Skip to main content
SpringerLink
Log in

Root-Associated Ectomycorrhizal Mycobionts as Forest Biofertilizers: Standardized Molecular Methods for Characterization of Ectomycorrhizal Wood Wide Web

  • Chapter
  • First Online:
Microbiota and Biofertilizers

Abstract

Ectomycorrhizal (ECM) fungi play a crucial role in nutrient mobilization and cycling, particularly in temperate forests dominated by coniferous species. The belowground ectomycorrhizal Wood Wide Web interconnects innumerable host plants and serves as a sustainable continuum for plant and soil health in forest ecosystems. Conifers, particularly conifer roots harbouring ectomycorrhizal fungi, are rich in phenolics and other secondary metabolites, which interfere and hamper their DNA extraction and inhibit all downstream processes like amplification and sequencing. The present study was projected for presenting the standardized molecular methodology for characterization of ectomycorrhizal fungi from conifer roots, starting from extraction of high-quality DNA and its PCR amplification, followed by DNA purification and loading, to final sequencing, all things reflected in a chronological manner. This chapter highlights the role of root-associated ectomycorrhizal fungi as biofertilizers in forest ecosystems and efficient molecular methods specially optimized for characterization of ectomycorrhizal fungi associated with conifers.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adeleke RA, Nunthkumar B, Roopnarain A, Obi L (2019) Applications of plant–microbe interactions in agro-ecosystems. In: Microbiome in plant health and disease. Springer, Singapore, pp 1–34

    Google Scholar 

  • Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microb Cell Factories 13:66

    Article  Google Scholar 

  • Bhat RA, Dervash MA, Mehmood MA, Skinder BM, Rashid A, Bhat JIA, Lone R (2017) Mycorrhizae: a sustainable industry for plant and soil environment. In: Mycorrhiza-nutrient uptake, biocontrol, ecorestoration. Springer, Cham, pp 473–502

    Chapter  Google Scholar 

  • Bücking H, Liepold E, Ambilwade P (2012) The role of the mycorrhizal symbiosis in nutrient uptake of plants and the regulatory mechanisms underlying these transport processes. In: Plant science, vol 4. IntechOpen, pp 107–138

    Google Scholar 

  • Chakrabarti R, Schutt CE (2001) The enhancement of PCR amplification by low molecular-weight sulfones. Gene 274:293–298

    Article  CAS  PubMed  Google Scholar 

  • Chatterjee A, Khan SR, Vaseem H (2019) Exploring the role of mycorrhizae as soil ecosystem engineer. In: Varma A, Choudhary DK (eds) Mycorrhizosphere and pedogenesis. Springer, Singapore, pp 73–93

    Chapter  Google Scholar 

  • Chavez D, Pereira G, Machuca Á (2014) Stimulation of Pinus radiata seedling growth using ectomycorrhizal and saprophytic fungi as biofertilizers. Bosque 35:57–63

    Google Scholar 

  • Chung H, Kim D, Cho N, Lee S (2003) Observation and distribution of ectomycorrhizal fungi in Pinus roots. Mycobiology 31:1–8

    Article  Google Scholar 

  • Domínguez JA, Selva J, Rodríguez Barreal JA, Saiz de Omeñaca JA (2006) The influence of mycorrhization with Tuber melanosporum in the afforestation of a Mediterranean site with Quercus ilex and Quercus faginea. For Ecol Manag 231:226–233

    Article  Google Scholar 

  • Domínguez-Núñez JA, Albanesi AS (2019) Ectomycorrhizal fungi as biofertilizers in forestry. In: Biostimulants in plant science. IntechOpen

    Google Scholar 

  • Domínguez-Núñez JA, Berrocal-Lobo M, Albanesi AS (2019) Ectomycorrhizal fungi: role as biofertilizers in forestry. In: Giri B et al (eds) Biofertilizers for sustainable agriculture and environment, Soil biology 55. Springer, Cham, pp 67–82

    Chapter  Google Scholar 

  • Farell EM, Alexandre G (2012) Bovine serum albumin further enhances the effects of organic solvents on increased yield of polymerase chain reaction of GC-rich templates. BMC Res Notes 5:257

    Article  PubMed  PubMed Central  Google Scholar 

  • Frąc M, Hannula SE, Bełka M, Jędryczka M (2018) Fungal biodiversity and their role in soil health. Front Microbiol 9:707

    Article  PubMed  PubMed Central  Google Scholar 

  • Frackman S, Kobs G, Simpson D, Storts D (1998) Betaine and DMSO: enhancing agents for PCR, Promega notes 65, pp 27–29

    Google Scholar 

  • Gil-Martínez M, López-García Á, Domínguez MT, Navarro-Fernández CM, Kjøller R, Tibbett M, Marañón T (2018) Ectomycorrhizal fungal communities and their functional traits mediate plant-soil interactions in trace element contaminated soils. Front Plant Sci 9:1682

    Article  PubMed  PubMed Central  Google Scholar 

  • Giovannetti M, Lucian A, Paola F, Elisa P, Cristiana S, Patrizia S (2006) At the root of the wood wide web. Plant Signal Behav 1:1–5

    Article  PubMed  PubMed Central  Google Scholar 

  • Hardjasa A, Ling M, Ma K, Yu H (2010) Investigating the effects of DMSO on PCR fidelity using a restriction digest-based method. JEMI 14:161–164

    Google Scholar 

  • Horton TR, Bruns TD (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 10:1855–1871

    Article  CAS  PubMed  Google Scholar 

  • Janowski D, Wilgan R, Leski T, Karliński L, Rudawska M (2019) Effective molecular identification of ectomycorrhizal fungi: revisiting DNA isolation methods. Forests 10:218

    Article  Google Scholar 

  • Jensen MA, Fukushima M, Davis RW (2010) DMSO and betaine greatly improve amplification of GC-rich constructs in de novo synthesis. PLoS One 5:e11024

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kinden DA, Brown MF (1975) Technique for scanning electron microscopy of fungal structures within plant cells. Phytopathology 65:74–76

    Article  Google Scholar 

  • Mahanty T, Bhattacharjee S, Goswami M, Bhattacharyya P, Das B, Ghosh A, Tribedi P (2017) Biofertilizers: a potential approach for sustainable agriculture development. Environ Sci Pollut R 24:3315–3335

    Article  CAS  Google Scholar 

  • Malusá E, Sas-Paszt L, Ciesielska J (2012) Technologies for beneficial microorganisms inocula used as biofertilizers. Sci World J:2012

    Google Scholar 

  • Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS (2016) Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol 14:760–773

    Article  CAS  PubMed  Google Scholar 

  • Marx DH, Cordell CE (1989) The use of specific ectomycorrhizas to improve artificial forestation practices. In: Whipps JM, Lumsden RD (eds) Biotechnology of fungi for improving plant growth: symposium of the British Cambridge University Press, Cambridge, pp 1–25

    Google Scholar 

  • McAfee BJ, Fortin JA (1986) Competitive interactions of ectomycorrhizal mycobionts under field conditions. Can J Bot 64:848–852

    Article  Google Scholar 

  • Molina R (1994) The role of mycorrhizal symbioses in the health of giant redwoods and other forest ecosystems1. Proceedings of the symposium on Giant Sequoias: their place in the ecosystem and society 151:78–81

    Google Scholar 

  • Mridha MAU (2003) Application of mycorrhizal technology in plantation forestry in Bangladesh. In: The XII World Forestry Congress, Canada

    Google Scholar 

  • Nagai M, Yoshida A, Sato N (1998) Additive effects of bovine serum albumin, dithiothreitol and glycerol on PCR. IUBMB Life 44:157–163

    Article  CAS  Google Scholar 

  • Nilsson HR, Tedersoo L, Lindahl BD, Kjøller R, Carlsen T, Quince C, Abarenkov K, Pennanen T, Stenlid J, Bruns T, Larsson K, Kõljalg U, Kauserud H (2011) Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytol 191:314–318

    Article  Google Scholar 

  • Nuti M, Giovannetti G (2015) Borderline products between bio-fertilizers/bio-effectors and plant protectants: the role of microbial consortia. J Agric Sci Technol A 5:305–315

    Google Scholar 

  • Olivier JM (2000) Progress in the cultivation of truffles. In: Van Griensven LJLD (ed) Mushroom science XV: science and cultivation of edible fungi, vol 2. Balkema, Rotterdam, pp 937–942

    Google Scholar 

  • Pal S, Singh HB, Farooqui A, Rakshit A (2015) Fungal biofertilizers in Indian agriculture: perception, demand and promotion. J Eco-friendly Agric 10:101–113

    Google Scholar 

  • Saravanan RS, Natarajan K (1996) Effect of Pisolithus tinctorius on the nodulation and nitrogen fixing potential of Acacia nilotica seedlings. Kavaka 24:41–49

    Google Scholar 

  • Saravanan RS, Natarajan K (2000) Effect of ecto- and endomycorrhizal fungi along with Bradyrhizobium sp. on the growth and nitrogen fixation in Acacia nilotica seedlings in the nursery. J Trop For Sci 12:348–356

    Google Scholar 

  • Schrey SD, Erkenbrack E, Früh E, Fengler S, Hommel K, Horlacher N, Schulz D, Ecke M, Kulik A, Fiedler HP, Hampp R, Tarkka MT (2012) Production of fungal and bacterial growth modulating secondary metabolites is widespread among mycorrhiza–associated streptomycetes. BMC Microbiol 12:164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schwartz MW, Hoeksema JD, Gehring CA, Johnson NC, Klironomos JN, Abbott LK, Pringle A (2006) The promise and the potential consequences of the global transport of mycorrhizal fungal inoculum. Ecol Lett 9:501–515

    Article  PubMed  Google Scholar 

  • Sharma R (2017) Ectomycorrhizal mushrooms: their diversity, ecology and practical applications. In: Varma A, Prasad R, Tuteja N (eds) Mycorrhiza – function, diversity, state of the art. Springer, Berlin, pp 99–131

    Chapter  Google Scholar 

  • Sim MY, Eom AH (2006) Effects of ectomycorrhizal fungi on growth of seedlings of Pinus densiflora. Mycobiology 34:191–195

    Article  PubMed  PubMed Central  Google Scholar 

  • Simard SW (2012) Mycorrhizal networks: mechanisms, ecology and modeling. Fungal Biol Rev26:39–60

    Google Scholar 

  • Smith D, Peay KG (2014) Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 92:e90234

    Article  CAS  Google Scholar 

  • Tarkka MT, Drigo B, Deveau A (2018) Mycorrhizal microbiomes. Mycorrhiza 28:403–409

    Article  CAS  PubMed  Google Scholar 

  • Thomas L, Singh I (2019) Microbial biofertilizers: types and applications. In: Biofertilizers for sustainable agriculture and environment. Springer, Cham, pp 1–19

    Google Scholar 

  • Vecstaudža D, Seņkovs M, Nikolajeva V, Mutere O (2018) Characteristics of an endophytic microbial consortium and its impact on rhizosphere microbiota of barley. Environ Exp Biol 16:177–183

    Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors profoundly acknowledge G.B. Pant National Institute of Himalayan Environment and Sustainable Development (NMHS-IERP) for providing financial support under the Grant number GBPI/IERP-NMHS/15-16/10/03. We thank the director of the University Scientific Instrumentation Centre (USIC), University of Kashmir, for providing the necessary SEM facility. We also thank the head of the Department of Botany, University of Kashmir, India, for providing the necessary laboratory facilities.

Conflict of Interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India

    Rezwana Assad, Zafar Ahmad Reshi & Irfan Rashid

Authors
  1. Rezwana Assad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zafar Ahmad Reshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Irfan Rashid
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Khalid Rehman Hakeem

  2. Department of Environmental Science, Sri Pratap College, Cluster University, Higher Education Department, Srinagar, Jammu and Kashmir, India

    Gowhar Hamid Dar

  3. Department of Environment & Water Management, Sri Pratap College, Cluster University, Srinagar, Jammu and Kashmir, India

    Mohammad Aneesul Mehmood

  4. Division of Environmental Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir-Srinagar, Srinagar, Jammu and Kashmir, India

    Rouf Ahmad Bhat

10.1 Electronic Supplementary Material

Data 7.2

(DOCX 78 kb)

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Assad, R., Reshi, Z.A., Rashid, I. (2021). Root-Associated Ectomycorrhizal Mycobionts as Forest Biofertilizers: Standardized Molecular Methods for Characterization of Ectomycorrhizal Wood Wide Web. In: Hakeem, K.R., Dar, G.H., Mehmood, M.A., Bhat, R.A. (eds) Microbiota and Biofertilizers. Springer, Cham. https://doi.org/10.1007/978-3-030-48771-3_10

Download citation

Publish with us

Policies and ethics

Search

Navigation