Calcification. Net calcification was determined using the buoyant weight technique (Jokiel et al 1978). Each coral fragment was weighed at the beginning and end of the experiment. Buoyant weight was normalized to dry weight.

Gross photosynthesis. Gross photosynthesis was calculated from net photosynthesis and respiration; these measurements were made on the live coral fragments incubated in sealed chambers (Hoadley et al. 2016).

CZAR, CHARtoc, CTAR. Gross photosynthesis and respiration were used to calculate CZAR (Muscatine et al. 1981). Dissolved and particulate organic carbon samples (DOC and POC) were collected following incubations. DOC samples were analyzed using a Shimadzu TOC-L total organic carbon analyzer (using the 680°C combustion catalytic oxidation method) (Levas et al 2015). POC filters (GF/F) were acid fumigated (Levas et al 2015) and combusted in an Elementar Vario EL Cube/Micro Cube elemental analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer at the stable isotope facility at the University of California - Davis. CHARtoc was calculated using methods modified from Levas et al (2015). CZAR and CHARZOO were summed to yield CTAR (Grottoli et al. 2014).

For tissue analyses, corals were frozen at -80 degrees C and samples were either ground of airbrushed for further analyses.

Surface area. Surface area was measured on Acropora millepora using the wax-dipping technique (Veal et al. 2010) and on Turbinaria reniformis using the aluminum foil method (Marsh 1970).

Tissue biomass. Ash free dry weight was calculated using methods in McLachlan et al. (2020) on ground growing tips of A. millepora and water-picked tissue slurry of T. reniformis.

Chlorophyll a. A. millepora chlorophyll a was measured from tissue slurry using 100% acetone (Jeffrey & Humphrey 1975). T. reniformis chlorophyll data was from Hoadley et al. (2016).

Protein. Protein was measured using the bicinchoninic method (Smith et al. 1985) with bovine serum albumin as a standard (Pierce BCA Protein Assay Kit). This was carried out on air-brushed tissue slurry of A. millepora and water-picked and freeze-dried tissue slurry for T. reniformis. Protein was reported in Joules (Gnaiger & Bitterlich, 1984) and standardized to total biomass of the sub-sample.

Carbohydrates. Carbohydrates were measured using the phenol-sulfuric acid spectrophotometric method (Dubois et al. 1956) with glucose standards. This was carried out on air-brushed tissue slurry of A. millepora and ground T. reniformis. Carbohydrates were reported in Joules (Gnaiger & Bitterlich, 1984) and standardized to total biomass of the sub-sample.

Total lipids. Total lipids were measured using chloroform:methanol (2:1, v:v) with two KCl rinses (Baumann et al. 2014). This was carried out on air-brushed tissue slurry of A. millepora and water-piked and freeze-dried tissue slurry for T. reniformis. Total lipids were reported in Joules (Gnaiger & Bitterlich, 1984) and standardized to total biomass of the sub-sample.

δ15N isotopes (coral host, algal endosymbiont, whole tissue). Samples were prepped for isotopic analysis using a method modified from Hughes and Grottoli (2010). All A. millepora host and algal endosymbiont fractions, partitioned from airbrushed tissue slurry, were combusted in a Costech elemental analyzer and the resulting N2 gas analyzed with a Thermo Finnigan Delta IV stable isotope ratio mass spectrometer (SIRMS) via a ConFlow open split interface in the Grottoli Stable Isotope Biogeochemistry Lab at The Ohio State University. All T. reniformis whole (freeze-dried tissue slurry) and algal endosymbiont fractions were combusted in an Elementar Vario EL Cube/Micro Cube elemental analyzer interfaced to a PDZ Europa 20-20 SIRMS at the stable isotope facility at University of California - Davis. Repeated measurements of an internal standard had an average SD ±0.08‰ δ15N. The δ15N values of both species are reported as the per mil deviation of the ratio of stable nitrogen isotopes 15N:14N relative to air. Approximately 10% of A. millepora samples were run in duplicate with an average SD ± 0.21‰.

A Euclidean distance-based resemblance matrix was constructed using normalized data of primary physiological variables: P, calcification, biomass, protein, and total lipids. Non-metric multi-dimensional scaling (NMDS) plots were generated to visualize relationships between each coral ramet across all treatments, for each species. Analysis of similarities (ANOSIM) was used to evaluate the degree of dissimilarity among treatments. All multivariate analyses were conducted using the software package Primer v6 (Clarke & Gorley 2006). Prior to further statistical analysis, all data were tested for normality by a Shapiro-Wilk’s test and homogeneity of variance was assessed with plots of expected vs. residual values. Univariate three-way analysis of variance (ANOVA) was used to test the effects of temperature, pCO2, nutrients, and genotype on each measured variable for each species. Temperature was fixed with 2 levels (26.4°C, 29.8°C), pCO2 fixed with 2 levels (401 μatm, 760 μatm), nutrients fixed with 2 levels (ambient, moderate). All univariate parametric statistics were generated using SAS software, Version 9.3 of the SAS System for Windows. Values of p ≤ 0.05 were considered significant.

Additional details of the statistical analysis are outlined in Dobson et al. 2020.