Genomic potential of Marinobacter aquaeolei, a biogeochemical "Opportunitroph"

Applied and Environmental Microbiology

Volumn 77, Issue 8, 2011, Pages 2763-2771

  Singer, Esther ^a   Webb, Eric A ^a   Nelson, William C ^a   Heidelberg, John F ^a   Ivanova, Natalia ^b   Pati, Amrita ^b   Edwards, Katrina J ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE STRATEGY; BIOGEOCHEMICAL CYCLE; DEFENSE MECHANISM; ELECTRON DONORS; ENVIRONMENTAL CONDITIONS; ENVIRONMENTAL FLUCTUATIONS; GENETIC CHARACTERISTICS; GENOME ANALYSIS; GENOME STRUCTURES; GLOBAL OCEAN; HEAVY METAL RESISTANCE; HORIZONTAL GENE TRANSFER; MARINOBACTER; PHOSPHONATES; POLLUTED WATER; TERMINAL ELECTRON ACCEPTORS;

ANALYTICAL GEOCHEMISTRY; BIOGEOCHEMISTRY; ECOLOGY; GENE TRANSFER; HEAVY METALS; HEAVY WATER; HYDROCARBONS; METABOLISM; OXYGEN; SENSORY PERCEPTION; UREA; WATER POLLUTION;

GENES;

BACTERIAL DNA; IRON; NITROGEN; PHOSPHONIC ACID DERIVATIVE; UREA;

ADAPTIVE RADIATION; ANTIBIOTICS; BACTERIUM; BIODEGRADATION; BIOGEOCHEMICAL CYCLE; ELECTRON; ENVIRONMENTAL CONDITIONS; GENETIC ANALYSIS; GENOME; GENOMICS; GLOBAL OCEAN; HEAVY METAL; HYDROCARBON; METABOLISM; NITRATE; OXYGEN; PERCEPTION; SURVIVAL; TOXIN; UREA; WATER POLLUTION;

ARTICLE; BACTERIAL GENOME; CHEMISTRY; DNA SEQUENCE; GENETICS; MARINOBACTER; METABOLISM; OXYGEN CONSUMPTION; PHYLOGENY; SIGNAL TRANSDUCTION;

DNA, BACTERIAL; GENOME, BACTERIAL; IRON; MARINOBACTER; NITROGEN; OXYGEN CONSUMPTION; PHOSPHONIC ACIDS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; UREA;

MARINOBACTER; MARINOBACTER HYDROCARBONOCLASTICUS;

EID: 79955587314     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01866-10     Document Type: Article

References (72)

1. Antunes, A., L. Franca, and F. Rainey. 2007. Marinobacter salsuginis sp. nov., isolated from the brine-seawater interface of the Shaban Deep, Red Sea. Int. J. Syst. Evol. Microbiol. 57:1035-1040.
2. Aziz, R. K., M. Breitbart, and R. A. Edwards. 2010. Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 38: 4207-4217.
3. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512-524.
4. Bhaskar, P., H.-P. Grossart, N. Bhosle, and M. Simon. 2005. Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin. FEMS Microbiol. Ecol. 53:255-264.
5. Burrows, L. L. 2005. Weapons of mass retraction. Mol. Microbiol. 57:878-888.
6. Button, D. K., B. R. Robertson, P. W. Lepp, and T. M. Schmidt. 1998. A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl. Environ. Microbiol. 64:4467-4476.
7. Chain, P., et al. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185:2759-2773.
8. Clark, L. L., E. D. Ingall, and R. Benner. 1998. Marine phosphorus is selectively remineralized. Nature 393:426.
9. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
10. Dhillon, A., K. J. Edwards, E. Webb, D. Rogers, and M. L. Sogin. 2005. Marinobacter aquaeolei gene expression studies for clues to neutrophilic iron oxidation, abstr. 829. NAI Bienn. Meet. University of Colorado, Boulder, CO.
11. Dyhrman, S. T., et al. 2006. Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nat. Lett. 439:68-71.
12. Eisen, J., et al. 2002. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc. Natl. Acad. Sci. U. S. A. 99:9509-9514.
13. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
14. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
15. Fontaine, S., A. Mariotti, and L. Abbadie. 2003. The priming effect of organic matter: a question of microbial competition? Soil Biol. Biochem. 35:837-843.
16. Gauthier, M. J., et al. 1992. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int. J. Syst. Bacteriol. 42:568-576.
17. Gerhardt, M. B., P. C. Stern, P. M. Maroney, and S. C. Mitchell. 1992. Removal of selenium from petroleum refinery waste-waters, abstr. 497. AIChE Summer Natl. Meet. 1992, Miami, FL.
18. Giovannoni, S. J., et al. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1-5.
19. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
20. Gorshkova, N. M., et al. 2003. Marinobacter excellens sp. nov., isolated from sediments of the Sea of Japan. Int. J. Syst. Evol. Microbiol. 53:2073-2078.
21. Gu, J., H. Cai, S. Yu, R. Qu, and B. Yin. 2007. Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield. Int. J. Syst. Evol. Microbiol. 57:250-254.
22. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
23. Guo, B., J. Gu, Y. Ye, and Y. Tang. 2007. Marinobacter segnicrescens sp. nov., a moderate halophile isolated from benthic sediment of the South China Sea. Int. J. Syst. Evol. Microbiol. 57:1970-1974.
24. Han, C. S., and P. Chain. 2006. Finishing repeat regions automatically with Dupfinisher, p. 141-146. In H. R. Arabnia and H. Valafar (ed.), Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology. CSREA Press, Las Vegas, NV.
25. Handley, K., M. Hery, and J. Lloyd. 2009. Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment. Int. J. Syst. Evol. Microbiol. 59:886-892.
26. Heidelberg, J. F., I. T. Paulsen, J. Eisen, K. H. Nealson, and C. M. Fraser. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-1123.
27. Homann, V. V., K. J. Edwards, E. A. Webb, and A. Butler. 2009. Siderophores of Marinobacter aquaeolei: petrobactin and its sulfonated derivatives. Biometals 22:565-571.
28. Huo, Y., C. Wang, J. Yang, M. Wu, and X. Xu. 2008. Marinobacter mobilis sp. nov. and Marinobacter zhejiangensis sp. nov., halophilic bacteria isolated from the East China Sea. Int. J. Syst. Evol. Microbiol. 58:2885-2889.
29. Jørgensen, B., S. D'Hondt, and D. Miller. 2006. 2. Microbial community composition in deep marine subsurface sediments of ODP Leg 201: sequencing surveys and cultivations. Proc. Ocean Drill. Prog. Sci. Res. 201:1-19.
30. Juteau, P., R. Larocque, D. Rho, and A. LeDuy. 1999. Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter. Appl. Microbiol. Biotechnol. 52:863-868.
31. Karp, P. D., et al. 2005. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33:6083-6089.
32. Kassen, R. 2002. The experimental evolution of specialists, generalists, and the maintenance of diversity. J. Evol. Biol. 15:173-190.
33. Kaye, J. Z., and J. A. Baross. 2000. High incidence of halotolerant bacteria in Pacific hydrothermal-vent and pelagic environments. FEMS Microbiol. Ecol. 32:249-260.
34. Kaye, J. Z., J. B. Sylvan, K. J. Edwards, and J. A. Baross. 2011. Halomonas and Marinobacter ecotypes from hydrothermal vent, subseafloor, and deepsea environments. FEMS Microbiol. Ecol. 75:123-133.
35. Koebnik, R. 2005. TonB-dependent trans-envelope signalling: the exception or the rule? Trends Microbiol. 13:343-347.
36. Kononova, S. V., and M. A. Nesmeyanova. 2002. Phosphonates and their degradation by microorganisms. Biochemistry 67:184-195.
37. Konstantinidis, K. T., and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102: 2567-2572.
38. Lander, E. S., and M. S. Waterman. 1988. Genomic mapping by fingerprinting random cones: a mathematical analysis. Genomics 2:213-239.
39. Lauro, F. M., et al. 2009. The genomic basis of trophic strategy in marine bacteria. Proc. Natl. Acad. Sci. U. S. A. 106:15527-15533.
40. Liebgott, P., L. Casalot, and S. Paillard. 2006. Marinobacter vinifirmus sp. nov., a moderately halophilic bacterium isolated from a wine-barrel-decalcification wastewater. Int. J. Syst. Evol. Microbiol. 56:2511-2516.
41. MacArthur, R. H., and E. O. Wilson. 1967. The theory of island biogeography. Princeton University Press, Princeton, NJ.
42. Markowitz, V. M., et al. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34:D344-D348.
43. Martín, S., et al. 2003. Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity. Int. J. Syst. Evol. Microbiol. 53:1383-1387.
44. Matthijs, S., et al. 2011. Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila L48 and its close relative Pseudomonas putida KT2440. Biometals 22:951-964.
45. Metcalf, W. W., and R. S. Wolfe. 1998. Molecular genetic analysis of phosphite and hypophosphite oxidation by Pseudomonas stutzeri WM88. J. Bacteriol. 180:5547-5558.
46. Moran, M., A. Buchan, J. Gonzalez, and J. Heidelberg. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
47. Myers, J., and C. Myers. 2002. Genetic complementation of an outer membrane cytochrome omcB mutant of Shewanella putrefaciens MR-1 requires omcB plus downstream DNA. Appl. Environ. Microbiol. 68:2781-2793.
48. Nelson, K. E., et al. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4:799-808.
49. Nguyen, B. H., E. Denner, T. Ha Dang, G. Wanner, and H. Stan-Lotter. 1999. Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Int. J. Syst. Bacteriol. 49:367-375.
50. Nowack, B. 2003. Environmental chemistry of phosphonates. Water Res. 37:2533-2546.
51. Paul, E. A., and D. A. Clark. 2007. Soil microbiology, ecology and biochemistry. Academic Press, New York, NY.
52. Pianka, E. R. 1972. r and K selection or b and d selection? Am. Nat. 106:581-588.
53. Polz, M. F., D. E. Hunt, S. P. Preheim, and D. M. Weinreich. 2006. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Biol. Sci. 361:2009-2021.
54. Proft, T., and E. N. Baker. 2009. Pili in Gram-negative and gram-positive bacteria-structure, assembly and their role in disease. Cell. Mol. Life Sci. 66:613-635.
55. Reguera, G., et al. 2005. Extracellular electron transfer via microbial nanowires. Nature 435:1098-1101.
56. Reysenbach, A.-L., and N. Hamamura. 2008. A geobiological perspective on metagenomics. Geobiology 6:337-340.
57. Riemann, L., and H.-P. Grossart. 2008. Elevated lytic phage production as a consequence of particle colonization by a marine flavobacterium (Cellulophaga sp.). Microb. Ecol. 56:505-512.
58. Rogers, D. R., C. M. Santelli, and K. J. Edwards. 2003. Geomicrobiology of deep-sea deposits: estimating community diversity from low-temperature seafloor rocks and minerals. Geobiology 1:109-117.
59. Romanenko, L. A., et al. 2005. Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment. Int. J. Syst. Evol. Microbiol. 55:143-148.
60. Schwartz, E. 2009. Microbial megaplasmids. Springer-Verlag, Heidelberg, Germany.
61. Shieh, W. Y., W. D. Jean, Y.-T. Lin, and M. Tseng. 2003. Marinobacter lutaoensis sp. nov., a thermotolerant marine bacterium isolated from a coastal hot spring in Lutao, Taiwan. Can. J. Microbiol. 49:244-252.
62. Shivaji, S., P. Gupta, P. Chaturvedi, K. Suresh, and D. Delille. 2005. Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from sea water off the sub-Antarctic Kerguelen Islands. Int. J. Syst. Evol. Microbiol. 55: 1453-1456.
63. Sorek, R., V. Kunin, and P. Hugenholtz. 2008. CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. 6:181-186.
64. Tate, R. L. 1995. Soil microbiology. Wiley, New York, NY.
65. Templeton, A., H. Staudigel, and B. Tebo. 2005. Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi Seamount. Geomicrobiol. J. 22:127-139.
66. Valdés, J., et al. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9:597.
67. Varela, M. M., H. M. van Aken, and G. J. Herndl. 2008. Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso-and bathypelagic waters of the (sub)tropical Atlantic. Environ. Microbiol. 10:1903-1911.
68. Vaysse, P.-J., et al. 2009. Proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation. Res. Microbiol. 160:829-837.
69. West, A. H., and A. M. Stock. 2001. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem. Sci. 26:369-376.
70. White, A. K., and W. W. Metcalf. 2004. Two COP lyase operons in Pseudomonas stutzeri and their roles in the oxidation of phosphonates, phosphite, and hypophosphite. J. Bacteriol. 186:4730-4739.
71. Yoon, J., M. Lee, S. Kang, and T. Oh. 2007. Marinobacter salicampi sp. nov., isolated from a marine solar saltern in Korea. Int. J. Syst. Evol. Microbiol. 57:2102-2105.
72. Yoon, J.-H., D.-Y. Shin, I.-G. Kim, K. H. Kang, and Y.-H. Park. 2003. Marinobacter litoralis sp. nov., a moderately halophilic bacterium isolated from sea water from the East Sea in Korea. Int. J. Syst. Evol. Microbiol. 53:563-568.