Table 1.

Length in nucleotides between positions homologous toE. coli SSU rDNA positions 8 through 355 (domain A) or 8 through 536 (domain B) for a variety of marine bacteriaa

Accession no.Cellular strain or environ-mental gene cloneTaxonomic affiliationSize of domain (bp)
AB
env.OCS28 [A]α312468
U70681 env.OM55α312468
U75264 env.SAR490α312ND
X52170 env SAR12c313ND
U75260 env.SAR418α313ND
U75262 env.SAR440α313ND
U75263 env.SAR466α313ND
X52169 env.SAR6c313470
Synechococcus sp. strain WH8101c313471
Synechococcus sp. strain WH8103c313472
U78945 env.OCS122 [B]α314470
U75259 env.SAR414α314ND
env.SAR420α314472
X52171 env.SAR7c314471
U64002 Rhizobium sp. strain BAL25α314470
U63957 Zoogloea sp. strain BAL43α314470
L10934 env.FL1α315470
L10935 env.FL11α315471
env.OCS24 [C]α315471
U70678 env.OM25α315471
U75258 env.SAR241α315471
U75254 env.SAR464α315471
X78315 Roseobacter algicola α315471
L15345 Strain LFRα315472
U63935 Caulobacter sp. strain BAL3α316472
U75252 env.OCS12 [D]α316472
env.OCS126 [D]α316472
U78942 env.OCS19 [D]α316ND
U78943 env.OCS84 [D]α316ND
U70684 env.OM136α316472
U70585 env.OM143α316471
U70686 env.OM155α316472
U70692 env.OM299α316ND
U70679 env.OM38α316472
U70680 env.OM42α316472
U70682 env.OM65α316473
X52280 env.SAR1α316473
X52172 env.SAR11α316473
U75255 env.SAR203α316472
U75256 env.SAR211α316472
U75257 env.SAR220α316472
env.SAR402α316472
U64003 Erythrobacter sp. strain BAL26α316472
U64005 Erythrobacter sp. strain BAL28α316472
U64011 Erythrobacter sp. strain SCB34α316472
U64025 Erythrobacter sp. strain SCB48α316472
U63952 Erythromicrobium sp. strain BAL34α316472
U63958 Flavobacterium sp. strain BAL44α316ND
U63939 Rhizomonas sp. strain BAL11α316472
U63934 Rhodobacter sp. strain BAL2α316472
U63949 Rhodobactersp. strain BAL27α316472
U63956 Sphingomonas sp. strain BAL40α316472
U63959 Sphingomonas sp. strain BAL45α316472
U63960 Sphingomonassp. strain BAL46α316472
U63962 Sphingomonas sp. strain BAL48α316485
U63937 Sphingomonas sp. strain BAL5α316470
U63998 Sphingomonassp. strain SCB21α316472
U78913 Strain R2A114 [D]α316ND
U78918 Strain R2A163 [D]α316ND
U78919 Strain R2A166 [D]α316ND
U78910 Strain R2A62 [D]α316ND
U78912 Strain R2A84 [D]α316ND
env.OCS138 [E]α317473
env.OCS154 [E]α317473
env.OCS180 [E]α317473
env.OCS53 [E]α317473
U70687 env.OM188α317473
U70689 env.OM242α317ND
U75649 env.SAR193α317473
env.SAR222α317ND
env.SAR239α317ND
env.SAR258α317ND
U75253 env.SAR407α317473
U14583 Strain 307α318474
U64009 Strain BAL32α318474
U78909 Strain R2A57 [F]α318ND
U64019 Strain SCB42α318472
env.OCS14 [J]α324480
env.OCS27 [J]α324483
U70683 env.OM75 [J]α326482
U78944 env.OCS116 [M]α328484
U70714 env.OM110γ328ND
U78917 Strain R2A153 [M]α328ND
U65915 env.SAR276δ329ND
env.OCS124 [N]α330486
M58793 Microscilla marina f330505
U20797 env.SAR202x331488
U20798 env.SAR307x331488
env.OCS2γ334ND
U63945 Aeromonas sp. strain BAL19γ336ND
U05570 Methylobacterium pelagicum γ338518
U14585 Strain 34-pα338520
U70702 env.OM241γ339520
U70696 env.OM60γ339520
L35470 env.SAR160γ339520
U85887 Flavobacterium sp. strain A103f339515
U85888 Flavobacterium sp. strain A265f339515
D32219 Strain K189Cγ339ND
U64010 Aeromonas sp. strain SCB33γ340ND
X82144 Alteromonas luteoviolacea γ340522
X82147 Alteromonas rubra γ340522
M93352 Deleya aquamarina γ340521
env.OCS111 [Q]β340521
env.OCS7 [Q]β340521
L35469 env.SAR156γ340521
U85873 Halomonas variabilis γ340521
U85872 Halomonas variabilis γ340521
U85871 Halomonas variabilis γ340521
L42618 Halomonas variabilis γ340521
L35540 Methylobacterium pelagicum γ340521
X72775 Methylomicrobium pelagicum γ340521
RDP Oceanospirillum kriegii γ340521
U63961 Rhodoferaxsp. strain BAL47β340461
U85854 Strain C079γ340521
D32220 Strain K189Bγ340ND
D32221 Strain unid gamma-proteobacteriumγ340ND
U78920 Strain R2A9 [Q]γ340ND
X82143 Alteromonas espejiana γ341522
X67024 Alteromonas haloplanktis γ341522
L10938 Alteromonas macleodii γ341522
X82140 Alteromonas undina γ341523
env.OCS43 [R]β341ND
L35471 env.SAR166γ341519
env.SAR470γ341ND
env.SAR471γ341523
U63946 Flavobacterium sp. strain BAL22f341ND
U63938 Flavobacterium sp. strain BAL9f341ND
X87339 Methylophaga thalassica γ341521
X98336 Pseudoalteromonas antarctica γ341522
U85857 Pseudoalteromonas sp. strain MB6-03γ341522
U85858 Pseudoalteromonassp. strain MB8-02γ341522
U64012 Aeromonas sp. strain SCB35γ342ND
U64020 Aeromonas sp. strain SCB43γ342523
U63953 Alcaligenes sp. strain BAL37β342ND
X82141 Alteromonas piscicida γ342524
U63943 Cytophaga sp. strain BAL17f342ND
U78946 env.OCS181γ342523
env.OCS44γ342523
env.OCS5γ342523
env.OCS66β342523
env.OCS98β342521
U70718 env.OM111γ342ND
U70698 env.OM133γ342ND
U70694 env.OM23γ342523
U70697 env.OM93γ342523
U63954 Flavobacterium sp. strain BAL38f342ND
X82134 Pseudoalteromonas atlantica γ342523
X82136 Pseudoalteromonas carrageenovora γ342523
U85856 Pseudoalteromonas sp. strain IC006γ342523
U85859 Pseudoalteromonassp. strain IC013γ342523
U85860 Pseudoalteromonas sp. strain MB6-05γ342523
U85861 Pseudoalteromonassp. strain SW08γ342523
U85862 Pseudoalteromonassp. strain SW29γ342523
U85870 Pseudomonas sp. strain A177γ342523
U85868 Pseudomonas sp. strain ACAM213γ342523
U63942 Pseudomonas sp. strain BAL16γ342ND
U63944 Pseudomonas sp. strain BAL18γ342ND
U63947 Pseudomonas sp. strain BAL23γ342ND
U64001 Pseudomonas sp. strain BAL24γ342523
U85869 Pseudomonas sp. strain IC038γ342523
U65012 Pseudomonas stutzeri γ342523
U26420 Pseudomonas stutzeri ZoBellγ342523
U78922 Strain R2A30γ342ND
U63941 Zoogloea sp. strain BAL15β342ND
U85897 Arthrobacter sp. strain MB6-07h343504
U85896 Arthrobacter sp. strain MB8-13h343516
U85893 Arthrobactersp. strain MB90h343503
U63940 Cytophagasp. strain BAL13f343ND
U70693 env.OM10γ343523
U65912 env.SAR248δ343499
U65908 env.SAR324δ343499
U85890 Flavobacterium sp. strain ACAM123f343519
U85889 Flavobacterium sp. strain IC001f343519
U85891 Marine psychrophile IC025f343519
X95640 Methylophaga thalassica γ343524
U78924 Strain R2A103 [S]f343ND
U64027 Alteromonas sp. strain SCB50γ344525
X82061 Corynebacterium glutamicum h344507
U70706 env.OM156β344525
U70707 env.OM180β344525
env.SAR267x344502
M63811 env.SAR92γ344525
L35461 env.SAR86γ344525
U85879 Psychrobacter glacincola γ344525
U85878 Psychrobacter glacincola γ344525
U85877 Psychrobacter glacincola γ344525
U85876 Psychrobacter glacincola γ344525
U85875 Psychrobacter sp. strain IC008γ344525
U85874 Psychrobacter sp. strain MB6-21γ344525
U78941 Strain R2A170h344ND
U64026 Strain SCB49f344ND
M58794 Microscilla sericea f345520
U64021 Antarcticum sp. strain SCB44f345521
X80629 Corynebacterium glutamicum h345508
X84257 Corynebacterium glutamicum h345508
Z46753 Corynebacterium glutamicum h345508
M62796 Cytophaga lytica f345521
L10948 env.AGG13f345521
L10945 env.AGG41f345520
L10946 env.AGG58f345519
env.SAR242x345ND
M58775 Flectobacillus glomeratus f345521
X67022 Marinobacter hydrocarbonoclasticus γ345527
U63999 Marinobacter sp. strain SCB22γ345526
X67025 Marinomonas vaga γ345526
U14586 Strain 301f345521
U85883 Strain IC054f345ND
U85885 Strain IC063f345521
U85884 Strain IC066f345ND
U78933 Strain R2A10f345ND
U78935 Strain R2A132f345ND
U78940 Strain R2A160h345ND
U78939 Strain R2A54f345ND
U64015 Strain SCB38f345462
M61002 Vesiculatum antarcticum f345521
X82135 Alteromonas aurantia γ346527
X82137 Alteromonas citrea γ346527
X82137 Alteromonas denitrificans γ346528
U85895 Arthrobacter sp. strain IC044h346507
U64000 Chromohalobacter sp. strain SCB23γ346ND
U85844 Colwellia sp. strain IC068γ346527
U85845 Colwellia sp. strain ICP11γ346527
L42615 Deleya cupida γ346527
M93354 Deleya marina γ346527
L42616 Deleya pacifica γ346527
env.OCS178β346527
U70699 env.OM182γ346527
U70704 env.OM43β346527
U70705 env.OM58β346ND
U70695 env.OM59γ346527
env.SAR226x346504
env.SAR250x346503
env.SAR259x346501
env.SAR269x346504
U85863 Marinobacter sp. strain IC022γ346527
U85864 Marinobacter sp. strain IC032γ346527
RDP Marinomonas communis γ346527
RDP Marinomonas vaga γ346527
RDP Oceanospirillum beijerincki γ346527
U85880 Psychrobacter immobilis γ346527
U78930 Strain R2A148γ346ND
U85881 Strain IC051f346522
U78931 Strain R2A173γ346ND
U78924 Strain R2A44γ346ND
U78927 Strain R2A86γ346ND
U78928 Strain R2A88γ346ND
U64017 Strain SCB40f346489
U64022 Strain SCB45γ346472
M62788 Cyclobacterium marinus f347522
L10944 env.AGG32f347522
U70703 env.OM252γ347528
env.SAR251x347504
env.SAR432h347503
U63955 Flavobacterium sp. strain BAL39f347ND
U64023 Flexibacter sp. strain SCB46f347523
X87755 Kytococcus sedentarius h347508
DEW Serratia rubidacea γ347527
U85906 Shewanella frigidimarina γ347528
U85882 Strain IC076f347523
Z25522 Strain purpleγ347524
U78929 Strain R2A113γ347ND
U78932 Strain R2A5f347ND
U85900 Arthrobacter sp. strain MB6-20h348509
U63951 Azospirillum sp. strain BAL31γ348ND
U85841 Colwellia sp. strain IC062γ348529
U85842 Colwellia sp. strain IC064γ348529
L10950 env.AGG53γ348528
X54745 env.WHB461γ348529
X54744 env.WHB462γ348529
M58784 Flexibacter litoralis f348525
RDP Oceanospirillum jannaschii γ348529
M22365 Oceanospirillum linum γ348529
U85855 Pseudoalteromonas sp. strain MB8-11γ348529
U85905 Shewanella frigidimarina γ348529
U85904 Shewanella frigidimarina γ348529
U85903 Shewanella frigidimarina γ348529
U85902 Shewanella frigidimarina γ348529
U85907 Shewanella gelidimarina γ348529
X81623 Shewanella putrefaciens γ348529
U85886 Strain ACAM210f348524
X76334 Vibrio vulnificus γ348529
X74727 Vibrio vulnificus γ348529
X74726 Vibrio vulnificus γ348529
X76333 Vibrio vulnificus γ348529
Z22992 Vibrio vulnificus γ348529
X56582 Vibrio vulnificus γ348529
U64004 Xanthomonas sp. strain BAL27γ348ND
U85846 Colwellia sp. strain ACAM179γ349530
U85843 Colwellia sp. strain IC072γ349530
M58770 Cytophaga marinoflava f349525
U70708 env.OM271f349525
U70709 env.OM273f349525
env.SAR196n349520
L35504 Nitrospina gracilis δ349508
RDP Oceanospirillum maris γ349530
U64014 Strain SCB37f349480
X74685 Photobacterium angustum γ350531
D25310 Photobacterium phosphoreum γ350532
X74687 Photobacterium phosphoreum γ350531
Z19107 Photobacterium phosphoreum γ350531
U85908 Shewanella hanedai γ350531
X82133 Shewanella putrefaciens γ350532
U63948 Shewanella sp. strain BAL25γ350ND
U14582 Strain 90-P(gv)1γ350531
U85849 Strain IC004γ350531
U85852 Strain IC085γ350531
U78923 Strain R2A37 [U]γ350ND
U14581 Strain S51-W(gv)1γ350531
RDP Vibrio marinus γ350531
X82134 Vibrio marinus γ350533
U85847 Colwellia sp. strain IC035γ351532
U85853 Strain IC067γ351532
U64018 Strain SCB41f351ND
L35468 env.SAR145γ352532
M96493 Nitrococcus mobilis β352533
X82132 Shewanella hanedai γ352533
env.OCS155h353509
U70710 env.OM1h353509
U70711 env.OM231h353ND
U41450 env.OCS307fb353535
U85851 Strain IC059γ353534
X56756 Vibrio alginolyticus γ353535
U34043 env.SAR406fb354536
D55729 Planococcus okeanokoites 1354534
U85899 Planococcus sp. strain IC0241354534
X56578 Vibrio harveyi γ354536
X56581 Vibrio natriegens γ354536
D25308 Photobacterium histaminum γ355537
D25309 Photobacterium leiognathi γ355537
X62172 Planococcus citreus 1355535
U85898 Planococcussp. strain MB6-161355535
D83367 Staphylococcus halodurans 1355534
Z26896 Staphylococcus halodurans 1355536
X66100 Staphylococcus halodurans 1355536
L37600 Staphylococcus halodurans 1355538
U78937 Strain R2A180 [V]1355ND
X56575 Vibrio campbellii γ355537
env.SAR272x356514
U14584 Flectobacillus sp. strain S38-W(gv)1f356537
U78938 Strain R2A1611356ND
env.SAR256x357514
X70642 Listonella pelagia γ357ND
U85867 Marinobacter sp. strain IC065γ357ND
X74722 Listonella pelagia γ358539
X74686 Photobacterium leiognathi γ358539
X74691 Vibrio alginolyticus γ358539
X74690 Vibrio alginolyticus γ358539
X74692 Vibrio campbellii γ358539
X74702 Vibrio fischeri γ358539
X70640 Vibrio fischeri γ358538
X74706 Vibrio harveyi γ358539
X74710 Vibrio mediterranei γ358539
X74714 Vibrio natriegens γ358539
X74716 Vibrio nereis γ358539
X74717 Vibrio nigripulchritudo γ358539
X74719 Vibrio orientalis γ358539
U64016 Vibrio sp. strain SCB39γ358524
U64024 Vibrio sp. strain SCB47γ358523
Z31657 Vibrio splendidus γ358538
X74724 Vibrio splendidus γ358539
U64013 Flexibacter sp. strain SCB36f360527
U64006 Vibrio sp. strain BAL29γ360ND
U64007 Vibrio sp. strain BAL30γ360526
X62171 Marinococcus halophilus 1363545
X90835 Marinococcus halophilus 1374556
U85901 Halobacillus sp. strain MB6-081392574
  • a Lengths were calculated for bacteria and plastids isolated from seawater, as well as for SSU rDNAs cloned from community DNA. Published sequences were obtained from the RDP, GenBank, and ARB databases. We also included unpublished sequences of genes cloned from environmental DNA from the Oregon coast (12, 15) (prefix env.OCS) and the Sargasso Sea (prefix env.SAR). Letters in brackets correspond to the peaks in Fig. 1. α, β, γ, and δ, alpha, beta, gamma, and delta subdivisions, respectively, of the Proteobacteria; f,Flexibacter, Bacteroides, andCytophaga phylum; l, low-G+C gram-positive phylum; h, high-G+C gram-positive phylum; x, Chloroflexus andHerpetosiphon phylum; c, cyanobacteria; fb,Fibrobacter phylum; n, Nitrospira phylum; ND, not determined.