Scientific Background Synechococcus pigment types

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1 Scientific Background Synechococcus pigment types Oligotrophic Mesotrophic Coastal 0 m Nutrients 50 m 100 m 150 m

Scientific Background Synechococcus Genomes BL107 CA RS9917 Clade I

VII Clade X HL H L L LL 1300 1200 1100 1000 900 800 700 600 500 400 300

cladespecific genes RS9917 WH7805 MED4 Strain-specific genes MED4 SS120

2 Scientific Background Synechococcus Genomes BL107 CA RS9917 Clade I Clade II Clade III Clade IV Clade VIII Clade IX Clade V Clade VI Clade VII Clade X HL H L L LL Core genome Main Title Genus- / cladespecific genes RS9917 WH7805 MED4 Strain-specific genes MED4 SS120 MIT9313 WH7803 WH7805 CC9902 CC9605 CC9311 WH8102 RS9917 RS9916 RCC307 WH5701

3 BOUM Cruise Main Objectives 1) Study the physiological response of Prochlorococcus cells to various environmental factors and its consequences on the distribution of these organisms 2) Determine the impact of Synechococcus pigmentation on the distribution of this organism 3) Identify the set of genes that allow specific lineages to occupy distinct niches in the water column 4) Correlate these informations to better understand the community structure of these organisms and the relationship with their phylogeny.

4 BOUM Cruise PE PEII 2 cg ec ee pespetper aplacp unk5 cp mped cpunk6 mpee unk1unk3 c cc unk4 2 FISH Cultures BL107 CC9605 WH8102 RS9916 WH /100/100 WH /88/66 CC9311 Diversity Diversity markers (DNA) PC U pe m BA pe pe mpeym m ev p unk10 m ba bb cb ca pe pe rp rprpct unk12 rpcs A B ey ez cp pe pe cp unk11 c c ba bb cb A rpcspe pe rp rpcrpct rpce rpcf unk12 ev p unk10 m ey cp unk11 ez ee ea eb cp mp cp cp PEIIsubunit PEIsubunit 2 PCsubunit ev ba bb cb ca p cg ec ee pes etper rpcspe pe rp rprpce c cp c unk10 m unk12 rpcf unk1cpct PEassociatedlinker unk4 cp unk5 cp cped cpunk6 PCassociatedlinker WH780 Rod-corelinker Z A B PEgeneregulation ey e e e 5 unk2 cp unk11 cp cp cp Phycobilin lyase (or homolog) Bilin synthesis Phosphatase cpcs cpcg1 unk1 cpct cpcg2cpcc cpcd cpcb cpca cpcccpcb cpca cpce cpcf Conservedhypothetical RS9917 Hypothetical unk9 unk8+7 WH5701 unk2 ITS2 ITS1 16S PE ba bb cb ca rpcspe pe rp rp rpct unk12 WH7803 unk2 Pigment markers ITS BA C pe pe pe ee pes pet er RS9916 mpezmpefmpee unk1unk3unk4aplacpcgunk5 cpec mped cpunk6 c c cp mpey m m m RCC307 BL107 CC9902 CC9311 unk2 unk7 unk8 unk9 2 cg ec ee pespetper c cc unk1unk4 apla cp unk5cp mped cpunk6 unk10 ez ey ea eb cp cp unk11 cp cp unk9 unk7 unk8 unk2 CC9902 PEI BA C U pe pe pe pe mpey m m m m ce rp cf WH8102 CC9605 rp Methodology 5S 23S RS9917 WH5701 RCC307 Gloeobacter P hos phate Molybdate 1533, ? Cation trans porterdi-,tri-dic arboxylate 0097 A T P as e , 1577 Gly cine 0095 Xy lulose -5-P Alanine Leucine Valine 1362, 0766 D -Sedoheptulose -7-P 0890? Chlorophy llidea2 5-Phosphoribosy l diphosphate Histidine Purines, Py rimidines Ribof lav in, FAD, Folate cis-aconitate Nicotinamide N icotinam ide mononucleotide m ononucleotide Malate 1620 Fe ? Fe2+ or Mn2+ NRAMP-type 1203 TCA Cycle Cobalamine C obalam ine Fumarate NAD N AD Succinate Zn2+ or Mn Chl b Chl Cycle Chlide b Citrate Oxaloacetate Pcb PsaJF Flvd PsaE PsaC PsaB FeS PsaD PsaA Isocitrate 1752 Oxalosuccinate Protopor phy rin IX ATP Synthase NADH N AD H d eh yd ro g en ase dehydrogenase D1 D2 Cyt b Cyt C yt b6/f Pcb Cyt b559 D1 D2 Mg-Protoporphy rin IX PS I Cyt f SIV F es Cytb6 FNR PQ/PQH2 Mg-2,4-div iny l phaeoporphy rin a5monomethy lester Mg-Protoporphy rin IX monomethy lester Plas to Plasto cyanin c yanin PsaLIKM Heme 1866 H+ Cytochrome C yto ch ro me o xid ase oxidase Chl a Ribose-5-P DV-Protochlorophy llide L-Aspartate Oligopeptides Py ruv ate Acety l-coa Spermidine/Putrescine 0881 K+ Kef-type 1227 Chl b CO Na+/bicarbonate, Na+/bic arbonate, SbtA 0241 Glucose-6-P D-Erythrose-4-P 0855, 0856 D-Sedoheptulose-1,7-PP D -Sedoheptulose-1,7-PP 1770 Asparagine Threonine Methionine Leucine Isoleucine SO , 0804 Polar amino acids Calvin Cycle D-Ribulose Phosphoenolpy ruv ate-5-p PAPS 0190 APS , D-Ribulose-1,5-PP 2-P-Gly cerate ATP ADP O-acety lserine Dihy droxy acetone-p F Fructoseructose1,6-PP , 0856 Fructose-6-P F ructose-6-p P-Gly cerate CO2 Serine 0143 SO 3 2- Try ptophane Ty rosine Pheny lalanine 0505,1157, Cy steine H 2S D eoxy -D -ribose 2-Deoxy -D-ribose-5-P Gly ceral1,3-pp-gly ceratedehy de-3-p Cobalt 0389,10 26? F es CP43 Real time PCR PsbO CP47 CP47 PsbO PS II dimer d imer CP43 P cb 2 Oxoglutarate 1668 Arginine Proline L-Glutamate Na+/galac tos idena+/alanine Na+/galactoside 1625 Na+/proline 0784 Na+/glutamate L-Glutamine NH Cl Na+/H+ K+/H Ca2+/Na+ Genomics Cell sorting Whole genome amplification 454 sequencing Physiology Physiological markers (RNA) UV stress (reca) Cell cycle (ftsz) Phosphate limitation Temperature Oxygen evolution PAM fluorimetry

L/depth) Cycle experiments (A, A, B, C, 72 h) 3 CTD/day QPCR DNA (6 depths, 2L/depth) QPCR RNA (6 depths, 12L/depth) Flow

5 BOUM Cruise Sampling 24 stations Short Stations QPCR DNA (6 depths, 2L/depth) FISH (6 depths, 150 ml/depth) 6 stations Cultures (2 depths, 500 ml/depth) 3 stations Env Genomic (1 depths, 3 L/depth) 2 stations (B, C) Long Stations Env Genomic (1 depths, 3 L/depth) Cycle experiments (A, A, B, C, 72 h) 3 CTD/day QPCR DNA (6 depths, 2L/depth) QPCR RNA (6 depths, 12L/depth) Flow cytometry (12 depth, 5 ml/depth) Surface QPCR DNA (2L every 2-3 h) QPCR RNA (12 L every 2-3 h) Flow cytometry (12 depth, 5 ml/depth)

Aménagements intérieurs : revêtement de sol 575 255 87 233 Plaques

7 Aménagements intérieurs : revêtement de sol Plaques quadrillées en plastique, épaisses et amovibles

Objectif/Methodology BOUM Cruise Physiological status of

Experiments (Light, nutrient, temp, etc) Microarray Real

optimisation Elaboration of sequence data base Design of

8 Objectif/Methodology BOUM Cruise Physiological status of Prochlorococcus Prochlorococcus Genome Comparison Stress Experiments (Light, nutrient, temp, etc) Microarray Real time PCR Identification of potentiel markers and optimisation Elaboration of sequence data base Design of specific primers Check for specificity QPCR Optimisation Application to natural samples

Methodology Synechococcus Functional diversity Physiological status Pigment type/its Genomic UV stress (reca) Cell cycle (ftsz) Phosphate limitation Temperature Oxygen evolution Real time PCR Design

9 Methodology Synechococcus Functional diversity Physiological status Pigment type/its Genomic UV stress (reca) Cell cycle (ftsz) Phosphate limitation Temperature Oxygen evolution Real time PCR Design specific primers Optimisation of RT-PCR conditions Flow cytometry cell sorting Whole genome amplification 454 Sequencing Additional sample Culture FISH PAM sepctrofluorimetry Synechococcus Functionnal Diversity

10 Objectives for the BOUM Cruise Effets des facteurs environnementaux Understand repartition en clades des syn Parametres influencant la repartition des differents clades L effet de la pigmentation sur la repartition de ces organismes 1: Study the physiological status of Prochlorococcus cell using molecular markers: UV stress (reca) Cell cycle (ftsz) Phosphate Limitation Temperature Oxygen evolution 2: Study the Functional Diversity of Marine Synechococcus using : Pigment content ITS Genomic approach

11 Thématique 3: Diversité fonctionnelle des cyanobactéries marines et acclimatation aux facteurs environnementaux Simulation des conditions environnementales IN flux set up Fresh culture medium Peristaltic pump Rapid clip Filtration cartwridge 0.2 µm UVA, UVB Automatic sampling (Cell cycle, growth rate) Waste Culture Manual sampling (ARN)

MODEL 1. provides additional information about the performance of the CeSS algorithm.

MODEL 1. provides additional information about the performance of the CeSS algorithm. MODEL 1 Sections 1 to 4 describe Model 1, a metabolic model of E. coli s Central Carbon Metabolism. Section 5 provides additional information about the performance of the CeSS algorithm. 1 Model structure: