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Original Articles

Vertical distribution of fungal communities in tallgrass prairie soil

, &
Pages 1027-1041 | Received 21 Dec 2009, Accepted 07 Mar 2010, Published online: 20 Jan 2017

LITERATURE CITED

  • Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143–169.
  • An ZQ, Grove JH, Hendrix JW, Hershman DE, Henson GT. 1990. Vertical distribution of endogonaceous mycorrhizal fungi associated with soybean, as affected by soil fumigation. Soil Biol Biochem 22:715–719.
  • Anderson IC, Parkin PI. 2007. Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. J Microbiol Methods 68:248–253.
  • ———, ———, Campbell CD. 2008. DNA- and RNA-derived assessments of fungal community composition in soil amended with sewage sludge rich in cadmium, copper and zinc. Soil Biol Biochem 40:2358–2365.
  • Baier R, Ingenhaag J, Blaschke H, Gottlein A, Agerer R. 2006. Vertical distribution of an ectomycorrhizal community in upper soil horizons of a young Norway spruce (Picea abies [L.] Karst.) stand of the Bavarian limestone alps. Mycorrhiza 16:197–206.
  • Borneman J, Hartin RJ. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360.
  • Buée EL, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009. 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456.
  • Cardenas E, Tiedje JM. 2008. New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19:544–549.
  • Colwell RK. 2006. EstimateS: statistical estimation of species richness and shared species from samples. Version 8. http://viceroy.eeb.uconn.edu/estimates
  • Cooke RC, Rayner ADM. 1984. Ecology of saprobic fungi. London: Longman. 415 p.
  • Crous PW, Schubert K, Braun U, de Hoog GS, Hocking AD, Shin H, Groenewald JZ. 2007. Opportunistic, human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae. Stud Mycol 58:185–234.
  • Dickie IA, Xu B, Koide RT. 2002. Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol 156:527–535.
  • Domsch KH, Gams W, Anderson T. 1980. Compendium of soil fungi. New York: Academic Press. 1264 p.
  • Egerton-Warburton LM, Graham RC, Hubbert KR. 2003. Spatial variability in mycorrhizal hyphae and nutrient and water availability in a soil-weathered bedrock profile. Plant Soil 249:331–342.
  • Fay PA, Carlisle JD, Knapp AK, Blair JM, Collins SL. 2000. Altering rainfall timing and quantity in a mesic grassland ecosystem: design and performance of rainfall manipulation shelters. Ecosystems 3:308–319.
  • Fierer N, Schimel JP, Holden PA. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem 35:167–176.
  • Fisher RA, Corbet AS, Williams CB. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. J Animal Ecol 12:42–58.
  • Fritze H, Pietikäinen J, Pennanen T. 2000. Distribution of microbial biomass and phospholipid fatty acids in podzol profiles under coniferous forest. Eur J Soil Sci 51:565–573.
  • Goos RD. 1987. Fungi with a twist—the helicosporous hyphomycetes. Mycologia 79:1–22.
  • Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5:235–237.
  • Henk DA, Vilgalys R. 2007. Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium. Am J Bot 94:1515–1526.
  • Hoffmann C, Minkah N, Leipzig J, Wang GP, Tebas P, Bushman FD. 2007. DNA bar-coding and pyrophosphate sequencing reveals rare HIV drug resistance mutations of potential clinical significance. Antiviral Therapy (London) 12:S152–S152.
  • Huang XQ, Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Res 9:868–877.
  • Jakobsen I, Nielsen NE. 1983. Vesicular arbuscular mycorrhiza in field-grown crops 1. Mycorrhizal infection in cereals and peas at various times and soil depths. New Phytol 93:401–413.
  • Jumpponen A, Johnson LC. 2005. Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations—a case study from tallgrass prairie. Mycologia 97:1177–1194.
  • ———, Jones KL. 2009. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184: 438–448.
  • ———, ———, Mattox JD, Yeage C. 2010. Massively parallel 454 sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 19(S1):41–53.
  • Kabir Z, O’Halloran IP, Widden P, Hamel C. 1998. Vertical distribution of arbuscular mycorrhizal fungi under corn (Zea mays L.) in no-till and conventional tillage systems. Mycorrhiza 8:53–55.
  • Lai X, Cao L, Tan H, Fang S, Huang Y, Zhou S. 2007. Fungal communities from methane hydrate-bearing deep-sea marine sediments in South China Sea. ISME J 1:756–762.
  • Lenz R, Eisenbeis G. 1998. The vertical distribution of decomposition activity and of litter-colonizing nematodes in soils under different tillage. Pedobiologia 42: 193–204.
  • Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Hogberg P, Stenlid J, Finlay RD. 2007. Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytol 173:611–620.
  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380.
  • Mather PM. 1976. Computational methods of multivariate analysis in physical geography. London: J Wiley & Sons. 532 p.
  • McCune B, Mefford MJ. 1999. PC-ORD multivariate analysis of ecological data. Version 4.1. Glendale Beach, Oregon: MjM Software.
  • Meyer M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nature Protocols 3: 267–278.
  • Nilsson RH, Ryberg M, Abarenkov K, Sjokvist E, Kristiansson E. 2009. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 296:97–101.
  • Oehl F, Sieverding E, Ineichen K, Ris EA, Boller T, Wiemken A. 2005. Community structure of arbuscular mycorrhizal fungi at different soil depths in extensively and intensively managed agroecosystems. New Phytol 165:273–283.
  • Porter TM, Schadt CW, Rizvi L, Martin AP, Schmidt SK, Scott-Denton L, Vilgalys R, Moncalvo JM. 2008. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Mol Phylogenet Evol 46:635–644.
  • Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6:639–641.
  • Ransom MD, Rice CW, Todd TC, Wehmueller WA. 1998. Soils and soil biota. In: Knapp AK, Briggs JM, Hartnett DC, Collins SL, eds. Grassland dynamics: long-term ecological research in tallgrass prairie. New York: Oxford. p 48–67.
  • Renker C, Alphei J, Buscot F. 2003. Soil nematodes associated with the mammal pathogenic fungal genus Malassezia (Basidiomycota: Ustilaginomycetes) in central European forests. Biol Fertility Soils 37:70–72.
  • Rillig MC, Field CB. 2003. Arbuscular mycorrhizae respond to plants exposed to elevated atmospheric CO2 as a function of soil depth. Plant Soil 254:383–391.
  • Roesch LF, Fulthorpe RR, Riva A, Gasella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290.
  • Rosling A, Landeweert R, Lindahl BD, Larsson KH, Kuyper TW, Taylor AFS, Finlay RD. 2003. Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytol 159:775–783.
  • Schadt CW, Martin AP, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359–1361.
  • Smith SE, Read DJ. 2008. Mycorrhizal symbiosis. 3rd ed. London: Academic Press. 800 p.
  • Snajdr J, Valaskova V, Merhautova V, Herinkova J, Cajthaml T, Baldrian P. 2008. Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biol Biochem 40:2068–2075.
  • 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.
  • Towne EG. 2002. Vascular plants of Konza Prairie Biological Station: an annotated checklist of species in a Kansas tallgrass prairie. Sida 20:269–294.
  • Vilgalys R. 2003. Taxonomic misidentification inPUBLIC DNA databases. New Phytol 160:4–5.
  • Wang Z, Binder M, Hibbett DS. 2005. Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological and molecular studies. Am J Bot 92:1565–1574.
  • White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. New York: Academic Press. p 315–325.
  • Zajicek JM, Hetrick BAD, Owensby CE. 1986. The influence of soil depth on mycorrhizal colonization of forbs in the tallgrass prairie. Mycologia 78:316–320.
  • Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214.

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