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Congruence of ribosomal DNA sequencing, fatty acid methyl ester profiles and morphology for characterization of the genus Rhizophagus (arbuscular mycorrhiza fungus)

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Abstract

Difficulties in obtaining sterile axenic cultures and heterogeneity in nuclear-encoded ribosomal DNA (n-rDNA) sequences within a single arbuscular mycorrhizal spore make genetic analysis of arbuscular mycorrhizal fungi (AMF) a complicated task, and currently available methods of genotyping are inadequate for identification to the species level. Therefore, we applied a multipronged approach on different isolates grown in root organ culture (ROC) belonging to the genus Rhizophagus which were not characterized at species level. Each strain was characterized using the fatty acid methyl ester profile (FAME), partial sequencing of a small subunit-internal transcribed spacer (SSU-ITS) and a large subunit (LSU) region of n-rDNA, and morphological examination of spores. Neighbor-joining trees obtained from the SSU-ITS rDNA sequences were broadly similar to those obtained from the LSU rDNA sequences. FAME profiles of the same isolates used for molecular characterization were obtained using fatty acid datasets, and results were compared to a neighbor-joining tree of n-rDNA sequence. Based on the results of these studues, a combination of morphology, biomarkers (FAME), and molecular sequencing (of highly variable D1-D2 of LSU and ITS) is recommended for phylogenetic analysis and characterization of species/strain of Glomeromycota.

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Acknowledgments

The author thanks the University Grants Commission (UGC) of the Govt of India for the award of a senior research fellowship to carry out doctoral work at The Energy and Resources Institute (TERI), New Delhi. This research was supported by funds provided to TERI by the Department of Biotechnology; Govt of India. The author also gratefully acknowledges Mr Yattendra Joshi for revising the manuscript.

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Authors and Affiliations

  1. TERI University, 10 Institutional Area, Vasant Kunj, New Delhi, 10070, India

    Sanjeev Kumar

  2. Centre for Mycorrhizal Research (CMR), Biotechnology and Bioresources Division, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India

    Shanuja Beri & Alok Adholeya

  3. Centre for Mycorrhizal Research, The Energy and Resources Institute, India Habitat Center, D.S Block, Lodhi Road, New Delhi, 110003, India

    Alok Adholeya

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  1. Sanjeev Kumar
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  2. Shanuja Beri
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  3. Alok Adholeya
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Correspondence to Alok Adholeya.

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Kumar, S., Beri, S. & Adholeya, A. Congruence of ribosomal DNA sequencing, fatty acid methyl ester profiles and morphology for characterization of the genus Rhizophagus (arbuscular mycorrhiza fungus). Ann Microbiol 63, 1405–1415 (2013). https://doi.org/10.1007/s13213-013-0601-5

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