Sarah N. Brown Dr. Stephen Giovannoni Dr. Jang-Cheon Cho Department of Microbiology HHMI D structures of Pelagibacter ubique (2006) (Pelagibacter means "bacterium of the sea")
The most abundant marine bacteria (~30% in euphotic) Proteorhodopsin –containing (photoheterotroph) Importance in biogeochemical cycles Global climate & weather regulation (DMSP) FIGURE 1. Distribution of the SAR11 clade in the world's oceans.
In 2002, SAR11 cells were first isolated in seawater-based medium (no colonies produced). Growth of Pelagibacter in artificial seawater medium (ASW) is a recent advancement. Non-colony forming property and oligotrophy made it difficult for taxonomy Purpose: To characterize & provide official nomenclature for SAR11 (strains 1062 & 7211) SAR11: Candidatus Pelagibacter Fig. 4. Cultures of oligotrophic marine bacteria growing in carboys of autoclaved seawater.
Incorporates multiple methods for identification & description of new species Species: the basic unit of bacterial taxonomy SAR11 clade Class: Alphaproteobacteria GENOTYPIC INFORMATION PHENOTYPIC INFORMATION
>98.7% 16S rRNA gene sequence similarity between 1062 & 7211 Consequently, we can’t tell whether these strains are the same species. Therefore, genomic comparisons should be performed. 16S rRNA gene sequence similarity HTCC7211 HTCC % (Dr. Jang Cheon-Cho, 2011)
>95-96% average nucleotide identity (ANI b /ANI m ) indicates ‘true (same) species’ Fig., m= MUMmer computer algorithm; b= BLAST algorithm ANI b HTCC7211 HTCC ANI m HTCC7211 HTCC Strains show <95-96% average nucleotide identity (ANI b/m ) Therefore, HTCC1062 & HTCC7211 represent separate genomic species (Dr. Jang Cheon-Cho, 2011) Different species <95-96% ANIm/b Same species
HTCC1062 HTCC1002 HTCC7211 HIMB P. ubiquis P. bermudensis 1. HTCC1062→ Pelagibacter ubiquis gen. nov., sp. nov. 2. HTCC7211→ Pelagibacter bermudensis sp. nov. (Dr. Jang Cheon-Cho, 2011) Group Ia
Prepare artificial seawater medium (ASW) Salinity: w/out NaCl & w/10% NaCl pH: adjust w/0.1M NaOH & 0.1M HCl Add nutrients & inoculum Dispense into 156 flasks (triplicates of each growth condition) Incubate Temp (°C): 4, 8, 12, 16, 20, 23, 25, & 30 pH & salinity: 16ºC Screen for growth
µ max optimum maximum minimum optimum maximum SPECIFIC GROWTH RATE (µ) µ = the # of divisions per cell per unit time. It depends upon growth conditions.
µ max minimum optimum maximum µ max optimum minimum maximum optimum maximum minimum µ max
minimum optimum maximum SPECIFIC GROWTH RATE (µ) minimum µ max optimum maximum
PHENOTYPE SUMMARY CONCLUSIONS Growth data suggest that these strains are separate species. Genotypic & phenotypic data show that these are 2 distinct species. Therefore, we propose the following nomenclature : Strain HTCC1062→ Pelagibacter ubiquis gen. nov., sp. nov. Strain HTCC7211→ Pelagibacter bermudensis sp. nov. Optimum Growth Conditions Oregon Coast Strain HTCC1062 Sargasso Sea Strain HTCC7211 Temperature16ºC23ºC Salinity1.5% NaCl2% NaCl pH6.58
The Gordon & Betty Moore Foundation Dr. Stephen Giovannoni Dr. Jang Cheon-Cho Paul Carini Kevin Vergin Giovannoni Lab HHMI & Dr. Kevin Ahern
Konstantinidis, K., and J. M. Tiedje Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: Konstantinidis, K., and J. M. Tiedje Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187: Morris, R.M., Rappé, M.S., Connon,S.A., Vergin, K.L., Siebold, W.A., Carlson, C.A., and Giovannoni, S.J. (December 2002). SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: doi: /nature Nicastro, D., Schwartz, C., Pierson, J., Cho, J.-C.C., Giovannoni, S. J., and McIntosh, J. R. (2006). Three-dimensional structure of the tiny bacterium Pelagibacter ubique studied by cryo-electron tomography. Microsc. Microanal. 12(sup2): Richter, M., Rosselló-Móra, R. (October 2009). Shifting the genomic gold standard for the prokaryotic species definition. Biological Sciences - Microbiology: PNAS 106 (45): ; doi: /pnas