> 0.660.33 to 0.660 to 0.330-0.33 to 0-0.66 to -0.33< -0.66

Slope of the significantlinear correlation

RH

ma

x

PA

Rm

ax

Tm

in

PC

MI

Max 1 h [O

3]

Max 1 h [O

3] 14d

Ave 8 h [O

3] ]

Ave 8 h [O

3] 14d

14d AO

T40

Tmax     1   -1 -0 -1 -0 -0

RHmax

-1 -0 0          

PARmax 0            

Tmin -0 -1 -0 -0 -0 -0

PCMI          

Max 1 h [O3]   1 1 1 1

Max 1 h [O3] 14d   1 1 1

Ave 8 h [O3]   1 1

Ave 8 h [O3] 14d   1

Supplemental Figure S1. Pearson correlations between pairs of environmental variables. Maximum temperature during daylight hours (Tmax), maximum relative humidity during daylight hours (RHmax), maximum daily photosynthetically active radiation (PARmax), minimum temperature during the night before a sampling day (Tmin), Palmer’s Crop Moisture Index (PCMI), the 1 hour maximum [O3] during daylight hours (Max 1 h [O3]), the average of the maximum 1 h [O3] for the preceding 14 days before a sampling date (Max 1 h [O3] 14d), the average 8 h [O3] on the sampling date (Ave 8 h [O3]), the mean of the 8 h averages recorded for 14 days before a sampling date (Ave 8 h [O3] 14 d), and the accumulated dose of O3 over a threshold of 40 ppb for the 14 days preceding sampling (14 d AOT40). Significant correlations with a p-value less than 0.05 are displayed.

PC1O3

-4 -2 0 2 4 6

OR

AC

( m

ol

TE

g D

W-1

)

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0Ambient [CO2] ORAC = 0.0557x + 0.7685, P = 0.003

Elevated [CO2] ORAC = 0.0321x + 0.6521, P = 0.087

Higher [O3]Lower [O3]

Supplemental Figure S2. Total antioxidant capacity as affected by PC1O3. Open circles represent measurements at ambient [CO2] with the resulting linear regression (solid line). Closed circles represent measurements taken at elevated [CO2] with the resulting linear regression (dashed line).

H2O

H2O2

ASA

MDAMDHAR

NAD(P)H

NAD(P)+

DHA

ASA GSH

GSSG

DHARGR

APX

NAD(P)+

NAD(P)H

SOD

O2-

O2

CAT

O2

AOx

ASA MDA

GPxH2O

H2O2

Supplemental Figure S3. Transcripts coding for antioxidant recycling components that were significantly affected by PC1O3 at elevated [CO2]. Each box represents a unique transcript encoding an enzyme or protein structure. Blue

boxes denote a significant positive correlation between transcript abundance and PC1O3; yellow boxes denote a

significant negative correlation between transcript abundance and PC1O3. ROS are shown in red text, reduced

metabolites in blue text and oxidized metabolites in black text. Reduced ascorbic acid (ASA), monodehydroascorbate (MDA), dehydroascorbate (DHA), reduced glutathione (GSH), oxidized glutathione (GSSG), ascorbate oxidase (AOX), superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione peroxidase (GPX). Details of the transcriptional response and gene annotations are in Table S1.

Supplemental Fig. S4 % of transcripts of given function with significant differences in abundance due to principle component 2 (PC2ENV)

0 20 40 60 80

Biodegradation of XenobioticsPolyamine metabolism

Hormone metabolismCell wall

StressDevelopment

DNACell

MiscellaneousSecondary metabolism

RNANucleotide metabolism

SignallingMinor CHO metabolism

Co-factor and vitamin metabolismProtein

Lipid metabolismTransport

Amino acid metabolismGluconeogenesis/ glyoxylate cycle

S-assimilationMajor CHO metabolism

Metal handlingGlycolysis

FermentationN-metabolism

RedoxOPP

TCA cycleMitochondrial e- transport

C1-metabolismPhotosynthesis

Tetrapyrrole synthesis

Ambient [CO2]

Elevated [CO2]

**

***

***

*

*

****

*

*

**

**

****

**

**

*

**

**

*

Supplemental Figure S4. Percentage of transcripts in each of 33 functional groups from MapMan software that displayed significant average differences in abundance due to principle component 2 (PC2ENV) in ambient [CO2] (open bars) and elevated [CO2] (closed bars). The solid gray line is the average number of all transcripts tested that responded significantly to PC2ENV in the elevated [CO2] treatment (35%) and the dashed gray line is the average number that responded significantly in ambient [CO2] (38 %).

Supplemental Figure S5. Transcripts coding for components of tetrapyrrole synthesis significantly affected by PC1O3 at elevated [CO2]. Each box represents a unique transcript encoding an enzyme or protein structure. Blue boxes denote a significant positive correlation between transcript abundance and PC1O3. Yellow boxes denote a significant negative correlation between transcript abundance and PC1O3. Three key regulatory steps in this pathway are: 1) the activation of glutamate by glutamyl tRNA synthetase; 2) the conversion of glutamate-1-smialdehyde to 5-aminolevulinic acid (ALA) by GSA aminotransferase; and 3) an ATP dependant insertion of Mg 2+ into protoporphyrin IX by magnesium chelatase (Tanaka et al., 2007). Details of the transcriptional response and gene annotations are in Table S1.

Supplemental Fig. S6

Supplemental Figure S6. Transcripts coding for components of the TCA cycle and mitochondrial electron transport significantly affected by PC1O3 at elevated [CO2]. Each box represents a unique transcript encoding an enzyme or protein structure. Blue boxes denote a significant positive correlation between transcript abundance and PC1O3. Yellow boxes denote a significant negative correlation between transcript abundance and PC1O3. Details of the transcriptional response and gene annotations are in Table S1.

resp

iratio

n r

ate

(n

mo

l CO

2 g

-1 s

-1)

0

20

40

60

growth [O3] (ppb)

0 50 100 150 200

resp

iratio

n r

ate

(n

mo

l CO

2 g

-1 s

-1)

0

20

40

60

growth [O3] (ppb)

0 50 100 150 200

2009 2010

DOY 208

DOY 222

DOY 195

DOY 238

y = 0.10x + 23.74p = 0.07R2 = 0.46

y = 0.0012x2 -0.123x + 36.6p = 0.0025R2 = 0.91

y = -0.0013x2 + 0.36x - 3.25p = 0.13R2 = 0.56

p = 0.45

Supplemental Fig. S7

Supplemental Figure S7. Scatterplot of nighttime rates of respiratory CO2 efflux per unit leaf mass from mature leaves grown at [O3] ranging from 40 to 200 ppb. Data were collected during the first 4-hours of after sunset on day of year (DOY) 208 and 222 in 2009 and DOY 195 and 238 in 2010. The line of best fit and statistical results from regression analysis are shown on each panel.