#### 4.1. Chlorophyll a Fluorescence Measurements

(a) Normalizations and Subtractions

The chlorophyll

a fluorescence polyphasic O-J-I-P kinetics of dark-adapted samples grown under C1, C2, C3, and C4, for 1, 5, and 8 days are evident in

Figure 1. Each kinetic is the average of six replicates, after each of the kinetics Ft = f(t) was normalized on its initial value; i.e., the averages are plotted as F

_{t}/F

_{0} = f(t). This normalization was permitted as the minor variations observed among the raw F

_{20μs} values were random and not depending on the treatment. Hence, the experimental F

_{20μs} was reasonably taken as the real F

_{0}. The kinetics demonstrated clearly that high light levels (C3 and C4) result in a pronounced suppression of the variable fluorescence (F

_{t} − F

_{0}) throughout the entire time course of the 1 s.

(b) The JIP-Test Parameters

The trapped energy flux per RC (TR

_{0}/RC) was not affected by irradiance or salinity and their interaction (

Figure 2A,

Table S1), but the effect of irradiance was significant on RCs per PSII antenna Chl

a (RC/ABS;

p < 0.001,

Table S1). Mean RC/ABS values (

Figure 2B) were higher at 100 μmol photons m

^{−2} s

^{−1} (C1, C2) than at 400 μmol photons m

^{−2} s

^{−1} (C3, C4). The maximum RC/ABS values were observed at C2 and at C1 on the 5th day, while the minimum values were observed at C3 on the 5th day and at C4 on the 1st day. Post hoc comparisons (

Table S2) showed that RC/ABS values were significantly lower in C3 and C4 than in C1 and C2.

The effect of irradiance was significant on the light absorption flux of antenna chlorophyll molecules per RC (also a measure of PSII apparent antenna size-ABS/RC;

p < 0.001,

Table S1). Mean ABS/RC values (

Figure 2C) were higher at 400 μmol photons m

^{−2} s

^{−1} (C3, C4) than at 100 μmol photons m

^{−2} s

^{−1} (C1, C2). The maximum values of ABS/RC were observed at C3 on the 5th day and at C4 on the 1st day, while the minimum values were observed at C1 on the 5th day and at C2 on the 8th day. Post hoc comparisons (

Table S3) showed that ABS/RC values were significantly lower in C1 and C2 than in C3 and C4 conditions. There was a significant interaction between salinity and treatment time on ABS/RC (

p < 0.01,

Table S1). At salinity 19 (C2, C4), no significant differences were observed. At 400 μmol photons m

^{−2} s

^{−1} (C3), ABS/RC values increased from the 1st to the 5th day, but they decreased on the 8th day.

The effect of irradiance was significant on the dissipated energy flux per RC (DI

_{0}/RC;

p < 0.001,

Table S1). Mean DI

_{0}/RC values were higher at 400 μmol photons m

^{−2} s

^{−1} (C3, C4) than at 100 μmol photons m

^{−2} s

^{−1} (C1, C2). The maximum of DI

_{0}/RC were observed at C3 on the 5th day and at C4 on the 1st day, while the minimum values were observed at C2 on the 8th day and at C2 on the 1st day. Post hoc comparisons (

Table S4) showed that DI

_{0}/RC values were significantly lower in C1 and C2 than in C3 and C4 conditions.

The effect of irradiance was significant on φ

_{P0}, i.e., the efficiency by which PSII transforms excitation energy to oxido-reduction energy (reduction of the primary electron quinone acceptor Q

_{A} to Q

_{A}^{−}) (

p < 0.01,

Table S1). Mean φ

_{P0} values (

Figure 3A) were higher at 100 μmol photons m

^{−2} s

^{−1} (C1, C2) than at 400 μmol photons m

^{−2} s

^{−1} (C3, C4). The maximum φ

_{P0} values were observed at C1 on the 1st day and at C2 on the 8th day, while the minimum values were observed at C3 on the 5th day and at C4 on the 1st day. Post hoc comparisons (

Table S5) showed that φ

_{P0} values were significantly lower in C3 and C4 than in C1 and C2. There was also a significant interaction between salinity, irradiance and treatment time on φ

_{P0} (

p < 0.01,

Table S1). At salinity 9 and irradiance 400 μmol photons m

^{−2} s

^{−1} (C3), φ

_{P0} values decreased on the 5th day, but they partly recovered on the 8th day. In the other conditions (C1, C3, C4), φ

_{P0} did not exert significant changes over time.

The effect of irradiance was significant on the quantum yields for electron transport to the plastoquinone (PQ) pool (φ

_{E0};

p < 0.01,

Table S1). Mean φ

_{E0} values (

Figure 3B) were higher at 100 μmol photons m

^{−2} s

^{−1} (C1, C2) than at 400 μmol photons m

^{−2} s

^{−1} (C3, C4). The maximum φ

_{E0} values were observed at C2 and at C1 on the 1st day, while the minimum values were observed at C3 on the 5th day and at C4 on the 1st day. Post hoc comparisons (

Table S6) showed that φ

_{E0} values were significantly lower in C3 and C4 than in C1 and C2. The effect of treatment time was significant on φ

_{E0} (

p < 0.01,

Table S1). φ

_{E0} values in C3 decreased on the 5th day, but they partly recovered on the 8th day.

The effect of irradiance was significant on the quantum yields for electron transport to the electron acceptors at the PSI acceptor side (φ

_{R0};

p < 0.01,

Table S1). Mean φ

_{R0} values (

Figure 3C) were higher at 100 μmol photons m

^{−2} s

^{−1} (C1, C2) than at 400 μmol photons m

^{−2} s

^{−1} (C3, C4). The maximum φ

_{R0} values were observed at C2 on the 1st day and at C2 on the 5th day, while the minimum values were observed at C3 and at C4 on the 5th day. Post hoc comparisons (

Table S7) showed that φ

_{R0} values were significantly lower in C3 and C4 than in C1 and C2. There was also a significant interaction between irradiance and treatment time on φ

_{R0} (

p < 0.01,

Table S1). At irradiance 400 μmol photons m

^{−2} s

^{−1} (C3, C4), φ

_{R0} decreased from the 1st to the 5th day, but they partly recovered on the 8th day, while at 100 μmol photons m

^{−2} s

^{−1} (C1, C2), φ

_{R0} decreased over time.

The effect of irradiance was significant on the efficiency/probability that an electron moves further than Q

_{A}^{−} (ψ

_{E0};

p < 0.01,

Table S1). Mean ψ

_{E0} values (

Figure 4A) were higher at 100 μmol photons m

^{−2} s

^{−1} (C1, C2) than at 400 μmol photons m

^{−2} s

^{−1} (C3, C4). The maximum ψ

_{E0} values were observed at C1 on the 1st day and at C2 on the 1st day, while the minimum values were observed at C3 on the 5th day and at C4 on the 5th day. Post hoc comparisons (

Table S8) showed that ψ

_{E0} values were significantly lower in C3 and C4 than in C1 and C2. The effect of treatment time was significant on ψ

_{E0} (

p < 0.01,

Table S1). Ψ

_{E0} values decreased on the 5th day, but they partly recovered on the 8th day.

The effect of irradiance was significant on the efficiency/probability that an electron from the intersystem electron carriers is transferred to reduce end electron acceptors at the PSI acceptor side (δ

_{R0};

p < 0.01,

Table S1). Mean δ

_{R0} values (

Figure 4B) were higher at 400 μmol photons m

^{−2} s

^{−1} (C3, C4) than at 100 μmol photons m

^{−2} s

^{−1} (C1, C2). The maximum δ

_{R0} values were observed at C4 on the 1st day and at C3 on the 5th day, while the minimum values were observed at C2 and at C1 on the 8th day. Post hoc comparisons (

Table S9) showed that δ

_{R0} values were significantly higher in C3 and C4 than in C1 and C2.

The effect of irradiance was significant on the connectivity of PSII photosynthetic units (M

_{0}’/M

_{0};

p < 0.01,

Table S1). Mean M

_{0}’/M

_{0} values (

Figure 4C) were higher at 400 μmol photons m

^{−2} s

^{−1} (C3, C4) than at 100 μmol photons m

^{−2} s

^{−1} (C1, C2). The maximum M

_{0}’/M

_{0} values were observed at C3 and at C4 on the 5th day, while the minimum values were observed at C1 on the 1st day and at C2 on the 8th day. Post hoc comparisons (

Table S10) showed that M

_{0}’/M

_{0} values were significantly lower in C3 and C4 than in C1 and C2. Differences due to salinity and time are found not to be statistically significant.