Adaptation, ecology, and evolution of the halophilic stromatolite archaeon halococcus hamelinensis inferred through genome analyses

Archaea

Volumn 2015, Issue , 2015, Pages

  Gudhka, Reema K ^a   Neilan, Brett A ^a   Burns, Brendan P ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; HALOCOCCUS;

ARCHAEAL DNA;

ADAPTATION; ARCHAEAL GENOME; CHEMISTRY; CYANOBACTERIUM; DNA BASE COMPOSITION; DNA SEQUENCE; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; HALOCOCCUS; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; OPEN READING FRAME;

ADAPTATION, BIOLOGICAL; BASE COMPOSITION; CYANOBACTERIA; DNA, ARCHAEAL; ECOSYSTEM; EVOLUTION, MOLECULAR; GENOME, ARCHAEAL; HALOCOCCUS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SEQUENCE ANALYSIS, DNA;

EID: 84932606697     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2015/241608     Document Type: Article

References (50)

1. M. R. Walter, R. Buick, and J. S. R. Dunlop, "Stromatolites 3,400-3,500 Myr old from the North Pole area, Western Australia," Nature, vol. 284, no. 5755, pp. 443-445, 1980.
2. J. W. Schopf, "Fossil evidence of Archaean life," Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 361, no. 1470, pp. 869-885, 2006.
3. C. Dupraz and P. T. Visscher, "Microbial lithification in marine stromatolites and hypersalinemats," Trends inMicrobiology, vol. 13, no. 9, pp. 429-438, 2005.
4. R. P. Reid, P. T. Visscher, A. W. Decho et al., "The role of microbes in accretion, lamination and early lithification of modern marine stromatolites," Nature, vol. 406, no. 6799, pp. 989-992, 2000.
5. F. Goh, M. A. Allen, S. Leuko et al., "Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay," The ISME Journal, vol. 3, no. 4, pp. 383-396, 2009.
6. M. A. Allen, F. Goh, B. P. Burns, and B. A. Neilan, "Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay," Geobiology, vol. 7, no. 1, pp. 82-96, 2009.
7. B. P. Burns, F. Goh, M. Allen, and B. A. Neilan, "Microbial diversity of extant stromatolites in the hypersalinemarine environment of Shark Bay, Australia," Environmental Microbiology, vol. 6, no. 10, pp. 1096-1101, 2004.
8. A. Oren, "Population dynamics of halobacteria in the Dead Sea water column," Limnology and Oceanography, vol. 28, no. 6, pp. 1094-1103, 1983.
9. S. Benlloch, S. G. Acinas, J. Antón, S. P. Luz, and F. Rodríguez-Valera, "Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR," Microbial Ecology, vol. 41, no. 1, pp. 12-19, 2001.
10. F. Goh, S. Leuko, M. A. Allen et al., "Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated fromstromatolites in Shark Bay, Australia," International Journal of Systematic and Evolutionary Microbiology, vol. 56, no. 6, pp. 1323-1329, 2006.
11. W. D. Grant, M. Kamekura, T. J. McGenity, and A. Ventosa, "The Archaea and the deeply branching and phototrophic Bacteria," in Class III. Halobacteria class. nov In Bergey'sManual of Systematic Bacteriology, D. R. Boone, R. W. Castenholz, and G. M. Garrity, Eds., vol. 1, Springer, New York, NY, USA, 2nd edition, 2001.
12. F. Goh, Y. J. Jeon, K. Barrow, B. A. Neilan, and B. P. Burns, "Osmoadaptive strategies of the archaeon Halococcus hamelinensis isolated from a hypersaline stromatolite environment," Astrobiology, vol. 11, no. 6, pp. 529-536, 2011.
13. S. Leuko, B. A. Neilan, B. P. Burns, M. R. Walter, and L. J. Rothschild, "Molecular assessment of UVC radiation-induced DNA damage repair in the stromatolitic halophilic archaeon, Halococcus hamelinensis," Journal of Photochemistry and Photobiology B: Biology, vol. 102, no. 2, pp. 140-145, 2011.
14. S. Leuko, F. Goh, R. Ibáñez-Peral, B. P. Burns, M. R. Walter, and B. A. Neilan, "Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment," Extremophiles, vol. 12, no. 2, pp. 301-308, 2008.
15. R. K. Aziz, D. Bartels, A. Best et al., "The RAST Server: rapid annotations using subsystems technology," BMC Genomics, vol. 9, article 75, 2008.
16. V. M. Markowitz, F. Korzeniewski, K. Palaniappan et al., "The integrated microbial genomes (IMG) system," Nucleic acids research., vol. 34, pp. D344-D348, 2006.
17. A. L. Delcher, K. A. Bratke, E. C. Powers, and S. L. Salzberg, "Identifying bacterial genes and endosymbiont DNA with Glimmer," Bioinformatics, vol. 23, no. 6, pp. 673-679, 2007.
18. K. Lagesen, P.Hallin, E. A. Rødland, H.-H. Stærfeldt, T. Rognes, and D.W. Ussery, "RNAmmer: consistent and rapid annotation of ribosomal RNA genes," Nucleic Acids Research, vol. 35, no. 9, pp. 3100-3108, 2007.
19. T. M. Lowe and S. R. Eddy, "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence," Nucleic Acids Research, vol. 25, no. 5, pp. 955-964, 1997.
20. M. A. Larkin, G. Blackshields, N. P. Brown et al., "ClustalWand Clustal X version 2.0," Bioinformatics, vol. 23, no. 21, pp. 2947-2948, 2007.
21. K. Tamura, J. Dudley, M. Nei, and S. Kumar, "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0," Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596-1599, 2007.
22. E. Saunders, B. J. Tindall, R. Fähnrich et al., "Complete genome sequence of Haloterrigena turkmenica type strain (4kT)," Standards in Genomic Sciences, vol. 2, no. 1, pp. 107-116, 2010.
23. A. Witte, U. Baranyi, R. Klein et al., "Characterization of Natronobacterium magadii phage φCh1, a unique archaeal phage containing DNA and RNA,"MolecularMicrobiology, vol. 23, no. 3, pp. 603-616, 1997.
24. M. C. Gutiérrez, A. M. Castillo, M. Kamekura et al., "Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in InnerMongolia, China," International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 7, pp. 1402-1407, 2007.
25. A. Oren, "Molecular ecology of extremely halophilic Archaea and Bacteria," FEMSMicrobiology Ecology, vol. 39, no. 1, pp. 1-7, 2002.
26. R. T. Papke, C. J. Douady, W. F. Doolittle, and F. Rodríguez-Valera, "Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern," EnvironmentalMicrobiology, vol. 5, no. 11, pp. 1039-1045, 2003.
27. S. P. Balashov, E. S. Imasheva, V. A. Boichenko, J. Antón, J. M. Wang, and J. K. Lanyi, "Xanthorhodopsin: a proton pumpwith a light-harvesting carotenoid antenna," Science, vol. 309, no. 5743, pp. 2061-2064, 2005.
28. E. F. DeLong and O. Béjà, "The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times," PLoS Biology, vol. 8, no. 4,Article ID e1000359, 2010.
29. A. Copeland, S. Spring, M. Göker et al., "Complete genome sequence of Desulfomicrobium baculatum type strain (XT)," Standards in Genomic Sciences, vol. 1, no. 1, pp. 29-37, 2009.
30. A. Justé, B. Lievens, I. Frans et al., "Genetic and physiological diversity of Tetragenococcus halophilus strains isolated from sugar-and salt-rich environments," Microbiology, vol. 154, no. 9, pp. 2600-2610, 2008.
31. J. C. Yang, R.Madupu, A. S. Durkin et al., "The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms)," PLoS ONE, vol. 4, no. 7,Article ID e6085, 2009.
32. A. Ventosa, J. J. Nieto, and A. Oren, "Biology of moderately halophilic aerobic bacteria,"Microbiology and Molecular Biology Reviews, vol. 62, no. 2, pp. 504-544, 1998.
33. L. Lyngberg, J. Healy, W. Bartlett et al., "KefF, the regulatory subunit of the potassium efflux system KefC, shows quinone oxidoreductase activity," Journal of Bacteriology, vol. 193, no. 18, pp. 4925-4932, 2011.
34. T. Allers and M. Mevarech, "Archaeal genetics-the third way," Nature Reviews Genetics, vol. 6, no. 1, pp. 58-73, 2005.
35. P. Horvath and R. Barrangou, "CRISPR/Cas, the immune system of bacteria and Archaea," Science, vol. 327, no. 5962, pp. 167-170, 2010.
36. B. P. Burns, R. Anitori, P. Butterworth et al., "Modern analogues and the early history of microbial life," Precambrian Research, vol. 173, no. 1-4, pp. 10-18, 2009.
37. D. D. Martin, R. A. Ciulla, andM. F. Roberts, "Osmoadaptation in Archaea," Applied and Environmental Microbiology, vol. 65, no. 5, pp. 1815-1825, 1999.
38. M. A. Webber and L. J. V. Piddock, "The importance of efflux pumps in bacterial antibiotic resistance," Journal of Antimicrobial Chemotherapy, vol. 51, no. 1, pp. 9-11, 2003.
39. A. Castañeda-García, T. T. Do, and J. Blázquez, "The K+ uptake regulator trka controls membrane potential, pH homeostasis and multidrug susceptibility in Mycobacterium smegmatis," Journal of Antimicrobial Chemotherapy, vol. 66, no. 7, pp. 1489-1498, 2011.
40. J. Su, H. Gong, J. Lai, A. Main, and S. Lu, "The potassium transporter Trk and external potassium modulate Salmonella enterica protein secretion and virulence," Infection and Immunity, vol. 77, no. 2, pp. 667-675, 2009.
41. S. P. Kennedy, W. V. Ng, S. L. Salzberg, L. Hood, and S. DasSarma, "Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence," Genome Research, vol. 11, no. 10, pp. 1641-1650, 2001.
42. G. Storz and R. Hengge-Aronis, Bacterial Stress Responses, ASM Press, Washington, DC, USA, 2000.
43. M. R. Diaz and B. F. Taylor, "Metabolism of methylated osmolytes by aerobic bacteria from Mono Lake, a moderately hypersaline, alkaline environment," FEMS Microbiology Ecology, vol. 19, no. 4, pp. 239-247, 1996.
44. F. Goh, K. D. Barrow, B. P. Burns, and B. A. Neilan, "Identification and regulation of novel compatible solutes from hypersaline stromatolite-associated cyanobacteria," Archives of Microbiology, vol. 192, no. 12, pp. 1031-1038, 2010.
45. M. Kolbe, H. Besir, L.-O. Essen, and D. Oesterhelt, "Structure of the light-driven chloride pump halorhodopsin at 1.8 Å Resolution," Science, vol. 288, no. 5470, pp. 1390-1396, 2000.
46. C. P.Marshall, S. Leuko, C. M. Coyle, M. R. Walter, B. P. Burns, and B. A. Neilan, "Carotenoid analysis of halophilic archaea by resonance Raman spectroscopy," Astrobiology, vol. 7, no. 4, pp. 631-643, 2007.
47. B.Morton, "The biology and functional morphology of Fragum erugatum (Bivalvia: Cardiidae) from Shark Bay, Western Australia: the significance of its relationship with entrained zooxanthellae," Journal of Zoology, vol. 251, no. 1, pp. 39-52, 2000.
48. H.-P. Fiedler, C. Bruntner, A. T. Bull et al., "Marine actinomycetes as a source of novel secondary metabolites," Antonie van Leeuwenhoek, vol. 87, no. 1, pp. 37-42, 2005.
49. E. A. Lynch, G. I. Langille, A. Darling et al., "Sequencing of seven haloarchael genomes reveals patterns of genomci flux," Plos ONE, vol. 7, pp. 1-13, 2012.
50. G. Popescu and L. Dumitru, "Biosorption of some heavy metals from media with high salt concentrations by halophilic Archaea," Biotechnology & Biotechnological Equipment, vol. 23, supplement 1, pp. 791-795, 2014.