TABLE 4.
Phylogenetic affinity of sequences co-migrating with DGGE bands in Fig. 2a
| Band | Sample | Accession no. of cloned sequence | Closest sequenceb (accession no.) | Groupc | % Similarity | No. of clones |
|---|---|---|---|---|---|---|
| A | 96BD | 125 BP (not submitted) | Sva0996 (AJ241005) | High G+C, gram positive | 96 | 0 |
| B | 96BD | AF355053 | Clone SAR307 (U20798) | GNSB | 97 | 2 |
| C | 97A | AF355044 | Nitrospina gracilis (L35504) | δ | 91 | 1 |
| D | 96A | AF353233 | Clone OM38 (U70679) | α, SAR116 | 98 | 1 |
| E | 95C | AF355042 | Nitrospina gracilis (L35504) | δ | 89 | 2 |
| F | 95A | AF353227 | Clone SAR407 (U75253) | α, SAR11 | 98 | 4 |
| G | 96AD | AF353212 | Clone SAR203 (U75255) | α, SAR11 | 97 | 1 |
| H | 96A | AF353208 | Clone SAR407 (U75253) | α, SAR11 | 98 | 23 |
| H | 96A | AF353234 | Clone NAC1-19 (AF245628) | α, Roseo | 97 | 1 |
| I | 96B | AF354595 | Fundibacter jadensis (AJ001150) | γ | 88 | 1 |
| I | 96BD | AF355041 | Clone NAC60-12 (AF245652) | δ | 98 | 1 |
| I | 96B | AF353224 | Clone SAR407 (U75253) | α, SAR11 | 96 | 5 |
| I | 96A | AF353235 | Clone NAC11-3 (AF245632) | α, Roseo | 99 | 8 |
| I | 95B | AF353214 | Clone ZD0410 (AJ400351) | α, SAR11 | 99 | 7 |
| J | 96AD | AF354601 | Pseudoalteromonas atlantica (AF173963) | γ | 99 | 2 |
| K | 96AD | AF355040 | Clone NAC60-12 (AF245652) | δ | 99 | 5 |
| L | 96B | AF353229 | Clone OM155 (U70686) | α, SAR11 | 95 | 2 |
| M | 96B | AF353242 | No match | γ | 3 | |
| M | 95B | AF353241 | Oceanospirillum sp. (AJ302699) | γ | 90 | 1 |
| N | 95A | AF354598 | Alteromonas macleodii (Y18228) | γ | 99 | 10 |
| O | 95B | AF353239 | Oceanospirillum sp. (AJ302699) | γ | 96 | 7 |
| P | 96AD | AF354604 | Alcanivorax borkumensis (Y12579) | γ | 96 | 2 |
| P | 96B | AF354597 | Pseudoalteromonas atlantica (AF173963) | γ | 98 | 1 |
| P | 96A | AF354611 | Clone ZD0424 (AJ400355) | γ | 97 | 2 |
| P | 95B | AF354609 | Fundibacter jadensis (AJ001150) | γ | 98 | 1 |
| Q | 96B | AF354596 | Pseudomonas fluorescens (AF094726) | γ | 91 | 1 |
| R | 96AD | AF354607 | Thiomicrospira sp. (AJ237758) | γ | 90 | 1 |
| S1 | 96A | AF354610 | Fundibacter jadensis (AJ001150) | γ | 98 | 3 |
| S1 | 96BD | AF354605 | Alcanivorax borkumensis (Y12579) | γ | 94 | 2 |
| S2 | 95D | AF354615 | Clone OM241 (U70702) | γ | 93 | 1 |
| S3 | 96B | AF354616 | Clone ZD0403 (AJ400347) | Cyto | 91 | 1 |
| T | 97A | AF354617 | Strain agg58 (L10946) | Cyto | 85 | 1 |
| U1 | 96BD | AF354606 | Clone ZD0405 (AJ400348) | γ | 99 | 1 |
| U2 | 97A | AF354613 | Clone OCS5 (AF001651) | γ, SAR86 | 99 | 1 |
| V1 | 96BD | AY08221 | Clone DEV005 (AJ401105) | Verr | 88 | 1 |
| V2 | 96B | AF354621 | Polaribacter irgensii (M61002) | CFB | 97 | 1 |
| V2 | 97A | AF354618 | Clone OM271 (U70708) | Cyto | 93 | 1 |
| V3 | 97A | AF355051 | Clone ZD0403 (AJ400347) | Cyto | 91 | 1 |
| W | 97A | AF354620 | Polaribacter irgensii (M61002) | CFB | 95 | 2 |
With the exception of band A, which was identified by sequencing DNA contained in the band, identifications were made by comparing the mobility of fragments amplified from cloned inserts with the mobility of fragments amplified from samples. Where more than one clone contained an insert of a given phylotype that matched a band, the accession number given is for the clone with the longest sequence with the greatest BLAST similarity value to the database sequence and the number of clones matching that phylotype is given. Twenty-one clones contained sequences that could not be assigned to bands in Fig. 2.
As determined by BLAST.
Abbreviations are as defined in Table 2, footnote b.