Development of Oligonucleotide Microarrays for Simultaneous Multi-species Identification of Phellinus Tree-pathogenic Fungi

Overview

Journal Microb Biotechnol

Specialties Biotechnology
Microbiology

Date 2016 Feb 9

PMID 26853539

Authors

Yuh Tzean

Po-Yao Shu

Ruey-Fen Liou

Shean-Shong Tzean

Affiliations

Soon will be listed here.

Abstract

Polyporoid Phellinus fungi are ubiquitously present in the environment and play an important role in shaping forest ecology. Several species of Phellinus are notorious pathogens that can affect a broad variety of tree species in forest, plantation, orchard and urban habitats; however, current detection methods are overly complex and lack the sensitivity required to identify these pathogens at the species level in a timely fashion for effective infestation control. Here, we describe eight oligonucleotide microarray platforms for the simultaneous and specific detection of 17 important Phellinus species, using probes generated from the internal transcribed spacer regions unique to each species. The sensitivity, robustness and efficiency of this Phellinus microarray system was subsequently confirmed against template DNA from two key Phellinus species, as well as field samples collected from tree roots, trunks and surrounding soil. This system can provide early, specific and convenient detection of Phellinus species for forestry, arboriculture and quarantine inspection, and could potentially help to mitigate the environmental and economic impact of Phellinus-related diseases.

References

Hsiao C, Huang L, Bouchara J, Barton R, Li H, Chang T . Identification of medically important molds by an oligonucleotide array. J Clin Microbiol. 2005; 43(8):3760-8. PMC: 1233923. DOI: 10.1128/JCM.43.8.3760-3768.2005. View

Guglielmo F, Bergemann S, Gonthier P, Nicolotti G, Garbelotto M . A multiplex PCR-based method for the detection and early identification of wood rotting fungi in standing trees. J Appl Microbiol. 2007; 103(5):1490-507. DOI: 10.1111/j.1365-2672.2007.03378.x. View

Martin R, James D, Levesque C . Impacts of Molecular Diagnostic Technologies on Plant Disease Management. Annu Rev Phytopathol. 2001; 38:207-239. DOI: 10.1146/annurev.phyto.38.1.207. View

Tiquia S, Wu L, Chong S, Passovets S, Xu D, Xu Y . Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 2004; 36(4):664-70, 672, 674-5. DOI: 10.2144/04364RR02. View

Schoch C, Seifert K, Huhndorf S, Robert V, Spouge J, Levesque C . Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A. 2012; 109(16):6241-6. PMC: 3341068. DOI: 10.1073/pnas.1117018109. View

Olive D, Bean P . Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol. 1999; 37(6):1661-9. PMC: 84917. DOI: 10.1128/JCM.37.6.1661-1669.1999. View

Guglielmo F, Gonthier P, Garbelotto M, Nicolotti G . A PCR-based method for the identification of important wood rotting fungal taxa within Ganoderma, Inonotus s.l. and Phellinus s.l. FEMS Microbiol Lett. 2008; 282(2):228-37. DOI: 10.1111/j.1574-6968.2008.01132.x. View

Ann P, Chang T, Ko W . Phellinus noxius Brown Root Rot of Fruit and Ornamental Trees in Taiwan. Plant Dis. 2019; 86(8):820-826. DOI: 10.1094/PDIS.2002.86.8.820. View

Rihn B, Coulais C, Bottin M, Martinet N . Evaluation of non-radioactive labelling and detection of deoxyribonucleic acids. Part One: Chemiluminescent methods. J Biochem Biophys Methods. 1995; 30(2-3):91-102. DOI: 10.1016/0165-022x(94)00068-o. View

10.

Dai Y, Zhou L, Cui B, Chen Y, Decock C . Current advances in Phellinus sensu lato: medicinal species, functions, metabolites and mechanisms. Appl Microbiol Biotechnol. 2010; 87(5):1587-93. DOI: 10.1007/s00253-010-2711-3. View

11.

Rhee S, Liu X, Wu L, Chong S, Wan X, Zhou J . Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol. 2004; 70(7):4303-17. PMC: 444823. DOI: 10.1128/AEM.70.7.4303-4317.2004. View

12.

Brown T, Anthony R . The addition of low numbers of 3' thymine bases can be used to improve the hybridization signal of oligonucleotides for use within arrays on nylon supports. J Microbiol Methods. 2000; 42(2):203-7. DOI: 10.1016/s0167-7012(00)00175-5. View

13.

Burdon J, Thrall P, Ericson A . The current and future dynamics of disease in plant communities. Annu Rev Phytopathol. 2005; 44:19-39. DOI: 10.1146/annurev.phyto.43.040204.140238. View

14.

Turenne C, Sanche S, Hoban D, Karlowsky J, Kabani A . Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J Clin Microbiol. 1999; 37(6):1846-51. PMC: 84966. DOI: 10.1128/JCM.37.6.1846-1851.1999. View

15.

Gauthier M, Blais B . Comparison of different approaches for the incorporation of non-radioactive labels into polymerase chain reaction products. Biotechnol Lett. 2003; 25(16):1369-74. DOI: 10.1023/a:1024944823516. View

16.

Thorn R, Reddy C, Harris D, Paul E . Isolation of saprophytic basidiomycetes from soil. Appl Environ Microbiol. 1996; 62(11):4288-92. PMC: 1388993. DOI: 10.1128/aem.62.11.4288-4292.1996. View

17.

Lievens B, Thomma B . Recent developments in pathogen detection arrays: implications for fungal plant pathogens and use in practice. Phytopathology. 2008; 95(12):1374-80. DOI: 10.1094/PHYTO-95-1374. View

18.

Lafontaine D, Tollervey D . The function and synthesis of ribosomes. Nat Rev Mol Cell Biol. 2001; 2(7):514-20. DOI: 10.1038/35080045. View

19.

Letowski J, Brousseau R, Masson L . Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods. 2004; 57(2):269-78. DOI: 10.1016/j.mimet.2004.02.002. View

20.

Saiki R, Walsh P, Levenson C, Erlich H . Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A. 1989; 86(16):6230-4. PMC: 297811. DOI: 10.1073/pnas.86.16.6230. View