Denaturing gradient gel electrophoresis Denaturing

Denaturing gradient gel electrophoresis Denaturing gradient: 41-44% Electrophoresis: 60˚C, 100V, 14h ADS GLS Flooded treatment + +

Bradyrhizobium strain USDA 6

76

110

123

Image analysis

Measurement of peak area Fig. S1. Schematic representation of a DGGE analysis and the image analysis procedure for the estimation of community structures.

Table S1 pH, EC values, and population densities of bradyrhizobia in soil microcosms. pH(H2 O) 1:5 extract * 0 day 30 day ANW_H

5.93 ± 0.02 a

ANW_M ANW_L

6.09 ± 0.05 ab

60 day 6.05 ± 0.00 b

6.06 ± 0.01 b 6.11 ± 0.07 ab

6.05 ± 0.02 b 6.05 ± 0.00 b

EC (dS m-1) 1:5 extract* 0 day 30 day 0.38 ± 0.00 a

0.28 ± 0.02 b

60 day 0.33 ± 0.01 b

0.31 ± 0.01 b 0.31 ± 0.04 a

0.35 ± 0.01 a 0.34 ± 0.02 a

Population density (CFU g -1 dry soil) 0 day 30 day (1.26 ± 0.45) × 10

6

60 day 7

(3.64 ± 1.30) × 107

7

(3.09 ± 1.25) × 10 (3.17 ± 1.56) × 107

(3.81 ± 2.09) × 107 (8.38 ± 1.22) × 106

(3.17 ± 0.28) × 10

AFW_H AFW_M AFW_L

5.93 ± 0.02 a

6.80 ± 0.13 b 6.65 ± 0.02 b 6.81 ± 0.18 b

6.78 ± 0.05 b 6.74 ± 0.08 b 6.63 ± 0.02 b

0.38 ± 0.00 a

0.21 ± 0.05 ab 0.18 ± 0.00 b 0.17 ± 0.01 b

0.19 ± 0.00 b 0.18 ± 0.00 b 0.16 ± 0.01 b

(1.26 ± 0.45) × 106

(1.04 ± 0.56) × 108 (1.27 ± 0.30) × 108 (9.83 ± 1.84) × 107

(1.09 ± 0.39) × 107 (3.85 ± 0.80) × 107 (1.18 ± 1.62) × 107

AND_H AND_M AND_L

6.49 ± 0.02 a

6.21 ± 0.19 ab 6.13 ± 0.04 b 6.18 ± 0.05 b

6.33 ± 0.04 b 6.19 ± 0.03 b 6.17 ± 0.01 b

0.41 ± 0.02 a

0.37 ± 0.01 b 0.40 ± 0.01 a 0.42 ± 0.07 ab

0.32 ± 0.02 b 0.31 ± 0.03 a 0.31 ± 0.01 b

(8.82 ± 3.29) × 105

(1.04 ± 0.33) × 108 (1.04 ± 0.11) × 108 (1.27 ± 0.75) × 108

(4,72 ± 1.09) × 107 (5.48 ± 0.76) × 107 (8.20 ± 1.16) × 107

AFD_H AFD_M AFD_L

6.49 ± 0.02 a

6.92 ± 0.05 b 6.94 ± 0.03 b 6.95 ± 0.04 b

6.98 ± 0.04 b 6.92 ± 0.16 a 7.20 ± 0.05 c

0.41 ± 0.02 a

0.25 ± 0.01 b 0.25 ± 0.01 b 0.24 ± 0.01 b

0.23 ± 0.01 b 0.22 ± 0.01 b 0.26 ± 0.01 b

(8.82 ± 3.29) × 105

(2.76 ± 0.95) × 108 (1.37 ± 0.25) × 108 (1.14 ± 0.27) × 108

(7.77 ± 4.44) × 107 (8.76 ± 1.68) × 107 (1.01 ± 0.82) × 108

GNW_H GNW_M GNW_L

6.09 ± 0.02 a

5.88 ± 0.03 b 6.00 ± 0.07 a 5.99 ± 0.02 b

5.95 ± 0.02 c 5.89 ± 0.12 a 5.96 ± 0.03 b

0.28 ± 0.01 a

0.32 ± 0.04 a 0.33 ± 0.01 a 0.26 ± 0.03 a

0.33 ± 0.03 a 0.28 ± 0.04 a 0.31 ± 0.08 a

(1.33 ± 1.00) × 106

(3.81 ± 1.28) × 107 (6.76 ± 2.36) × 107 (5.59 ± 0.43) × 107

(4.78 ± 1.76) × 107 (3.26 ± 1.44) × 107 (3.25 ± 1.65) × 107

GFW_H GFW_M GFW_L

6.09 ± 0.02 a

6.51 ± 0.21 ab 6.68 ± 0.10 b 6.53 ± 0.11 ab

6.42 ± 0.06 b 6.20 ± 0.08 a 6.28 ± 0.05 b

0.28 ± 0.01 a

0.13 ± 0.01 b 0.14 ± 0.02 b 0.12 ± 0.01 b

0.16 ± 0.03 b 0.12 ± 0.00 b 0.12 ± 0.08 b

(1.33 ± 1.00) × 106

(1.43 ± 0.25) × 108 (9.24 ± 1.74) × 107 (1.64 ± 0.51) × 108

(1.06 ± 1.21) × 108 (9.81 ± 5.87) × 107 (1.83 ± 1.41) × 107

GND_H GND_M GND_L

6.09 ± 0.02 a

6.01 ± 0.07 a 5.96 ± 0.09 a 5.85 ± 0.02 b

5.99 ± 0.06 a 6.01 ± 0.03 a 6.10 ± 0.10 ab

0.28 ± 0.01 a

0.35 ± 0.04 a 0.34 ± 0.02 a 0.36 ± 0.05 a

0.34 ± 0.05 a 0.33 ± 0.03 a 0.28 ± 0.02 a

(1.13 ± 0.95) × 106

(4.81 ± 1.78) × 107 (6.26 ± 3.66) × 107 (5.60 ± 0.34) × 107

(3.65 ± 0.78) × 107 (3.61 ± 0.55) × 107 (3.16 ± 0.74) × 107

GFD_H GFD_M GFD_L

6.09 ± 0.02 a

6.69 ± 0.05 c 6.53 ± 0.13 a 6.57 ± 0.09 b

6.28 ± 0.04 b 6.42 ± 0.21 a 6.33 ± 0.10 ab

0.28 ± 0.01 a

0.18 ± 0.01 b 0.17 ± 0.01 b 0.16 ± 0.00 b

0.16 ± 0.00 b 0.16 ± 0.01 b 0.16 ± 0.01 b

(1.13 ± 0.95) × 106

(1.03 ± 0.61) × 108 (8.43 ± 0.49) × 107 (1.87 ± 0.62) × 108

(7.22 ± 0.50) × 107 (6.73 ± 0.60) × 107 (7.50 ± 2.57) × 107

Each value is the mean±SD (n=3). Community nomenclature is indicated as follows: A: andosol (ADS) or G: gray lowland soil (GLS), and N: non-flooded or F: flooded conditions, and W: microcosm with the USDA110T wild type or D: microcosm with the USDA110ΔnosZ variant. Additionally, High: high incubation temperature (H: 30˚C), Medium: medium incubation temperature (M: 25˚C), Low: low incubation temperature (L: 20˚C). Although these incubations were conducted using sterile soil, and sterile water was supplied where necessary, the water supply was conducted under semi-sterile conditions. These cfu values are indicated as references. a,b,c: different characters indicate significant differences among incubation periods (0, 30, 60 d) in the treatment (Bonferroni, p