picoeukaryotes (< 3 µm) diversity coastal site of the english channel khadidja romari &...
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Picoeukaryotes (< 3 µm) diversity
coastal site of the English Channel
Khadidja Romari & Daniel Vaulot
PICODIV meeting
Oslo - March 2003
Roscoff
Station: Astan Year 2000April June
SeptemberDecember
Year 2001AprilMayJune
Year 2001May
Sampling strategy
RFLP Analysis of environmental clone libraries
Rarefaction curves
0
10
20
30
40
50
60
70
0 20 40 60 80 100
Number of clones
Cum
ulat
ive
RFLP
- t
ype
Num
ber
June 2001
Sept.2001
Dourd. May 2001May 2001
Apri. 2000
Apri. 2001
Dec. 2000
June 2000
Clone library
Astan
Dourduff
Date
12 April 2000 65 35
9 June 2000 54 46
7 Sept 2000 68 32
19 Dec 2000 60 40
12 April 2001 54 46
16 May 2001 65 35
13 June 2001 41 59
# of RFLP types Coverage value (%)
17 May 2001 52 48
* 100 positives clones were screened by RFLP for each clone library* Coverage value (C) = 1- n/N, (n = number of RFLP type; N = number of clone analysed)
RFLP-Analysis of environmental clone libraries
Clones 99.5 %sequence simil.
OTU OTU
OTU with similarity 98 %
Phylotype
OTU
OTU : Operational taxonomic unit
Phylotype : Genus/species levelOTU: Ecotype level
Groups # phylotypes # OTUs
Prasinophyceae 9 28 Cryptophyceae 6 22 Prymnesiophyceae 3 6 Dinophyceae 7 11 Cercozoa 19 25 Choanoflagellates 5 6 Stramenopiles 26 40 Alveolate group I 4 7 Alveolate group II 25 42 Ciliates 23 38 Rosko II 6 12 Rosko I (Telonema ) 4 8
Total 137 245
Diversity inside the groups
• OTUs : Clones with similarity 98% and < 99,5 %• Phylotypes : OTUs with similarity < 98 %
• Phylotype level: Heterotrophs are more diverse than phototrophs
Groups # Phylotypes
Heterotrophs 108
Phototrophs 21
# OTUs
164
83
Diversity : Phototrophs vs heterotrophs
• OTU level: Phototrophs are relatively more diverse than heterotrophs
Photosynthetic groups
• Prasinophyceae•Micromonas, Bathycoccus, Ostreococcus also Pyramimonas, CCMP 1205
• Cryptophyceae (nucleus and nucleomorph)
•Geminigera
• Prymnesiophyceae•uncultivated group, Chrysochromulina
• Dinophyceae•Gymnodinium, Prorocentrum, Dinophysis
Ostreococcus
Non photosynthetic groups• Stramenopiles
•all clades defined by Ramon plus a new one•Cafeteria
• Uncultivated alveolates•mostly group II (Amoebophrya)
• Ciliates•no strong identity with known species
• Cercozoa•Cryothecomonas, Cercomonas
Picture from S. Kuhn
Cryothecomonas
• Choanoflagellates•no strong identity with known species
• Telonema
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
april 00 june 00 sept 00 dec 00 april 01 may 01 june 01 may 01(Dourduff)
# O
TU
s
Prasinophyceae Cryptophyceae Prymnesiophyceae Dinophyceae Choanoflagellates
Stramenopiles Cercozoa Alveolate group II Alveolate group I Perkinsozoa
Ciliates Rosko I (Telonema) Rosko II
Temporal and spatial variability
Astan StationSporadic phylotypes (appearing only
once)observed
Apr-00 Jun-00 Sep-00 Dec-00 Apr-01 May-01 Jun-01 Total % of all phylotypes
Prasinophyceae 8 1 1 2 25%
Cryptophyta (includes nucleomorph) 6 1 1 17%
Haptophyta 3 1 1 2 67%
Cercozoa 18 2 3 7 2 2 16 89%
Choanoflagellates 4 1 2 3 75%
Stramenopiles 26 5 3 2 1 1 5 17 65%
Perkinsozoa 1 1 1
Dinophyceae 7 4 1 5 71%
Alveolate group I 4 1 1 2 50%
Alveolate group II 25 4 1 3 4 2 6 20 80%
Ciliates 14 1 2 2 1 6 43%
Rosko I 6 2 2 4 67%
Rosko II 4 1 1 1 3 75%
Fungi 1 1 1
RA000609.30 1 1 1
Total number of phylotypes observed only once 14 14 9 11 12 6 18 84 66%
Total number of phylotypes 128 44 31 28 26 29 27 30
% of phylotypes observed once 32% 45% 32% 42% 41% 22% 60%
Conclusions• High diversity (not fully covered by clone
sampling)• Confirm ubiquity of novel alveolates and
stramenopiles• Specificity of coastal areas (temperate ?)
•Mamiellales•Cryptophyceae•Ciliates•Cercozoa•Two novel groups ?
• Diatom bloom library has unique features• low diversity•mostly sporadic phylotypes
• Estuarine library very different from Astan library•dominated by Ciliates•some groups absent (Cryptophyceae)
Acknowledgements
PICODIV
CNRS-Aventis Foundation
BIOSOPE (funded by CNRS)
PICOMANCHE(Brittany region program)
The Mysis crew
Fabrice Not(Collecting samples)