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TABLE 1 Oligonucleotide primers and probes used in dot blots and DGGE analysis
PCR Primers Specific target DNA Sequence 5´-3´
OXY107F* Oxygenic phototroph biased GGA CGG GTG AGT AAC GC G TG R
Prochlorococcus dot blot data : Coastal Chile (20.4°S, 70.6°W) low oxygen environment
Sept chlorophyll field for Arabian Sea(SeaWiFS)
March chlorophyll field for Arabian Sea(SeaWiFS)
• oligotophy/eutrophy gradient of surface waters along the transect• oxygen-depleted (ca 2-10 µM O2) waters that occur at depths from ca 200 - 2500 metres throughout the basin. • divergent driven, gentle but continual upwelling of the Equator and adjacent downwelling waters
Indian Ocean - Arabian Sea - cruise Sept 2001
Marine Synechococcus strains: Roscoff
Strain Origin Isolator Location PUB:PEB
Minos 1
Minos 2
Minos 11
Minos 12
Max 42
Almo 3
Eum 14
Oli 31
Mediterranean Sea
Mediterranean Sea
Mediterranean Sea
Mediterranean Sea
Sargasso Sea
Alboran Sea
Tropical Atlantic
Equatorial Pacific
F. Partensky
F. Partensky
F. Partensky
F. Partensky
D. Vaulot
D. Vaulot
D. Vaulot
D. Vaulot
39°10’N 6 °10’E
39°10’N 6 °10’E
34°0’N 18 °10’E
34°0’N 18 °10’E
26°18’N 63°26’W
36°11’N 1°51’W
21°02’N 31°0’W
5°N 150° 0°W
PEB>PUB
PEB>PUB
PEB>PUB
PEB>PUB
PEB<PUB
PEB<PUB
PEB<PUB
PEB<PUB
Analysis of Synechococcus strains III : Red Sea
Strain Date of Depth of Colour PUB/PEB Motility N source ntcA RFLP 16S sequenceisolation isolation ratio type
RS9901 29.3.99 0 m Red 0.7 - NO3-/NH4
+ I +RS9902 29.3.99 0 m Orange 1.4 - NO3
-/NH4+ II +
RS9903 11.5.99 10 m Orange 2.0 - NO3-/NH4
+ III +RS9904 14.6.99 10 m Orange 1.5 - NO3
-/NH4+ III +
RS9905 18.7.99 10 m Orange/Red 1.0 - (+) NO3-/NH4
+ IV +RS9906 23.8.99 10 m Green - - NO3
-/NH4+ N/A +
RS9907 23.8.99 10 m Red 0.5 - NO3-/NH4
+ II +RS9908 7.9.99 10 m Red 0.5 - NO3
-/NH4+ II +
RS9909 7.9.99 10 m Green - - NO3-/NH4
+ N/A +RS9910 7.9.99 10 m Red 0.5 - NO3
-/NH4+ II +
RS9911 11.5.99 10 m Red 0.8 - NH4+ V +
RS9912 23.8.99 10 m Red 0.5 - NH4+ N/A +
RS9913 7.9.99 10 m Green - - NH4+ N/A +
RS9914 18.10.99 10 m Green - - NH4+ N/A +
RS9915 18.10.99 10 m Red 0.8 - NH4+ IV +
RS9916 22.11.99 10 m Red 0.7 - NH4+ I +
RS9917 22.11.99 10 m Green - - NH4+ N/A +
RS9918 22.11.99 10 m Green - - NH4+ N/A +
RS9919 22.11.99 50 m Orange NO3- V -
RS9920 22.11.99 150 m Orange NO3- VI -
Synechococcus genes being used for multi-locus sequence typing and community structure analysis
Gene Encoding
rpoC1 DNA-dependent polymerase
petB/D fragments b-type cytochrome & subunit of the photosynthetic
& intergenic region cytochrome b6/f complex, respectively
rnpB ribonucleoprotein enzyme (RNase P)
pstS periplasmic phosphate-binding protein
16S rDNA small subunit rRNA
ntcA global N transcriptional regulator
16S rRNA
petB-D
rpoC1 pstS
Distinguishing alleles
petBD intergenic region - sequence length
rpoC1 pstS 5% divergence
16S rDNA 1% divergence
12C14C
12C
14C
14C labelling of DNA : growth of Prochlorococcus NATL1-MIT on 14C NaHCO3
55,000 x g o/n40,000 x g o/n
Environmental DNA received from partners :
ROSCOFF BLANES HELGOLAND
Name DNA amplifiable
RA000404 x x
RA000609 faint
RA000709 faint x
RA001006
Name DNA amplifiable
BL000921
BL001221
Name DNA amplifiable
HE000803
HE001005
HE001206 x x
Full length clone libraries generated : pA (8-28) pHr (1542-1522)
Site Primers Identifier
HE000803 pA/pHr He(H) 25/02/01
Mio (Prosope cruise) pA/pHr Mio(M) 25/02/01
Dyf (Prosope cruise) pA/pHr Dyf (D) 25/02/01
Prosope cruise track
Sample Name DYF MIO Helgoland
Number of clones 70 70 75
% Containing Insert 95.7 98.6 98.6
% Amplified with Primer couple 359F/1313R 72.9 72.9 61.3 (oxygenic-phototroph specific)
% Amplified with Primer couple 359F/1038R 14.3 22.9 9.3(1038r amplifies all marine Syns& Pros, ACE/PS680 cluster, PCC9005 = marine cyano-specific)
Analysis of full length environmental clone libraries
Sequence analysis of Cyanobacterial/plastid sequences from full length clone libraries