FigureS1. Measures of intra-group diversity using QIIME 1.8.0. (a) Alpha diversity rarefaction using observed species in Chao1 analysis. (b) Shannon score for evenness. Colors are: red (Garden Soil), blue (Hospital soil).

(A)(B)

Figure S2. Relative abundance of phylum level taxonomic bins in the 16S rRNA gene sequence datasets.

Figure S3. Statistical analyses of metabolic profiles for the hospital soil and the garden soil at STAMP level 1. Total numbers of sequences in the different categories are shown in the bar graph; the blue bar represents the garden soil, while the yellow bar represents the hospital soil. Subsystems in the hospital soil community have negative differences between proportions (yellow dots). Subsystems overrepresented in the garden soil samples have positive differences between proportions (blue dots). Features with a q value of >0.05 were considered significant.

Figure S4. Statistical analyses of metabolic profiles for the hospital soil and the garden soil at STAMP level 2. Total numbers of sequences in the different categories are shown in the bar graph; the blue bar represents the garden soil, while the yellow bar represents the hospital soil. Subsystems in the hospital soil community have negative differences between proportions (yellow dots). Subsystems overrepresented in the garden soil samples have positive differences between proportions (blue dots). Features with a q value of >0.05 were considered significant.

Table S1. Data summary of metagenome data used for comparative metagenomics.

MG-RAST ID / Name
4548402.3 / Hospital Soil
4548916.3 / Garden Soil
4491955.3 / Soil 1
4569430.3 / Soil 2
4520195.3 / Soil 3
4603397.3 / Soil 4
4507647.3 / Soil 5
4507646.3 / Soil 6

Table S2. Relative sequence abundance of all detected bacterial classes in the samples. Relative sequence abundances higher than 1% are highlighted.

Sample Name / Garden Soil / Incinerator Plant Soil / Garden Soil (%) / Incinerator Plant Soil (%)
Taxon
Acidobacteria / 0.120345352 / 0.132797858 / 12.03453523 / 13.27978581
Actinobacteria / 0.03288922 / 0.032663989 / 3.288922016 / 3.266398929
Armatimonadetes / 0.002111867 / 0.007764391 / 0.211186683 / 0.77643909
BRC1 / 0.000124227 / 0 / 0.012422746 / 0
Bacteroidetes / 0.110873008 / 0.161178046 / 11.08730085 / 16.11780455
Chlorobi / 0.002764061 / 0.010174029 / 0.2764061 / 1.017402945
Chloroflexi / 0.003602596 / 0.004016064 / 0.360259635 / 0.401606426
Cyanobacteria / 0.000217398 / 0.002141901 / 0.021739806 / 0.214190094
Elusimicrobia / 0.000434796 / 0 / 0.043479611 / 0
FBP / 6.21E-05 / 0 / 0.006211373 / 0
Fibrobacteres / 0.000341626 / 0 / 0.034162552 / 0
Firmicutes / 0.009782913 / 0.026506024 / 0.978291251 / 2.65060241
GAL15 / 0 / 0.000267738 / 0 / 0.026773762
GN04 / 0.00059008 / 0.013654618 / 0.059008044 / 1.365461847
Gemmatimonadetes / 0.042082052 / 0.058366801 / 4.208205224 / 5.836680054
Kazan-3B-28 / 3.11E-05 / 0 / 0.003105687 / 0
NKB19 / 9.32E-05 / 0 / 0.00931706 / 0
Nitrospirae / 0.011335756 / 0.005087015 / 1.133575577 / 0.508701473
OD1 / 6.21E-05 / 0.000267738 / 0.006211373 / 0.026773762
OP11 / 3.11E-05 / 0 / 0.003105687 / 0
Planctomycetes / 0.029410851 / 0.042302544 / 2.941085127 / 4.230254351
Proteobacteria / 0.617410479 / 0.472824632 / 61.74104786 / 47.28246319
Spirochaetes / 0.000155284 / 0 / 0.015528433 / 0
TM6 / 0.003788938 / 0.008299866 / 0.378893754 / 0.829986613
TM7 / 0.000310569 / 0.003212851 / 0.031056865 / 0.321285141
Verrucomicrobia / 0.003260971 / 0.013922356 / 0.326097084 / 1.392235609
WS2 / 0.000310569 / 0 / 0.031056865 / 0
WS3 / 0.007546818 / 0.004551539 / 0.754681822 / 0.455153949
Thermi / 3.11E-05 / 0 / 0.003105687 / 0

Table S3. Detailed information of metagenomic processing of garden and hospital soil.

Hospital Soil / Garden Soil
Upload: bp Count / 120,124,962 bp / 142,119,629 bp
Upload: Sequences Count / 276227 / 321048
Upload: Mean Sequence Length / 434 ± 119 bp / 442 ± 114 bp
Upload: Mean GC percent / 64 ± 7 % / 63 ± 8 %
Artificial Duplicate Reads: Sequence Count / 1251 / 3720
Post QC: bp Count / 117,082,985 bp / 137,341,683 bp
Post QC: Sequences Count / 252889 / 292390
Post QC: Mean Sequence Length / 462 ± 74 bp / 469 ± 68 bp
Post QC: Mean GC percent / 64 ± 7 % / 63 ± 7 %
Processed: Predicted Protein Features / 278128 / 323342
Processed: Predicted rRNA Features / 25509 / 27317
Alignment: Identified Protein Features / 134283 / 171610
Alignment: Identified rRNA Features / 213 / 302
Annotation: Identified Functional Categories / 108613 / 135379

Table S4. Relative sequence abundance of all detected bacterial classes in the samples.

Phyla / Hospital Soil / Garden Soil / Hospital Soil (%) / Garden Soil (%)
Proteobacteria / 134450 / 152306 / 53.93901221 / 45.93216301
Actinobacteria / 24192 / 50704 / 9.705411553 / 15.29121895
Planctomycetes / 18917 / 41190 / 7.589172882 / 12.42200435
Firmicutes / 12698 / 14057 / 5.094217754 / 4.239284174
Acidobacteria / 11131 / 16175 / 4.465564484 / 4.878026714
Bacteroidetes / 9416 / 14552 / 3.777536177 / 4.388565363
Chloroflexi / 8854 / 8958 / 3.552071507 / 2.701537144
Verrucomicrobia / 7880 / 9413 / 3.16131957 / 2.838755206
Cyanobacteria / 6675 / 7962 / 2.677894433 / 2.401165298
Gemmatimonadetes / 4590 / 3679 / 1.841428531 / 1.109506045
Deinococcus-Thermus / 2364 / 2568 / 0.948395871 / 0.774452711
unclassified (derived from Bacteria) / 2170 / 2780 / 0.87056643 / 0.838387281
Chlorobi / 1362 / 1815 / 0.546410819 / 0.547364358
Nitrospirae / 940 / 1238 / 0.377111725 / 0.37335376
Spirochaetes / 689 / 733 / 0.276414871 / 0.22105679
Aquificae / 603 / 643 / 0.24191316 / 0.193914756
Thermotogae / 506 / 547 / 0.202998439 / 0.164963253
Chlamydiae / 360 / 464 / 0.144425767 / 0.139932266
Synergistetes / 283 / 372 / 0.1135347 / 0.112187075
Deferribacteres / 218 / 282 / 0.087457826 / 0.085045041
Lentisphaerae / 215 / 337 / 0.086254278 / 0.101631839
Fusobacteria / 154 / 225 / 0.061782134 / 0.067855086
Dictyoglomi / 150 / 134 / 0.060177403 / 0.040411473
Poribacteria / 142 / 173 / 0.056967941 / 0.052173021
Elusimicrobia / 108 / 59 / 0.04332773 / 0.017793111
Chrysiogenetes / 97 / 105 / 0.038914721 / 0.031665707
Fibrobacteres / 50 / 57 / 0.020059134 / 0.017189955
Tenericutes / 49 / 61 / 0.019657952 / 0.018396268