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 Partnerships 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)

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

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

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

5. 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

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

3. 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

2. JD Cybulski, S Husa, NN Duprey, B Mamo, T Tsang, M Yasuhara, JY Xie, JW Qiu, Y Yokohama, DM Baker (in revision) Local stressors are the main driver of past diversity decline in coral reef communities. Science Advances

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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