Novel psychropiezophilic oceanospirillales species profundimonas piezophila gen. nov., sp. nov., isolated from the deep-sea environment of the puerto rico trench

Applied and Environmental Microbiology

Volumn 80, Issue 1, 2014, Pages 54-60

  Cao, Yi ^a,b   Chastain, Roger A ^a   Eloe, Emiley A ^a   Nogi, Yuichi ^c   Kato, Chiaki ^c   Bartletta, Douglas H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b ZHEJIANG UNIVERSITY   (China)

^c JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR FATTY ACIDS; DEEPWATER HORIZON OIL SPILLS; HETEROTROPHS; NEW SPECIES; OPTIMAL GROWTH; PHYLOGENETIC ANALYSIS; POLYUNSATURATED FATTY ACIDS (PUFAS); PUERTO RICO;

HYDROSTATIC PRESSURE; MONOUNSATURATED FATTY ACIDS; OIL SPILLS; POLYUNSATURATED FATTY ACIDS;

BACTERIA;

BACTERIUM; DEEP SEA; FATTY ACID; GROWTH RATE; MONOCULTURE; NEW GENUS; NEW SPECIES; NUTRIENT ENRICHMENT; PRESSURE EFFECT; SEAWATER; TAXONOMY;

ATLANTIC OCEAN; PUERTO RICO TRENCH;

BACTERIAL DNA; FATTY ACID; RIBOSOME DNA; RNA 16S; SEA WATER;

ARTICLE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HYDROSTATIC PRESSURE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OCEANOSPIRILLACEAE; PHYLOGENY; PUERTO RICO; TEMPERATURE;

CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; HYDROSTATIC PRESSURE; MOLECULAR SEQUENCE DATA; OCEANOSPIRILLACEAE; PHYLOGENY; PUERTO RICO; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 84891103031     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02288-13     Document Type: Article

References (43)

1. Eloe EA, Malfatti F, Gutierrez J, Hardy K, Schmidt WE, Pogliano K, Pogliano J, Azam F, Bartlett DH. 2011. Isolation and characterization of a psychropiezophilic alphaproteobacterium. Appl. Environ. Microbiol. 77:8145-8153. http://dx.doi.org/10.1128/AEM.05204-11.
2. Bartlett DH. 1992. Microbial life at high-pressures. Sci. Prog. 76:479- 496. 3. Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH. 2007. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl. Environ. Microbiol. 73:838-845. http://dx.doi.org /10.1128/AEM.01726-06.
3. Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH. 2007. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl. Environ. Microbiol. 73:838-845. http://dx.doi.org/10.1128/AEM.01726-06.
4. Bartlett DH. 2002. Pressure effects on in vivo microbial processes. Biochim. Biophys. Acta 1595:367-381. http://dx.doi.org/10.1016/S0167-4838(01)00357-0.
5. Abe F. 2007. Exploration of the effects of high hydrostatic pressure on microbial growth, physiology and survival: perspectives from piezophysiology. Biosci. Biotechnol. Biochem. 71:2347-2357. http://dx.doi.org/10.1271/bbb.70015.
6. Meersman F, Daniel I, Bartlett DH, Winter R, Hazael R, McMillan PF. 2013. High-pressure biochemistry and biophysics. Rev. Mineral. Geochem. 75:607-648. http://dx.doi.org/10.2138/rmg.2013.75.19.
7. Allen EE, Facciotti D, Bartlett DH. 1999. Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl. Environ. Microbiol. 65:1710-1720.
8. Kawamoto J, Sato T, Nakasone K, Kato C, Mihara H, Esaki N, Kurihara T. 2011. Favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, Shewanella violacea DSS12, at high-hydrostatic pressures. Environ. Microbiol. 13:2293-2298. http://dx.doi.org/10.1111/j.1462-2920.2011.02487.x.
9. Usui K, Hiraki T, Kawamoto J, Kurihara T, Nogi Y, Kato C, Abe F. 2012. Eicosapentaenoic acid plays a role in stabilizing dynamic membrane structure in the deep-sea piezophile Shewanella violacea: a study employing high-pressure time-resolved fluorescence anisotropy measurement. Biochim. Biophys. Acta 1818:574-583. http://dx.doi.org/10.1016/j.bbamem.2011.10.010.
10. Lauro FM, Tran K, Vezzi A, Vitulo N, Valle G, Bartlett DH. 2008. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure. J. Bacteriol. 190: 1699-1709. http://dx.doi.org/10.1128/JB.01176-07.
11. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. 2010. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204-208. http://dx.doi.org/10.1126/science.1195979.
12. Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK. 2012. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 6:1715-1727. http://dx.doi.org/10.1038/ismej.2012.59.
13. Verna C, Ramette A, Wiklund H, Dahlgren TG, Glover AG, Gaill F, Dubilier N. 2010. High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic. Environ. Microbiol. 12:2355-2370. http://dx.doi.org/10.1111/j.1462-2920.2010.02299.x.
14. Goffredi SK, Johnson SB, Vrijenhoek RC. 2007. Genetic diversity and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Appl. Environ. Microbiol. 73: 2314-2323. http://dx.doi.org/10.1128/AEM.01986-06.
15. Tresguerres M, Katz S, Rouse GW. 2013. How to get into bones: proton pump and carbonic anhydrase in Osedax boneworms. Proc. R. Soc. B 280:20130625. http://dx.doi.org/10.1098/rspb.2013.0625.
16. Goffredi SK, Orphan VJ, Rouse GW, Jahnke L, Embaye T, Turk K, Lee R, Vrijenhoek RC. 2005. Evolutionary innovation: a bone-eating marine symbiosis. Environ. Microbiol. 7:1369-1378. http://dx.doi.org/10.1111/j.1462-2920.2005.00824.x.
17. Rouse GW, Goffredi SK, Vrijenhoek RC. 2004. Osedax: bone-eating marine worms with dwarf males. Science 305:668-671. http://dx.doi.org/10.1126/science.1098650.
18. Hedlund BP, Geiselbrecht AD, Bair TJ, Staley JT. 1999. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl. Environ. Microbiol. 65:251-259.
19. Miyazaki M, Nogi Y, Fujiwara Y, Kawato M, Kubokawa K, Horikoshi K. 2008. Neptunomonas japonica sp. nov., an Osedax japonicus symbiont-like bacterium isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan. Int. J. Syst. Evol. Microbiol. 58:866-871. http://dx.doi.org/10.1099/ijs.0.65509-0.
20. Dietz AS, Yayanos AA. 1978. Silica gel media for isolating and studying bacteria under hydrostatic pressure. Appl. Environ. Microbiol. 36:966- 968.
21. Yayanos AA, Dietz AS, Van Boxtel R. 1981. Obligately barophilic bacterium from the Mariana trench. Proc. Natl. Acad. Sci. U. S. A. 78:5212- 5215. http://dx.doi.org/10.1073/pnas.78.8.5212.
22. Hugh R, Leifson E. 1953. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram-negative bacteria. J. Bacteriol. 66:24-26.
23. Edwards PR, Ewing WH. 1972. Identification of Enterobacteriaceae, 3rd ed. Burgess Publishing Company, Minneapolis, MN.
24. Nogi Y, Kato C. 1999. Taxonomic studies of extremely barophilic bacteria isolated from the Mariana Trench and description of Moritella yayanosii sp. nov., a new barophilic bacterial isolate. Extremophiles 3:71-77. http://dx.doi.org/10.1007/s007920050101.
25. Baumann P, Baumann L. 1979. The marine gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes, p 1302-1331. In Starr MP, Stolp H, Truper HG, Balows A, Schlegel HH (ed), The prokaryotes. Springer-Verlag, New York, NY.
26. DeLong EF, Franks DG, Yayanos AA. 1997. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl. Environ. Microbiol. 63:2105-2108.
27. 3+. J. Bacteriol. 176:1468-1474.
28. Sasser M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. MIDI Inc., Newark, DE.
29. Saito H, Miura K. 1963. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim. Biophys. Acta 72:612-629.
30. Tamaoka J, Komagata K. 1984. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25:125-128. http://dx.doi.org/10.1111/j.1574-6968.1984.tb01388.x.
31. Lane DJ. 1991. 16S/23S rRNA sequencing, p 115-148. In Stackebrandt E, GoodfellowM(ed), Nucleic acid techniques in bacterial systematics. Wiley, Chichester, United Kingdom.
32. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2.
33. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, 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. 32:1363-1371. http://dx.doi.org/10.1093/nar/gkh293.
34. Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5:164-166.
35. Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum- evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26:1641-1650. http://dx.doi.org/10.1093/molbev/msp077.
36. Zobell CE, Cobet AB. 1964. Filament formation by Escherichia coli at increased hydrostatic pressures. J. Bacteriol. 87:710-719.
37. Lee HW, Shin NR, Lee J, Roh SW, Whon TW, Bae JW. 2012. Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas. Int. J. Syst. Evol. Microbiol. 62:2657-2661. http://dx.doi.org/10.1099/ijs.0.037473-0.
38. Nogi Y, Hosoya S, Kato C, Horikoshi K. 2004. Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench. Int. J. Syst. Evol. Microbiol. 54:1627-1631. http://dx.doi.org/10.1099/ijs.0.03049-0.
39. Katz S, Klepal W, Bright M. 2011. The Osedax trophosome: organization and ultrastructure. Biol. Bull. 220:128-139. http://www.biolbull.org/content/220/2/128.long.
40. Rouse GW, Wilson NG, Goffredi SK, Johnson SB, Smart T, Widmer C, Young CM, Vrijenhoek RC. 2009. Spawning and development in Osedax boneworms (Siboglinidae, Annelida). Mar. Biol. 156:395-405. http://dx.doi.org/10.1007/s00227-008-1091-z.
41. Salathé RM, Vrijenhoek RC. 2012. Temporal variation and lack of host specificity among bacterial endosymbionts of Osedax bone worms (Polychaeta: Siboglinidae). BMC Evol. Biol. 12:189. http://dx.doi.org/10.1186/1471-2148-12-189.
42. Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK. 2012. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ. Microbiol. 14:2405-2416. http://dx.doi.org/10.1111/j.1462-2920.2012.02780.x.
43. Zhang XY, Zhang YJ, Yu Y, Li HJ, Gao ZM, Chen XL, Chen B, Zhang YZ. 2010. Neptunomonas antarctica sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 60:1958-1961. http://dx.doi.org/10.1099/ijs.0.017756-0.