Table 3. Contamination correction method tested on post USEARCH data for microbial aerosol communities at urban parks measured using 16S and ITS DNA sequencing with a combined taxonomy table.
| Dataset | 16S | ITS | |
|---|---|---|---|
| Metrics | |||
| ASVs flagged as contaminates | “microDecon” adjusted 350 ASVs for contamination. “decontam” flagged frequency—117 combination—340, prevalence 13–217 ASVs depending on threshold. | “microDecon” adjusted 303 for contamination, “decontam” flagged frequency—104 combination—251 prevalence 1–77 ASVs depending on threshold. | |
| Alpha diversity (Hills numbers) | Observed (D0) | 236 | 388 |
| expShannon (D1) | 15.92 | 28.2 | |
| invSimpson (D2) | 10.45 | 18.03 | |
| Beta diversity (Bray–Curtis) | Mean | 0.86 | 0.91 |
| Median | 0.91 | 0.94 | |
| Range | 0.21–1 | 0.25–1 | |
| Standard deviation | 0.14 | 0.1 | |
| Number of ASVs significantly differentially abundant (by location) | 144 | 54 | |
Note:
For both ITS and 16S “microDecon” was used on default settings. The decontaminated ASV table produced was checked for consistency against contaminant ASVs identified in “decontam” on a range of its options (frequency, prevalence and combination). 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.