Evaluating Coral Diversity Across Zones

Shannon diversity metrics were generated with the phyloseq function rarefy_even_depth with option replace = TRUE, and a minimum sequence depth for a sample of 1000. Prior to rarefaction, taxa with a sum of zero across the subsetted data were removed. Two sets of alpha-diversity analyses were run: [1 (link)] evaluated differences across the three zones (vulnerable, endemic, and epidemic) in field-sourced apparently healthy (AH) corals, and [2 ] evaluated differences across disease states (AH, unaffected tissue [DU], and lesion tissue [DL] on a diseased colony) in SCTLD-susceptible corals (i.e., without Acropora spp.). Significance was tested with linear mixed models with the R packages lme4 v1.1.21 [68 ], and emmeans v1.4.3.1 [69 (link)], and Tukey’s HSD was used for pairwise comparisons. For zones and disease states, coral species was used as a random effect.

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Rosales S.M., Huebner L.K., Evans J.S., Apprill A., Baker A.C., Becker C.C., Bellantuono A.J., Brandt M.E., Clark A.S., del Campo J., Dennison C.E., Eaton K.R., Huntley N.E., Kellogg C.A., Medina M., Meyer J.L., Muller E.M., Rodriguez-Lanetty M., Salerno J.L., Schill W.B., Shilling E.N., Stewart J.M, & Voss J.D. (2023). A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies. ISME Communications, 3, 19.

Publication 2023

Coral Epidemic Tissue

Corresponding Organization :

Other organizations : National Oceanic and Atmospheric Administration, University of Miami, NOAA Atlantic Oceanographic and Meteorological Laboratories, Florida Fish and Wildlife Conservation Commission, United States Geological Survey, Woods Hole Oceanographic Institution, Florida International University, University of the Virgin Islands, Florida Keys Community College, Mote Marine Laboratory, Institut de Biologia Evolutiva, Pompeu Fabra University, Pennsylvania State University, University of Florida, George Mason University, Harbor Branch Oceanographic Institute, Florida Atlantic University

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Variable analysis

independent variables

Zone (vulnerable, endemic, epidemic)
Disease state (apparently healthy [AH], unaffected tissue [DU], lesion tissue [DL])

dependent variables

Shannon diversity metrics

control variables

Coral species (used as a random effect)

controls

The study used a minimum sequence depth of 1000 for rarefaction, and taxa with a sum of zero across the subsetted data were removed prior to rarefaction.

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