Bacterial diversity and occurrence of ammonia-oxidizing bacteria in the Atacama Desert soil during a " desert bloom" event

Soil Biology and Biochemistry

Volumn 42, Issue 7, 2010, Pages 1183-1188

  Orlando, Julieta ^a   Alfaro, Marco ^b   Bravo, Lorena ^a   Guevara, Rafael ^a   Carú, Margarita ^a  

^a UNIVERSITY OF CHILE   (Chile)

^b LIAP   (Chile)

Author keywords

Ammonia oxidizing bacteria; Atacama Desert; Bacterial diversity; Desert bloom event

Indexed keywords

16S RRNA GENE; AMMONIA OXIDIZING BACTERIA; ARID SOILS; ATACAMA DESERT; BACTERIAL COMMUNITY; BACTERIAL COMPOSITION; BACTERIAL DIVERSITY; CLONING AND SEQUENCING; GENE CLONES; NORTHERN CHILE;

AMMONIA; ARID REGIONS; BACTERIOLOGY; BLOOMS (METAL); CLONING; RNA; SOIL MOISTURE;

LANDFORMS;

BACTERIUM; COMMUNITY COMPOSITION; DESERT SOIL; GENETIC ANALYSIS; MICROBIAL COMMUNITY; RAINFALL; SOIL MICROORGANISM; SOIL MOISTURE; SPECIES DIVERSITY; TAXONOMY;

ATACAMA DESERT; CHILE;

BACTERIA (MICROORGANISMS); NITROSOMONADALES; NITROSOSPIRA;

EID: 77954862112     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2010.03.025     Document Type: Article

References (52)

1. Adams M.B. Ecological issues related to N deposition into natural ecosystems: research needs. Environment International 2003, 29:189-199.
2. Almeyda E. Pluviometría de las zonas del desierto y las estepas cálidas de Chile 1948, Editorial Universitaria, Santiago, Chile.
3. Begon M., Harper J.L., Townsend C.R. Ecology. Individuals, Populations and Communities 1990, Blanckwell Scientific Publications Inc, Cambridge. second ed.
4. Bhatnagar A., Bhatnagar M. Microbial diversity in desert ecosystems. Current Science 2005, 89:91-100.
5. Bowman W.D., Steltzer H. Positive feedbacks to anthropogenic nitrogen deposition in Rocky Mountain alpine tundra. Ambio 1998, 27:514-517.
6. Bruns M.A., Stephen J.R., Kowalchuk G.A., Prosser J.I., Paul E.A. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Applied and Environmental Microbiology 1999, 65:2994-3000.
7. Connon S.A., Lester E.D., Shafaat H.S., Obenhuber D.C., Ponce A. Bacterial diversity in hyperarid Atacama Desert soils. Journal of Geophysical Research 2007, 112. 10.1029/2006JG000311.
8. Drees K.P., Neilson J.W., Betancourt J.L., Quade J., Henderson D.A., Pryor B.M., Maier R.M. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Applied and Environmental Microbiology 2006, 72:7902-7908.
9. Ewing S.A., Michalski G., Thiemens M., Quinn R.C., Macalady J.L., Kohl S., Wankel S.D., Kendall C., McKay C.P., Amundson R. Rainfall limit of the N cycle on Earth. Global Biogeochemical Cycles 2007, 21. 10.1029/2006GB002838.
10. Ewing S., Macalady J., Warren-Rhodes K., McKay C., Amundson R. Changes in the soil C cycle at the arid-hyperarid transition in the Atacama Desert. Journal of Geophysical Research 2008, 113. 10.1029/2007JG000495.
11. Feng Q., Endo K.N., Guodong C. Soil carbon in desertified land in relation to site characteristics. Geoderma 2002, 106:21-43.
12. Fierer N., Schimel J.P., Holden P.A. Influence of drying-rewetting frequency on soil bacterial community structure. Microbial Ecology 2003, 45:63-71.
13. Forster J.C. Soil sampling, handling, storage and analysis. Methods in Applied Soil Microbiology and Biochemistry 1995, 49-121. Academic Press Ltd., London, England. K. Alef, P. Nannipieri (Eds.).
14. Fritz P., Suzuki O., Silva C., Salati E. Isotope hydrology of groundwaters in the Pampa Del Tamarugal, Chile. Journal of Hydrology 1981, 53:161-184.
15. Girvan M.S., Bullimore J., Pretty J.N., Osborn A.M., Ball A.S. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Applied and Environmental Microbiology 2003, 69:1800-1809.
16. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
17. Hartsough P., Tyler S.W., Sterling J., Walvoord M. A 14.6kyr record of nitrogen flux from desert soil profiles as inferred from vadose zone waters. Geophysical Research Letters 2001, 28:2955-2958.
18. He J.Z., Shen J.P., Zhang L.M., Zhu Y.Q., Zheng Y.M., Xu M.G., Di H. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environmental Microbiology 2007, 9:2364-2374.
19. Hutcheson K. A test for comparing diversities based on the Shannon formula. Journal of Theoretical Biology 1970, 29:151-154.
20. Jaksic F.M. Ecological effects of El Niño in terrestrial ecosystems of western South America. Ecography 2001, 24:241-250.
21. Johnson S.L., Budinoff C.R., Belnap J., Garcia-Pichel F. Relevance of ammonium oxidation within biological soil crust communities. Environmental Microbiology 2005, 7:1-12.
22. Jukes T.H., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. Academic Press, New York, USA. H.M. Munro (Ed.).
23. Kowalchuk G.A., Stienstra A.W., Heilig G.H.J., Stephen J.R., Woldendorp J.W. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environmental Microbiology 2000, 2:99-110.
24. Lester E.D., Satomi M., Ponce A. Microflora of extreme arid Atacama Desert soils. Soil Biology & Biochemistry 2007, 39:704-708.
25. Lipson D.A., Schmidt S.K. Seasonal changes in an alpine soil bacterial community in the Colorado rocky mountains. Applied and Environmental Microbiology 2004, 70:2867-2879.
26. Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 2005, 71:8228-8235.
27. Maier R.M., Drees K.P., Neilson J.W., Henderson D.A., Quade J., Betancourt J.L. Microbial life in the Atacama Desert. Science 2004, 306:1289-1290.
28. Martin A.P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Applied and Environmental Microbiology 2002, 68:3673-3682.
29. McKay C.P., Friedmann E.I., Gomez-Silva B., Caceres-Villanueva L., Andersen D.T., Landheim R. Temperature and moisture conditions for life in the extreme arid region of the Atacama Desert: four years of observations including the El Nino of 1997-1998. Astrobiology 2003, 3:393-406.
30. Mendum T.A., Sockett R.E., Hirsch P.R. Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the β-subdivision of the class proteobacteria in arable soils to nitrogen fertilizer. Applied and Environmental Microbiology 1999, 65:4155-4162.
31. Navarro-González R., Rainey F.A., Molina P., Bagaley D.R., Hollen B.J., de la Rosa J., Small A.M., Quinn R.C., Grunthaner F.J., Cáceres L., Gomez-Silva B., McKay C.P. Mars-like soils in the Atacama Desert, Chile, and the dry limit of microbial life. Science 2003, 302:1018-1021.
32. Nejidat A. Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev Desert soils. FEMS Microbiology Ecology 2005, 52:21-29.
33. Nelson D.W. Determination of ammonium in KCl extracts by the salicylate method. Commun. Soil Science and Plant Analysis 1983, 14:1051-1062.
34. Peterjohn W.T., Schlesinger W.H. Nitrogen loss from deserts in the southwestern United States. Biogeochemistry 1990, 10:67-79.
35. Rainey, F.A., Ray, K.E., Ward-Rainey, N., 1999. The camels of the prokaryotic world. In: Eighth International Symposium on Microbial Ecology, held in Halifax, Nova Scotia, Canada.
36. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 1997, 63:4704-4712.
37. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 1987, 4:406-425.
38. Schlesinger W.H., Reynolds J.F., Cunningham G.L., Huenneke L.F., Jarrell W.M., Virginia R.A., Whitford W.G. Biological feedbacks in global desertification. Science 1990, 247:1043-1048.
39. Stephen J.R., McCaig A.E., Smith Z., Prosser J.I., Embley T.M. Molecular diversity of soil and marine 16S rDNA sequences related to β-subgroup ammonia-oxidizing bacteria. Applied and Environmental Microbiology 1996, 62:4147-4154.
40. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
41. Van de Peer Y., De Wachter R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computer Applications in the Biosciences 1994, 10:569-570.
42. Vidiella P.E., Armesto J.J., Gutierrez J.R. Vegetation changes and sequential flowering after rain in the southern Atacama Desert. Journal of Arid Environments 1999, 43:449-458.
43. Walvoord M.A., Phillips F.M., Stonestrom D.A., Evans R.D., Hartsough P.C., Newman B.D., Striegl R.G. A reservoir of nitrate beneath desert soils. Science 2003, 302:1021-1024.
44. Warren-Rhodes K.A., Dungan J.L., Piatek J., Stubbs K., Gómez-Silva B., Chen Y.P., McKay C. Ecology and spatial pattern of cyanobacterial community island patches in the Atacama Desert, Chile. Journal of Geophysical Research 2007, 112. 10.1029/2006JG000305.
45. Webster G., Embley T.M., Prosser J.I. Grassland management regimens reduce small-scale heterogeneity and species diversity of β-protobacteria ammonia oxidizer populations. Applied and Environmental Microbiology 2002, 68:20-30.
46. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 1991, 173:697-703.
47. Wieland G., Neumann R., Backhaus H. Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Applied and Environmental Microbiology 2001, 67:5849-5854.
48. Yang J.E., Skogley E.O., Schaff B.E., Kim J.J. Simple spectrophotometric determination of nitrate in water, resin, and soil extracts. Soil Science Society of America Journal 1998, 62:1108-1115.
49. Yeager C.M., Northup D.E., Grow C.C., Barns S.M., Kuske C.R. Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Applied and Environmental Microbiology 2005, 71:2713-2722.
50. Zaady E. Seasonal change and nitrogen cycling in a patchy Negev Desert: a review. Arid Land Research and Management 2005, 19:111-124.
51. Zhou J., Beicheng X., Treves D.S., Wu L.Y., Marsh T.L., O'Neill R.V., Palumbo A.V., Tiedje J.M. Spatial and resource factors influencing high microbial diversity in soil. Applied and Environmental Microbiology 2002, 68:326-334.
52. Zhou J., Xia B., Huang H., Palumbo A.V., Tiedje J.M. Microbial diversity and heterogeneity in sandy subsurface soils. Applied and Environmental Microbiology 2004, 70:1723-1734.