TABLE 2
FROM:
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
Mary Beth Leigh, Vivian H Pellizari, Ond
ej Uhlík, Robin Sutka, Jorge Rodrigues, Nathaniel E Ostrom, Jizhong Zhou and James M Tiedje
Table 2. Phylogenetic identification of organisms based on 16S rRNA gene sequences using RDP Classifier
| Identity (PHYLUM, family) | Number of sequences detected | |||||||
|---|---|---|---|---|---|---|---|---|
| Total DNA clone library | 13 C-DNA clone libraries | BPl-utilizing isolates | ||||||
| t=0 | Genera | 1 d | 4 d | 14 d | Genera | t=0 | Genera | |
| ACIDOBACTERIA | ||||||||
| Acidobacteriaceae | 0 | 0 | 0 | 2 | Geothrix a | 0 | ||
| ACTINOBACTERIA | ||||||||
| Acidimicrobiaceae | 1 | Acidimicrobium | 0 | 1 | 0 | Acidimicrobium | 0 | |
| Geodermatophilaceae | 0 | 1 | 1 | 0 | Blastococcus | 0 | ||
| Intrasporangiaceae | 3 | Janibacter a | 1 | 1 | 0 | Tetraspaera a , Terrabacter | 0 | |
| Microbacteriaceae | 4 | Agromyces, Leifsonia | 1 | 0 | 0 | Leifsonia b | 0 | |
| Micrococcaceae | 0 | 0 | 1 | 2 | Arthrobacter | 2 | Arthrobacter | |
| Micromonosporaceae | 0 | 0 | 4 | 1 | Actinoplanes, Spirilliplanes a , Asanoa a | 0 | ||
| Nocardiaceae | 3 | 0 | 0 | 0 | 16 | Rhodococcus | ||
| Nocardioidaceae | 3 | Aeromicrobium, Nocardioides, Kribbella | 4 | 4 | 6 | Kribbella, Nocardioides | 0 | |
| Pseudonocardiaceae | 1 | Pseudonocardia | 0 | 9 | 8 | Pseudonocardia | 0 | |
| Rubrobacteraceae | 1 | Solirubrobacter | 1 | 3 | 0 | Solirubrobacter | 0 | |
| Streptomycetaceae | 2 | Streptomyces | 0 | 0 | 2 | Streptomyces | 0 | |
| Unclassifieda | 11 | Acidimicrobium a , Acidothermus b , Micropruina b , Modestobacter b , Solirubrobacter b , Unclassified c | 10 | 7 | 6 | Acidimicrobium b , Solirubrobacter b , Spirillospora b , Unclassified c | 0 | |
| BACTERIODETES | ||||||||
| Crenotrichaceae | 5 | Chitinophaga | 0 | 2 | 1 | Chitinophaga | 0 | |
| Flavobacteriaceae | 1 | Flavobacterium | 0 | 0 | 0 | 0 | ||
| Flexibacteraceae | 3 | Dyadobacter, Reichenbachia b, Sporocytophaga b | 0 | 0 | 0 | 0 | ||
| Sphingobacteriaceae | 0 | 1 | 0 | 0 | Pedobacter | |||
| Unclassified | 2 | Chitinophaga b , Ulvibacter b | 0 | 2 | 0 | Gramella b | 0 | |
| CHLOROFLEXI | ||||||||
| Anaerolinaeceea | 0 | 0 | 0 | 2 | Anaerolinea | |||
| FIRMICUTES | ||||||||
| Staphylococcaceae | 0 | 0 | 0 | 0 | 1 | Staphylococcus | ||
| GEMMATIMONADETES | ||||||||
| Gemmatimonadaceae | 2 | Gemmatimonas | 0 | 3 | 3 | Gemmatimonas | 0 | |
| PLANCTOMYCETES | ||||||||
| Planctomycetaceae | 0 | 2 | 2 | 2 | Isospaera, Pirellula | 0 | ||
| PROTEOBACTERIA | ||||||||
 -Acetobacteraceae | 1 | Rhodopila | 0 | 0 | 1 | Stella | 0 | |
| Bradyrhizobiaceae | 2 | Afipia b , Bradyrhizobium | 2 | 1 | 2 | Afipia b , Agromonas b , Bradyrhizobium, Nitrobacter b | 0 | |
| Caulobacteraceae | 0 | 0 | 1 | 0 | Caulobacter | 0 | ||
| Hyphomicrobiaceae | 1 | Rhodoplanes | 1 | 1 | 0 | Blastochloris, Rhodoplanes | 0 | |
| Phyllobacteriaceae | 0 | 0 | 0 | 1 | Mesorhizobium | 0 | ||
| Rhodobacteraceae | 0 | 0 | 1 | 0 | Roseivirga | 0 | ||
| Rhodobiaceae | 0 | 1 | 0 | 0 | Rhodobium | 0 | ||
| Sphingomonadaceae | 6 | Sphingomonas | 3 | 7 | 10 | Sphingomonas | 0 | |
| Unclassified | 4 | Blastochloris b , Hyphomicrobium b , Nitrobacter b , Unclassified c | 9 | 2 | 3 | Afipia b , Blastochloris b , Devosia b , Filomicrobium b , Methylocystis b , Methylosinus b , Microvirg b , Rhodobium b , Rhodoplanes b , Rhodopseudomonas b , Stella b , Teichococcus b | 0 | |
 -Burkholderiaceae | 0 | 1 | 2 | 0 | Ralstonia, Cupriavidus b | 0 | ||
| Comamonadaceae | 0 | 0 | 5 | 8 | Comamonas, Hydrogenophaga, Polaromonas, Variovorax | 0 | ||
| Hydrogenophilaceae | 0 | 0 | 0 | 1 | Thiobacillus | 0 | ||
| Oxalobacteraceae | 0 | 0 | 1 | 0 | Herbaspirillum b | 0 | ||
| Rhodocyclaceae | 0 | 0 | 0 | 2 | Sterolibacterium | 0 | ||
| Unclassified | 1 | Caenibacterium b | 1 | 2 | 3 | Caenibacterium b , Thiobacter b , Variovorax b , Zoogloea b | 0 | |
 -Bdellovibrionaceae | 0 | 0 | 0 | 1 | Bdellovibrio | 0 | ||
| Unclassified | 1 | Anaeromyxobacter | 0 | 1 | 2 | Desulforhabdus b , Haliangium b , Smithella b , Unclassified c | 0 | |
 -Coxiellaceae | 0 | 1 | 0 | 0 | Rickettsiella | 0 | ||
| Pseudomonadaceae | 0 | 0 | 1 | 1 | Pseudomonas | 2 | Pseudomonas | |
| Xanthomonadaceae | 3 | Pseudoxanthomonas b , Thermomonas | 0 | 0 | 2 | Lysobacter | 1 | Stenotrophomonas |
| Unclassified | 4 | Alkalispirillum a , Balneatrix b , Rhabdochromatium b | 1 | 4 | 1 | Alkanindiges b , Methylococcus b , Thiorhodospira a , Unclassified c | 0 | |
| UNCLASSIFIED | 20 | 9 | 8 | 13 | 0 | |||
| Total sequences analyzed | 85 | 50 | 77 | 86 | 22 | |||
Abbreviation: BP, biphenyl.
a Unclassified denotes that phylogenetic assignment by RDP Classifier has bootstrap value below 80%.
b RDP Classifier bootstrap value below 80% for genus assignment.
c RDP Classifier bootstrap value below 20% for genus.
