Table 1. Summary of metrics computed for datasets derived from the USEARCH and “Dada2” pipelines for ITS and 16S amplicons for microbial aerosol communities at urban parks.
| 16S | ITS | |||||||
|---|---|---|---|---|---|---|---|---|
| Metrics | 16S Dada2 | 16S USEARCH | P value 16S Dada2 v USEARCH | ITS Dada2 | ITS USEARCH | P value ITS Dada2 v USEARCH | ||
| Raw abundance | Total reads | 507,586 | 754,752 | 0.03 | 1,687,012 | 2,222,530 | 0.10 | |
| Mean (SD) reads per sample | 9,399 (7,808) | 10,938 (9,381) | 0.37 (0.3) | 25,179 (26,742) | 33,172 (35,256) | 0.09 (0.07) | ||
| Raw diversity | Total ASVs | 7,503 | 4,400 | 0.01 | 7,507 | 5,519 | 0.02 | |
| Samples with no reads completing pipeline | 3 | 0 | 0.08 | 1 | 0 | 0.36 | ||
| Alpha diversity (Hill numbers) | Observed (D0) | 151 | 315 | 0.00 | 255 | 441 | 0.01 | |
| Exp Shannon (D1) | 16.46 | 23.8 | 0.19 | 18.88 | 29.48 | 0.10 | ||
| Inv Simpson (D2) | 17.25 | 16.66 | 0.90 | 14.8 | 17.15 | 0.61 | ||
| Beta diversity (Bray–Curtis) | Mean | 0.84 | 0.87 | 0.37 | 0.9 | 0.9 | 0.70 | |
| Median | 0.89 | 0.91 | 0.95 | 0.94 | 0.93 | 0.57 | ||
| Range | 0.12–1 | 0.13–1 | N/A | 0.17–1 | 0.22–1 | N/A | ||
| Standard deviation | 0.16 | 0.15 | 0.40 | 0.12 | 0.11 | 0.90 | ||
| No. ASVs sig. differentially abundant (by location) | 174 | 180 | 0.01 | 41 | 51 | 0.25 | ||
Note:
SD is the standard deviation. 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. No, is number; sig, is significantly. 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.