[1] | Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105: 1422–1432.
|
[2] | O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Env Microbiol 71: 5544–5550.
|
[3] | Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Oxon: CAB International. 771 p.
|
[4] | Schmit JP, Mueller GM (2007) An estimate of the lower limit of global fungal diversity. Biodiv Conserv 16: 99–111.
|
[5] | Allen MF (1991) The ecology of mycorrhizae. New York: Cambridge University Press. 200 p.
|
[6] | Smith SE, Read DJ (2008) New York: Academic Press. 800 p.
|
[7] | Clay K. 1988. Fungal endophytes of grasses: a defensive mutualism between plants and fungi. Ecology 69: 10–16.
|
[8] | Santamaría J, Bayman P (2005) Fungal epiphytes and endophytes of coffee leaves (Coffea arabica). Microb Ecol 50: 1–8.
|
[9] | Jumpponen A, Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184: 438–448.
|
[10] | Kagami M, de Bruin A, Ibelings BW, Van Donk E (2007) Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics. Hydrobiologia 578: 113–129.
|
[11] | Kagami M, von Elert E, Ibelings BW, de Bruin A, Van Donk E (2007) The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella. Proc R Soc Lond Ser B 274: 1561–1566.
|
[12] | Robinson CH (2001) Cold adaptation in Arctic and Antarctic fungi. New Phytol 151: 341–353.
|
[13] | Berg B, McClaugherty C (2003) Plant litter: decomposition, humus formation, carbon sequestration. Berlin: Springer. 300 p.
|
[14] | Vega FE, Blackwell M (2005) Insect-fungal associations: ecology and evolution. New York: Oxford University Press. 333 p.
|
[15] | Mangan SA, Schnitzer SA, Herre EA, Mack KML, Valencia MC, et al. (2010) Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466: 752–755.
|
[16] | Cardoso IM, Kuyper TW (2006) Mycorrhizas and tropical soil fertility. Agr Ecosyst Env 116: 72–84.
|
[17] | Sawers RJH, Gutjahr C, Paszkowski U (2008) Cereal mycorrhiza: an ancient symbiosis in modern agriculture. Trends Plant Sci 13: 93–97.
|
[18] | Kayser O, Kiderlen AF, Croft SL (2003) Natural products as antiparasitic drugs. Parasitol Res 90: 55–62.
|
[19] | Zjawiony JK (2004) Biologically active compounds from Aphyllophorales (Polypore) fungi. J Natur Prod 67: 300–310.
|
[20] | Mortimer RK (2000) Evolution and variation of the yeast (Saccharomyces) genome. Genome Res 10: 403–409.
|
[21] | Wang J, Chen C (2006) Biosorption of heavy metals by Saccharomyces cerevisiae: a review. Biotechnol Adv 24: 427–451.
|
[22] | Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Res 9: 83–89.
|
[23] | Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, et al. (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25: 38–47.
|
[24] | Nilsson RH, Tedersoo L, Lindahl BD, Kj?ller R, Carlsen T, et al. (2011) Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytol 191: 314–318.
|
[25] | Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. (2012) Proc Natl Acad Sci USA 109: 6241–6246.
|
[26] | Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B 270: 313–321.
|
[27] | CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794–12797.
|
[28] | Valentini A, Pompanon F, Taberlet P (2009) DNA barcoding for ecologists. Trends Ecol Evol 24: 110–117.
|
[29] | Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87: 99–108.
|
[30] | Corse E, Costedoat C, Chappaz R, Pech N, Martin J, Gilles A (2010) A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces. Mol Ecol Res 10: 96–108.
|
[31] | Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, et al. (2011) DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytol 191: 288–300.
|
[32] | Sato H, Murakami N (2008) Reproductive isolation among cryptic species in the ectomycorrhizal genus Strobilomyces: Population-level caps marker-based genetic analysis. Mol Phyl Evol 48: 326–334.
|
[33] | Sato H, Yumoto T, Murakami N (2007) Cryptic species and host specificity in the ectomycorrhizal genus Strobilomyces (Strobilomycetaceae). Am J Bot 94: 1630–1641.
|
[34] | Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V (2009) Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Env Microbiol 12: 2165–2179.
|
[35] | Dumbrell AJ, Ashton PD, Aziz N, et al. (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190: 794–804.
|
[36] | Moora M, Berger S, Davison J, ?pik M, Bommarco R, et al. (2011) Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: Evidence from a continental-scale study using massively parallel 454 sequencing. J Biogeogr 38: 1305–1317.
|
[37] | Arfi Y, Buée M, Marchand C, Levasseur A, Record E (2012) Multiple markers pyrosequencing reveals highly diverse and host specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa. FEMS Microbiol Ecol 79: 433–444.
|
[38] | Lekberg Y, Schnoor T, Kj?ller R, Gibbons SM, Hansen LH, et al. (2011) 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. J Ecol 100: 151–160.
|
[39] | Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 10: 189.
|
[40] | White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols a guide to methods and applications, 315–322. Academic Press, San Diego.
|
[41] | Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113–118.
|
[42] | Egger KN (1995) Molecular analysis of ectomycorrhizal fungal communities. Canadian J Bot 73: 1415–1415.
|
[43] | Martin KJ, Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5: 28.
|
[44] | Manter DK, Vivanco JM (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.
|
[45] | Wallander H, Johansson U, Sterkenburg E, Durling MB, Lindahl BD (2010) Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests. New Phytol 187: 1124–1134.
|
[46] | Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188: 291–301.
|
[47] | Huang X, Wang J, Aluru S, Yang SP, Hillier LD (2003) PCAP: a whole-genome assembly program. Genome Res 13: 2164.
|
[48] | Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868.
|
[49] | Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511–518.
|
[50] | Jumpponen A, Jones KL (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186: 496–513.
|
[51] | Buée M, Reich M, Murat C, Morin E, Nilsson RH, et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: 449–456.
|
[52] | Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, et al. (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathogens 6: e1000713.
|
[53] | Amend AS, Seifert KA, Samson R, Bruns TD (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci USA 107: 13748–13753.
|
[54] | Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH (2008) Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinfo 4: 193–201.
|