Skip to main content
SpringerLink
Log in
Book cover

Mycorrhizosphere and Pedogenesis pp 207–219Cite as

Metagenomics as a Tool to Explore Mycorrhizal Fungal Communities

  • Chapter
  • First Online:

Abstract

Fungi are important inhabitants of soil communities and help in providing nutrition to plants in symbiont form, act as decomposers and also harm the plants playing the role of monstrous pathogens. Arbuscular mycorrhizal fungus (AMF) is a heterogeneous group of fungal species associated with the roots of over 90% of higher plant species. The exploration and study of AMF diversity in ecosystems is carried out for many different reasons. The most fundamental reason is to find out more about the basic ecology of AMF. New knowledge about AMF ecology has being successfully uncovered with the application of metagenomics and has added to our knowledge of the vast pool of microbes. Metagenomics assess the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. DNA pyrosequencing along with metabarcoding is being extensively used in investigating the prokaryotic and eukaryotic assemblages in soil ecosystems. The aim of this chapter is to focus on the role of metagenomic analysis in exploring the AMF which is the most widespread symbionts in agri ecosystems worldwide.

This is a preview of subscription content, 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   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

References

  • Alguacil, M. M., Roldán, A., & Torres, M. P. (2009). Complexity of semiarid gypsophilous shrub communities mediates the AMF biodiversity at the plant species level. Microbial Ecology, 57(4), 718–727.

    Google Scholar 

  • 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. Environmental Microbiology Reports, 2(4), 594–604.

    Article  Google Scholar 

  • Bhargava, P., Gupta, N., Vats, S., & Goel, R. (2017a). Health issues and heavy metals. Austin Journal of Environmental Toxicology, 3(1), 3018.

    Google Scholar 

  • Bhargava, P., Singh, A. K., & Goel, R. (2017b). Microbes: Bioresource in agriculture and environmental sustainability. In Plant-microbe interactions in agro-ecological perspectives (pp. 361–376). Singapore: Springer.

    Chapter  Google Scholar 

  • Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R. H., Uroz, S., & Martin, F. (2009). 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184(2), 449–456.

    Article  Google Scholar 

  • Colombo, R. P., Fernandez Bidondo, L., Silvani, V. A., Carbonetto, M. B., Rascovan, N., Bompadre, M. J., & Godeas, A. M. (2014). Diversity of arbuscular mycorrhizal fungi in soil from the Pampa Ondulada, Argentina, assessed by pyrosequencing and morphological techniques. Canadian Journal of Microbiology, 60(12), 819–827.

    Article  CAS  Google Scholar 

  • Cristescu, M. E. (2014). From barcoding single individuals to metabarcoding biological communities: Towards an integrative approach to the study of global biodiversity. Trends in Ecology & Evolution, 29(10), 566–571.

    Article  Google Scholar 

  • Dai, M., Hamel, C., St. Arnaud, M., He, Y., Grant, C., Lupwayi, N., & Zhou, Z. (2012). Arbuscular mycorrhizal fungi assemblages in Chernozem great groups revealed by massively parallel pyrosequencing. Canadian Journal of Microbiology, 58(1), 81–92.

    Article  CAS  Google Scholar 

  • Daniell, T. J., Husband, R., Fitter, A. H., & Young, J. P. W. (2001). Molecular diversity of arbuscularmycorrhizal fungi colonising arable crops. FEMS Microbiology Ecology, 36(2–3), 203–209.

    Article  CAS  Google Scholar 

  • Douhan, G. W., Vincenot, L., Gryta, H., & Selosse, M. A. (2011). Population genetics of ectomycorrhizal fungi: From current knowledge to emerging directions. Fungal Biology, 115(7), 569–597.

    Article  Google Scholar 

  • Dumbrell, A. J., Ashton, P. D., Aziz, N., Feng, G., Nelson, M., Dytham, C., & Helgason, T. (2011). Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytologist, 190(3), 794–804.

    Article  CAS  Google Scholar 

  • Gai, J. P., Christie, P., Feng, G., & Li, X. L. (2006). Twenty years of research on community composition and species distribution of arbuscular mycorrhizal fungi in China: A review. Mycorrhiza, 16(4), 229–239.

    Article  CAS  Google Scholar 

  • Grant, S., Grant, W. D., Cowan, D. A., Jones, B. E., Ma, Y., Ventosa, A., & Heaphy, S. (2006). Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. Applied and Environmental Microbiology, 72(1), 135–143.

    Article  CAS  Google Scholar 

  • Helgason, T., Daniell, T. J., Husband, R., Fitter, A. H., & Young, J. P. W. (1998). Ploughing up the wood-wide web? Nature, 394(6692), 431.

    Article  CAS  Google Scholar 

  • Helgason, T., Fitter, A. H., & Young, J. P. W. (1999). Molecular diversity of arbuscularmycorrhizal fungi colonisingHyacinthoides non-scripta (bluebell) in a seminatural woodland. Molecular Ecology, 8(4), 659–666.

    Article  CAS  Google Scholar 

  • Hollister, E. B., Schadt, C. W., Palumbo, A. V., Ansley, R. J., & Boutton, T. W. (2010). Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains. Soil Biology and Biochemistry, 42(10), 1816–1824.

    Article  CAS  Google Scholar 

  • Husband, R., Herre, E. A., Turner, S. L., Gallery, R., & Young, J. P. (2002). Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest. Molecular Ecology, 11(12), 2669–2678.

    Article  CAS  Google Scholar 

  • Jumpponen, A., & Jones, K. L. (2009). Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, 184(2), 438–448.

    Article  CAS  Google Scholar 

  • Kernaghan, G. (2005). Mycorrhizal diversity: Cause and effect? Pedobiologia, 49(6), 511–520.

    Article  Google Scholar 

  • Leal, P. L., Carvalho, T. S., Siqueira, J. O., & Moreira, F. (2017). Assessment of the occurrence and richness of arbuscular mycorrhizal fungal spores by direct analysis of field samples and trap culture-a comparative study. Anais da Academia Brasileira de Ciências, (AHEAD), 0–0.

    Google Scholar 

  • Lennon, J. T. (2011). Replication, lies and lesser-known truths regarding experimental design in environmental microbiology. Environmental Microbiology, 13(6), 1383–1386.

    Article  Google Scholar 

  • Ligrone, R., Carafa, A., Lumini, E., Bianciotto, V., Bonfante, P., & Duckett, J. G. (2007). Glomeromycotean associations in liverworts: A molecular, cellular, and taxonomic analysis. American Journal of Botany, 94(11), 1756–1777.

    Article  CAS  Google Scholar 

  • Lim, Y. W., Kim, B. K., Kim, C., Jung, H. S., Kim, B. S., Lee, J. H., & Chun, J. (2010). Assessment of soil fungal communities using pyrosequencing. The Journal of Microbiology, 48(3), 284–289.

    Article  Google Scholar 

  • Lindahl, B. D., De Boer, W., & Finlay, R. D. (2010). Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi. The ISME Journal, 4(7), 872–881.

    Article  Google Scholar 

  • 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. Environmental Microbiology, 12(8), 2165–2179.

    CAS  PubMed  Google Scholar 

  • Mathimaran, N., Ruh, R., Vullioud, P., Frossard, E., & Jansa, J. (2005). Glomus intraradices dominates arbuscular mycorrhizal communities in a heavy textured agricultural soil. Mycorrhiza, 16(1), 61–66.

    Article  CAS  Google Scholar 

  • Nam, Y. J., Kim, H., Lee, J. H., Yoon, H., & Kim, J. G. (2015). Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands. The Journal of General and Applied Microbiology, 61(3), 67–74.

    Article  CAS  Google Scholar 

  • Öpik, M., Metsis, M., Daniell, T. J., Zobel, M., & Moora, M. (2009). Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, 184(2), 424–437.

    Article  Google Scholar 

  • Parniske, M. (2008). Arbuscular mycorrhiza: The mother of plant root endosymbioses. Nature Reviews Microbiology, 6(10), 763–775.

    Article  CAS  Google Scholar 

  • Peay, K. G., Baraloto, C., & Fine, P. V. (2013). Strong coupling of plant and fungal community structure across western Amazonian rainforests. The ISME Journal, 7(9), 1852–1861.

    Article  CAS  Google Scholar 

  • Prosser, J. I. (2010). Replicate or lie. Environmental Microbiology, 12(7), 1806–1810.

    Article  CAS  Google Scholar 

  • Read, D. J. (1996). The structure and function of the ericoid mycorrhizal root. Annals of Botany, 77(4), 365–374.

    Article  CAS  Google Scholar 

  • Reigstad, L. J., Bartossek, R., & Schleper, C. (2011). Preparation of high-molecular weight DNA and metagenomic libraries from soils and hot springs. In Methods in enzymology (Vol. 496, pp. 319–344). San Diego: Academic.

    Google Scholar 

  • Säle, V., Aguilera, P., Laczko, E., Mäder, P., Berner, A., Zihlmann, U., & Oehl, F. (2015). Impact of conservation tillage and organic farming on the diversity of arbuscular mycorrhizal fungi. Soil Biology and Biochemistry, 84, 38–52.

    Article  Google Scholar 

  • Schechter, S. P., & Bruns, T. D. (2008). Serpentine and non-serpentine ecotypes of Collinsia sparsiflora associate with distinct arbuscular mycorrhizal fungal assemblages. Molecular Ecology, 17(13), 3198–3210.

    Article  CAS  Google Scholar 

  • Vallino, M., Massa, N., Lumini, E., Bianciotto, V., Berta, G., & Bonfante, P. (2006). Assessment of arbuscular mycorrhizal fungal diversity in roots of Solidago gigantea growing in a polluted soil in Northern Italy. Environmental Microbiology, 8(6), 971–983.

    Article  Google Scholar 

  • Wang, B., & Qiu, Y. L. (2006). Phylogenetic distribution and evolution of mycorrhizas in land plants. Mycorrhiza, 16(5), 299–363.

    Article  CAS  Google Scholar 

  • Wang, C., Gu, Z., Cui, H., Zhu, H., Fu, S., & Yao, Q. (2015). Differences in arbuscular mycorrhizal fungal community composition in soils of three land use types in subtropical hilly area of southern China. PLoS One, 10(6), e0130983.

    Article  Google Scholar 

  • Wirsel, S. G. (2004). Homogenous stands of a wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology, 48(2), 129–138.

    Article  CAS  Google Scholar 

  • Wu, B., Hogetsu, T., Isobe, K., & Ishii, R. (2007). Community structure of arbuscular mycorrhizal fungi in a primary successional volcanic desert on the southeast slope of Mount Fuji. Mycorrhiza, 17, 495–506.

    Article  CAS  Google Scholar 

  • Zak, D. R., Holmes, W. E., White, D. C., Peacock, A. D., & Tilman, D. (2003). Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology, 84(8), 2042–2050.

    Article  Google Scholar 

Download references

Acknowledgements

PB thanks DST-SERB: SB/YS/LS-213/2013 for the financial support.

Author information

Authors and Affiliations

  1. Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India

    Prachi Bhargava, Siddharth Vats & Neeraj Gupta

Authors
  1. Prachi Bhargava
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Siddharth Vats
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Neeraj Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Prachi Bhargava .

Editor information

Editors and Affiliations

  1. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Ajit Varma

  2. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Devendra K. Choudhary

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bhargava, P., Vats, S., Gupta, N. (2019). Metagenomics as a Tool to Explore Mycorrhizal Fungal Communities. In: Varma, A., Choudhary, D. (eds) Mycorrhizosphere and Pedogenesis. Springer, Singapore. https://doi.org/10.1007/978-981-13-6480-8_13

Download citation

Publish with us

Policies and ethics

Search

Navigation