Table 2. Comparison of taxonomy assignments of 16S and ITS USEARCH ASVs for urban parks bioaerosol communities with the RDP and SILVA (16S)/UNITE(ITS) taxonomy databases, and with a combined database approach.
| Taxonomy database used | RDP training set (16S) | SILVA (16S) |
P-value between 16S databases |
RDP training set (ITS) | UNITE (ITS) |
P-value Between ITS databases |
|
|---|---|---|---|---|---|---|---|
| Metrics | |||||||
| Total genera identified by pipeline | 517 | 694 | 0.02 | 501 | 696 | 0.06 | |
| Alpha diversity of genera (Hill numbers) | Observed (D0) | 112 | 127 | 0.30 | 121 | 123 | 0.75 |
| expShannon (D1) | 11.31 | 12.56 | 0.52 | 14 | 8.56 | 0.02 | |
| invSimpson (D2) | 7.99 | 8.98 | 0.56 | 8.71 | 5.3 | 0.00 | |
| Beta diversity of genera (Bray–Curtis) | Mean | 0.78 | 0.8 | 0.56 | 0.84 | 0.82 | 0.61 |
| Median | 0.8 | 0.83 | 0.52 | 0.86 | 0.85 | 0.75 | |
| Range | 0.08–1 | 0.09–1 | NA | 0.17–1 | 0.10–1 | NA | |
| Standard deviation | 0.19 | 0.18 | 0.44 | 0.14 | 0.18 | 0.17 | |
| Unassigned ASVs at genus level | Number | 2,479 | 1,681 | 0.02 | 3,899 | 3,559 | 0.28 |
| % total ASVs | 56% | 38% | 0.00 | 71% | 64% | 0.01 | |
| Unassigned ASVs at genus level with both databases | Number | 1,011 | 2,871 | ||||
| % total ASVs | 23% | 53% | |||||
Note:
Observed (D0) is the raw diversity or number of unique ASVs detected. ExpShannon (D1) refers to the exponential of the Shannon diversity index and invSimpson (D2) refers to the inverse of the Simpson diversity index. Ranges are not appropriate for statistical testing so an N/A appears instead of a p value for them. P values that are significant at the 0.05 threshold appear in bold.