In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections
© The Author(s) 2016
Received: 22 April 2016
Accepted: 19 July 2016
Published: 27 July 2016
Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here.
To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues.
This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.
KeywordsBasidiomycota Pucciniomycotina Rust fungus In situ hybridization Puccinia horiana Uromyces transversalis Phakopsora pachyrhizi Chrysanthemum × morifolium Gladiolus × hortulanus Glycine max
Rust fungi (Basidiomycota, Pucciniomycotina) are obligate parasites that infect many species of vascular plants [1, 2]. Recent studies in this laboratory have focused on Chrysanthemum white rust, caused by Puccinia horiana, Gladiolus rust, caused by Uromyces transversalis and Asian soybean rust, caused by Phakopsora pachyrhizi. [3, 4]. Studies on the interactions between these pathogenic fungi and plants would benefit from approaches that allow visualization of the pathogen within host plant tissue, including the use of in situ hybridization (ISH) technology.
ISH was first used to localize specific DNA sequences on chromosomes using probes labeled with radioisotopes [5, 6]. The technique was later used for the detection of viral particles and high copy number mRNA in cultured cells and sectioned tissue making it useful for localizing gene expression patterns [6–10]. Non-radioactive methods were also developed that employed digoxygenin or biotin-conjugated nucleotides allowing for detection with antibody and streptavidin conjugates [9–11]. The development of non-radioactive methods eventually gave rise to fluorescent ISH (FISH), which employs various fluorescent-labeling techniques to produce fluorescence at the site of hybridization [12–14]. Non-radioactive ISH methods have been used to accomplish such tasks as chromosome mapping [14–16], gene expression localization [6, 8, 9, 11], and pathogen detection [17–26]. Chromogenic ISH (CISH) is an alternative to FISH that has become popular in diagnostic laboratories studying human pathogens [19–24].
Recently ISH has been used to identify microorganisms by targeting rRNA [18, 21, 24, 27–32]. The abundance of rRNA in the cell offers ample target for probes to bind to allowing for clear visualization of microorganisms within the sample being assayed. This technique has been used to identify and characterize prokaryotic organisms [27, 29, 32] and has been used for the detection of fungi in cultures [24, 31], plant [17, 18, 20, 30] and animal tissue [19, 21–23, 25].
The aim of this study was to develop a basic ISH protocol that plant pathologists can use for the detection of rust pathogens in paraffin embedded plant tissue. Here we report the development of an optimized protocol tested on three genera of rust fungi from three plant species. The results of this investigation demonstrate the utility of ISH as a tool for visualizing the infection of plant tissue by rust fungi.
Generation of infected leaf material
Leaves of Chrysanthemum × morifolium infected with Puccinia horiana isolate PA-11 , Gladiolus × hortulanus infected with Uromyces transversalis isolate CA-07 , and Glycine max infected with Phakopsora pachyrhizi isolate Taiwan 72-1  were generated for experiments as described. These plant pathogens are regulated under the Plant Protection Act of 2000 and inoculations were conducted in a BSL-3 Plant Pathogen Containment Facility at Ft. Detrick MD under conditions specified in valid USDA APHIS PPQ 526 permits.
DNA extraction and sequencing for ISH probe design
Genomic DNA was extracted from 50 mg of fungal basidiospores of Puccinia horiana using a hexadecyltrimethylammonium bromide (CTAB) extraction protocol beginning with 1 min of homogenization in 500 µL of CTAB extraction buffer (1 % CTAB, 0.7 M NaCl, 100 mM Tris (pH 7.5), 10 mM EDTA, 0.3 mg/mL proteinase K). Homogenized samples were incubated at 65 °C for 30 min, placed on ice for 2 min, and extracted with 500 µL of chloroform: isoamyl alcohol (24:1) by 10 s of vortexing followed by centrifugation at 14,000×g for 10 min. A volume of 300 µL of aqueous phase liquid was collected from each sample, combined with an equal volume of CTAB extraction buffer, re-extracted with 500 µL of chloroform: isoamyl alcohol (24:1), vortexed, and centrifuged at 14,000×g for 10 min. An equal volume of isopropanol was added to 400 µL of aqueous phase extract, which was gently mixed, and centrifuged at 14,000×g for 15 min. Following removal of isopropanol, DNA pellets were washed with 500 µL of 70 % ethanol, and centrifuged at 14,000×g for 20 min at 4 °C. Once 70 % ethanol was removed and nucleic acid pellets were allowed to dry a volume of 50 µL of TE buffer (10 mM Tris, pH 8.0, 1 mM EDTA) containing 1 mg/mL RNase A was added to each sample. Final concentrations of extracted DNA were determined using a Nanodrop 2000 (Thermo Fisher Scientific Inc, Waltham, MA).
Basidiospore DNA was amplified using primers for 18S rDNA (Table 2) in conventional PCR reactions and products were verified by gel electrophoresis. Post-amplification products were purified using ExoSAP-IT reagent (USB Corporation) before sequencing with BigDye Terminator version 3.1 cycle sequencing kit (ABI, Foster, CA). BigDye reaction products were purified using a DyeEx® 2.0 Spin Kit (Qiagen), and analyzed on an ABI 3130XL sequencer (Applied Biosystems).
Tissue sample collection and fixation
Rectangular leaf tissue samples measuring 4 cm by 1 cm were cut from infected leaves using a sterile razor blade and placed into a 50 mL conical tube containing 30 mL of FAE fixative (2 % formaldehyde, 5 % acetic acid, 60 % ethanol) (see supplementary protocol). After 48 h of incubation at 4 °C FAE fixative was removed from the sample tubes and samples were washed with 70 % ethanol for 5 min before incubation at room temperature in 70 % ethanol for one week. After fixation in FAE fixative and clearing in 70 % ethanol samples were shipped to American Histolabs (Rockville, MD) for RNase-free preparation, including paraffin embedding, sectioning, mounting on positively charged microscope slides, and deparaffinization. All microscope slide samples were stored at −80 °C prior to pre-hybridization.
All steps listed in the pre-hybridization protocol were carried out under ribonuclease (RNase) free conditions (see supplementary protocol). Slide mounted tissue samples were rehydrated by incubation in 100 % ethanol, 50 % ethanol, and diethylpyrocarbonate (DEPC)-treated water for 3 min each. Following rehydration samples were treated with 0.2 M HCl for 20 min, washed for 2 min in DEPC-treated water, and incubated at 70 °C for 20 min in 2× SSPE (0.3 M NaCl, 2 mM EDTA, 20 mM NaH2PO4, pH 7.4), before digestion with 10ug/mL proteinase K in proteinase K buffer (20 mM Tris–HCl, pH 7.0, 2 mM CaCl2). Digestion was stopped by washing with 2× SSPE for 5 min at room temperature, and tissue was treated with 0.1 M TEA (0.1 M triethanolamine-Cl, pH 8.0) containing 0.5 % acetic anhydride (Sigma, St. Louis, MO) (v/v) for 10 min preceding treatment with biotin and streptavidin blocking solutions. Blocking of endogenous biotin is achieved by treating samples with 1 mL of 1× Blocking Reagent (Roche, Indianapolis, IN) containing 4 drops/mL of streptavidin blocker (Vector Laboratories, Burlingame, CA) for 15 min, and washing for 5 min in 2× SSPE before applying 1 mL of 1× Blocking Reagent containing 4 drops/mL of biotin blocker (Vector Laboratories, Burlingame, CA) for 15 min. After blocking, slides were washed in 2× SSPE for 5 min and dehydrated by incubation with DEPC-treated water, 50 % ethanol, and 100 % ethanol consecutively for 3 min each. Samples were allowed to air dry while hybridization mixture was prepared.
Hybridization mixture (0.3 M NaCl, 20 mM Tris (pH 7.5), EDTA 2 mM, 500 µg/mL tRNA, 500 µg/mL poly(A) RNA, 1× Denhardt’s Solution , 10 % deionized formamide, 9 ng/µL DNA probe) was prepared and heated to 85–95 °C for 2 min before being placed into ice for 2 min. After the hybridization mixture was prepared, a volume of 100 µL was added to each sample slide, a coverslip was applied, and sample slides were placed into a plastic container lined with paper towels moistened with 4X SSPE. Sample slides were incubated overnight at 42 °C in one pint polypropylene snap-lid plastic containers in a H9270 Dual-Chamber Hybridization Oven (Thermo Fisher Scientific, Waltham, MA).
Post hybridization, staining, and permanent mounting
Slides were removed from the 42 °C hybridization oven and dipped in 2× SSPE to aid in coverslip removal. Once coverslips were removed slides were washed in 2× SSPE for 30 min at room temperature, 1× SSPE for 30 min at 52 °C, and blocked for 30 min at room temperature using 1× Blocking Reagent. Samples were treated with Streptavidin-HRP at a concentration of 1:2500 (Invitrogen Carlsbad, CA.) in 1× PBS for 1 h at room temperature, and washed three times in 1× PBS, prior to application of ImmPACT™ VIP Peroxidase Substrate Kit (Vector Laboratories) following manufacturer’s instructions. To rinse and dehydrate tissue samples slides were placed consecutively into DEPC-treated water for 5 min, and 50 % ethanol and 100 % ethanol for 3 min each. Slides were allowed to dry completely before application of Permaslip Mounting Medium and Liquid Coverslip Solution (American MasterTech, Lodi, CA). Immediately following the addition of mounting media, a new coverslip was applied to permanently mount and preserve the tissue sections.
All images were captured using a Nikon DS-Fi1 camera coupled with a Nikon Eclipse 80i microscope and NIS Elements imaging software (Nikon Inc., Melville, NY). The images reported here were produced through differential interference contrast (DIC) microscopy using a Nikon D-DA DIC light filter. A Nikon CFI Plan Achromat DL 10× objective lens was used to magnify samples to 100×.
Results and discussion
Sequencing for probe design
Accession numbers of sequences used in CLUSTALW and BLAST alignments
List of sequencing primers and ISH probes used in this study
Primer 1 Puccinia 18S Forward (30 bp)
5′ CAATTGGAGGGCAAGTCTGGTGCCAGCAGC 3′
Primer 2 Puccinia 18S Reverse (30 bp)
5′ TGGACCTGGTGAGTTTCCCCGTGTTGAGTC 3′
Puccinia horiana 18S Anti-Sense
5′/biotin/AAGTTCACCAAGAGGTAAGCCTCCAACAA ATCAGTACACACCAAAAGGCAGACCAACTGC 3′
Puccinia horiana 18S Sense
5′/biotin/GCAGTTGGTCTGCCTTTTGGTGTGTACT GATTTGTTGGAGGCTTACCTCTTGGTGAACTT 3′
Uromyces transversalis 18S Anti-Sense
5′/biotin/AAGTTCACCAAGAGGTAAGCCTCCAACA AATCAGTACACACCAAAAGGCGGACCAACTGC 3′
Uromyces transversalis 18S Sense
5′/biotin/GCAGTTGGTCCGCCTTTTGGTGTGTACT GATTTGTTGGAGGCTTACCTCTTGGTGAACTT 3′
Phakopsora pachyrhizi 18S Anti-Sense
5′/biotin/AGGTTCACCAAGAGGTAAGCCTCCAAC AAATCAGTACACACCAAATGGCGGACCAACTGC 3′
Phakopsora pachyrhizi 18S Sense
5′/biotin/GCAGTTGGTCCGCCATTTGGTGTGTACT GATTTGTTGGAGGCTTACCTCTTGGTGAACCT 3′
CLUSTALW alignment of anti-sense probes
* ******************************************* *** **********
Development of an optimized ISH protocol
Application of the protocol to rust fungi
The images presented here are at relatively low magnification, and resolution is therefore at the tissue level. Further magnification of images did not resolve at the intracellular level (not shown). Use of a fluorescent label rather than precipitable stain may result in higher-level resolution.
We present here a generalized ISH protocol for localization of rust fungi in paraffin embedded sections of host tissues. This technique provides plant pathologists with a tool to study the morphology of rust fungi within the plants they infect, which may aid in the elucidation of the life cycles of these plant pathogenic fungi and determination of fungal growth patterns in host tissue. We have demonstrated that this protocol can be applied to pathogens from different genera of rust fungi residing in different plant hosts with little to no non-specific background staining of plant tissue. Our protocol is easy to apply and modify if necessary. The generic protocol thus serves as a starting point that may be modified to suit other plant pathogen systems of interest.
MAE co-conceived the project, adapted methods, conducted the experiments, tested protocols and wrote the manuscript, MBM co-conceived the project, provided guidance, improvements and reagents, and edited the manuscript, MRB and CLP edited the manuscript, DGL co-conceived the project and edited the manuscript. All authors read and approved the final manuscript.
The authors thank Dr. Kerry Pedley and Amy Ruck for providing U. transversalis spore DNA and P. pachyrhizi infected soybean samples, Dr. Reid Frederick for advice and healthy soybean tissue, and Susan Nester for providing P. horiana—infected Chrysanthemum tissue and U. transversalis—infected Gladiolus tissue. MAE wishes to thank Dr. Oney P. Smith, Hood College, for many stimulating ideas and discussions.
The authors declare that they have no competing interests.
Commercial endorsement disclaimer
The use of trade, firm, or corporation names on this page is for the information and convenience of the reader. Such use does not constitute an official endorsement of approval by the USDA Agricultural Research Service, NAL or BIC of any product or service to the exclusion of others that may be suitable.
Equal opportunity statement
USDA is an equal opportunity provider and employer.
This work was supported by USDA, ARS and by USDA APHIS Farm Bill 10007 research grants coordinated by author Dr. Cristi L. Palmer, IR-4 Project, Rutgers University.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, et al. The Top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol. 2012;13:414–30.View ArticlePubMedGoogle Scholar
- Yamaoka Y. Recent outbreaks of rust diseases and the importance of basic biological research for controlling rusts. J Gen Plant Pathol. 2014;80:375–88.View ArticleGoogle Scholar
- Bromfield KR. Soybean Rust (Monograph). St. Paul: APS Press; 1984.Google Scholar
- Schneider RW, Hollier CA, Whitam HK. First report of soybean rust caused by Phakopsora pachyrhizi in the continental United States. Plant Dis. 2005;89:774.View ArticleGoogle Scholar
- Gall JG, Pardue ML. Nucleic acid hybridization in cytological preparations. Methods Enzymol. 1971;21:470–80.View ArticleGoogle Scholar
- Zeller R, Rogers M, Haramis AG. In situ hybridization to cellular RNA. Curr Protoc Mol Biol. 2001:14.13. 11–14.13. 16.
- Brahic M, Haase AT. Detection of viral sequences of low reiteration frequency by in situ hybridization. Proc Natl Acad Sci USA. 1978;75:6125–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Haramis A, Carrasco A. Whole-mount in situ hybridization and detection of RNAs in vertebrate embryos and isolated organs. Curr Protoc Mol Biol. 1996:14.19.
- Lawrence JB, Singer RH. Quantitative analysis of in situ hybridization methods for the detection of actin gene expression. Nucleic Acids Res. 1985;13:1777–99.View ArticlePubMedPubMed CentralGoogle Scholar
- Singer R, Lawrence JB, Villnave C. Optimization of in situ hybridization using isotopic and nonisotopic detection methods. Biotechniques. 1986;4:230–50.Google Scholar
- Singer RH, Ward DC. Actin gene expression visualized in chicken muscle tissue culture by using in situ hybridization with a biotinated nucleotide analog. Proc Natl Acad Sci USA. 1982;79:7331–5.View ArticlePubMedPubMed CentralGoogle Scholar
- Landegent J, De Wal NJI, Baan R, Hoeijmakers J, Van der Ploeg M. 2-Acetylaminofluorene-modified probes for the indirect hybridocytochemical detection of specific nucleic acid sequences. Exp Cell Res. 1984;153:61–72.View ArticlePubMedGoogle Scholar
- Pinkel D, Landegent J, Collins C, Fuscoe J, Segraves R, Lucas J, Gray J. Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. Proc Natl Acad Sci USA. 1988;85:9138–42.View ArticlePubMedPubMed CentralGoogle Scholar
- Pinkel D, Straume T, Gray J. Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA. 1986;83:2934–8.View ArticlePubMedPubMed CentralGoogle Scholar
- Brandriff B, Gordon L, Fertitta A, Olsen A, Christensen M, Ashworth L, Nelson D, Carrano A, Mohrenweiser H. Human chromosome 19p: a fluorescence in situ hybridization map with genomic distance estimates for 79 intervals spanning 20 Mb. Genomics. 1994;23:582–91.View ArticlePubMedGoogle Scholar
- Gordon L, Bergmann A, Christensen M, Danganan L, Lee D, Ashworth L, Nelson D, Olsen A, Mohrenweiser H, Carrano A. A 30-Mb metric fluorescence in situ hybridization map of human chromosome 19q. Genomics. 1995;30:187–92.View ArticlePubMedGoogle Scholar
- Assmus B, Hutzler P, Kirchhof G, Amann R, Lawrence JR, Hartmann A. In situ localization of azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl Environ Microbiol. 1995;61:1013–9.PubMedPubMed CentralGoogle Scholar
- Glöckner FO, Amann R, Alfreider A, Pernthaler J, Psenner R, Trebesius K, Schleifer K-H. An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst Appl Microbiol. 1996;19:403–6.View ArticleGoogle Scholar
- Li AY, Crone M, Adams PJ, Fenwick SG, Hardy GE, Williams N. The microscopic examination of Phytophthora in plant tissues using fluorescent in situ hybridization. J Phytopathol. 2014;162:747–57.View ArticleGoogle Scholar
- Montone KT, Guarner J. In situ hybridization for rRNA sequences in anatomic pathology specimens, applications for fungal pathogen detection: a review. Adv Anat Pathol. 2013;20:168–74.View ArticlePubMedGoogle Scholar
- Montone KT, LiVolsi VA, Lanza DC, Kennedy DW, Palmer J, Chiu AG, Feldman MD, Loevner LA, Nachamkin I. In situ hybridization for specific fungal organisms in acute invasive fungal rhinosinusitis. Am J Clin Pathol. 2011;135:190–9.View ArticlePubMedGoogle Scholar
- Schröder S, Hain M, Sterflinger K. Colorimetric in situ hybridization (CISH) with digoxigenin-labeled oligonucleotide probes in autofluorescent hyphomycetes. Int Microbiol. 2010;3:183–6.Google Scholar
- Shinozaki M, Okubo Y, Sasai D, Nakayama H, Ishiwatari T, Murayama S, Tochigi N, Wakayama M, Nemoto T, Shibuya K. Development and evaluation of nucleic acid-based techniques for an auxiliary diagnosis of invasive fungal infections in formalin-fixed and paraffin-embedded (FFPE) tissues. Med Mycol. 2012;53:241–5.View ArticleGoogle Scholar
- Sterflinger K, Hain M. In situ hybridization with rRNA targeted probes as a new tool for the detection of black yeasts and meristematic fungi. Stud Mycol. 1999;43:23–30.Google Scholar
- Tanaka E. Specific in situ visualization of the pathogenic endophytic fungus Aciculosporium take, the cause of witches’ broom in bamboo. Appl Environ Microbiol. 2009;75:4829–34.View ArticlePubMedPubMed CentralGoogle Scholar
- Vági P, Knapp DG, Kósa A, Seress D, Horváth ÁN, Kovács GM. Simultaneous specific in planta visualization of root-colonizing fungi using fluorescence in situ hybridization (FISH). Mycorrhiza. 2014;24:259–66.View ArticlePubMedGoogle Scholar
- Amann R, Fuchs BM, Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol. 2001;12:231–6.View ArticlePubMedGoogle Scholar
- Bloch B. Biotinylated probes for in situ hybridization histochemistry: use for mRNA detection. J Histochem Cytochem. 1993;41:1751–4.View ArticlePubMedGoogle Scholar
- Brigati DJ, Myerson D, Leary JJ, Spalholz B, Travis SZ, Fong CK, Hsiung G, Ward DC. Detection of viral genomes in cultured cells and paraffin-embedded tissue sections using biotin-labeled hybridization probes. Virology. 1983;126:32–50.View ArticlePubMedGoogle Scholar
- Moter A, Göbel UB. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods. 2000;41:85–112.View ArticlePubMedGoogle Scholar
- Wagner M, Horn M, Daims H. Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol. 2003;6:302–9.View ArticlePubMedGoogle Scholar
- Zachgo S. In situ hybridization. In: Gilmartin PM, Bowler C, editors. Molecular plant biology. 2nd ed. New York: Oxford University Press; 2002. p. 41–63.Google Scholar
- Bonde MR, Palmer CL, Luster DG, Nester SE, Revell JM, Berner DK. Sporulation capacity and longevity of Puccinia horiana teliospores in infected chrysanthemum leaves. Plant Health Prog. 2013. doi:10.1094/PHP-2013-0823-01-RS.Google Scholar
- Bonde MR, Nester SE, Luster DG, Palmer CL. Longevity of Uromyces transversalis, causal agent of gladiolus rust, under various environmental conditions. Plant Health Prog. 2015. doi:10.1094/PHP-RS-14-0036.Google Scholar
- Lamour KH, Finley L, Snover-Clift KL, Stack JP, Pierzynski J, Hammerschmidt R, Jacobs JL, Byrne JM, Harmon PF, Vitoreli AM, et al. Early detection of Asian soybean rust using PCR. Plant Health Prog. 2006. doi:10.1094/PHP-2006-0524-01-RS.Google Scholar
- Denhardt DT. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966;23:641–6.View ArticlePubMedGoogle Scholar
- McManus J, Cason JE. Carbohydrate histochemistry studied by acetylation techniques: I. Periodic acid methods. J Exp Med. 1950;91:651.View ArticlePubMedPubMed CentralGoogle Scholar