TABLE 3.
Composition of root and potting mix bacterial communitiesa
| Taxon and organism (GenBank no.) | Relative abundance of partial 16S rRNA gene sequences
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| All (%) | Root (%)
|
Potting mix (%)
|
|||||||||
| C | Cmp1 | Cmp2 | S1 | S2 | C | Cmp1 | Cmp2 | S1 | S2 | ||
| Actinobacteria | 4.2 | 2.3 | 6.5 | 5.3 | 11.4 | 13.9 | |||||
| Streptomyces | 2.5 | 11.4 | 13.9 | ||||||||
| Other Actinobacteria | 1.7 | 2.3 | 6.5 | 5.3 | |||||||
| Bacteroidetes | 19.8 | 11.9 | 27.5 | 16.3 | 25.0 | 16.1 | 5.9 | 45.2 | 44.7 | 2.9 | 5.6 |
| Flavobacteriaceae | 5.3 | 11.9 | 5.0 | 4.7 | 16.1 | 2.9 | 3.2 | 2.6 | 2.9 | 2.8 | |
| Flavobacteriumsp. (AJ786797) | 3.4 | 9.5 | 2.5 | 4.7 | 12.9 | 2.9 | |||||
| Cryomorphaceae | 1.9 | 7.5 | 10.7 | 3.2 | |||||||
| Crenotrichaceae | 0.3 | 2.6 | |||||||||
| Flexibacteraceae | 5.0 | 11.6 | 3.6 | 2.9 | 12.9 | 15.8 | 2.8 | ||||
| Sphingobacteriaceae | 1.1 | 6.5 | 5.3 | ||||||||
| Other Bacteroidetes | 6.1 | 15.0 | 10.7 | 19.4 | 18.4 | ||||||
| Alphaproteobacteria | 31.8 | 11.9 | 20.0 | 27.9 | 42.9 | 58.1 | 32.4 | 19.4 | 18.4 | 51.4 | 47.2 |
| Rhizobiaceae | 17.1 | 11.9 | 7.5 | 20.9 | 17.9 | 32.3 | 26.5 | 2.6 | 14.3 | 38.9 | |
| Rhizobium/Agrobacterium | 12.9 | 7.1 | 2.5 | 16.3 | 25.8 | 26.5 | 11.4 | 38.9 | |||
| Agrobacterium tumefaciens (AY972364) | 9.2 | 2.4 | 19.4 | 23.5 | 11.4 | 38.9 | |||||
| Caulobacteraceae | 1.7 | 4.7 | 3.6 | 3.2 | 5.7 | ||||||
| Phyllobacteriaceae | 0.3 | 2.6 | |||||||||
| Hyphomicrobiaceae | 1.4 | 3.6 | 6.5 | 5.3 | |||||||
| Rhodobacteraceae | 0.3 | 2.9 | |||||||||
| Rhodospirillaceae | 1.7 | 2.5 | 7.1 | 9.7 | |||||||
| Azospirillum lipoferumsp. (AY998242) | 1.4 | 2.5 | 7.1 | 9.7 | |||||||
| Sphingomonadaceae | 9.2 | 10.0 | 2.3 | 10.7 | 6.5 | 5.9 | 16.1 | 7.9 | 28.6 | 8.3 | |
| Unclassified | 0.3 | 3.2 | |||||||||
| Betaproteobacteria | 29.1 | 73.8 | 15.0 | 23.3 | 14.3 | 16.1 | 50.0 | 16.1 | 5.3 | 34.3 | 33.3 |
| Oxalobacteraceae | 7.0 | 52.4 | 7.0 | ||||||||
| Burkholderiaceae | 5.9 | 29.4 | 2.6 | 11.4 | 16.7 | ||||||
| Limnobacter thiooxidans (AJ289885) | 3.9 | 23.5 | 2.9 | 13.9 | |||||||
| Alcaligenaceae | 0.6 | 2.5 | 2.3 | ||||||||
| Comamonadaceae | 6.4 | 16.7 | 2.5 | 4.7 | 3.2 | 5.9 | 14.3 | 13.9 | |||
| Hydrogenophaga atypica(AJ585992) | 2.8 | 5.9 | 11.4 | 11.1 | |||||||
| Unclassified Burkholderiales | 1.9 | 4.8 | 2.3 | 2.9 | 8.6 | ||||||
| Methylophilaceae | 5.6 | 10.0 | 7.0 | 14.3 | 12.9 | 8.8 | 12.9 | ||||
| Methylophilussp. strain EHg7 (AY43679) | 2.5 | 4.6 | 12.9 | 8.8 | |||||||
| Methylovorus glucosetrophus(AY486133) | 1.9 | 10.0 | 7.1 | 3.2 | |||||||
| Nitrosomonadaceae | 0.3 | 2.6 | |||||||||
| Unclassified | 0.8 | 3.2 | 2.8 | ||||||||
| Gammaproteobacteria | 10.3 | 2.4 | 27.5 | 18.6 | 7.1 | 9.7 | 8.8 | 6.5 | 18.4 | ||
| Enterobacteriaceae | 1.1 | 10.0 | |||||||||
| Pseudomonadaceae | 3.4 | 2.4 | 18.6 | 3.2 | 5.9 | ||||||
| Xanthomonadaceae | 5.6 | 17.5 | 7.1 | 6.5 | 2.9 | 6.5 | 15.8 | ||||
| Unclassified | 0.3 | 2.6 | |||||||||
| Chloroflexi, unclassified | 0.8 | 3.2 | 5.3 | ||||||||
| Firmicutes | 3.9 | 10.0 | 11.6 | 10.7 | 2.9 | 3.2 | 2.6 | ||||
| Bacillaceae | 1.9 | 10.0 | 9.3 | ||||||||
| Clostridiaceae | 0.6 | 7.1 | |||||||||
| Thermoactinomycetaceae | 0.8 | 2.3 | 3.6 | 2.6 | |||||||
| Unclassified | 0.6 | 2.9 | 3.2 | ||||||||
a
The relative abundances of partial 16S rRNA gene sequences affiliated with the different taxonomic groups are presented. The different amendments are denoted as follows: C, untreated control; Cmp1, biosolid compost; Cmp2, straw compost; S1, Streptomyces sp. isolated from Cmp1; S2, Streptomyces sp. isolated from Cmp2. Relative abundance is expressed as the percentage of the total number of clone sequences from each library. “All” refers to the relative abundance in the complete set of sequences (358 clones). Specific subfamily taxa are denoted in boldface in column 1.