Moving from pattern to process in fungal symbioses: Linking functional traits, community ecology and phylogenetics

New Phytologist

Volumn 185, Issue 4, 2010, Pages 882-886

  Parrent, Jeri L ^a   Peay, Kabir ^b   Arnold, A Elizabeth ^c   Comas, Louise H ^d   Avis, Peter ^e   Tuininga, Amy ^f  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e INDIANA UNIVERSITY NORTHWEST   (United States)

^f FORDHAM UNIVERSITY   (United States)

Author keywords

Community phylogenetics; Endophytes; Functional diversity; Fungal Environmental Sampling and Informatics Network (FESIN); Molecular ecology; Mycorrhizal fungi

Indexed keywords

ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; FUNGUS; GENETICS; GENOMICS; LETTER; PHYLOGENY; PHYSIOLOGY; QUANTITATIVE TRAIT; SYMBIOSIS;

ECOLOGICAL AND ENVIRONMENTAL PHENOMENA; FUNGI; GENOMICS; PHYLOGENY; QUANTITATIVE TRAIT, HERITABLE; SYMBIOSIS;

FUNGI;

EID: 77949339232     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03190.x     Document Type: Letter

References (46)

1. Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F. A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Systematic Biology 2009, 58:283-297.
2. Arnold AE, Lamit LJ, Bidartondo MI, Gehring CA, Callahan H. Interwoven branches of the plant and fungal trees of life. New Phytologist 2010, 185:874-878.
3. Avis PG, McLaughlin DJ, Dentinger BC, Reich PC. Long-term increase in nitrogen supply alters above- and below-ground ectomycorrhizal communities and increases the dominance of Russula spp. in a temperate oak savanna. New Phytologist 2003, 160:239-253.
4. Avis PG, Mueller GM, Lussenhop J. Ectomycorrhizal fungal communities in two North American oak forests respond to nitrogen addition. New Phytologist 2008, 179:472-483.
5. Avis PG, Branco S, Tang Y, Mueller G. Pooled samples bias fungal community descriptions. Molecular Ecology Resources 2010, 10:135-141.
6. Bidartondo MI, Gardes M. Fungal diversity in molecular terms: profiling, identification, and quantification in the environment. The fungal community 2005, 215-239. Dighton J, White JFOudemans PV. In, eds, Boca Raton, FL, USA, CRC Press, Taylor & Francis Group
7. Blackwood CB, Waldrop MP, Zak DR, Sinsabaugh RL. Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition. Environmental Microbiology 2007, 9:1306-1316.
8. Bonito G, Isikhuemhen OS, Vilgalys R. Identification of fungi associated with municipal compost using DNA-based techniques. Bioresource Technology 2010, 101:1021-1027.
9. Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist 2009, 184:449-456.
10. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW. The merging of community ecology and phylogenetic biology. Ecology Letters 2009, 12:693-715.
11. Courty PE, Pritsch K, Schloter M, Hartmann A, Garbaye J. Activity profiling of ectomycorrhiza communities in two forest soils using multiple enzymatic tests. New Phytologist 2005, 167:309-319.
12. Diaz S, Cabido M. Vive la difference: plant functional diversity matters to ecosystem processes. Trends in Ecology & Evolution 2001, 16:646-655.
13. Dickie IA, FitzJohn RG. Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review. Mycorrhiza 2007, 17:259-270.
14. Dong S, Brooks D, Jones MD, Grayston SJ. A method for linking in situ activities of hydrolytic enzymes to associated organisms in forest soils. Soil Biology and Biochemistry 2007, 39:2414-2419.
15. Edwards IP, Upchurch RA, Zak DR. Isolation of fungal cellobiohydrolase genes from sporocarps and forest soils by PCR. Applied and Environmental Microbiology 2008, 74:3481-3489.
16. Geml J, Laursen GA, Timling I, McFarland JM, Booth MG, Lennon N, Nusbaum C, Taylor DL. Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales, Basidiomycota) in Alaska, based on soil and sporocarp DNA. Molecular Ecology 2009, 18:2213-2227.
17. Govindarajulu M, Pfeffer PE, Jin HR, Abubaker J, Douds DD, Allen JW, Bucking H, Lammers PJ, Shachar-Hill Y. Nitrogen transfer in the arbuscular mycorrhizal symbiosis. Nature 2005, 435:819-823.
18. van der Heijden MGA, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 1998, 396:69-72.
19. Hibbett DS, Gilbert L-B, Donoghue MJ. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 2000, 407:506-508.
20. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadikowska J. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
21. Jargeat P, Rekangalt D, Verner M-C, Gay G, Debaud J-C, Marmeisse R, Fraissinet-Tachet L. Characterisation and expression analysis of a nitrate transporter and nitrite reductase genes, two members of a gene cluster for nitrate assimilation from the symbiotic basidiomycete Hebeloma cylindrosporum. Current Genetics 2003, 43:199-205.
22. Jumpponen A, Jones KL. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist 2009, 184:438-448.
23. Kraft NJB, Cornwell WK, Webb CO, Ackerly DD. Trait evolution, community assembly, and the phylogenetic structure of ecological communities. American Naturalist 2007, 170:271-283.
24. Lozupone C, Hamady M, Knight R. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 2006, 7:371.
25. Maherali H, Klironomos JN. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 2007, 316:1746-1748.
26. Martin F, Aerts A, Ahrén D, Brun A, Danchin EGJ, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008, 452:88-92.
27. McGill BJ, Enquist BJ, Weiher E, Westoby M. Rebuilding community ecology from functional traits. Trends in Ecology & Evolution 2006, 21:178-185.
28. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics 2009, 4:193-201.
29. Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K-H, Kõljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 2006, 1:e59.
30. Nygren C, Eberhardt U, Karlsson M, Parrent JL, Lindahl B, Taylor AFS. Growth on nitrate and occurrence of nitrate reductase-encoding genes in a phylogenetically diverse range of ectomycorrhizal fungi. New Phytologist. 2008, 180:875-889.
31. Parrent JL, James TY, Vasaitis R, Taylor AFS. Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evolutionary Biology 2009, 9:148.
32. Peay KG, Kennedy PG, Bruns TD. Fungal community ecology: a hybrid beast with a molecular master. BioScience 2008, 58:799-810.
33. Peay KG, Bidartondo MI, Arnold AE. Not every fungus is everywhere: scaling to the biogeography of fungal-plant interactions across roots, shoots and ecosystems. New Phytologist 2010, 185:878-882.
34. Phillips RP, Erlitz Y, Bier R, Bernhardt ES. New approach for capturing soluble root exudates in forest soils. Functional Ecology 2008, 22:990-999.
35. Powell JR, Parrent JL, Maherali H, Hart MM, Rillig MC, Klironomos JN. Phylogenetic trait conservatism and the evolution of functional tradeoffs in arbuscular mycorrhizal fungi. Proceedings of the Royal Society B 2009, 276:4237-4245.
36. Pritsch K, Luedemann G, Matyssek R, Hartmann A, Schloter M, Scherb H, Grams TEE. Mycorrhizosphere responsiveness to atmospheric ozone and inoculation with Phytophthora citricola in a phytotrone experiment with spruce/beech mixed cultures. Plant Biology 2005, 7:718-727.
37. Rodriguez RJ, White JF, Arnold AE, Redman RS. Fungal endophytes: diversity and functional roles. New Phytologist 2009, 182:314-330.
38. Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, Contosta AR, Cusack D, Frey S, Gallo ME. Stoichiometry of soil enzyme activity at global scale. Ecology Letters 2008, 11:1252-1264.
39. Smith SE, Read DJ. Mycorrhizal symbiosis 2008, San Diego, CA, USA, Academic Press
40. Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Oliver SG, Talbot NJ. Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS ONE 2008, 3:e2300.
41. Taylor DL, Booth MG, McFarland JW, Herriott IC, Lennon NJ, Nusbaum C, Marr TG. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Molecular Ecology Resources 2008, 8:742-752.
42. U'Ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM, Arnold AE. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: A case study for analysing fungal environmental samples. Mycological Research 2009, 113:432-449.
43. Vilgalys R. Taxonomic misidentification in public DNA databases. New Phytologist 2003, 160:4-5.
44. Webb CO, Ackerly DD, Kembel SW. Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 2008, 24:2098-2100.
45. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. Phylogenies and community ecology. Annual Review of Ecology and Systematics 2002, 33:475-505.
46. Westoby M, Wright IJ. Land-plant ecology on the basis of functional traits. Trends in Ecology & Evolution 2006, 21:261-268.