Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism
- 774 Downloads
Biodiversity research rapidly progresses due to the continuous improvement of high-throughput analysis platforms, which facilitate detailed analyses of the composition and architecture of microbial communities in various environmental niches. In the fields of applied forestry and agriculture, microbial communities are also increasingly considered, because they are involved in various kinds of biotic interactions with plants and therefore have high diagnostic value for assessing the health status of plants and soils. While in-depth identification of microbial species in environmental samples is currently achieved by next generation sequencing or microarray techniques, profiling of whole microbial communities can be accomplished via less labor-intensive approaches. We modified the protocol for automated ribosomal intergenic spacer analysis (ARISA) by targeting length polymorphism of the fungal ITS1 rRNA gene for a rapid diagnostic assessment of fungal community composition and surveyed its application spectrum. The approach allowed for spatial and temporal differentiation among fungal assemblages in soil samples and different plant species, and is therefore particularly useful for environmental screening and monitoring projects. Standardized experimental conditions permit the cumulative gathering of data, for instance during long-term projects.
KeywordsARISA Endophytic fungi Soil fungi Fungal community profiles Environmental diagnostics Metagenome analysis Fungal diversity
We would like to thank Nancy Stolle, Julia Segert, Anja Zigan and Michaela Hochholzer (all Bayreuth) for assistance with preparing the DNA samples. Jonny Neumann (Matzner lab, Univ. Bayreuth) helped in determining the soil profiles of the ‘Steigerwald’ and ‘Hohe Warte’ sites.
Conflicts of interest
The authors declare that they have no conflict of interest.
- Butler JM, Hill CR (2010) Scientific Issues with Analysis of Low Amounts of DNA. http://www.promega.com/resources/articles/profiles-in-dna/2010/scientific-issues-with-analysis-of-low-amounts-of-dna/ Updated 2010
- de Baere T, van Keerberghen A, van Hauwe P, de Beenhouwer H, Boel A, Verschraegen G, Claeys G, Vaneechoutte M (2005) An interlaboratory comparison of ITS2-PCR for the identification of yeasts, using the ABI Prism 310 and CEQ8000 capillary electrophoresis systems. BMC Microbiol 5:14PubMedCrossRefGoogle Scholar
- Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee Y, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kues U, Hibbett DS, Hoffmeister D, Hogberg N, Martin F, Grigoriev IV, Watkinson SC (2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333:762–765PubMedCrossRefGoogle Scholar
- Oros-Sichler M, Costa R, Heuer H, Small K (2007) Molecular fingerprinting techniques to analyze soil microbial communities. In: van Elsas JD, Janson JK, Trevors JT (eds) Modern soil microbiology, 2nd edn. CRC Press, Madison, pp 355–386Google Scholar
- Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188:291–301PubMedCrossRefGoogle Scholar
- Werner S, Peršoh D, Rambold, G (2012) Basidiobolus haptosporus is frequently associated with the gamasid mite Leptogamasus obesus. Fungal Biol 116:90–97Google Scholar
- White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315–322Google Scholar