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 clonesaGroupbClosest relative (accession no.)% SimilarityBand position
96BD-6 (AF355053 )1,4562/24GNSBClone SAR307 (U20798 )97B
96A-18 (AF353233 )1,4421/24α, SAR116Clone OM38 (U70679 )98D
97A-12 (AF355044 )1,4461/16δ Nitrospina gracilis (L35504 )91C
95A-16 (AF353227 )1,3971/20α, SAR11Clone SAR407 (U75253 )98F
95C-6 (AF355042 )1,4732/10δ Nitrospina gracilis (L35504 )89E
96A-3 (AF353218 )6521/24α, SAR11Clone SAR407 (U75253 )98F
96B-5 (AF353219 )6411/23α, SAR11Clone SAR407 (U75253 )98F
96BD-18c (AF355034 )1,1001/24α, SAR11Clone SAR407 (U75253 )98F
96AD-8 (AF353212 )1,4301/20α, SAR11Clone SAR203 (U75255 )97G
95A-12 (AF353230 )9672/20α, SAR11Clone PLY43 (U13159 )99H
95B-11 (AF353220 )6501/17α, SAR11Clone PLY43 (U13159 )99H
95C-1 (AF353221 )6273/10α, SAR11Clone OM188 (U70687 )99H
96A-20 (AF353208 )1,4303/24α, SAR11Clone SAR407 (U75253 )98H
96B-3 (AF353209 )1,4305/23α, SAR11Clone SAR407 (U75253 )98H
96B-15 (AF353213 )668Dupα, SAR11Clone SAR407 (U75253 )98H
97A-2 (AF353231 )9945/16α, SAR11Clone SAR407 (U75253 )98H
97A-8 (AF353232 )721Dupα, SAR11Clone SAR407 (U75253 )98H
97B-2 (AF353216 )6453/10α, SAR11Clone SAR407 (U75253 )98H
97B-10 (AF353217 )609Dupα, SAR11Clone OM188 (U70687 )100H
97C-1 (AF353210 )1,4301/10α, SAR11Clone SAR407 (U75253 )98H
96A-8 (AF353234 )1,421Comigrated with 96A-20α, RoseoClone NAC1-19 (AF245628 )97H
96A-1 (AF353235 )1,4208/24α, RoseoClone NAC11-3 (AF245632 )99I
96B-6 (AF353224 )1,4293/34α, SAR11Clone SAR407 (U75253 )96I
97B-5 (AF353225 )1,4292/10α, SAR11Clone SAR407 (U75253 )94I
95B-1 (AF353214 )1,3963/17α, SAR11Clone ZD0410 (AJ400351 )99I
95C-4 (AF353222 )619Dupα, SAR11Clone ZD0410 (AJ400351 )96I
95C-7 (AF353215 )1,4402/10α, SAR11Clone ZD0410 (AJ400351 )98I
95D-8 (AF353223 )1,4411/12α, SAR11Clone ZD0410 (AJ400351 )97I
97A-1 (AF353228 )1,4071/16α, SAR11Clone ZD0410 (AJ400351 )95I
96BD-3 (AF355041 )1,4721/24δClone NAC60-12 (AF245652 )98I
96B-16 (AF354595 )1,5001/23γ Fundibacter jadensis (AJ001150 )88I
96AD-16 (AF354601 )1,4912/20γ Pseudoalteromonas atlantica (AF173963 )99J
96AD-23 (AF354602 )629Dupγ Pseudoalteromonas atlantica (AF173963 )99J
95A-13 (AF355038 )1,4393/20δClone NAC60-12 (AF245652 )98K
95C-5 (AF355039 )1,4721/10δClone NAC60-12 (AF245652 )98K
96AD-7 (AF355040 )1,4721/20δClone NAC60-12 (AF245652 )99K
96A-7 (AF353226 )1,4391/24α, SAR11Clone OM155 (U70686 )94L
96B-22d (AF353229 )1,3301/23α, SAR11Clone OM155 (U70686 )95L
96B-1 (AF353242 )1,4932/23γ-eM
97A-11 (AF355037 )1,4621/16γ-M
95B-17 (AF353241 )1,4611/17γ Oceanospirillum sp. (AJ302699 )90M
95A-1 (AF354599 )650Dupγ Alteromonas macleodii (Y18228 )99N
95A-15 (AF354598 )1,45510/20γ Alteromonas macleodii (Y18228 )99N
95A-4 (AF354600 )650Dupγ Alteromonas macleodii (Y18228 )99N
95B-13 (AF353237 )1,461Dupγ Oceanospirillum sp. (AJ302699 )90O
95B-19 (AF353240 )644Dupγ Oceanospirillum sp. (AJ302699 )96O
95B-7 (AF353238 )1,4617/17γ Oceanospirillum sp. (AJ302699 )90O
95B-8 (AF353239 )1,455Dupγ Oceanospirillum sp. (AJ302699 )96O
96AD-24 (AF354604 )1,4971/20γ Alcanivorax borkumensis (Y12579 )96P
96BD-24 (AF354603 )1,4971/24γ Alcanivorax borkumensis (Y12579 )96P
96A-14 (AF354611 )1,4891/24γClone ZD0424 (AJ400355 )97P
97A-6 (AF354612 )1,4561/16γClone ZD0424 (AJ400355 )97P
95B-15 (AF354609 )1,4641/17γ Fundibacter jadensis (AJ001150 )98P
96B-17 (AF354597 )1,4911/23γ Pseudoalteromonas atlantica (AF173963 )98P
96B-9 (AF354596 )1,4921/23γ Pseudomonas fluorescens (AF094726 )91Q
96AD-3 (AF354607 )1,5021/20γ Thiomicrospira sp. (AJ237758 )90R
96BD-1 (AF354605 )1,4942/24γ Alcanivorax borkumensis (Y12579 )94S1
96A-12 (AF354610 )1,4983/24γ Fundibacter jadensis (AJ001150 )98S1
95D-6 (AF354615 )6171/12γClone OM241 (U70702 )93S2
96B-24 (AF354616 )1,4851/23CytoClone ZD0403 (AJ400347 )91S3
97A-17 (AF354617 )1,4441/16CytoStrain agg58 (L10946 )85T
96BD-19 (AF354606 )1,4951/24γClone ZD0405 (AJ400348 )99U1
97A-18 (AF354613 )1,4571/16γ, SAR86Clone OCS5 (AF001651 )99U2
96BD-2c (AY08221 )1,2691/24VerrClone DEV005 (AJ401105 )88V1
97A-13 (AF354618 )1,4441/16CytoClone OM271 (U70708 )93V2
96B-11 (AF354621 )1,4771/23CFB Polaribacter irgensii (M61002 )97V2
97A-14 (AF355051 )1,4521/16CytoClone ZD0403 (AJ400347 )91V3
97A-15 (AF354620 )1,4402/16CFB Polaribacter irgensii (M61002 )95W
97A-5 (AF355052 )650DupCFB Polaribacter irgensii (M61002 )97W
95A-3 (AF355043 )1,4571/20δClone BD4-10 (AB015560 )87-
95D-9 (AY08220 )1,4921/12VerrClone DEV022 (AJ401118 )94-
95A-2 (AF355046 )1,4851/20δ, SAR406Clone OCS307 (U41450 )89-
97B-4 (AY08219 )1,5231/10VerrClone OPB35 (AF027005 )83-
96B-13 (AF355050 )1,4651/23εClone PVB-55 (U15105 )95-
96A-24 (AF355048 )6501/24δ, SAR406Clone SAR406 (U34043 )80-
96B-7 (AF355047 )1,5181/23δ, SAR406Clone SAR406 (U34043 )90-
96BD-15 (AF355049 )6381/24δ, SAR406Clone SAR406 (U34043 )80-
96B-10 (AF353211 )1,4302/23α, SAR11Clone SAR407 (U75253 )98-
95B-10 (AY08222 )1,4441/17VerrClone VadinHB65 (U81755 )83-
95B-14 (AF355055 )1,4441/17VerrClone VadinHB65 (U81755 )83-
95A-18 (AF355054 )1,4211/20GNSBClone WS52f (AF186417 )80-
97C-5 (AF354614 )1,4951/10γClone ZD0408 (AJ400349 )98-
96BD-22d (AF355045 )1,2791/24δ Nitrospina gracilis (L35504 )92-
95B-2 (AF355036 )1,4191/17α Olavius loisae symbiont (AF104473 )89-
97A-7 (AF353236 )1,4261/16α Olavius loisae symbiont (AF104473 )88-
96AD4 (AF354619 )1,4812/20Cyto Psychroserpens burtonensis (U62913 )93-
95B-9c (AF355035 )1,3641/17αStrain BD1-17 (AB015526 )88-
96AD-9 (AF354608 )1,4991/20γ 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 ε, α-, δ-, γ-, and ε-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.