TABLE 2.
Cloned sequences with phylogenetic affiliation, nearest neighbor from GenBank, percent similarity based on aligned base pairs, band position in DGGE (Fig. 2), and total clones migrated with each band
| Clone (accession no.) | Sequence length (bp) | No. of clonesa | Groupb | Closest relative (accession no.) | % Similarity | Band position |
|---|---|---|---|---|---|---|
| 96BD-6 (AF355053) | 1,456 | 2/24 | GNSB | Clone SAR307 (U20798) | 97 | B |
| 96A-18 (AF353233) | 1,442 | 1/24 | α, SAR116 | Clone OM38 (U70679) | 98 | D |
| 97A-12 (AF355044) | 1,446 | 1/16 | δ | Nitrospina gracilis (L35504) | 91 | C |
| 95A-16 (AF353227) | 1,397 | 1/20 | α, SAR11 | Clone SAR407 (U75253) | 98 | F |
| 95C-6 (AF355042) | 1,473 | 2/10 | δ | Nitrospina gracilis (L35504) | 89 | E |
| 96A-3 (AF353218) | 652 | 1/24 | α, SAR11 | Clone SAR407 (U75253) | 98 | F |
| 96B-5 (AF353219) | 641 | 1/23 | α, SAR11 | Clone SAR407 (U75253) | 98 | F |
| 96BD-18c (AF355034) | 1,100 | 1/24 | α, SAR11 | Clone SAR407 (U75253) | 98 | F |
| 96AD-8 (AF353212) | 1,430 | 1/20 | α, SAR11 | Clone SAR203 (U75255) | 97 | G |
| 95A-12 (AF353230) | 967 | 2/20 | α, SAR11 | Clone PLY43 (U13159) | 99 | H |
| 95B-11 (AF353220) | 650 | 1/17 | α, SAR11 | Clone PLY43 (U13159) | 99 | H |
| 95C-1 (AF353221) | 627 | 3/10 | α, SAR11 | Clone OM188 (U70687) | 99 | H |
| 96A-20 (AF353208) | 1,430 | 3/24 | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 96B-3 (AF353209) | 1,430 | 5/23 | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 96B-15 (AF353213) | 668 | Dup | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 97A-2 (AF353231) | 994 | 5/16 | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 97A-8 (AF353232) | 721 | Dup | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 97B-2 (AF353216) | 645 | 3/10 | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 97B-10 (AF353217) | 609 | Dup | α, SAR11 | Clone OM188 (U70687) | 100 | H |
| 97C-1 (AF353210) | 1,430 | 1/10 | α, SAR11 | Clone SAR407 (U75253) | 98 | H |
| 96A-8 (AF353234) | 1,421 | Comigrated with 96A-20 | α, Roseo | Clone NAC1-19 (AF245628) | 97 | H |
| 96A-1 (AF353235) | 1,420 | 8/24 | α, Roseo | Clone NAC11-3 (AF245632) | 99 | I |
| 96B-6 (AF353224) | 1,429 | 3/34 | α, SAR11 | Clone SAR407 (U75253) | 96 | I |
| 97B-5 (AF353225) | 1,429 | 2/10 | α, SAR11 | Clone SAR407 (U75253) | 94 | I |
| 95B-1 (AF353214) | 1,396 | 3/17 | α, SAR11 | Clone ZD0410 (AJ400351) | 99 | I |
| 95C-4 (AF353222) | 619 | Dup | α, SAR11 | Clone ZD0410 (AJ400351) | 96 | I |
| 95C-7 (AF353215) | 1,440 | 2/10 | α, SAR11 | Clone ZD0410 (AJ400351) | 98 | I |
| 95D-8 (AF353223) | 1,441 | 1/12 | α, SAR11 | Clone ZD0410 (AJ400351) | 97 | I |
| 97A-1 (AF353228) | 1,407 | 1/16 | α, SAR11 | Clone ZD0410 (AJ400351) | 95 | I |
| 96BD-3 (AF355041) | 1,472 | 1/24 | δ | Clone NAC60-12 (AF245652) | 98 | I |
| 96B-16 (AF354595) | 1,500 | 1/23 | γ | Fundibacter jadensis (AJ001150) | 88 | I |
| 96AD-16 (AF354601) | 1,491 | 2/20 | γ | Pseudoalteromonas atlantica (AF173963) | 99 | J |
| 96AD-23 (AF354602) | 629 | Dup | γ | Pseudoalteromonas atlantica (AF173963) | 99 | J |
| 95A-13 (AF355038) | 1,439 | 3/20 | δ | Clone NAC60-12 (AF245652) | 98 | K |
| 95C-5 (AF355039) | 1,472 | 1/10 | δ | Clone NAC60-12 (AF245652) | 98 | K |
| 96AD-7 (AF355040) | 1,472 | 1/20 | δ | Clone NAC60-12 (AF245652) | 99 | K |
| 96A-7 (AF353226) | 1,439 | 1/24 | α, SAR11 | Clone OM155 (U70686) | 94 | L |
| 96B-22d (AF353229) | 1,330 | 1/23 | α, SAR11 | Clone OM155 (U70686) | 95 | L |
| 96B-1 (AF353242) | 1,493 | 2/23 | γ | -e | M | |
| 97A-11 (AF355037) | 1,462 | 1/16 | γ | - | M | |
| 95B-17 (AF353241) | 1,461 | 1/17 | γ | Oceanospirillum sp. (AJ302699) | 90 | M |
| 95A-1 (AF354599) | 650 | Dup | γ | Alteromonas macleodii (Y18228) | 99 | N |
| 95A-15 (AF354598) | 1,455 | 10/20 | γ | Alteromonas macleodii (Y18228) | 99 | N |
| 95A-4 (AF354600) | 650 | Dup | γ | Alteromonas macleodii (Y18228) | 99 | N |
| 95B-13 (AF353237) | 1,461 | Dup | γ | Oceanospirillum sp. (AJ302699) | 90 | O |
| 95B-19 (AF353240) | 644 | Dup | γ | Oceanospirillum sp. (AJ302699) | 96 | O |
| 95B-7 (AF353238) | 1,461 | 7/17 | γ | Oceanospirillum sp. (AJ302699) | 90 | O |
| 95B-8 (AF353239) | 1,455 | Dup | γ | Oceanospirillum sp. (AJ302699) | 96 | O |
| 96AD-24 (AF354604) | 1,497 | 1/20 | γ | Alcanivorax borkumensis (Y12579) | 96 | P |
| 96BD-24 (AF354603) | 1,497 | 1/24 | γ | Alcanivorax borkumensis (Y12579) | 96 | P |
| 96A-14 (AF354611) | 1,489 | 1/24 | γ | Clone ZD0424 (AJ400355) | 97 | P |
| 97A-6 (AF354612) | 1,456 | 1/16 | γ | Clone ZD0424 (AJ400355) | 97 | P |
| 95B-15 (AF354609) | 1,464 | 1/17 | γ | Fundibacter jadensis (AJ001150) | 98 | P |
| 96B-17 (AF354597) | 1,491 | 1/23 | γ | Pseudoalteromonas atlantica (AF173963) | 98 | P |
| 96B-9 (AF354596) | 1,492 | 1/23 | γ | Pseudomonas fluorescens (AF094726) | 91 | Q |
| 96AD-3 (AF354607) | 1,502 | 1/20 | γ | Thiomicrospira sp. (AJ237758) | 90 | R |
| 96BD-1 (AF354605) | 1,494 | 2/24 | γ | Alcanivorax borkumensis (Y12579) | 94 | S1 |
| 96A-12 (AF354610) | 1,498 | 3/24 | γ | Fundibacter jadensis (AJ001150) | 98 | S1 |
| 95D-6 (AF354615) | 617 | 1/12 | γ | Clone OM241 (U70702) | 93 | S2 |
| 96B-24 (AF354616) | 1,485 | 1/23 | Cyto | Clone ZD0403 (AJ400347) | 91 | S3 |
| 97A-17 (AF354617) | 1,444 | 1/16 | Cyto | Strain agg58 (L10946) | 85 | T |
| 96BD-19 (AF354606) | 1,495 | 1/24 | γ | Clone ZD0405 (AJ400348) | 99 | U1 |
| 97A-18 (AF354613) | 1,457 | 1/16 | γ, SAR86 | Clone OCS5 (AF001651) | 99 | U2 |
| 96BD-2c (AY08221) | 1,269 | 1/24 | Verr | Clone DEV005 (AJ401105) | 88 | V1 |
| 97A-13 (AF354618) | 1,444 | 1/16 | Cyto | Clone OM271 (U70708) | 93 | V2 |
| 96B-11 (AF354621) | 1,477 | 1/23 | CFB | Polaribacter irgensii (M61002) | 97 | V2 |
| 97A-14 (AF355051) | 1,452 | 1/16 | Cyto | Clone ZD0403 (AJ400347) | 91 | V3 |
| 97A-15 (AF354620) | 1,440 | 2/16 | CFB | Polaribacter irgensii (M61002) | 95 | W |
| 97A-5 (AF355052) | 650 | Dup | CFB | Polaribacter irgensii (M61002) | 97 | W |
| 95A-3 (AF355043) | 1,457 | 1/20 | δ | Clone BD4-10 (AB015560) | 87 | - |
| 95D-9 (AY08220) | 1,492 | 1/12 | Verr | Clone DEV022 (AJ401118) | 94 | - |
| 95A-2 (AF355046) | 1,485 | 1/20 | δ, SAR406 | Clone OCS307 (U41450) | 89 | - |
| 97B-4 (AY08219) | 1,523 | 1/10 | Verr | Clone OPB35 (AF027005) | 83 | - |
| 96B-13 (AF355050) | 1,465 | 1/23 | ɛ | Clone PVB-55 (U15105) | 95 | - |
| 96A-24 (AF355048) | 650 | 1/24 | δ, SAR406 | Clone SAR406 (U34043) | 80 | - |
| 96B-7 (AF355047) | 1,518 | 1/23 | δ, SAR406 | Clone SAR406 (U34043) | 90 | - |
| 96BD-15 (AF355049) | 638 | 1/24 | δ, SAR406 | Clone SAR406 (U34043) | 80 | - |
| 96B-10 (AF353211) | 1,430 | 2/23 | α, SAR11 | Clone SAR407 (U75253) | 98 | - |
| 95B-10 (AY08222) | 1,444 | 1/17 | Verr | Clone VadinHB65 (U81755) | 83 | - |
| 95B-14 (AF355055) | 1,444 | 1/17 | Verr | Clone VadinHB65 (U81755) | 83 | - |
| 95A-18 (AF355054) | 1,421 | 1/20 | GNSB | Clone WS52f (AF186417) | 80 | - |
| 97C-5 (AF354614) | 1,495 | 1/10 | γ | Clone ZD0408 (AJ400349) | 98 | - |
| 96BD-22d (AF355045) | 1,279 | 1/24 | δ | Nitrospina gracilis (L35504) | 92 | - |
| 95B-2 (AF355036) | 1,419 | 1/17 | α | Olavius loisae symbiont (AF104473) | 89 | - |
| 97A-7 (AF353236) | 1,426 | 1/16 | α | Olavius loisae symbiont (AF104473) | 88 | - |
| 96AD4 (AF354619) | 1,481 | 2/20 | Cyto | Psychroserpens burtonensis (U62913) | 93 | - |
| 95B-9c (AF355035) | 1,364 | 1/17 | α | Strain BD1-17 (AB015526) | 88 | - |
| 96AD-9 (AF354608) | 1,499 | 1/20 | γ | Thiomicrospira sp. (AJ237758) | 96 | - |
a
Number of clones in a library out of the total number screened in that library that gave DGGE bands migrating to the position indicated in the column marked “Band position.” We usually only sequenced one of these clones, but in some instances we sequenced additional clones. When these contained the same sequence as the first clone sequenced, they are listed as “Dup” in the column headed “No. of clones”; if they contained a different sequence, they were listed as “comigrated with (Clone ID).”
b
α, δ, γ, and ɛ, α-, δ-, γ-, and ɛ-Proteobacteria, respectively; Roseo, Roseobacter spp.; Cyto, Cytophaga spp.; Verr, Verrucomicrobium spp.
c
Chimeric sequences and portion of sequences were deleted.
d
Partial inserts.
e
-, Band position was not identified.