TABLE 3.
Clone composition and distribution of bacterioplankton ribosomal operon libraries from the Chesapeake Bay
| Bacterial group | No. (%) of clones
|
|||||
|---|---|---|---|---|---|---|
| September 2002
|
March 2003
|
|||||
| Station 908, CB01 | Station 804, CB11 | Station 707, CB22 | Station 908, CB31 | Station 804, CB41 | Station 707, CB51 | |
| Alphaproteobacteria | 13 (14.3) | 18 (21.7) | 23 (26.7) | 51 (60.0) | 33 (38.8) | 40 (48.8) |
| SAR11 | ||||||
| SAR11-I | 8 (8.8) | 7 (8.4) | 9 (10.5) | |||
| SAR11-II | 3 (3.3) | 2 (2.4) | 5 (5.8) | |||
| SAR11-III | 2 (2.4) | 1 (1.2) | ||||
| Rhodospirillalles | ||||||
| SPOTSAUG01_5m94 | 1 (1.2) | 1 (1.2) | ||||
| SAR116-IIIa | 3 (3.5) | |||||
| Roseobacter | ||||||
| Chesapeake Roseobacter I (ChesI)b | 1 (1.1) | 5 (6.0) | 4 (4.7) | |||
| Chesapeake Roseobacter II (ChesII)b | 1 (1.2) | 1 (1.2) | 5 (6.1) | |||
| Chesapeake Roseobacter III (ChesIII)b | 2 (2.4) | 5 (5.9) | 6 (7.3) | |||
| Chesapeake Roseobacter IV (ChesIV)b | 4 (4.7) | 5 (5.9) | 2 (2.4) | |||
| Chesapeake Roseobacter V (ChesV)b | 1 (1.1) | 1 (1.2) | ||||
| DG1128 | 2 (2.4) | 2 (2.4) | 1 (1.2) | |||
| GAI-37 | 1 (1.2) | 1 (1.2) | 3 (3.7) | |||
| AS26 | 1 (1.2) | |||||
| Slope strain DI4b | 5 (5.9) | 14 (16.5) | 13 (15.9) | |||
| Arctic sea ice strain ARK9990b | 15 (17.6) | 2 (2.4) | ||||
| Sulfitobacter mediterraneus | 1 (1.2) | 1 (1.2) | ||||
| Rhodobacter | ||||||
| Pseudorhodobacter ferrugineus | 15 (17.6) | 1 (1.2) | 1 (1.2) | |||
| Other | 5 (5.9) | |||||
| Sphigomonas | 1 (1.2) | |||||
| Other | ||||||
| Ahrensia sp. strain DFL-42 | 1 (1.2) | 6 (7.3) | ||||
| Defluvibacter lusatiae | 1 (1.2) | |||||
| Betaproteobacteria | 0 | 3 (3.6) | 2 (2.3) | 14 (16.5) | 21 (24.7) | 6 (7.3) |
| OM 156c | 1 (1.2) | 1 (1.2) | ||||
| OM 43c | 2 (2.4) | |||||
| SPOTS_APR01_5m110 | 1 (1.2) | |||||
| GKS16d | 1 (1.2) | |||||
| Polynucleobacter necessariusd | 3 (3.5) | |||||
| GKS98d | 10 (11.8) | 21 (24.7) | 6 (7.3) | |||
| Gammaproteobacteria | 4 (4.4) | 12 (14.5) | 10 (11.6) | 2 (2.4) | 0 | 3 (3.7) |
| Gamma strain AGG47a | 1 (1.1) | 1 (1.2) | 1 (1.2) | |||
| Novel clade strain SAR86-IV | 1 (1.1) | 4 (4.8) | 3 (3.5) | |||
| SDF1-40 | 1 (1.1) | |||||
| CHAB-III-7 | 1 (1.2) | |||||
| OM60c | 1 (1.2) | |||||
| SPOTSOCT00_5m87 | 1 (1.2) | |||||
| Marine gamma strain HTCC2188 | 1 (1.2) | 1 (1.2) | ||||
| Acinetobacter junii | 1 (1.2) | |||||
| RedeBAC7D11 | 1 (1.2) | |||||
| KTC1119a | 1 (1.2) | |||||
| SAR86-II | 2 (2.3) | |||||
| Pseudomonas syringae | 1 (1.2) | |||||
| Psychrobacter submarinus | 1 (1.2) | |||||
| Gamma strain Sva0091 | 1 (1.2) | |||||
| Psychromonas antarctica | 1 (1.2) | |||||
| Unidentified Gammaproteobacteria | 1 (1.1) | 3 (3.6) | 1 (1.2) | |||
| Deltaproteobacteria | 1 (1.1) | 1 (1.2) | 2 (2.3) | 0 | 0 | 1 (1.2) |
| Bacteroidetes | 11 (12.1) | 12 (14.5) | 6 (7.0) | 2 (2.4) | 4 (4.7) | 3 (3.7) |
| Flavobacteria | ||||||
| Flavobacteriaceae UC1 | 4 (4.4) | |||||
| Unidentified strain CB22B12 | 1 (1.2) | |||||
| Antarctic bacterium strain R-9033 | 1 (1.2) | 1 (1.2) | ||||
| ATAM173_A3 | 1 (1.2) | |||||
| Cellulophaga sp. | 3 (3.5) | |||||
| Sphingobacteria | ||||||
| Unclassified strain CB11C03 | 1 (1.1) | 1 (1.2) | ||||
| Unidentified strain CB22A10 | 1 (1.2) | |||||
| Antarctic bacterium strain R-9286 | 1 (1.2) | 1 (1.2) | ||||
| TM18_28 | 1 (1.2) | |||||
| Unclassified Bacteroidetes | ||||||
| Unclassified strain CB11B01 | 1 (1.1) | 6 (7.2) | ||||
| Unidentified strain CB11D01 | 2 (2.2) | 2 (2.4) | 1 (1.2) | |||
| RW262e | 3 (3.3) | 1 (1.2) | ||||
| Bacteroidetes strain OM 273 | 2 (2.4) | 1 (1.2) | ||||
| Bacteroidetes strain AGG58e | 1 (1.2) | |||||
| Unidentified strain CB22H06 | 1 (1.2) | |||||
| Cyanobacteria/Synechococcus | 5 (5.5) | 12 (14.5) | 7 (8.1) | 0 | 0 | 0 |
| Plastids | 0 | 0 | 8 (9.3) | 0 | 1 (1.2) | 0 |
| Actinobacteria | 57 (62.6) | 22 (26.5) | 27 (31.4) | 15 (17.6) | 25 (29.4) | 27 (32.9) |
| Freshwater acIf | 3 (3.3) | 4 (4.8) | 2 (2.4) | 11 (12.9) | 6 (7.3) | |
| Freshwater acIIf | 7 (7.7) | 1 (1.2) | 9 (10.6) | 5 (5.9) | 5 (6.1) | |
| Freshwater acIIIf | 2 (2.2) | 1 (1.2) | 4 (4.7) | 2 (2.4) | 8 (9.4) | 13 (15.9) |
| Freshwater acIVf | 7 (7.7) | 2 (2.4) | 1 (1.2) | 1 (1.2) | 2 (2.4) | |
| Plankton marine Actinobacterium | 37 (40.7) | 12 (14.5) | 23 (26.7) | |||
| Sediment marine Actinobacterium | 2 (2.4) | |||||
| Novel Actinobacterium strain CB31D05 | 1 (1.1) | 1 (1.2) | 1 (1.2) | |||
| Fibrobacters | 0 | 1 (1.2) | 0 | 0 | 0 | 0 |
| Verrucomicrobia | 0 | 2 (2.4) | 1 (1.2) | 1 (1.2) | 1 (1.2) | 2 (2.4) |
| Total valid clones | 91 | 83 | 86 | 85 | 85 | 82 |
| Chimeras or short inserts | 5 | 13 | 10 | 11 | 11 | 14 |