Article Figures & Data
Figures
- Fig. 1.
DGGE gel separating eukaryotic 18S rDNA fragments from the populations retained on prefilters and from the populations appearing in filtrates from the five samples used to generate genetic libraries. The filtrate samples analyzed by using genetic libraries are circled.
- Fig. 2.
Numbers of bands that were unique to the filtrates, that were shared, and that were unique to the prefilters for the five samples used to generate genetic libraries after quantitative analysis of the DGGE gel shown in Fig. 1. The values above the bars for unique bands are the percentages of band intensity accounted for by these bands in the DGGE profile.
- Fig. 3.
Phylogenetic tree for partial sequences of environmental clones and the most closely related cultured organisms. Environmental clones are indicated by boldface type and each clone is designated by the library designation followed by a number. One clone representing each different OTU detected by the RFLP analysis of the five genetic libraries is included. The bar indicates 10% estimated sequence divergence. The number of clones in each genetic library belonging to each phylogenetic group is indicated on the right.
Tables
- Table 1.
Characteristics of the samples used to generate the five libraries of eukaryotic 18S rRNA genes
Library System Characteristics Coordinates Date (day/mo/yr) Temp (°C) Fraction analyzed (μm) Chl a concn (μg liter−1) Total In fraction ME-1 Mediterranean (Alborán Sea) Upwelling 36°14′N, 4°15′W 9/11/97 18.0 0.2–5 0.87 0.72 ANT37 Antarctica (Weddell Sea) Ice edge 60°32′S, 44°12′W 26/1/98 −1.8 0.2–1.6 0.35 0.01 ANT12 Antarctica (Scotia Sea) Open ocean 58°16′S, 44°27′W 23/1/98 1.9 0.2–1.6 0.29 0.02 NA11 North Atlantic Within eddy 59°30′N, 21°8′W 14/6/98 11.2 0.2–2 0.87 0.22 NA37 North Atlantic Outside eddy 59°34′N, 21°3′W 21/6/98 10.5 0.2–2 0.59 0.19 - Table 2.
Concentrations of heterotrophic and phototrophic picoeukaryotes, Prochlorococcus and Synechococcusin whole water and in the fractions passing through the prefilters for the samples used to generate eukaryotic genetic libraries
Library Sample Concn (103 cells ml−1) ofa: Picoeukaryotes Prochlorococcus Synechococcus Heterotrophic Phototrophic P1 P2 P3 ME1 Whole water 1.5 13.9 12.7 12.9 <5-μm fraction NDb 14.1 14.8 12.7 ANT37 Whole water 0.4 9.9 2.5 5.2 2.2 0 0 <1.6-μm fraction ND 0.5 0.4 0.1 0 0 0 ANT12 Whole water 0.7 3.2 1.3 1.5 0.4 0 0 <1.6-μm fraction ND 1.0 0.8 0.2 0.0 0 0 NA11 Whole water ND 6.6 4.8 1.8 0 4.6 <2-μm fraction ND 6.6 4.6 2.0 0 2.6 NA37 Whole water ND 3.2 0 7.3 <2-μm fraction ND 4.6 0 6.8 ↵a Heterotrophic picoeukaryotes were counted by the epifluorescence method, and phototrophic picoplankton (both eukaryotic and prokaryotic) were counted by the flow cytometry method. P1, P2, and P3 are distinct phototrophic picoeukaryote populations (P1 cells are smaller than P3 cells).
↵b ND, not determined.
- Table 3.
Results of RFLP analysis of the five genetic libraries
Library No. of clones No. of OTUs Coverage (%) No. of OTUs unique to library No. of OTUs found in libraries from the same system No. of OTUs found in libraries from different systems ME1 63 28 81 17 NAa 11 ANT37 58 29 66 20 4 5 ANT12 67 23 82 8 4 11 NA11 17 12 47 7 1 4 NA37 20 10 75 5 1 4 ↵a NA, not applicable.
- Table 4.
Number of clones belonging to each OTU in genetic libraries and phylogenetic affiliations of the representative clones sequenced
Taxon OTU No. of clones in libraries Clone Closest relative (% similarity) ME1 ANT37 ANT12 NA11 NA37 Prasinophytes 1 6 ME1-1 Ostreococcus tauri (98.1) 2 8 16 5 ME1-2 Mantoniella squamata (96.8) 3 2 1 3 ME1-3 Ostreococcus tauri (94.1) 4 1 ANT37-3 Mantoniella squamata (99.9) 5 1 ANT37-4 Mantoniella squamata (96.1) 6 1 NA11-1 Micromonas pusilla (99.0) 7 2 NA37-1 Micromonas pusilla (99.1) Prymnesiophytes 8 1 2 ME1-4 Prymnesium patelliferum (94.3) 9 5 16 1 ANT37-5 Phaeocystis antarctica (99.8) 10 1 ANT12-2 Phaeocystis antarctica (97.6) 11 1 NA11-2 Emiliania huxleyi (96.0) 12 1 NA11-7 Emiliania huxleyi (95.6) Diatoms 13 3 1 ME1-14 Papiliocellulus elegans (95.5) 14 1 ME1-15 Chaetoceros rostratus (96.7) 15 2 1 ME1-16 Skeletonema costatum (96.8) 16 1 ANT37-10 Corethron criophilum (95.9) 17 5 ANT37-11 Corethron criophilum (89.0) 18 1 ANT37-12 Corethron criophilum (95.3) 19 2 ANT37-9 Chaetocerossp. (86.7) 20 1 ANT12-3 Pseudonitzschia multiseries (98.6) Dinophytes 21 1 ME1-8 Lepidodinium viride (76.0) 22 2 1 3 6 ANT37-6 Gymnodinium mikimotoi (96.7) 23 1 ANT37-8 Lepidodinium viride (98.5) Pelagophytes 24 1 6 ME1-27 Pelagomonas calceolata (100) Glaucocystophytes 25 1 ANT12-4 Cyanophora paradoxa (84.9) 26 2 ANT37-26 Cyanophora paradoxa (80.0) 27 1 ANT37-27 Cyanophora paradoxa (85.8) Dictyochales 28 1 ANT37-15 Dictyocha speculum (90.3) 29 1 NA11-6 Dictyocha speculum (91.0) 30 1 NA37-4 Dictyocha speculum (91.5) Cryptophytes 31 3 ME1-5 Geminigera cryophila (98.5) Eustigmatophytes 32 2 ME1-25 Nannochloropsissp. (89.0) Bolidophytes 33 1 ANT37-30 Bolidomonas pacifica (94.6) Novel stramenopiles 34 1 ME1-17 Hyphochytrium catenoides (90.8) 35 3 ME1-18 Hyphochytrium catenoides (87.6) 36 2 ME1-19 Hyphochytrium catenoides (87.8) 37 2 ME1-20 Hyphochytrium catenoides (88.3) 38 1 ME1-21 Hyphochytrium catenoides (90.9) 39 1 ME1-22 Hyphochytrium catenoides (90.3) 40 1 5 ANT12-6 Hyphochytrium catenoides (89.2) 41 6 ANT12-7 Hyphochytrium catenoides (88.8) 42 1 5 ANT12-24 Hyphochytrium catenoides (89.4) 43 1 ANT12-9 Hyphochytrium catenoides (88.5) 44 2 2 ANT12-10 Hyphochytrium catenoides (88.0) 45 1 1 ANT12-11 Hyphochytrium catenoides (93.7) 46 1 ANT37-19 Hyphochytrium catenoides (90.0) 47 1 ANT37-20 Hyphochytrium catenoides (85.5) 48 1 ANT37-21 Hyphochytrium catenoides (92.9) 48 1 ANT37-22 Hyphochytrium catenoides (85.4) 50 1 ANT37-23 Hyphochytrium catenoides (90.3) 51 1 NA11-4 Hyphochytrium catenoides (86.4) 52 3 1 NA11-5 Hyphochytrium catenoides (87.7) 53 2 ANT37-13 Hyphochytrium catenoides (87.7) 54 1 ANT37-16 Hyphochytrium catenoides (87.5) 55 2 1 ME1-24 Hyphochytrium catenoides (90.2) 56 1 ANT12-8 Hyphochytrium catenoides (88.9) 57 1 ANT12-5 Hyphochytrium catenoides (87.4) Novel alveolates 58 6 1 3 ME1-6 Pentapharsodinium tyrrhenicum (87.2) 59 2 ME1-7 Heterocapsa triquetra (87.8) 60 1 ME1-9 Heterocapsa triquetra (89.3) 61 3 ME1-10 Heterocapsa triquetra (85.8) 62 2 NA37-2 Gymnodinium catenatum (89.2) 63 1 NA37-3 Lepidodinium viride (89.3) Ciliates 64 2 1 1 ME1-11 Strombidium purpureum (93.3) 65 1 ME1-12 Oxytricha granulifera (92.2) 66 1 2 ME1-13 Oxytricha granulifera (87.5) 67 1 ME1-31 Oxytricha granulifera (91.3) 68 1 NA11-3 Oxytricha granulifera (88.1) 69 1 ANT37-24 Oxytricha granulifera (93.5) Chrysophytes 70 3 2 ME1-23 Paraphysomonas foraminifera (98.7) 71 1 NA11-11 Paraphysomonas foraminifera (95.3) Cercomonads 72 1 ME1-26 Heteromita globosa (88.1) 73 1 ANT12-14 Thaumatomonassp. (82.9) 74 1 ANT37-28 Thaumatomonassp. (89.6) 75 2 NA37-5 Cercomonasstrain ATCC 50318 (83.0) Fungi 76 2 3 ANT12-13 Stenocybe pullatula (80.0) Metazoans 77 36 Oikopleurasp. (99.2) 78 43 Cancrincola plumipes (94.0)
