Prochlorococcus (a model marine microbe)

Transcription

1 chlorococcus (a model marine microbe) 0.5μm Features of a Model Organism for Microbial Oceanography Widespread Abundant Predictable Simple Culture collection Amenable to study in the field Genomic Database Genetic System chlorococcus Divinyl Chl a Divinyl Chl b chlorococcus: the minimal phototroph Discovered in 1985 karyotic Cyanobacterium Divinyl chlorophylls a and b Most abundant oxygenic phototroph 0.6 microns wavelength [nm] Light CO N,P,S,Fe, Co etc. (only inorganic compounds) 1700 genes LIFE (that dominates the oceans) Cascade of Scales chlorococcus Ranges of reported values: Percent of total chlorophyll 670% 558% 58% 67% 57% Record concentration: 700,000 cells ml 1 Global Abundance: 10 5 cells 5 Gt C yr 1 SeaWiFS ject, NASA 1

2 Unique properties of photosynthesis Photosynthetic apparatus comprised of Chl a, Chl b1, b and phycobiliproteins Photosynthesis occurs over orders of magnitude of light High photosynthetic yield Red shifted (~10nm) Chl a & b Higher probability of absorbing than scattering light due to small size Photosynthetic antenna architecture Laser Flow Cytometry Cells Forward light scatter detector Pigment fluorescence detector DNA per cell Chlorophyll (Red) Fluorescence Pennates Nano Ultra Syn Forward Angle Light Scatter (Size) K. Bares chlorococcus Biomass 10 8 cholorococcus and Synechococcus integrated abundance at BATS chlorococcus Cells mm Synechococcus Partensky et al Sep89 Sep90 Sep91 Sep9 Sep9 Sep9 DuRand et al 001 DSR 8:198

3 red fluorescence chlorococcus highlight/lowlight populations 5m 75m 15m red fluorescence red fluorescence forward scatter forward scatter forward scatter chlorococcus spp. strain diversity Photophysiological differences among high and low light ecotypes 5 psba (108bp) NJ MIT90 MIT91 MIT901 MIT91 MIT90 MIT911 High Light Low Light a* (m (mg Chl a) 1 ) g C g Chl a 1 hr Irradiance (μmol quanta m sec 1 ) Chl b / a (g/g) growth rate (d 1 ) Growth Irradiance (μmol quanta m sec 1 ) Wavelength (nm) Growth Irradiance (μmol quanta m sec 1 ) After Moore and Chisholm, 1999 chlorococcus spp. strain diversity of N utilization psba (108bp) NJ N utilization key: MIT90 NH MIT91 NH MIT901, NO MIT91 NH, NO, NO MIT90 MIT911 after Moore et al 00 Cells mm and Syn abundance in N. Atlantic (Integrated abundance) chlorococcus Synechococcus Sep89 Sep90 Sep91 Sep9 Sep9 Sep9 Winter Deep Mixing High NO Spring Bloom of Syn DuRand et al 001 DSR 8:198

4 Question chlorococcus genetic diversity clusters into clades What are the important other niche dimensions?.let the cells tell us MIT90 MIT91 MIT901 MIT91 MIT90 e e e e e MIT911 emit911 psba (108bp) NJ N1 o N5 o N8 o 0 0 Red Fls o C e 50 e e 50 depth (m) 100 e depth (m) 100 Total e1 1e 1e5 1e1 1e 1e5 1e1 1e 1e5 cells/ml cells/ml cells/ml after Johnson et al. 006 Integrated Total Abundance Clade Abundance cells/mm o C 1e7 1e6 1e5 1e 1e Σ chlorococcus e e e e emit911 o C S0 S0 EQ N0 N0 after Johnson et al. 006 after Johnson et al. 006

5 Question: What is the lower bound of Ecologically relevant Taxonomic Units (ETUs? Genomovars?) within a group of organisms? How many different ETUs exist at HOT? at BATS? in the oceans? chlorococcus genetic diversity psba (108bp) NJ MIT90 MIT91 MIT901 MIT91 MIT90 MIT911 chlorococcus genomics Genome Feature Length (bp) 1,657,990,10,87 GC content (%) tein Coding 88 8 tein coding genes with assigned function conserved hypothetical hypothetical Genes with orthologs: chlorococcus 15 chlorococcus 15 Synechococcus Genes without orthologue in: and 57 and 8 Transfer RNA 7 Ribosomal RNA operons 1 Other structures RNAs after Rocap et al. 00 Sequence alignment shows conservation, loss, gain, and extensive rearrangement (HL) Genome features reflect niche dimensions NH NO org P Temperature Upwelling Mixed Layer High Light Ecotype Alk phosphatase HLIP DNA Repair No nitrite reductase no nitrate reductase (LL) NO, PO Low Light Ecotype No Alk phosphatase Fewer HLIP LL adap.. Genes nitrite reductase no nitrate reductase 5

6 As we learn the function of more of the ecotype specific genes. Cell surface properties are likely important in selection (HL) (LL) 171 genes 5 genes 59 genes 15 genes 909 genes we will learn more about niche differentiation Analysis of genomes revealed many LPS insertions and deletions Comparison of Cultures with Fosmid from HOT reveals cell envelope insertions Gene Function lowaffinity P transporter out membrane porin highaddinity P i binding Gene Name pita,b phoe psts Syn uvrd cpeb cpea cpez mpex cpey cpet cpes ppec pucc xylb metk LL P i channel components Plimitationinducible porins phosphonate ABCtype transport psta,b,c som phnc,d,e LL phosphonate operon regulator phosphonate biodegradation phno phnfn,p Fosmid clone HF101F1 alkaline phosphatase 5 nucleotidase APaselike phoa usha deda exopolyphosphatase gppa Epimerases (cell envelope) Unknown function Potentially cell envelope Fosmid clone HF101D8 polyphosphate utilization (kinase) P i sensor kinase response regulator modulator of P i transduction potential transcriptional regulator P i starvationinducible ppk phor phob phou ptra phohlike Coleman et al. 006 P i starvationinducible psip1 after Moore et al. 005 Whole Genome Analysis: nitrogen utilization nira narb NO NO NH chlorococcus spp. strain diversity of N utilization nira Syn HY1 cysg ppk tet HY HY HY5 nira ppk moabhymoea moac CA tet cysg deletion G narbnapa HY1 cysg F deletion E moaa moba orfg urec B A D D A B urec E after Post et al. psba (108bp) NJ N utilization key: MIT90 NH MIT91 NH MIT901, NO MIT91 NH, NO, NO MIT90 MIT911 after Moore et al 00 6

7 What other environmental variables are important Cu More chlorococcus genomes Depth NH NO Light NO Temperature Upwelling Mixed Layer MIT90 MIT91 MIT901 MIT91 MIT90 MIT911 What genes are shared by all ecotypes in the chlorococcus cluster? Core of common genes How are the remaining genes distributed among ecotypes? Myoviridae chlorococcus Cyanophage Siphoviridae Podoviridae 100nm Sullivan et al 7

8 Cyanophage Genomes (JGI) Host Range Oxygenic Photosynthesis Core reaction Center teins Podovirus (6 kb) Host Specific HL D1 e D e NADPH Myovirus 1 (55 kb) different LL,, MIT911 PSII PSI Ferridoxin Myovirus (181 kb) different HL and LL,,, HLIP H O O Plastocyanin Sullivan et al 005 Photosynthetic Genes in Encoded Photosynthetic Genes = overlapping start / stop codons Podovirus = contiguous ORFs HLIP D1 Myovirus PC HLIPs Fd D1 1kb kb Myovirus HLIPs D1 D ~500 bp Cluster with chlorococcus Functional Widespread bable reciprocal evolutionary influence Other host genes 6.kb Lindell, Sullivan et al.8kb 8