Ecological Archives E096-211-A3
Anna R. Peschel, Donald R. Zak, Lauren C. Cline, and Zachary Freedman. 2015. Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function. Ecology 96:2383–2393. http://dx.doi.org/10.1890/15-0164.1
Appendix C. Fungal and bacterial orders, and, functional genes which significantly drive the difference in taxonomic composition and functional dissimilarity respectively, between treatments.
Table C1. Bacterial orders significantly driving difference in taxonomic composition between treatments. Pearson’s r correlation coefficient shows direction and degree of correlation of orders to PCo axis 1 or 2.
Order |
Axis correlation |
P value |
Pearson’s r correlation coefficient |
Actinomycetales |
1(-) |
<0.0001 |
-0.93 |
Pseudomonadales |
1(-) |
<0.0001 |
-0.93 |
Bacteroidales |
1(-) |
<0.0001 |
-0.93 |
Rhizobiales |
1(-) |
<0.0001 |
-0.92 |
Rhodobacterales |
1(-) |
<0.0001 |
-0.91 |
Xanthomonadales |
1(-) |
<0.0001 |
-0.89 |
Bacillales |
1(-) |
<0.0001 |
-0.88 |
Lactobacillales |
1(-) |
<0.0001 |
-0.87 |
Clostridiales |
1(-) |
<0.0001 |
-0.87 |
Burkholderiales |
1(-) |
<0.0001 |
-0.86 |
Enterobacteriales |
1(-) |
<0.0001 |
-0.85 |
Sphingomonadales |
1(-) |
<0.0001 |
-0.85 |
Chroococcales |
1(-) |
<0.0001 |
-0.84 |
Bdellovibrionales |
1(-) |
<0.0001 |
-0.84 |
Selenomonadales |
1(-) |
<0.0001 |
-0.83 |
Spirochaetales |
1(-) |
<0.0001 |
-0.83 |
Vibrionales |
1(-) |
<0.0001 |
-0.82 |
Deinococcales |
1(-) |
<0.0001 |
-0.80 |
Nitrospirales |
1(-) |
<0.0001 |
-0.79 |
Myxococcales |
1(-) |
<0.0001 |
-0.78 |
Erysipelotrichales |
1(-) |
<0.0001 |
-0.78 |
Bifidobacteriales |
1(-) |
<0.0001 |
-0.77 |
Fibrobacterales |
1(-) |
<0.0001 |
-0.77 |
Oscillatoriales |
1(-) |
<0.0001 |
-0.77 |
Cytophagales |
1(-) |
<0.0001 |
-0.77 |
Gloeobacterales |
1(-) |
<0.0001 |
-0.76 |
Caulobacterales |
1(-) |
<0.0001 |
-0.72 |
Desulfuromonadales |
1(-) |
<0.0001 |
-0.71 |
Flavobacteriales |
1(-) |
<0.0001 |
-0.69 |
Verrucomicrobiales |
1(-) |
<0.0001 |
-0.68 |
Thermotogales |
1(-) |
<0.0001 |
-0.65 |
Thermales |
1(-) |
<0.0001 |
-0.64 |
Sphingobacteriales |
1(-) |
<0.001 |
-0.60 |
Solibacterales |
1(-) |
<0.001 |
-0.60 |
Candidatus |
1(-) |
<0.001 |
-0.59 |
Caldilineales |
1(-) |
<0.001 |
-0.58 |
Nostocales |
1(-) |
<0.001 |
-0.57 |
Synergistales |
1(-) |
<0.001 |
-0.56 |
Rhodospirillales |
1(-) |
<0.001 |
-0.56 |
Chlorobiales |
1(-) |
<0.001 |
-0.55 |
Herpetosiphonales |
1(-) |
<0.001 |
-0.54 |
Methylococcales |
1(-) |
<0.001 |
-0.53 |
Neisseriales |
1(-) |
<0.01 |
-0.51 |
Phycisphaerales |
1(-) |
<0.01 |
-0.46 |
Oceanospirillales |
1(-) |
<0.01 |
-0.41 |
Thiotrichales |
1(+) |
<0.0001 |
0.70 |
Caldilineales |
2(-) |
<0.01 |
0.50 |
Chlamydiales |
2(+) |
<0.01 |
0.41 |
Ktedonobacterales |
2(+) |
<0.01 |
0.41 |
Rubrobacterales |
2(+) |
<0.01 |
0.43 |
Hydrogenophilales |
2(+) |
<0.01 |
0.51 |
Thermoanaerobacterales |
2(+) |
<0.001 |
0.52 |
Aeromonadales |
2(+) |
<0.001 |
0.58 |
Rhodocyclales |
2(+) |
<0.0001 |
0.64 |
Acidithiobacillales |
2(+) |
<0.0001 |
0.70 |
Table C2. Fungal orders significantly driving the difference in taxonomic composition between treatments. Pearson’s r correlation coefficient shows the direction and degree of correlation for bacterial orders to PCo axis 1 or 2.
Order |
Axis correlation |
P-value |
Pearson's r correlation coefficient |
Agaricales |
1(-) |
<0.0001 |
-0.90 |
Eurotiales |
1(-) |
<0.0001 |
-0.88 |
Sordariales |
1(-) |
<0.0001 |
-0.86 |
Onygenales |
1(-) |
<0.0001 |
-0.81 |
Glomerellales |
1(-) |
<0.0001 |
-0.81 |
Saccharomycetales |
1(-) |
<0.0001 |
-0.79 |
Hypocreales |
1(-) |
<0.0001 |
-0.76 |
Dothideales |
1(-) |
<0.0001 |
-0.74 |
Magnaporthales |
1(-) |
<0.0001 |
-0.74 |
Pleosporales |
1(-) |
<0.001 |
-0.68 |
Auriculariales |
1(-) |
<0.001 |
-0.67 |
Microascales |
1(-) |
<0.001 |
-0.66 |
Mucorales |
1(-) |
<0.01 |
-0.62 |
Helotiales |
1(-) |
<0.01 |
-0.54 |
Schizosaccharomycetales |
2(+) |
<0.05 |
0.45 |
Xylariales |
2(+) |
<0.01 |
0.57 |
Capnodiales |
2(+) |
<0.0001 |
0.77 |
Table C3. Bacterial gene variants, that encode for lignocellulolytic enzymes, which are responsible for functional dissimilarity between treatments. Pearson’s r correlation coefficient shows the degree and direction of correlation of a gene variant to PCo axis 1 or 2.
Enzymes encoded by gene variants |
Gene family |
PCo axis |
P value |
Pearson’s r correlation coefficient |
alpha-amylase |
starch |
1(-) |
<0.001 |
-0.97 |
cellobiase |
cellulose |
1(-) |
<0.001 |
-0.96 |
alpha-L-arabinofuranosidase |
hemicellulose |
1(-) |
<0.001 |
-0.95 |
xylose isomerase |
hemicellulose |
1(-) |
<0.001 |
-0.93 |
D-alanine—(R) lactate ligase |
vanillin/lignin |
1(-) |
<0.001 |
-0.93 |
phenol oxidase |
lignin |
1(-) |
<0.001 |
-0.92 |
pullulanase |
starch |
1(-) |
<0.001 |
-0.92 |
endoglucanase |
cellulose |
1(-) |
<0.001 |
-0.91 |
isoamylase |
starch |
1(-) |
<0.001 |
-0.89 |
cutinase |
cutin |
1(-) |
<0.001 |
-0.85 |
glucoamylase |
starch |
1(-) |
<0.001 |
-0.80 |
neopullulanase |
starch |
1(-) |
0.022 |
-0.46 |
exoglucanase |
cellulose |
2(-) |
0.004 |
-0.56 |
glyoxal oxidase |
lignin |
2(-) |
0.005 |
-0.55 |
Table C4. Fungal gene variants that encode for lignocellulolytic enzymes, which are responsible for functional dissimilarity between treatments. Pearson’s r correlation coefficient shows the degree and direction of correlation of a gene variant to PCo axis 1 or 2.
Enzymes encoded by gene variants |
Gene family |
PCo axis |
P value |
Pearson’s r correlation coefficient |
phenol oxidase |
lignin |
1(-) |
<0.0001 |
-0.94 |
xylanase |
hemicellulose |
1(-) |
<0.0001 |
-0.93 |
exoglucanase |
cellulose |
1(-) |
<0.0001 |
-0.92 |
Alpha-L-arabinofuranosidase |
hemicellulose |
1(-) |
<0.0001 |
-0.90 |
endoglucanase |
cellulose |
1(-) |
<0.0001 |
-0.90 |
glucoamylase |
starch |
1(-) |
<0.001 |
-0.89 |
glyoxal oxidase |
lignin |
1(-) |
<0.0001 |
-0.89 |
cellobiase |
cellulose |
1(-) |
<0.0001 |
-0.88 |
alpha-amylase |
starch |
1(-) |
<0.001 |
-0.87 |
acetylxylan esterase |
cellulose |
1(-) |
<0.0001 |
-0.87 |
manganese peroxidase |
lignin |
1(-) |
<0.000001 |
-0.82 |
mannanase |
hemicellulose |
1(-) |
<0.001 |
-0.71 |
ligninase |
lignin |
1(-) |
<0.0001 |
-0.69 |
cutinase |
cutin |
1(-) |
<0.001 |
-0.63 |
vanillin dehydrogenase |
vanillin/lignin |
1(-) |
<0.01 |
-0.59 |
Literature cited
Riccardi, C. L., S. J. Prichard, D. V. Sandberg, and R. D. Ottmar. 2007. Quantifying physical characteristics of wildland fuels using the Fuel Characteristic Classification System. Canadian Journal of Forest Research 37:2413–2420.
Reiner, A. L., R. J. Tausch, and R. F. Walker. 2010. Estimation procedures for understory biomass and fuel loads in sagebrush steppe invaded by woodlands. Western North American Naturalist 70:312–322.