Table 3.
A comparison of alpha-diversity estimators among the RNA-seq and RNA/DNA Amplicon-seq datasets.
| Bacteria | Archaea | |||||
|---|---|---|---|---|---|---|
| RNA-seq | RNA Amplicon-seq (Mean ± SEM) | DNA Amplicon-seq | RNA-seq | RNA Amplicon-seq (Mean ± SEM) | DNA Amplicon-seq | |
| Number of observed phylotypes | 45.4 ± 2.8*1 | 33.2 ± 2.9# | 35.6 ± 3.1# | 11.8 ± 0.4a | 6.2 ± 0.2b | 7.6 ± 0.5c |
| Chao | 52.1 ± 3.8* | 43.0 ± 7.3*# | 40.4 ± 3.3# | 12.7 ± 0.5a | 6.2 ± 0.2b | 8.4 ± 1.0b |
| Shannon2 | 1.9 ± 0.3 | 1.8 ± 0.3 | 2.0 ± 0.2 | 1.2 ± 0.1 | 1.0 ± 0.0 | 1.1 ± 0.1 |
| Inverse Simpson | 4.3 ± 1.2 | 4.2 ± 1.3 | 4.8 ± 1.0 | 2.5 ± 0.2 | 2.3 ± 0.1 | 2.5 ± 0.3 |
| Good's coverage | 99.7% | 99.8% | 99.8% | 99.8% | 100% | 99.9% |
1
Within a row, means with different superscript tend to be different at P < 0.1. Comparison was conducted using paired Wilcoxon signed rank test for bacterial and archaeal communities separately, and thus estimators between bacterial and archaeal groups are not comparable.
2
Shannon indices showed in the table are the raw values, and the comparison of Shannon indices among datasets was based on the exponentially transformed values (Jost, 2007) using paired Wilcoxon signed rank test.