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

Email:

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 / % Removed
Bacteria
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:N
Moisture / -
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 / Fusobacteriales
2 / 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 / Agaricostilbomycetes
2 / 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 / Fungi
Total 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 / N
Total / 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