TABLE 3.
Species richness estimates obtained using long and short sequences from the Soil-Okla-A clone library at different taxonomic cutoffsa
| Regionb | Species richness estimation method | Species richness (mean ± SD) at indicated taxonomic cutoff (%)
|
||||
|---|---|---|---|---|---|---|
| 3 | 6 | 8 | 10 | 15 | ||
| V1+V2 | Chao | 1,874 ± 198 | 1,256 ± 151 | 802 ± 89 | 682 ± 86 | 397 ± 57 |
| ACE | 2,041 ± 209 | 1,169 ± 105 | 797 ± 68 | 649 ± 60 | 380 ± 38 | |
| Parametric | 4,589 ± 178 | 2,360 ± 94 | 1,616 ± 70 | 1,275 ± 59 | 737 ± 41 | |
| V3 | Chao | 1,050 ± 107 | 602 ± 72 | 418 ± 52 | 303 ± 41 | 145 ± 17 |
| ACE | 1,098 ± 94 | 562 ± 46 | 387 ± 31 | 286 ± 25 | 147 ± 13 | |
| Parametric | 2,273 ± 91 | 1,397 ± 68 | 686 ± 34 | 627 ± 37 | 190 ± 11 | |
| V4 | Chao | 1,704 ± 182 | 908 ± 110 | 611 ± 74 | 464 ± 60 | 211 ± 28 |
| ACE | 1,848 ± 171 | 913 ± 86 | 624 ± 60 | 455 ± 44 | 206 ± 19 | |
| Parametric | 3,428 ± 125 | 2,223 ± 100 | 1,034 ± 48 | 792 ± 40 | 305 ± 17 | |
| V5+V6 | Chao | 1,479 ± 161 | 784 ± 91 | 674 ± 95 | 546 ± 91 | 225 ± 30 |
| ACE | 1,576 ± 147 | 785 ± 69 | 594 ± 54 | 451 ± 44 | 219 ± 19 | |
| Parametric | 2,759 ± 125 | 1,539 ± 68 | 1,129 ± 53 | 904 ± 46 | 324 ± 17 | |
| V6 | Chao | 1,503 ± 158 | 1,031 ± 109 | 806 ± 85 | 736 ± 89 | 481 ± 60 |
| ACE | 1,728 ± 164 | 1,062 ± 94 | 827 ± 70 | 716 ± 64 | 454 ± 39 | |
| Parametric | 3,179 ± 121 | 2,302 ± 95 | 1,488 ± 62 | 1,407 ± 63 | 845 ± 41 | |
| V6+V7 | Chao | 1,246 ± 139 | 669 ± 69 | 494 ± 57 | 390 ± 52 | 187 ± 25 |
| ACE | 1,264 ± 115 | 704 ± 60 | 479 ± 39 | 370 ± 33 | 193 ± 20 | |
| Parametric | 2,688 ± 108 | 1,684 ± 79 | 1,023 ± 50 | 865 ± 48 | 292 ± 19 | |
| V7 | Chao | 660 ± 82 | 329 ± 56 | 209 ± 32 | 149 ± 25 | 76 ± 20 |
| ACE | 665 ± 63 | 298 ± 31 | 200 ± 20 | 148 ± 18 | 75 ± 12 | |
| Parametric | 1,209 ± 57 | 547 ± 32 | 343 ± 22 | 207 ± 13 | 91 ± 7 | |
| V7+V8 | Chao | 796 ± 85 | 373 ± 44 | 266 ± 33 | 206 ± 32 | 94 ± 22 |
| ACE | 807 ± 68 | 381 ± 36 | 276 ± 28 | 206 ± 25 | 91 ± 13 | |
| Parametric | 1,959 ± 87 | 706 ± 38 | 383 ± 20 | 288 ± 17 | 123 ± 10 | |
| NFL | Chao | 1,631 ± 161 | 805 ± 95 | 510 ± 57 | 429 ± 63 | 197 ± 34 |
| ACE | 1,833 ± 179 | 752 ± 64 | 517 ± 45 | 411 ± 42 | 192 ± 23 | |
| Parametric | 2,819 ± 98 | 1,790 ± 80 | 1,036 ± 51 | 912 ± 52 | 347 ± 24 | |
| LM | Chao | 868 ± 99 | 455 ± 60 | 310 ± 46 | 230 ± 35 | 125 ± 35 |
| ACE | 840 ± 70 | 448 ± 43 | 299 ± 31 | 229 ± 25 | 114 ± 18 | |
| Parametric | 2,183 ± 96 | 953 ± 52 | 463 ± 25 | 382 ± 24 | 187 ± 16 | |
a
Species richness estimates were obtained using the nearly full-length sequences with and without the Lane mask filter and each of the eight studied short, pyrosequencing-simulating regions from the Soil-Okla-A clone library at five different taxonomic cutoffs.
b
NFL, nearly full-length region (8F-1492R); LM, nearly full-length region with the Lane mask applied.