Skip to main content

Advertisement

SpringerLink
Log in

Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism

  • Original Article
  • Published:
Mycological Progress Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21:51–66

    Article  Google Scholar 

  • Baldrian P, Kolařík M, Stursová M, Kopecký J, Valášková V, Větrovský T, Zifčáková L, Snajdr J, Rídl J, Vlček C, Voříšková J (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6:248–258

    Article  PubMed  CAS  Google Scholar 

  • Banning NC, Gleeson DB, Grigg AH, Grant CD, Andersen GL, Brodie EL, Murphy DV (2011) Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol 77:6158–6164

    Article  PubMed  CAS  Google Scholar 

  • Bredemeier M, Blanck K, Dohrenbusch A, Lamersdorf N, Meyer AC, Murach D, Parth A, Xu YJ (1998) The Solling roof project - site characteristics, experiments and results. Forest Ecol Manag 101:281–293

    Article  Google Scholar 

  • Buée 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

    Article  PubMed  Google Scholar 

  • 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

  • Carson JK, Gleeson DB, Clipson N, Murphy DV (2010) Afforestation alters community structure of soil fungi. Fungal Biol 114:580–584

    Article  PubMed  Google Scholar 

  • Cordier T, Robin C, Capdevielle X, Desprez-Loustau M, Vacher C (2012) Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecol 5:509–520

    Article  Google Scholar 

  • 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 5:14

    Article  PubMed  Google Scholar 

  • Dumbrell AJ, Ashton PD, Aziz N, Feng G, Nelson M, Dytham C, Fitter AH, Helgason T (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190:794–804

    Article  PubMed  CAS  Google 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 333:762–765

    Article  PubMed  CAS  Google Scholar 

  • Feldhaar H (2011) Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol 36:533–543

    Article  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636

    PubMed  CAS  Google Scholar 

  • Gams W (2007) Biodiversity of soil-inhabiting fungi. Biodivers Conserv 16:69–72

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Gewin V (2006) Genomics: discovery in the dirt. Nature 439:384–386

    Article  PubMed  CAS  Google Scholar 

  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77

    Article  PubMed  CAS  Google Scholar 

  • Jumpponen A, Jones KL, Mattox JD, Yaege C (2010) Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 19(Suppl 1):41–53

    Article  PubMed  Google Scholar 

  • Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Högberg P, Stenlid J, Finlay RD (2007) Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytol 173:611–620

    Article  PubMed  CAS  Google 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 355–386

    Google Scholar 

  • Osono T (2006) Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Can J Microbiol 52:701–716

    Article  PubMed  CAS  Google Scholar 

  • Peršoh D, Theuerl S, Buscot F, Rambold G (2008) Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J Microbiol Meth 75:19–24

    Article  Google Scholar 

  • Peršoh D, Melcher M, Flessa F, Rambold G (2010) First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and its host Pinus sylvestris. Fungal Biol 114:585–596

    Article  PubMed  Google Scholar 

  • Peršoh D, Weig AR, Rambold G (2012) A transcriptome—targeting EcoChip for assessing functional mycodiversity. Microarrays 1:25–41

    Article  Google Scholar 

  • Peršoh D, Segert J, Zigan A, Rambold G (2013) Fungal community composition shifts along a leaf degradation gradient in a European Beech forest. Plant Soil 362:175–186. doi:10.1007/s11104-012-1271-y

    Google Scholar 

  • Popa R, Popa R, Mashall MJ, Nguyen H, Tebo BM, Brauer S (2009) Limitations and benefits of ARISA intra-genomic diversity fingerprinting. J Microbiol Meth 78:111–118

    Article  CAS  Google Scholar 

  • Redman RS, Kim YO, Woodward CJDA, Greer C, Espino L, Doty SL, Rodriguez RJ (2011) Increased fitness of rice plants to abiotic stress via habitat adapted symbiosis: a strategy for mitigating impacts of climate change. PLoS One 6:e14823

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez RJ, White JF Jr, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182:314–330

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg E, Sharon G, Atad I, Zilber-Rosenberg I (2010) The evolution of animals and plants via symbiosis with microorganisms. Environ Microbiol Rep 2:500–506

    Article  PubMed  Google Scholar 

  • Sieber T (2007) Endophytic fungi in forest trees: are they mutualists? Fungal Biol Rev 21:75–89

    Article  Google Scholar 

  • Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H, Richards TA (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19(Suppl 1):21–31

    Article  PubMed  CAS  Google Scholar 

  • Stone J, Polishook J, White J Jr (2004) Endophytic fungi. In: Mueller GM, Bills GF, Foster MS (eds) Biodiversity of fungi. Inventory and monitoring methods. Elsevier Academic Press, Amsterdam, Boston, pp 241–270

    Chapter  Google 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 188:291–301

    Article  PubMed  CAS  Google Scholar 

  • Torzilli AP, Sikaroodi M, Chalkley D, Gillevet PM (2006) A comparison of fungal communities from four salt marsh plants using automated ribosomal intergenic spacer analysis (ARISA). Mycologia 98:690–698

    Article  PubMed  CAS  Google Scholar 

  • Unterseher M, Schnittler M (2009) Dilution-to-extinction cultivation of leaf-inhabiting endophytic fungi in beech (Fagus sylvatica L.) - different cultivation techniques influence fungal biodiversity assessment. Mycol Res 113:645–654

    Article  PubMed  Google Scholar 

  • Werner S, Peršoh D, Rambold, G (2012) Basidiobolus haptosporus is frequently associated with the gamasid mite Leptogamasus obesus. Fungal Biol 116:90–97

    Google 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 315–322

    Google Scholar 

  • Zak DR, Pregitzer KS, Burton AJ, Edwards IP, Kellner H (2011) Microbial responses to a changing environment: implications for the future functioning of terrestrial ecosystems. Fungal Ecol 4:386–395

    Article  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. DNA-Analytics and Ecoinformatics, University of Bayreuth, 95440, Bayreuth, Germany

    Alfons R. Weig & Gerhard Rambold

  2. Mycology, University of Bayreuth, 95440, Bayreuth, Germany

    Derek Peršoh, Sebastian Werner, Amelie Betzlbacher & Gerhard Rambold

Authors
  1. Alfons R. Weig
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Derek Peršoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sebastian Werner
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Amelie Betzlbacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gerhard Rambold
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Derek Peršoh.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weig, A.R., Peršoh, D., Werner, S. et al. Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism. Mycol Progress 12, 719–725 (2013). https://doi.org/10.1007/s11557-012-0883-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11557-012-0883-1

Keywords

Search

Navigation