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-FL2BAL4798.1 Rubrivivaxspp.
CRO-FL17 Hydrogenophaga flava 93.7 Rubrivivax spp.
CRO-FL25???
γ-ProteobacteriaCRO-FL8NKB490.5
Gram-positive bacteriaCRO-FL9, -14ACK-M194.2, 94.9ACK-4
CRO-FL22OCS15599.8OM1
CyanobacteriaCRO-FL18, -24 Prochlorococcussp. strain MIT930398.6, 97.8 Prochlorococcus spp.
CRO-FL13SAR799.5SAR7
Coastal ocean, particle-attachedα-ProteobacteriaCRO1OM4298.9MarineRhodobacter spp.
γ-ProteobacteriaCRO2, -21 Legionella lytica 95.1, 94.7 Legionella spp.
CRO33 Legionella feeleii 94.7 Legionella spp.
CRO14, -19 Pseudomonas syringae 99.4 Pseudomonas spp.
CFBb CRO4MED2592.2 Cytophagaspp.
Planctomycesspp.CRO13 Planctomyces limnophilus 98.5 Planctomyces limnophilus
CyanobacteriaCRO15, -34 Prochlorococcus sp. strain MIT930398.1, 97.3 Prochlorococcus spp.
CRO16, -24, -27, -29, -31, -35SAR798.9–99.7SAR7
ChloroplastsCRO11, -22, -28, -32OM8191.0 Chrysophyceae
CRO17OM8187.5–88.0 Chrysophyceae
UnknownCRO6???
CRO18???
Columbia River, free-livingα-ProteobacteriaCR-FL10LD12100.0Freshwater SAR11
CR-FL11Soil clone (AF010012)96.6 Rhizobium-Agrobacterium
β-ProteobacteriaCR-FL2, -6, -9BAL4796.3–96.5 Rubrivivax spp.
CR-FL8* MT1194.6 Rubrivivax spp.
CR-FL13, -22LD1797.0, 96.7 Polynucleobacter necessarius
CR-FL23ACK-L696.1 Polynucleobacter necessarius
CR-FL21ACK-C3099.8 Methylophilus spp.
γ-ProteobacteriaCR-FL28 Vibrio marinus 92.9?
CR-FL29 Pseudomonassp. clone (U63942)95.8 Pseudomonas spp.
Gram-positive bacteriaCR-FL16, -18MC1984.2, 86.3CR-FL16
CR-FL3, -20ACK-M188.6, 91.1ACK-4
CR-FL30 Agrococcus jenensis 86.8?
CFBCR-FL26 Capnocytophaga gingivalis 85.4 Cytophaga spp.
CR-FL12???
Planctomycesspp.CR-FL15MC5588.7 Isophaera spp.
Verrucomicrobiales spp.CR-FL1, -25, -27VeSm1386.8–87.6 Verrucomicrobiales
CR-FL5MC1893.3 Verrucomicrobiales
UnknownCR-FL4???
Columbia River, particle-attachedα-ProteobacteriaCR-PA55 Rhodobacter sphaeroides 94.2Freshwater Rhodobacter spp.
CR-PA22 Beijerinckia indica 95.3 Rhizobium-Agrobacterium spp.
CR-PA53MHP1793.9 Rhizobium-Agrobacteriumspp.
β-ProteobacteriaCR-PA6, -11 Rhodoferax fermentans 98.3, 96.3 Rubrivivax spp.
CR-PA24 Alcaligenes denitrificans 92.5 Bordetella spp.
CR-PA50 Ralstonia pickettii 99.3 Ralstonia spp.
γ-ProteobacteriaCR-PA40 Methylobacter sp. strain BB5.196.2 Methylomonas spp.
CR-PA44 Legionella feeleii 96.0 Legionella 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)93.4 Saprospira spp.
Planctomycesspp.CR-PA16MC5588.7 Isophaera spp.
ChloroplastsCR-PA2, -20Chloroplast (Skeletonema pseudocostatum)98.6, 98.4 Bacillariophyta
CR-PA30, -43Hstp1498.1, 97.8 Bacillariophyta
UnknownCR-PA15???
Columbia River estuary, free-livingα-ProteobacteriaCRE-FL64OM4299.5MarineRhodobacter spp.
CRE-FL23MED2697.4MarineRhodobacterspp.
CRE-FL63OCS1298.7SAR11
CRE-FL21 Sphingomonas adhaesiva 95.3 Sphingomonas spp.
CRE-FL20??
CRE-FL1??
β-ProteobacteriaCRE-FL38, -49BAL4798.1 Rubrivivax spp.
CRE-FL16, -19 (-2, -65)BAL4795.5 Rubrivivax spp.
CRE-FL37c MT1195.0 Rubrivivaxspp.
CRE-FL62 Aquaspirillum delicatum 92.0 Rubrivivax spp.
CRE-FL35, -41, -50 Rhodoferax fermentans 96.1–97.2 Rubrivivax spp.
CRE-FL14, -26, -79ACK-L598.9–99.6 Polynucleobacter necessarius
CRE-FL11LD1797.0 Polynucleobacter necessarius
CRE-FL45, -78ACK-L696.5, 96.7 Polynucleobacter necessarius
CRE-FL73ACK-C30100.0 Methylophilusspp.
(CRE-FL15)ACK-C30(98.1) Methylophilusspp.
CRE-FL40ACK-C3095.0 Methylophilusspp.
CRE-FL44, -56 (-58) Alcaligenes denitrificans 93.1, 92.2 Bordetella spp.
CRE-FL33 Ralstonia pickettii 98.9 Ralstonia spp.
CRE-FL22 Ultramicrobacterium sp. strain ND595.7?
CRE-FL68 Gallionella ferruginea 95.5 Gallionella spp.
γ-ProteobacteriaCRE-FL4, -7, -61, -76, -77, -80, (-6, -9, -29, -30, -32, -34, -36, -42) Marinomonas vaga 89.2–89.8 Oceanospirillum spp.
CRE-FL8 Marinomonas aquaeolei 88.6 Oceanospirillum spp.
δ-ProteobacteriaCRE-FL54 Desulfosarcina variabilis 93.1 Desulfobacter 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, -60 Agrococcus jenensis 93.3, 94.2?
CRE-FL10, -72OCS15599.5, 99.8OM1
CFBCRE-FL46Sea ice psychrophile (U85888)93.4 Cytophaga spp.
CRE-FL24, -25TBS2296.1, 93.1 Cytophaga spp.
CRE-FL57OM27194.5 Cytophaga spp.
CRE-FL75 Psychroserpens burtonensis 88.1 Cytophaga spp.
(CRE-FL17)SCB37(93.1) Cytophaga spp.
CRE-FL3, -39 Flectobacillus major 86.2, 86.4 Flexibacter flexilis
OrderVerrucomicrobiales CRE-FL31TM1888.5 Verrucomicrobiales
CRE-FL59LD2987.3 Verrucomicrobiales
CRE-FL74 Verrucomicrobium spinosum 85.0 Verrucomicrobiales
ChloroplastCRE-FL52OM2090.5 Bacillariophyta
UnknownCRE-FL28???
CRE-FL69???
Columbia River estuary, particle-attachedα-ProteobacteriaCRE-PA76, -77KAT1095.0Marine Rhodobacter
CRE-PA4, -47, -80, -89 Rhodobacter capsulatus strain ATH97.4–98.4Freshwater Rhodobacter
CRE-PA51BAL2795.0FreshwaterRhodobacter
CRE-PA70OM188100.0SAR11
CRE-PA52, -53 Blastobacter natatorius 97.1 Sphingomonas spp.
β-ProteobacteriaCRE-PA69 Rubrivivax gelatinosus 93.3 Rubrivivax spp.
(CRE-PA65) Rhodoferax fermentans (96.1) Rubrivivax spp.
CRE-PA22???
CRE-PA84???
CRE-PA45ACK-C3098.1 Methylophilusspp.
γ-ProteobacteriaCRE-PA2, -16, -49, -86, -87, -88 (-5, -8, -20, -33, -48) Marinomonas vaga 89.2–89.8 Oceanospirillum spp.
CRE-PA40OM2397.9 Oceanospirillum spp.
CRE-PA14, -50Symbiont (hydrothermal vent mussel)92.3, 93.4 Thiothrix nivea
CRE-PA25NKB488.2?
CRE-PA78OM6092.8?
CRE-PA17TBS2389.0?
CRE-PA9 Methylococcus capsulatus 87.8 Methylomonas spp.
CRE-PA58, -74TRS2088.2, 89.4?
CRE-PA35 Xanthomonas vesicatoria 92.2 Xanthomonas spp.
δ-ProteobacteriaCRE-PA6, -66 Desulfurhopalus vacuolatus 91.8, 93.1 Desulfobacter spp.
CRE-PA18 Desulfovibrio sp. strain STL694.5 Desulfovibrio spp.
Gram-positive bacteriaCRE-PA41MC1987.3CR-FL16
CRE-PA39OCS15599.5OM1
CRE-PA63 (-67, -81)OPB9083.0?
CRE-PA72 Spiroplasmasp. strain Y3283.2Low G+C
CRE-PA64MB242488.5Low G+C
CFBCRE-PA32BAL1393.6 Cytophagaspp.
CRE-PA38Sea ice psychrophile (U85888)93.4 Cytophaga spp.
CRE-PA10, -79 (-43)MED2592.0 Cytophaga spp.
CRE-PA44MED1892.5 Cytophaga spp.
CRE-PA37SCB3793.1 Cytophaga spp.
CRE-PA11, -15, -85 Psychroserpens burtonensis 93.0 Cytophaga spp.
CRE-PA7 Flectobacillus major 86.7 Flexibacter flexilis
CRE-PA83Soil clone C12589.8 Saprospira spp.
CRE-PA30???
CRE-PA75???
CRE-PA82???
Planctomycesspp.CRE-PA34MC10094.6 Planctomyces limnophilus
Verrucomicrobiales CRE-PA23LD2987.9 Verrucomicrobiales
CRE-PA73MC1892.2 Verrucomicrobiales
CRE-PA29?? Verrucomicrobiales
ChloroplastCRE-PA60Chloroplast (Skeletonema pseudocostatum)98.4 Bacillariophyta
CRE-PA42Hstp1496.5 Bacillariophyta
CRE-PA59 (-19)AGG5697.3 Bacillariophyta
CRE-PA21OM8187.7 Chrysophyceae
CRE-PA27 Chlorella saccharophila 91.5Green 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.