Plant and Soil

, Volume 290, Issue 1–2, pp 259–268 | Cite as

A method for assessing arbuscular mycorrhizal fungi group distribution in tree roots by intergenic transcribed sequence variation

  • Mervyn Shepherd
  • Linh Nguyen
  • Megan E. Jones
  • J. Doland Nichols
  • F. Lynn Carpenter
Original Paper


We identified five taxonomic groups of arbuscular mycorrhizal fungi (AMF) inside roots of young trees of six species of legumes and six species of non-legumes from a field site in southern Costa Rica using an AMF group-specific PCR assay of the intergenic transcribed sequence and 18S rRNA gene fragment. Assay specificity was verified by cloning and sequencing representatives from four of the five AMF groups. We found no difference in overall AMF diversity levels between legumes and non-legumes or between plant species. Some groups of AMF may associate more frequently with legumes than others, as Glomus Group A (Glomus mosseae/intradices group) representatives were detected more frequently in legumes than non-legumes relative to Glomus Group B (Glomus etunicatum/claroideum) representatives.


Acaulosporaceae Gigasporaceae Glomales AMF diversity 



The authors thank Eduer Sandi Tapia, Rolando Mendez Rodriguez, and Leonel Figueroa Vargas for their conscientious assistance in the field work. We thank F. Eliott for technical assistance in the laboratory. Financial support was provided by University of California Research Expeditions Program and Rainforest Agrarian International Network.


  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  2. Binkley D, Giardina C (1997) Nitrogen fixation in tropical forest plantations. In: Nambiar EKS, Brown AG (eds) Management of soil, nutrients and water in tropical plantations. ACIAR, Canberra, Australia, pp 297–328Google Scholar
  3. Carpenter FL, Nichols D, Pratt RT, Young KC (2004) Methods of facilitating reforestation of tropical degraded land with the native timber tree, Terminalia amazonia. For Ecol Manag 202:281–291CrossRefGoogle Scholar
  4. Chelius MK, Triplett EW (1999) Rapid detection of arbuscular mycorrhizae in roots and soil of an intensively managed turfgrass system by PCR amplification of small subunit rDNA. Mycorrhiza 9:61–64CrossRefGoogle Scholar
  5. Clapp JP, Young JPW, Merryweather JW, Fitter AH (1995) Diversity of fungal symbionts in arbuscular mycorrhizas from a natural community. New Phytol 130:259–265CrossRefGoogle Scholar
  6. Gardes M, Bruns T (1993) ITS primers with enhanced specificity for basiomycetes – application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118PubMedGoogle Scholar
  7. Hijri M, Redecker D, MacDonald-Comber P, Voigt K, Wostemeyer J, Sanders IR (2002) Identification and isolation of two Ascomycete fungi from spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea. Appl Environ Micro 68:4567–4573CrossRefGoogle Scholar
  8. Israel D (1987) Investigation of the role of phosphorus in symbiotic nitrogen fixation. Plant Physiol 84:835–840PubMedCrossRefGoogle Scholar
  9. Jakobsen I, Gazery C, Abbott LK (2001) Phosphate transport by communities of arbuscular mycorrhizal fungi in intact soil cores. New Phytol 149:95–103CrossRefGoogle Scholar
  10. Kiers ET, Lovelock CE, Kruger EL, Herre EA (2000) Different effects of tropical arbuscular mycorrhizal fungal inocula on root colonization and tree seedling growth: implications for tropical forest diversity. Ecol Lett 3:106–113CrossRefGoogle Scholar
  11. Kowalchuk GA, De Souza FA, Van Veen JA (2002) Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria in Dutch coastal sand dunes. Mol Ecol 11:571–581PubMedCrossRefGoogle Scholar
  12. Nichols JD, Rosemeyer M, Carpenter FL, Kettler J (2001) Intercropping legume trees with native timber trees rapidly restores cover to eroded tropical pasture without fertilization. For Ecol Manag 152:195–209CrossRefGoogle Scholar
  13. Redecker D (2000) Specific PCR primers to identify arbuscular mycorrhizal fungi within colonized roots. Mycorrhiza 10:73–80CrossRefGoogle Scholar
  14. Redecker D (2002) Molecular identification and phylogeny of arbuscular mycorrhizal fungi. Plant Soil 244:67–73CrossRefGoogle Scholar
  15. Redecker D, Morton JB, Bruns TD (2000) Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). Mol Phyl Evol 14:276–284CrossRefGoogle Scholar
  16. Roux KH (1994) Using mismatched primer-template pairs in touchdown PCR. Bio Tech 16:812–814Google Scholar
  17. Roux KH (1995) Optimization and troubleshooting in PCR. PCR Meth Appl 4:884–999Google Scholar
  18. Sanchez PA, Logan TJ (1992) Myths and science about the chemistry and fertility of soils in the tropics. In: Lal R, Sanchez PA (eds) Myth and science of soils of the tropics. Proc. Int. Symp. sponsored by Division A-6 of the Am. Soc. of Agron., Madison, Wisconsin USA 1992, pp 35–46. SSSA Special Publication No. 29Google Scholar
  19. Shepherd M, Cross M, Stokoe RL, Scott LJ, Jones ME (2002) High-throughput DNA extraction from forest trees. Plant Mol Biol Rep 20:425a–425jGoogle Scholar
  20. van der Heijden M (1998) Different arbuscular mycorrhizal fungal species are potential determinants of plant community structure. Ecology 79:2082–2091CrossRefGoogle Scholar
  21. van der Heijden M, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69–72CrossRefGoogle Scholar
  22. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Extensive fungal diversity in plant roots. Science 295:2051PubMedCrossRefGoogle Scholar
  23. White TJ, Bruns T, Lee S, Taylor J (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 Press Inc, San Diego, pp 315–322Google Scholar
  24. Zhou MY, Clark SE, Gomez-Sanchez CE (1995) Universal cloning method by TA strategy. BioTech 19:34–35Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Mervyn Shepherd
    • 1
  • Linh Nguyen
    • 1
  • Megan E. Jones
    • 1
  • J. Doland Nichols
    • 2
  • F. Lynn Carpenter
    • 3
  1. 1.Centre for Plant Conservation GeneticsSouthern Cross UniversityLismoreAustralia
  2. 2.Sustainable Forestry Program, School of Environmental Science and ManagementSouthern Cross UniversityLismoreAustralia
  3. 3.Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineUSA

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