Article Figures & Data
Figures
- FIG 1
Distribution of mycobacterial relative abundances and clade richness across samples. Bars indicate either the number of samples containing the specified relative abundance of mycobacteria (% of all bacterial or archaeal 16S rRNA reads) (A) or the number of samples containing the specified number of mycobacterial clades (via hsp65 reads), which varies from 0 to 18 clades per sample (B).
- FIG 2
Relative abundances of mycobacteria across the 143 soils included in this study. Random forest analyses of 8 soil and site characteristics that described 25% of the variation in mycobacterial 16S rRNA gene relative abundances identified the most important environmental predictors as aridity index (A), soil pH (B), and minimum annual temperature (C). Boxplots show quartile ranges for each environmental category, with black dots indicating exact sample values. Significant differences between groups (determined using pairwise Wilcoxon signed-rank tests) are denoted by the asterisks with corresponding P values. Spearman correlations suggest that mycobacteria are more abundant in wetter, more acidic, and cooler soils. Aridity categories were based on site aridity index values: arid, 0 to 0.2; semiarid, 0.201 to 0.4; semihumid, 0.401 to 0.7; and Humid, 0.701 to 2.5. Categories for minimum annual temperature determined as cool, −35.0 to −9.0°C; temperate, −9.01 to 1.0°C; and warm, 1.0 to 22.0°C. (D) Differences in mycobacterial abundances across general ecosystem categories.
- FIG 3
Phylogenetic tree representing described and previously undescribed mycobacterial hsp65 sequences. (A) A total of 472 exact sequence variants (ESVs) were identified in soils sampled here, a majority of which represent novel and undescribed taxa. These ESVs span the known phylogenetic diversity of the genus. Colors indicate reference mycobacterial strains (blue) from Dai et al. (55) and sequences recovered from soils in this study (orange). (B) Closely related ESVs were grouped into 159 clades based on patristic distance. The top 20 most ubiquitous clades are highlighted in color, with yellow colors indicating higher ubiquity (clades found in more soil samples). Four of the clades included described members, as indicated by red symbols, namely, clade 10 (M. stomatepiae, M. genavense, M. florentinum, M. lentiflavum, M. montefiorense, and M. triplex), clade 12 (M. novocastrense and M. rutilum), clade 31 (including M. intracellulare, M. avium subsp. paratuberculosis, M. avium subsp. silvaticum, M. colombiense, M. chimaera, and M. avium subsp. avium), and clade 44 (M. doricum and M. monacense). Small black triangles mark sequences from the reference database. Both trees are rooted with the hsp65 sequence from Nocardia farcinica (DSM43665).
- FIG 4
Environmental preferences of selected mycobacterial clades. The environmental conditions associated with the presence of each clade shown here are significantly different from conditions in which the clade was absent, as determined by both Wilcoxon signed-rank tests and Spearman correlations (P < 0.05). Environmental variables that were consistently the most important for predicting clade presence in random forest models were aridity index (A), soil pH (B), and minimum annual temperature (C). Clades with notably strong environmental preferences are visualized in Fig. 1, and a comprehensive list of all significant relationships with supporting statistics is provided in Table S4 and S5. Three of these mycobacterial clades, namely, clade 10, clade 12, and clade 31, included described members (for a detailed list of named species, see Fig. 3 or Table S3).
Additional Files
Supplemental material
- Supplemental file 1 -
Tables S2 to S5, Fig. S1 and S2
PDF, 956K
- Supplemental file 2 -
Tables S2 to S5, Fig. S1 and S2
CSV, 20K
- Supplemental file 1 -
