Table 1.
Percent relative abundance of bacterial groups containing knowna PAH-degraders in 16S rRNA gene pyrosequence libraries
| Phylogenetic group | PAH(s)b | Monthly-fed bioreactor |
Weekly-fed bioreactor |
Feed soil |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0c | 28 | 56 | 84 | 112 | 140 | 0 | 28 | 56 | 84 | 112 | 140 | 0 | 140 | ||
| Achromobacter | N | <0.1 | <0.1 | −d | − | − | − | <0.1 | <0.1 | <0.1 | − | − | − | 0.1 | 0.9 |
| Acidovorax | N, Ph | 5.6 | 12.3 | 19.8 | 15.9 | 3.5 | 25.0 | 5.4 | 17.4 | 22.1 | 19.2 | 16.5 | 14.4 | 10.4 | 9.6 |
| “Anthracene Group 1” | A | 0.4 | 0.5 | 0.4 | 0.6 | 0.2 | 1.1 | 1.0 | 0.3 | 0.2 | 0.3 | 0.3 | 0.3 | 4.2 | 10.2 |
| Pigmentiphaga | A, N, Ph | <0.1 | <0.1 | <0.1 | <0.1 | − | <0.1 | 0.1 | − | − | − | − | − | 0.1 | 0.1 |
| Pseudomonase | A, N | 0.2 | 0.1 | 0.1 | 0.1 | 0.1 | 0.2 | 0.1 | 0.5 | 0.3 | 0.1 | 0.1 | <0.1 | 5.5 | 5.9 |
| Pseudoxanthomonase | A, N | 1.2 | 0.4 | 0.5 | 0.4 | 0.2 | 0.7 | 1.3 | 0.8 | 0.6 | 0.7 | 0.3 | 0.4 | 33.5 | 28.3 |
| “Pyrene Group 2” | B, F, Py | 1.7 | 2.3 | 4.1 | 3.3 | 1.4 | 4.0 | 2.7 | 9.8 | 8.5 | 6.5 | 6.5 | 6.2 | 0.2 | 0.1 |
| Rhizobiume | A, B | 0.4 | 0.1 | 0.3 | 0.3 | <0.1 | 0.3 | 0.2 | 0.2 | 0.1 | 0.1 | 0.1 | 0.3 | 0.1 | 0.1 |
| Rhodobacter | B | − | − | <0.1 | <0.1 | − | − | <0.1 | − | − | − | − | − | <0.1 | − |
| Sphingobium | F, N, Ph | 1.7 | 1.6 | 1.6 | 2.5 | 0.6 | 1.7 | 2.0 | 1.3 | 0.4 | 0.3 | 0.2 | 0.3 | 7.6 | 6.3 |
| Sphingomonas | F | 0.6 | 1.1 | 3.3 | 5.4 | 2.5 | 4.3 | 1.1 | 1.4 | 1.7 | 1.3 | 2.1 | 2.6 | 0.2 | 0.3 |
| Variovorax | A, B, N | 0.4 | 0.2 | 0.1 | 0.1 | <0.1 | 0.1 | 0.2 | 0.1 | 0.1 | <0.1 | <0.1 | − | 0.4 | 0.9 |
| Percentage of library | 12.2 | 18.6 | 30.2 | 28.6 | 8.5 | 37.4 | 14.1 | 31.8 | 34.0 | 28.5 | 26.1 | 24.5 | 62.3 | 61.9 | |
| Total seqs in library | 4,514 | 6,352 | 7,553 | 5,375 | 6,010 | 4,621 | 10,565 | 12,010 | 11,430 | 10,194 | 9,804 | 10,415 | 10,693 | 9,441 | |
a
As determined by stable-isotope probing of the untreated feed soil (Jones 2010)
b
PAH metabolized during SIP: A anthracene, B benz[a]anthracene, F fluoranthene, N naphthalene, Ph phenanthrene, Py pyrene
c
Day of sampling after implementation of semi-continuous feeding
d
Dashes indicate that sequences belonging to this group were not found in the library
e
Sequences from these genera were found in 13C-enriched DNA from incubations with anthracene but were not verified as having increased in response to the substrate by quantitative PCR (qPCR)