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Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

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Abstract

Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36–361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon–Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.

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Acknowledgments

The authors are grateful to the financial support from Chinese National Science Foundation (31270545) and Tianjin Research Program for Advanced Technology (12JCZDJC29700).

Conflict of interest

The authors declare that they have no conflict of interest and the research does not involve Human Participants and/or Animals.

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Authors and Affiliations

  1. Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China

    Jie Liu, Yaoyao Yu, Zhang Cai & Yingying Wang

  2. John and Willie Leone Family Department of Energy and Mineral Engineering, The Pennsylvania State University, University Park, PA, 16802, USA

    Zhang Cai

  3. State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300071, China

    Mark Bartlam

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  1. Jie Liu
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  2. Yaoyao Yu
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Correspondence to Yingying Wang.

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Liu, J., Yu, Y., Cai, Z. et al. Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE. World J Microbiol Biotechnol 31, 1387–1395 (2015). https://doi.org/10.1007/s11274-015-1890-6

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  • DOI: https://doi.org/10.1007/s11274-015-1890-6

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