Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean

FEMS Microbiology Letters - Tập 295 Số 2 - Trang 141-147 - 2009
Jaeho Song1, Hyun-Myung Oh1, Jang‐Cheon Cho1
1Division of Biology and Ocean Sciences, Inha University, Incheon, Korea.

Tóm tắt

Từ khóa


Tài liệu tham khảo

Altschul SF , Madden TL , Schäfer 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: 3389–3402.

Béjà O , Aravind L , Koonin EV et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–1906.

Cho JC & Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microb 70: 432–440.

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 , Stapels MD , Morris RM , Vergin KL , Schwalbach MS , Givan SA , Barofsky DF & Giovannoni SJ (2007) Polyphyletic photosynthetic reaction centre genes in oligotrophic marine Gammaproteobacteria. Environ Microbiol 9: 1456–1463.

Chun J , Lee JH , Jung Y , Kim M , Kim S , Kim BK & Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57: 2259–2261.

Connon SA & Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microb 68: 3878–3885.

Davis, 1958, USFWS Fish Bull, 58, 293

Don RH , Cox PT , Wainwright BJ , Baker K & Mattick JS (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19: 4008.

Field KG , Gordon D , Wright T , Rappé M , Urback E , Vergin K & Giovannoni SJ (1997) Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microb 63: 63–70.

Giovannoni SJ , Bibbs L , Cho JC et al. (2005a) Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438: 82–85.

Giovannoni SJ , Tripp HJ , Givan S et al. (2005b) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242–1245.

Giovannoni SJ , Hayakawa DH , Tripp HJ , Stingl U , Givan SA , Cho JC , Oh HM , Kitner JB , Vergin KL & Rappé MS (2008) The small genome of an abundant coastal ocean methylotroph. Environ Microbiol 10: 1771–1782.

Ludwig W , Strunk O , Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363–1371.

Morris RM , Rappé MS , Connon SA , Vergin KL , Siebold WA , Carlson CA & Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806–810.

Morris RM , Vergin KL , Cho JC , Rappé MS , Carlson CA & Giovannoni SJ (2005) Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site. Limnol Oceanogr 50: 1687–1696.

Morris RM , Longnecker K & Giovannoni SJ (2006) Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. Environ Microbiol 8: 1361–1370.

Rappé MS , Vergin K & Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33: 219–232.

Rappé MS , Connon SA , Vergin KL & Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630–633.

Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.

Stingl U , Desiderio RA , Cho JC , Vergin KL & Giovannoni SJ (2007a) The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microb 73: 2290–2296.

Stingl U , Tripp HJ & Giovannoni SJ (2007b) Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J 1: 361–371.

Stingl U , Cho JC , Foo W , Vergin KL , Lanoil B & Giovannoni SJ (2008) Dilution-to-extinction culturing of psychrotolerant planktonic bacteria from permanently ice-covered lakes in the McMurdo dry valleys, Antarctica. Microb Ecol 55: 395–405.

Swofford, 2002, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods)

Tripp HJ , Kitner JB , Schwalbach MS , Dacey JW , Wilhelm LJ & Giovannoni SJ (2008) SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452: 741–744.

Wilhelm LJ , Tripp HJ , Givan SA , Smith DP & Giovannoni SJ (2007) Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol Direct 2: 27.