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Microbial Ecology Microbial Ecology Soil Fungal Communities Underneath Willow Canopies on a Primary Successional Glacier Forefront: rDNA Sequence Results Can Be Affected by Primer Selection and Chimeric Data Ari Jumpponen Division of Biology, Kansas State University, 125 Ackert Hall, Manhattan, KS 66506, USA Received: 7 January 2004 / Accepted: 9 March 2004 / Online publication: 3 November 2006 Abstract amplification and a smaller number of PCR cycles are necessary precautions to allow collection of reliable Soil fungal communities underneath willow canopies environmental sequence data. that had established on the forefront of a receding glacier were analyzed by cloning the polymerase chain reaction (PCR)-amplified partial small subunit (18S) of the ribosomal (rRNA) genes. Congruence between two sets Introduction of fungus-specific primers targeting the same gene region was analyzed by comparisons of inferred neighbor-joining Fungi perform important ecosystem functions by partic- topologies. The importance of chimeric sequences was ipating in the decomposition of dead tissues as well as evaluated by Chimera Check (Ribosomal Database Proj- plant uptake of water and nutrients [6, 34]. Assessment ect) and by data reanalyses after omission of potentially of fungal community composition is difficult because of unreliable and ephemeral production of identifiable chimeric regions at the 50- and 30-ends of the cloned amplicons. Diverse communities of fungi representing macroscopic fruiting bodies [11, 27, 35]. Many fungi Ascomycota, Basidiomycota, Chytridiomycota, and Zygo- also produce microscopic, sexual or asexual fruiting mycota were detected. Ectomycorrhizal fungi comprised a structures or fruit below ground escaping detection in major component in the early plant communities in assessments relying exclusively on the collection of primary successional ecosystems, as both primer sets epigeous fruiting bodies. Pure culture techniques allow frequently detected basidiomycetes (Russulaceae and fungal community assays of soil and tissue samples in the Thelephoraceae) forming mycorrhizal symbioses. Various absence of identifiable macroscopic fruiting bodies. ascomycetes (Ophiostomatales, Pezizales, and Sordar- However, similar to bacteria [38], it is likely that large iales) of uncertain function dominated the clone libraries numbers of fungi would be missed in such pure culture amplified from the willow canopy soil with one set of assays (see [31, 41]). To overcome these problems in primers, whereas the clone libraries of the amplicons fungal community analysis, molecular means specifically generated with the second primer set were dominated by targeting fungi in environmental samples have been basidiomycetes. Accordingly, primer bias is an important developed [3, 9, 14, 25, 28, 32, 33, 40]. factor in fungal community analyses using DNA extracted Direct molecular assessment of the fungal commu- from environmental samples. A large proportion (930%) nities allows analyses without relying on whether or not of the cloned sequences were concluded to be chimeric the fungi can be grown in pure culture or produce based on their changing positions in inferred phylogenies fruiting bodies. However, polymerase chain reaction after omission of possibly chimeric data. Many chimeric (PCR) artifacts, such as chimeric sequences resulting sequences were positioned basal to existing classes of from amplification of more than one template, can cause fungi, suggesting that PCR artifacts may cause frequent problems in environmental samples with unknown discovery of new, higher level taxa (order, class) in direct sources of diverse initial template DNA [13, 19, 24, 42, PCR analyses. Longer extension times during the PCR 43]. Various coextracted substances and low concen- trations of the target template in the presence of highly similar competing target and nontarget templates may Correspondence to: Ari Jumpponen; E-mail: [email protected] further influence the fidelity of PCR reactions [42]. DOI: 10.1007/s00248-004-0006-x & Volume 53, 233–246 (2007) & * Springer Science + Business Media, Inc. 2006 233 234 A. JUMPPONEN: FUNGI IN THE WILLOW CANOPY SOIL ON A GLACIER FOREFRONT 0.60 0.14 0.20 0.31 0.20 0.10 0.11 0.08 0.20 0.40 0.20 0.29 0.43 0.27 0.06 0.22 0.11 0.11 0.15 0.46 0.20 0.33 0.22 0.14 0.07 0.33 0.13 0.94 0.14 0.43 0.33 0.29 0.10 0.11 0.14 0.44 r Frequency glacie c , c a a a 95 96 98 96 96 97 97/97 97 97 97 97 99 97 98 99 94 95 98 99 98 93 98 96 96 95 95 99 98 97 98 96 99 97 98 98 99/99 Similarity receding a of forefront the Phylum Ascomycota Basidiomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Basidiomycota Ascomycota Contaminant Basidiomycota Ascomycota Ascomycota Basidiomycota Ascomycota Ascomycota Basidiomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota on established canopies Prismatolaimidae) sedis) willow (Unknown) (Chaetothyriales) (Incertae (Xylariales) (Enoplida; the (Onygenales) (Onygenales) (Onygenales) (Onygenales) (Agyriales) (Hypocreales) (Hypocreales) (Chaetothyriales) (Hypocreales) (Hypocreales) (Helotiales) (Helotiales) (Ophiostomatales) (Order) (Lecanorales) (Chaetothyriales) (Chaethothyriales/Dothidiales) (Chaethothyriales/Dothidiales) (Chaethothyriales/Dothidiales) (Pleosporales) (Eurotiales) [AF168167] (Pezizales) (Pezizales) (Pezizales) (Pezizales) [AY016351] (Agaricales) (Cortinariaceae) (Agaricales) (Agaricales) (Ceratobasidiales) [AY204613] [AF346544] [AF036603] (Pezizales) (Pezizales) underneath [AB015787] [AB015787] [AB015787] [AB015787] [AF119501] [U43463] [M89993] [M89993] [AB027339] [AB027339] [U45445] number] DS16b [Y18702] [AY228753] [AJ243294] from [U42483] [AF241544] [AF338393] [AF338393] [AF338393] [AF096174] [D85643] [AF133150] [AF133150] [AF133150] [AF133150] [AF287835] [AF287835] [U62012] [U62012] longisetosum [AF287838] [AF287838] ericea intermedius mycopappi pulcherrima [accession tenuissimum tenuissimum tenuissimum tenuissimum marchalianum petricola endophyte juniperi premnophila piliferum solani obtained chrysospermus chrysospermus chrysospermus chrysospermus submonticulosum rilstonii archeri archeri oleaginea oleaginea oleaginea sulphurina pumila pumila geophylla geophylla match griseorosea griseorosea griseorosea griseorosea septate sequences BLAST Spilocaea Spilocaea Hymenoscyphus Cladonia Hypoxylon Neobulgaria Inocybe Dark Oidiodendron Prismatolaimus Inocybe Peziza Anamylopsora Pulvinula Hypomyces Ophiostoma Hypomyces Sarcinomyces Laccaria Peziza Pulvinula Hypomyces Peziza Peziza Tetracladium Laccaria Oidiodendron Oidiodendron Oidiodendron Rhizoctonia Hypomyces Spilocaea Raciborskiomyces Herpotrichia Connersia Mycosphaerella at 20) 40) 80) 40) 40) 20) 40) 20) 40) 40) 80) 40) 40) 80) 20) 40) 80) 40) 20) 20) 20) 20) 40) 40) 40) 40) 40) 20) 40) 40) 40) 100) G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( RDP environmental Yes Yes Yes Yes Yes No No Yes Yes Yes Yes Yes Yes Yes Yes No Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes No Yes Chimera the of analyses [AY382404] [AY382405] [AY382410] [AY382412] [AY382414] [AY382426] [AY382427] [AY382428] [AY382429] [AY382431] [AY382432] [AY382433] [AY382435] [AY382401] [AY382402] [AY382403] [AY382413] [AY382430] [AY382411] [AY382436] [AY382416] [AY382415] [AY382406] [AY382407] [AY382408] [AY382434] [AY382417] [AY382421] [AY382418] [AY382419] [AY382420] [AY382419] [AY382423] [AY382424] [AY382422] [AY382425] b b b b b b b b b b b b b RDP and clone BLAST 1. ble B_Canopy_300_01_08 B_Canopy_300_01_14 B_Canopy_300_01_16 Ta B_Canopy_300_03_17 B_Canopy_300_02_04 B_Canopy_750_01_07 B_Canopy_750_02_13 B_Canopy_300_03_06 B_Canopy_300_03_12 B_Canopy_750_01_10 B_Canopy_750_01_15 B_Canopy_750_03_11 Environmental B_Canopy_450_01_06 B_Canopy_450_01_02 B_Canopy_300_03_19 B_Canopy_300_02_05 B_Canopy_300_02_06 B_Canopy_300_02_10 B_Canopy_750_02_15 B_Canopy_750_03_03 B_Canopy_750_03_04 B_Canopy_750_03_08 B_Canopy_450_02_13 B_Canopy_450_01_13 B_Canopy_450_01_14 B_Canopy_450_01_18 B_Canopy_450_02_02 B_Canopy_300_02_14 B_Canopy_300_01_18 B_Canopy_300_02_12 B_Canopy_450_03_05 B_Canopy_450_03_07 B_Canopy_750_02_19 B_Canopy_450_03_02 B_Canopy_450_03_14 B_Canopy_750_01_01 A. JUMPPONEN: FUNGI IN THE WILLOW CANOPY SOIL ON A GLACIER FOREFRONT 235 0.11 0.14 0.14 0.14 0.50 0.13 0.09 0.13 0.75 0.14 0.29 0.14 0.14 0.77 0.23 0.25 0.89 0.13 0.25 0.33 0.25 0.08 0.43 0.14 1.00 0.29 0.40 0.20 0.92 0.40 0.63 0.55 0.09 0.18 1.00 0.09 0.67 c 98 95 96 95 98 94 97 98 94 94 94 95 97 98 97 96 98 97 93 97 94 92 94 97 97 97 96 98 93 98 99 99 98 95 98 97/94 97 Ascomycota Ascomycota Ascomycota Ascomycota Ascomycota Basidiomycota Ascomycota Basidiomycota Ascomycota Basidiomycota Basidiomycota Chytridiomycota Basidiomycota Basidiomycota Basidiomycota Basidiomycota Basidiomycota Basidiomycota Ascomycota Basidiomycota Basidiomycota Ascomycota Basidiomycota Basidiomycota Basidiomycota Basidiomycota Zygomycota Basidiomycota Basidiomycota Ascomycota Basidiomycota Basidiomycota Ascomycota Ascomycota Ascomycota Ascomycota Basidiomycota . sample (Aphyllophorales) (Unknown one (Onygenales) (Mucorales) (Hypocreales) (Hypocreales) rom (Aphyllophorales) f (Onygenales) (Cantharellales) (Spizellomycetales) (Ophiostomatales) ined (Sordariales) (Helotiales) (Helotiales) (Helotiales) (Helotiales) (Helotiales) [AF334910] (Agaricales) [AF168167] (Agaricales) (Agaricales) (Agaricales)
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