The Baker Lab

85. R Goetama, DM Baker, I Guibert, SE McIlroy, BD Russell (in press) How a coastal megacity affects marine biodiversity and ecosystem function: impacts of reduced water quality and other anthropogenic stressors Ecological Indicators

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84. V Denis, C Ferrier-Pagès, N Schubert, M Coppari, DM Baker, EF Camp, A Gori, AG Grottoli, F Houlbrèque, SR Maier, G Mancinelli, S Martinez, Ş Yalçın Özdilek, VZ Radice, M Ribes, C Richter, N Viladrich, S Rossi (2024) Heterotrophy in marine animal forests in an era of climate change. Biological Reviews DOI: 10.1111/brv.13053

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83. JD Cybulski, NN Duprey, B Thibodeau, M Yasuhara, N Geeraert, N Leonard, HB Vonho, A Martínez-Garcia, DM Baker (in press) Coral carbonate-bound isotopes reveal monsoonal influence on nitrogen

sources in Southeastern China's Greater Bay Area from the mid-Holocene until the Anthropocene. Marine Pollution Bulletin.

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82. JD Cybulski, KS Leung, CON Leung, DM Baker, TKW Lee (2023) Protocol to track the biosynthesis of cholesterol in cultured HCC cells using 13C compound-specific stable isotopic tracers. STAR Protocols 4 (3), 102506.

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81. BL Mamo, JDCybulski, YHong, PGHarnik, A Chao, A Tsujimoto, CL Wei, DM Baker, M Yasuhara (2023) Modern biogeography of benthic foraminifera in an urbanized tropical marine ecosystem. Geological Society, London, Special Publications 529, 79-98.

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80. HS Yang, T Kim, KT Lee, T Kim, DM Baker, DH Kang (2023) Use of Autonomous Reef Monitoring Structures to Monitor Changes in the Marine Environment in Jeju, South Korea: A Brief Review. Ocean Science Journal 58(2), 17

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79. G Puntin, J Craggs, R Hayden, KE Engelhardt, S McIlroy, M Sweet, DM Baker, M Zeigler (2023) The reef-building coral Galaxea fascicularis: a new model system for coral symbiosis research. Coral Reefs 42, 239–252.

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78. J. Hui, Y Yu, W Nong, WL So, Y Xie, HY Yip, J Haimovitz, T Swale, DM Baker, W Bendena, TF Chan, APY Chui, KF Lau, PY Qian, JW Qiu, B Thibodeau, F Xu (2022) Genome of elegance coral Catalaphyllia jardinei (Euphylliidae). Frontiers in Marine Science. 9, https://doi.org/10.3389/fmars.2022.991391

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77. S Martinez, R Grover, DM Baker, C Ferrier-Pagès (2022) Symbiodiniaceae are the first site of heterotrophic nitrogen assimilation in reef-building corals. mBio. 13(5). DOI: https://doi.org/10.1128/mbio.01601-22

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76. J Cybulski, C Skinner, Z Wan, C Wong, R Toonen, M Gaither, K Soong, A Wyatt, DM Baker (2022) Improving stable isotope assessments of inter- and intra-species variation in coral reef fish trophic strategies. Ecology & Evolution. 12(9), e9221.

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75.  E Mok, CO Leung, L Zhou, MML Lei, HW Leung, MTong, TL Wong, E Lau, IO Ng, J Ding, JP Yun, J Yu, H Zhu, CH Lin, D Lindholm, KS Leung, JD Cybulski, DM Baker, S Ma, and T Lee (2022) Caspase-3-induced SREBP2 activation drives drug resistance via promotion of cholesterol biosynthesis in hepatocellular carcinoma. Cancer Research. 82(17):3102-3115. DOI: 10.1158/0008-5472.CAN-21-2934

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74. LH Chow, VPF Yu, ZY Kho, GCL See, A Wang, DM Baker, LM Tsang (2022) An updated checklist of sea slugs (Gastropoda, Heterobranchia) from Hong Kong supported by citizen science. Zoological Studies. 61:e52. doi: 10.6620/ZS.2022.61-52

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73. Y Yau, N Geeraert, DM Baker, B Thibodeau (2022) Elucidating sources of atmospheric NOX pollution in a heavily urbanised environment using multiple stable isotopes. Science of the Total Environment. 832, 154781.

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72.  M Medina, DM Baker, D Baltrus, GM Bennett, U Cardini, AMS Correa, SM Degnan, G Chrisa, E Kim, J Li, DR Nash, EM Marzinelli, MK Nishiguchi, C Prada, MS Roth, M Saha, C Irwin-Smith, KR Theis, JR Zaneveld (2022) Grand Challenges in Coevolution. Frontiers in Ecology & Evolution; Coevolution. https://doi.org/10.3389/fevo.2021.618251

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71. JL Richards, V Sheng, WY Chung, M Liu, HH Tsang, SE McIlroy, DM Baker (2022) Development of an eDNA-based survey method for urban fish markets. Methods in Ecology & Evolution.

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70. M Moynihan, N Goodkin, KM Morgan, PYY Kho, A Lopes dos Santos, FM Lauro, DM Baker, P Martin (2022) Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef. The ISME Journal 16, 233–246.

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69. T Röthig, G Puntin, JCY Wong, A Burian, W McLeod, DM Baker (2021) Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish. Microbiome 9, 127.

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68. T Kim, J Lee, DM Baker (2021) Modification of fatty acid profile and biosynthetic pathway in symbiotic corals under eutrophication. Science of the Total Environment 771, 145336.

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67. AA Andersson, LG Gibson, DM Baker, S Wang, B Leung, LM Chu, C Dingle (2021) Applying stable isotope analysis to detect laundering of yellow-crested cockatoos (Cacatua sulphurea) in wildlife trade. Animal Conservation 24, 1021-1031.

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66. M Santos, DM Baker, I Conti-Jerpe, J Reimer (2021) Populations of a widespread hexacoral have trophic plasticity and flexible syntrophic interactions across the Indo-Pacific Ocean. Coral Reefs https://doi.org/10.1007/s00338-021-02055-4.

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65. JCY Wong, S Enriquez, DM Baker (2021) Towards a trait-based understanding of Symbiodiniaceae nutrient acquisition strategies. Coral Reefs 40, 625-639. 

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64. N Geeraert, A Archana, MN Xu, SJ Kao, DM Baker, B Thibodeau (2021) Investigating the link between Pearl River-induced eutrophication and hypoxia in Hong Kong shallow coastal waters. Science of the Total Environment 771, 145007.

 

63. A Archana, DM Baker (2020) Multifunctionality of an urbanized coastal marine ecosystem. Frontiers in Marine Science doi.org/10.3389/fmars.2020.557145

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62.  JD Cybulski, S Husa, NN Duprey, B Mamo, T Tsang, M Yasuhara, JY Xie, JW Qiu, Y Yokohama, DM Baker (2020) Coral reef diversity losses in China’s Greater Bay Area were driven by regional stressors  Science Advances 6(40), eabb1046

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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 185:116264.

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60. SE McIlroy, JCY Wong, DM Baker (2020) Competitive traits of coral symbionts may alter the structure and function of the microbiome. The ISME Journal 14, 2424-2432.

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59. T Röthig, H Bravo, A Corley, T Prigge, A Chung, V Yu, SE McIlroy, M Bulling, M Sweet, DM Baker (2020) Environmental flexibility in Oulastrea crispata in a highly urbanised environment - a microbial perspective. Coral Reefs 39:649-662.

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58. C Hatten, A Whitfort, DM Baker, CE Dingle (2020) Wildlife forensic science in Hong Kong. WIREs Forensic Science

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57. YY Yau, DM Baker, B Thibodeau (2020) Quantifying the impact of anthropogenic atmospheric nitrogen deposition on the generation of hypoxia under future emission scenarios in Chinese coastal waters. Environmental Science & Technology 54(7):3920-3928.

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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

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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 14:1571-1583.

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54. A Wang*, IE Conti-Jerpe, JL Richards, DM Baker (2020) Phestilla subodiosus, sp. nov., (Nudibranchia: Trinchesiidaea) a corallivorous pest species in the aquarium trade. Zookeys 909:1-24.

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53. N Geeraert, NN Duprey, S McIlroy, PD Thompson, BR Goldstein, C LaRoche, K Kim, LJ Raymundo, DM Baker (2020) The anthropogenic nitrogen footprint of a tropical lagoon: spatial variability in Padina δ15N. Pacific Science 74(1):19-29.

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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.

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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

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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.

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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.

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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.

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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​

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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.

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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.

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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.

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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 ​

doi.org/10.1371/journal.pone.0199680

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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.

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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.

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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 Resistome. Cell Reports 24:1190-1202 (link)

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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.

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37. A Ohdera , MJ Abrams, CL Ames, DM Baker, LP Suescun Bolivar, AG Collins, CJ Freeman, Edgar Gamero-Mora, TL Goulet, DK Hofmann, A Jaimes-Becerra, PF 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)

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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)

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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.

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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.

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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.

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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)

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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.

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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 xamachana. Marine 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 acoroides. Marine 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.