Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano

FEMS Microbiology Ecology

Volumn 73, Issue 2, 2010, Pages 291-302

  Dorador, Cristina ^a,b,c   Vila, Irma ^d   Remonsellez, Francisco ^e   Imhoff, Johannes F ^b   Witzel, Karl Paul ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b GEOMAR HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL   (Germany)

^c UNIVERSIDAD DE ANTOFAGASTA   (Chile)

^d UNIVERSITY OF CHILE   (Chile)

^e UNIVERSIDAD CATÓLICA DEL NORTE   (Chile)

Author keywords

16S rRNA gene; Andean Altiplano; archaeal amoA gene; archaeal diversity; Chile

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; FRESH WATER; RNA 16S;

ABUNDANCE; CLUSTER ANALYSIS; COMMUNITY COMPOSITION; GENETIC ANALYSIS; MARINE ECOSYSTEM; METHANOGENIC BACTERIUM; SALINITY; SPECIES DIVERSITY; WETLAND;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CHILE; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; SEDIMENT; WETLAND; ARCHAEON; BACTERIA;

ARCHAEA; BACTERIA; CHILE; DNA, ARCHAEAL; DNA, BACTERIAL; FRESH WATER; GEOLOGIC SEDIMENTS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY; WETLANDS;

ALTIPLANO; CHILE;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; HALOBACTERIA; HALOBACTERIUM; METHANOBACTERIA;

EID: 77954413876     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.00891.x     Document Type: Article

References (70)

1. Auguet J-C Casamayor EO (2008) A hotspot for cold crenarchaeota in the neuston of high mountain lakes. Environ Microbiol 10 : 1080 1086.
2. Beal EJ, House CH Orphan VJ (2009) Manganese- and iron-dependent marine methane oxidation. Science 325 : 184 187.
3. Biddle JF, Lipp JS, Lever MA et al 2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. P Natl Acad Sci USA 103 : 3846 3851.
4. Bräuer SL, Cadillo-Quiroz H, Yashiro E, Yavitt JB Zinder SH (2006) Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442 : 192 194.
5. Briée C, Moreira D López-García P (2007) Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Microbiol Res 158 : 213 227.
6. Cadillo-Quiroz H, Yashiro E, Yavitt JB Zinder SH (2008) Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl Environ Microb 74 : 2059 2068.
7. Casamayor EO, Schäfer H, Bañeras L, Pedrós-Alió C Muyzer G (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microb 66 : 499 508.
8. Chaban B, Ng SYM Jarrell KF (2006) Archaeal habitats - from the extreme to the ordinary. Can J Microbiol 52 : 73 116.
9. Chao A (1984) Non-parametric estimation of the classes in a population. Scand J Statistics 11 : 265 270.
10. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43 : 783 791.
11. Cui H-L, Tohty D, Zhou P-J Liu S-J (2006) Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China. Int J Syst Evol Micr 56 : 1631 1634.
12. de la Torre JR, Walker CB, Ingalls AE, Könneke M Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10 : 810 818.
13. DeLong EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 89 : 5685 5689.
14. DeLong EF (1998) Everything in moderation: archaea as 'non-extremophiles'. Curr Opin Genet Dev 8 : 649 654.
15. Demergasso C, Casamayor E, Chong G, Galleguillos P, Escudero L Pedrós-Alió C (2004) Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama desert, Northern Chile. FEMS Microbiol Ecol 48 : 57 69.
16. Demergasso C, Escudero L, Casamayor EO, Chong G, Balagué V Pedrós-Alió C (2008) Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama). Extremophiles 12 : 491 504.
17. Dojka MA, Hugenholtz P, Haack SK Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microb 64 : 3869 3877.
18. Dong H, Zhang G, Jiang H, Yu B, Chapman LR, Lucas CR Fields MW (2006) Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology. Microbiol Ecol 51 : 65 82.
19. Dorador C (2007) Microbial diversity in high altitude wetlands of the Chilean Altiplano: phylogeny, diversity and function. PhD Thesis, University of Kiel, Germany.
20. Dorador C, Busekow A, Vila I, Imhoff J Witzel K-P (2008a) Molecular analysis of enrichment cultures of ammonia oxidizers from the Salar de Huasco, a high altitude saline wetland in northern Chile. Extremophiles 12 : 405 414.
21. Dorador C, Vila I, Imhoff J Witzel K-P (2008b) Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in northern Chile: an example of geographical dispersion? FEMS Microbiol Ecol 64 : 419 432.
22. Dorador C, Meneses D, Urtuvia V, Demergasso C, Vila I, Witzel K-P Imhoff JF (2009) Diversity of Bacteroidetes in high-altitude saline evaporitic basins in northern Chile. J Geophys Res 114 : G00D05, DOI :.
23. Eggen R, Harmsen H, Geerling A de Vos WM (1989) Nucleotide sequence of a 16S rRNA encoding gene from the archaebacterium Methanothrix soehngenii. Nucleic Acids Res 17 : 9469.
24. Francis CA, Roberts KJ, Beman JM, Santoro AE Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. P Natl Acad Sci USA 102 : 14683 14688.
25. Fuhrman JA, McCallum K Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356 : 148 149.
26. Galand PE, Lovejoy C Vincent WF (2006) Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean. Aquat Microb Ecol 44 : 115 126.
27. Guindon S, Lethiec F, Duroux P Gascuel O (2005) PHYML Online, a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33 : W557 W559.
28. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. P Natl Acad Sci USA 105 : 2134 2139.
29. Holmer M Storkholm P (2001) Sulphate reduction and sulphur cycling in lake sediments: a review. Freshwater Biol 46 : 431 451.
30. Inagaki F, Suzuki M, Takai K et al 2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microb 69 : 7224 7235.
31. Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM Pearson A (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. P Natl Acad Sci USA 103 : 6442 6447.
32. Jiang H, Dong H, Yu B, Lv G, Deng S, Berzins N Dai M (2009) Diversity and abundance of ammonia-oxidizing Archaea and bacteria in Qinghai Lake, Northwestern China. Geomicrobiol J 26 : 199 211.
33. Jiang H, Dong H, Yu B, Ye Q, Shen J, Rowe H Zhang C (2008) Dominance of putative marine benthic Archaea in Qinghai Lake, north-western China. Environ Microbiol 10 : 2355 2367.
34. Jurgens G, Glöckner FO, Amann R, Saano A, Montonen L, Likolammi M Münster U (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34 : 45 56.
35. Karner MB, DeLong EF Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409 : 507 510.
36. Karr E, Ng J, Belchik S, Sattley W, Madigan M Achenbach LA (2006) Biodiversity of methanogenic and other archaea in the permanently frozen lake Fryxell, Antarctica. Appl Environ Microb 72 : 1663 1666.
37. Kemp P Aller J (2004) Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnol Oceanogr-Meth 2 : 114 125.
38. Kendall MM, Wardlaw GD, Tang CF, Bonin AS, Liu Y Valentine DL (2007) Diversity of archaea in marine sediments from Skan bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov. Appl Environ Microb 73 : 407 414.
39. Könneke M, Bernhard AE, Torre JRDL, Walker CB, Waterbury JB Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 : 543 546.
40. Liu Y, Boone DR Choy C (1990) Methanohalophilus oregonense sp. nov., a methylotrophic methanogen from an alkaline, saline aquifer. Int J Syst Bacteriol 40 : 111 116.
41. Lomans BP, Maas R, Luderer R, Camp HOD, Pol A, Drift CVD Vogels GD (1999) Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microb 65 : 3641 3650.
42. Martin-Cuadrado A-B, Rodriguez-Valera F, Moreira D et al 2008) Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J 2 : 865 886.
43. Muyzer G, de Waal EC Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb 59 : 695 700.
44. Nadkarni MA, Martin FE, Jacques NA Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148 : 257 266.
45. Oren A (2002) Molecular ecology of extremely halophilic Archaea and Bacteria. FEMS Microbiol Ecol 39 : 1 7.
46. Oren A (2006) Life at high salt concentrations. The Prokaryotes, Vol. 2 (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H Stackebrandt E, eds), pp. 263 282. Springer
47. Raskin L, Poulsen L, Noguera D, Rittmann B Stahl D (1994) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl Environ Microb 60 : 1241 1248.
48. Risacher F, Alonso H Salazar C (1999) Geoquímica de aguas en cuencas cerradas: I, II y III regiones - Chile. Ministerio de Obras Públicas, Dirección General de Aguas
49. Risacher F, Alonso H Salazar C (2003) The origin of brines and salts in Chilean salars: a hydrochemical review. Earth-Sci Rev 63 : 249 293.
50. Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H Kamagata Y (2007) Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. Appl Environ Microb 73 : 4326 4331.
51. Schleper C, Jurgens G Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3 : 479 488.
52. Shao P, Chen YQ, Zhou H et al 2004) Phylogenetic diversity of Archaea in aquafarm sediment. Mar Biol 146 : 133 142.
53. Sørensen KB Teske A (2006) Stratified communities of active Archaea in deep marine subsurface sediments. Appl Environ Microb 72 : 4596 4603. (Pubitemid 44078783)
54. Sørensen KB, Lauer A Teske A (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru basin, ODP leg 201, site 1231. Geobiology 2 : 151 161.
55. Sørensen KB, Canfield DE, Teske AP Oren A (2005) Community composition of a hypersaline endoevaporitic microbial mat. Appl Environ Microb 71 : 7352 7365.
56. Stackebrandt E Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33 : 152 155.
57. Stackebrandt E Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44 : 846 849.
58. Stahl DA Amann R (1991) Development and application of nucleic acid probes. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E Goodfellow M, eds), pp. 205 248. John Wiley & Sons Ltd
59. Takai K Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152 : 1285 1297.
60. Takai K Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microb 66 : 5066 5072.
61. Takai K, Moser DP, DeFlaun M, Onstott TC Fredrickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microb 67 : 5750 5760.
62. Tamura K, Dudley J, Nei M Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24 : 1596 1599.
63. Teske A (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23 : 357 368. (Pubitemid 44446542)
64. Teske A Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2 : 3 18.
65. van der Wielen P, Voost S van der Kooij D (2009) Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems. Appl Environ Microb 74 : 4687 4695.
66. Ventosa A, Nieto JJ Oren A (1998) Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol R 62 : 504 544.
67. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microb 65 : 4375 4384.
68. Vila I Mühlhauser HA (1987) Dinámica de lagos de altura, perspectivas de investigación. Arch Biol Med Exp 20 : 95 103.
69. Weidler GW, Dornmayr-Pfyffenhuemer M, Gerbl FW, Heinen W Stan-Lotter H (2007) Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota. Appl Environ Microb 73 : 259 270.
70. Yan B, Hong K Yu ZM (2006) Archaeal communities in mangrove soil characterized by 16S rRNA gene clones. J Microbiol 44 : 566 571.