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Plant and Soil

, Volume 358, Issue 1–2, pp 225–233 | Cite as

Succession of root-associated fungi in Pisum sativum during a plant growth cycle as examined by 454 pyrosequencing

  • L. Yu
  • M. Nicolaisen
  • J. Larsen
  • S. Ravnskov
Regular Article

Abstract

Purpose

Roots are inhabited by a broad range of fungi, including pathogens and mycorrhizal fungi, with functional traits related to plant health and nutrition. Management of these fungi in agroecosystems requires profound knowledge about their ecology. The main objective of this study was to examine succession patterns of root-associated fungi in pea during a full plant growth cycle.

Methods

Plants were grown in pots with field soil in a growth chamber under controlled conditions. Fungal communities in pea roots were analyzed at different plant growth stages including the vegetative growth, flowering and senescence, using 454 pyrosequencing.

Results

One hundred and twenty one non-singleton operational taxonomic units (OTUs) representing fungal species were detected. Pathogenic and arbuscular mycorrhizal fungi dominated during the vegetative growth stage, whereas saprotrophic fungi dominated during plant senescence.

Conclusions

In conclusion, the results from the present study demonstrated highly diverse fungal communities in pea roots with clear succession patterns related to fungal traits.

Keywords

fungal diversity arbuscular mycorrhizal fungi pathogens Pisum sativum 

Notes

Acknowledgements

We thank Karsten Malmskov (Ardo A/S) and Steen Meier for help sampling soil in the field, Anne-Pia Larsen and Jacob I. Bañuelos Trejo for assistance with root staining, Henriette Nyskjold for technical assistance, Bernd Wollenweber for critical review on the manuscript and Kirsten Jensen for linguistic editing.

Supplementary material

11104_2012_1188_MOESM1_ESM.docx (29 kb)
ESM 1 (DOCX 28 kb)

References

  1. 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 40:2562–2570CrossRefGoogle Scholar
  2. 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 10:189PubMedCrossRefGoogle Scholar
  3. Blackwell M (2011) The Fungi: 1, 2, 3, … 5, 1 million species? Biodiversity special issue. Am J Bot 98:426–438PubMedCrossRefGoogle Scholar
  4. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 pyrosequencing analyses of forest soils reveal on unexpectedly high fungal diversity. New Phytol 184:449–456PubMedCrossRefGoogle Scholar
  5. 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
  6. Eissenstat DM, Yanai RD (2002) Root life span, efficiency, and turnover. In: Waisel Y, Eshel S, Kafkafi U (eds) Plant root: the hidden half. Marcel Dekker, New York, pp 221–238Google Scholar
  7. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes application to the identification of mycorrhizal and rusts. Mol Ecol 2:113–118PubMedCrossRefGoogle Scholar
  8. Gianinazzi S, Trouvelot A, Lovato P, Tuinen DV, Franken P, Gianinazzi-Pearson V (1995) Arbuscular Mycorrhizal Fungi in Plant Production of Temperate Agroecosystems. Crit Rev Biotech 15:305–311CrossRefGoogle Scholar
  9. Giovannetti M, Mosse B (1980) An evaluation of techniques for measuring vesicular arbuscular mycorrhizal infection in roots. New Phytol 84:489–500CrossRefGoogle Scholar
  10. Gransee A, Wittenmayer L (2000) Qualitative and quantitative analysis of water-soluble root exudates in relation to plant species and development. J Plant Nutr Soil Sci 163:381–385CrossRefGoogle Scholar
  11. Houlden A, Timms-Wilson TM, Day MJ, Bailey MJ (2008) Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops. FEMS Microbiol Ecol 65:193–201PubMedCrossRefGoogle Scholar
  12. Hui N, Jumpponen A, Niskanen T, Liimatainen K, Jones KL, Koivula T (2011) EcM fungal community structure, but not diversity, altered in a Pb-contaminated shooting range in a boreal coniferous forest site in Southern Finland. FEMS Microbiol Ecol 76:121–132PubMedCrossRefGoogle Scholar
  13. Jumpponen A, Jones KL, Mattox JD, Yaege C (2010) Massively parallel in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 19:41–53PubMedCrossRefGoogle Scholar
  14. 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 105:1027–1032CrossRefGoogle Scholar
  15. 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 37–45Google Scholar
  16. Kraft JM, Pfleger FL (2001) Compendium of pea diseases and pests. In: Kraft JM, Pfleger FL (eds) The disease compendium series of the American Phytopathological Society. Am Phytopathol Soci, St. PaulGoogle Scholar
  17. Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. J Plant Nutr Soil Sci 163:421–431CrossRefGoogle Scholar
  18. Larsen J, Bødker L (2002) Interactions between pea root-associated fungi examined using signature fatty acids. New Phytol 149:487–493CrossRefGoogle Scholar
  19. 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 Phythol 173:611–620CrossRefGoogle Scholar
  20. Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V (2010) Disclosing arbuscualr mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Environ Microbiol 12:2165–2179PubMedGoogle Scholar
  21. Margulies M, Egholm M, Altman WE, Attiya S et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedGoogle Scholar
  22. Martin KJ, Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5:28PubMedCrossRefGoogle Scholar
  23. Monchy S, Sanciu G, Jobard M, Rasconi S, Gerphagnon M, Chabé 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 13:1433–1453PubMedCrossRefGoogle Scholar
  24. O’Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550PubMedCrossRefGoogle Scholar
  25. Ravnskov S, Jakobsen I (1995) Functional compatibility in arbuscular mycorrhizas measured as hyphal P transport to the plant. New Phytol 129:611–618CrossRefGoogle Scholar
  26. Rossman AY, Tulloss RE, O’Dell TE, Thorn RG (1998) Protocols for an all taxa biodiversity inventory of fungi in a Costa Rican conservation area. Parkway, BooneGoogle Scholar
  27. Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH (2009) An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytol 181:471–474PubMedCrossRefGoogle Scholar
  28. Scheublin TR, Ridgway KP, Young PW, van der Heijden MGA (2004) Nonlegumes, legumes, and nodules harbor different arbuscular mycorrhizal fungal communities. Appl Environ Microbiol 70:6240–6246PubMedCrossRefGoogle Scholar
  29. Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Academic, LondonGoogle Scholar
  30. Unterseher M, Jumpponen A, Öpik M, Tedersoo L, Moora M, Dormann CF, Schnittler M (2011) Species abundance distributions and richness estimations in fungal metagenomics – lessons learned from community ecology. Mol Ecol 20:275–285PubMedCrossRefGoogle Scholar
  31. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Extensive fungal diversity in plant roots. Science 295:2051PubMedCrossRefGoogle Scholar
  32. 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 Natl Acad Sci USA 104:16970–16975PubMedCrossRefGoogle Scholar
  33. Voisin AS, Salon C, Jeudy C, Warembourg R (2003) Root and nodule growth in Pisum sativum L. in relation to photosynthesis: Analysis using 13 C-labelling. Ann Bot 92:557–563PubMedCrossRefGoogle Scholar
  34. Vrålstad T, Myhre E, Schumacher T (2002) Molecular diversity and phylogenetic affinities of symbiotic root-associated ascomycetes of the Helotiales in burnt and metal polluted habitats. New Phytol 155:131–148CrossRefGoogle Scholar
  35. Whipps JM (2004) Prospects and limitations for mycorrhizas in biocontrol of root pathogens. Can J Bot 82:1198–1225CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Department of Agroecology, Aarhus UniversityResearch Centre FlakkebjergSlagelseDenmark
  2. 2.Centro de Investigaciones en EcosistemasUniversidad Nacional Autónoma de MéxicoMoreliaMexico

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