Amino acid compound specific isotope analyses (AA-CSIA) of reef corals and their endosymbiont algae

Wall CB, Wallsgrove NJ, Gates RD, Popp BN. 20201. Amino acid δ13C and δ15N analyses reveal distinct species-specific patterns of trophic plasticity in a marine symbiosis. Limnology and Oceanography

Compound specific isotope analyses (CSIA) and multivariate ‘isotope fingerprinting’ track biosynthetic sources and reveal trophic interactions in food webs. However, CSIA have not been widely applied in the study of marine symbioses. Here, we exposed a reef coral (Montipora capitata) in symbiosis with Symbiodiniaceae algae to experimental treatments (autotrophy, mixotrophy, heterotrophy) to test for trophic shifts and amino acid (AA) sources using paired bulk (δ13C, δ15N) and AA-CSIA (δ13CAA, δ15NAA).

Directory information

CSIA-AA-corals.html

html file for Rmd output
To open the html output you must first download it and open it in from your computer (it opens with plots and code embedded).

CSIA-AA-corals.Rmd

R markdown for project
This is the markdown script that generates the html and executes all code

CSIA-AA.Rproj

R project to run Rmd and directory
If you open RStudio-- load the Project, open the Rmd and code away!

DATA houses the following folders and files

bulkCN.isotopes.csv
- bulk isotope data for corals, their symbionts, plankton sample
d13C.CSIA.long.csv
- long format carbon AA-CSIA data
d13C.CSIA.wide.csv
- wide format carbon AA-CSIA data
d15N.CSIA.long.csv
- long format nitrogen AA-CSIA data
d15N.CSIA.wide.csv
- wide format nitrogen AA-CSIA data
Pacif_RedS_Aloha_source_AAd13C.csv
- data from Palmyra, Red Sea, Station Aloha, present study (Oahu) -- includes coral, symbionts, cultured algae and POM/plankton
Pacific.Redsea.EAA_full.df
- data for Palmyra, Red Sea, Hawaii exclusive to corals, symbionts, POM/plankton
Palmyra_AAd13C.csv
- coral, symbiont, POM/plankton data from Fox et al. 2019 Functional Ecology
sumV.csv
- AA-CSIA for sumV calculations
wt.means.d15N.csv
- AA-CSIA for weighted mean calculations

percent heterotrophy folder
- spreadsheets to calculate percent heterotrophy in mixing models

FIGURES folder

execute code -- these are outputs from the code chunks in R
Main Tables and Figures -- these are found in the manuscript text, slightly modified figure outputs

OUTPUT folder

assorted outputs from running Rmd code, some used in figure and table summaries

cbwall/CSIA-corals