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Su Z, Liu G, Li C, Liu X, Guo Q, Wang P, Dong L, Lu X, Zhao W, Zhang X, Qu Y, Zhang J, Mo S, Li S, Ma P. Establishment and application of quantitative detection of Bacillus velezensis HMB26553, a biocontrol agent against cotton damping-off caused by Rhizoctonia. Biotechnol J 2024; 19:e2300412. [PMID: 38375560 DOI: 10.1002/biot.202300412] [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: 08/15/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
A highly sensitive quantitative PCR (qPCR) method was developed for detection and quantification of Bacillus velezensis HMB26553 in cotton rhizosphere. The study aimed to develop a quantitative detection method for the strain HMB26553, and explore the relationship between its colonization of the cotton rhizosphere and its control effect. The whole genome sequence of strain HMB26553 was obtained by genome sequencing and a unique specific sequence pB-gene0026 on plasmid plaBV2 was identified by using high-throughput alignment against NCBI. Plasmid plaBV2 could be stably genetically inherited. Based on this sequence, specific primers for amplifying 106 bp and a minor groove binder (MGB) TaqMan probe for enhancing sensitivity were designed. The copy number of plaBV2 in strain HMB26553, which was 2, was confirmed by internal reference primers and the MGB TaqMan probe based on housekeeping gene gyrB. The established detection technique based on these primers and probes had high specificity and sensitivity compared to traditional plate counting method, with a detection limit of 1.5 copy genome. Using this method, the study discovered a likely correlation between the quantity of colonization in cotton rhizosphere and efficacy against cotton damping-off caused by Rhizoctonia after seed soaking and irrigation with strain HMB26553. Thus, this method provides scientific support for the rational application of strain HMB26553 in the future.
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Affiliation(s)
- Zhenhe Su
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Gaoge Liu
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Cong Li
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Xiaomeng Liu
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Qinggang Guo
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Peipei Wang
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Lihong Dong
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Xiuyun Lu
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Weisong Zhao
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Xiaoyun Zhang
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Yuanghang Qu
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Jiaqi Zhang
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Shaojing Mo
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Shezeng Li
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
| | - Ping Ma
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding, China
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Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1. IMA Fungus 2023; 14:21. [PMID: 37803441 PMCID: PMC10559472 DOI: 10.1186/s43008-023-00121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 10/08/2023] Open
Affiliation(s)
- Cobus M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Felipe Balocchi
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ales Eichmeier
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, Private Bag X1, Stellenbosch, 7602 South Africa
| | - Scott E. Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
- DOE Joint Bioenergy Institute, Emeryville, CA 94608 USA
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/a, 70126 Bari, Italy
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Eliska Hakalova
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Richard D. Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720 USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Catarina Leal
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jakub Pecenka
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Anja Piso
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Milan Spetik
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Leal C, Gramaje D, Fontaine F, Richet N, Trotel-Aziz P, Armengol J. Evaluation of Bacillus subtilis PTA-271 and Trichoderma atroviride SC1 to control Botryosphaeria dieback and black-foot pathogens in grapevine propagation material. PEST MANAGEMENT SCIENCE 2023; 79:1674-1683. [PMID: 36573682 DOI: 10.1002/ps.7339] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Grapevine trunk diseases (GTDs) are a complex group of diseases that lead to major economic losses in all wine-producing countries. The investigation of biocontrol agents (BCAs) capable of forestalling or at least minimizing the development of GTDs has, recently, become a priority. Nursery experiments were set up to (i) assess the biocontrol effect of Trichoderma atroviride (Ta) SC1 and Bacillus subtilis (Bs) PTA-271, alone and in simultaneous application, against Botryosphaeria dieback (BOT)- and black-foot (BF)- associated pathogens during the grapevine propagation process and (ii) evaluate the success of the BCA inoculation during the grapevine propagation process, using quantitative reverse-transcription polymerase chain reaction techniques. RESULTS The results demonstrated a significant reduction in the percentage of potentially infected plants and the percentage of fungal isolation from wood fragments of BOT and BF pathogens in nursery material treated with Ta SC1 and Bs PTA-271, respectively. In one of the experiments, simultaneous treatments with Bs PTA-271 and Ta SC1 caused a reduction in percentages of potentially infected plants and fungal isolation, from wood fragments containing BOT and BF pathogens. CONCLUSION These biological treatments may be relevant components of an integrated approach, using complementary management strategies to limit infection by GTD pathogens, but further research is still needed to elucidate the effectiveness of Bs PTA-271 and the benefits of simultaneous application with Ta SC1 for the control of GTD pathogens in nurseries. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Catarina Leal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, Logroño, Spain
| | - Florence Fontaine
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Nicolas Richet
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Patricia Trotel-Aziz
- University of Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes Research Unit, EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
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Lee G, Choi H, Liu H, Han YH, Paul NC, Han GH, Kim H, Kim PI, Seo SI, Song J, Sang H. Biocontrol of the causal brown patch pathogen Rhizoctonia solani by Bacillus velezensis GH1-13 and development of a bacterial strain specific detection method. FRONTIERS IN PLANT SCIENCE 2023; 13:1091030. [PMID: 36699832 PMCID: PMC9868939 DOI: 10.3389/fpls.2022.1091030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Brown patch caused by the basidiomycete fungus Rhizoctonia solani is an economically important disease of cool-season turfgrasses. In order to manage the disease, different types of fungicides have been applied, but the negative impact of fungicides on the environment continues to rise. In this study, the beneficial bacteria Bacillus velezensis GH1-13 was characterized as a potential biocontrol agent to manage brown patch disease. The strain GH1-13 strongly inhibited the mycelial growth of turf pathogens including different anastomosis groups of R. solani causing brown patch and large patch. R. solani AG2-2(IIIB) hyphae were morphologically changed, and fungal cell death resulted from exposure to the strain GH1-13. In addition, the compatibility of fungicides with the bacterial strain, and the combined application of fungicide azoxystrobin and the strain in brown patch control on creeping bentgrass indicated that the strain could serve as a biocontrol agent. To develop strain-specific detection method, two unique genes from chromosome and plasmid of GH1-13 were found using pan-genome analysis of 364 Bacillus strains. The unique gene from chromosome was successfully detected using both SYBR Green and TaqMan qPCR methods in bacterial DNA or soil DNA samples. This study suggests that application of GH1-13 offers an environmentally friendly approach via reducing fungicide application rates. Furthermore, the developed pipeline of strain-specific detection method could be a useful tool for detecting and studying the dynamics of specific biocontrol agents.
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Affiliation(s)
- Gahee Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Hyeongju Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Haifeng Liu
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Yun-Hyeong Han
- Division of Food and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
- Damyang-gun Agricultural Technology Center, Damyang, Republic of Korea
| | - Narayan Chandra Paul
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - Gui Hwan Han
- Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup, Republic of Korea
| | | | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup, Republic of Korea
| | - Sun-Il Seo
- Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
- Division of Food and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, Republic of Korea
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Ambreetha S, Balachandar D. SCAR marker: A potential tool for authentication of agriculturally important microorganisms. J Basic Microbiol 2023; 63:4-16. [PMID: 35916264 DOI: 10.1002/jobm.202200419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/23/2022] [Indexed: 01/04/2023]
Abstract
Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Chervin J, Romeo-Oliván A, Fournier S, Puech-Pages V, Dumas B, Jacques A, Marti G. Modification of Early Response of Vitis vinifera to Pathogens Relating to Esca Disease and Biocontrol Agent Vintec ® Revealed By Untargeted Metabolomics on Woody Tissues. Front Microbiol 2022; 13:835463. [PMID: 35308402 PMCID: PMC8924477 DOI: 10.3389/fmicb.2022.835463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Esca disease is one of the most destructive grapevine trunk diseases. Phaeoacremonium minimum and Phaeomoniella chlamydospora are two of the known fungal pathogens associated with this disease. Today, biocontrol agents against Esca are mainly based on the use of the strain of the mycoparasite fungal genus Trichoderma such as the Vintec® product. The aim of this study was to investigate early response of woody tissues to Esca pathogens and identify metabolites that could be correlated with a biocontrol activity within a complex woody matrix. An untargeted liquid chromatography–high-resolution mass spectrometry metabolomic approach coupled to a spectral similarity network was used to highlight clusters of compounds associated with the plant response to pathogens and biocontrol. Dereplication highlighted the possible role of glycerophospholipids and polyphenol compounds, the latest mainly belonging to stilbenoids. Antifungal activity of some relevant biomarkers, evaluated in vitro on Phaeomoniella chlamydospora and Botrytis cinerea, suggests that some of these compounds can play a role to limit the development of Esca pathogens in planta.
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Affiliation(s)
- Justine Chervin
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Ana Romeo-Oliván
- Unité de Recherche Physiologie, Pathologie, et Génétique Végétales (PPGV), INP PURPAN, Université de Toulouse, Toulouse, France
| | - Sylvie Fournier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Virginie Puech-Pages
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - Alban Jacques
- Unité de Recherche Physiologie, Pathologie, et Génétique Végétales (PPGV), INP PURPAN, Université de Toulouse, Toulouse, France
| | - Guillaume Marti
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
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Chammem H, Nesler A, Pertot I. Wood pellets as carriers of conidia of Trichoderma atroviride SC1 for soil application. Fungal Biol 2021; 125:989-998. [PMID: 34776236 DOI: 10.1016/j.funbio.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022]
Abstract
The use of biocontrol agents to control soilborne diseases is a promising alternative to chemical pesticides, however, obtaining a homogeneous distribution and incorporation of conidia of fungal biocontrol agents into the soil is often difficult. Several carriers/formulations have been proposed over time, unfortunately without offering an ultimate solution. We propose the use of wood pellets as a carrier of conidia of a saprophytic fungus that has good biodegradation and biocontrol properties (Trichoderma atroviride SC1). The coating process is based on the direct spraying of wood pellets with a conidial suspension at different rates. Beech, fir, and chestnut wood pellets were compared in terms of relevant physicochemical traits and efficacy in supporting the growth of the fungus. Beech wood pellets displayed the best characteristics in terms of water holding capacity, swelling properties, and disintegration time. T. atroviride SC1 grows best on beech and fir wood pellets and reaches a plateau after nine days of incubation, regardless of the initial coating concentrations. The addition of small quantities of a nitrogen source as tryptone or soy flour, soy proteins, and a mixture of animal proteins used as pet food to the conidial suspension can increase the growth by ten-folds on all types of wood pellets. Our results demonstrate that beech and fir wood pellets could be suitable carriers to deliver and sustain the growth of T. atroviride SC1.
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Affiliation(s)
- Hamza Chammem
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 20, 38123, Trento, TN, Italy.
| | - Andrea Nesler
- Bi-PA nv (Biological Products for agriculture), Technologielaan 7, B-1840, Londerzeel, Belgium.
| | - Ilaria Pertot
- Center Agriculture Food Environment, University of Trento, via E. Mach 1, 38010, San Michele all'Adige, TN, Italy; Research and Innovation Centre, Fondazione Edmund Mach (FEM), via E. Mach 1, 38010, San Michele all'Adige, TN, Italy.
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Chammem H, Antonielli L, Nesler A, Pindo M, Pertot I. Effect of a Wood-Based Carrier of Trichoderma atroviride SC1 on the Microorganisms of the Soil. J Fungi (Basel) 2021; 7:751. [PMID: 34575789 PMCID: PMC8467423 DOI: 10.3390/jof7090751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023] Open
Abstract
Wood pellets can sustain the growth of Trichoderma spp. in soil; however, little is known about their side effects on the microbiota. The aims of this study were to evaluate the effect of wood pellets on the growth of Trichoderma spp. in bulk soil and on the soil microbial population's composition and diversity. Trichoderma atroviride SC1 coated wood pellets and non-coated pellets were applied at the level of 10 g∙kg-1 of soil and at the final concentration of 5 × 103 conidia∙g-1 of soil and compared to a conidial suspension applied at the same concentration without the wood carrier. Untreated bulk soil served as a control. The non-coated wood pellets increased the total Trichoderma spp. population throughout the experiment (estimated as colony-forming unit g-1 of soil), while wood pellets coated with T. atroviride SC1 did not. The wood carrier increased the richness, and temporarily decreased the diversity, of the bacterial population, with Massilia being the most abundant bacterial genus, while it decreased both the richness and diversity of the fungal community. Wood pellets selectively increased fungal species having biocontrol potential, such as Mortierella, Cladorrhinum, and Stachybotrys, which confirms the suitability of such carriers of Trichoderma spp. for soil application.
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Affiliation(s)
- Hamza Chammem
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 20, 38123 Trento, TN, Italy;
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria;
| | - Andrea Nesler
- Bi-PA nv (Biological Products for Agriculture), Technologielaan, 7, B-1840 Londerzeel, Belgium;
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
| | - Massimo Pindo
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
| | - Ilaria Pertot
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
- Center Agriculture Food Environment, University of Trento, Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy
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9
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Gao C, Wang B, Ma GC, Zeng H. Green Fluorescent Protein-Tagged Bacillus axarquiensis TUBP1 Reduced Cotton Verticillium Wilt Incidence by Altering Soil Rhizosphere Microbial Communities. Curr Microbiol 2021; 78:3562-3576. [PMID: 34347145 DOI: 10.1007/s00284-021-02618-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
Verticillium wilt is a major disease of cotton that considerably decreases yield and crop quality. Soil microbial communities play an important role in plant health. Therefore, biocontrol bacteria that regulate microbial communities in rhizosphere soil can improve plant resistance to pathogens. Previously, the antagonistic strain Bacillus axarquiensis TUBP1 was screened and found to act against Verticillium dahliae with 43% biocontrol effect in cotton fields. We studied the effect of Bacillus axarquiensis TUBP1 with a green fluorescent protein (GFP) gene marker on the microbial community structure of cotton rhizosphere soil and cotton yield and quality. Cotton Verticillium wilt incidence, soil biochemical properties, and soil bacterial and fungal communities were analyzed. Results showed that bacterial and fungal abundance in cotton rhizosphere soil was temporarily changed after applying B. axarquiensis TUBP-315GFP. However, Bacillus significantly increased, whereas V. dahliae significantly decreased. The incidence of cotton Verticillium wilt after treatment with B. axarquiensis TUBP-315GFP was significantly lower and cotton production increased by 40.6%. Our findings indicated that the application of B. axarquiensis TUBP-315GFP can change microbial community structure of cotton rhizosphere soil, leading to a reduction in the incidence of cotton Verticillium wilt and increasing cotton yield.
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Affiliation(s)
- Chang Gao
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Bo Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Guo-Cai Ma
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Hong Zeng
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China.
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10
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Kumar A, Rodrigues V, Baskaran K, Shukla AK, Sundaresan V. DNA barcode based species-specific marker for Ocimum tenuiflorum and its applicability in quantification of adulteration in herbal formulations using qPCR. J Herb Med 2020. [DOI: 10.1016/j.hermed.2020.100376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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11
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Hilje-Rodríguez I, Albertazzi FJ, Rivera-Coto G, Molina-Bravo R. A multiplex qPCR TaqMan-assay to detect fungal antagonism between Trichoderma atroviride (Hypocreaceae) and Botrytis cinerea (Sclerotiniaceae) in blackberry fruits using a de novo tef1-α- and an IGS-sequence based probes. BIOTECHNOLOGY REPORTS 2020; 27:e00447. [PMID: 32528864 PMCID: PMC7276392 DOI: 10.1016/j.btre.2020.e00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Quantitative polymerase chain reactions specifically detect Trichoderma atroviride. The method uses a probe based on the tef-1α for the detection. The method simultaneously detects T. atroviride and Botrytis cinerea in blackberries.
The aim of this study was to design a Trichoderma atroviride-specific qPCR oligo set, evaluate its specificity, and standardize a methodology that quantifies antagonism against Botrytis cinerea in blackberry fruits (Rubus adenotrichos Schltdl.). Primers and probe were designed based on the nuclear translation elongation factor 1-alpha (tef1-α) of T. atroviride. A commercial IGS-based oligo set was used to quantify B. cinerea. The specificity of the designed oligo set, along with ITS-based oligo sets, was assessed using other Trichoderma species and B. cinerea. Multiplex qPCR assays were performed using DNA from B. cinerea, T. atroviride, and blackberries inoculated with these fungi. Assays with the tef1-α oligo set showed high sensitivity and reproducibility. In inoculated fruits, T. atroviride and B. cinerea were quantified simultaneously, including in symptomless tissues. This work standardized a qPCR methodology that specifically targets a T. atroviride isolate. This newly-designed qPCR oligo set could be useful in future biological control programs.
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Affiliation(s)
- Irena Hilje-Rodríguez
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
- Corresponding author.
| | - Federico J. Albertazzi
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Apartado Postal 11501-2060, San José, Costa Rica
| | - German Rivera-Coto
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
| | - Ramón Molina-Bravo
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
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12
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Stummer BE, Zhang Q, Zhang X, Warren RA, Harvey PR. Quantification of Trichoderma afroharzianum, Trichoderma harzianum and Trichoderma gamsii inoculants in soil, the wheat rhizosphere and in planta suppression of the crown rot pathogen Fusarium pseudograminearum. J Appl Microbiol 2020; 129:971-990. [PMID: 32320112 DOI: 10.1111/jam.14670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 11/29/2022]
Abstract
AIMS Develop quantitative assays (qPCR) to determine the detection threshold limits, colonization and persistence of Trichoderma gamsii, Trichoderma afroharzianum and T. harzianum inoculants in cropping soils, the wheat rhizosphere and their in planta suppressive efficacy against the crown rot pathogen Fusarium pseudograminearum. METHODS AND RESULTS Trichoderma qPCR primers were designed from the internal transcribed spacer region of 5.8S rDNA and from sequences of DNA fragments diagnostic for each inoculant genotype. The minimum detection thresholds of qPCR assays varied between 1 × 103 (log 3) and 8 × 104 (log 4·9) conidia (genome) equivalents per gram of soil for multi- and single-copy target sequences, respectively and were independent of soil type. There was a strong correlation (r > 0·974) between culture-dependent and culture-independent (qPCR) quantification methods. In wheat bioassays, Trichoderma inoculants colonized rhizosphere soils and wheat roots at 56-112 days postemergence to a depth of 20 cm but were more abundant (P < 0·001) at 0-10 cm root depth, means ranging from 2 × 102 (log 2·3) to 4 × 105 (log 5·6) conidia equivalents per gram of rhizosphere soil or root tissue. Inoculants reduced (P < 0·001) F. pseudograminearum biomass in wheat crown and root tissue by up to 5754-fold and increased (P = 0·008) plant biomass, relative to the pathogen control. CONCLUSIONS The qPCR assays provided sensitive and accurate assessment of wheat root and rhizosphere soil colonization of Trichoderma inoculants. Strains persisted through to grain maturity at levels shown to significantly suppress F. pseudograminearum in planta. SIGNIFICANCE AND IMPACT OF THE STUDY The qPCR assays developed here were used to determine the wheat rhizosphere dynamics of T. harzianum, T. afroharzianum and T. gamsii inoculants and their suppressive efficacy against F. pseudograminearum in planta. These assays can be applied to monitor inoculant dynamics in suppressing crown rot and other wheat root diseases in the field.
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Affiliation(s)
- B E Stummer
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia
| | - Q Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - X Zhang
- Ecology Research Institute, Shandong Academy of Sciences, Jinan, Shandong, China
| | - R A Warren
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia
| | - P R Harvey
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia.,Ecology Research Institute, Shandong Academy of Sciences, Jinan, Shandong, China
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13
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Zhang J, Fu B, Lin Q, Riley IT, Ding S, Chen L, Cui J, Yang L, Li H. Colonization of Beauveria bassiana 08F04 in root-zone soil and its biocontrol of cereal cyst nematode (Heterodera filipjevi). PLoS One 2020; 15:e0232770. [PMID: 32369513 PMCID: PMC7199937 DOI: 10.1371/journal.pone.0232770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Cereal cyst nematodes cause serious yield losses of wheat in Hunaghuai winter wheat growing region in China. Beauveria bassiana 08F04 isolated from the surface of cysts is a promising biological control agent for cereal cyst nematodes. As the colonization capacity is a crucial criteria to assess biocontrol effectiveness for a microbial agent candidate, we aimed to label B. bassiana 08F04 for efficient monitoring of colonization in the soil. The binary pCAM-gfp plasmid containing sgfp and hph was integrated into B. bassiana 08F04 using the Agrobacterium tumefaciens-mediated transformation. The transformation caused a significant change in mycelial and conidial yields, and in extracellular chitinase activity in some transformants. The cultural filtrates of some transformants also decreased acetylcholinesterase activity and the survival of Heterodera filipjevi second-stage juveniles relative to the wild-type strain. One transformant (G10) had a growth rate and biocontrol efficacy similar to the wild-type strain, so it was used for a pilot study of B. bassiana colonization conducted over 13 weeks. Real-time PCR results and CFU counts revealed that the population of G10 increased quickly over the first 3 weeks, then decreased slowly over the following 4 weeks before stabilizing. In addition, the application of wild-type B. bassiana 08F04 and transformant G10 significantly reduced the number of H. filipjevi females in roots by 64.4% and 60.2%, respectively. The results of this study have practical applications for ecological, biological and functional studies of B. bassiana 08F04 and for bionematicide registration.
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Affiliation(s)
- Jie Zhang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bo Fu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, China
| | - Qitong Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ian T. Riley
- Department of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Shengli Ding
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Linlin Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Jiangkuan Cui
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Lirong Yang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (LY); (HL)
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- * E-mail: (LY); (HL)
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14
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Berbegal M, Ramón-Albalat A, León M, Armengol J. Evaluation of long-term protection from nursery to vineyard provided by Trichoderma atroviride SC1 against fungal grapevine trunk pathogens. PEST MANAGEMENT SCIENCE 2020; 76:967-977. [PMID: 31472038 DOI: 10.1002/ps.5605] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Fungal grapevine trunk diseases (GTDs) represent a threat to viticulture, being responsible for important economic losses worldwide. Nursery and vineyard experiments were set up to evaluate the ability of Trichoderma atroviride SC1 to reduce infections of GTD pathogens in grapevine planting material during the propagation process and to assess the long-term protection provided by this biocontrol agent on grapevine plants in young vineyards during two growing seasons. RESULTS Reductions of some GTD pathogen incidence and severity were found on grapevine propagation material after nursery application of T. atroviride SC1 during the grafting process, and also after additional T. atroviride SC1 treatments performed during two growing seasons in young vineyards, when compared with untreated plants. CONCLUSION Trichoderma atroviride SC1 showed promise to reduce infections caused by some GTD pathogens in nurseries, and also when establishing new vineyards. This biological control agent could possibly be a valuable component in an integrated management approach where various strategies are combined to reduce GTD infections. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Mónica Berbegal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Antonio Ramón-Albalat
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Maela León
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
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15
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Zhang Y, Wang X, Pang G, Cai F, Zhang J, Shen Z, Li R, Shen Q. Two-step genomic sequence comparison strategy to design Trichoderma strain-specific primers for quantitative PCR. AMB Express 2019; 9:179. [PMID: 31707479 PMCID: PMC6842373 DOI: 10.1186/s13568-019-0904-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Survival of inoculated fungal strains in a new environment plays a critical role in functional performance, but few studies have focused on strain-specific quantitative PCR (qPCR) methods for monitoring beneficial fungi. In this study, the Trichoderma guizhouense strain NJAU 4742 (transformed with the gfp gene and named gfp-NJAU 4742), which exhibits a growth-promoting effect by means of phytohormone production and pathogen antagonism, was selected as a model to design strain-specific primer pairs using two steps of genomic sequence comparison to detect its abundance in soil. After a second comparison with the closely related species T. harzianum CBS 226-95 to further differentiate the strain-specific fragments that had shown no homology to any sequence deposited in the databases used in the first comparison, ten primer pairs were designed from the whole genome. Meanwhile, 3 primer pairs, P11, P12 and P13, were also designed from the inserted fragment containing the gfp gene. After verification testing with three types of field soils, primer pairs P6, P7 and P8 were further selected by comparison with P11, P12 and P13. A practical test using a pot experiment showed that stable colonization of gfp-NJAU 4742 in pepper rhizosphere soil could be detected using primer pairs P6 and P7, showing no significant difference from the results of primers P11 and P12. Hence, the strategy described here for designing fungal-strain-specific primers may theoretically be used for any other fungi for which the whole genome sequence is available in a database, and the qPCR methodology developed can also be used to further monitor the population dynamics of different strains based on the designed primers.
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16
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Li Y, Shi H, Zhang H, Chen S. Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer. PeerJ 2019; 7:e6073. [PMID: 30643688 PMCID: PMC6330032 DOI: 10.7717/peerj.6073] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/06/2018] [Indexed: 11/20/2022] Open
Abstract
Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng-1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng-1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in response to drought stress. To the best of our knowledge, this is the first report about the effect of synergistic use of biofertilizer and SAP on plant growth under drought stress.
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Affiliation(s)
- Yongbin Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowen Shi
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowei Zhang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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17
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Gerin D, Pollastro S, Raguseo C, De Miccolis Angelini RM, Faretra F. A Ready-to-Use Single- and Duplex-TaqMan-qPCR Assay to Detect and Quantify the Biocontrol Agents Trichoderma asperellum and Trichoderma gamsii. Front Microbiol 2018; 9:2073. [PMID: 30233545 PMCID: PMC6127317 DOI: 10.3389/fmicb.2018.02073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/14/2018] [Indexed: 11/13/2022] Open
Abstract
Trichoderma asperellum strain icc012 and Trichoderma gamsii strain icc080, the microbial active ingredients of RemedierTM (ISAGRO, Novara, Italy), are biocontrol agents (BCAs) employable for crop protection against a wide range of fungal pathogens, including soil-borne pathogens and fungi involved in grapevine trunk disease. In this study, single and duplex real-time quantitative PCR (qPCR) methods to detect and quantify T. asperellum and T. gamsii were developed. Primers/probe sets were designed on the T. asperellum and T. gamsii rpb2 genes and tested for specificity on a panel of microorganisms commonly associated with grape wood and soil. No differences were observed comparing single- and duplex-qPCR assays on different BCAs, 1 pg of target DNA was detected approximately at Cq = 34. R2-values and the efficiency were always equal to 0.99 and >80%, respectively. The detection limit of the duplex-qPCR assay on artificially inoculated samples was 2 × 103 and 4 × 104 conidia g-1 of grape wood tissue and soil, respectively. The methods will be useful to better schedule BCA application in the field and in grapevine nurseries, as well as for investigating the dynamic of BCA populations.
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Affiliation(s)
- Donato Gerin
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Public Laboratory of Research SELGE Network No. 14, Bari, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Rita M. De Miccolis Angelini
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Public Laboratory of Research SELGE Network No. 14, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Public Laboratory of Research SELGE Network No. 14, Bari, Italy
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18
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Kredics L, Chen L, Kedves O, Büchner R, Hatvani L, Allaga H, Nagy VD, Khaled JM, Alharbi NS, Vágvölgyi C. Molecular Tools for Monitoring Trichoderma in Agricultural Environments. Front Microbiol 2018; 9:1599. [PMID: 30090089 PMCID: PMC6068273 DOI: 10.3389/fmicb.2018.01599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Various Trichoderma species possess significance in agricultural systems as biofertilizers or biocontrol agents (BCAs). Besides these beneficial features, certain Trichoderma species can also act as agricultural pests, causing the green mold disease of cultivated mushrooms. This double-faced nature of the genus in agricultural environments points at the importance of proper monitoring tools, which can be used to follow the presence and performance of candidate as well as patented and/or registered biocontrol strains, to assess the possible risks arising from their application, but also to track harmful, unwanted Trichoderma species like the green molds in mushroom growing facilities. The objective of this review is to discuss the molecular tools available for the species- and strain-specific monitoring of Trichoderma, ranging from immunological approaches and fingerprinting tools to exogenous markers, specific primers used in polymerase chain reaction (PCR) as well as "omics" approaches.
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Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Orsolya Kedves
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Rita Büchner
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lóránt Hatvani
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Henrietta Allaga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Viktor D Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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19
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Manjunatha C, Sharma S, Kulshreshtha D, Gupta S, Singh K, Bhardwaj SC, Aggarwal R. Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification. PLoS One 2018; 13:e0196409. [PMID: 29698484 PMCID: PMC5919678 DOI: 10.1371/journal.pone.0196409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/12/2018] [Indexed: 10/26/2022] Open
Abstract
Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease.
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Affiliation(s)
- C. Manjunatha
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Sapna Sharma
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Deepika Kulshreshtha
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Sangeeta Gupta
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Kartar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Subhash C. Bhardwaj
- ICAR—Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, India
| | - Rashmi Aggarwal
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
- * E-mail:
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Babu BK, Mesapogu S, Sharma A, Somasani SR, Arora DK. Quantitative real-time PCR assay for rapid detection of plant and human pathogenic Macrophomina phaseolina from field and environmental samples. Mycologia 2017; 103:466-73. [DOI: 10.3852/10-181] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | - Dilip K. Arora
- National Bureau of Agriculturally Important Microorganisms (NBAIM), Post Box 06, Maunath Bhanjan, Uttar Pradesh-275 101, India
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Mosimann C, Oberhänsli T, Ziegler D, Nassal D, Kandeler E, Boller T, Mäder P, Thonar C. Tracing of Two Pseudomonas Strains in the Root and Rhizoplane of Maize, as Related to Their Plant Growth-Promoting Effect in Contrasting Soils. Front Microbiol 2017; 7:2150. [PMID: 28119675 PMCID: PMC5222796 DOI: 10.3389/fmicb.2016.02150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/20/2016] [Indexed: 11/18/2022] Open
Abstract
TaqMan-based quantitative PCR (qPCR) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (PGPR), Pseudomonas fluorescens Pf153 and Pseudomonas sp. DSMZ 13134, in the root and rhizoplane of inoculated maize plants. This was performed in pot experiments with three contrasting field soils (Buus, Le Caron and DOK-M). Potential cross-reactivity of the qPCR assays was assessed with indigenous Pseudomonas and related bacterial species, which had been isolated from the rhizoplane of maize roots grown in the three soils and then characterized by Matrix-Assisted Laser Desorption Ionization (MALDI) Time-of-Flight (TOF) mass spectrometry (MS). Sensitivity of the qPCR expressed as detection limit of bacterial cells spiked into a rhizoplane matrix was 1.4 × 102 CFU and 1.3 × 104 CFU per gram root fresh weight for strain Pf153 and DSMZ 13134, respectively. Four weeks after planting and inoculation, both strains could readily be detected in root and rhizoplane, whereas only Pf153 could be detected after 8 weeks. The colonization rate of maize roots by strain Pf153 was significantly influenced by the soil type, with a higher colonization rate in the well fertile and organic soil of Buus. Inoculation with strain DSMZ 13134, which colonized roots and rhizoplane to the same degree, independently of the soil type, increased yield of maize, in terms of biomass accumulation, only in the acidic soil of Le Caron, whereas inoculation with strain Pf153 reduced yield in the soil Buus, despite of its high colonization rate and persistence. These results indicate that the colonization rate and persistence of inoculated Pseudomonas strains can be quantitatively assessed by the TaqMan-based qPCR technique, but that it cannot be taken for granted that inoculation with a well-colonizing and persistent Pseudomonas strain has a positive effect on yield of maize.
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Affiliation(s)
- Carla Mosimann
- Department of Environmental Sciences, Botany, Zürich-Basel Plant Science Center, University of BaselBasel, Switzerland; Research Institute of Organic Agriculture (FIBL)Frick, Switzerland
| | | | | | - Dinah Nassal
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zürich-Basel Plant Science Center, University of Basel Basel, Switzerland
| | - Paul Mäder
- Research Institute of Organic Agriculture (FIBL) Frick, Switzerland
| | - Cécile Thonar
- Research Institute of Organic Agriculture (FIBL) Frick, Switzerland
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Abbasi S, Safaie N, Shams-bakhsh M, Shahbazi S. Biocontrol Activities of Gamma Induced Mutants of Trichoderma harzianum against some Soilborne Fungal Pathogens and their DNA Fingerprinting. IRANIAN JOURNAL OF BIOTECHNOLOGY 2016; 14:260-269. [PMID: 28959344 PMCID: PMC5434996 DOI: 10.15171/ijb.1224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/01/2015] [Accepted: 05/31/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Random induced mutation by gamma radiation is one of the genetic manipulation strategies to improve the antagonistic ability of biocontrol agents. OBJECTIVES This study aimed to induce mutants with more sporulation, colonization rate leading to enhanced antagonistic ability (in vitro assay) comparing to wild type (WT) and the assessment of genetic differences (in situ evaluation) using molecular markers. The superior mutants could be appropriate biocontrol agents against soil borne fungal diseases. MATERIALS AND METHODS In this research sampling and isolation of Trichoderma isolates were performed from soils with low incidence of soil borne disease. T. harzianum 65 was selected and irradiation was conducted with gammacell at optimal dose 250 Gray/s. Mutants (115) were obtained from the WT. The antagonistic abilities of twenty-four mutants were evaluated using dual culture and culture filtrate tests. RESULTS The results of in vitro assays revealed that Th15, Th11 and Th1 mutants exhibited stronger growth inhibition (GI) and colonization rate on Macrophomina phaseolina and Rhizoctonia solani AG4 compared to the wild type. Th15 and Th11 mutants exhibited stronger GI and colonization rate on Sclerotinia sclerotiorum in dual culture and culture filtrate tests and Th1 and Th11 mutants exhibited stronger GI on Fusarium grminearum in culture filtrate test. The DNA fingerprinting was carried out using RAPD and rep-PCR markers. Two (Th9 and Th17) out of the 24 mutants categorized distantly from the rest based on different polymorphism obtained by molecular markers. However, Th9 was different in GI% from Th17. RAPD analysis separated WT from mutants, Th9 from Th17 and also phenotypically superior mutants from other mutants. Meanwhile, rep-PCR analysis categorized WT isolate and mutants according to their antagonistic properties. CONCLUSIONS The latter marker (rep-PCR) appeared to be reproducible and simple to distinguish mutants from a single isolate of T. harzianum. Mutants (3 isolates) were phenotypically and genotypically distinct from WT. These mutants demonstrated a pronounced biocontrol activities against soilborne fungal phytopathogens.
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Affiliation(s)
- Sakineh Abbasi
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University of Tehran, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University of Tehran, Tehran, Iran
| | - Masoud Shams-bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University of Tehran, Tehran, Iran
| | - Samira Shahbazi
- Nuclear Science and Technology Research Institute, Atomic Energy Organization of Iran, Karaj, Iran
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Canfora L, Malusà E, Tkaczuk C, Tartanus M, Łabanowska B, Pinzari F. Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil. Sci Rep 2016; 6:22933. [PMID: 26975931 PMCID: PMC4791642 DOI: 10.1038/srep22933] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/25/2016] [Indexed: 11/30/2022] Open
Abstract
A culture independent method based on qPCR was developed for the detection and quantification of two fungal inoculants in soil. The aim was to adapt a genotyping approach based on SSR (Simple Sequence Repeat) marker to a discriminating tracing of two different species of bioinoculants in soil, after their in-field release. Two entomopathogenic fungi, Beauveria bassiana and B. brongniartii, were traced and quantified in soil samples obtained from field trials. These two fungal species were used as biological agents in Poland to control Melolontha melolontha (European cockchafer), whose larvae live in soil menacing horticultural crops. Specificity of SSR markers was verified using controls consisting of: i) soil samples containing fungal spores of B. bassiana and B. brongniartii in known dilutions; ii) the DNA of the fungal microorganisms; iii) soil samples singly inoculated with each fungus species. An initial evaluation of the protocol was performed with analyses of soil DNA and mycelial DNA. Further, the simultaneous detection and quantification of B. bassiana and B. brongniartii in soil was achieved in field samples after application of the bio-inoculants. The protocol can be considered as a relatively low cost solution for the detection, identification and traceability of fungal bio-inoculants in soil.
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Affiliation(s)
- L. Canfora
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
| | - E. Malusà
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - C. Tkaczuk
- Department of Plant Protection and Breeding, Siedlce University of Natural Sciences and Humanities, Prusa 14 Street, 08-110 Siedlce, Poland
| | - M. Tartanus
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - B.H. Łabanowska
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - F. Pinzari
- Council for Agricultural Research and Economics - Research Centre for the Soil-Plant System, Via della Navicella 2-4, 00184 Rome, Italy
- Life Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Pasini L, Prodorutti D, Pastorelli S, Pertot I. Genetic Diversity and Biocontrol of Rosellinia necatrix Infecting Apple in Northern Italy. PLANT DISEASE 2016; 100:444-452. [PMID: 30694124 DOI: 10.1094/pdis-04-15-0480-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The soilborne fungus Rosellinia necatrix is the causal agent of white root rot disease on numerous plant species, including apple, which, together with the ability to survive in soil for long periods, makes this pathogen difficult to control. To understand the origins of pathogen infestation, a survey of diseased apple orchards in the northeast of Italy was conducted and 35 isolates of R. necatrix were characterized with intersimple sequence repeat markers. High genetic heterogeneity among the collected isolates suggested multiple preexisting sources of inoculum and not movement of infected soil or plant material from a single source. Greenhouse trials confirmed that, as with some other crops, soil water content and temperature were the main factors influencing infection of apple plants, while organic fertilizers and the incorporation of apple wood residues were less important. The efficacy of Trichoderma atroviride SC1 as a biocontrol agent against R. necatrix greatly depended on the timing of application. It reduced white root rot incidence on apple seedlings only if treatment was applied at least 1 week before planting.
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Affiliation(s)
- Luca Pasini
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre
| | | | - Sandro Pastorelli
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre
| | - Ilaria Pertot
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, TN, Italy
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25
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Horn IR, van Rijn M, Zwetsloot TJJ, Basmagi S, Dirks-Mulder A, van Leeuwen WB, Ravensberg WJ, Gravendeel B. Development of a multiplex Q-PCR to detect Trichoderma harzianum Rifai strain T22 in plant roots. J Microbiol Methods 2016; 121:44-9. [PMID: 26747625 DOI: 10.1016/j.mimet.2015.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 11/16/2022]
Abstract
The fungal species Trichoderma harzianum is widely used as a biological agent in crop protection. To verify the continued presence of this fungus on plant roots manually inoculated with T. harzianum strain T22, a Q-PCR was designed using specific probes for this particular strain. To develop these molecular diagnostic tools, genome mining was first carried out to retrieve putative new regions by which different strains of T. harzianum could be distinguished. Subsequently, Sanger sequencing of the L-aminoacid oxidase gene (aox1) in T. harzianum was applied to determine the mutations differing between various strains isolated from the Trichoderma collection of Koppert Biological Systems. Based on the sequence information obtained, a set of hydrolysis probes was subsequently developed which discriminated T. harzianum T22 strains varying in only a single nucleotide. Probes designed for two strains uniquely recognized the respective strains in Q-PCR with a detection limit of 12,5ng DNA. Titration assays in which T. harzianum DNA from distinct strains was varied further underscored the specificity of the probes. Lastly, fungal DNA extracted from roots of greenhouse cultured tomato plants was analyzed using the probe-based assay. DNA from T. harzianum strain T22 could readily be identified on roots of greenhouse reared tomato plants inoculated with varying concentrations up to one week after treatment with a detection limit of 3e6 colony forming units of T. harzianum T22. We conclude that the Q-PCR method is a reliable and robust method for assessing the presence and quantity of T. harzianum strain T22 in manually inoculated plant material. Our method provides scope for the development of DNA based strain specific identification of additional strains of Trichoderma and other fungal biological control agents.
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Affiliation(s)
- Ivo R Horn
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands
| | - Menno van Rijn
- Koppert Biological Systems, Veilingweg 14, 2651, BE, Berkel en Rodenrijs, The Netherlands
| | - Tom J J Zwetsloot
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands
| | - Said Basmagi
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands
| | - Anita Dirks-Mulder
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands
| | - Willem B van Leeuwen
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands
| | - Willem J Ravensberg
- Koppert Biological Systems, Veilingweg 14, 2651, BE, Berkel en Rodenrijs, The Netherlands
| | - Barbara Gravendeel
- University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK, Leiden, The Netherlands; Naturalis Biodiversity Center, Darwinweg 2, 2333, CR Leiden, The Netherlands; Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.
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26
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Martini M, Moruzzi S, Ermacora P, Loi N, Firrao G. Quantitative real-time PCR and high-resolution melting (HRM) analysis for strain-specific monitoring of fluorescent pseudomonads used as biocontrol agents against soil-borne pathogens of food crops. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Skoneczny D, Oskiera M, Szczech M, Bartoszewski G. Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity. Folia Microbiol (Praha) 2015; 60:297-307. [PMID: 25791292 PMCID: PMC4445485 DOI: 10.1007/s12223-015-0385-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 03/05/2015] [Indexed: 11/30/2022]
Abstract
Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the ribosomal RNA (rRNA) gene cluster, a fragment of the translation elongation factor 1-alpha (tef1) gene, and random amplified polymorphic DNA (RAPD) markers were applied to determine the genetic diversity of Trichoderma atroviride strains collected in Poland, and also in order to identify loci and PCR-based molecular markers useful in genetic variation assessment of that fungus. Although tef1 and RAPD analysis showed limited genetic diversity among T. atroviride strains collected in Poland, it was possible to distinguish major groups that clustered most of the analyzed strains. Polymorphic RAPD amplicons were cloned and sequenced, yielding sequences representing 13 T. atroviride loci. Based on these sequences, a set of PCR-based markers specific to T. atroviride was developed and examined. Three cleaved amplified polymorphic sequence (CAPS) markers could assist in distinguishing T. atroviride strains. The genomic regions identified may be useful for further exploration and development of more precise markers suitable for T. atroviride identification and monitoring, especially in environmental samples.
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Affiliation(s)
- Dominik Skoneczny
- Department of Plant Genetics Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warszawa, Poland
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28
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Pérez G, Verdejo V, Gondim-Porto C, Orlando J, Carú M. Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities. J Zhejiang Univ Sci B 2014; 15:966-78. [PMID: 25367789 PMCID: PMC4228509 DOI: 10.1631/jzus.b1400063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/22/2014] [Indexed: 11/11/2022]
Abstract
Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20-23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community.
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29
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Tsai TT, Liu JK, Chang YM, Chen KF, Kao CM. Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study. JOURNAL OF HAZARDOUS MATERIALS 2014; 268:92-101. [PMID: 24468531 DOI: 10.1016/j.jhazmat.2014.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/30/2013] [Accepted: 01/05/2014] [Indexed: 06/03/2023]
Abstract
The objectives of this pilot-scale study were to (1) evaluate the effectiveness of bioremediation of trichloroethylene (TCE)-contaminated groundwater with the supplement of slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, surfactants) under reductive dechlorinating conditions, (2) apply gene analyses to confirm the existence of TCE-dechlorinating genes, and (3) apply the real-time polymerase chain reaction (PCR) to evaluate the variations in TCE-dechlorinating bacteria (Dehalococcoides spp.). Approximately 350L of SPRS solution was supplied into an injection well (IW) and groundwater samples were collected and analyzed from IW and monitor wells periodically. Results show that the SPRS caused a rapid increase of the total organic carbon concentration (up to 5794mg/L), and reductive dechlorination of TCE was significantly enhanced. TCE dechlorination byproducts were observed and up to 99% of TCE removal (initial TCE concentration=1872μg/L) was observed after 50 days of operation. The population of Dehalococcoides spp. increased from 4.6×10(1) to 3.41×10(7)cells/L after 20 days of operation. DNA sequencing results show that there were 31 bacterial species verified, which might be related to TCE biodegradation. Results demonstrate that the microbial analysis and real-time PCR are useful tools to evaluate the effectiveness of TCE reductive dechlorination.
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Affiliation(s)
- T T Tsai
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - J K Liu
- Department of Biological Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y M Chang
- Institute of Environmental Engineering and Management, National Taipei University of Technology, Taipei, Taiwan
| | - K F Chen
- Department of Civil Engineering, National Chi Nan University, Nantou, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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Corneo PE, Pellegrini A, Cappellin L, Roncador M, Chierici M, Gessler C, Pertot I. Microbial community structure in vineyard soils across altitudinal gradients and in different seasons. FEMS Microbiol Ecol 2013; 84:588-602. [PMID: 23398556 DOI: 10.1111/1574-6941.12087] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 11/27/2022] Open
Abstract
Microbial communities living in nine vineyards distributed over three altitudinal transects were studied over 2 years. Fungal and bacterial community dynamics were explored using automated ribosomal intergenic spacer analysis (ARISA) and by determining bacterial cells and fungal colony-forming units (CFUs). Moreover, extensive chemical and physical analyses of the soils were carried out. Multivariate analyses demonstrated that bacterial and fungal communities are affected by altitude, which acts as a complex physicochemical gradient. In fact, soil moisture, Al, Mg, Mn and clay content are changing with altitude and influencing the bacterial genetic structure, while in the case of fungi, soil moisture, B and clay content are found to be the main drivers of the community. Moreover, other exchangeable cations and heavy metals, not correlating with altitude, are involved in the ordination of the sites, especially Cu. Qualitative ARISA revealed the presence of a stable core microbiome of operational taxonomic units (OTUs) within each transect, which ranged between 57% and 68% of total OTUs in the case of fungi and between 63% and 72% for bacteria. No seasonal effect on the composition of microbial communities was found, demonstrating that bacterial and fungal communities in vineyards are mostly stable over the considered seasons.
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Affiliation(s)
- Paola E Corneo
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Fernández-Baldo MA, Fernández JG, Pereira SV, Messina GA, Salinas E, Raba J, Sanz Ferramola MI. Development of an indirect competitive enzyme-linked immunosorbent assay applied to the Botrytis cinerea quantification in tissues of postharvest fruits. BMC Microbiol 2011; 11:220. [PMID: 21970317 PMCID: PMC3197504 DOI: 10.1186/1471-2180-11-220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 10/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Botrytis cinerea is a phytopathogenic fungus responsible for the disease known as gray mold, which causes substantial losses of fruits at postharvest. This fungus is present often as latent infection and an apparently healthy fruit can deteriorate suddenly due to the development of this infection. For this reason, rapid and sensitive methods are necessary for its detection and quantification. This article describes the development of an indirect competitive enzyme-linked immunosorbent assay (ELISA) for quantification of B. cinerea in apple (Red Delicious), table grape (pink Moscatel), and pear (William's) tissues. RESULTS The method was based in the competition for the binding site of monoclonal antibodies between B. cinerea antigens present in fruit tissues and B. cinerea purified antigens immobilized by a crosslinking agent onto the surface of the microtiter plates. The method was validated considering parameters such as selectivity, linearity, precision, accuracy and sensibility. The calculated detection limit was 0.97 μg mL-1 B. cinerea antigens. The immobilized antigen was perfectly stable for at least 4 months assuring the reproducibility of the assay. The fungus was detected and quantified in any of the fruits tested when the rot was not visible yet. Results were compared with a DNA quantification method and these studies showed good correlation. CONCLUSIONS The developed method allowed detects the presence of B. cinerea in asymptomatic fruits and provides the advantages of low cost, easy operation, and short analysis time determination for its possible application in the phytosanitary programs of the fruit industry worldwide.
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Affiliation(s)
- Martín A Fernández-Baldo
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - Jorge G Fernández
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - Sirley V Pereira
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - Germán A Messina
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - Eloy Salinas
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - Julio Raba
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
| | - María I Sanz Ferramola
- INQUISAL, Departamento de Química. Universidad Nacional de San Luis, CONICET. Chacabuco 917. D5700BWS. San Luis, Argentina
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Comparison of real-time PCR and microscopy to evaluate sclerotial colonisation by a biocontrol fungus. Fungal Biol 2011; 115:317-25. [DOI: 10.1016/j.funbio.2010.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 12/08/2010] [Accepted: 12/20/2010] [Indexed: 11/24/2022]
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33
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Naeimi S, Kocsubé S, Antal Z, Okhovvat SM, Javan-Nikkhah M, Vágvölgyi C, Kredics L. Strain-specific SCAR markers for the detection of Trichoderma harzianum AS12-2, a biological control agent against Rhizoctonia solani, the causal agent of rice sheath blight. ACTA BIOLOGICA HUNGARICA 2011; 62:73-84. [PMID: 21388921 DOI: 10.1556/abiol.61.2011.1.8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In order to identify a specific marker for T. harzianum AS12-2, a strain capable of controlling rice sheath blight caused by Rhizoctonia solani, UP-PCR was performed using five universal primers (UP) both separately and in pairwise combinations. The application of two UP primers resulted in the amplification of unique fragments from the genomic DNA of T. harzianum AS12-2, clearly distinguishing it from other Trichoderma strains. The unique fragments had no significant sequence homology with any other known sequence available in databases. Based on the sequences of the unique fragments, 14 oligonucleotide primers were designed. Two primer sets amplified a fragment of expected size from the DNA of strain T. harzianum AS12-2 but not from any other examined strains belonging to T. harzianum, to other Trichoderma species assayed, or to other common fungi present in paddy fields of Mazandaran province, Iran. In conclusion, SCAR (sequence characterized amplified regions) markers were successfully identified and rapid, reliable tools were provided for the detection of an effective biocontrol Trichoderma strain, which can facilitate studies of its population dynamics and establishment after release into the natural environment.
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Affiliation(s)
- S Naeimi
- Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran
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Beaulieu R, López-Mondéjar R, Tittarelli F, Ros M, Pascual JA. qRT-PCR quantification of the biological control agent Trichoderma harzianum in peat and compost-based growing media. BIORESOURCE TECHNOLOGY 2011; 102:2793-2798. [PMID: 21030250 DOI: 10.1016/j.biortech.2010.09.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 09/27/2010] [Accepted: 09/29/2010] [Indexed: 05/30/2023]
Abstract
To ensure proper use of Trichoderma harzianum in agriculture, accurate data must be obtained in population monitoring. The effectiveness of qRT-PCR to quantify T. harzianum in different growing media was compared to the commonly used techniques of colony counting and qPCR. Results showed that plate counting and qPCR offered similar T. harzianum quantification patterns of an initial rapid increase in fungal population that decreased over time. However, data from qRT-PCR showed a population curve of active T. harzianum with a delayed onset of initial growth which then increased throughout the experiment. Results demonstrated that T. harzianum can successfully grow in these media and that qRT-PCR can offer a more distinct representation of active T. harzianum populations. Additionally, compost amended with T. harzianum exhibited a lower Fusarium oxysporum infection rate (67%) and lower percentage of fresh weight loss (11%) in comparison to amended peat (90% infection rate, 23% fresh weight loss).
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Affiliation(s)
- Robert Beaulieu
- Department of Soil Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Espinardo, Murcia, Spain
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Guidi V, De Respinis S, Benagli C, Lüthy P, Tonolla M. A real-time PCR method to quantify spores carrying the Bacillus thuringiensis var. israelensis cry4Aa and cry4Ba genes in soil. J Appl Microbiol 2010; 109:1209-17. [DOI: 10.1111/j.1365-2672.2010.04741.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Von Felten A, Défago G, Maurhofer M. Quantification of Pseudomonas fluorescens strains F113, CHA0 and Pf153 in the rhizosphere of maize by strain-specific real-time PCR unaffected by the variability of DNA extraction efficiency. J Microbiol Methods 2010; 81:108-15. [DOI: 10.1016/j.mimet.2010.02.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/04/2010] [Accepted: 02/06/2010] [Indexed: 11/28/2022]
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Lorito M, Woo SL, Harman GE, Monte E. Translational research on Trichoderma: from 'omics to the field. ANNUAL REVIEW OF PHYTOPATHOLOGY 2010; 48:395-417. [PMID: 20455700 DOI: 10.1146/annurev-phyto-073009-114314] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Structural and functional genomics investigations are making an important impact on the current understanding and application of microbial agents used for plant disease control. Here, we review the case of Trichoderma spp., the most widely applied biocontrol fungi, which have been extensively studied using a variety of research approaches, including genomics, transcriptomics, proteomics, metabolomics, etc. Known for almost a century for their beneficial effects on plants and the soil, these fungi are the subject of investigations that represent a successful case of translational research, in which 'omics-generated novel understanding is directly translated in to new or improved crop treatments and management methods. We present an overview of the latest discoveries on the Trichoderma expressome and metabolome, of the complex and diverse biotic interactions established in nature by these microbes, and of their proven or potential importance to agriculture and industry.
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Affiliation(s)
- Matteo Lorito
- Dipartimento di Arboricoltura, Botanica e Patologia Vegetale (ArBoPaVe), Università di Napoli Federico II, Portici, Napoli, Italy 80138.
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Longa CMO, Pertot I. An intact soil-core microcosm method to evaluate the survival and vertical dispersal ofTrichoderma atrovirideSC1. Lett Appl Microbiol 2009; 49:609-14. [PMID: 19780964 DOI: 10.1111/j.1472-765x.2009.02715.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C M O Longa
- IASMA Research and Innovation Center, Fondazione Edmund Mach, 38010 S. Michele all'Adige (TN), Italy.
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Longa C, Savazzini F, Tosi S, Elad Y, Pertot I. Evaluating the survival and environmental fate of the biocontrol agentTrichoderma atrovirideSC1 in vineyards in northern Italy. J Appl Microbiol 2009; 106:1549-57. [DOI: 10.1111/j.1365-2672.2008.04117.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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