Human The great divide: constreined sex (a.k.a. meiosis) 70% Drosophila70% genes in common
All this diversity only withdifferent alleles of the samegenes
Metagenome B +viriome Global GenomeThe shape of prokaryotic biodiversity Metagenome A+ viriome Pan-genome species A Species A core Pan-genome species B Species B core Species C core Metagenome C +viriome
Periodic-Selection (Atwood et al, 1951) The unit of selection: The clone? Giovannoni Nature 430: 515 (2004)
• How to reconcile PS with large pan- genomes?• Study the genes found in the accessory pool
Solar SalternEvapora. Carbonate Gypsum Halite Ratio Domain Domain Domain No Intermediate (Vi/Vo) 36-70 g/l 70-140 g/l 220-290 g/l >290 g/l life 140-220 g/l Diatoms Haloarchaea Cyanobacteria Haloquadratum Green Algae Sulphur Phototrophic Bacteria Artenia Salina walsbyi Dunaliella up to 70-95% of the population Along many years: “unique” low GC content
H. walsbyi is a unique specie Num. Mbp over 95% id (in 70% length) = 398.8A 100 95 90%id 85 80 75 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Haloquadratum walsbyi HSBQ001 chr. (3132494 bp)B C House-keeping genes Metagenome AtpB SecY Tef2 RadA Num. Seqs.Num. Seqs. %id 398.8Mp %id
Environmental pan-genome of H. walsbyi GI 1 GI 2 GI 3 GI 4 (promer) (BLASTN) H. Walsbyi (3132494 bp)
e-fosmids of H. walsbyi Variability of GI 1 Cell surface glycoprotein 100 90 80 70 60 50 40 30 %sim. Cell surface adhesin Putative S-layer protein Dentin-sialophosphoprotrein 23-cyclic-nucleotide 2-phosphodiesterase IS element 240631 279189 Ig-like domain-containing protein H.w. C23 Protease ABC-type cobalamin/iron(III) eHw-1 Hmu2 H.w. 239281 312087 HBSQ001 eHw-4 eHw-7 eHw-559 eHw-5 eHw-12 eHw-6 eHw-9
METAGENOMIC ISLANDS GOS marine metagenomes GENOMIC ISLANDS O-chain LPS Giant protein Transporters EXTRACELLULAR COMPONENTS IN GENOMIC ISLANDS Pili Exo-polysaccharide Other Prochlorococcus marinus MED4 Prochlorococcus marinus MIT9301 Pelagibacter ubique HTCC1062100%% sim. Pelagibacter ubique HTCC1062 (1308759 bp) 50% Burkholderia sp. 383 chr.1 Shewanella sp. MR-4 Pili O-chain LPS Giant Exo- Pili Transporters protein polysaccharide related Pelagibacter ubique HTCC1002 contigs100% Aeromonas hydrophila subs. hydrophila ATCC 7966 Synechococcus sp. WH812% sim. 50% Transmembrane/ O-chain LPS Pili Respiratory system Giant Outer membrane Transporters Fe transporter protein proteins Pili Solar salter metagenomes Pelagibacter ubique HTCC7211100% Salinibacter ruber DSM 13855 Haloquadratum walsbyi DSM 16790 100 100% sim. 95 95 Y Axis Title Y Axis Title 90 90 85 8550% 80 80 O-chain LPS Pili Zn transporter, Phosphonate Pili O-chain 75 Exo-polysaccharide 75 Cell surface Cell surface and Phosphate metabolism LPS 0 500000 1000000 1500000 2000000 2500000 3000000 3500000 glycoproteins 0 500000 1000000 1500000 2000000 glycoproteins 2500000 3000000 X Axis Title X Axis Title
Low recruiting genes (MGIs and islets)• Coding for exposed features: O-chain of LPS, glycoproteins etc, pili, flagella• Transporters• Sensors and regulators (behaviour)• Sub-niche specialization e.g. microaerophilic growth
Alteromonas macleodii• Proteobacterium isolated by Baumann from surface waters near Hawaii in the ‘60s• Common isolate• Heterotrophic aerobe, wide range of substrates as C,E source, 2-3 m long, typical copiotroph r strategist• Mostly found in the particulate fraction
160 isolates on MA characterized by 16S rRNA sequencing , 28% A. macleodii 2% Alteromonas macleodii DE strain genome 4% 2% 2% Alteromonas sp. SequencedSample from 6% Bacillus sp.1000 m deep 5% 28% Sulfitobacter sp.South Adriatic 10% Rhodobacteraceae 28% 5% bacterium SCSWE04 8% Oceanobacillus iheyensis 3 other strains17/05/2003; 22:14 R/V UraniaBottom ca. 1100 m sequenced now200 L retrieved by rossete(single cast) from 1000 m AD1000 Metagenomic fosmid library ca. 38,000 clones (1.75 Gbp or 600 prokaryotic genomes) Sampling site
Variation of A. macleodii in a single sample of 200 L If we consider that the cell density atthe location is 105 cells per ml andaccept the figure of 5% belonging toA. macleodii, in 200 liters we willhave about 5x108 cells of A.macleodii (about the population thatyou have in a common 100 mllaboratory culture)
End sequencing of ca 8000 fosmids• 15968 individual reads• 424 (2.6%) could be affiliated to A. macleodii DE (>98% nuc identity over 300 nucs), average 99.04% Purificación López-García
Synonymous 128 FlaL Non-synonymous 44 85%(sensor of two-component system) FlaL Sensory box TM1 Variable region in AD1000-39-B06
Flagellum cluster VariabilityExtracellular>Regulation>>cytoplasmic Acetyl CoA Diguanalate Transglycosilase cyclase STL Smr Domain ABC Transporter carboxylase containing p. RTX Toxin DNA pol Cell cycle p. Kef-type K+ FGAM Thrombospondin type 3 subunit α MesJ transport system Synthetase repeat:OmpA/MotB Synonymous 151 181 38 69 110 155 31 32 12 16 28 10 15 75 75 31 33 Non-synymous 28 19 6 3 16 23 9 0 6 4 4 10 3 15 18 6 2 Mer B,A,R eAmacleodii AD1000-7-B08 A. macleodii DE 98% 98% 60% 78% 83% 83% 1.483.121 99% 1.518.371A. macleodii DE HlyD Sterol 3.203.823 HKLuxR UmuC desaturase Mer B,A,R FliD FliC FlgL FlgK FlgJ FlgL FlgG FlgE FlgC FlgA FlgN Transposase FlaG FlgH FlgF FlgD FlgB FlgM CheR/V GI 9
Different exposed receptors, flagelins and theirglycosilation BUT ALSObehaviour at the level of flagellum synthesis i.e. thelineage represented by the sequenced strain and thatrepresented by fosmid eAmacleodii AD1000-39-B06could have different responses to environmental signalsthat either induce or block synthesis of the flagellum i.e.produce flagella under different conditions.
Constant-Diversity Nature Reviews Microbiology , November 2009
San Francisco Bay salt pond POM Alteromonas macleodii and Co CO2 + H2O 300 major organic compoundsProblem: Solution:only the transporters will to have manyoccupy the 3 Mpb of oneindividual cell DNA ? lineages sharing the feast (3132494 pb)Problem: what about clonal sweeps? Solution: phages One lineage will be more efficient in consuming the limiting nutrient
What does natural selection act upon – genes,individuals, groups of individuals (such as a kin group), or the species as a whole?• The unit of selection in the prokaryotic world might be a complex consortium that includes several clonal cellular lineages sharing a core genome but differing in an adaptive gene complements that allows the population a much more efficient exploitation of available resources. These pan-clonal populations are maintained equalized by phage predation in an analogous way as the immune system in a mammal maintains in check tumors. If this is so, phage populations should be considered as belonging to the same selection unit.
Alicante (Spain), EvolutionaryUniversity Miguel Hernández Genomics Group Ana Belén Rohit Ghai Post-doc. Post-doc. Inma García Pre-doc. Carol Mizuno Aitor Gonzaga Pre-doc. Pre-doc. Sandra Rocamora Pre-doc.
Thank you very much! Alicante (Spain), University Miguel HernándezAitor GonzagaAna-BelénMartín-CuadradoRohit Ghai
OBJETIVE HOW MANY DIFFERENT Haloquadratum walsbyi clones exists? Core-genome how different Pan-genome “In situ”, from thedo they they are? of H. walsbyi metagenomevary alongtime? are equally Accesory-genome distributed ?
What we have?: SequencesTwo genomes Haloquadratum walsbyi strains sequenced (in theory) HBSQ001 C23 4 SAGs of H. + (2000) Sanger (2011) 454 pyro. walsbyi 3132494 bp 3148034 bpMetagenomic collections of Santa Pola saltern : DNA Bulk DNA pyrosequencing (FLX, 400pb) 5 m 0.22 m extraction sp37 (2008) sp33 (2010) sp32 (2007) prokariots time-series (2005) 1041 Mpb + Torrevieja (Alicante) Saltern (2010) 145 MbpFosmids libraries. 33 Sequenced fosmids Analysis of 2947 fosmid ends DNA Metagenomic fosmids library (35 Kb) 5 m 0.22 m extraction sp (2002) 2000 clones sp37 (2008) 5952 clones 23 fosmids (2006) (Sanger) prokariots Torrevieja saltern: 2880 clones 10 fosmids GI1 (2009) FLX