Naked eye evaluation and quantitative detection of the sugarcane leaf scald pathogen, Xanthomonas albilineans, in sugarcane xylem sap
Muhammad Umer
A , Nahian Binte Aziz B C , Salma Al Jabri B , Shamsul A. Bhuiyan A C D and Muhammad J. A. Shiddiky A B D
+ Author Affiliations
- Author Affiliations
A Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Qld 4111, Australia.
B School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, Qld 4111, Australia.
C Sugar Research Australia, Woodford, Qld 4514, Australia.
D Corresponding authors. Email: sbhuiyan@sugarresearch.com.au; m.shiddiky@griffith.edu.au
Crop and Pasture Science 72(5) 361-371 https://doi.org/10.1071/CP20416
Submitted: 22 October 2020 Accepted: 10 March 2021 Published: 26 May 2021
Journal Compilation © CSIRO 2021 Open Access CC BY-NC-ND
Abstract
Sugarcane leaf scald caused by the bacterium Xanthomonas albilineans is a major disease of sugarcane worldwide. Whereas erratic symptoms make phenotypic detection challenging, molecular methods require expensive instruments and labour, and longer sample-to-answer times. We report a novel method for detection of X. albilineans DNA in sugarcane xylem sap. The method involves (i) boiling lysis-based DNA extraction from sugarcane sap; (ii) magnetic purification of target sequences directly from the lysate through use of magnetic bead-bound capture probes; and (iii) DNA sandwich hybridisation platform for HRP/TMB/H2O2 reaction-based naked eye visualisation and electrochemical detection of the target. The method is sensitive (limit of detection 100 fM) and reproducible (relative standard deviation <7%) with linear dynamic range 100 fM–1 nM (R2 = 0.99). The method was tested on a range of sugarcane cultivars of known resistance ratings (susceptible, intermediate resistant, and resistant) for leaf scald disease from an inoculated field trial. Detection levels agreed with the resistance rating of cultivars tested. In addition, qPCR results strongly correlated with our assay (r = 0.91–0.99, P < 0.01) and cultivar resistance rating. We believe that our assay could be useful for rapid screening as well as sensitive quantification of target pathogen DNA in infected sugarcane plants.
Keywords: leaf scald disease, Xanthomonas albilineans detection, naked eye evaluation of leaf scald disease, electrochemical detection of leaf scald disease, sugarcane xylem sap.
References
Birch RG (2001) Xanthomonas albilineans and the antipathogenesis approach to disease control. Molecular Plant Pathology 2, 1–11.| Xanthomonas albilineans and the antipathogenesis approach to disease control.Crossref | GoogleScholarGoogle Scholar | 20572987PubMed |
Birch RG, Patil SS (1985) Preliminary characterization of an antibiotic produced by Xanthomonas albilineans which inhibits DNA synthesis in Escherichia coli. Microbiology 131, 1069–1075.
| Preliminary characterization of an antibiotic produced by Xanthomonas albilineans which inhibits DNA synthesis in Escherichia coli.Crossref | GoogleScholarGoogle Scholar |
Birch RG, Bower R, Elliott A, Hansom S, Basnayake S, Zhang L (2000) Regulation of transgene expression: progress towards practical development in sugarcane, and implications for other plant species. In ‘Developments in plant genetics and breeding’. Vol. 5. (Ed. AD Arencibia) pp. 118–125. (Elsevier)
Boriachek K, Umer M, Islam MN, Gopalan V, Lam AK, Nguyen NT, Shiddiky MJA (2018) An amplification-free electrochemical detection of exosomal miRNA-21 in serum samples. Analyst 143, 1662–1669.
| An amplification-free electrochemical detection of exosomal miRNA-21 in serum samples.Crossref | GoogleScholarGoogle Scholar | 29512659PubMed |
Cociancich S, Pesic A, Petras D, Uhlmann S, Kretz J, Schubert V, Vieweg L, Duplan S, Marguerettaz M, Noëll J, Pieretti I, Hügelland M, Kemper S, Mainz A, Rott P, Royer M, Süssmuth RD (2015) The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine. Nature Chemical Biology 11, 195–197.
| The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine.Crossref | GoogleScholarGoogle Scholar | 25599532PubMed |
Comstock JC, Irey MS (1992) Detection of the sugarcane leaf scald pathogen, Xanthomonas albilineans, using tissue blot immunoassay, ELISA, and isolation techniques. Plant Disease 76, 1033–1035.
| Detection of the sugarcane leaf scald pathogen, Xanthomonas albilineans, using tissue blot immunoassay, ELISA, and isolation techniques.Crossref | GoogleScholarGoogle Scholar |
Comstock JC, Wang Z, Perdomo R (1997) The incidence of leaf scald and its effect on yield components. Sugar Cane 4, 18–22.
Davis MJ, Rott P, Baudin P, Dean J (1994) Evaluation of selective media and immunoassays for detection of Xanthomonas albilineans, causal agent of sugarcane leaf scald disease. Plant Disease 78, 78–82.
| Evaluation of selective media and immunoassays for detection of Xanthomonas albilineans, causal agent of sugarcane leaf scald disease.Crossref | GoogleScholarGoogle Scholar |
Davis MJ, Rott P, Warmuth C, Chatenet M, Baudin P (1997) Intraspecific genomic variation within Xanthomonas albilineans, the sugarcane leaf scald pathogen. Phytopathology 87, 316–324.
| Intraspecific genomic variation within Xanthomonas albilineans, the sugarcane leaf scald pathogen.Crossref | GoogleScholarGoogle Scholar | 18945175PubMed |
Drummond TG, Hill MG, Barton JK (2003) Electrochemical DNA sensors. Nature Biotechnology 21, 1192–1199.
| Electrochemical DNA sensors.Crossref | GoogleScholarGoogle Scholar | 14520405PubMed |
Fang Y, Ramasamy RP (2015) Current and prospective methods for plant disease detection. Biosensors 5, 537–561.
| Current and prospective methods for plant disease detection.Crossref | GoogleScholarGoogle Scholar | 26287253PubMed |
Ferapontova EE (2018) DNA electrochemistry and electrochemical sensors for nucleic acids. Annual Review of Analytical Chemistry 11, 197–218.
| DNA electrochemistry and electrochemical sensors for nucleic acids.Crossref | GoogleScholarGoogle Scholar | 29894229PubMed |
Garces FF, Gutierrez A, Hoy JW (2014) Detection and quantification of Xanthomonas albilineans by qPCR and potential characterization of sugarcane resistance to leaf scald. Plant Disease 98, 121–126.
| Detection and quantification of Xanthomonas albilineans by qPCR and potential characterization of sugarcane resistance to leaf scald.Crossref | GoogleScholarGoogle Scholar | 30708616PubMed |
Hoy J (1994) Sugarcane leaf scald distribution, symptomatology. Plant Disease 78, 1083–1087.
| Sugarcane leaf scald distribution, symptomatology.Crossref | GoogleScholarGoogle Scholar |
Islam MN, Masud MK, Nguyen NT, Gopalan V, Alamri HR, Alothman ZA, Hossain MSA, Yamauchi Y, Lam AK, Shiddiky MJA (2018) Gold-loaded nanoporous ferric oxide nanocubes for electrocatalytic detection of microRNA at attomolar level. Biosensors & Bioelectronics 101, 275–281.
| Gold-loaded nanoporous ferric oxide nanocubes for electrocatalytic detection of microRNA at attomolar level.Crossref | GoogleScholarGoogle Scholar |
Khater M, de la Escosura-Muñiz A, Merkoçi A (2017) Biosensors for plant pathogen detection. Biosensors & Bioelectronics 93, 72–86.
| Biosensors for plant pathogen detection.Crossref | GoogleScholarGoogle Scholar |
Khater M, de la Escosura-Muñiz A, Quesada-González D, Merkoçi A (2019) Electrochemical detection of plant virus using gold nanoparticle-modified electrodes Analytica Chimica Acta 1046, 123–131.
| Electrochemical detection of plant virus using gold nanoparticle-modified electrodesCrossref | GoogleScholarGoogle Scholar | 30482289PubMed |
Koo KM, Carrascosa LG, Shiddiky MJA, Trau M (2016) Poly(A) extensions of miRNAs for amplification-free electrochemical detection on screen-printed gold electrodes. Analytical Chemistry 88, 2000–2005.
| Poly(A) extensions of miRNAs for amplification-free electrochemical detection on screen-printed gold electrodes.Crossref | GoogleScholarGoogle Scholar | 26814930PubMed |
Lau HY, Wu H, Wee EJH, Trau T, Wang Y, Botella JR (2017) Specific and sensitive isothermal electrochemical biosensor for plant pathogen DNA detection with colloidal gold nanoparticles as probes. Scientific Reports 7, 38896
| Specific and sensitive isothermal electrochemical biosensor for plant pathogen DNA detection with colloidal gold nanoparticles as probes.Crossref | GoogleScholarGoogle Scholar | 28094255PubMed |
Masud MK, Islam MN, Haque MH, Tanaka S, Gopalan V, Alici G, Nguyen NT, Lam AK, Hossain MSA, Yamauchi Y, Shiddiky MJA (2017) Gold-loaded nanoporous superparamagnetic nanocubes for catalytic signal amplification in detecting miRNA. Chemical Communications 53, 8231–8234.
| Gold-loaded nanoporous superparamagnetic nanocubes for catalytic signal amplification in detecting miRNA.Crossref | GoogleScholarGoogle Scholar |
McLeod R, McMahon G, Allsopp P (1999) Costs of major pests and diseases to the Australian sugar industry. Plant Protection Quarterly 14, 42–46.
Nezhad AS (2014) Future of portable devices for plant pathogen diagnosis. Lab on a Chip 14, 2887–2904.
| Future of portable devices for plant pathogen diagnosis.Crossref | GoogleScholarGoogle Scholar | 24920461PubMed |
Pan YB, Grisham MP, Burner DM, Legendre BL, Wei Q (1999) Development of polymerase chain reaction primers highly specific for Xanthomonas albilineans, the causal bacterium of sugarcane leaf scald disease. Plant Disease 83, 218–222.
| Development of polymerase chain reaction primers highly specific for Xanthomonas albilineans, the causal bacterium of sugarcane leaf scald disease.Crossref | GoogleScholarGoogle Scholar | 30845497PubMed |
Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Cociancich S, Couloux A, Darrasse A, Gouzy J, Jacques M-A, Lauber E, Manceau C, Mangenot S, Poussier S, Segurens B, Szurek B, Verdier V, Arlat M, Rott P (2009) The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 10, 616
| The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae.Crossref | GoogleScholarGoogle Scholar | 20017926PubMed |
Plant Health Australia (2019) The National Plant Biosecurity Status Report 2018 and 2019. Plant Health Australia, Canberra, ACT.
Qavi AJ, Kindt JT, Bailey RC (2010) Sizing up the future of microRNA analysis. Analytical and Bioanalytical Chemistry 398, 2535–2549.
| Sizing up the future of microRNA analysis.Crossref | GoogleScholarGoogle Scholar | 20680616PubMed |
Ricaud C, Ryan CC (1989) Leaf scald. In ‘Diseases of sugarcane’. Chapter III. (Eds C Ricaud, BT Egan, AG Gillaspie, CG Hughes) pp. 39–58. (Elsevier: Amsterdam)
Rott P (1995) Leaf scald of sugarcane. Agriculture for Development 6, 49–56.
Rott P, Davis M (1995) Recent advances in research on variability of Xanthomonas albilineans, causal agent of sugarcane leaf scald disease. In ‘Proceedings of the International Society of Sugarcane Technologists Congress’. Vol. 22, pp. 498–503. (International Society of Sugarcane Technologists)
Rott P, Davis MJ (2000) Leaf scald. In ‘A guide to sugarcane diseases’. (Eds P Rott, R Bailey, J Comstock, B Croft, A Saumtally) pp. 38–44. (CIRAD Publication Services: Montepellier, France)
Rott P, Mohamed I, Klett P, Soupa D, de Saint-Albin A, Feldmann P, Letourmy P (1997) Resistance to leaf scald disease is associated with limited colonization of sugarcane and wild relatives by Xanthomonas albilineans. Phytopathology 87, 1202–1213.
| Resistance to leaf scald disease is associated with limited colonization of sugarcane and wild relatives by Xanthomonas albilineans.Crossref | GoogleScholarGoogle Scholar | 18945019PubMed |
Royer M, Costet L, Vivien E, Bes M, Cousin A, Damais A, Pieretti I, Savin A, Megessier S, Viard M, Frutos R, Gabriel DW, Rott PC (2004) Albicidin pathotoxin produced by Xanthomonas albilineans is encoded by three large PKS and NRPS genes present in a gene cluster also containing several putative modifying, regulatory, and resistance genes. Molecular Plant-Microbe Interactions 17, 414–427.
| Albicidin pathotoxin produced by Xanthomonas albilineans is encoded by three large PKS and NRPS genes present in a gene cluster also containing several putative modifying, regulatory, and resistance genes.Crossref | GoogleScholarGoogle Scholar | 15077674PubMed |
Shiddiky MJA, Rahman MA, Shim YB (2007) Hydrazine-catalyzed ultrasensitive detection of DNA and proteins. Analytical Chemistry 79, 6886–6890.
| Hydrazine-catalyzed ultrasensitive detection of DNA and proteins.Crossref | GoogleScholarGoogle Scholar |
Shiddiky MJA, Torriero AAJ, Zhao C, Burgar I, Kennedy G, Bond AM (2009) Nonadditivity of faradaic currents and modification of capacitance currents in the voltammetry of mixtures of ferrocene and the cobaltocenium cation in protic and aprotic ionic liquids. Journal of the American Chemical Society 131, 7976–7989.
| Nonadditivity of faradaic currents and modification of capacitance currents in the voltammetry of mixtures of ferrocene and the cobaltocenium cation in protic and aprotic ionic liquids.Crossref | GoogleScholarGoogle Scholar |
Shiddiky MJA, Torriero AAJ, Zeng Z, Spiccia L, Bond AM (2010) Highly selective and sensitive DNA assay based on electrocatalytic oxidation of ferrocene bearing zinc(ii)−cyclen complexes with diethylamine. Journal of the American Chemical Society 132, 10053–10063.
| Highly selective and sensitive DNA assay based on electrocatalytic oxidation of ferrocene bearing zinc(ii)−cyclen complexes with diethylamine.Crossref | GoogleScholarGoogle Scholar |
Siddiquee S, Rovina K, Yusof NA, Rodrigues KF, Suryani S (2014) Nanoparticle-enhanced electrochemical biosensor with DNA immobilization and hybridization of Trichoderma harzianum gene. Sensing and Bio-Sensing Research 2, 16–22.
| Nanoparticle-enhanced electrochemical biosensor with DNA immobilization and hybridization of Trichoderma harzianum gene.Crossref | GoogleScholarGoogle Scholar |
Wang ZK, Comstock JC, Hatziloukas E, Schaad NW (1999) Comparison of PCR, BIO-PCR, DIA, ELISA and isolation on semiselective medium for detection of Xanthomonas albilineans, the causal agent of leaf scald of sugarcane. Plant Pathology 48, 245–252.
| Comparison of PCR, BIO-PCR, DIA, ELISA and isolation on semiselective medium for detection of Xanthomonas albilineans, the causal agent of leaf scald of sugarcane.Crossref | GoogleScholarGoogle Scholar |
Wong ELS, Gooding JJ (2003) Electronic detection of target nucleic acids by a 2,6-disulfonic acid anthraquinone intercalator. Analytical Chemistry 75, 3845–3852.
| Electronic detection of target nucleic acids by a 2,6-disulfonic acid anthraquinone intercalator.Crossref | GoogleScholarGoogle Scholar |
Wongkaew P, Poosittisak S (2014) Diagnosis of sugarcane white leaf disease using the highly sensitive DNA based voltammetric electrochemical determination. American Journal of Plant Sciences 5, 2256–2268.
| Diagnosis of sugarcane white leaf disease using the highly sensitive DNA based voltammetric electrochemical determination.Crossref | GoogleScholarGoogle Scholar |
Zhang J, Song S, Wang L, Pan D, Fan C (2007) A gold nanoparticle-based chronocoulometric DNA sensor for amplified detection of DNA. Nature Protocols 2, 2888–2895.
| A gold nanoparticle-based chronocoulometric DNA sensor for amplified detection of DNA.Crossref | GoogleScholarGoogle Scholar | 18007624PubMed |
