Diversity and distribution of soil fungal communities in a semiarid grassland

Mycologia

Volumn 103, Issue 1, 2011, Pages 10-21

  Porras Alfaro, Andrea ^a   Herrera, Jose ^b   Natvig, Donald O ^c   Lipinski, Kendra ^c   Sinsabaugh, Robert L ^c  

^a WESTERN ILLINOIS UNIVERSITY   (United States)

^b TRUMAN STATE UNIVERSITY   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Biological soil crust; Bouteloua gracilis; Dark septate fungi; Rhizosphere soil; Semiarid grassland

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA; RNA 18S;

ABUNDANCE; FERTILIZER APPLICATION; FUNGUS; GRASSLAND; MICROTOPOGRAPHY; POPULATION DISTRIBUTION; RHIZOSPHERE; SAMPLING; SEMIARID REGION; SOIL CRUST; SOIL MICROORGANISM; SPATIOTEMPORAL ANALYSIS; SPECIES DIVERSITY;

ARTICLE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; ECOSYSTEM; FUNGUS; GENETIC VARIABILITY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POACEAE; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; RANDOMIZATION; RHIZOSPHERE; SEQUENCE ALIGNMENT; UNITED STATES;

BASE SEQUENCE; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; FUNGI; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; NEW MEXICO; PHYLOGENY; POACEAE; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; RANDOM ALLOCATION; RHIZOSPHERE; RNA, RIBOSOMAL, 18S; SEQUENCE ALIGNMENT; SOIL MICROBIOLOGY;

NEW MEXICO; UNITED STATES;

ASCOMYCOTA; BOUTELOUA GRACILIS; FUNGI; OTUS; PLEOSPORALES;

EID: 78751520814     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/09-297     Document Type: Article

References (56)

1. Allen MF. 2006. Water dynamics of mycorrhizas in arid soils. In: Gadd GM, ed. Fungi in biogeochemical cycles. New York: Cambridge Univ Press. p 74-97.
2. Allen MF, Smith WK, Moore TS, Christensen M. 1981. Comparative water relation and photosynthesis of mycorrhizal and non-mycorrhizal Bouteloua gracilis H.B.K Lag Ex Steud. New Phytol 88:683-693, doi:10.1111/j.1469-8137.1981.tb01745.x
3. Allison SD, Hanson CA, Treseder KK. 2007. Nitrogen fertilization reduces diversity and alters community structure of active fungi in boreal ecosystems. Soil Biol Biochem 39:1878-1887, doi:10.1016/j.soilbio.2007.02.001
4. Báez S, Fargione J, Moore DI, Collins SL, Gosz JR. 2007. Atmospheric nitrogen deposition in the northern Chihuahuan desert: temporal trends and potential consequences. J Arid Environ 68:640-651, doi:10.1016/j.jaridenv.2006.06.011
5. Bates ST, Garcia-Pichel F. 2008. A culture-independent study of free-living fungi in biological soil crusts of the Colorado Plateau: their diversity and relative contribution to microbial biomass. Environ Microbiol 11:56-67, doi:10.1111/j.1462-2920.2008.01738.x
6. Bayman P, Angulo-Sandoval P, Baéz-Ortíz Z, Lodge DJ. 1998. Distribution and dispersal of Xylaria endophytes in two tree species in Puerto Rico. Mycol Res 102:944-948, doi:10.1017/S095375629700590X
7. Bell AA, Wheeler MH. 1986. Biosynthesis and functions of fungal melanins. Ann Rev Phytopathol 24:411-451, doi:10.1146/annurev.py.24.090186.002211
8. Belnap J. 2002. Nitrogen fixation in biological soil crusts from southeast Utah, USA. Biol Fertility Soils 35:128-135, doi:10.1007/s00374-002-0452-x
9. Collins SL, Sinsabaugh RL, Crenshaw C, Porras-Alfaro A, Stursova M, Zeglin L. 2008. The threshold-delay nutrient dynamics model for aridland ecosystem processes. J Ecol 96:413-420, doi:10.1111/j.1365-2745.2008.01362.x
10. Crenshaw C, Lauber CL, Sinsabaugh RL, Stavely LK. 2008. Fungal control of nitrous oxide production in semiarid grassland. Biogeochemistry 87:17-27, doi:10.1007/s10533-007-9165-4
11. Durrell LW, Shields LM. 1960. Fungi isolated in culture from soils of the Nevada test site. Mycologia 52:639-641.
12. Eldridge DJ, Semple WS, Koen TB. 2000. Dynamic of cryptogamic soil crusts in a derived grassland in southeastern Australia. Austral Ecol 25:232-240.
13. Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package). Version 3.6. Seattle: Department of Genome Sciences, Univ Washington. Distributed by the author.
14. Frey SD, Knorr M, Parrent JL, Simpson RT. 2004. Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests. Forest Ecol Manage 196:159-171, doi:10.1016/j.foreco.2004.03.018
15. Garcia-Pichel F, Johnson SL, 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, doi:10.1007/s00248-003-1004-0
16. Gardes M, Bruns TM. 1993. ITS primers with enhanced specificity of Basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2:113-118, doi:10.1111/j.1365-294X.1993.tb00005.x
17. Green L, Porras-Alfaro A, Sinsabaugh RL. 2008. Translocation of nitrogen and carbon integrates biotic crusts and grass production in desert semiarid grassland. J Ecol 96:1076-1085, doi:10.1111/j.1365-2745.2008.01388.x
18. Grishkan I, Zaady E, Nevo E. 2006. Soil crust microfungi along a southward rainfall gradient in desert ecosystems. Eur J Soil Biol 42:33-42, doi:10.1016/j.ejsobi.2005.09.014
19. Hansen K, Pfister DH. 2006. Systematics of the Pezizomycetes-the operculate discomycetes. Mycologia 98: 1029-1040, doi:10.3852/mycologia.98.6.1029
20. Helgason T, Daniell TJ, Husband R, Fitter AH, Young JPW. 1998. Ploughing up the wood-wide web? Nature 394: 431, doi:10.1038/28764
21. Herrera J, Kramer CL, Reichman OJ. 1997. Patterns of fungal communities that inhabit rodent foot stores: effect of substrate and infection time. Mycologia 86: 846-857, doi:10.2307/3761105
22. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G-H, Johnson D, O'Rourke, Crockett M, Binder M, Curtis JM, Slot JC, et al. 2006a. Reconstructing the early evolution of fungi using a sixgene phylogeny. Nature 443:818-822, doi:10.1038/nature05110
23. James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Powell MJ, Griffith GW, Vilgalys R. 2006b. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860-871, doi:10.3852/mycologia.98.6.860
24. Johnson NC. 1993. Can fertilization of soil select less mutualistic mycorrhizae? Ecol Appl 3:749-757, doi:10.2307/1942106
25. Johnson NC, Rowland DL, Corkidi L, Egerton-Warburton LM, Allen EM. 2003. Nitrogen enrichment alters mycorrhizal allocation at five mesic to semiarid grasslands. Ecology 84:1895-1908, doi:10.1890/0012-9658(2003) 084[1895:NEAMAA]2.0.CO;2
26. Jumpponen A, Johnson L. 2005. Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulation? A case study from tallgrass prairie. Mycologia 97:1177-1194, doi:10.3852/mycologia.97.6.1177
27. Jumpponen A, Trowbridge J, Mandyam K, Johnson L. 2005. Nitrogen enrichment causes minimal changes in arbuscular mycorrhizal colonization but shifts community composition-evidence from rDNA data. Biol Fertility Soils 41:217-224, doi:10.1007/s00374-005-0845-8
28. Khidir HH, Eudy DM, Porras-Alfaro A, Herrera J, Natvig DO, Sinsabaugh RL. 2010. A general suite of fungal endophytes dominate the roots of two dominant grasses in a semiarid grassland. J Arid Environ 74:35-42, doi:10.1016/j.jaridenv.2009.07.014
29. Lumbsch HT, Huhndorf SM. 2007. Outline of Ascomycota 2007. Myconet 13:1-58.
30. Luzopone C, Knight R. 2005. Unifrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microb 71: 8228-8235, doi:10.1128/AEM.71.12.8228-8235.2005
31. Maestre FT, Escudero A, Martinez I, Guerrero G, Rubio A. 2005. Does spatial pattern matter to ecosystem functioning? Insights from biological soil crusts. Funct Ecol 19:566-573, doi:10.1111/j.1365-2435.2005.01000.x
32. Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo J, Zai-Wei Ge Z, Yang Z, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RJ, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982-995, doi:10.3852/mycologia.98.6.982
33. McLain JET, Martens DA. 2005. Nitrous oxide flux from amino acid mineralization. Soil Biol Biochem 37:289-299, doi:10.1016/j.soilbio.2004.03.013
34. 2O production by heterotrophic N transformations in a semiarid soil. Appl Soil Ecol 32: 253-263, doi:10.1016/j.apsoil.2005.06.005
35. Morgan JAW, Bending GD, White PJ. 2005. Biological costs and benefits to plant-microbe interactions in the rhizosphere. J Exp Bot 56:1729-1739, doi:10.1093/jxb/eri205
36. O'Brien HE, Parrent JL, Jackson JA, Moncalvo J, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microb 71: 5544-5550, doi:10.1128/AEM.71.9.5544-5550.2005
37. Parker AEC, Vellinga R, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982-995, doi:10.3852/mycologia. 98.6.982
38. Pennington D, Collins SL. 2007. Remotely sensed response of an aridland ecosystem to pervasive drought. Landscape Ecol 22:897-910, doi:10.1007/s10980-006-9071-5
39. Porras-Alfaro A, Herrera J, Natvig DO, Sinsabaugh RL. 2007. Effect of long-term nitrogen fertilization on mycorrhizal fungi associated with a dominant grass in a semiarid grassland. Plant Soil 296:65-75, doi:10.1007/s11104-007-9290-9
40. Porras-Alfaro A, Herrera J, Sinsabaugh RL, Odenbach KJ, Lowrey T, Natvig DO. 2008. A novel root fungal consortium associated with a dominant desert grass. Appl Environ Microb 74:2805-2813, doi:10.1128/AEM.02769-07
41. Schlesinger WH, Raikes JA, Hartley AE, Cross AF. 1996. Spatial pattern of soil nutrients in desert ecosystems. Ecology 77:364-374, doi:10.2307/2265615
42. Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microb 71:1501-1506, doi:10.1128/AEM.71.3.1501-1506. 2005
43. Schloss PD, Handelsman J. 2006. Introducing SONS, a tool for OTUbased comparisons of membership and structure between microbial communities. Appl Environ Microbiol 72:6773-6779, doi:10.1128/AEM.00474-06
44. Schloss PD, Larget BR, Handelsman J. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microb 70:5485-5492, doi:10.1128/AEM.70.9.5485-5492.2004
45. Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous RW. 2006. A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041-1052, doi:10.3852/mycologia. 98.6.1041
46. Scorzetti G, Fell JW, Fonseca S, Statzell-Tallman. 2002. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res 2:495-517.
47. Simon L, Lalonde M, Bruns TD. 1992. Specific amplification of 18S fungal ribosomal genes from VA endomycorrhizal fungi colonizing roots. Appl Environ Microb 58:291-295.
48. Sinsabaugh RL, Carreiro MM, Repert DA. 2002. Allocation of extracellular enzymatic activity in relation to litter decomposition, N deposition and mass loss. Biogeochemistry 60:1-24, doi:10.1023/A:1016541114786
49. Smith SE, Read DJ. 1997. Mycorrhizal symbiosis. 2nd ed. New York: Academic Press. 605 p.
50. Spatafora JW, Sung G-H, Johnson D, Hesse C, O'Rourje B, Serdani M, Spotts R, Lutzoni F, Hofstetter V, Miadlikowska J, Reeb V, Gueidan C, Fraker E, Lumbsch T, Lücking R, Schmitt I, Hosaka K, Aptroot A, Roux C, Miller AN, Geiser DM, Hafellner J, Hestmark G, Arnold AE, Büdel B, Rauhut A, Hewitt D, Untereiner WA, Cole MS, Scheidegger C, Schultz M, Sipman H, Schoch CL. 2006. A five-gene phylogeny of Pezizomycota. Mycologia 98:1018-1028, doi:10.3852/mycologia.98.6.1018
51. States JS, Christensen M. 2001. Fungi associated with biological soil crusts in desert grasslands of Utah and Wyoming. Mycologia 93:432-439, doi:10.2307/3761728
52. States JS, Christensen M., Kinter CL. 2001. Soil fungi as components of biological soil crusts. In: Belnap J, Lange OL, eds. Biological soil crust: structure, function and management. Ecological Studies 150. Berlin, Heidelberg: Springer-Verlag. p 155-166.
53. Stursova M, Crenshaw CL, Sinsabaugh RL. 2006. Microbial responses to long-term N deposition in a semiarid grassland. Microb Ecol 51:90-98, doi:10.1007/s00248-005-5156-y
54. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.
55. Zak J. 2005. Fungal communities of desert ecosystems: links to climate change. In:Dighton J, White JF, Oudemans P, eds. The fungal community: its organization and role in the ecosystems. Boca Raton, Florida: CRC Press. p 659-681.
56. Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung G. 2006. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 98:1076-1087, doi:10.3852/mycologia.98.6.1076