Archaeal and bacterial diversity in five different hydrothermal ponds in the Copahue region in Argentina

Systematic and Applied Microbiology

Volumn 37, Issue 6, 2014, Pages 429-441

  Urbieta, María Sofía ^a   Toril, Elena González ^b   Alejandra Giaveno, M ^c   Bazán, Ángeles Aguilera ^b   Donati, Edgardo R ^a  

^a Universidad Nacional de La Plata   (Argentina)

^b INSTITUTO NACIONAL DE TÉCNICA AEROESPACIAL   (Spain)

^c UNIVERSIDAD NACIONAL DEL COMAHUE   (Argentina)

Author keywords

Environmental 16S rRNA clone libraries; Extremophiles; FISH; Geothermal environment biodiversity; Sulphur cycle

Indexed keywords

ARSENIC DERIVATIVE; BACTERIAL RNA; CADMIUM; CALCIUM ION; CHROMIUM; COBALT; FERRIC ION; MAGNESIUM ION; MANGANESE; NICKEL; POTASSIUM; RNA 16S; SODIUM; SULFATE; ZINC ION;

ACID MINE DRAINAGE; ACIDIPHILIUM; ACIDITHIOBACILLUS; ALPHAPROTEOBACTERIA; AQUIFICALES; ARCHAEAL GENE; ARCHAEON; ARGENTINA; ARTICLE; ATOMIC ABSORPTION SPECTROMETRY; BACTERIAL GENE; BETAPROTEOBACTERIA; COMMUNITY STRUCTURE; CONTROLLED STUDY; ELECTRIC CONDUCTIVITY; FLUORESCENCE IN SITU HYBRIDIZATION; GAMMAPROTEOBACTERIA; GENE SEQUENCE; HIGH TEMPERATURE; HYDROTHERMAL POND; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOLECULAR CLONING; MOLECULAR ECOLOGY; NITROSPIRAE; NONHUMAN; PH; PHYLOGENETIC TREE; PHYSICAL CHEMISTRY; PLANCTOMYCES; POND; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA SEQUENCE; SULFOLOBALES; SULFUR CYCLE; THERMAL SPRING; THERMOPHILIC BACTERIUM; THERMOPLASMATALES; WATER SAMPLING; BACTERIUM; BIODIVERSITY; CLASSIFICATION; GENETICS; GEOGRAPHY; MICROBIOLOGY; PHYLOGENY;

ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA; SULFOLOBALES; THERMOPLASMATALES;

ARCHAEA; ARGENTINA; BACTERIA; BIODIVERSITY; GENES, ARCHAEAL; GEOGRAPHY; HOT SPRINGS; PHYLOGENY; PHYSICOCHEMICAL PHENOMENA; PONDS; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY;

EID: 84925033965     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2014.05.012     Document Type: Article

References (56)

1. Achenbach L., Woese C. 16S and 23S rRNA-like primers. Archaea: A Laboratory Manual 1995, 521-523. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA. K.R. Sower, H.J. Schreier (Eds.).
2. Amann R.I. In situ identification of microorganisms by whole cell hybridization with rRNA-targeted nucleic acid probes. Molecular Microbial Ecology Manual 1995, 1-15. Kluwer Academic Publishers, Dordrecht, Netherlands. A.D.L. Akkermans, J.D. van Elsas, F.J. de Bruijn (Eds.).
3. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 1990, 56:1919-1925.
4. Amaral-Zettler L.A., Zettler E.R., Theroux S.M., Palacios C., Aguilera A., Amils R. Microbial community structure across the tree of life in the extreme Río Tinto. ISME J. 2011, 5:42-50.
5. Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weightman A.J. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 2006, 72:5734-5741.
6. Auchtung T.A., Takacs-Vesbach C.D., Cavanaugh C.M. 16S rRNA phylogenetic investigation of the candidate division Korarchaeota. Appl. Environ. Microbiol. 2006, 72:5077-5082.
7. Ayton J., Aislabie J., Barker G.M., Saul D., Turner S. Crenarchaeota affiliated with group 1.1b are prevalent in coastal mineral soils of the Ross Sea region of Antarctica. Environ. Microbiol. 2010, 12:689-703.
8. Benson C.A., Bizzoco R.W., Lipson D.A., Kelley S.T. Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents. FEMS Microbiol. Ecol. 2011, 76:74-88.
9. Bond P.L., Banfield J.F. Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. Microb. Ecol. 2001, 41:149-161.
10. Burgess A.E., Unrine J.M., Mills G.L., Romanek C.S., Wiegel J. Comparative geochemical and microbiological characterization of two thermal ponds in the Uzon Caldera, Kamchatka, Russia. Microb. Ecol. 2012, 63:471-489.
11. Chao A. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 1984, 11:265-270.
12. Chiacchiarini P., Lavalle L., Giaveno A., Donati E. First assessment of acidophilic microorganisms from geothermal Copahue-Caviahue system. Hydrometallurgy 2010, 104:334-341.
13. Daims H., Bruhl A., Amann R., Schleifer K.H., Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 1999, 22:434-444.
14. Daims H., Nielsen P., Nielsen J.L., Juretschko S., Wagner M. Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology. Water Sci. Technol. 2001, 41:85-90.
15. Donahoe-Christiansen J., D'Imperio S., Jackson C.R., Inskeep W.P., Mcdermott T.R. Arsenite-oxidizing Hydrogenobaculum strain isolated from an acid-sulfate-chloride geothermal spring in Yellowstone National Park. Appl. Environ. Microbiol. 2004, 70:1865-1868.
16. Farnfield H.R., Marcillab A.L., Warda N.I. Arsenic speciation and trace element analysis of the volcanic Río Agrio and the geothermal waters of Copahue, Argentina. Sci. Total Environ. 2012, 433:371-378.
17. Ghosh W., Roy P. Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int. J. Syst. Evol. Microbiol. 2006, 56:91-97.
18. Giaveno A., Pettinari G., González Toril E., Aguilera A., Urbieta M.S., Donati E. The influence of two thermophilic consortia on troilite (FeS) dissolution. Hydrometallurgy 2011, 106:19-25.
19. Giaveno M.A., Urbieta M.S., Ulloa R., González Toril E., Donati E. Physiologic versatility and growth flexibility as the main characteristics of a novel thermoacidophilic Acidianus strain isolated from Copahue geothermal area in Argentina. Microb. Ecol. 2013, 65:336-346.
20. Good I.J. The population frequencies of species and the estimation of population parameters. Biometrica 1953, 40:237-264.
21. Gonzalez-Toril E., Llobet-Brossa E., Casamayor E.O., Amann R., Amils R. Microbial ecology of an extreme acidic environment, the Tinto River. Appl. Environ. Microbiol. 2003, 69:4853-4865.
22. Hallberg K.B., Coupland K., Kimura S., Johnson D.B. Macroscopic streamer growths in acidic, metal rich mine waters in North Wales consist of novel and remarkably simple bacterial communities. Appl. Environ. Microb. 2005, 72:2022-2030.
23. Hamamura N., Macur R.E., Korf S., Ackerman G., Taylor W.P., Kozubal M., Reysenbach A.L., Inskeep W.P. Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments. Environ. Microbiol. 2009, 11:421-431.
24. Hammer Ø., Harper D.A.T., Ryan P.D. PAST: paleontological statistics software package for education and data analysis. Paleontol. Electron. 2001, 4:9-17.
25. Hanson C.A., Fuhrman J.A., Horner-Devine M.C., Martiny J.B. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol 2012, 10:497-506.
26. Hetzer A., Morgan H.W., Mcdonald I.R., Daughney C.J. Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand. Extremophiles 2007, 11:605-614.
27. Hou W., Wang S., Dong H., Jiang H., Briggs B.R. A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province, China using 16S rRNA gene pyrosequencing. PLOS ONE 2013, 8(1):e53350. 10.1371/journal.pone.0053350.
28. Ikenaga M., Guevara R., Dean A.L., Pisani C., Boyer J.N. Changes in community structure of sediment bacteria along the Florida Coastal Everglades Marsh-Mangrove-Seagrass salinity gradient. Microb. Ecol. 2010, 59:284-295.
29. Johnson D.B. Geomicrobiology of extremely acidic subsurface environments. FEMS Microbiol. Ecol. 2012, 81:2-12.
30. Johnson D.B., Hallberg K. The microbiology of acidic mine waters. Res. Microbiol. 2003, 154:466-473.
31. Kato S., Itoh T., Yamagishi A. Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes. FEMS Microbiol. Lett. 2011, 319:34-43.
32. Kelly D.P., Wood A.P. Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int. J. Syst. Evol. Microbiol. 2000, 50:511-516.
33. Kelly L.C., Cockell C.S., Piceno Y.M., Andersen G.L., Thorsteinsson T., Marteinsson V. Bacterial diversity of weathered terrestrial Icelandic volcanic glasses. Microb. Ecol. 2010, 60:740-752.
34. Kozubal M.A., Macur R.E., Jay Z.J., Beam J.P., Malfatti S.A. Microbial iron cycling in acidic geothermal springs of Yellowstone National Park: integrating molecular surveys, geochemical processes, and isolation of novel Fe-active microorganisms. Front. Microbiol. 2012, 3:1-16.
35. Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. John Wiley & Sons, Chichester, United Kingdom. E. Stackebrandt, M. Goodfellow (Eds.).
36. Lavalle L., Chiacchiarini P., Pogliani C., Donati E. Isolation and characterization of acidophilic bacteria from Patagonia, Argentina. Process. Biochem. 2005, 40:1095-1099.
37. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Buchner A., Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
38. Manz W., Amann R., Ludwig W., Wagner M., Schleifer K.H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst. Appl. Microbiol. 1992, 15:593-600.
39. Mas G., Mas L., Bengochea L. Alteración ácido-sulfática en el campo geotérmico Copahue, Provincia de Neuquén. Rev. Asoc. Geol. Argentina 1996, 51:78-86.
40. Mas G., Mas L., Bengochea L. Hydrothermal, surface alteration in the Copahue geothermal field (Argentina). Proceedings of the Twenty-first Workshop on Geothermal Reservoir Engineering 1996, 22-24. Stanford University, Stanford, CA.
41. Mathur J., Bizzoco R.W., Ellis D.G., Lipson D.A., Poole A.W., Levine R., Kelley S.T. Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs. Appl. Environ. Microbiol. 2007, 73:2612-2623.
42. Neef A. Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populations analyse in komplexen mikrobiellen Biozonösen. Ph.D. thesis 1997, Technical University of Munich, Munich, Germany.
43. Pernthaler A., Pernthaler J., Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 2002, 68:3094-3101.
44. Reysenbach A.L., Ehringer M., Hershberger K. Microbial diversity at 83°C in Calcite Springs, Yellowstone National: another environment where Aquificales and Korarchaeota coexist. Extremophiles 2000, 4:61-67.
45. Rusch A., Amend J.P. Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper)thermophilic archaea and bacteria. Extremophiles 2004, 8:357-366.
46. Santofimia E., Gonzalez Toril E., Lopez Pamo E., Gomariz M., Amils R., Aguilera A. Microbial diversity and its relationship to physicochemical characteristics of the water in two extreme acidic pit lakes from the Iberian Pyrite Belt (SW Spain). PLOS ONE 2013, 8:e66746. 10.1371/journal.pone.0066746.
47. Schloss P.D. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 2005, 71:1501-1506.
48. Sclesceri L.S., Greenberg A.E., Eaton A.D. Standard Methods for the Examination of Water and Wastewaters 1998, American Public Health Association, Washington, USA. 20th ed.
49. Sorokin D.Y., Teske A., Robertson L.A., Kuenen G. Anaerobic oxidation of thiosulfate to tetrathionate by obligately heterotrophic bacteria, belonging to the Pseudomonas stutzeri group. FEMS Microb. Ecol. 1999, 30:113-123.
50. Stahl D.A., Amann R. Development and application of nucleic acid probes. Nucleic Acid Techniques in Bacterial Systematics 1991, 205-248. John Wiley & Sons Ltd., Chichester, England. E. Stackebrandt, M. Goodfellow (Eds.).
51. Ter Braak C.J.F., Smilauer P. CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (Version 4.5) 2002, Microcomputer Power, Ithaca, USA.
52. Urbieta M.S., González Toril E., Aguilera A., Giaveno M.A., Donati E. First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina. Microb. Ecol. 2012, 64:91-104.
53. Vallés J., Pettinari G., Baschini M., Grathoff G. Characterization of muds and waters of the Copahue Geothermal Field, Neuquén Province, Patagonia Argentina. Int. Cong. Appl. Mineral. 2005, 1:507-510.
54. Whitaker R.J., Grogan D.W., Taylor J.W. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003, 301:976-978.
55. Williams K.P., Kelly D.P. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int. J. Syst. Evol. Microbiol. 2013, 63:2901-2906.
56. Willis G., Hedrich S., Ñancucheo I., Johnson D.B., Donati E.R. Microbial diversity in acidic anaerobic sediments at the geothermal Caviahue-Copahue System, Argentina. Adv. Mater. Res. 2013, 825:7-10.