Advertisement

Characterization of Arbuscular Mycorrhizal Communities in Roots of Vineyard Plants

Chapter
Part of the Rhizosphere Biology book series (RHBIO)

Abstract

We developed a new protocol to study arbuscular mycorrhizal fungal (AMF) communities in Bordeaux vineyards in a standardized way, in order to compare results obtained over years and between locations. To this end, we first used grapevine root samples instead of soil samples to avoid AMF spores or hyphae interacting with cover plants. We next increased the number of grapevine samples to obtain more representative coverage of AMF communities while decreasing variability intra-vineyard, especially for the larger parcels. In addition, we adapted the DNA extraction protocol dedicated to soil samples to grapevine roots, as a way to increase the yield and the purity of samples. These features, coupled to the choice of the LSU-D2 region as the molecular marker for high-throughput sequencing (MiSeq® technology), further allowed us to assess the AMF populations of Bordeaux vineyards.

Notes

Acknowledgements

The authors acknowledge the financial support provided by the Bureau Interprofessionnel des Vins de Bourgogne (MYCOVITI Project), the Conseil Interprofessionel du Vin de Bordeaux (project 41971/41975), the Plant Health and Environment department from INRA and funding bodies within the H2020 ERA-net project, CORE Organic Cofund, and with cofunds from the European Commission (BIOVINE project).

References

  1. Balestrini R, Magurno F, Walker C, Lumini E, Bianciotto V (2010) Cohorts of arbuscular mycorrhizal fungi (AMF) in Vitis vinifera, a typical Mediterranean fruit crop. Environ Microbiol Rep 2:594–604CrossRefGoogle Scholar
  2. Basu S, Rabara RC, Negi S (2018) AMF: the future prospect for sustainable agriculture. Physiol Mol Plant Pathol 102:36–45CrossRefGoogle Scholar
  3. Bouffaud M-L, Bernaud E, Colombet A, van Tuinen D, Wipf D, Redecker D (2016) Regional-scale analysis of arbuscular mycorrhizal fungi: the case of Burgundy vineyards. J Int Sci Vigne Vin 50:1–8Google Scholar
  4. Cameron DD, Neal AL, van Wees SCM, Ton J (2013) Mycorrhiza-induced resistance: more than the sum of its parts? Trends Plant Sci 18:539–545CrossRefGoogle Scholar
  5. Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G (2016) FROGS: find, rapidly, OTUs with galaxy solution. Bioinformatics 40:1–4Google Scholar
  6. Gianinazzi S, Gollotte A, Binet M-N, van Tuinen D, Redecker D, Wipf D (2010) Agroecology: the key role of arbuscular mycorrhizas in ecosystem services. Mycorrhiza 20:519–530CrossRefGoogle Scholar
  7. Gollotte A, van Tuinen D, Atkinson D (2004) Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment. Mycorrhiza 14:111–117CrossRefGoogle Scholar
  8. Hart MM, Aleklett K, Chagnon P-L, Egan C, Ghignone S, Helgason T, Lekberg Y, Öpik M, Pickles BJ, Waller L (2015) Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. New Phytol 207:235–247CrossRefGoogle Scholar
  9. Holland TC, Bowen P, Bogdanoff C, Hart MM (2013) How distinct are arbuscular mycorrhizal fungal communities associating with grapevines? Biol Fertil Soils 50:667–674CrossRefGoogle Scholar
  10. Lee E-H, Eo J-K, Ka K-H, Eom A-H (2013) Diversity of arbuscular mycorrhizal fungi and their roles in ecosystems. Mycobiology 41:121CrossRefGoogle Scholar
  11. Likar M, Hančević K, Radić T, Regvar M (2012) Distribution and diversity of arbuscular mycorrhizal fungi in grapevines from production vineyards along the eastern Adriatic coast. Mycorrhiza 23:209–219CrossRefGoogle Scholar
  12. Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J et al (2013) Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytol 199:288–299CrossRefGoogle Scholar
  13. Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V (2010) Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Environ Microbiol 12:2165–2179PubMedGoogle Scholar
  14. Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol 188:223–241CrossRefGoogle Scholar
  15. Plassart P, Terrat S, Thomson B, Griffiths R, Dequiedt S, Lelievre M, Regnier T, Nowak V, Bailey M, Lemanceau P et al (2012) Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure. PLoS One 7:e44279CrossRefGoogle Scholar
  16. Redecker D, Schüßler A, Stockinger H, Stürmer SL, Morton JB, Walker C (2013) An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). Mycorrhiza 23:515–531CrossRefGoogle Scholar
  17. Rillig MC, Wright SF, Eviner VT (2002) The role of arbuscular mycorrhizal fungi and glomalin in soil aggregation: comparing effects of five plant species. Plant Soil 238:325–333CrossRefGoogle Scholar
  18. Schlaeppi K, Bender SF, Mascher F, Russo G, Patrignani A, Camenzind T, Hempel S, Rillig MC, van der Heijden MGA (2016) High-resolution community profiling of arbuscular mycorrhizal fungi. New Phytol 212:780–791CrossRefGoogle Scholar
  19. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A et al (2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108:1028–1046CrossRefGoogle Scholar
  20. Smith SE, Read D (2008) Mycorrhizal Symbiosis, 3rd edn. Academic Press, AmsterdamGoogle Scholar
  21. Stockinger H, Krüger M, Schüßler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187:461–474CrossRefGoogle Scholar
  22. Trouvelot S, Bonneau L, Redecker D, Tuinen DV, Adrian M, Wipf D (2015) Arbuscular mycorrhiza symbiosis in viticulture: a review. Agron Sustain Dev 35:1449–1467CrossRefGoogle Scholar
  23. van Tuinen D, Jacquot E, Zhao B, Gollotte A, Gianinazzi-Pearson V (1998) Characterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR. Mol Ecol 7:879–887CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Agroécologie, AgroSup Dijon, CNRS, INRAUniversité Bourgogne Franche-ComtéDijonFrance

Personalised recommendations