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)1,4461/16δNitrospina gracilis (L35504)91C
95A-16 (AF353227)1,3971/20α, SAR11Clone SAR407 (U75253)98F
95C-6 (AF355042)1,4732/10δNitrospina 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)1,5001/23γFundibacter jadensis (AJ001150)88I
96AD-16 (AF354601)1,4912/20γPseudoalteromonas atlantica (AF173963)99J
96AD-23 (AF354602)629DupγPseudoalteromonas 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)1,4611/17γOceanospirillum sp. (AJ302699)90M
95A-1 (AF354599)650DupγAlteromonas macleodii (Y18228)99N
95A-15 (AF354598)1,45510/20γAlteromonas macleodii (Y18228)99N
95A-4 (AF354600)650DupγAlteromonas macleodii (Y18228)99N
95B-13 (AF353237)1,461DupγOceanospirillum sp. (AJ302699)90O
95B-19 (AF353240)644DupγOceanospirillum sp. (AJ302699)96O
95B-7 (AF353238)1,4617/17γOceanospirillum sp. (AJ302699)90O
95B-8 (AF353239)1,455DupγOceanospirillum sp. (AJ302699)96O
96AD-24 (AF354604)1,4971/20γAlcanivorax borkumensis (Y12579)96P
96BD-24 (AF354603)1,4971/24γAlcanivorax borkumensis (Y12579)96P
96A-14 (AF354611)1,4891/24γClone ZD0424 (AJ400355)97P
97A-6 (AF354612)1,4561/16γClone ZD0424 (AJ400355)97P
95B-15 (AF354609)1,4641/17γFundibacter jadensis (AJ001150)98P
96B-17 (AF354597)1,4911/23γPseudoalteromonas atlantica (AF173963)98P
96B-9 (AF354596)1,4921/23γPseudomonas fluorescens (AF094726)91Q
96AD-3 (AF354607)1,5021/20γThiomicrospira sp. (AJ237758)90R
96BD-1 (AF354605)1,4942/24γAlcanivorax borkumensis (Y12579)94S1
96A-12 (AF354610)1,4983/24γFundibacter 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)1,4771/23CFBPolaribacter irgensii (M61002)97V2
97A-14 (AF355051)1,4521/16CytoClone ZD0403 (AJ400347)91V3
97A-15 (AF354620)1,4402/16CFBPolaribacter irgensii (M61002)95W
97A-5 (AF355052)650DupCFBPolaribacter 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)1,2791/24δNitrospina gracilis (L35504)92-
95B-2 (AF355036)1,4191/17αOlavius loisae symbiont (AF104473)89-
97A-7 (AF353236)1,4261/16αOlavius loisae symbiont (AF104473)88-
96AD4 (AF354619)1,4812/20CytoPsychroserpens burtonensis (U62913)93-
95B-9c (AF355035)1,3641/17αStrain BD1-17 (AB015526)88-
96AD-9 (AF354608)1,4991/20γThiomicrospira 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.