Metagenomics as a Tool to Explore Mycorrhizal Fungal Communities
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.
KeywordsMycorrhizosphere AMF diversity Shotgun sequencing Metagenomics Pyrosequencing Metabarcoding
PB thanks DST-SERB: SB/YS/LS-213/2013 for the financial support.
- 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
- Bhargava, P., Gupta, N., Vats, S., & Goel, R. (2017a). Health issues and heavy metals. Austin Journal of Environmental Toxicology, 3(1), 3018.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.CrossRefGoogle 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.CrossRefGoogle 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
- 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