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Mycology
An International Journal on Fungal Biology
Volume 3, 2012 - Issue 1: The impact of fungi on other organisms
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Invited Articles

Endophytic fungal diversity: review of traditional and molecular techniques

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Pages 65-76 | Received 14 Dec 2011, Accepted 09 Jan 2012, Published online: 21 Feb 2012

References

  • Albrectsen , BR , Bjorken , L , Varad , A , Hagner , A , Wedin , M , Karlsson , J and Jansson , S. 2010 . Endophytic fungi in European aspen (Populus tremula) leaves: diversity, detection, and a suggested correlation with herbivory resistance . Fungal Divers. , 41 : 17 – 28 .
  • Aly , AH , Debbab , A , Kjer , J and Proksch , P. 2010 . Fungal endophytes from higher plants: a prolific source of phytochemicals and other bioactive natural products . Fungal Divers. , 41 : 1 – 16 .
  • Anderson , IC and Cairney , JWG. 2004 . Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques . Environ Microbiol. , 6 : 769 – 779 .
  • Arnold , AE , Henk , DA , Eells , RL , Lutzoni , F and Vilgalys , R. 2007 . Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR . Mycologia , 99 : 185 – 206 .
  • Azevedo , JL and Araújo , WL. 2007 . “ Diversity and applications of endophytic fungi isolated from tropical plants ” . In Fungi: multifaceted microbes , Edited by: Ganguli , BN and Deshmukh , SK . 189 – 207 . Boca Raton , FL : CRC Press .
  • Baumgartner , K , Bhat , R and Fujiyoshi , P. 2010 . A rapid infection assay for Armillaria and real-time PCR quantitation of the fungal biomass in planta . Fungal Biol. , 114 : 107 – 119 .
  • Bayman , P , Lebrón , LL , Tremblay , RL and Lodge , DJ. 1997 . Variation in endophytic fungi from roots and leaves of Lepanthes (Orchidaceae) . New Phytol. , 135 : 143 – 149 .
  • Begerow , D , Nilsson , H , Unterseher , M and Maier , W. 2010 . Current state and perspectives of fungal DNA barcoding and rapid identification procedures . Appl Microbiol Biotechnol. , 87 : 99 – 108 .
  • Bell , AS , Blanford , S , Jenkins , N , Thomas , MB and Read , AF. 2009 . Real-time quantitative PCR for analysis of candidate fungal biopesticides against malaria: Technique validation and first applications . J Invertebr Pathol. , 100 : 160 – 168 .
  • Bellemain , E , Carlsen , T , Brochmann , C , Coissac , E , Taberlet , P and Kauserud , H. 2010 . ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases . BMC Microbiol. , 10 : 189 – 197 .
  • Bills , GF. 1996 . “ Isolation and analysis of endophytic fungal communities from wood plants ” . In Endophytic fungi in grasses and woody plants: systematics, ecology, and evolution , Edited by: Redlin , SC and Carris , LM . 31 – 65 . St. Paul , MN : APS Press .
  • Botella , L and Diez , JJ. 2011 . Phylogenic diversity of fungal endophytes in Spanish stands of Pinus halepensis . Fungal Divers. , 47 : 9 – 18 .
  • Burgess , T , Wingfield , MJ and Wingfield , BW. 2001 . Simple sequence repeat markers distinguish among morphotypes of Sphaeropsis sapinea . Appl Environ Microbiol. , 67 : 354 – 362 .
  • Camacho , FJ , Gernandt , DS , Liston , A , Stone , JK and Klein , AS. 1997 . Endophytic fungal DNA, the source of contamination in spruce needle DNA . Mol Ecol. , 6 : 983 – 987 .
  • Cannon , PF and Simmons , CM. 2002 . Diversity and host preference of leaf endophytic fungi in the Iwokrama Forest Reserve, Guyana . Mycologia , 94 : 210 – 220 .
  • Carbone , I and Kohn , LM. 1993 . Ribosomal DNA sequence divergence within internal transcribed spacer 1 of the Sclerotiniaceae . Mycologia , 85 : 415 – 427 .
  • Carroll , GC. 1986 . “ The biology of endophytism in plants with particular reference to woody plants ” . In Microbiology of the phyllosphere , Edited by: Fokkema , NJ and van den Heuvel , J . 205 – 222 . Cambridge , UK : Cambridge University Press .
  • Charles , TC. 2010 . “ The potential for investigation of plant-microbe interactions using metagenomics methods ” . In Metagenomics: Theory, methods and applications , Edited by: Marco , D . 107 – 118 . Norfolk , UK : Marco D Caister/Academic Press .
  • Cheplick , GP , Clay , K and Marks , S. 1989 . Interactions between infection by endophytic fungi and nutrient limitation in the grasses Lolium perenne and Festuca arundinacea . New Phytol. , 111 : 89 – 97 .
  • Clardy , J , Fischbach , MA and Walsh , CT. 2006 . New antibiotics from bacterial natural products . Nat Biotechnol. , 24 : 1541 – 1550 .
  • Crozier , J , Thomas , SE , Aime , MC , Evans , HC and Holmes , KA. 2006 . Molecular characterization of fungal endophytic morphospecies isolated from stems and pods of Theobroma cacao . Plant Pathol. , 55 : 783 – 791 .
  • Davey , ML and Currah , RS. 2006 . Interactions between mosses (Bryophyta) and fungi . Can J Bot. , 84 : 1509 – 1519 .
  • de Bary , A. 1866 . Morphologie und Physiologie der Pilze, Flechten, und Myxomyceten , Leipzig : W. Engelmann .
  • Deckert , RJ , Melville , LH and Peterson , RL. 2001 . Structural features of a Lophodermium endophyte during the cryptic life-cycle phase in the foliage of Pinus strobus . Mycol Res. , 105 : 991 – 997 .
  • Ding , G , Zheng , Z , Liu , S , Zhang , H , Guo , LD and Che , YS. 2009 . Photinides A-F, cytotoxic benzofuranone-derived γ-lactones from the plant endophytic fungus Pestalotiopsis photiniae . J Nat Prod. , 72 : 942 – 945 .
  • Druzhinina , IS , Kopchinskiy , AG , Komon , M , Bissett , J , Szakacs , G and Kubicek , CP. 2005 . An oligonucleotide barcode for species identification in Trichoderma and Hypocrea . Fungal Genet Biol. , 42 : 813 – 828 .
  • Dumbrell , AJ , Ashton , PD , Aziz , N , Feng , G , Nelson , M , Dytham , C , Fitter , AH and Helgason , T. 2011 . Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing . New Phytol. , 190 : 794 – 804 .
  • Duong , LM , Jeewon , R , Lumyong , S and Hyde , KD. 2006 . DGGE coupled with ribosomal DNA gene phylogenies reveal uncharacterized fungal phylotypes . Fungal Divers. , 23 : 121 – 138 .
  • Fisher , PJ , Petrini , O and Sutton , BC. 1993 . A comparative study of fungal endophytes in leaves, xylem and bark of Eucalyptus nitens in Australia and England . Sydowia , 45 : 338 – 345 .
  • Frøslev , TG , Jeppesen , TS , Laessoe , T and Kjoller , R. 2007 . Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe . Mol Phylogenet Evol. , 44 : 217 – 227 .
  • Gamboa , MA , Laureano , S and Bayman , P. 2002 . Measuring diversity of endophytic fungi in leaf fragments: Does size matter? . Mycopathologia , 156 : 41 – 45 .
  • Gao , XX , Zhou , H , Xu , DY , Yu , CH , Chen , YQ and Qu , LH. 2005 . High diversity of endophytic fungi from the pharmaceutical plant, Heterosmilax japonica Kunth revealed by cultivation-independent approach . FEMS Microbiol Lett. , 249 : 255 – 266 .
  • Gazis , R , Rehner , S and Chaverri , P. 2011 . Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences . Mol Ecol. , 20 : 3001 – 3013 .
  • Gharizadeh , B , Norberg , E , Löffler , J , Jalal , S , Tollemar , J , Einsele , H , Klingspor , L and Nyrén , P. 2004 . Identification of medically important fungi by the Pyrosequencing (TM) technology . Mycoses , 47 : 29 – 33 .
  • Ghimire , SR , Charlton , ND , Bell , JD , Krishnamurthy , YL and Craven , KD. 2011 . Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma . Fungal Divers. , 47 : 19 – 27 .
  • Gillevet , PM , Sikaroodi , M and Torzilli , AP. 2009 . Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing . Fungal Ecol. , 2 : 160 – 167 .
  • González , V and Tello , ML. 2011 . The endophytic mycota associated with Vitis vinifera in central Spain . Fungal Divers. , 47 : 29 – 42 .
  • Götz , M , Nirenberg , H , Krause , S , Wolters , H , Draeger , S , Buchner , A , Lottmann , J , Berg , G and Smalla , K. 2006 . Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods . FEMS Microbiol Ecol. , 58 : 404 – 413 .
  • Groppe , K and Boller , T. 1997 . PCR assay based on a microsatellite-containing locus for detection and quantification of Epichloë endophytes in grass tissue . Appl Environ Microbiol. , 63 : 1543 – 1550 .
  • Guo , LD. 2001 . Advances of endophytic fungi . Mycosystema , 20 : 148 – 152 . in Chinese with English abstract
  • Guo , LD , Hyde , KD and Liew , ECY. 1998 . A method to promote sporulation in palm endophytic fungi . Fungal Divers. , 1 : 109 – 113 .
  • Guo , LD , Hyde , KD and Liew , ECY. 2000 . Identification of endophytic fungi from Livistona chinensis (Palmae) using morphological and molecular techniques . New Phytol. , 147 : 617 – 630 .
  • Guo , LD , Hyde , KD and Liew , ECY. 2001 . Detection and identification of endophytic fungi within frond tissues of Livistona chinensis based on rDNA sequence . Mol Phylogenet Evol. , 20 : 1 – 13 .
  • Guo , LD , Huang , GR , Wang , Y , He , WH , Zheng , WH and Hyde , KD. 2003 . Molecular identification of white morphotype strains of endophytic fungi from Pinus tabulaeformis . Mycol Res. , 107 : 680 – 688 .
  • Guo , LD , Huang , GR and Wang , Y. 2008 . Seasonal and tissue age influences on endophytic fungi of Pinus tabulaeformis (Pinaceae) in Dongling Mountain, Beijing . J Integr Plant Biol. , 50 : 997 – 1003 .
  • Hajibabaei , M , Janzen , DH , Burns , JM , Hallwachs , W and Hebert , PDN. 2006 . DNA barcodes distinguish species of tropical Lepidoptera . Proc Natl Acad Sci USA , 103 : 968 – 971 .
  • Hallmann , J , Berg , G and Schulz , B. 2006 . “ Isolation procedures for endophytic microorganisms ” . In Microbial root endophytes , Edited by: Schulz , BJE , Boyle , CJC and Sieber , TN . 299 – 319 . Berlin : Springer .
  • Hawksworth , DL. 1991 . The fungal dimension of biodiversity: magnitude, significance, and conservation . Mycol Res. , 95 : 641 – 655 .
  • Hawksworth , DL. 2004 . ‘Misidentifications’ in fungal DNA sequence databanks . New Phytol. , 161 : 13 – 15 .
  • Hebert , PDN , Cywinska , A , Ball , SL and de Waard , JR. 2003 . Biological identifications through DNA barcodes . Proc R Soc (Lond) B , 270 : 313 – 321 .
  • Higgins , KL , Arnold , AE , Miadlikowska , J , Sarvate , SD and Lutzoni , F. 2007 . Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages . Mol Phylogenet Evol. , 42 : 543 – 555 .
  • Hoff , JA , Klopfenstein , NB , McDonald , GI , Tonn , JR , Kim , MS , Zambino , PJ , Hessburg , PF , Rogers , JD , Peever , TL and Carris , LM. 2004 . Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa) . For Pathol. , 34 : 255 – 271 .
  • Hui , N , Jumpponen , A , Niskanen , T , Liimatainen , K , Jones , KL , Koivula , T , Romantschuk , M and Strömmer , R. 2011 . EcM fungal community structure, but not diversity, altered in a Pb contaminated shooting range in a boreal coniferous forest site in Southern Finland . FEMS Microbiol Ecol. , 76 : 121 – 132 .
  • Hyde , KD and Soytong , K. 2008 . The fungal endophyte dilemma . Fungal Divers. , 33 : 163 – 173 .
  • Jargeat , P , Martos , F , Carriconde , F , Gryta , H , Moreau , PA and Gardes , M. 2010 . Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota) . Mol Ecol. , 19 : 5216 – 5230 .
  • Jumpponen , A and Jones , KL. 2009 . Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere . New Phytol. , 18 : 438 – 444 .
  • Jumpponen , A , Jones , KL and Blair , J. 2010 . Vertical distribution of fungal communities in tallgrass prairie soil . Mycologia , 102 : 1027 – 1041 .
  • Kelly , LJ , Hollingsworth , PM , Coppins , BJ , Ellis , CJ , Harrold , P , Tosh , J and Yahr , R. 2011 . DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context . New Phytol. , 191 : 288 – 300 .
  • Khin , L , Mika , H , Tomomi , B-T and Hiroki , M. 2011 . Real-time PCR assays for monitoring anaerobic fungal biomass and population size in the rumen . Curr Microbiol. , 62 : 1147 – 1151 .
  • Kõljalg , U , Larsson , KH , Abarenkov , K , Nilsson , RH , Alexander , IJ , Eberhardt , U , Erland , S , Høiland , K , Kjøller , R Larsson , E . 2005 . UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi . New Phytol. , 166 : 1063 – 1068 .
  • Krings , M , Taylor , TN , Hass , H , Kerp , H , Dotzler , N and Hermsen , EJ. 2007 . Fungal endophytes in a 400-million-yr-old land plant: infection pathways, spatial distribution, and host responses . New Phytol. , 174 : 648 – 657 .
  • Kumaresan , V and Suryanarayanan , TS. 2002 . Endophytic assemblages in young, mature and senescent leaves of Rhizophora apiculata: evidence for the role of endophytes in mangrove litter degradation . Fungal Divers. , 9 : 91 – 91 .
  • Lacap , DC , Hyde , KD and Liew , ECY. 2003 . An evaluation of the fungal ‘morphotype’ concept based on ribosomal DNA sequences . Fungal Divers. , 12 : 53 – 66 .
  • Letourneau , A , Seena , S , Marvanová , L and Bärlocher , F. 2010 . Potential use of barcoding to identify aquatic hyphomycetes . Fungal Divers. , 40 : 51 – 64 .
  • Levinson , G and Gutman , GA. 1987 . Slipped-strand mispairing: a major mechanism for DNA sequence evolution . Mol Biol Evol. , 4 : 203 – 221 .
  • Li , J , Li , L , Si , YK , Jiang , XJ , Guo , LD and Che , YS. 2011 . Virgatolides A–C, benzannulated spiroketals from the plant endophytic fungus Pestalotiopsis virgatula . Org Lett. , 13 : 2670 – 2673 .
  • Li , WC , Guo , SY and Guo , LD. 2007a . Endophytic fungi associated with lichen Physcia stellaris using different surface sterilization methods . J Fungal Res. , 5 : 202 – 206 .
  • Li , WC , Zhou , J , Guo , SY and Guo , LD. 2007b . Endophytic fungi associated with lichens in Baihua mountain of Beijing, China . Fungal Divers. , 25 : 69 – 80 .
  • Liang , Y , Guo , LD and Ma , KP. 2005 . Population genetic structure of an ectomycorrhizal fungus Amanita manginiana in a subtropical forest over two years . Mycorrhiza , 15 : 137 – 142 .
  • Liu , L , Liu , SC , Jiang , LH , Chen , XL , Guo , LD and Che , YS. 2008 . Chloropupukeananin, the first chlorinated pupukeanane derivative and its precursors from Pestalotiopsis fici . Org Lett. , 10 : 1397 – 1400 .
  • Liu , L , Li , Y , Liu , SC , Zheng , ZH , Chen , XL , Zhang , H , Guo , LD and Che , YS. 2009 . Chloropestolide A, an antitumor metabolite with an unprecedented spiroketal skeleton from Pestalotiopsis fici . Org Lett. , 11 : 2836 – 2839 .
  • Liu , L , Niu , SB , Lu , XH , Chen , XL , Zhang , H , Guo , LD and Che , YS. 2010 . Unique metabolites of Pestalotiopsis fici suggest a biosynthetic hypothesis involving a Diels-Alder reaction and then mechanistic diversification . Chem Commun. , 46 : 460 – 462 .
  • Liu , L , Bruhn , T , Guo , LD , Götz , DCG , Brun , BR , Stich , A , Che , YS and Bringmann , G. 2011 . Chloropupukeanolides C–E, cytotoxic pupukeanane chlorides with a spiroketal skeleton from Pestalotiopsis fici . Chem Eur J. , 17 : 2604 – 2613 .
  • Lucero , ME , Unc , A , Cooke , P , Dowd , S and Sun , SL. 2011 . Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var. griffithsii . PLoS ONE. , 6 : e17693
  • Lumini , E , Orgiazzi , A , Borriello , R , Bonfante , P and Bianciotto , V. 2010 . Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach . Environ Microbiol. , 12 : 2165 – 2179 .
  • Maciá-Vicente , JG , Jansson , H-B , Talbot , NJ and Lopez-Llorca , LV. 2009 . Real-time PCR quantification and live-cell imaging of endophytic colonization of barley. Hordeum vulgare. roots by Fusarium equiseti and Pochonia chlamydosporia . New Phytol. , 182 : 213 – 228 .
  • Margulies , M , Egholm , M , Altman , WE , Attiya , S , Bader , JS , Bemben , LA , Berka , J , Braverman , MS , Chen , YJ Chen , ZT . 2005 . Genome sequencing in microfabricated high-density picolitre reactors . Nature , 437 : 376 – 380 .
  • May , LA , Smiley , B and Schmidt , MG. 2001 . Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage . Can J Microbiol. , 47 : 829 – 841 .
  • Medinger , R , Nolte , V , Pandey , RM , Jost , S , Ottenwälder , B , Schlötterer , C and Boenigk , J. 2010 . Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms . Mol Ecol. , 19 : 32 – 40 .
  • Mohamed , R , Jong , PL and Zali , MS. 2010 . Fungal diversity in wounded stems of Aquilaria malaccensis . Fungal Divers. , 43 : 67 – 74 .
  • Monchy , S , Sanciu , G , Jobard , M , Rasconi , S , Gerphagnon , M , Chabé , M , Cian , A , Meloni , D , Niquil , N Christaki , U . 2011 . Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing . Environ Microbiol. , 13 : 1433 – 1453 .
  • Morakotkarn , D , Kawasaki , H and Seki , T. 2007 . Molecular diversity of bamboo-associated fungi isolated from Japan . FEMS Microbiol Lett. , 266 : 10 – 19 .
  • Morales , VM , Pelcher , LE and Taylor , JL. 1993 . Comparison of the 5.8S rDNA and internal transcribed spacer sequences of isolates of Leptosphaeria maculans from different pathogenicity groups . Curr Genet. , 23 : 490 – 495 .
  • Müller , CB and Krauss , J. 2005 . Symbiosis between grasses and asexual fungal endophytes . Curr Opin Plant Biol. , 8 : 450 – 456 .
  • Murali , TS , Suryanarayanan , TS and Venkatesan , G. 2007 . Fungal endophyte communities in two tropical forests of southern India: diversity and host affiliation . Mycol Progress , 6 : 191 – 199 .
  • Nilsson , RH , Ryberg , M , Abarenkov , K , Sjökvist , E and Kristiansson , E. 2009 . The ITS region as a target for characterization of fungal communities using emerging sequencing technologies . FEMS Microbiol Lett. , 296 : 97 – 101 .
  • Nilsson , RH , Tedersoo , L , Lindah , B D , Kjøller , R , Carlsen , T , Quince , C , Abarenkov , K , Pennanen , T , Stenlid , J Bruns , T . 2011 . Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities . New Phytol. , 191 : 314 – 318 .
  • Öpik , M , Metsis , M , Daniell , TJ , Zobel , M and Moora , M. 2009 . Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest . New Phytol. , 184 : 424 – 437 .
  • Ovaskainen , O , Nokso-Koivista , J , Hottola , J , Rajala , T , Pennanen , T , Ali-Kovero , H , Miettinen , O , Oinonen , P , Auvinen , P Paulin , L . 2010 . Identifying wood-inhabiting fungi with 454 sequencing - what is the probability that BLAST gives the correct species? . Fungal Ecol. , 3 : 274 – 283 .
  • Peay , KG , Martin , I. , Bidartondo , MI and Arnold , AE. 2010 . Not every fungus is everywhere: scaling to the biogeography of fungal-plant interactions across roots, shoots and ecosystems . New Phytol. , 185 : 878 – 882 .
  • Peever , TL , Ibañez , A , Akimitsu , K and Timmer , LW. 2002 . Worldwide phylogeography of the citrus brown spot pathogen, Alternaria alternata . Phytopathology , 92 : 794 – 802 .
  • Petrini , O. 1991 . “ Fungal endophytes of tree leaves ” . In Microbial ecology of leaves , Edited by: Andrews , JH and Hirano , SS . 179 – 197 . New York : Springer .
  • Petrini , O , Stone , J and Carroll , FE. 1982 . Endophytic fungi in evergreen shrubs in western Oregon: A preliminary study . Can J Bot. , 60 : 789 – 796 .
  • Petrini , O , Sieber , TN , Toti , L and Viret , O. 1992 . Ecology, metabolite production, and substrate utilization in endophytic fungi . Nat Toxins , 1 : 185 – 196 .
  • Photita , W , Lumyong , S , Lumyong , P and Hyde , KD. 2001 . Endophytic fungi of wild banana (Musa acuminata) at doi Suthep Pui National Park, Thailand . Mycol Res. , 105 : 1508 – 1513 .
  • Promputtha , I , Jeewon , R , Lumyong , S , McKenzie , EHC and Hyde , KD. 2005 . Ribosomal DNA fingerprinting in the identification of non sporulating endophytes from Magnolia liliifera (Magnoliaceae) . Fungal Divers. , 20 : 167 – 186 .
  • Promputtha , I , Lumyong , S , Dhanasekaran , V , McKenzie , EHC , Hyde , KD and Jeewon , R. 2007 . A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence . Microb Ecol. , 53 : 579 – 590 .
  • Purahong , W and Hyde , KD. 2011 . Effects of fungal endophytes on grass and non-grass litter decomposition rates . Fungal Divers. , 47 : 1 – 7 .
  • Reinhold-Hurek , B and Hurek , T. 2011 . Living inside plants: bacterial endophytes . Curr Opin Plant Biol. , doi: 10.1016/j.pbi.2011.04.004
  • Rodrigues , KF and Samuels , GJ. 1990 . Preliminary study of endophytic fungi in a tropical palm . Mycol Res. , 94 : 827 – 830 .
  • Rondon , MR , August , PR , Bettermann , AD , Brady , SF , Grossman , TH , Liles , MR , Loiacono , KA , Lynch , BA , MacNeil , IA Minor , C . 2000 . Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms . Appl Environ Microbiol. , 66 : 2541 – 2547 .
  • Saikkonen , K , Saari , S and Helander , M. 2010 . Defensive mutualism between plants and endophytic fungi? . Fungal Divers. , 41 : 101 – 113 .
  • Schwarz , P , Bretagne , S , Gantier , JC , Garcia-Hermoso , D , Lortholary , O , Dromer , F and Dannaoui , E. 2006 . Molecular identification of Zygomycetes from culture and experimentally infected tissues . J Clin Microbiol. , 44 : 340 – 349 .
  • Seena , S , Pascoal , C , Marvanová , L and Cássio , F. 2010 . DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species . Fungal Divers. , 44 : 77 – 87 .
  • Seifert , KA. 2009 . Progress towards DNA barcoding of fungi . Mol Ecol Res , 9 ( Suppl.1 ) : 83 – 89 .
  • Seifert , KA , Samson , RA , de Waard , JR , Houbraken , J , Lévesque , CA , Moncalvo , JM , Louis-Seize , G and Hebert , PDN. 2007 . Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case . Proc Natl Acad Sci USA , 104 : 3901 – 3906 .
  • Sinclair , JB and Cerkauskas , RF. 1996 . “ Latent infection vs. endophytic colonization by fungi ” . In Endophytic fungi in grasses and woody plants: systematics, ecology, and evolution , Edited by: Redlin , SC and Carris , LM . 3 – 29 . St. Paul , MN : APS Press .
  • Sogin , ML , Morrison , HG , Huber , JA , Welch , DM , Huse , SM , Neal , PR , Arrieta , JM and Herndl , GJ. 2006 . Microbial diversity in the deep sea and the underexplored “rare biosphere” . Proc Natl Acad Sci USA , 103 : 12115 – 12120 .
  • Stockinger , H , Krüger , M and Schüßler , A. 2010 . DNA barcoding of arbuscular mycorrhizal fungi . New Phytol , 187 : 461 – 474 .
  • Stoyke , G and Currah , RS. 1991 . Endophytic fungi from the mycorrhizae of alpine ericoid plants . Can J Bot , 69 : 347 – 352 .
  • Su , YY , Guo , LD and Hyde , KD. 2010 . Response of endophytic fungi of Stipa grandis to experimental plant function group removal in Inner Mongolia steppe, China . Fungal Divers , 43 : 93 – 101 .
  • Sun , JQ , Guo , LD , Zang , W , Ping , WX and Chi , DF. 2008 . Diversity and ecological distribution of endophytic fungi associated with medicinal plants . Sci China Ser C. , 51 : 751 – 759 .
  • Sun , X , Guo , LD and Hyde , KD. 2011 . Community composition of endophytic fungi in Acer truncatum and their role in decomposition . Fungal Divers , 47 : 85 – 95 .
  • Suryanarayanan , TS , Thirunavukkarasu , N , Hariharan , GN and Balaji , P. 2005 . Occurrence of non-obligate microfungi inside lichen thalli . Sydowia , 57 : 119 – 129 .
  • Swatzell , LJ , Powell , MJ and Kiss , JZ. 1996 . The relationship of endophytic fungi to the gametophyte of the fern Schizaea pusilla . Int J Plant Sci , 157 : 53 – 62 .
  • Taylor , DL and McCormick , MK. 2008 . Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas . New Phytol , 177 : 1020 – 1033 .
  • Taylor , JE , Hyde , KD and Jones , EBG. 1999 . Endophytic fungi associated with the temperate palm, Trachycarpus fortunei, within and outside its natural geographic range . New Phytol , 142 : 335 – 346 .
  • Tedersoo , L , Jairus , T , Horton , BM , Abarenkov , K , Suvi , T , Saar , I and Kõljalg , U. 2008 . Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers . New Phytol , 180 : 479 – 490 .
  • Tedersoo , L , Nilsson , RH , Abarenkov , K , Jairus , T , Sadam , A , Saar , I , Bahram , M , Bechem , E , Chuyong , G and Kõljalg , U. 2010 . 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases . New Phytol , 188 : 291 – 301 .
  • Tejesvi , MV , Kajula , M , Mattila , S and Pirttilä , AM. 2011 . Bioactivity and genetic diversity of endophytic fungi in Rhododendron tomentosum Harmaja . Fungal Divers , 47 : 97 – 107 .
  • Ting , ASY , Meon , S , Kadir , J , Radu , S and Singh , G. 2008 . Endophytic microorganisms as potential growth promoters of banana . Biocontrol , 53 : 541 – 553 .
  • U'Ren , JM , Dalling , JW , Gallery , RE , Maddison , DR , Davis , EC , Gibson , CM and Arnold , AE. 2009 . Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples . Mycol Res , 113 : 432 – 449 .
  • Vialle , A , Feau , N , Allaire , M , Didukh , M , Martin , F , Moncalvo , JM and Hamelin , RC. 2009 . Evaluation of mitochondrial genes as DNA barcode for Basidiomycota . Mol Ecol Resour , 9 : 99 – 113 .
  • Vieira , PDS , de Souza Motta , CM , Lima , D , Torres , JB , Quecine , MC , Azevedo , JL and de Oliveira , NT. 2011 . Endophytic fungi associated with transgenic and non-transgenic cotton . Mycology , 2 : 91 – 97 .
  • Vilgalys , R. 2003 . Taxonomic misidentification in public DNA database . New Phytol , 160 : 4 – 5 .
  • Wang , Q and Guo , LD . 2010 . Ectomycorrhizal community composition of Pinus tabulaeformis assessed by ITS-RFLP and ITS sequences . Botany , 88 : 590 – 595 .
  • Wang , Q , Gao , C and Guo , LD. 2011a . Ectomycorrhizae associated with Castanopsis fargesii (Fagaceae) in a subtropical forest, China . Mycol Progress , 10 : 323 – 332 .
  • Wang , Q , He , XH and Guo , LD. 2011b . Ectomycorrhizal fungus communities of Quercus liaotugensis Koidz of different ages in a northern China temperate forest . Mycorrhiza , doi: 10.1007/s00572-011-0423-x
  • Wang , Y and Guo , LD. 2007 . A comparative study of endophytic fungi in needles, bark, and xylem of Pinus tabulaeformis . Can J Bot , 85 : 911 – 917 .
  • Wang , Y , Guo , LD and Hyde , KD. 2005 . Taxonomic placement of sterile morphotypes of endophytic fungi from Pinus tabulaeformis (Pinaceae) in northeast China based on rDNA sequences . Fungal Divers , 20 : 235 – 260 .
  • Wang , YC , Zheng , ZH , Liu , SC , Zhang , H , Li , EW , Guo , LD and Che , YS. 2010 . Oxepinochromenones, furochromenone, and their putative precursors from the endolichenic fungus Coniochaeta sp . J Nat Prod , 73 : 920 – 924 .
  • Xiang , MC , Xiang , PA , Jiang , XZ , Duan , WJ and Liu , XZ. 2010 . Detection and quantification of the nematophagous fungus Hirsutella minnesotensis in soil with real-time PCR . Appl Soil Ecol , 44 : 170 – 175 .
  • Xu , J , Ebada , SS and Proksch , P. 2010 . Pestalotiopsis a highly creative genus: chemistry and bioactivity of secondary metabolites . Fungal Divers , 44 : 15 – 31 .
  • Zhang , P , Chen , ZH , Xiao , B , Tolger , B , Bao , HY and Yang , ZL. 2010 . Lethal amanitas of East Asia characterized by morphological and molecular data . Fungal Divers , 42 : 119 – 133 .
  • Zhao , P , Luo , J and Zhuang , WY. 2011 . Practice towards DNA barcoding of the nectriaceous fungi . Fungal Divers , 46 : 183 – 191 .
  • Zheng , RY and Jiang , H. 1995 . Rhizomucor endophyticus sp. nov., an endophytic zygomycetes from higher plants . Mycotaxon , 56 : 455 – 466 .

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