Table 3.

Clone sequences from each clone library, listed with phylum affiliation, nearest neighbor from the global database, percent similarity based on alignable base pairs, and grouping within each phylum

Sample location and typeCategoryClone no.aNearest neighbor% SimilarityAssemblage
Coastal ocean, free-livingα-ProteobacteriaCRO-FL4, -10, -15, -23OCS1297.6–99.7SAR11
CRO-FL1, -3, -7, -12, -26OCS15496.3–98.4SAR11
CRO-FL11OCS12499.7OCS124
CRO-FL5, -16?d??
β-ProteobacteriaCRO-FL2BAL4798.1Rubrivivaxspp.
CRO-FL17Hydrogenophaga flava93.7Rubrivivax spp.
CRO-FL25???
γ-ProteobacteriaCRO-FL8NKB490.5
Gram-positive bacteriaCRO-FL9, -14ACK-M194.2, 94.9ACK-4
CRO-FL22OCS15599.8OM1
CyanobacteriaCRO-FL18, -24Prochlorococcussp. strain MIT930398.6, 97.8Prochlorococcus spp.
CRO-FL13SAR799.5SAR7
Coastal ocean, particle-attachedα-ProteobacteriaCRO1OM4298.9MarineRhodobacter spp.
γ-ProteobacteriaCRO2, -21Legionella lytica95.1, 94.7Legionella spp.
CRO33Legionella feeleii94.7Legionella spp.
CRO14, -19Pseudomonas syringae99.4Pseudomonas spp.
CFBbCRO4MED2592.2Cytophagaspp.
Planctomycesspp.CRO13Planctomyces limnophilus98.5Planctomyces limnophilus
CyanobacteriaCRO15, -34Prochlorococcus sp. strain MIT930398.1, 97.3Prochlorococcus spp.
CRO16, -24, -27, -29, -31, -35SAR798.9–99.7SAR7
ChloroplastsCRO11, -22, -28, -32OM8191.0Chrysophyceae
CRO17OM8187.5–88.0Chrysophyceae
UnknownCRO6???
CRO18???
Columbia River, free-livingα-ProteobacteriaCR-FL10LD12100.0Freshwater SAR11
CR-FL11Soil clone (AF010012)96.6Rhizobium-Agrobacterium
β-ProteobacteriaCR-FL2, -6, -9BAL4796.3–96.5Rubrivivax spp.
CR-FL8*MT1194.6Rubrivivax spp.
CR-FL13, -22LD1797.0, 96.7Polynucleobacter necessarius
CR-FL23ACK-L696.1Polynucleobacter necessarius
CR-FL21ACK-C3099.8Methylophilus spp.
γ-ProteobacteriaCR-FL28Vibrio marinus92.9?
CR-FL29Pseudomonassp. clone (U63942)95.8Pseudomonas spp.
Gram-positive bacteriaCR-FL16, -18MC1984.2, 86.3CR-FL16
CR-FL3, -20ACK-M188.6, 91.1ACK-4
CR-FL30Agrococcus jenensis86.8?
CFBCR-FL26Capnocytophaga gingivalis85.4Cytophaga spp.
CR-FL12???
Planctomycesspp.CR-FL15MC5588.7Isophaera spp.
Verrucomicrobiales spp.CR-FL1, -25, -27VeSm1386.8–87.6Verrucomicrobiales
CR-FL5MC1893.3Verrucomicrobiales
UnknownCR-FL4???
Columbia River, particle-attachedα-ProteobacteriaCR-PA55Rhodobacter sphaeroides94.2Freshwater Rhodobacter spp.
CR-PA22Beijerinckia indica95.3Rhizobium-Agrobacterium spp.
CR-PA53MHP1793.9Rhizobium-Agrobacteriumspp.
β-ProteobacteriaCR-PA6, -11Rhodoferax fermentans98.3, 96.3Rubrivivax spp.
CR-PA24Alcaligenes denitrificans92.5Bordetella spp.
CR-PA50Ralstonia pickettii99.3Ralstonia spp.
γ-ProteobacteriaCR-PA40Methylobacter sp. strain BB5.196.2Methylomonas spp.
CR-PA44Legionella feeleii96.0Legionella spp.
CR-PA27TRS2088.2?
Gram-positive bacteriaCR-PA52MC1986.5CR-FL16
CR-PA21, -26, -38MC1986.1–87.3CR-FL16
CR-PA36ACK-M194.7ACK-4
CR-PA13OPB9083.0?
CFBCR-PA19Soil clone C125 (AF013539)93.4Saprospira spp.
Planctomycesspp.CR-PA16MC5588.7Isophaera spp.
ChloroplastsCR-PA2, -20Chloroplast (Skeletonema pseudocostatum)98.6, 98.4Bacillariophyta
CR-PA30, -43Hstp1498.1, 97.8Bacillariophyta
UnknownCR-PA15???
Columbia River estuary, free-livingα-ProteobacteriaCRE-FL64OM4299.5MarineRhodobacter spp.
CRE-FL23MED2697.4MarineRhodobacterspp.
CRE-FL63OCS1298.7SAR11
CRE-FL21Sphingomonas adhaesiva95.3Sphingomonas spp.
CRE-FL20??
CRE-FL1??
β-ProteobacteriaCRE-FL38, -49BAL4798.1Rubrivivax spp.
CRE-FL16, -19 (-2, -65)BAL4795.5Rubrivivax spp.
CRE-FL37cMT1195.0Rubrivivaxspp.
CRE-FL62Aquaspirillum delicatum92.0Rubrivivax spp.
CRE-FL35, -41, -50Rhodoferax fermentans96.1–97.2Rubrivivax spp.
CRE-FL14, -26, -79ACK-L598.9–99.6Polynucleobacter necessarius
CRE-FL11LD1797.0Polynucleobacter necessarius
CRE-FL45, -78ACK-L696.5, 96.7Polynucleobacter necessarius
CRE-FL73ACK-C30100.0Methylophilusspp.
(CRE-FL15)ACK-C30(98.1)Methylophilusspp.
CRE-FL40ACK-C3095.0Methylophilusspp.
CRE-FL44, -56 (-58)Alcaligenes denitrificans93.1, 92.2Bordetella spp.
CRE-FL33Ralstonia pickettii98.9Ralstonia spp.
CRE-FL22Ultramicrobacterium sp. strain ND595.7?
CRE-FL68Gallionella ferruginea95.5Gallionella spp.
γ-ProteobacteriaCRE-FL4, -7, -61, -76, -77, -80, (-6, -9, -29, -30, -32, -34, -36, -42)Marinomonas vaga89.2–89.8Oceanospirillum spp.
CRE-FL8Marinomonas aquaeolei88.6Oceanospirillum spp.
δ-ProteobacteriaCRE-FL54Desulfosarcina variabilis93.1Desulfobacter spp.
Gram-positive bacteriaCRE-FL67MC1984.9CR-FL16
CRE-FL47, -53MC1986.8, 85.8CR-FL16
CRE-FL18, -70 (-66)ACK-M190.8, 90.6ACK-4
CRE-FL13ACK-M188.6ACK-4
CRE-FL43, -60Agrococcus jenensis93.3, 94.2?
CRE-FL10, -72OCS15599.5, 99.8OM1
CFBCRE-FL46Sea ice psychrophile (U85888)93.4Cytophaga spp.
CRE-FL24, -25TBS2296.1, 93.1Cytophaga spp.
CRE-FL57OM27194.5Cytophaga spp.
CRE-FL75Psychroserpens burtonensis88.1Cytophaga spp.
(CRE-FL17)SCB37(93.1)Cytophaga spp.
CRE-FL3, -39Flectobacillus major86.2, 86.4Flexibacter flexilis
OrderVerrucomicrobialesCRE-FL31TM1888.5Verrucomicrobiales
CRE-FL59LD2987.3Verrucomicrobiales
CRE-FL74Verrucomicrobium spinosum85.0Verrucomicrobiales
ChloroplastCRE-FL52OM2090.5Bacillariophyta
UnknownCRE-FL28???
CRE-FL69???
Columbia River estuary, particle-attachedα-ProteobacteriaCRE-PA76, -77KAT1095.0Marine Rhodobacter
CRE-PA4, -47, -80, -89Rhodobacter capsulatus strain ATH97.4–98.4Freshwater Rhodobacter
CRE-PA51BAL2795.0FreshwaterRhodobacter
CRE-PA70OM188100.0SAR11
CRE-PA52, -53Blastobacter natatorius97.1Sphingomonas spp.
β-ProteobacteriaCRE-PA69Rubrivivax gelatinosus93.3Rubrivivax spp.
(CRE-PA65)Rhodoferax fermentans(96.1)Rubrivivax spp.
CRE-PA22???
CRE-PA84???
CRE-PA45ACK-C3098.1Methylophilusspp.
γ-ProteobacteriaCRE-PA2, -16, -49, -86, -87, -88 (-5, -8, -20, -33, -48)Marinomonas vaga89.2–89.8Oceanospirillum spp.
CRE-PA40OM2397.9Oceanospirillum spp.
CRE-PA14, -50Symbiont (hydrothermal vent mussel)92.3, 93.4Thiothrix nivea
CRE-PA25NKB488.2?
CRE-PA78OM6092.8?
CRE-PA17TBS2389.0?
CRE-PA9Methylococcus capsulatus87.8Methylomonas spp.
CRE-PA58, -74TRS2088.2, 89.4?
CRE-PA35Xanthomonas vesicatoria92.2Xanthomonas spp.
δ-ProteobacteriaCRE-PA6, -66Desulfurhopalus vacuolatus91.8, 93.1Desulfobacter spp.
CRE-PA18Desulfovibrio sp. strain STL694.5Desulfovibrio spp.
Gram-positive bacteriaCRE-PA41MC1987.3CR-FL16
CRE-PA39OCS15599.5OM1
CRE-PA63 (-67, -81)OPB9083.0?
CRE-PA72Spiroplasmasp. strain Y3283.2Low G+C
CRE-PA64MB242488.5Low G+C
CFBCRE-PA32BAL1393.6Cytophagaspp.
CRE-PA38Sea ice psychrophile (U85888)93.4Cytophaga spp.
CRE-PA10, -79 (-43)MED2592.0Cytophaga spp.
CRE-PA44MED1892.5Cytophaga spp.
CRE-PA37SCB3793.1Cytophaga spp.
CRE-PA11, -15, -85Psychroserpens burtonensis93.0Cytophaga spp.
CRE-PA7Flectobacillus major86.7Flexibacter flexilis
CRE-PA83Soil clone C12589.8Saprospira spp.
CRE-PA30???
CRE-PA75???
CRE-PA82???
Planctomycesspp.CRE-PA34MC10094.6Planctomyces limnophilus
VerrucomicrobialesCRE-PA23LD2987.9Verrucomicrobiales
CRE-PA73MC1892.2Verrucomicrobiales
CRE-PA29??Verrucomicrobiales
ChloroplastCRE-PA60Chloroplast (Skeletonema pseudocostatum)98.4Bacillariophyta
CRE-PA42Hstp1496.5Bacillariophyta
CRE-PA59 (-19)AGG5697.3Bacillariophyta
CRE-PA21OM8187.7Chrysophyceae
CRE-PA27Chlorella saccharophila91.5Green plant chloroplasts
UnknownCRE-PA24, -26???
  • a Clone numbers in parentheses were categorized by RFLP pattern.

  • b CFB,Cytophaga-Flexibacter-Bacteroides.

  • c Clone that is most closely related to known contaminants from a negative-control library (43).

  • d ?, nearest neighbor could not be determined.