Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322
Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydro-genase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceis-pirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.
KeywordsCanididatus Puniceispirillum marinum carbon monoxide dimethylsulfoniopropionate light-emitting diode mitomycin C proteorhodopsin SAR116
Unable to display preview. Download preview PDF.
This research was supported by the Marine Biotechnology Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) [No. 20180430]; and by the Korea National Research Fund [NRF-2017R1D1A1B03034706].
- Britschgi, T.B. and Giovannoni, S.J. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57, 1707–1713.Google Scholar
- Choo, Y.J., Lee, K., Song, J., and Cho, J.C. 2007. Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int. J. Syst. Evol. Microbiol. 57, 532–537.CrossRefGoogle Scholar
- Dupont, C.L., Rusch, D.B., Yooseph, S., Lombardo, M.J., Richter, R.A., Valas, R., Novotny, M., Yee-Greenbaum, J., Selengut, J.D., Haft, D.H., et al. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6, 1186- 1199.Google Scholar
- Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L., et al. 2008. The Pfam protein families database. Nucleic Acids Res. 36, D281- D288.Google Scholar
- Giovannoni, S.J. and Rappé, M.S. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes, pp. 47–84. In Kirchman, D.L.E. (ed.), Microbial ecology of the oceans. Wiley-Liss New York, USA.Google Scholar
- Gómez-Consarnau, L., Akram, N., Lindell, K., Pedersen, A., Neutze, R., Milton, D.L., González, J.M., and Pinhassi, J. 2010. Proteor-hodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol. 8, e1000358.Google Scholar
- González, J.M., Fernández-Gómez, B., Fernàndez-Guerra, A., Gomez-Consarnau, L., Sánchez, O., Coll-Lladó, M., Del Campo, J., Escudero, L., Rodríguez-Martínez, R., Alonso-Saez, L., et al. 2008. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc. Natl. Acad. Sci. USA 105, 8724–8729.CrossRefGoogle Scholar
- Grote, J., Bayindirli, C., Bergauer, K., Carpintero de Moraes, P., Chen, H., D’Ambrosio, L., Edwards, B., Fernandez-Gómez, B., Hamisi, M., Logares, R., et al. 2011. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand. Genomic Sci. 5, 269–278.CrossRefGoogle Scholar
- Jorgensen, J.H., Turnidge, J.D., and Washington, J.A. 1999. Antibacterial susceptibility tests: dilution and disk diffusion method, pp. 1526–1543. In Murray, P.R., Baron, E.J., Pfaller, M.A., Tenover, F.C., and Yolken, R.H. (eds.), Manual of clinical microbiology. American Society for Microbiology, Washington, DC, USA.Google Scholar
- Macleod, R.A. 1965. The question of the existence of specific marine bacteria. Bacteriol. Rev. 29, 9–24.Google Scholar
- Ohta, K. 1997. Diurnal variations of carbon monoxide concentration in the equatorial Pacific upwelling region. Oceanogr. Lit. Rev. 44, 1258.Google Scholar
- Reasoner, D.J. and Geldreich, E.E. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Microbiol. 49, 1–7.Google Scholar
- Reisch, C.R., Moran, M.A., and Whitman, W.B. 2011. Bacterial cata-bolism of dimethylsulfoniopropionate (DMSP). Front. Micro-biol. 2, 172.Google Scholar
- Swofford, D.L. 2002. PAUP: phylogenetic analysis using parsimony, version 4.0b10. Sinauer Associates, Sunderland, MA, USA.Google Scholar