Fungal communities in soils along a vegetative ecotone

Mycologia

Volumn 105, Issue 1, 2013, Pages 61-70

  Karst, Justine ^a   Piculell, Bridget ^a   Brigham, Christy ^b   Booth, Michael ^c   Hoeksema, Jason D ^a  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b Santa Monica Mountains National Recreation Area   (United States)

^c UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

Clone library; Diversity; Ecotone; Grassland; Plant

Indexed keywords

FUNGAL DNA; RIBOSOME DNA;

CLONE; COASTAL ZONE; ECOTONE; FUNGUS; GRASSLAND; PLANT COMMUNITY; SCRUB; SOIL MICROORGANISM; SPECIES DIVERSITY; SPECIES RICHNESS; TAXONOMY;

ARTICLE; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; FUNGUS; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POACEAE; SALVIA OFFICINALIS; SOIL; UNITED STATES;

BIODIVERSITY; CALIFORNIA; DNA, FUNGAL; DNA, RIBOSOMAL; ECOSYSTEM; FUNGI; MOLECULAR SEQUENCE DATA; PHYLOGENY; POACEAE; SALVIA OFFICINALIS; SOIL; SOIL MICROBIOLOGY;

CALIFORNIA; UNITED STATES;

EID: 84874685940     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/12-042     Document Type: Article

References (39)

1. Amend AS, Seifert KA, Bruns TD. 2010. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19:5555-5565
2. Anderson IC, Cairney JWG. 2004. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Enviro Microbiol 6:769-779
3. Avis PG, Branco S, Tang Y, Mueller GM. 2010. Pooled samples bias fungal community descriptions. Mol Ecol Resour 10:135-141
4. Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 10
5. Buee M, 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
6. Christensen M. 1989. A view of fungal ecology. Mycologia 81:1-19
7. Colwell RK, Coddington JA. 1994. Estimating terrestrial biodiversity through extrapolation. Philos TR Soc B 345:101-118
8. de Bellis T, Kernaghan G, Widden P. 2007. Plant community influences on soil microfungal assemblages in boreal mixed-wood forests. Mycologia 99:356-367
9. de Deyn GB, van der Putten WH. 2005. Linking aboveground and belowground diversity. Trends Ecol Evol 20:625-633
10. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH. 2010. Idiosyncrasy and overdominance in the structure of natural communities of arbuscular mycorrhizal fungi: is there a role for stochastic processes? J Ecol 98:419-428
11. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB. 2007. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microb 73:7059-7066
12. Fierer N, McCain CM, Meir P, Zimmermann M, Rapp JM, Silman MR, Knight R. 2011. Microbes do not follow the elevational diversity patterns of plants and animals. Ecology 92:797-804
13. 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
14. Huang XQ, Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Res 9:868-877
15. Hunt J, Boddy L, Randerson PF, Rogers HJ. 2004. An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microbial Ecol 47: 385-395
16. 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 GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schußler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer KE, Langer G, Untereiner WA, Lücking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822
17. 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
18. Jumpponen A, Jones KL. 2009. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184: 438-448
19. Kageyama SA, Posavatz NR, Waterstripe KE, Jones SJ, Bottomley PJ, Cromack K, Myrold DD. 2008. Fungal and bacterial communities across meadow-forest ecotones in the western Cascades of Oregon. Can J Forest Res 38:1053-1060
20. Kwasna H, Bateman GL, Ward E. 2008. Determining species diversity of microfungal communities in forest tree roots by pure-culture isolation and DNA sequencing. Appl Soil Ecol 40:44-56
21. Meyer M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nature Protocols 3: 267-278
22. O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microb 71:5544-5550
23. Orpurt PA, Curtis JT. 1957. Soil microfungi in relation to the prairie continuum in Wisconsin. Ecology 38:628-637
24. Peay KG, Kennedy PG, Davies SJ, Tan S, Bruns TD. 2010. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. New Phytol 185:529-542
25. Reeder J, Knight R. 2009. The 'rare biosphere': a reality check. Nat Methods 6:636-637
26. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet 16:276-277
27. Robinson CH, Szaro TM, Izzo AD, Anderson IC, Parkin PI, Bruns TD. 2009. Spatial distribution of fungal communities in a coastal grassland soil. Soil Biol Biochem 41: 414-416
28. Rooney AP, Ward TJ. 2005. Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. P Natl Acad Sci-Biol 102:5084-5089
29. Sampo S, Bergero R, Buffa G, LuppiMosca AM. 1997. Soil fungal communities in a young and an old Alnus viridis coenosis. Mycologia 89:837-845
30. Schadt CW, Martin AP, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359-1361
31. Seena S, Wynberg N, Barlocher F. 2008. Fungal diversity during leaf decomposition in a stream assessed through clone libraries. Fungal Divers 30:1-14.
32. Taylor DL, Herriott IC, Long J, O'Neill K. 2007. TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction. Environ Microbiol 9:1329-1334
33. Taylor DL, Herriott IC, Stone KE, McFarland JW, Booth MG, Leigh MB. 2010. Structure and resilience of fungal communities in Alaskan boreal forest soils. C J Forest Res 40: 1288-1301
34. U'Ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM, 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
35. Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH. 2004. Ecological linkages between aboveground and belowground biota. Science 304:1629-1633
36. Wicklow DT, Whitting WF. 1974. Soil microfungal changes among profiles of disturbed conifer-hardwood forests. Ecology 55:3-16
37. Wicklow MC, Bollen WB, Denison WC. 1974. Comparison of soil microfungi in 40-year-old stands of pure alder, pure conifer, and alder-conifer mixtures. Soil Biol Biochem 6:73-78
38. Widden P. 1986. Microfungal community structure from forest soils in southern Quebec, using discriminant function and factor-analysis. CJ Bot 64:1402-1412
39. Zinger L, Lejon DPH, Baptist F, Bouasria A, Aubert S, Geremia RA, Choler P. 2011. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS One 6.