Table 3.
Number of archaeal sequences before and after quality management, barcode, number of OTUs, coverage, Chao1 and inverted Simpson index of the environmental samples analyzed by 454-pyrosquencing.
| Gene | Name | Growth Stage | Plant | Barcode | Accession | Raw seqs | No. seqs* | No. OTU | Good's coverage | Chao1 | 1/Simpson |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 16S rDNA | RWVF3 | Vegetative | Rice | ACGTAC | SRS715481 | 4063 | 1956 | 164 | 0.97 | 208 | 32 |
| RWVF6 | Vegetative | Rice | ACTGCA | SRS715482 | 2572 | 1326 | 140 | 0.96 | 205 | 24 | |
| RWVF9 | Vegetative | Rice | AGAGTC | SRS715483 | 4886 | 2828 | 177 | 0.98 | 293 | 29 | |
| RWRF3 | Reproductive | Rice | ATCGAT | SRS715487 | 7437 | 3753 | 231 | 0.98 | 359 | 30 | |
| RWRF6 | Reproductive | Rice | ATGCTA | SRS715488 | 5458 | 2410 | 188 | 0.97 | 264 | 32 | |
| RWRF9 | Reproductive | Rice | CACAGT | SRS715489 | 1414 | 929 | 112 | 0.95 | 168 | 18 | |
| RWMF3 | Maturity | Rice | CAGTCA | SRS715493 | 6656 | 3630 | 202 | 0.98 | 291 | 25 | |
| RWMF6 | Maturity | Rice | CATGAC | SRS715494 | 4312 | 2137 | 176 | 0.97 | 284 | 31 | |
| RWMF9 | Maturity | Rice | CGATAT | SRS715495 | 6515 | 3250 | 201 | 0.97 | 492 | 26 | |
| MMRF4 | Repoductive | Maize | CAGTCA | SRS715490 | 8727 | 4644 | 206 | 0.99 | 256 | 17 | |
| MMRF7 | Reproductive | Maize | CATGAC | SRS715491 | 7723 | 3378 | 192 | 0.98 | 251 | 29 | |
| MMRF10 | Reproductive | Maize | CGATAT | SRS715492 | 6280 | 2894 | 164 | 0.99 | 194 | 23 | |
| MMVF4 | – | Unplanted | AGCTGA | SRS715484 | 6678 | 3369 | 168 | 0.99 | 215 | 10 | |
| MMVF7 | – | Unplanted | AGTCAG | SRS715485 | 2918 | 1504 | 128 | 0.97 | 185 | 16 | |
| MMVF10 | – | Unplanted | ATATCG | SRS715486 | 3909 | 2049 | 159 | 0.98 | 208 | 23 | |
| 16S rRNA | RWRF3 | Reproductive | Rice | ATCGAT | SRS715487 | 3232 | 1962 | 169 | 0.97 | 232 | 36 |
| RWRF6 | Reproductive | Rice | ATGCTA | SRS715488 | 2797 | 1727 | 128 | 0.97 | 239 | 25 | |
| RWRF9 | Reproductive | Rice | CACAGT | SRS715489 | 572 | 565 | 74 | 0.95 | 126 | 19 | |
| MMRF4 | Repoductive | Maize | CAGTCA | SRS715490 | 7914 | 804 | 74 | 0.96 | 115 | 8 | |
| MMRF7 | Reproductive | Maize | CATGAC | SRS715491 | 1459 | 775 | 85 | 0.96 | 109 | 14 | |
| MMRF10 | Reproductive | Maize | CGATAT | SRS715492 | 831 | 532 | 55 | 0.96 | 78 | 10 |
Raw data were deposited under the study accession numbers SRP047229 for archaeal sequences in the NCBI Sequence Read Archive (SRA). Sample from one field (A–C) was randomly chosen and analyzed as representative of the field.
*
number of sequences after quality analysis.
Partial 16S rRNA primers: Archaea: Arch344F (5′-ACGGGGYGCAGCAGGCGCGA), Arch934br (5′-GTGCTCCCCCGCCAATTCCT).
Adaptor primes: forward (5′-GATGGCCATTACGGCC), reverse (5′-GGTGGCCGAGGCGGCC).