Table 1. OTUs recovered in this study (clustering at a 98% similarity threshold).
| Distribution of clones | ||||||||||||
| OTU | Division | Class/or other group | Closest match | Accession | Identity (%) | Origin (for uncultured clones) | Closest cultured match | Identity (%) | Total | VIRE | ESTUARY | BAY |
| V99 | Stramenopiles | Chrysophyceae | Mallomonas portae-ferreae | GU935618 | 99.6 | 1 | 1 | 0 | 0 | |||
| B83 | Uncult. eukaryote clone LG47-07 | AY919816 | 99.8 | Lake George, oligotrophic (USA) | Paraphysomonas foraminifera | 99.4 | 4 | 1 | 0 | 3 | ||
| V56 | Uncult. eukaryote clone AMT15_15_10m | GQ863816 | 98.8 | Upwelling region, Atlantic (Canaries) | Paraphysomonas butcheri | 98.7 | 1 | 1 | 0 | 0 | ||
| V09 | Uncult. stramenopile clone MLB53.161 | EU143922 | 97.4 | Lake Taihu, subtropical (China) | Uroglena sp. | 94.4 | 1 | 1 | 0 | 0 | ||
| V92 | Uncult. eukaryote clone RW2_2011 | AB721074 | 96.5 | Freshwater, Kiryu (Japan) | Uroglena sp. | 96.1 | 2 | 2 | 0 | 0 | ||
| V69 | Spumella-like flagellate (isolate JBAS36) | AY651079 | 99.6 | Freshwater, Nag Pokhari (Nepal) | Pedospumella encystans | 99 | 2 | 2 | 0 | 0 | ||
| V78 | Spumella-like flagellate (isolate JBC27) | AY651093 | 93.3 | Small pond, Huqiu (China) | Chrysosphaera parvula | 90.9 | 2 | 2 | 0 | 0 | ||
| V97 | Uncult. eukaryote clone PG5.22 | AY642735 | 97.5 | Lake Godivelle, oligotrophic (France) | Paraphysomonas imperforata | 95.1 | 1 | 1 | 0 | 0 | ||
| V145 | Uncult. eukaryote clone Ch8A2mF4 | JF730784 | 99.2 | Char Lake (Arctic) | Ochromonas tuberculata | 95.5 | 13 | 13 | 0 | 0 | ||
| V81 | Uncult. eukaryote clone WH8eA1 | JF730838 | 99.8 | Ward hunt Lake (Arctic) | Ochromonas tuberculata | 96.4 | 1 | 1 | 0 | 0 | ||
| B18 | Uncult eukaryote clone CYSGM-7 | AB275090 | 98 | Marine sediment, methane seep (Japan) | Kephyrion sp. | 96.7 | 21 | 0 | 1 | 20 | ||
| B59 | Uncult. eukaryote clone Q2B03N10 | EF172974 | 97.6 | Sargasso Sea (25m depth) | Synura curtispina | 91 | 1 | 0 | 0 | 1 | ||
| Es64 | Bacillariophyceae | Thalassiosira guillardii | AF374478 | 99.7 | 68 | 0 | 68 | 0 | ||||
| Es37 | Thalassiosira pseudonana | DQ093367 | 99.8 | 4 | 0 | 4 | 0 | |||||
| V141 | Cyclotella meneghinia | AY496207 | 100 | 6 | 6 | 0 | 0 | |||||
| V105 | Stephanodiscus hantzschii | DQ514914 | 99.8 | 26 | 10 | 16 | 0 | |||||
| V38 | Discostella pseudostelligera | DQ514905 | 99.8 | 10 | 7 | 3 | 0 | |||||
| Es86 | Thalassiosira nordenskioeldii | DQ514886 | 99.9 | 1 | 0 | 1 | 0 | |||||
| Es109 | Diatoma tenuis var. elongatus | EF423403 | 99.9 | 1 | 0 | 1 | 0 | |||||
| Es123 | Asterionellopsis glacialis | X77701 | 99.8 | 1 | 0 | 1 | 0 | |||||
| Es110 | Navicula phyllepta | EU938308 | 100 | 1 | 0 | 1 | 0 | |||||
| V154 | Navicula gregaria | HM805037 | 99.9 | 1 | 1 | 0 | 0 | |||||
| V163 | Surirella brebissoni | AJ867029 | 99.7 | 1 | 1 | 0 | 0 | |||||
| B128 | Rhizosolenia imbricata | AY485510 | 100 | 7 | 0 | 0 | 7 | |||||
| B140 | Bolidophyceae | Uncult. eukaryote clone BLACKSEA_48 | HM749950 | 99.5 | Southern Black Sea | Bolidomonas pacifica | 95.7 | 1 | 0 | 0 | 1 | |
| V16 | Bicosoecids | Uncult. eukaryote clone P34.6 | AY642710 | 98.1 | Lake Pavin, oligomesotrophic (France) | Adriamonas peritocrescens | 93.4 | 1 | 1 | 0 | 0 | |
| V44 | MAST-2 | Uncult. eukaryote clone W8eD9 | JF730854 | 99.9 | Ward hunt Lake (Arctic) | Pirsonia verrucosa | 88.5 | 1 | 1 | 0 | 0 | |
| B110 | MAST-4 | Uncult. eukaryote clone H3S8Ae5 | JQ781882 | 100 | North pacific ocean | Pirsonia verrucosa | 88.9 | 1 | 0 | 0 | 1 | |
| B75 | MAST-12 | Uncult. eukaryote clone BAQA21 | AF372755 | 96 | Marine anoxic sediments, Berkeley (USA) | Oblongichytrium sp. | 84.1 | 1 | 0 | 0 | 1 | |
| V122 | Cryptophyta | (nucleus) | Cryptomonas curvata | AM051189 | 99.9 | 21 | 21 | 0 | 0 | |||
| V83 | Cryptomonas pyrenoidifera/C. marssonii | EU163587/AM051192 | 99.7 | 1 | 1 | 0 | 0 | |||||
| V42 | Cryptomonas tetrapyrenoidosa/C. ovata | AB240954/AF508270 | 100 | 3 | 3 | 0 | 0 | |||||
| V151 | Cryptomonas borealis/C. ovata | AM051188/AB240952 | 93.9 | 1 | 1 | 0 | 0 | |||||
| V23 | Uncult. Cryptophyte, clone STFeb_146 | HM135081 | 99.9 | Lake Stechlin, oligotrophic (Germany) | Teleaulax amphioxeia | 98.7 | 1 | 1 | 0 | 0 | ||
| V113 | Uncult. eukaryote, clone D7 | FN263278 | 100 | Southern Baltic sea | Geminigera cryophila | 99.6 | 6 | 1 | 1 | 4 | ||
| B67 | Teleaulax acuta | AB471786 | 100 | 3 | 0 | 0 | 3 | |||||
| B147 | Cryptophyceae sp. | GQ375265 | 99.7 | Northern Baffin Bay (Arctic ocean) | Falcomonas daucoides | 98.6 | 3 | 0 | 0 | 3 | ||
| B96 | (nucleomorph) | Falcomonas daucoides | AJ420689 | 86.2 | 2 | 0 | 0 | 2 | ||||
| B23 | Haptophyta | Prymnesiophyceae | Haptolina hirta | AJ246272 | 98.7 | 1 | 0 | 0 | 1 | |||
| B121 | Phaeocystis globosa | AF182112 | 99.6 | 1 | 0 | 0 | 1 | |||||
| B01 | Picobiliphytes | Uncult. eukaryote clone RA000907 | DQ222877 | 99.2 | English Channel | 1 | 0 | 0 | 1 | |||
| B107 | Centrohelids | Pterocystis sp. unidentified helio 5 | AY749610 | 95.6 | Okareka Lake (New Zealand) | Heterophrys myriopoda | 94.9 | 1 | 0 | 0 | 1 | |
| V33 | Alveolata | Dinophyceae | Gymnodinium eucyaneum | JQ639760 | 99.8 | 1 | 1 | 0 | 0 | |||
| B131 | Gyrodinium spirale | AB120001 | 99.7 | 8 | 0 | 0 | 8 | |||||
| B49 | Uncult. eukaryote clone M1_18B06 | DQ103837 | 99.5 | The anoxic Mariager Fjord (Denmark) | Peridinium umbonatum | 93.4 | 5 | 0 | 0 | 5 | ||
| B115 | Uncult eukaryote clone SA1_4B9 | EF527151 | 99.4 | The anoxic Framvaren Fjord (Norway) | Euduboscquella sp. | 96.2 | 1 | 0 | 0 | 1 | ||
| V98 | Ciliophora | Uncult. eukaryote clone VNP11 | DQ409125 | 99.4 | Lacustrine reservoir, hyper-eutrophic (France) | Strobilidium caudatum | 90.1 | 2 | 2 | 0 | 0 | |
| V84 | Uncult. alveolate clone 1-D5 | FN689891 | 99.8 | Gulf of Finland (Finland) | Tintinnidium sp. 1 | 90.5 | 1 | 1 | 0 | 0 | ||
| V85 | Uncult. ciliate clone AY2009D10 | HQ219435 | 100 | Lake Aydat, eutrophic (France) | Strobilidium caudatum | 90 | 1 | 1 | 0 | 0 | ||
| V61 | Uncult. eukaryote clone VNP38 | DQ409135 | 100 | Lacustrine reservoir, hyper-eutrophic (France) | Pseudochilodonopsis fluviatilis | 93.2 | 2 | 2 | 0 | 0 | ||
| B116 | Tintinnopsis rapa (isolate 241) | JN831834 | 99.4 | 2 | 0 | 0 | 2 | |||||
| V127 | Chlorophyta | Chlorophyceae | Chlamydomonas noctigama | JN903979 | 99.7 | 2 | 2 | 0 | 0 | |||
| V102 | Uncult. eukaryote clone KRL01E11 | JN090871 | 100 | Lake Karla (Greece) | Chlamydomonas kuwadae | 99.4 | 7 | 5 | 1 | 1 | ||
| V140 | Neochlorosarcina negevensis | AB218715 | 99.1 | 1 | 1 | 0 | 0 | |||||
| V146 | Mychonastes huancayensi/M. jurisii | GQ477050/GQ477038 | 99.9 | 2 | 2 | 0 | 0 | |||||
| V131 | Atractomorpha echinata | AF302772 | 100 | 1 | 1 | 0 | 0 | |||||
| Es74 | Prasinophyceae | Nephroselmis olivacea | X74754 | 98,1 | 1 | 0 | 1 | 0 | ||||
| B125 | Uncult Crustomastix, clone PROSOPE.CM-5m. | EU143398 | 96.9 | Mediterranean Sea | Crustomastix stigmatica (pras1) | 94.6 | 1 | 0 | 0 | 1 | ||
| B129 | Micromonas pusilla strain | AY955010 | 99.7 | 1 | 0 | 0 | 1 | |||||
| V05 | Fungi | Chytridiomycota | Uncult. eukaryote clone B86-172 | EF196796 | 98.2 | Freshwater, Alpen (France) | Spizellomyces pseudodichotomus | 94.4 | 1 | 1 | 0 | 0 |
| Es32 | Uncult. Chytridiomycota clone PFD5SP2005 | EU162640 | 99.6 | Lake Pavin, oligomesotrophic (France) | Kappamyces laurelensi | 94.8 | 9 | 7 | 2 | 0 | ||
| V31 | Environmental clade LKM | Uncult. eukaryote clone E-C4_1 | HM628660 | 99.7 | Slow sand filter biofilm | Mortierella microzygospora | 87.1 | 2 | 2 | 0 | 0 | |
| V136 | Unknown lineage | Uncult. fungus clone C10 | JN054676 | 100 | Wastewater treatment plant | Rhizophlyctis rosea | 87.5 | 1 | 1 | 0 | 0 | |
| B64 | Cercozoa | Phytomyxea | Uncult. eukaryote clone TAGIRI-5 | AB191413 | 96.3 | Anoxic marine sediment (Japan) | Phagomyxa bellerocheae | 87.8 | 1 | 0 | 0 | 1 |
| B65 | Filosoa | Uncult. eukaryote clone 9_149 | EU545751 | 99.8 | Marine sediment, East Sea | Botuliforma benthica | 95,4 | 1 | 0 | 0 | 1 | |
| B87 | Uncult. eukaryote clone 9_25 | EU087251 | 100 | Marine sediment, East Sea | Protaspis oviformis | 98,8 | 3 | 0 | 0 | 3 | ||
| B144 | Thaumatomastix sp. | GQ144681 | 100 | Boundary Bay (Canada) | Thaumatomonas coloniensi | 94.4 | 1 | 0 | 0 | 1 | ||
A representative clone for each OTU and its phylogenetic affiliation are provided. Highest BLAST match and closest cultured organisms from GenBank are given with accession numbers and percentage similarity. The remaining columns indicate the distribution and the number of clones found in each clone library (VIRE River, ESTUARY, and BAY).