Karl J. Romanowicz, Zachary B. Freedman, Rima A. Upchurch, William A. Argiroff, and Donald
SUPPLEMENTARY DATA
Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture
Karl J. Romanowicz, Zachary B. Freedman, Rima A. Upchurch, William A. Argiroff, and Donald R. Zak
Corresponding author: Karl J. Romanowicz
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FEMS Microbiology Ecology
The supplementary information includes Figures S1-S2 and Tables S1-S6
Figure S1. Approximate locations for four replicate northern hardwood forest stands (A-D) across upper and lower Michigan, USA.
Figure S2.Mean percent change of bacterial or fungal taxa(relative abundance) from the total community by sites. Significant site × community interactions within taxa (P < 0.05 via ANOVA) indicated by *.
Table S1. Sequence loss in MOTHUR quality control bioinformatic pipeline.
Initial Sequences / Final Sequences / % RemovedBacteria
Total / 57,929 / 47,496 / 18
Active / 54,856 / 39,100 / 29
Fungi
Total / 47,337 / 36,583 / 23
Active / 62,733 / 41,084 / 35
Table S2.Collinearity between environmental determinants from z-score transformations. Significant collinearity (|r| ≥ 0.80) in bold.
Moisture / pH / Aryl / Alkyl / O/N-alkyl / Carboxyl / C / N / C:NMoisture / -
pH / 0.78 / -
Aryl / -0.58 / -0.22 / -
Alkyl / 0.52 / 0.24 / -0.51 / -
O/N-alkyl / 0.09 / 0.03 / -0.38 / -0.58 / -
Carboxyl / -0.78 / -0.40 / 0.91 / -0.47 / -0.41 / -
C / -0.57 / -0.59 / 0.10 / -0.27 / 0.12 / 0.25 / -
N / 0.72 / 0.76 / -0.03 / 0.34 / -0.24 / -0.25 / -0.49 / -
C:N / -0.80 / -0.77 / 0.10 / -0.41 / 0.24 / 0.33 / 0.73 / -0.95 / -
Table S3. List of “Other” bacterial orders presented in Table 3.
1 / Acidimicrobiales / 30 / Fusobacteriales2 / Acidobacteria_Gp10_order_incertae_sedis / 31 / Gammaproteobacteria_order_incertae_sedis
3 / Acidobacteria_Gp16_order_incertae_sedis / 32 / Gemmatimonadales
4 / Acidobacteria_Gp2_order_incertae_sedis / 33 / Ktedonobacterales
5 / Acidobacteria_Gp3_order_incertae_sedis / 34 / Lactobacillales
6 / Acidobacteria_Gp3_order_incetae_sedis / 35 / Legionellales
7 / Acidobacteria_Gp4_order_incertae_sedis / 36 / Methylophilales
8 / Acidobacteria_Gp5_order_incertae_sedis / 37 / Myxococcales
9 / Acidobacteria_Gp6_order_incertae_sedis / 38 / Neisseriales
10 / Acidobacteria_Gp7_order_incertae_sedis / 39 / Nitrosomonadales
11 / Alphaproteobacteria_order_incertae_sedis / 40 / Oceanospirillales
12 / Alteromonadales / 41 / OD1_order_incertae_sedis
13 / Anaerolineales / 42 / Opitutales
14 / Armatimonadales / 43 / Pasteurellales
15 / Armatimonadetes_gp4_order_incetae_sedis / 44 / Phycisphaerales
16 / Armatimonadetes_gp5_order_incetae_sedis / 45 / Rhodobacterales
17 / Bacillales / 46 / Rhodocyclales
18 / Bacteroidales / 47 / Rickettsiales
19 / Bacteroidetes_incertae_sedis_order_incertae_sedis / 48 / Selenomonadales
20 / Bdellovibrionales / 49 / Solirubrobacterales
21 / Caldilineales / 50 / Spartobacteria_order_incertae_sedis
22 / Chloroflexales / 51 / Spirochaetales
23 / Chthonomonadales / 52 / SR1_order_incertae_sedis
24 / Clostridiales / 53 / Subdivision3_order_incertae_sedis
25 / Coriobacteriales / 54 / Thiotrichales
26 / Deinococcales / 55 / TM7_order_incertae_sedis
27 / Enterobacteriales / 56 / Verrucomicrobiales
28 / Entomoplasmatales / 57 / Xanthomonadales
29 / Erysipelotrichales
Table S4. List of “Other” fungal classes presented in Table 3.
1 / Agaricostilbomycetes2 / Ascomycota_incertae_sedis
3 / Cystobasidiomycetes
4 / Fungi_incertae_sedis
5 / Pezizomycetes
6 / Saccharomycetes
7 / Ustilaginomycetes
8 / Arthoniomycetes
9 / Chytridiomycetes
10 / Exobasidiomycetes
11 / Lecanoromycetes
12 / Pucciniomycetes
13 / Taphrinomycetes
Table S5. Influence of individual environmental factors on total and active bacterial and fungal composition. Significant variations in microbial composition attributed to an environmental factor (P < 0.05 via marginal DistLM) are in bold.
Bacteria / FungiTotal R2 / Active R2 / Total R2 / Active R2
Physical
Moisture 1 / 0.104 / 0.100 / 0.142 / 0.138
pH / 0.105 / 0.096 / 0.135 / 0.130
Chemical
Alkyl / 0.092 / 0.091 / 0.104 / 0.104
O/N-alkyl / 0.090 / 0.091 / 0.080 / 0.084
Carboxyl 2 / 0.099 / 0.098 / 0.121 / 0.120
Biogeochemical
C / 0.096 / 0.095 / 0.110 / 0.110
N 3 / 0.099 / 0.096 / 0.122 / 0.124
1 Moisture collinear with factor C:N (r = -0.80; Table S2); C:N excluded from marginal DistLM
2 Carboxyl collinear with factor Aryl (r = 0.91; Table S2); Aryl excluded from marginal DistLM
3 N content collinear with factor C:N (r = -0.95; Table S2); C:N excluded from marginal DistLM
Table S6. Spearman’s rank correlations between bacterial and fungal taxa representing significant community effects and environmental factors representing significant site effects. Significant correlations (|rs| > 0.59) are in bold.
Moisture / pH / Carboxyl / C1 / NTotal / Active / Total / Active / Total / Active / Total / Active / Total / Active
Bacteria
Caulobacterales / -0.50 / -0.82 / -0.71 / -0.66 / 0.50 / 0.41 / - / 0.59 / -0.50 / -0.92
Planctomycetales / 0.26 / 0.32 / 0.57 / 0.37 / -0.29 / -0.49 / - / -0.43 / 0.34 / 0.27
Pseudomonadales / -0.38 / 0.22 / -0.13 / 0.28 / 0.61 / -0.05 / - / -0.32 / -0.10 / 0.37
Rhizobiales / 0.46 / -0.70 / 0.55 / -0.66 / -0.57 / 0.32 / - / 0.33 / 0.45 / -0.73
Sphingobacteriales / 0.12 / 0.29 / -0.13 / 0.21 / 0.40 / -0.71 / - / 0.03 / 0.21 / 0.13
Fungi
Agaricomycetes / 0.57 / 0.71 / 0.71 / 0.64 / -0.58 / -0.52 / - / -0.44 / 0.69 / 0.83
Dothideomycetes / 0.34 / 0.53 / 0.34 / 0.21 / -0.55 / -0.28 / - / -0.09 / 0.31 / 0.51
Leotiomycetes / -0.41 / -0.29 / -0.36 / -0.46 / 0.71 / 0.56 / - / 0.34 / -0.13 / -0.13
Microbotryomycetes / 0.33 / 0.25 / 0.37 / 0.56 / -0.54 / -0.30 / - / -0.57 / 0.39 / 0.44
Tremellomycetes / -0.20 / 0.01 / -0.23 / 0.39 / -0.05 / -0.27 / - / -0.55 / -0.25 / 0.18
1 C content correlations excluded from total communities as factor was not significant in marginal DistLM