Genomic Taxonomy of the Genus Prochlorococcus

Ahlgren NA, Rocap G, Chisholm SW (2006) Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies. Environ Microbiol 8(3):441–454

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134

Auch AF, Klenk HP, Göker M (2010) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2(1):142–148

Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D (2011) Genomic island variability facilitates Prochlorococcus–virus coexistence. Nature 474:604–608

Binder BJ, Chisholm SW, Olson RJ, Frankel SL, Worden AZ (1996) Dynamics of picophytoplankton, ultraphytoplankton and bacteria in the central equatorial Pacific. Deep-Sea Res 43:907–931

Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury J, Welschmeyer N (1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340–343

Chisholm SW, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury JB, West-Johnsrud L, Zettler ER (1992) Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll aa and bb. Arch Microbiol 157:297–300

Cho JC, Giovannoni SJ (2004) Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order ‘Rhodobacterales’. Int J Syst Evol Microbiol 54:1129–1136

Cho JC, Vergin KL, Morris RM, Giovannoni SJ (2004) Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae. Environ Microbiol 6:611–621

Cho JC, Giovannoni SJ (2006) Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 56:855–859

Coleman ML et al (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:1768–1770

Coleman ML, Chisholm SW (2010) Ecosystem-specific selection pressures revealed through comparative population genomics. Proc Natl Acad Sci U S A 107:18634–18639

Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104(1):410–433

Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F et al (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A 100:10020–10025

Dufresne A, Garczarek L, Partensky F (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 6(2):R14

Emerson D, Rentz JA, Lilburn TG, Davis RE, Aldrich H et al (2007) A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One 2(8):e667

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

Ferris MJ, Palenik B (1998) Niche adaptation in ocean cyanobacteria. Nature 396:226–228

Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240

Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152

Fuhrman JA, McCallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl Environ Microbiol 59:1294–1302

Garcia-Fernandez JM, Hess WR, Houmard J, Partensky F (1998) Expression of the psbA gene in the marine oxyphotobacteria Prochlorococcus spp. Arch Biochem Biophys 359:17–23

Garcia-Fernandez JM, de Marsac NT, Diez J (2004) Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments. Microbiol Mol Biol Rev 68:630–638

Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3(9):733–739, Review

Goericke R, Repeta DJ (1992) The pigments of Prochlorococcus marinus: the presence of divinyl-chlorophyll aa and bb in a marine prokaryote. Limnol Oceanogr 37:425–433

Guinebretière MH, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M, De Vos P (2008) Ecological diversification in the Bacillus cereus group. Environ Microbiol 10(4):851–865

Heywood JL, Zubkov MV, Tarran GA, Fuchs BM, Holligan PM (2006) Prokaryoplankton standing stocks in oligotrophic gyre and equatorial provinces of the Atlantic Ocean: evaluation of inter-annual variability. Deep Sea Res II 53:1530–1547

Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320(5879):1081–1085

Johnson FH, Shunk IV (1936) An interesting new species of luminous bacteria. J Bacteriol 31(6):585–593

Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EM, Chisholm SW (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737–1740

Karlin S, Mrazek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179(12):3899–3913

Karlin S (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1(5):598–610

Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537:39–64

Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J et al (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 3:e231

Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. PNAS Sci N Y 102:2567–2572

Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264

Konstantinidis KT, Stackebrandt E (2013) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson FL (eds) The prokaryotes (4th edition): prokaryotic biology and symbiotic associations. Springer, Heidelberg, p 229

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948

Lawrence JG, Retchless AC (2009) The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol 532:29–53

Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32(4):1363–1371

Martiny AC, Coleman M, Chisholm SW (2006) Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc Natl Acad Sci USA 103:12552–12557

Martiny AC, Huang Y, Li W (2009) Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions. Environ Microbiol 11:1340–1347

Moore LR, Chisholm SW (1999) Photophysiology of the marine cyanobacterium Prochlorococcus: ecotypic differences among cultured isolates. Limnol Oceanogr 44:628–638

Moore LR, Post AF, Rocap G, Chisholm SW (2002) Utilization of different nitrogen sources by the marine cyanobacteria Prochlorococcus and Synechococcus. Limnol Oceanogr 47:989–996

Olson RJ (1981) 15N tracer studies of the primary nitrite maximum. J Mar Res 39:1033–1051

Oren A (2004) A proposal for further integration of the cyanobacteria under the bacteriological code. Int J Syst Evol Microbiol 54:1895–1902

Partensky F, Hess WR, Vaulot D (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63:106–127

Preheim SP, Timberlake S, Polz MF (2011) Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl Environ Microbiol 77(20):7195–7206

Rippka R, Coursin T, Hess W, Lichtlé C, Scanlan DJ, Palinska KA, Iteman I, Partensky F, Houmard J, Herdman M (2000) Prochlorococcus marinus Chisholm et al. 1992 subsp. pastoris subsp. nov. strain PCC 9511, the first axenic chlorophyll a2/b2-containing cyanobacterium (Oxyphotobacteria). Int J Syst Evol Microbiol 5:1833-47

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR et al (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047

Rocap G, Distel DL, Waterbury JB, Chisholm SW (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68(3):1180–1191

Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184(16):4529–4535

Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F (2009) Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73(2):249–99

Schleifer KH (2009) Classification of Bacteria and Archaea: past, present and future. Syst Appl Microbiol 32(8):533–542

Sher D, Thompson JW, Kashtan N, Croal L, Chisholm SW (2011) Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria. ISME J 5(7):1125–1132

Stackebrandt E, Goebel BM (1994) A place for DNA–DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 49:846–849

Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

Sullivan MB, Waterbury JB, Chisholm SW (2003) Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424:1047–1051

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739

Thompson FL, Iida T, Swings J (2004) Biodiversity of vibrios. Microbiol Mol Biol Rev 68(3):403–431

Thompson AW, Huang K, Saito MA, Chisholm SW (2011) Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. ISME J 5:1580–1594

Thompson CC, Vicente ACP, Souza RC, Vasconcelos ATR, Vesth T, Jr NA, Ussery DW, Iida T, Thompson FL (2009) Genomic taxonomy of vibrios. BMC Evol Biol 9:258

Thompson CC, Vieira NM, Vicente ACP, Thompson FL (2011) Infection, genetics and evolution towards a genome based taxonomy of mycoplasmas. infection, genetics and evolution. Elsevier BV 11:1798–1804

Thompson CC, Emmel VE, Fonseca EL, Marin MA, Vicente ACP (2013) Streptococcal taxonomy based on genome sequence analyses. F1000Research 2:67

Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW (2006) Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol 2:53

Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60(2):407–438, Review

West NJ, Scanlan DJ (1999) Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean. Appl Environ Microbiol 65(6):2585–2591

West NJ, Schönhuber WA, Fuller NJ, Amann RI, Rippka R, Post AF, Scanlan DJ (2001) Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology 147(Pt 7):1731–1744

Zinser ER, Coe A, Johnson ZI, Martiny AC, Fuller NJ, Scanlan DJ, Chisholm SW (2006) Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method. Appl Environ Microbiol 72(1):723–732

Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R, McNulty N et al (2009) Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus. PLoS One 4:e5135