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Da Silva CGN, Monteiro EDC, Diniz PP, Terra LA, Schwab S, Reis VM, Simoes-Araujo JL, Urquiaga S. Designing and validation of specific primers for the quantitative detection of bacteria in sugarcane inoculant. Braz J Microbiol 2023; 54:2627-2640. [PMID: 37843794 PMCID: PMC10689644 DOI: 10.1007/s42770-023-01144-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Endophytic diazotrophic plant growth-promoting bacteria Herbaspirillum rubrisubalbicans (HCC103), Herbaspirillum seropedicae (HRC54), Paraburkholderia tropica (Ppe8T), Gluconacetobacter diazotrophicus (Pal5T), and Nitrospirillum amazonense (CBAmC) have been used as inoculants for sugarcane. The genome sequences of these strains were used to design a set of specific primers for the real-time PCR (qPCR) assay. Primer specificity was confirmed by conventional PCR using the genomic DNAs of 25 related bacterial species and the five target strains. The qPCR assays were conducted using root and shoot samples from two sugarcane varieties (RB867515 and RB92579). These samples were collected both with and without inoculation, using the target strains specified in this study. The sugarcane plants were grown in a greenhouse, utilizing a substrate composed of sterile sand and vermiculite in a 2:1 ratio, for a duration of 55 days. The primers designed for this study successfully amplified target DNA fragments from each of the bacterial species, enabling their differentiation at the species level. The total bacterial population present in the sugarcane quantified using qPCR was on average 105.2 cells g-1 of fresh tissue. Across both evaluated varieties, it was observed that the population of inoculated bacteria tended to decrease over time and became more concentrated in the sugarcane roots compared to the aerial parts. The qPCR results suggest that both the host and the microbes influence the endophytic population and the bacterial number decreases with plant age.
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Affiliation(s)
- Cleudison Gabriel Nascimento Da Silva
- Instituto de Agronomia, Programa de Pós Graduação em Fitotecnia, Universidade Federal Rural Do Rio de Janeiro (UFRRJ), Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil.
| | - Edevaldo de Castro Monteiro
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Priscila Pereira Diniz
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Leonardo Araujo Terra
- Instituto de Agronomia, Programa de Pós Graduação em Ciência, Tecnologia e Inovação Agropecuária, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | | | | | - Segundo Urquiaga
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
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Duong HT, Williams B, White D, Burgess TI, Hardy GESJ. qPCR Assays for Sensitive and Rapid Detection of Quambalaria Species from Plant Tissues. PLANT DISEASE 2022; 106:107-113. [PMID: 34261359 DOI: 10.1094/pdis-04-21-0816-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Several species from the genus Quambalaria (order Microstromatales) cause diseases on eucalypts (Eucalyptus and related genera) both in plantations and natural ecosystems. We developed real-time quantitative PCR (qPCR) assays to rapidly detect and distinguish five Quambalaria species. The design of the species-specific qPCR assay for each species, Q. pitereka (PIT), Q. coyrecup (COR), Q. cyanescens (CYN), Q. pusilla (PUS), and Q. eucalypti (EUC), was based on the ITS region and was evaluated for specificity and sensitivity. The PIT, COR, and CYN qPCR assays could amplify as little as 10 fg µl-1 from pure cultures, whereas PUS and EUC qPCR assays could amplify 100 fg µl-1 of their target species. The PIT, COR, and CYN qPCR assays were further validated using naturally and artificially infected samples of their plant host Corymbia calophylla. These assays will be used for rapid diagnostics and future experiments on the infection process.
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Affiliation(s)
- Hoa T Duong
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
- Institute of Forest Tree Improvement and Biotechnology, Hanoi 10000, Vietnam
| | - Briony Williams
- ArborCarbon, PO Box 1065, Willagee Central 6163, Western Australia, Australia
| | - Diane White
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
| | - Treena I Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
| | - Giles E St J Hardy
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, 6150 Perth, Western Australia, Australia
- ArborCarbon, PO Box 1065, Willagee Central 6163, Western Australia, Australia
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Cheng Y, Tang X, Gao C, Li Z, Chen J, Guo L, Wang T, Xu J. Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops. Pathogens 2020; 9:pathogens9030223. [PMID: 32197350 PMCID: PMC7157645 DOI: 10.3390/pathogens9030223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
Bast fibers and products derived from them are undergoing a resurgence in demand in the global market. However, fungal diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of bast fiber crops in many parts of the world. Thus, there is a high demand for effective control and prevention strategies against fungal pathogens. Having rapid, specific, sensitive, and cost-effective tests that can be used for early and accurate diagnosis of disease agents is an essential step of such strategies. The objective of this study was to review the current status of research on molecular diagnosis of fungal pathogens on bast fiber crops. Our search of PubMed identified nearly 20 genera of fungal pathogens on bast fiber crops, among which the five most common genera were Colletotrichum, Pythium, Verticillium, Fusarium, and Golovinomyces. The gene regions that have been used for molecular identifications of these fungi include internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), ß-tubulin, calmodulin (CAL), histone subunit 3 (H3), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), etc. We summarize the molecular assays that have been used to identify these fungi and discuss potential areas of future development for fast, specific, and accurate diagnosis of fungal pathogens on bast fiber crops.
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Affiliation(s)
- Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Xiaoyu Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
- Department of Biology, McMaster University, Hamilton, L8S 4K1, Canada
- Correspondence:
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Luchi N, Ioos R, Santini A. Fast and reliable molecular methods to detect fungal pathogens in woody plants. Appl Microbiol Biotechnol 2020; 104:2453-2468. [PMID: 32006049 PMCID: PMC7044139 DOI: 10.1007/s00253-020-10395-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 01/19/2020] [Indexed: 12/11/2022]
Abstract
Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.
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Affiliation(s)
- Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy.
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Unit of Mycology, Domaine de Pixérécourt, 54220, Malzéville, France
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy
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Luchi N, Santini A, Salvianti F, Pinzani P. Early Detection of Fungal Plant Pathogens by Real-Time Quantitative PCR: The Case of Diplodia sapinea on Pine. Methods Mol Biol 2020; 2065:95-104. [PMID: 31578690 DOI: 10.1007/978-1-4939-9833-3_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter reports the use of real-time quantitative PCR to detect Diplodia sapinea, a fungal plant pathogen that causes shoot tip dieback and tree mortality on pine trees. This molecular approach represents a reliable and sensitive tool to detect fungal pathogens in DNA extracted from plant tissues and its use can be also recommended to study fungal behavior in host tissues by quantifying fungal growth in the latent phase, when symptoms in the host are not present yet.
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Affiliation(s)
- Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Florence, Italy.
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Florence, Italy
| | - Francesca Salvianti
- Molecular and Clinical Biochemistry Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Careggi Hospital, University of Florence, Florence, Italy
| | - Pamela Pinzani
- Molecular and Clinical Biochemistry Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Careggi Hospital, University of Florence, Florence, Italy
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