Table 1 Mean relative abundance (%) of bacterial phyla calculated based on copies per million reads across feces, manure, lagoon and soil samples from both farm types
Phylum | CF | CL | CM | CS | OF | OL | OM | OS | RS | Overall |
|---|---|---|---|---|---|---|---|---|---|---|
Proteobacteria | 16.78 | 59.72 | 63.16 | 53.06 | 17.38 | 42.58 | 63.86 | 57.17 | 56.77 | 35.40 |
Actinobacteria | 8.18 | 8.50 | 13.30 | 37.31 | 11.93 | 9.40 | 11.33 | 32.51 | 33.65 | 15.88 |
Bacteroidetes | 34.36 | 19.40 | 12.07 | 2.24 | 27.67 | 19.27 | 12.29 | 4.05 | 2.27 | 21.04 |
Planctomycetes | 0.17 | 0.19 | 0.36 | 2.09 | 0.22 | 0.37 | 0.13 | 1.90 | 2.25 | 0.67 |
Firmicutes | 35.06 | 8.37 | 7.05 | 2.13 | 38.06 | 16.77 | 9.69 | 1.74 | 1.74 | 22.04 |
Acidobacteria | 0.14 | 0.09 | 0.15 | 0.95 | 0.15 | 0.17 | 0.06 | 0.78 | 1.01 | 0.32 |
Gemmatimonadetes | 0.02 | 0.03 | 0.11 | 0.52 | 0.03 | 0.06 | 0.04 | 0.36 | 0.50 | 0.14 |
Verrucomicrobia | 0.30 | 0.10 | 0.44 | 0.35 | 0.39 | 0.64 | 0.09 | 0.33 | 0.53 | 0.35 |
Deinococcus-Thermus | 0.14 | 0.11 | 0.20 | 0.31 | 0.19 | 0.21 | 0.25 | 0.30 | 0.29 | 0.20 |
Cyanobacteria | 0.70 | 0.35 | 0.32 | 0.32 | 0.81 | 0.96 | 0.29 | 0.28 | 0.32 | 0.60 |
Chloroflexi | 0.15 | 0.18 | 0.28 | 0.25 | 0.19 | 0.61 | 0.09 | 0.21 | 0.20 | 0.23 |
Nitrospirae | 0.04 | 0.02 | 0.03 | 0.16 | 0.05 | 0.06 | 0.02 | 0.11 | 0.15 | 0.06 |
Kiritimatiellaeota | 0.01 | 0.03 | 0.02 | 0.06 | 0.02 | 0.17 | 0.01 | 0.05 | 0.06 | 0.04 |
Spirochaetes | 1.48 | 1.54 | 0.76 | 0.05 | 1.04 | 5.46 | 0.14 | 0.04 | 0.05 | 1.33 |
Chlorobi | 0.12 | 0.08 | 0.06 | 0.04 | 0.14 | 0.21 | 0.04 | 0.04 | 0.05 | 0.11 |
Armatimonadetes | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 |
Synergistetes | 0.08 | 0.13 | 0.05 | 0.03 | 0.09 | 0.32 | 0.02 | 0.03 | 0.02 | 0.09 |
Unclassfied | 0.01 | 0.01 | 0.07 | 0.01 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 |
Thermotogae | 0.13 | 0.08 | 0.12 | 0.01 | 0.14 | 0.23 | 0.04 | 0.01 | 0.01 | 0.10 |
Tenericutes | 0.68 | 0.73 | 0.75 | 0.01 | 0.67 | 1.69 | 1.17 | 0.01 | 0.01 | 0.63 |
Fusobacteria | 0.73 | 0.14 | 0.11 | 0.01 | 0.38 | 0.27 | 0.17 | 0.01 | 0.01 | 0.34 |
Candidatus Bipolaricaulota | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 |
Aquificae | 0.06 | 0.02 | 0.01 | 0.01 | 0.08 | 0.04 | 0.01 | 0.01 | 0.01 | 0.04 |
Chrysiogenetes | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 |
Chlamydiae | 0.07 | 0.03 | 0.03 | 0.01 | 0.08 | 0.04 | 0.03 | 0.00 | 0.01 | 0.05 |
Thermodesulfobacteria | 0.03 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 |
Balneolaeota | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 |
Deferribacteres | 0.04 | 0.02 | 0.03 | 0.00 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 |
Calditrichaeota | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
Ignavibacteriae | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 |
Elusimicrobia | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 |
Fibrobacteres | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 |
Caldiserica | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Coprothermobacterota | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Candidatus Saccharibacteria | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 |
Candidatus Cloacimonetes | 0.38 | 0.03 | 0.42 | 0.00 | 0.01 | 0.15 | 0.15 | 0.00 | 0.00 | 0.14 |
Dictyoglomi | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |