Skip to main content
SpringerLink
Log in

Molecular characterization of root-associated fungal communities in relation to health status of Pisum sativum using barcoded pyrosequencing

  • Regular Article
  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Background and Aims

Root-associated fungi are known to be important for plant health and nutrition, but only few studies have addressed their diversity in relation to plant health status.

Methods

Fungal diversity in roots of healthy and diseased Pisum sativum plants was examined in terms of barcoded pyrosequencing of the nuclear ribosomal internal transcribed spacer 1. The CLOTU program was used for filtering and clustering of sequences, and Chao 1 estimator was used to calculate fungal richness.

Results

Principal component analyses (PCA) showed that the structure of root-associated fungal communities differed between sites and a clear relationship between root-associated fungal communities and plant health status was found. For example, the arbuscular mycorrhizal (AM) fungus Glomus caledonium was prevalent in roots of healthy plants, whereas the pathogenic fungus Phoma sojicola was prevalent in roots of diseased plants.

Conclusions

The present study revealed clear differences in composition of root-associated fungi from four field sites, and correlations between abundance of several root-associated fungi and plant health status were found.

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

  • Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-enhanced pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770

    Article  Google Scholar 

  • 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 10:189

    Article  PubMed  Google Scholar 

  • Borowicz VA (2001) Do arbuscular mycorrhizal fungi alter plant-pathogen relations? Ecology 82:3057–3068

    Google Scholar 

  • Bretag TW, Keane PJ, Price TV (2006) The epidemiology and control of ascochyta blight in field peas: a review. Aust J Agric Res 57:883–902

    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 

  • Bødker L, Kjøller R, Kristensen K (2002) Interactions between indigenous arbuscular mycorrhizal fungi and Aphanomyces euteiches in field-grown pea. Mycorrhiza 12:7–12

    Article  PubMed  Google Scholar 

  • Colwell RK (2009) EstimateS: Statistical estimation of species richness and shared species from samples. Version 8.2. User’s Guide and application. http://purl.oclc.org/estimates

  • Domsch KH, Gams W, Anderson T (2007) Compendium of soil fungi, 2nd edn. IHW Verlag, Eching

    Google Scholar 

  • EPPO standards (2004) PP 1/172 (2) Bulletin 2:176–178

  • Filion M, Hamelin RC, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl Environ Microbiol 70:3541–3551

    Article  PubMed  CAS  Google Scholar 

  • Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes application to the identification of mycorrhizal and rusts. Mol Ecol 2:113–118

    Article  PubMed  CAS  Google Scholar 

  • Giovannetti M, Mosse B (1980) An evaluation of techniques for measuring vesicular arbuscular mycorrhizal infection in roots. New Phytol 84:489–500

    Article  Google Scholar 

  • Gianinazzi S, Gollotte A, Binet MN, van Tuinen D, Redecker D, Wipf D (2010) Agroecology: the key role of arbuscular mycorrhizas in ecosystem services. Mycorrhiza 20:519–530

    Article  PubMed  Google Scholar 

  • Irinyi L, Kövics GJ, Sándor E (2009) Taxonomical re-evaluation of Phoma-like soybean pathogenic fungi. Mycol Res 113:249–260

    Article  PubMed  Google Scholar 

  • Jumpponen A, Jones KL (2010) Seasonally dynamics of fungal communities in the Querus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186:496–513

    Article  PubMed  CAS  Google Scholar 

  • Kane RT, Smiley RW (1987) Relative pathogenicity of selected Fusarium species and Microdochium bolleyi to winter wheat in New York. Plant Dis 71:177–181

    Article  Google Scholar 

  • Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–36

    Article  PubMed  CAS  Google Scholar 

  • Kjøller R, Rosendahl S (1998) Enzymatic activity of the mycelium compared with oospore development during infection of pea roots by Aphanomyces euteiches. Phytopathology 88:992–996

    Article  PubMed  Google Scholar 

  • Kjøller R, Rosendahl S (2001) Molecular diversity of glomalean (arbuscular mycorrhizal) fungi determined as distinct Glomus specific DNA sequences from roots of field grown peas. Mycol Res 105:1027–1032

    Article  Google Scholar 

  • Kormanik PP, McGraw AC (1982) Quantification of vesicular-arbuscular mycorrhiza in plant roots. In: Schenck NC (ed) Methods and principles of mycorrhizal research. American Phytopathological Society, St. Paul, pp 37–45

    Google Scholar 

  • Kraft JM, Pfleger FL (2001) Compendium of pea diseases and pests. In: Kraft JM, Pfleger FL (eds) American Phytopathological Society. St. Paul, MN, USA

  • Krüger M, Stockinger H, Krüger C, Schüßler A (2009) DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytol 183:212–223

    Article  PubMed  Google Scholar 

  • Kövics GJ, de Gruyter J, van der Aa HA (1999) Phoma sojicola comb. nov. and other hyaline-spored coelomucetes pathogenic on soybean. Mycol Res 103:1065–1070

    Article  Google Scholar 

  • Larsen J, Bødker L (2001) Interactions between pea root-associated fungi examined using signature fatty acids. New Phytol 149:487–493

    Article  CAS  Google Scholar 

  • Lemanczyk G, Sadowski CK (2002) Fungal community and health status of roots of winter wheat cultivated after oats and oats mixed with other crops. BioControl 47:349–361

    Article  Google Scholar 

  • Letourneau A, Seena S, Marvanová L, Bärlocher F (2010) Potential use of barcoding to identify aquatic hyphomycetes. Fungal Divers 40:51–64

    Article  Google Scholar 

  • Li S, Hartman GL, Jarvis BB, Tak H (2001) A Stachybotrys chartarum isolate from soybean. Mycopathologia 154:41–49

    Article  Google Scholar 

  • Monchy S, Sanciu G, Jobard M, Rasconi S, Gerphagnon M, Chabe M, Cian A, Meloni D, Niquil N, Christaki U, Viscogliosi E, Sime-Ngando T (2011) Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environ Microbiol 13:1433–1453

    Article  PubMed  Google Scholar 

  • Nilsson RH, Abarenkov K, Veldre V, Nylinder S, de Wit P, Broshce S, Alfredsson JF, Ryberg M, Kristiansson E (2010) An open source chimera checker for the fungal ITS region. Mol Ecol Res 10:1076–1081

    Article  CAS  Google Scholar 

  • Öpik M, Metsis M, Daniell TJ, Zobel M, Moora M (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a borenemoral forest. New Phytol 184:424–437

    Article  PubMed  Google Scholar 

  • Papavizas GC, Ayers WA (1974) Aphanomyces species and their root diseases in pea and sugarbeet. A review USDA Tech Bull 1485:1–158

    Google Scholar 

  • Persson L, Bødker L, Larsson-Wikström M (1997) Prevalence and pathogenicity of foot and root rot pathogens of pea in southern Scandinavia. Plant Dis 81:171–174

    Article  Google Scholar 

  • Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan W (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Method 6:639–641

    Article  CAS  Google Scholar 

  • Quince C, Lanzén A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38

    Article  PubMed  Google Scholar 

  • Selosse MA, Vohnik M, Chauvet E (2008) Out of the rivers: are some aquatic hyphomycetes plant endophytes? New Phytol 178:3–7

    Article  PubMed  Google Scholar 

  • Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Academic, London

    Google Scholar 

  • Stark C, Babik W, Durka W (2009) Fungi from the roots of the common terrestrial orchid Gymnadenia conopsea. Mycol Res 113:952–959

    Article  PubMed  Google Scholar 

  • St-Arnaud M, Vujanovic V (2007) Effect of the arbuscular mycorrhizal symbiosis on plant diseases and pests. In: Hame C, Plenchette C (eds) Mycorrhizae in crop production. Haworth’s Food Products Press, New York

    Google Scholar 

  • Seifert KA (2009) Progress towards DNA barcoding the fungi. Mol Ecol Resour 9(suppl):83–89

    Article  PubMed  CAS  Google Scholar 

  • Stockinger H, Krüger M, Schüßler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187:461–474

    Article  PubMed  CAS  Google Scholar 

  • Thygesen K, Larsen J, Bødker L (2004) Arbuscular mycorrhizal fungi reduce development of pea root-rot caused by Aphanomyces euteiches using oopores as pathogen inoculum. Eur J Plant Pathol 110:411–419

    Article  CAS  Google Scholar 

  • Unterseher M, Jumpponen A, Öpik M, Tedersoo L, Moora M, Dormann CF, Schnittler M (2011) Species abundance distridutions and richness estimations in fungal metagenomics-lessons learned from community ecology. Mol Ecol 20:275–285

    Article  PubMed  Google Scholar 

  • Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Extensive fungal diversity in plant roots. Science 259:2051

    Article  Google Scholar 

  • Vandenkoornhuyse P, Maheé S, Ineson P, Staddon P, Ostle N, Cliquet JB (2007) Active root-associated microbes identified by rapid incorporation of plant-derived carbon into RNA. Proc Nat Acad Sci USA 104:16970–16975

    Article  PubMed  CAS  Google Scholar 

  • Vujanovic V, Hamelin RC, Bernier L, Vujanovic G, St-Arnaud M (2007) Fungal diversity, dominance, and community structure in the Rhizosphere of clonal Picea mariana Plants throughout nursery production chronosequences. Microb Ecol 54:672–684

    Article  PubMed  CAS  Google Scholar 

  • Wehner J, Antunes PM, Powell JR, Mazukatow J, Rillig MC (2010) Plant pathogen protection by arbuscular mycorrhizas: A role for fungal diversity? Pedobiologia 53:197–201

    Article  Google Scholar 

  • Whipps JM (2004) Prospects and limitations for mycorrhizas in biocontrol of root pathogens. Can J Bot 82:1198–1227

    Article  Google Scholar 

  • Wieland G, Neumann R, Backhaus H (2001) Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 67:5849–5854

    Article  PubMed  CAS  Google Scholar 

  • Yergeau E, Labour K, Hamel C, Vujanovic V, Nakano-Hylander A, Jeannotte R, St-Arnaud M (2009) Patterns of Fusarium community structure and abundance in relation to spatial, abiotic and biotic factors in soil. FEMS Microbiol Ecol 71:34–42

    Article  Google Scholar 

Download references

Acknowledgements

We thank Karsten Malmskov (Ardo A/S), Lihui Xu and Steen Meier for support with field soil sampling and Anne-Pia Larsen and Henriette Nyskjold for their excellent technical laboratory assistance, and Annemarie Fejer Justesen for critical review of the manuscript.

Author information

Authors and Affiliations

  1. Faculty of Science and Technology, Department of Agroecology, Aarhus University, Research Centre Flakkebjerg, DK-4200, Slagelse, Denmark

    L. Yu, M. Nicolaisen & S. Ravnskov

  2. Universidad Nacional Autónoma de México, Centro de Investigaciones en Ecosistemas, Antigua Carretera a Pátzcuaro 8701, Col. Ex Hacienda de San José de la Huerta, C.P. 58190, Morelia, Michoacán, Mexico

    J. Larsen

Authors
  1. L. Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Nicolaisen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Larsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. Ravnskov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. Ravnskov.

Additional information

Responsible Editor: Erik J. Joner.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table 1

Supplementary Material_ The list of all 142 OTUs (DOCX 34 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yu, L., Nicolaisen, M., Larsen, J. et al. Molecular characterization of root-associated fungal communities in relation to health status of Pisum sativum using barcoded pyrosequencing. Plant Soil 357, 395–405 (2012). https://doi.org/10.1007/s11104-012-1180-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11104-012-1180-0

Keywords

Search

Navigation