Energetics and isotopes in bleached and recovering corals

Wall C.B., Ritson-Williams R., Popp B.N., and Gates R.D. (2019) Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery. Limnology and Oceanography 64(5): 2011-2028 (https://doi.org/10.1002/lno.11166).

An update has been made to the code following a Corrigendum related to coloring of points in NMDS plots. Conclusion of analyses were unchanged: https://doi.org/10.1002/lno.11662

This project assessed the energetic and isotopic changes in bleached and non-bleached colonies of two Hawaiian reef coral species at three reef sites in Kāne'ohe Bay, Hawai'i, following a rare archipelagic bleaching event in October 2014 and the subsequent recovery from bleaching in January 2015.

Files and Folders

• Bleach.Recovery.Isotope.Rproj -- the R project in Rstudio
• Wall et al_LnO_markdown_publish.Rmd -- the codes and script in Rmarkdown file
• Wall_et_al_LnO_markdown_publish.html -- this is the html export from Rmd

data

• Biological responses_BNB.final -- the biological properties of all corals. Metadata for this file can be found in Rmd file and below.
  • 'Time.point' -- 2014 October or 2015 January
  • 'Period' -- either Bleaching or Recovery
  • 'Site' -- 3 sites HIMB (Hawai'i Institute of Marine Biology), Reef 25, and Reef 44
  • 'Species' -- MC = Montipora capitata, or PC = Porites compressa
  • 'Condition' -- B = Bleached, NB = Non-bleached
  • 'Sample.ID' -- arbitrary colony ID #
  • 'Pair' -- bleached-nonbleached pair of neighboring colonies
  • 'Depth.m' -- colony depth in meters
  • 'surface.area.cm2' -- colony surface area in cm2
  • 'blastate.ml' -- tissue extract in ml
  • 'cells.ml' -- (unused data) symbiont cells per ml blastate
  • 'AFDW.g.ml' -- g ash-free dry weight per ml blastate
  • 'mg.carb.ml' -- mg of carbohydrates per ml blastate
  • 'mg.protein.ml' -- mg of proteins per ml blastate
  • 'ug.chl.a.ml' -- μg of chlorophyll a per ml blastate
  • 'ug.chl.c2.ml' -- μg of chlorophyll a per ml blastate
  • 'g.lipids.gdw' -- g of lipids per g ash-free dry-weight
  • 'lipid.freeze.dry.g' -- (unused data) g lipid biomass as a function of freeze-dried tissue
  • 'lipid.extract.mass.g' -- g of lipids extracted from 3ml freeze-dried aliquot of holobiont tissue
  • 'AFDW.burned+lipids.g' -- total mass of AFDW and lipids in grams from lipid extractions
  • 'AFDW.freeze.ml' -- g AFDW per ml aliquot of freeze-dried tissue used in lipid extractions
  • 'host.ug.N' -- μg of nitrogen in host tissue
  • 'host.d15N' -- δ15N of host tissues in permil
  • 'host.ug.C' -- μg of carbon in host tissue
  • 'host.d13C' -- δ13C of host tissues in permil
  • 'host.C.N' -- molar ratio of carbon : nitrogen in symbiont tissues
  • 'symb.ug.N' -- μg of nitrogen in symbiont tissue
  • 'symb.d15N' -- δ15N of symbiont tissues in permil
  • 'symb.ug.C' -- μg of carbon in host tissue
  • 'symb.d13C' -- δ13C of symbiont tissues in permil
  • 'symb.C.N' -- molar ratio of carbon : nitrogen in symbiont tissues
  • 'd15N.H.S' -- difference in δ15N of host minus symbiont
  • 'd13C.H.S' -- difference in δ13C of host minus symbiont
  • 'symb.comm' -- symbiont clade where qPCR had been previously run (see Cunning et al. 2016)

API ESRI tiles

• ESRI tiles to make a DIY map without Google API

coastn83.shp

• shape files to generate map -- NOTE need user Google API account as of 2019

environmental

• abiotic data
  • KBay_temp_1612480_20140601-20150228_phys.csv -- weather station temperature data
  • light_reef44_2014.csv -- 2014 light at Reef 44
  • light_reef44_2015.csv -- 2015 light at Reef 44
  • light_reefHIMB_2014.csv -- 2014 light at HIMB
  • light_reefHIMB_2015.csv -- 2015 light at HIMB
  • nutrients_BNB.update -- dissolved nutrients at three reef sites
  • Reefs_lat_long -- latitude and longitude of reef sites
  • sediment_long_KBay -- short-term sedimentation data
  • sediment_short_KBay -- long-term (annual) sedimentation data
  • temp_reef44_2014.csv -- 2014 temperature at Reef 44
  • temp_reef44_2015.csv -- 2015 temperature at Reef 44
  • temp_reefHIMB_2014.csv -- 2014 temperature at HIMB
  • temp_reefHIMB_2015.csv -- 2015 temperature at HIMB

figures

These figures are exports from Rmarkdown (Fig 1, 3) and images of bleached and non-bleached corals (Fig 2)

• Fig1a_sitemap.png -- this is the map generated from Google with sites identified
• Fig1bc.corals.png -- bleached and non-bleached corals

Final Figures

Figures here are exported from Rmd and used in publication with minor edits in Illustrator

• Fig 1. Map and corals.pdf
• Fig 2 Nutrients.pdf
• Fig 3. NMDS_MC.pdf
• Fig 4. NMDS_PC.pdf
• Fig 5. MC.PC.chla.pdf
• Fig 6. Energy reserves.pdf
• Fig 7. MC.PC.fig.isotopes.pdf
• Fig 8. Mass balance d13C.pdf
• Fig S1. Temp.PAR.color.pdf
• Fig S2. C.N hostsymb.pdf
• Fig S3. Compound to d13C.pdf