A culture-independent study of free-living fungi in biological soil crusts of the Colorado Plateau: Their diversity and relative contribution to microbial biomass

Environmental Microbiology

Volumn 11, Issue 1, 2009, Pages 56-67

  Bates, Scott T ^a   Garcia Pichel, Ferran ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; FUNGAL RNA; RIBOSOME DNA; RIBOSOME RNA; RNA, RIBOSOMAL, 26S;

ARTICLE; BIODIVERSITY; BIOMASS; CHEMISTRY; CLASSIFICATION; DNA DENATURATION; DNA FINGERPRINTING; DNA SEQUENCE; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; RNA GENE; UNITED STATES;

BIODIVERSITY; BIOMASS; COLORADO; DNA FINGERPRINTING; DNA, FUNGAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FUNGI; GENES, RRNA; NUCLEIC ACID DENATURATION; PHYLOGENY; RNA, FUNGAL; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

ACREMONIUM (ASCOMYCOTA); ALTERNARIA; ASCOMYCOTA; BACTERIA (MICROORGANISMS); BASIDIOMYCOTA; CYANOBACTERIA; FUNGI;

EID: 58149269395     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01738.x     Document Type: Article

References (68)

1. Altschul, S.F., Madden, T.J., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
2. Anderson, D.C., Harper, K.T. Rushforth, S.R. (1982) Recovery of cryptogamic soil crusts from grazing on Utah winter ranges. J Range Manage 35 : 355 359.
3. Anderson, I.C. Cairney, J.W.G. (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6 : 769 779.
4. Bakken, L.R. Olsen, R.A. (1983) Buoyant densities and dry-matter contents of microorganisms: conversion of a measured biovolume into biomass. Appl Environ Microbiol 45 : 1188 1195.
5. Bamforth, S.S. (1984) Microbial distributions in Arizona deserts and woodlands. Soil Biol Biochem 16 : 133 137.
6. Bates, S.T., Reddy, G.S.N. Garcia-Pichel, F. (2006) Exophiala crusticola anam. nov. (affinity Herpotrichiellaceae), a novel black yeast from biological soil crusts in the western United States. Int J Syst Evol Microbiol 56 : 2697 2702.
7. Belnap, J. (1995) Surface disturbances: their role in accelerating desertification. Environ Monit Assess 37 : 39 57.
8. Belnap, J. Gillette, D.A. (1998) Vulnerability of desert biological soil crusts to wind erosion: the influence of crust development, soil texture, and disturbance. J Arid Environ 39 : 133 142.
9. Belnap, J. Lange, O.L. (eds) 2001) Biological Soil Crusts: Structure, Function, and Management. Berlin, Germany : Springer-Verlag.
10. Belnap, J., Welter, J.R., Grimm, N.B., Barger, N. Ludwig, J.A. (2005) Linkages between microbial and hydrologic processes in arid and semiarid watersheds. Ecology 86 : 298 307.
11. Bhatnagar, A. Bhatnagar, M. (2005) Microbial diversity in desert ecosystems. Curr Sci 89 : 91 100.
12. Bridge, P. Spooner, B. (2001) Soil fungi: diversity and detection. Plant Soil 232 : 147 154.
13. Christensen, M. (1981) Species diversity and dominance in fungal communities. In The Fungal Community: Its Organization and Role in the Ecosystem, 1st edn. Wicklow, D.T. Carroll, G.C. (eds). New York, NY, USA : Marcel Dekker, pp. 201 232.
14. Christensen, M. (1989) A view of fungal ecology. Mycologia 81 : 1 19.
15. Cocolin, L., Manzano, M., Aggio, D., Cantoni, C. Comi, G. (2001) A novel polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) for the identification of Micrococcaceae strains involved in meat fermentations. Its application to naturally fermented Italian sausages. Meat Sci 57 : 59 64.
16. Collins, S.L., Sinsabaugh, R.L., Crenshaw, C., Green, L., Porras-Alfaro, A., Martina Stursova, M. Zeglin, L.H. (2008) Pulse dynamics and microbial processes in aridland ecosystems. J Ecol 96 : 413 420.
17. Crenshaw, C., Lauber, C. Sinsabaugh, R.L. (2008) Fungal control of nitrous oxide production in semiarid grassland. Biogeochemistry 87 : 17 27.
18. Döbbeler, P. (1997) Biodiversity of bryophilous ascomycetes. Biodivers Conserv 6 : 721 738.
19. Domsch, K.H., Gams, W. Anderson, T.H. (1980) Compendium of Soil Fungi, Vol. I. London, UK : Academic Press.
20. Durrell, L.W. (1964) The composition and structure of walls of dark fungus spores. Mycopathologia 4 : 339 345.
21. Evans, R.D. Johansen, J.R. (1999) Microbiotic crusts and ecosystem processes. Crit Rev Plant Sci 18 : 183 225.
22. Evans, R.D. Lange, O.L. (2001) Biological soil crusts and ecosystem nitrogen and carbon dynamics. In Biological Soil Crusts: Structure, Function, and Management. Belnap, J. Lange, O.L. (eds). Berlin, Germany : Springer-Verlag, pp. 263 279.
23. Ferre, F. (1992) Quantitative or semi-quantitative PCR: reality versus myth. PCR Methods Appl 2 : 1 9.
24. Fierer, N., Jackson, J.A., Vilgalys, R. Jackson, R.B. (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71 : 4117 4120.
25. Filion, M., St-Arnaud, M. Jabaji-Hare, S.H. (2003) Direct quantification of fungal DNA from soil substrate using real-time PCR. J Microbiol Methods 53 : 67 76.
26. Fletcher, J.E. Martin, W.P. (1948) Some effects of algae and molds in the rain-crust of desert soils. Ecology 29 : 95 100.
27. Fogel, G.B., Collins, C.R., Li, J. Brunk, C.F. (1999) Prokaryotic genome size and SSU rDNA copy number: estimates of microbial relative abundance from a mixed population. Microb Ecol 38 : 93 113.
28. Galagan, J.E., Calvo, S.E., Borkovich, K.A., Selker, E.U., Read, N.D., Jaffe, D., et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422 : 859 868.
29. Garcia-Pichel, F. Belnap, J. (1996) Microenvironments and microscale productivity of cyanobacterial desert crusts. J Phycol 32 : 774 782.
30. Garcia-Pichel, F., López-Cortéz, A. Nübel, U. (2001) Phylogenetic and morophological diversity of cyanobacteria in soil desert crusts from the Colorado Plateau. Appl Environ Microbiol 67 : 1902 1910.
31. Garcia-Pichel, F., Johnson, S.L., Youngkin, D. Belnap, J. (2003) Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid-lands in the Colorado plateau. Microb Ecol 46 : 312 321.
32. Gosset, W.S. (as 'Student') (1908) The probable error of a mean. Biometrika 6 : 1 25.
33. Green, L.E., Porras-Alfaro, A. Sinsabaugh, R.L. (2008) Translocation of nitrogen and carbon integrates biotic crust and grass production in desert grassland. J Ecol 96 : 1076 1085.
34. Grishkan, I., Zaady, E. Nevo, E. (2006) Soil crust microfungi along a southward rainfall gradient in desert ecosytems. Eur J Soil Biol 43 : 33 42.
35. Gundlapally, S.R. Garcia-Pichel, F. (2006) The community and phylogenetic diversity of biological soil crusts in the Colorado Plateau studied by molecular fingerprinting and intensive cultivation. Microb Ecol 52 : 345 357.
36. Haugland, R.A., Varma, M., Wymer, L.J. Vesper, S.J. (2004) Quantitative PCR analysis of selected Aspergillus, Penicillium and Paecilomyces species. Syst Appl Microbiol 2 : 198 210.
37. Hayatsu, M., Tago, K. Saito, M. (2008) (2008) Various players in the nitrogen cycle: diversity and functions of the microorganisms involve in nitrification and denitrification. Soil Sci Plant Nutr 54 : 33 45.
38. Hoppert, M., Reimer, R., Kemmling, A., Schröder, A., Günzl, B. Heinken, T. (2004) Structure and reactivity of a biological soil crust from a xeric sandy soil in central Europe. Geomicrobiol J 21 : 183 191.
39. Hosny, M., Hijri, M., Passerieux, E. Dulieu, H. (1999) rDNA units are highly polymorphic in Scutellospora castanea (Glomales, Zygomycetes). Gene 226 : 61 71.
40. Ingraham, J.L., Maaløe, O. Neidhardt, F.C. (1983) Growth of the Bacterial Cell. Sunderland, USA : Sinauer Associates.
41. Johnson, S.L., Charles, R., Budinoff, C.R., Belnap, J. Garcia-Pichel, F. (2005) Relevance of ammonium oxidation within biological soil crust communities. Environ Microbiol 7 : 1 12.
42. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 : 111 120.
43. Kowalchuk, G.A., Gerards, S. Woldendorp, J.W. (1997) Detection and characterization of fungal infections of Ammophila arenaria (Marram Grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl Environ Microbiol 63 : 3858 3865.
44. Lange, O.L., Kidron, G.J., Büdel, B., Meyer, A., Kilian, E. Abeliovich, A. (1992) Taxonomic composition and photosynthetic characteristics of the 'biological soil crusts' covering sand dunes in the western Negev Desert. Funct Ecol 6 : 519 527.
45. Lawrey, J.D. Diederich, P. (2003) Lichenicolous fungi: interactions, evolution and biodiversity. Bryologist 106 : 80 120.
46. McCune, B. Rosentreter, R. (2007) Biotic soil crust lichens of the Columbia Basin. Monogr North Am Lichenol 1 : 1 105.
47. Manter, D.K. Vivanco, J.M. (2007) Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Methods 71 : 7 14.
48. Morrison, T., Weis, J.J. Wittwer, C.T. (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24 : 954 962.
49. Muyzer, G., de Waal, E.C. Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59 : 695 700.
50. Muyzer, G., Teske, A., Wirsen, C.O. Jannasch, H.W. (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gel electrophoresis of 16S rDNA fragments. Arch Micorbiol 164 : 165 172.
51. Nagy, M., Pérez, A. Garcia-Pichel, F. (2005) The prokaryotic diversity of biological soil crusts in the Sonoran desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiol Ecol 54 : 233 245.
52. Nash, T.H., III, White, S.L. Marsh, J.E. (1977) Lichen and moss distribution and biomass in hot desert ecosystems. Bryologist 80 : 470 479.
53. Nübel, U., Garcia-Pichel, F., Kühl, M. Muyzer, G. (1999) Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65 : 422 430.
54. O'Donnell, K. (1993) Fusarium and its near relatives. In The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics. Reynolds, D.R. Taylor, J.W. (eds). Wallingford, UK : CAB International, pp. 225 233.
55. Ranzoni, F.V. (1968) Fungi isolated in culture from soils of the Sonaran Desert. Mycologia 60 : 356 371.
56. Rothrock, M.J. Garcia-Pichel, F. (2005) Microbial diversity of benthic mats along a tidal desiccation gradient. Environ Microbiol 7 : 593 601.
57. Shannon, C.E. Weaver, W. (1949) The Mathematical Theory of Communication. Urbana, USA : University of Illinois Press.
58. Smit, E., Leeflang, P., Glandorf, B., Van Elsas, J.D. Wernars, K. (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65 : 2614 2621.
59. Smith, S.M., Abed, R.M.M. Garcia-Pichel, F. (2004) Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA. Microb Ecol 28 : 200 208.
60. States, J.S. (1978) Soil fungi of cool-desert plant communities in northern Arizona and southern Utah. J Ariz Nev Acad Sci 13 : 13 17.
61. States, J.S. Christensen, M. (2001) Fungi associated with biological soil crusts in desert grasslands of Utah and Wyoming. Mycologia 93 : 432 439.
62. States, J.S., Christensen, M. Kinter, C.L. (2001) Soil fungi as components of biological soil crusts. In Biological Soil Crusts: Structure, Function, and Management. Belnap, J. Lange, O.L. (eds). Berlin, Germany : Springer-Verlag, pp. 155 166.
63. Suryanarayanan, T.S., Thirunavukkarasu, N., Hariharan, G.N. Balaji, P. (2005) Occurrence of non-obligate microfungi inside lichen thalli. Sydowia 57 : 120 130.
64. 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.
65. Van Elsas, J.D., Duarte, G.F., Keijzer-Wolters, A.C. Smit, E. (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microb Methods 43 : 133 151.
66. Wilcoxon, F. (1945) Individual comparisons by ranking methods. Biometrics 1 : 80 83.
67. Yeager, C.M., Kornosky, J.L., Housman, D.C., Grote, E.E., Belnap, J. Kuske, C.R. (2004) Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado Plateau and Chihuahuan Desert. Appl Environ Microbiol 70 : 973 983.
68. Zak, J. (2005) Fungal communities of desert ecosystems: links to climate change. In The Fungal Community: Its Organization and Role in the Ecosystem, 3rd edn. Dighton, J., White, J.F. Oudemans, P. (eds). Boca Raton, USA : CRC Press, pp. 659 681.