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Fontana DC, de Paula S, Torres AG, de Souza VHM, Pascholati SF, Schmidt D, Dourado Neto D. Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses. Pathogens 2021; 10:570. [PMID: 34066672 PMCID: PMC8151296 DOI: 10.3390/pathogens10050570] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
Plant diseases cause losses of approximately 16% globally. Thus, management measures must be implemented to mitigate losses and guarantee food production. In addition to traditional management measures, induced resistance and biological control have gained ground in agriculture due to their enormous potential. Endophytic fungi internally colonize plant tissues and have the potential to act as control agents, such as biological agents or elicitors in the process of induced resistance and in attenuating abiotic stresses. In this review, we list the mode of action of this group of microorganisms which can act in controlling plant diseases and describe several examples in which endophytes were able to reduce the damage caused by pathogens and adverse conditions. This is due to their arsenal of molecules generated during the interaction by which they form a kind of biological shield in the plant. Furthermore, considering that endophytic fungi can be an important tool in managing for biotic and abiotic stresses due to the large amount of biologically active substances produced, bioprospecting this class of microorganisms is tending to increase and generate valuable products for agriculture.
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Affiliation(s)
- Daniele Cristina Fontana
- Department of Plant Production, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (D.C.F.); (D.D.N.)
| | - Samuel de Paula
- Plant Pathology Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (A.G.T.); (V.H.M.d.S.); (S.F.P.)
| | - Abel Galon Torres
- Plant Pathology Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (A.G.T.); (V.H.M.d.S.); (S.F.P.)
| | - Victor Hugo Moura de Souza
- Plant Pathology Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (A.G.T.); (V.H.M.d.S.); (S.F.P.)
| | - Sérgio Florentino Pascholati
- Plant Pathology Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (A.G.T.); (V.H.M.d.S.); (S.F.P.)
| | - Denise Schmidt
- Department of Agronomy and Environmental Science, Frederico Westphalen Campus, Federal University of Santa Maria, Frederico Westphalen 98400000, Brazil;
| | - Durval Dourado Neto
- Department of Plant Production, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418900, Brazil; (D.C.F.); (D.D.N.)
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Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR. Sci Rep 2020; 10:16106. [PMID: 32999395 PMCID: PMC7528053 DOI: 10.1038/s41598-020-72976-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/28/2020] [Indexed: 01/15/2023] Open
Abstract
Common bunt of wheat caused by Tilletia laevis and/or T. caries (syn. T. tritici), is a major disease in wheat-growing regions worldwide that could lead to 80% or even total loss of production. Even though T. laevis can be distinguished from T. caries on the bases of morphology of teliospores using microscopy technique. However, molecular methods could serve as an additional method to quantify the pathogen. To develop a rapid diagnostic and quantify method, we employed the ISSR molecular marker for T. laevis in this study. The primer ISSR857 generated a polymorphic pattern displaying a 1385 bp T. laevis-specific DNA fragment. A pair of specific primers (L57F/L57R) was designed to amplify a sequence-characterized amplified region (SCAR) (763 bp) for the PCR detection assay. The primers amplified the DNA fragment in the tested isolates of T. laevis but failed in the related species, including T. caries. The detection limit of the primer set (L57F/L57R) was 5 ng/µl of DNA extracted from T. laevis teliospores. A SYBR Green I real-time PCR method for detecting T. laevis with a 100 fg/µl detection limit and droplet digital PCR with a high sensitivity (30 fg/µl detection limit) were developed; this technique showed the most sensitive detection compared to the SCAR marker and SYBR Green I real-time PCR. Additionally, this is the first study related the detection of T. laevis with the droplet digital PCR method.
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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Nawaz HH, Anam U, Rajaofera MJN, He Q, Liu W, Miao W. Development of SNP-Based Markers to Identify Colletotrichum gossypii in Upland Cotton. PLANT DISEASE 2018; 102:1426-1433. [PMID: 30673579 DOI: 10.1094/pdis-10-17-1672-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colletotrichum gossypii is a causal agent of anthracnose in upland cotton (Gossypii hirsutum). C. gossypii belongs to the C. gloeosporioides species complex. However, the high level of genetic similarity among the species within the C. gloeosporioides species complex makes the development of a diagnostic assay for C. gossypii challenging. Furthermore, the spore size and cultural characteristics of C. gossypii from different geographical areas can vary. In this study, we examined the morphological variance, growth pattern, and pathogenicity of C. gossypii and developed a molecular diagnostic assay to detect C. gossypii in cotton plants from different regions of China. To overcome any ambiguity in morphological and pathogenic characteristics, a set of primers targeting the β-tubulin (TUB) gene of C. gossypii was designed. Single-nucleotide polymorphisms (SNP) were used to identify C. gossypii at the species level using DNA sequence alignments of the TUB gene. The SPSCG/F and SPSCG/R primer pair only amplified C. gossypii, and was able to amplify C. gossypii in mixtures of other Colletotrichum spp., even when DNA concentrations were up to 10 times lower than that of the other species. This is the first report of the development of SNP-based markers for the specific identification of C. gossypii.
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Affiliation(s)
- Hafiz Husnain Nawaz
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Plant Protection, Hainan University, Haikou, Hainan Province, 570228, P.R. China
| | - Usmani Anam
- Chinese Academy of Sciences, South China Botanical Garden, Tianhi District, Guangzhou, 510000, Guangdong Province, P.R. China
| | - M J Nelly Rajaofera
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Plant Protection, Hainan University
| | - Qiguang He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Plant Protection, Hainan University
| | - Wenbo Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Plant Protection, Hainan University
| | - Weiguo Miao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Plant Protection, Hainan University
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Diagnostics of Seed-Borne Plant Pathogens for Safe Introduction and Healthy Conservation of Plant Genetic Resources. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Afanador-Kafuri L, González A, Gañán L, Mejía JF, Cardona N, Alvarez E. Characterization of the Colletotrichum Species Causing Anthracnose in Andean Blackberry in Colombia. PLANT DISEASE 2014; 98:1503-1513. [PMID: 30699787 DOI: 10.1094/pdis-07-13-0752-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Since 1992, anthracnose of Andean blackberry (Rubus glaucus) has generated losses as high as 40% for farmers in Colombia. In this study, our goal was to characterize 240 Colletotrichum isolates from Andean blackberry in eight areas of Colombia. These isolates were evaluated according to morphological characteristics, sensitivity to benomyl, pathogenicity, and genetic variability. Identification of the genus Colletotrichum was achieved by using species complex-specific polymerase chain reaction primers. A multilocus phylogeny approach was used to identify isolates to the species level with sequences from the ribosomal internal transcribed spacer region and partial sequences of the actin, β-tubulin 2, calmodulin, chitin synthase 1, glutamine synthetase, and glyceraldehyde-3-phosphate dehydrogenase genes. Most of the isolates were identified as Colletotrichum gloeosporioides sensu lato, were associated with the Castilla ecotype, showed high sensitivity to benomyl, and were highly aggressive. Isolates identified as C. acutatum sensu lato were found mainly on the Thornless ecotype, were highly resistant to benomyl, and showed intermediate aggressiveness. Only three isolates were identified as C. boninense sensu lato. The species identified included C. fructicola, C. kahawae subsp. ciggaro, C. godetiae, C. karstii, C. brassicicola, and undetermined Colletotrichum spp. This study is the first report of these species associated with anthracnose in Andean blackberry.
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Affiliation(s)
- Lucía Afanador-Kafuri
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia-Medellín, A. A. 1779, Medellín, Colombia
| | - Alonso González
- Tropical Fruit Project, International Center for Tropical Agriculture (CIAT), A. A. 6713, Cali, Colombia
| | - Lederson Gañán
- CIAT and Faculty of Agricultural Sciences, Universidad de Caldas, A. A. 275, Manizales, Colombia
| | | | - Nadya Cardona
- Universidad de Antioquia, A. A. 1226, Medellín, Colombia
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Damm U, Cannon P, Woudenberg J, Johnston P, Weir B, Tan Y, Shivas R, Crous P. The Colletotrichum boninense species complex. Stud Mycol 2012; 73:1-36. [PMID: 23136457 PMCID: PMC3458415 DOI: 10.3114/sim0002] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture. TAXONOMIC NOVELTIES New combination - Colletotrichum phyllanthi (H. Surendranath Pai) Damm, P.F. Cannon & Crous. Name replacement - C. petchii Damm, P.F. Cannon & Crous. New species - C. annellatum Damm, P.F. Cannon & Crous, C. beeveri Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. brassicicola Damm, P.F. Cannon & Crous, C. brasiliense Damm, P.F. Cannon, Crous & Massola, C. colombiense Damm, P.F. Cannon, Crous, C. constrictum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. cymbidiicola Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. dacrycarpi Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. novae-zelandiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. oncidii Damm, P.F. Cannon & Crous, C. parsonsiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. torulosum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir. Typifications: Epitypifications - C. dracaenae Petch.
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Affiliation(s)
- U. Damm
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - P.F. Cannon
- CABI Europe-UK, Bakeham Lane, Egham, Surrey TW20 9TY, UK and Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK
| | - J.H.C. Woudenberg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - P.R. Johnston
- Landcare Research, Private Bag 92170 Auckland, New Zealand
| | - B.S. Weir
- Landcare Research, Private Bag 92170 Auckland, New Zealand
| | - Y.P. Tan
- Plant Biosecurity Science, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - R.G. Shivas
- Plant Biosecurity Science, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Utrecht University, Department of Biology, Microbiology, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Abstract
A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.
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Affiliation(s)
- P.F. Cannon
- CABI Europe-UK, Bakeham Lane, Egham, Surrey TW20 9TY, UK and Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK
| | - U. Damm
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - P.R. Johnston
- Landcare Research, Private Bag 92170 Auckland, New Zealand
| | - B.S. Weir
- Landcare Research, Private Bag 92170 Auckland, New Zealand
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Lima JS, Figueiredo JG, Gomes RG, Stringari D, Goulin EH, Adamoski D, Kava-Cordeiro V, Galli-Terasawa LV, Glienke C. Genetic Diversity of Colletotrichum spp. an Endophytic Fungi in a Medicinal Plant, Brazilian Pepper Tree. ISRN MICROBIOLOGY 2012; 2012:215716. [PMID: 23724319 PMCID: PMC3658576 DOI: 10.5402/2012/215716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/14/2012] [Indexed: 11/23/2022]
Abstract
In this study, we reported thirty-nine endophytic fungi identified as Colletotrichum spp. associated with Brazilian pepper tree or aroeira (Schinus terebinthifolius Raddi. Anacardiaceae) in Paraná state, Brazil. These endophytes were identified by morphological and molecular methods, using PCR taxon-specific with CaInt/ITS4, CgInt/ITS4, and Col1/ITS4 primers, which amplify specific bands in C. acutatum, C. gloeosporioides lato sensu, and Colletotrichum boninensis, respectively, and by DNA sequence analysis of the nrDNA internal transcribed spacer region (ITS1, 5.8S, ITS2). We also assayed the presence of dsRNA particles in Colletotrichum spp. isolates. Combining both morphological characters and molecular data, we identified the species C. gloeosporioides, C. boninense, and C. simmondsii. However, we found a high genetic variability intraspecific in C. gloeosporioides which suggests the existence of several other species. Bands of double-stranded RNA (dsRNA) were detected in three of thirty-nine isolates. Identity of these bands was confirmed by RNAse, DNAse, and S1 nuclease treatments for the isolates LGMF633, LGMF726, and LGMF729. This is the first study reporting these particles of dsRNA in C. gloeosporioides.
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Affiliation(s)
| | | | | | | | | | | | | | | | - C. Glienke
- Department of Genetics, Centro Politécnico, Universidade Federal do Paraná (UFPR), Box 19071, 81531-990 Curitiba, PR, Brazil
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