David Michael Baker

Address: Kadoorie Biological Sciences Building, 6S-14

The University of Hong Kong

Pokfulam Road, Hong Kong, PRC

E-mail: dmbaker (at) hku.hk

Tel: 2299 0606


Ph.D. (2010) Ecology & Evolutionary Biology; Cornell University

M.S. (2004) Biology; American University

B.A. (2001) Biology; St. Mary's College of Maryland

Positions Held

Associate Professor,
The Swire Institute of Marine Science,
School of Biological Sciences
The University of Hong Kong

2013 - present

Chair, MarineGEO Community Committee
2020 - present
Director, HKU Stable Isotope Ratio Mass Spectrometry Laboratory (SIRMS)
2020 - present

MarineGEO Fellow (formerly Marine Science Network)

Smithsonian Institution

2011 - 2012

Post-doctoral Associate & Visiting Investigator

Carnegie Institution of Washington, Geophysical Laboratory

2010 - 2012

Peer-reviewed Publications (* indicates undergraduate advisee)

62.  JD Cybulski, S Husa, NN Duprey, B Mamo, T Tsang, M Yasuhara, JY Xie, JW Qiu, Y Yokohama, DM Baker (in press) Coral reef diversity losses in China’s Greater Bay Area were driven by regional stressors  Science Advances

61. X Li, M Yan, JR Gu, VTT Lam, TC Wai, DM Baker, PD Thompson, SKF Yiu, PKS Lam, PTY Leung (accepted) The effect of temperature on physiology, toxicity and toxin content of the benthic dinoflagellate Coolia malayensis from a seasonal tropical region. Water Research

60. SE McIlroy, JCY Wong, DM Baker (accepted) Competitive traits of coral symbionts may alter the structure and function of the microbiome. The ISME Journal

59. T Röthig, H Bravo, A Corley, T Prigge, A Chung, V Yu, SE McIlroy, M Bulling, M Sweet, DM Baker (in press) Environmental flexibility in Oulastrea crispata in a highly urbanised environment - a microbial perspective. Coral Reefs

58. C Hatten, A Whitfort, DM Baker, CE Dingle (accepted) Wildlife forensic science in Hong Kong. WIREs Forensic Science

57. YY Yau, DM Baker, B Thibodeau (accepted) Quantifying the impact of anthropogenic atmospheric nitrogen deposition on the generation of hypoxia under future emission scenarios in Chinese coastal waters. Environmental Science & Technology

56. I Conti-Jerpe, PD Thompson, CWM Wong, NL Oliveira, NN Duprey, MA Moynihan, DM Baker (2020) Trophic strategy and bleaching resistance in reef-building corals. Science Advances 6 (15), eaaz5443

55. CJ Freeman, CG Easson, KO Matterson, RW Thacker, DM Baker, V Paul (in press) Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association. The ISME Journal

54. A Wang*, IE Conti-Jerpe, JL Richards, DM Baker (accepted) Phestilla subodiosus, sp. nov., (Nudibranchia: Trinchesiidaea) a corallivorous pest species in the aquarium trade. Zookeys

53. N Geeraert, NN Duprey, S McIlroy, PD Thompson, BR Goldstein, C LaRoche, K Kim, LJ Raymundo, DM Baker (accepted) The anthropogenic nitrogen footprint of a tropical lagoon: spatial variability in Padina δ15N. Pacific Science

52. J Richards, V Sheng, WY Chung, LY Chan, ST Ng, Y Sadovy, DM Baker (2020) Prevalence of critically endangered European eel (Anguilla anguilla) in Hong Kong supermarkets. Science Advances 6(10), eaay0317. (link)


51. NN Duprey, XT Wang, T Kim, JD Cybulski, HB Vonhof, PJ Crutzen, GH Haug, DM Sigman, A Martínez-García, DM Baker (2020) Megacity development and the demise of coastal coral communities: evidence from coral skeleton δ15N records in the Pearl River Estuary. Global Change Biology 26:1138-1353.

50. DE Burkepile, AA Shantz, TC Adam, KS Munsterman, KE Speare, MC Ladd, MM Rice, SE McIlroy, JCY Wong, DM Baker, AJ Brooks, RJ Schmitt, and SJ Holbrook (2019) Nitrogen source drives differential impacts of nutrients on coral bleaching prevalence, duration, and mortality. Ecosystems doi.org/10.1007/s10021-019-00433-2

49. L Lachs, NA Mohd Johari, DQ Le, Z Bachok, CD Mohd Safuan, K Tanaka, DM Baker, NN Duprey, NC Ory, M Kochzius, TC Hong, K Shirai (2019) Effects of tourism-derived sewage on coral reefs: isotopic assessments identify effective bioindicators. Marine Pollution Bulletin 148:85-96.

48. SE McIlroy, PD Thompson, F Landry Yuan, TC Bonebrake, DM Baker (2019) Subtropical thermal variation supports persistence of corals but limits productivity of coral reefs. ProcB 286: 20190882.

47. J Chen, SE McIlroy, A Archana, DM Baker, G Panagiotou (2019) A pollution gradient shapes the microbiome, functionome and resistome in marine sediments. Microbiome 7:104.

46. TC Bonebrake, F Guo, C Dingle, DM Baker, RL Kitching, LA Ashton (2019) Integrating proximal and horizon threats for conservation. Trends in Ecology & Evolution  https://doi.org/10.1016/j.tree.2019.04.001

45.  CWM Wong, IE Conti-Jerpe, LJ Raymundo, CE Dingle, A Ponzo, DM Baker (2019) Whale shark ecotourism: impacts on coral reefs in the Philippines. Environmental Management 63(2):282-291.

44. MJ Kwon, C Tudge, K Kim, DM Baker, SE MacAvoy (2018) Museum collections yield information on nitrogen sources for coastal Gulf of Mexico, North Carolina, USA and Caribbean Sea invertebrates 1850 to 2004. Journal of Shellfish Research 37(5):1157-1165.

43. CP Shin*, A Hoffman, W Lee, RC Kendrick, DM Baker, TC Bonebrake (2018) Stable isotopes of Lithosiini and lichens in Hong Kong show the bioindicator potential of lichenivorous moths. Journal of Asia-Pacific Entomology 21:1110-1115.

42. MJ Perkins, YKY Mak, LSR Tao, ATL Wong, JKC Yau, DM Baker, KMY Leung (2018) Short-term tissue decomposition alters stable isotope values and C:N ratio but does not change relationships between lipid content, C:N ratio, and Δδ13C in marine animals. PLOS ONE 


41. A Archana, N Geeraert, MN Xu, SJ Kao, B Thibodeau, DM Baker (2018) Nitrogen sources and cycling revealed by dual isotopes of nitrate in a complex urbanized environment. Water Research 142(1):459-470.

40. LG Gibson, A Andersson, D Dudgeon, Y Song, Y Chen, DM Baker, A Hofford. (2018) Hong Kong's delayed ivory ban endangers African elephants. Frontiers in Ecology and the Environment 16(7):378-380.

39. K Kang, Y Ni, J Li, L Imamovic, C Sarkar, Y Heshiki, T Zheng, S Kumari, JCY Wong, A Archana, CWM Wong, CE Dingle, S Denizen, DM Baker, MOA Sommer, CJ Webster, G Panagiotou (2018) The Environmental Exposures and Inner-and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and ResistomeCell Reports 24:1190-1202 (link)

38. V Bacalan, T Poinsatte, DM Baker, ML Fogel, K Kim (2018) Stable isotope analyses of manatee bones measure historical nitrogen pollution in Florida waters, 1975 - 2010. Marine Biology 165:85.

37. A Ohdera , MJ Abrams, CL Ames, DM Baker, LP Suescun Bolivar, AG CollinsCJ Freeman, Edgar Gamero-Mora, TL Goulet, DK Hofmann, A Jaimes-BecerraPF Long, AC Marques, LA Miller, L Mydlarz Laura, AC Morandini, CR Newkirk, SP Putri, S Julia, N Stampar, B Steinworth, M Templeman, PE Thomé, M Vlok, C Woodley, JCY Wong, MQ Martindale, WK Fitt and M Medina (2018) Upside-down but headed in the right direction: The highly versatile Cassiopea xamachana system. Frontiers in Ecology and Evolution doi: 10.3389/fevo.2018.00035 (link)

36. DM Baker, CJ Freeman, JCY Wong, ML Fogel, N Knowlton (2018) Climate change promotes parasitism in a coral symbiosis. The ISME Journal 12(3):921-930 (link)

35. N Duprey, SE McIlroy, TPT Ng, PD Thompson, T Kim, JCY Wong, CWM Wong, SM Husa, SMH Li, GA Williams, DM Baker (2017) Facing a wicked problem with optimism: issues and priorities for coral conservation in Hong Kong. Biodiversity and Conservation 26(11): 2521-2545.

34. CJ Freeman, EW Stoner, CG Easson, KO Matterson, DM Baker (2017) Variation in δ13C and δ15N suggests a coupling of host and symbiont metabolism in the Symbiodinium - Cassiopea mutualism. Marine Ecology Progress Series 571: 245-251.

33. N Duprey, XT Wang, PD Thompson, J Pleadwell, LJ Raymundo, K Kim, DM Sigman, DM Baker (2017) Life and death of a sewage treatment plant recorded in a coral skeleton δ15N record. Marine Pollution Bulletin 120(1-2): 109-116.

32. Y Heshiki, T Dissanayake, T Zheng, K Kang, N Yueqiong, Z Xu, C Sarkar, PCY Woo, BKC Chow, DM Baker, A Yan, C Webster, G Panagiotou, and J Li. (2017) Towards a metagenomic understanding on the bacterial composition and resistome in Hong Kong banknotes. Frontiers in Microbiology 8:632. (link)

31. CWM Wong, N Duprey, DM Baker (2017) New insights on the nitrogen footprint of a coastal megalopolis from coral-hosted Symbiodinium δ15N. 51(4), 1981-1987. Environmental Science and Technology 51, 1981-1987.

30. DM Baker, T Murdoch, I Conti-Jerpe, ML Fogel (2017) Investigating Bermuda's pollution history through stable isotope analyses of modern and museum held gorgonian corals. Marine Pollution Bulletin 114, 169-175.

29. AH Yeung, DM Baker (2016) A turnaround at Sanya National Coral Reef Nature Reserve? Proceedings of the 13th International Coral Reef Symposium, Honolulu: 570 - 589. (link)


28. A Anand, L Li, SJ Kao, B Thibodeau, DM Baker (2016) Variations in nitrogen isotope composition of wastewater effluents by treatment type in Hong Kong. Marine Pollution Bulletin 111(1-2), 143-152.


27. F Stein, JCY Wong, V Sheng, SWC Law, B Schröder, DM Baker (2016) First genetic evidence of illegal trade in endangered European eel (Anguilla anguilla) from Europe to Asia. Conservation Genetics Resources 8(4), 533-537.


26. N Duprey, M Yasuhara, DM Baker (2016) Reefs of tomorrow: nutrients reduce coral biodiversity in an urbanized seascape. Global Change Biology 22(11), 3550-3568. 


25. JCY Wong, P Thompson, JY Xie, JW Qiu, DM Baker (2016) Symbiodinium clade C generality among common scleractinian corals in subtropical Hong Kong. Regional Studies in Marine Science 8(3), 439-444.


24. CJ Freeman, EW Stoner, CG Easson, KO Matterson, DM Baker (2016) Carbon and nitrogen metabolism by symbionts within Cassiopea xamachanaMarine Ecology Progress Series 544, 281-286.


23. CJ Freeman, CG Easson, DM Baker (2016) Niche structure of marine sponges from temperate hard-bottom habitats within Gray's Reef National Marine Sanctuary. Journal of the Marine Biological Association of the United Kingdom. 96(2), 559-565.

22. PK Cheung*, KK Yuen*, PF Li*, WH Lau*, CM Chiu*, M Yuen*, DM Baker (2015) To swim or not to swim? A disagreement between microbial indicators on beach water quality assessment in Hong Kong. Marine Pollution Bulletin 101, 53-60.


21.  DM Baker, CJ Freeman, N Knowlton, RW Thacker, K Kim, ML Fogel (2015) Productivity links morphology, symbiont specificity, and bleaching in the evolution of Caribbean octocoral symbioses. The ISME Journal 9, 2620-2629. (open access PDF)


20. CJ Freeman, DM Baker, CG Easson, RW Thacker (2015) Shifts in sponge-microbe mutualisms across an experimental irradiance gradient. Marine Ecology Progress Series 526, 41-53.


19. K Pinkerton, DM Baker, MR Cuddy, LJ Raymundo, KA Meyer, K Kim. (2015) Nitrogen dynamics on Guam as revealed by the seagrass Enhalus acoroidesMarine Ecology Progress Series 528, 117-126.

18. CJ Freeman, CG Easson, DM Baker (2014) Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras. Peer J 2:e695 (link)


17. CG Easson, M Slattery, DM Baker, D Gochfeld (2014) Complex ecological associations: Evidence for competition and facilitation in a sponge-algal interaction. Marine Ecology Progress Series 507, 153-167.


16. C Fiore, DM Baker, M Lesser (2013) Nitrogen biogeochemistry in the Caribbean sponge Xestospongia muta: A source or sink of dissolved inorganic nitrogen? PLOS ONE 8(8): e72961. (link)


15. JE Redding, RL Myers-Miller, DM Baker, ML Fogel, LJ Raymundo, K Kim (2013) Link between sewage-derived nitrogen pollution and coral disease severity. Marine Pollution Bulletin 73(1), 57-63. (link)


14. DM Baker, RE Rodríguez-Martínez, ML Fogel (2013) Tourism’s nitrogen footprint on a Meso-american coral reef. Coral Reefs 32(3), 691-699. (link)

13. CJ Freeman, RW Thacker, DM Baker, ML Fogel (2013) Quality or quantity: Is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance? The ISME Journal 7, 1116-1125. (link)


12. DM Baker, JP Andras, AG Jordán-Garza, ML Fogel (2013) Nitrate competition varies with temperature among Symbiodinium clades. The ISME Journal 7, 1248-1251. (link)


11. DM Baker, L Weigt, M Fogel, N Knowlton (2013) Ancient DNA from coral-hosted Symbiodinium reveal a static mutualism over the last 172 years. PLoS ONE 8(2): e55057.  (link)


10. M Moynihan*, DM Baker, AJ Mmochi (2012) Isotopic and microbial indicators of sewage pollution from Stone Town, Zanzibar. Marine Pollution Bulletin 64, 1348-1355.


9. RE Rodríguez-Martínez,, GA Jordán-Garza, DM Baker, E Jordán-Dahlgren (2012) Prevalence of coral-Trididemnum solidum interactions on Mexican Caribbean reefs. Coral Reefs 31(2), 571-577.


8. DM Baker, K Kim, JP Andras, JP Sparks (2011) Light-mediated 15N fractionation in Caribbean gorgonian corals: implications for pollution monitoring. Coral Reefs 30, 709-717.

7. DM Baker, E Jordán-Dahlgren, MA Maldonado, CD Harvell (2010) Sea fan corals provide a stable isotope baseline for assessing sewage pollution in the Mexican Caribbean. Limnology & Oceanography 55(5) 2139-2149.

6. DM Baker, K Webster, K Kim (2010) Caribbean octocorals record changing carbon and nitrogen sources from 1862-2005. Global Change Biology, 16(10), 2701-2710.

5. EB Rivest*, DM Baker, KL Rypien, CD Harvell (2010) Nitrogen preference of Aspergillus sydowii, an infective agent associated with aspergillosis of sea fan corals. Limnology & Oceanography, 55(1), 386-392.

4. KL Rypien, DM Baker (2009) Isotopic labeling and antifungal-resistance as tracers of gut passage of the sea fan pathogen Aspergillus sydowii. Diseases of Aquatic Organisms, 86, 1-7


3. CA Page, DM Baker, CD Harvell, Y Golbuu, L Raymundo, SJ Neale, KB Rosell, KL Rypien, JP Andras, BL Willis (2009) Influence of marine reserves on coral disease prevalence. Diseases of Aquatic Organisms. 87, 135-150

2. A Jordán-Garza, MA Maldonado, DM Baker, R. Rodríquez (2008) High abundance of Diadema antillarum on a Mexican reef. Coral Reefs 27(2), 295.

1. DM Baker, SA MacAvoy, K Kim (2007) Relationship between water quality, δ15N, and aspergillosis of Caribbean sea fan corals. Marine Ecology Progress Series. 343, 123-130.

Technical Reports

1. LI Raymundo, K Kim, J Redding, R Miller, K Pinkerton, DM Baker (2011) Links between deteriorating coral health and sewage pollution on Guam reef flats. University of Guam Marine Laboratory, Technical Report #131

Forthcoming Manuscripts

6. T Rothig, G Puntin, JCY Wong, W McLeod, DM Baker (in prep) Nutrient dynamics in the Cassiopea xamachana holobiont. Microbiome

5. I Conti-Jerpe, T Röthig, A Chung, DM Baker (in prep) Evidence for microbial engines: nitrate assimilation in low-light corals. 

4. M Santos, DM Baker, I Conti-Jerpe, J Reimer (in revision) How to become a widespread success: niche plasticity on coral reefs. Journal of Animal Ecology

3. JCY Wong, S Enriquez, DM Baker (in review) Towards a trait-based understanding of Symbiodiniaceae nutrient acquisition strategies. Coral Reefs

2. AA Andersson, LG Gibson, DM Baker, S Wang, B Leung, LM Chu, C Dingle (in revision) Applying stable isotope analysis to detect laundering of yellow-crested cockatoos (Cacatua sulphurea) in wildlife trade. Animal Conservation

1. A Archana, SE McIlroy, J Chen, CL Wang, T Rothig, T Kim, G Panagiotou, DM Baker (in prep) Eutrophication decreases carbon storage in urban marine sediments. Microbiome

Environment and Conservation Fund (Hong Kong), MarineGEO - Hong Kong: Towards an understanding of marine biodiversity and ecosystem function (67/2016; $3.2M HKD)
Ocean Park Conservation Foundation Hong Kong, Forming a scientific foundation for coral reef restoration and resilience in Hong Kong (OT01.1718; $466K HKD)


Research Grants Council Hong Kong, GRF; Sedimentary records of historical coral diversity and distribution in the South China Sea, (#17304116; $360K HKD)

University Grants Council, The University of Hong Kong Seed Funding for Basic Research;                   3-D printed coral reefs: exploring the relationship between rugosity and biodiversity ($80K HKD)



Research Grants Council Hong Kong, GRF; Determining the sources of nitrogen to the coral             skeletal organic matrix, (#17303615; $0.7M HKD)


University Grants Council, The University of Hong Kong Seed Funding for Basic Research;                   A Pilot Survey of Marine Biodiversity using Autonomous Reef Monitoring Structures (ARMS): A           First Step for MarineGEO Hong Kong ($47K)




Research Grants Council Hong Kong, GRF; Clash of the Dinoflagellates! Nitrogen competition among coral-hosted symbionts, (#17100014; $1.03M HKD)

Environment and Conservation Fund (Hong Kong), Two centuries of nitrogen pollution in Hong Kong’s coastal waters reconstructed from hard-coral and octocoral δ15N records (#2013-04; w. N. Duprey; $0.5M HKD)




NSF:RAPID Documenting bleaching susceptibility and resilience in Guam, Micronesia. (co-I w. K. Kim & L. Raymundo; $93,000 USD)


Research Grants Council Hong Kong, Early Career Scheme (RGC-ECS); A stable isotope survey of Hong Kong's corals: Assessing the impact of nitrogen pollution on coral health and community biodiversity, (#789913; 1.2M HKD)


University Grants Council, The University of Hong Kong Seed Funding for Basic Research ($120,000 HKD)



Bermuda Zoological Society, Investigating Bermuda’s marine pollution history through stable isotope analyses of modern and museum-held gorgonians, $1,750 USD



NSF: IGERT Program Small Grant, Stable isotope history of the Caribbean: Corals as sentinels for human perturbation, $3,860 USD



NSF: IGERT Program Small Grant, Monitoring coral reefs: 15N through space and time, $3,000 USD


Mario Einaudi Center for International Studies, Nitrogen isotope analyses of reef

corals: investigating the role of nutrients and coral disease, $1,000 USD



NSF: IGERT Program Small Grant, δ13C as a measure of photosynthetic efficiency in

modified symbioses: a test of the adaptive bleaching hypothesis, $4,000 USD

PADI Foundation Grant, A century of nitrogen perturbations in the Caribbean revealed using isotopic analysis of gorgonian coral skeletons, $4,000 USD

NSF: IGERT Program Small Grant, The effect of nitrate concentration on uptake in the Caribbean octocoral Gorgonia ventalina, $2,997 USD

NSF: IGERT Program Small Grant, Stable isotopes of coral reef invertebrates: developing assessment tools to monitor reef health, $1,000 USD



 Hemlinge Research Grant, American University $3,000 USD

© 2012 by David M. Baker. All rights reserved

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