Table 2.
Quality metrics of pyrosequencing analysis, co-amplification of non-target DNA, and amplification of bacterial rDNA reads.
| A. Total reads | 799F-1391R | 967F-1391R | 799F-1193R | 341F-785R | 68F-783Rabc | 68F-518R | 341F-783Rabc |
|---|---|---|---|---|---|---|---|
| Rhizosphere soil | 2235±165 | 2550±673 | 956±285 | 1961±119 | 3346±454 | 1519±217 | 2196 ± 317 |
| Root | 2728±74 | 2577±56 | 1943±129 | 2916±438 | 2484±155 | 3488±532 | 2548 ± 403 |
| Stem | 2811±117 | 2502±159 | 2456±486 | 2199±350 | 2068±384 | 3412±632 | 1386 ± 18 |
| Leaf | 2665±100 | 2402±231 | 2410±197 | 2621±134 | 1961±64 | 3257±367 | 1678 ± 81 |
| Read length before QC | 405±96 | 401±101 | 364±105 | 392±105 | 348±139 | 349±105 | 361 ± 129 |
| Read length after QC | 207±4 | 208±4 | 217±5 | 233±5 | 222±5 | 200±4 | 205 ± 4 |
| NORMALIZATION TO 1000 READS | |||||||
| B. Chloroplast DNA | 799F-1391R | 967F-1391R | 799F-1193R | 341F-785R | 68F-783Rabc | 68F-518R | 341F-783Rabc |
| Rhizosphere soil | 0 a | 0.2±0.3 (< 0.1)a | 0 a | 1±2 (0.1)a | 0 a | 0 a | 0.2±0.3 (< 0.1)a |
| Root | 0 a | 786±79 (79)b | 0 a | 863±54 (86)b | 736±90 (74)b | 975±8 (97)c | 270±87 (26)d |
| Stem | 2 ± 3(0.2)a | 997±3 (99)b | 0 a | 962±1 (96)b | 993±4 (99)b | 998±1 (99)b | 804±36 (80)c |
| Leaf | 0 a | 907±35 (91)b | 0 a | 910±29 (91)b | 894±12 (89)b | 985±4 (98)c | 518±71 (52)d |
| C. Mitochondrial DNA | 799F-1391R | 967F-1391R | 799F-1193R | 341F-785R | 68F-783Rabc | 68F-518R | 341F-783Rabc |
| Rhizosphere soil | 0 a | 0 a | 0.5±0.5 (< 0.1)a | 0 a | 0 a | 0 a | 0 a |
| Root | 0 a | 0 a | 9±1 (1)b | 45±17 (5) c | 15±5 (1) b | 4±1 (0.5)b | 136±17 (14)d |
| Stem | 0 a | 0 a | 19±11 (2)b | 35±1 (4)b | 6±3 (0.5)a | 1±1 (0.1)a | 173±25 (17)c |
| Leaf | 0 a | 0 a | 11±2.5 (1)b | 69±16 (7)c | 20±13 (2)b | 6±3 (0.5)b | 196±53 (20)d |
| D. Bacterial rDNA | 799F-1391R | 967F-1391R | 799F-1193R | 341F-785R | 68F-783Rabc | 68F-518R | 341F-783Rabc |
| Rhizosphere soil | 1000±0 (100)a | 999±0.26 (99)a | 999±0.3 (99)a | 998±3 (99)a | 1000±0 (100)a | 1000±0 (100)a | 999±0.52 (99)a |
| Root | 1000±0 (100)a | 414±79 (21)b | 992±1 (99)a | 92±41 (9)b | 250±88 (25)b | 22±7 (2)c | 594±72 (60)d |
| Stem | 997±3 (99)a | 2±3 (0.2)b | 982±11 (98)a | 4±2 (0.3)b | 1±1 (0.1)b | 1±2 (< 0.1)b | 25±12 (3)b |
| Leaf | 1000±0 (100)a | 93±35 (9)b | 989±3 (98)a | 22±15 (2)b | 85±37 (9)b | 10±6 (1)b | 278±25 (28)c |
(A) Total number of reads (± standard deviation) obtained per plant compartment for each primer pair and average read length (± standard deviation) before and after quality control (QC). Average number of chloroplast (B) and mitochondrial (C) sequences (non-target DNA) obtained from each plant compartment by the selected primer pairs. (D) Amplification of bacterial rDNA reads. Values were normalized to 1000 reads and are averages of three biologically independent replicates ± standard deviation. Values between brackets represent the average percentage (%) of reads. Sequence counts were statistically analyzed using a one-way ANOVA within each plant compartment to compare primer pairs. Differences at the 95% significance level are indicated with lower case letters (P < 0.05).