St. Petersburg Coastal and Marine Science Center
Coral diseases were first reported on reefs in the Florida Keys and Caribbean in the 1970s. In the decades since, they have been reported worldwide and with increasing frequency. Disease is now recognized as one of the major causes of reef degradation and coral mortality. Recent research has suggested that coral diseases may be secondary opportunistic infections, rather than the result of primary pathogens, making it imperative to understand the microbial shifts that accompany the transition from healthy to diseased corals. Additionally, we need to determine if the spread of coral disease is affected by the level of connectivity among water masses, organisms, trophic levels, or habitats. See black-band disease and coral bleaching galleries.
We are investigating coral disease processes and causes by characterizing microbial communities in diseased and healthy representatives of selected coral species both temporally and spatially by employing microarray technology. We are testing the diagnostic potential of coral fluorescence for identifying disease-induced physiological stress. This work links coral ecosystem studies in marine protected areas to better understand coral ecosystem health.
Specific efforts include:
Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit.
Five preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater®, DMSO–EDTA–salt (DESS), FTA® cards, and FTA Elute® cards. Microbial community fingerprinting analysis and DNA sequencing were used to detect specific changes in the known communities over weeks and months of storage. A previously known bias in FTA® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater®, and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.
Baker, E.J. and C.A. Kellogg, 2014, Comparison of three DNA extraction kits to establish maximum yield and quality of coral-associated microbial DNA: USGS Open-File Report 2014-1066, 14 p.
Kellogg, C.A., 2014, Section 3: Sampling from living organisms (Chapter 6: Sampling and experiments with biofilms in the environment), in Biofouling Methods (S. Dobretsov, D.N. Williams, and J. Thomason, Eds.), Wiley Blackwell, pp. 184 – 189.
Lisle, J.T., Garrison, V.H., and Gray, M.A., 2014, Evaluation of Coral Pathogen Growth Rates After Exposure to Atmospheric African Dust Samples: U.S. Geological Survey Open-File Report 2014–1017, 12 p., http://dx.doi.org/10.3133/ofr20141017.
Kellogg, C.A., Piceno, Y.M., Tom, L.M., DeSantis, T.Z., Gray, M.A., et al., 2013, Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in Orbicella annularis Using PhyloChip™ G3 Microarrays: PLoS ONE 8(11): e79801. doi:10.1371/journal.pone.0079801.
Gray, M.A., Pratte, Z.A., and Kellogg, C.A., 2013, Comparison of DNA preservation methods for environmental bacterial community samples: FEMS Microbiology Ecology 83: 468-477.
Kellogg, C.A., Piceno, Y.M., Tom, L.M., DeSantis, T.Z., Zawada, D.G., and Andersen, G.L., 2012, PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology: Journal of Microbiological Methods 88: 103-109.
Kellogg, C.A., and Zawada, D.G., 2010, Coral Paparazzi—Looking for a Quick Way to Spot Evidence of Coral Disease: Sound Waves, v. FY2011, p. 5-6.
Olson, J.B., and Kellogg C.A., 2010, Microbial ecology of corals, sponges, and algae in mesophotic coral environments: FEMS Microbiology Ecology 73: 17-30.
Kellogg, C.A., and Zawada, D.G., 2009, Applying new methods to diagnose coral diseases: U.S. Geological Survey Fact Sheet 2009-3113, 2 p.
Galkiewicz, J.P., and Kellogg C.A., 2008, Cross-kingdom amplification using bacterial-specific primers: complications for coral microbial ecology: Applied and Environmental Microbiology 74 (24): 7828-7831.