Life in extreme environments: Microbial diversity in Great Salt Lake, Utah

Extremophiles

Volumn 18, Issue 3, 2014, Pages 525-535

  Tazi, Loubna ^a   Breakwell, Donald P ^b   Harker, Alan R ^b   Crandall, Keith A ^c  

^a KANSAS STATE UNIVERSITY   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

^c GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

16S rRNA; Archaea; Bacteria; Biodiversity; GSL; Halophiles

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEON; BACTERIA; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; LAKE; MICROBIOLOGY; MICROFLORA; PHYLOGENY; SALINITY; SALT TOLERANCE; UNITED STATES;

ARCHAEA; BACTERIA; LAKES; MICROBIOTA; PHYLOGENY; SALINITY; SALT-TOLERANCE; UTAH;

EID: 84899475289     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-014-0637-x     Document Type: Article

References (71)

1. Baas-Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W. P. van Stockum and Zoon, The Hague.
2. Baxter BK, Litchfield CD, Sowers K, Griffith JD, DasSarma PA, DasSarma S (2005) Great Salt Lake microbial diversity. In: Gunde-Cimerron N, Oren A, Plemenita A (eds) Adaptation to life in high salt concentrations in Archaea, Bacteria, and Eukarya. Springer, The Netherlands.
3. Bell T, Ager D, Song JI, Newman JA, Thompson IP, Lilley AK, van der Gast CJ (2005) Larger islands house more bacterial taxa. Science 308: 1884.
4. Boujelben I, Gomariz M, Martínez-García M, Santos F, Peña A, López C, Antón J, Maalej S (2012) Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia. Antonie van Leeuwenhoek 101: 845-857.
5. Boutaiba S, Hacene H, Bidle KA, Maupin-Furlow JA (2011) Microbial diversity of the hypersaline Sidi Ameur and Himalatt salt lakes of the Algerian Sahara. J Arid Environ 75: 909-916.
6. Brakstad OG, Lødeng AG (2005) Microbial diversity during biodegradation of crude oil in seawater from the North Sea. Microb Ecol 49: 94-103.
7. Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML (2004) Combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an Australian crystallizer pond are cultivable. Appl Environ Microbiol 70: 5258-5265.
8. Cannon JS, Cannon MA (2002) The southern Pacific Railroad trestle: past and present. In: Gwynn JW (ed) Great Salt Lake, an overview of change. Special Publication of the Utah Department of Natural Resources, Salt Lake City pp 283-294.
9. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552.
10. Clementino MM, Vieira RP, Cardoso AM, Nascimento AP, Silveira CB, Riva TC, Gonzalez AS, Paranhos R, Albano RM, Ventosa A, Martins OB (2008) Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world. Extremophiles 12: 595-604.
11. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-D172.
12. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
13. Crandall KA, Fetzner JW, Lawler SH, Kinnersley M, Austin CM (1999) Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Austral J Zool 47: 199-214.
14. Cytryn E, Minz D, Oremland RS, Cohen Y (2000) Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl Environ Microbiol 66: 3269-3276.
15. Daffonchio D, Borin S, Brusa T, Brusetti L, van der Wielen PW, Bolhuis H, Yakimov MM, D'Auria G, Giuliano L, Marty D, Tamburini C, McGenity TJ, Hallsworth JE, Sass AM, Timmis KN, Tselepides A, de Lange GJ, Hübner A, Thomson J, Varnavas SP, Gasparoni F, Gerber HW, Malinverno E, Corselli C, Garcin J, McKew B, Golyshin PN, Lampadariou N, Polymenakou P, Calore D, Cenedese S, Zanon F, Hoog S (2006) Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline. Nature 440: 203-207.
16. de Souza MP, Amini A, Dojka MA, Pickering IJ, Dawson SC, Pace NR, Terry N (2001) Identification and characterization of bacteria in a selenium-contaminated hypersaline evaporation pond. Appl Environ Microbiol 67: 3785-3794.
17. de Wit R, Bouvier T (2006) 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say? Environ Microbiol 8: 755-758.
18. Eardley AJ (1963) Oil seeps at Rozel Point. Utah Geol Mineral Survey Spec Stud 5: 32.
19. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
20. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
21. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
22. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
23. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.
24. Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F (2011) New abundant microbial groups in aquatic hypersaline environments. Sci Rep 1: 135.
25. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59: 307-321.
26. Gwynn JW (1980) Great Salt Lake: a scientific, historical and economic overview. Utah Geol Mineral Surv Bull 116: 83-96.
27. Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR (2013) Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J 7: 50-60.
28. Hassibe WR, Keck WG (1978) The Great Salt Lake. US Geological Survey, Reston.
29. Head IM, Jones DM, Röling WF (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4: 173-182.
30. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJ (2004) A taxa-area relationship for bacteria. Nature 432: 750-753.
31. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63-67.
32. Konno U, Kouduka M, Komatsu DD, Ishii K, Fukuda A, Tsunogai U, Ito K, Suzuki Y (2013) Novel microbial populations in deep granitic groundwater from Grimsel Test Site, Switzerland. Microbiol Ecol 65: 626-637.
33. Lay CY, Mykytczuk NC, Niederberger TD, Martineau C, Greer CW, Whyte LG (2012) Microbial diversity and activity in hypersaline high Arctic spring channels. Extremophiles 16: 177-191.
34. Litchfield CD, Gillevet PM (2002) Microbial diversity and complexity in hypersaline environments: a preliminary assessment. J Ind Microbiol Biotechnol 28: 48-55.
35. Logares R, Lindström ES, Langenheder S, Logue JB, Paterson H, Laybourn-Parry J, Rengefors K, Tranvik L, Bertilsson S (2013) Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J 7: 937-948.
36. Maddison DR, Maddison WP (2005) MacClade 4: analysis of phylogeny and character evolution. Version 4. 08a. Sinauer Associates, Sunderland.
37. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreås L, Reysenbach AL, Smith VH, Staley JT (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-112.
38. Maturrano L, Santos F, Rosselló-Mora R, Antón J (2006) Microbial diversity in Maras salterns, a hypersaline environment in the Peruvian Andes. Appl Environ Microbiol 72: 3887-3895.
39. Mesbah NM, Abou-El-Ela SH, Wiegel J (2007) Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microbiol Ecol 54: 598-617.
40. Meuser JE, Baxter BK, Spear JR, Peters JW, Posewitz MC, Boyd ES (2013) Contrasting patterns of community assembly in the stratified water column of Great Salt Lake, Utah. Microb Ecol 66: 268-280.
41. Nam YD, Jung MJ, Roh SW, Kim MS, Bae JW (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6: e22109.
42. O'Malley MA (2007) The nineteenth century roots of 'everything is everywhere'. Nature Rev Microbiol 5: 647-651.
43. Oren A (2012) Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics. Int J Syst Evol Microbiol 62: 263-271.
44. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
45. Pagaling E, Wang H, Venables M, Wallace A, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S (2009) Microbial biogeography of six salt lakes in Inner Mongolia, China, and a salt lake in Argentina. Appl Environ Microbiol 75: 5750-5760.
46. Papke RT, Ward DM (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol Ecol 48: 293-303.
47. Parnell JJ, Crowl TA, Weimer BC, Pfrender ME (2009) Biodiversity in microbial communities: system scale patterns and mechanisms. Mol Ecol 18: 1455-1462.
48. Parnell JJ, Rompato G, Crowl TA, Weimer BC, Pfrender ME (2011) Phylogenetic distance in Great Salt Lake microbial communities. Aquat Microbiol Ecol 64: 267-273.
49. Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008) Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol 9: R70.
50. Pielou EC (1975) Ecological diversity. Wiley, New York.
51. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE (2013) Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 8: e61692.
52. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol 53: 793-808.
53. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
54. Post FJ (1977) The microbial ecology of the Great Salt Lake. Microbiol Ecol 3: 143-165.
55. Post FJ (1981) Microbiology of the Great Salt Lake North arm. Hydrobiologia 81: 59-69.
56. Raghavan TM, Furtado I (2000) Tolerance of an estuarine halophilic archaebacterium to crude oil and constituent hydrocarbons. Bull Environ Contam Toxicol 65: 725-731.
57. Rengefors K, Logares R, Laybourn-Parry J (2012) Polar lakes may act as ecological islands to aquatic protists. Mol Ecol 21: 3200-3209.
58. Riis V, Kleinsteuber S, Babel W (2003) Influence of high salinities on the degradation of diesel fuel by bacterial consortia. Can J Microbiol 49: 713-721.
59. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
60. Sinninghe Damsté JS, de Leeuw JW, Kock-van Dalen AC, de Zeeuw MA, de Lange F, Rijpstra WIC, Schenck PA (1987) The occurrence and identification of series of organic sulphur compounds in oils and sediment extracts: I. A study of Rozel Point Oil (USA). Geochim Cosmochim Acta 51: 2369-2391.
61. Sørensen KB, Canfield DE, Teske AP, Oren A (2005) Community composition of a hypersaline endoevaporitic microbial mat. Appl Environ Microbiol 71: 7352-7365.
62. Souza V, Espinosa-Asuar L, Escalante AE, Eguiarte LE, Farmer J, Forney L, Lloret L, Rodríguez-Martínez JM, Soberón X, Dirzo R, Elser JJ (2006) An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert. Proc Natl Acad Sci USA 103: 6565-6570.
63. Tapilatu YH, Grossi V, Acquaviva M, Militon C, Bertrand JC, Cuny P (2010) Isolation of hydrocarbon-degrading extremely halophilic archaea from an uncontaminated hypersaline pond (Camargue, France). Extremophiles 14: 225-231.
64. Tischer K, Zeder M, Klug R, Pernthaler J, Schattenhofer M, Harms H, Wendeberg A (2012) Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples. Syst Appl Microbiol 35: 526-532.
65. Tsai CR, Garcia JL, Patel BK, Cayol JL, Baresi L, Mah RA (1995) Haloanaerobium alcaliphilum sp. nov., an anaerobic moderate halophile from the sediments of Great Salt Lake, Utah. Int J Syst Bacteriol 45: 301-307.
66. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
67. Wainø M, Tindall BJ, Ingvorsen K (2000) Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah. Int J Syst Evol Microbiol 50: 183-190.
68. Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434: 1011-1014.
69. Weimer BC, Rompato G, Parnell JJ, Gann R, Ganesan B, Navas C, Gonzalez M, Clavel M, Albee-Scott S (2009) Microbial biodiversity of Great Salt Lake, Utah. In: Oren A, Naftz DL, Palacios P, Wurtsbaugh SJ (eds) Saline lakes around the world: unique systems with unique values (Natural Resources and Environmental Issues, vol. 15). S. J. and Jessie E. Quinney Natural Resources Research Library, Logan, pp 15-22.
70. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
71. Wright ES, Yilmaz LS, Noguera DR (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78: 717-725.