett, Stuart J. Campbell, Emily S. Darling, Estradivari, David Gill, Erika Gress, Georgina G. Gurney, Vera Horigue, Raymond Jakub, Emma V. Kennedy, Shauna L. Mahajan, Sangeeta Mangubhai, Shayle B. Matsuda, Nyawira A. Muthiga, Michael O. Navarro, Nadia Santodomingo, Henri Vallès, Laura Veve
Published in: Frontiers in Marine Science, Issue 8, 2021, ISSN 2296-7745
Publisher: Frontiers Media
DOI: 10.3389/fmars.2021.731037

Seeing the Forest for the Trees: Mapping Cover and Counting Trees from Aerial Images of a Mangrove Forest Using Artificial Intelligence

Author(s): Schürholz D, Castellanos-Galindo GA, Casella E, Mejía-Rentería JC, Chennu A
Published in: Remote Sensing, Issue 15, 2023, Page(s) 3334, ISSN 2072-4292
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/rs15133334

Hynes, M.G., O’Dea, A., Webster, J.M. and Renema, W., 2024. RADReef: A global Holocene Reef Rate of Accretion Dataset. Scientific Data, 11(1), p.398.

Author(s): Hynes, M.G., O’Dea, A., Webster, J.M. and Renema, W
Published in: Scientific Data, Issue 11, 2024, Page(s) 398, ISSN 2052-4463
Publisher: Springer
DOI: 10.1038/s41597-024-03228-w

Watching out for coral reefs with forams

Author(s): Elsa B Girard Willem Renema
Published in: Frontiers for Young Minds, Issue 12, 2024, Page(s) 1122119, ISSN 2296-6846
Publisher: Frontiers
DOI: 10.3389/frym.2024.1122119

Marine conservation beyond MPAs: Towards the recognition of other effective area-based conservation measures (OECMs) in Indonesia.

Author(s): Estradivari, Agung, Muh Firdaus Adhuri, Dedi Supriadi Ferse, Sebastian C. A. Sualia, Ita Andradi-Brown, Dominic A. Campbell, Stuart J. Iqbal, Mohamad Jonas, Harry D. Lazuardi, Muhammad Erdi Nanlohy, Hellen Pakiding, Fitryanti Pusparini, Ni Kadek Sri Ramadhana, Hikmah C. Ruchimat, Toni Santiadji, I. Wayan Veda Timisela, Natelda R. Veverka, Laura Ahmadia, Gabby N.
Published in: Marine Policy, Issue 137, 2022, Page(s) 104939, ISSN 0308-597X
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.marpol.2021.104939

First report of mitochondrial COI in foraminifera and implications for DNA barcoding

Author(s): Macher, J.-N., Wideman, J.G., Girard, E.B., Langerak, A., Duijm, E., Jompa, J., Sadekov, A., Vos, R., Wissels, R., Renema, W., 2021. First report of mitochondrial COI in foraminifera and implications for DNA barcoding. Sci. Rep. 11, 1–9.
Published in: Scientific Reports, Issue 11, 2021, Page(s) 1-9, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-01589-5

Simulation of the mid-Pliocene Warm Period using HadGEM3: experimental design and results from model–model and model–data comparison

Author(s): Charles J. R. Williams, Alistair A. Sellar, Xin Ren, Alan M. Haywood, Peter Hopcroft, Stephen J. Hunter, William H. G. Roberts, Robin S. Smith, Emma J. Stone, Julia C. Tindall, Daniel J. Lunt
Published in: Climate of the Past, Issue 17/5, 2021, Page(s) 2139-2163, ISSN 1814-9332
Publisher: European Geosciences Union
DOI: 10.5194/cp-17-2139-2021

A standardized database of Last Interglacial (MIS 5e) sea-level indicators in Southeast Asia

Author(s): Kathrine Maxwell, Hildegard Westphal, Alessio Rovere
Published in: Earth System Science Data, Issue 13/9, 2021, Page(s) 4313-4329, ISSN 1866-3516
Publisher: Copernicus Publications
DOI: 10.5194/essd-13-4313-2021

Dense and taxonomically detailed habitat maps of coral reef benthos machine-generated from underwater hyperspectral transects in Curaçao [dataset]

Author(s): Schürholz, Daniel; Chennu, Arjun
Published in: Pangaea, Issue 946315, 2022, ISSN 2378-1106
Publisher: Pangaea
DOI: 10.1594/pangaea.946315

Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera

Author(s): Girard, E.B., Langerak, A., Jompa, J., Wangensteen, O.S., Macher, J.-N., Renema, W
Published in: Frontiers in Marine Science, Issue 9, 2022, Page(s) 809659, ISSN 2296-7745
Publisher: Frontiers
DOI: 10.3389/fmars.2022.809659

Digitizing the coral reef: Machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats

Author(s): Schürholz, D., & Chennu, A.
Published in: Methods in Ecology and Evolution, Issue 14, 2023, Page(s) 596–613, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14029

The Punta de la Mona Rhodolith Bed: Shallow-Water Mediterranean Rhodoliths (Almuñecar, Granada, Southern Spain)

Author(s): Del Río J, Ramos DA, Sánchez-Tocino L, Peñas J and Braga JC
Published in: Frontiers in Earth Sciences, Issue 10:884685, 2022, ISSN 2296-6463
Publisher: Frontiers Media SA
DOI: 10.3389/feart.2022.884685

Rutterford, A., Bertini, L., Hendy, E. J., Johnson, K. G., Summerfield, R., & Burghardt, T. (2022). Towards the analysis of coral skeletal density-banding using deep learning. SN Applied Sciences, 4(2), 38

Author(s): Rutterford, A., Bertini, L., Hendy, E. J., Johnson, K. G., Summerfield, R., & Burghardt, T.
Published in: SN Applied Sciences, Issue 42, 2022, Page(s) 38, ISSN 2523-3971
Publisher: Springer
DOI: 10.1007/s42452-021-04912-x

The annelid community of a natural deep-sea whale fall off eastern Australia

Author(s): Georgieva, M.N., Wiklund, H., Ramos, D.A., Neal, L., Glasby, C.J., Gunton, L.M.
Published in: Records of the Australian Museum, Issue 75, 2023, Page(s) 167-213, ISSN 2201-4349
Publisher: Australian Museum
DOI: 10.3853/j.2201-4349.75.2023.1800

COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Author(s): Girard, E.B., Macher, J.-N., Jompa, J., Renema, W.
Published in: Ecology and Evolution, Issue 12, 2022, Page(s) e9549, ISSN 2045-7758
Publisher: John Wiley and Sons Ltd
DOI: 10.1002/ece3.9549

Biodiversity needs every tool in the box: use OECMs

Author(s): Georgina G. Gurney, Emily S. Darling, Gabby N. Ahmadia, Vera N. Agostini, Natalie C. Ban, Jessica Blythe, Joachim Claudet, Graham Epstein, Estradivari, Amber Himes-Cornell, Harry D. Jonas, Derek Armitage, Stuart J. Campbell, Courtney Cox, Whitney. R. Friedman, David Gill, Peni Lestari, Sangeeta Mangubhai, Elizabeth McLeod, Nyawira A. Muthiga, Josheena Naggea, Ravaka Ranaivoson, Amelia Wenger, Irf
Published in: Nature, Issue 595/7869, 2021, Page(s) 646-649, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/d41586-021-02041-4

Development and validation of an experimental life support system to study the impact of ultraviolet B radiation and temperature on coral reef microbial communities

Author(s): T.M. Stuij, D.F.R. Cleary, R.J.M. Rocha, A.R.M. Polonia, D.A.M. Silva, J.C. Frommlet, A. Louvado, Y. M. Huang, N. Van der Windt, N.J. De Voogd, N.C.M. Gomes
Published in: bioRxiv preprint, 2023
Publisher: Biorxiv

Humic substances mitigate adverse effects of elevated temperature with potentially critical repercussions for coral reef resilience

Author(s): T.M. Stuij, D.F.R. Cleary, N.J. de Voogd, R.J.M. Rocha, A.R.M. Polonia, D.A.M. Silva, J.C. Frommlet, A. Louvado, Y. M. Huang, N. van der Windt, N.C.M. Gomes
Published in: bioRxiv preprint, 2023
Publisher: bioRxiv

Quaternary coral, coralline algal and vermetid assemblages as sea-level indicators: a review

Author(s): Braga, JC, Humblet, M, Ramos, DAE, Dechnik, B, and Webster, JM
Published in: Special Publications of the International Association of Sedimentologists, Issue 29, 2022, Page(s) 1-38, ISBN 978-1-7398845-1-2
Publisher: International Association of Sedimentologists

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