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DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala Univ, Dept Informat Technol, Uppsala Multidisciplinary Ctr Adv Computat Sci, Box 137, S-75105 Uppsala, Sweden..
Univ Puerto Rico, Dept Biol, Mayaguez, PR 00681 USA..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2016 (English)In: Mycoscience, ISSN 1340-3540, E-ISSN 1618-2545, Vol. 57, no 3, 217-227 p.Article in journal (Refereed) PublishedText
Abstract [en]

Soil fungal communities in tropical regions remain poorly understood. In order to increase the knowledge of diversity of soil-inhabiting fungi, we extracted total DNA from top-organic soil collected in seven localities dominated by four major ecosystems in the tropical island of Puerto Rico. In order to comprehensively characterize the fungal community, we PCR-amplified the internal transcribed spacer 2 (ITS2) fungal barcode using newly designed degenerated primers and varying annealing temperatures to minimize primer bias. Sequencing results, obtained using Ion Torrent technology, comprised a total of 566,613 sequences after quality filtering. These sequences were clustered into 4140 molecular operational taxonomic units (MOTUs) after removing low frequency sequences and rarefaction to account for differences in read depth between samples. Our results demonstrate that soil fungal communities in Puerto Rico are structured by ecosystem. Ascomycota, followed by Basidiomycota, dominates the diversity of fungi in soil. Amongst Ascomycota, the recently described soil-inhabiting class Archaeorhizomycetes was present in all localities, and taxa in Archaeorhizomycetes were among the most commonly observed MOTUs. The Basidiomycota community was dominated by soil decomposers and ectomycorrhizal fungi with a distribution strongly affected by local variation to a greater degree than Ascomycota.

Place, publisher, year, edition, pages
2016. Vol. 57, no 3, 217-227 p.
Keyword [en]
Communities, Dikarya, High-throughput sequencing, Internal transcribed spacer, Molecular operational taxonomic unit
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-294653DOI: 10.1016/j.myc.2016.02.001ISI: 000373377800009OAI: oai:DiVA.org:uu-294653DiVA: diva2:932667
Funder
Swedish Research Council FormasCarl Tryggers foundation
Available from: 2016-06-02 Created: 2016-05-26 Last updated: 2016-06-02Bibliographically approved

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Scofield, Douglas G.Rosling, Anna
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