TABLE 1.
Distribution of clone and isolate sequences in phylogenetic groups
| Phylogenetic group | No. of clones from each librarya
|
% Of total library (clones)
|
% Of total library (isolates) from:
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Agricultural soil
|
Cast
|
Pooled clone reactions
|
Soil (1996) | Burrow (1996) | Casts (1997) | Soil (1999) | Casts (1999) | ||||||||
| 1 | 2 | 3 | 4 | 5 | 1 | 2 | Soil | Cast | |||||||
| Acidobacteria | 3 | 2 | 3 | 4 | 1 | 3 | 7 | 13.7 | 9.8 | ||||||
| Actinobacteria | 1 | 1 | 2 | 1 | 10 | 7 | 5.3 | 16.7 | 53.5 | 51.6 | 12.2 | 57.1 | 75.0 | ||
| Candidate division TM7 | 1 | 1 | 3 | 3 | 2.1 | 5.9 | |||||||||
| Cytophagales | 3 | 2 | 3 | 1 | 1 | 8 | 5 | 10.5 | 12.7 | 1.4 | |||||
| Fibrobacter | 1 | 2 | 1 | 1 | 4.2 | 1.0 | |||||||||
| Firmicutes | 4 | 11 | 1 | 4.2 | 11.8 | 15.2 | 19.4 | 4.1 | 21.4 | 16.7 | |||||
| Chloroflexi | 2 | 1 | 3 | 2 | 2 | 8.4 | 2.0 | ||||||||
| Nitrospira | 2 | 1 | 2 | 1 | 5.3 | 1.0 | |||||||||
| Planctomycetes | 1 | 2 | 3.2 | ||||||||||||
| Proteobacteria | |||||||||||||||
| α- | 1 | 1 | 2 | 8 | 2 | 4.2 | 9.8 | 5.1 | 6.5 | 1.4 | 7.1 | ||||
| β- | 1 | 3 | 3 | 1 | 1 | 2 | 8.4 | 2.9 | 5.1 | 9.7 | 4.1 | 7.1 | 8.3 | ||
| γ- | 1 | 1 | 1 | 1 | 15 | 7 | 4.2 | 21.6 | 21.2 | 12.9 | 77.0 | 7.1 | |||
| δ- | 2 | 2 | 1 | 1 | 5.3 | 1.0 | |||||||||
| Verrucomicrobia | 2 | 1 | 2.1 | 1.0 | |||||||||||
| Undescribed groupb | |||||||||||||||
| A | 3 | 1 | 2 | 6.3 | |||||||||||
| B | 1 | 1 | 1 | 1.1 | 2.0 | ||||||||||
| C | 1 | 1 | 1 | 3.2 | |||||||||||
| D | 1 | 1 | 1.1 | 1.0 | |||||||||||
| E | 1 | 1 | 2.1 | ||||||||||||
| F | 2 | 1 | 2.1 | ||||||||||||
| G | 1 | 1.1 | |||||||||||||
| H | 1 | 1.1 | |||||||||||||
| I | 1 | 1.1 | |||||||||||||
| Total sample size (n) | 17 | 27 | 20 | 21 | 10 | 64 | 38 | 95 | 102 | 99 | 31 | 74 | 14 | 12 | |
a
Each column represents the number of clones from a particular PCR. Each soil PCR was derived from a separate sample, while the cast PCRs originated from the same DNA extracted from pooled cast samples. All clone sequences are from 1999.
b
Clones which did not associate with a known phylum. Descriptions of each group are provided in the text.