Amatzia Genin

Amatzia is a visiting professor from Eilat, Israel, on 2 years of Sabbatical leave at CRE (November 2018 – September 2020)


I am a marine ecologist and biological oceanographer. My major interest is in the coupling between physical and biological processes in the marine environment, focusing on the effects of water motion on fundamental ecological processes, including predator-prey relationships, competition, symbiosis, mass transfer, and behavior. Research at my lab is process-oriented and inter-disciplinary, addressing mechanisms that operate at levels ranging from the individual to the ecosystem. Most of my studies are based on field experiments involving advanced technologies and novel approaches.

I completed my BSc (1977) and MSc (1981) at the Hebrew University of Jerusalem, Israel and PhD (1987) at Scripps Institute of Oceanography, UC San Diego, USA. I have been a faculty at the Hebrew University of Jerusalem and a resident researcher at the InterUniversity Institute for Marine Sciences of Eilat (IUI) since 1987. In the past 6 years (2012-2018) I was the scientific director of the IUI.

Some relaxation at the water front…

Dr. David Obura

David Obura is a Founding Director of, and works at CORDIOEast Africa, in Mombasa, Kenya –

CORDIO is a knowledge organization supporting sustainability of coral reef and marine systems in the Western Indian Ocean. CORDIO takes research to management and policy, builds capacity, and works with stakeholders, managers and policy makers.

David’s primary research is on coral reef resilience, in particular to climate change, and the biogeography of the Indian Ocean. At the boundary between science and action, David works to integrate conservation and development through inclusive blue economy principles and links provided by global sustainability goals and targets.

He works from the local scale, through fostering innovative action to promote sustainability, through regional scale alignment and integration such as in the Northern Mozambique Channel, to global scales of bringing knowledge and local-regional practice into decision-making circles. 2020 will be a critical year for ocean, biodiversity and climate targets in global conventions, and David is engaged in multiple processes (see expert groups) to bring coral reef science and learning into these global fora.

David contributes to The Conversation through his UQ affiliation on topical issues.

Online profiles

Expert groups

  • Earth Commission, Global Commons Alliance/Future Earth.
  • Technical Working Group (Kenya) and Expert Group, High Level Panel on Ocean Sustainability
  • IUCN Coral Specialist Group (chair) (International Union for the Conservation of Nature)
  • IPBES Global Assessment – Coordinating Lead Author, Chapter 2: Nature subsection
  • REVOcean Science and Innovation Committee
  • National Geographic Explorer. Updating the global coral Red List of Threatened Species
  • Informal Advisory Group (IAG), Ecologically and Biologically Significant Areas, CBD Secretariat
  • GOOS Biodiversity and Ecosystems Panel (Global Ocean Observing System, UNESCO-IOC)
  • GCRMN – Global Coral Reef Monitoring Network, Technical development and coordination

Selected publications

  1. Obura, D.O. (2020) Getting to 2030 – scaling effort to ambition through a narrative model of the SDGs. Marine Policy.
  2. Díaz S, Settele J, Brondízio ES, Ngo HT, Agard J et al. (2019) Pervasive human-driven decline of life on Earth points to the need for profound change. Science 366, eaax3100: 1-10
  3. Obura, D.O. (2019) A plot for sustainability -the Sustainable Development Goals as a narrative. Preprints 201910.0157 (doi:10.20944/preprints201910.0157.v2
  4. Gudka, M., Obura, D., Mbugua, J., Ahamada, S., Kloiber, U., Holter, T. (2019) Participatory reporting of the 2016 bleaching event in the Western Indian Ocea.n Coral Reefs 1-11.
  5. Obura DO, et al. (2019) Coral Reef Monitoring, Reef Assessment Technologies, and Ecosystem-Based Management. Front. Mar. Sci. 6:580. doi: 10.3389/fmars.2019.00580
  6. Bax NJ, Miloslavich P, Muller-Karger FE, Allain V, Appeltans W, Batten SD, Benedetti-Cecchi L, Buttigieg PL, Chiba S, Costa DP, Duffy JE, Dunn DC, Johnson CR, Kudela RM, Obura D, Rebelo L-M, Shin Y-J, Simmons SE and Tyack PL (2019) A Response to Scientific and Societal Needs for Marine Biological Observations. Front. Mar. Sci. 6:395. doi: 10.3389/fmars.2019.00395
  7. Gamoyo, M., Obura, D., & Reason, C. J. C. (2019). Estimating connectivity through larval dispersal in the Western Indian Ocean. Journal of Geophysical Research: Biogeosciences, 124. 2019JG005128
  8. Chassot E., Bodin N., Sardenne F., & Obura D.O. (2019) The key role of the Northern Mozambique Channel for Indian Ocean tropical tuna fisheries. Reviews in Fish Biology and Fisheries, 1–26.
  9. McLeod E., Anthony K.R.N., Mumby P.J., Maynard J., Beeden R., Graham N.A.J., Heron S.F., Hoegh-Guldberg O., Jupiter S., MacGowan P., Mangubhai S., Marshall N., Marshall P.A., McClanahan T.R., Mcleod K., Nyström M., Obura D.O., Parker B., possingham H.P., Salm R.V., & Tamelander J. (2019) The future of resilience-based management in coral reef ecosystems. Journal of Environmental Management, 233, 291–301
  10. Popova E., Vousden D., Sauer W.H.H., Mohammed E.Y., Allain V., Downey-Breedt N., Fletcher R., Gjerde K.M., Halpin P.N., Kelly S., Obura D.O., Pecl G., Roberts M., Raitsos D.E., Rogers A., Samoilys M., Sumaila U.R., Tracey S., & Yool A. (2019) Ecological connectivity between the areas beyond national jurisdiction and T coastal waters: Safeguarding interests of coastal communities in developing countries. Marine Policy, 104, 90–102.
  11. Obura, D.O. The Three Horses of Sustainability—Population, Affluence and Technology. Preprints2018, 2018120176 (doi: 10.20944/preprints201812.0176.v1)
  12. Obura, DO (2018) Ocean health in the blue economy. In: A Handbook on the Blue Economy in the Indian Ocean Region. Editor: Prof VN Attri. Indian Ocean Rim Association (IORA), ESRC/S Africa.
  13. Obura D, et al. (2018) East and southern Africa – coastal and ocean futures. Northern Mozambique Channel initiative (WWF/CORDIO),
  14. Obura, DO (2017) Refilling the coral reef glass. Science 357 (6357): 1215 DOI: 10.1126/science.aao5002
  15. Obura, DO et al.  2017. Reviving the Western Indian Ocean Economy: Implementing the SDGs to sustain a healthy ocean economy.  WWF International/Boston Consulting Group/CORDIO.
  16. Obura DO, et al. (2017) The Northern Mozambique Channel – a capitals approach to a Blue Economy future. In: Handbook on the Economics and Management for Sustainable Oceans. Editors: Svansson LE, Nunes PALD, Kumar P & Markandya A. Edward Elgar Publishing.
  17. Costello M.J., et al. (2016) Methods for the Study of Marine Biodiversity. The GEO Handbook on Biodiversity Observation Networks (ed. by M. Walters and R.J. Scholes), pp. 129–163. Springer.
  18. Obura, DO (2017), An Indian Ocean centre of origin revisited: Palaeogene and Neogene influences defining a biogeographic realm. Journal of Biogeography. 43:229–242 doi: 10.1111/jbi.12656
  19. Freestone, D. et al. (2016) World Heritage in the High Seas: An Idea Whose Time Has Come. World Heritage Centre reports, #44, United Nations Education, Science and Cultural Organization. 79 pp.
  20. Sale PF, & 24 others. (2014) Transforming management of tropical coastal seas to cope with challenges of the 21st century. Marine Pollution Bulletin: 1–16. doi:10.1016/j.marpolbul.2014.06.005
  21. Hoegh-Guldberg O. et al. (2013) Indispensable Ocean. Aligning ocean health and human well-being. Guidance from the Blue Ribbon Panel to the Global Partnership for Oceans
  22. Obura, DO (2012) The diversity and biogeography of Western Indian Ocean reef-building corals. PLOS ONE. 10.1371/0045013.
  23. Obura DO. (2009) Reef corals bleach to resist stress. Marine Pollution Bulletin 58:206-212. DOI 10.1016/j.marpolbul.2008.10.002
  24. Carpenter KE, et al. (2008). One-Third of Reef-Building Corals Face Elevated Extinction Risk from Climate Change and Local Impacts. Science 321: 560-563
  25. Obura DO (2005) Resilience and climate change – lessons from coral reefs and bleaching in the Western Indian Ocean. Estuarine Coastal and Shelf Science 603: 353-372.

Calcification calculation by Delta alkalinity

Calcification calculation by Delta alkalinity

ALK units: 2.2 µmol g (SW)-1 or 2200 µmol Kg (SW)-1

SW Density units: 1.03 gL-1

MW of CaCO3 = 100 g mol-1


AT = [HCO3]T + 2[CO32−]T + [B(OH)4]T + [OH]T − [H+]



Delta CaCO3 µg L(SW)-1 =

Delta ALK µmol g-1 x Density of SW gL-1 x MW of CaCO3 g mol-1 x ½

(NB in bold underlined units remain after nominator denominator cancellation)

Clearly then need to Multiply by Volume of seawater (L) and normalise to time and some other factor such as surface area or weight of organism.

Research on ocean acidification and coral bleaching in Hawaii

The effects of climate change on coral reefs are well known. We know that as the climate changes, the ocean temperature is rising, and that rising temperature is leading to coral bleaching. We also know that as the carbon dioxide concentration in the atmosphere increases, the ocean is becoming more acidic, and that is reducing coral growth (as more acidic water impairs the growth of skeleton by corals).

Does rising temperature also affect coral growth, and does ocean acidification also affect coral bleaching? Well, rising temperature (beyond a certain limit) has also been irrefutably found to reduce coral growth.

Coral bleaching in Kaneohe Bay, Hawaii, 2014.

Well, rising temperature (beyond a certain limit) has also been irrefutably found to reduce coral growth. But the effects of ocean acidification on coral bleaching are less clear. In some studies, ocean acidification increases coral bleaching. However, in other studies, ocean acidification does not seem to have an impact.

The Hawaii Institute for Marine Biology in Kaneohe Bay, Oahu.

To try to clarify this problem, I performed an experiment at the Hawaii Institute of Marine Biology from November 2014 to January 2015. Collaborating with local researchers (Dr. Ruth Gates, Dr. Ross Cunning and Chris Wall), we exposed colonies of the lace coral, Pocillopora damicornis, to two levels of ocean acidification.

One of these levels (7.95 on the pH scale) will be seen in the near future whilst the other level (7.75 on the pH scale) is what the world could see towards the end of the twenty-first century, if we don’t reduce greenhouse gas emissions enough. At first there may not seem to be much between 7.95 and 7.75, however the pH scale is logarithmic (not linear), so a decrease of 0.2 pH units actually amounts to a huge increase in the level of ocean acidification.

Coral micro colonies used in the ocean acidification experiment.

After two months of exposure to these two levels, we then divided the corals at each level of ocean acidification into a further two groups: one that would experience no increase in water temperature (remaining at 24°C), and one that would experience an increase of 6°C (to a final temperature of 30°C). An increase of that level is often sufficient to cause coral bleaching.

What we wanted to know is, will coral bleaching be worse in the corals that experienced end-of-century ocean acidification, compared to those that experienced less ocean acidification? After one week of temperature exposure, corals were snap frozen, preserving their biology for later analysis in a laboratory.

Using an airbrush of the same type used by artists, we removed the thin layer of tissue from the surface of each coral fragment to collect the single-celled algae that live within the tissue. As photosynthetic organisms, these algae provide the organic molecules that the coral tissue uses for energy. It is the loss of these algal cells from coral tissues that is the cause of the whitening (bleaching) of the coral during high temperatures. Using a microscope, we counted the number of single-celled algae from the tissue of each coral, and then calculated the total number of algal cells per square centimetre of area of coral tissue. This provided a measure of coral bleaching that could be compared between all the corals in our experiment.

In statistical analyses now underway, we are examining whether there is in fact more coral bleaching in those corals exposed to high ocean acidification compared to those that experienced less ocean acidification. This information will help us to plan for the impacts of climate change on coral reefs, and will further help to focus attention on the plight of marine ecosystems in our changing planet.

No better reason could be found for this research than in September 2014, when a coral bleaching event occurred on reefs beside the Hawaii Institute for Marine Biology due to high water temperatures. Scientists and coral reef managers in Hawaii are now planning for a second bleaching event at the same location, anticipated to occur this coming summer in 2015.

Catherine Kim, PhD Student

 Contact   About   Publications   Photos   Video    Blog


Catherine Kim
XL Catlin Oceans Scholar
ARC Centre of Excellence for Coral Reef Studies
University of Queensland Australia
Level 7 Gehrmann Labs (60)
St. Lucia, QLD 4072
+617 3365 3548
c dot kim at



Catherine hails from Virginia and completed her BSc in Science of Earth Systems concentrating in Oceanography at Cornell University.  Following graduation, she worked for Professor Drew Harvell coordinating her National Science Foundation Research Coordination Network Grant in the Ecology of Infectious Marine Disease.  She participated in seagrass wasting disease projects in the San Juan Islands, Washington and coral health and water quality surveys in Puakō, Hawai’i.  In 2013, she was also a program assistant for Cornell’s Earth and Environmental Systems Sustainability Semester based in Waimea, Hawai’i Island.

Currently, Catherine is an XL Catlin Oceans Scholar PhD student in the Coral Reef Ecosystems Lab and is fortunate to have been a part of the XL Catlin Seaview Survey global coral reef survey Indo-Pacific campaign in 2014.  Following the survey in Timor-Leste, Catherine is focusing her thesis work  in the newly independent nation combining XL Catlin and NOAA datasets.  As a former NOAA Pacific Islands Fisheries Science Center intern, she is excited to initiate a research partnership between the XL Catlin Seaview Survey and NOAA in an effort to better understand the coral reefs of Timor-Leste.  She will be investigating questions on coral reef benthic composition, marine biodiversity of crabs and fishes, and coral health.  Hopefully, her work will contribute to in-country marine resource management at this critical point of development in Timor-Leste.


Groner ML, Burge CA, Kim CJS, Rees E, Van Alstyne KL, Yang S, Wyllie-Echeverria S, Harvell CD (2015). Widespread variation in eelgrass wasting disease in the Salish Sea. Diseases of Aquatic Organisms.

Yoshioka RM, Kim CJS, Tracy AM, Most R, Harvell CD (2015). Linking sewage pollution and water quality to spatial patterns of Porites lobata growth anomalies in Puakō, Hawai‘i. Marine Pollution Bulletin.

Groner ML, Burge CA, Couch CS, Kim CJS, Siegmund GF, Singhal S, Smoot SC, Harvell CD, Wyllie-Echeverria S, Jarrell A & JK Gaydos (2014). Diseases of Aquatic Organisms 108: 165-175. Host demography influences the prevalence and severity of seagrass wasting disease. doi: 10.3354/dao02709

Burge CA, Kim CJS, Lyles JM, & CD Harvell (2013). Special Issue Oceans and Humans Health: The Ecology of Marine Opportunists. Microb Ecol 65(4): 869-79. doi:10.1007/s00248-013-0190-7



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