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Manfredini A, Malusà E, Costa C, Pallottino F, Mocali S, Pinzari F, Canfora L. Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil. Front Microbiol 2021; 12:698491. [PMID: 34531836 PMCID: PMC8438429 DOI: 10.3389/fmicb.2021.698491] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.
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Affiliation(s)
- Andrea Manfredini
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Eligio Malusà
- National Research Institute of Horticulture, Skierniewice, Poland
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Corrado Costa
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Federico Pallottino
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Stefano Mocali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy (CNR), Rome, Italy
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
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Xu WF, Yang JL, Meng XK, Gu ZG, Zhang QL, Lin LB. Understanding the Transcriptional Changes During Infection of Meloidogyne incognita Eggs by the Egg-Parasitic Fungus Purpureocillium lilacinum. Front Microbiol 2021; 12:617710. [PMID: 33897634 PMCID: PMC8058359 DOI: 10.3389/fmicb.2021.617710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/17/2021] [Indexed: 12/03/2022] Open
Abstract
The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs, and thus, it is used as a good biocontrol agent against plant root-knot nematodes. However, little is known about the transcriptional response of P. lilacinum while infecting nematode eggs. This study presents the whole transcriptome sequencing of P. lilacinum and transcriptome-wide gene expression analysis of P. lilacinum upon infecting the eggs of Meloidogyne incognita compared to non-infecting controls. A transcriptomic library of P. lilacinum was used as reference gene set and six transcriptomic libraries of the non-infecting control and P. lilacinum infecting M. incognita eggs were constructed, respectively, comprising three biological replicates of each. A total of 1,011 differently expressed genes (DEGs) were identified in the infecting samples, including 553 up-regulated and 458 down-regulated genes compared to the non-infecting control samples. Furthermore, functional enrichment analysis exhibited that these DEGs were primarily involved in oxidative phosphorylation, oxidoreductase activity, and metabolic processes. Fifteen DEGs were randomly selected to verify the RNA sequencing results through quantitative real-time polymerase chain reaction (qPCR). The study focused on P. lilacinum genes that were strongly expressed upon infecting M. incognita eggs. These DEGs were primarily involved in detoxification, parasitic behavior, and nutritional utilization. This study contributes significantly to the understanding of the molecular mechanisms underlying the parasitic action of P. lilacinum on nematode eggs and provides a valuable genetic resource for further research on parasitic behavior of P. lilacinum. Notably, this study examined the transcriptomics of P. lilacinum infecting M. incognita eggs at only one time point. Since there were fungi at different stages of the infection process at that time point, the transcriptional profiles are not precisely examining one specific stage in this process.
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Affiliation(s)
- Wen-Feng Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Kingenta Ecological Engineering Group Co., Ltd., Linyi, China
| | - Jia-Lin Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, China
| | - Xiang-Kun Meng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Kingenta Ecological Engineering Group Co., Ltd., Linyi, China
| | - Zhi-Guang Gu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Kingenta Ecological Engineering Group Co., Ltd., Linyi, China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, China
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McKinnon AC, Glare TR, Ridgway HJ, Mendoza-Mendoza A, Holyoake A, Godsoe WK, Bufford JL. Detection of the Entomopathogenic Fungus Beauveria bassiana in the Rhizosphere of Wound-Stressed Zea mays Plants. Front Microbiol 2018; 9:1161. [PMID: 29942287 PMCID: PMC6004820 DOI: 10.3389/fmicb.2018.01161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Entomopathogenic fungi from the genus Beauveria (Vuillemin) play an important role in controlling insect populations and have been increasingly utilized for the biological control of insect pests. Various studies have reported that Beauveria bassiana (Bals.), Vuill. also has the ability to colonize a broad range of plant hosts as endophytes without causing disease but while still maintaining the capacity to infect insects. Beauveria is often applied as an inundative spore application, but little research has considered how plant colonization may alter the ability to persist in the environment. The aim of this study was to investigate potential interactions between B. bassiana and Zea mays L. (maize) in the rhizosphere following inoculation, in order to understand the factors that may affect environmental persistence of the fungi. The hypothesis was that different isolates of B. bassiana have the ability to colonize maize roots and/or rhizosphere soil, resulting in effects to the plant microbiome. To test this hypothesis, a two-step nested PCR protocol was developed to find and amplify Beauveria in planta or in soil; based on the translation elongation factor 1-alpha (ef1α) gene. The nested protocol was also designed to enable Beauveria species differentiation by sequence analysis. The impact of three selected B. bassiana isolates applied topically to roots on the rhizosphere soil community structure and function were consequently assessed using denaturing gradient gel electrophoresis (DGGE) and MicroRespTM techniques. The microbial community structure and function were not significantly affected by the presence of the isolates, however, retention of the inocula in the rhizosphere at 30 days after inoculation was enhanced when plants were subjected to intensive wounding of foliage to crudely simulate herbivory. The plant defense response likely changed under wound stress resulting in the apparent recruitment of Beauveria in the rhizosphere, which may be an indirect defensive strategy against herbivory and/or the result of induced systemic susceptibility in maize enabling plant colonization.
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Affiliation(s)
- Aimee C McKinnon
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
| | - Hayley J Ridgway
- The New Zealand Institute for Plant & Food Research Limited, Christchurch, New Zealand
| | | | - Andrew Holyoake
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
| | - William K Godsoe
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
| | - Jennifer L Bufford
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
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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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Lacey L, Grzywacz D, Shapiro-Ilan D, Frutos R, Brownbridge M, Goettel M. Insect pathogens as biological control agents: Back to the future. J Invertebr Pathol 2015. [DOI: 10.1016/j.jip.2015.07.009] [Citation(s) in RCA: 545] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Johny S, Kyei-Poku G. A molecular tool for detection and tracking of a potential indigenous Beauveria bassiana strain for managing emerald ash borer populations in Canada. J Invertebr Pathol 2014; 122:16-21. [PMID: 25110340 DOI: 10.1016/j.jip.2014.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/30/2014] [Accepted: 07/30/2014] [Indexed: 11/29/2022]
Abstract
Emerald ash borer is an invasive species from Asia. Beauveria bassiana strain L49-1AA is being tested for the control of emerald ash borer in Canada, using an autocontamination trapping system. We have developed a simplified allele discrimination polymerase chain reaction (PCR) assay to screen B. bassiana strain, L49-1AA from other Beauveria species by targeting the inter-strain genetic differences in 5' end of EF1-α gene of the genus Beauveria. A single nucleotide polymorphism (SNP) site, T→C was identified only in L49-1AA and was used to develop a simplified allele discrimination polymerase chain reaction (PCR) assay based on a modified allelic inhibition of displacement activity (AIDA) approach for distinguishing B. bassiana L49-1AA from all background Beauveria isolates. The SNP site was employed to design inner primers but with a deliberate mismatch introduced at the 3' antepenultimate from the mutation site in order to maximize specificity and detection efficiency. Amplification was specific to L49-1AA without cross-reaction with DNA from other Beauveria strains. In addition, the designed primers were also tested against environmental samples in L49-1AA released plots and observed to be highly efficient in detecting and discriminating the target strain, L49-1AA from both pure and crude DNA samples. This new method can potentially allow for more discriminatory tracking and monitoring of released L49-1AA in our autocontamination and dissemination projects for managing EAB populations. Additionally, the modified-AIDA format has potential as a tool for simultaneously identifying and differentiating closely related Beauveria species, strains/isolates as well as general classification of other pathogens or organisms.
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Affiliation(s)
- Shajahan Johny
- Canadian Forestry Service, Great Lakes Forestry Centre, Natural Resources Canada, 1219 Queen Street East, Sault Ste. Marie, Ontario P6A 2E5, Canada
| | - George Kyei-Poku
- Canadian Forestry Service, Great Lakes Forestry Centre, Natural Resources Canada, 1219 Queen Street East, Sault Ste. Marie, Ontario P6A 2E5, Canada.
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Hirsch J, Galidevara S, Strohmeier S, Devi KU, Reineke A. Effects on diversity of soil fungal community and fate of an artificially applied Beauveria bassiana strain assessed through 454 pyrosequencing. MICROBIAL ECOLOGY 2013; 66:608-620. [PMID: 23736813 DOI: 10.1007/s00248-013-0249-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 05/17/2013] [Indexed: 06/02/2023]
Abstract
The entomopathogenic fungus Beauveria bassiana is widely used as a biological control agent (BCA) for insect pest control, with fungal propagules being either incorporated into the potting media or soil or sprayed directly onto the foliage or soil. To gain a better understanding of entomopathogenic fungal ecology when applied as a BCA to the soil environment, a case study using tag-encoded 454 pyrosequencing of fungal ITS sequences was performed to assess the fate and potential effect of an artificially applied B. bassiana strain on the diversity of soil fungal communities in an agricultural field in India. Results show that the overall fungal diversity was not influenced by application of B. bassiana during the 7 weeks of investigation. Strain-specific microsatellite markers indicated both an establishment of the applied B. bassiana strain in the treated plot and its spread to the neighboring nontreated control plot. These results might be important for proper risk assessment of entomopathogenic fungi-based BCAs.
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Affiliation(s)
- Jacqueline Hirsch
- Institute of Phytomedicine, Geisenheim University, Von-Lade-Str. 1, 65366, Geisenheim, Germany
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A PCR-based tool for the cultivation-independent monitoring of Pandora neoaphidis. J Invertebr Pathol 2008; 99:49-56. [DOI: 10.1016/j.jip.2008.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/19/2008] [Accepted: 03/20/2008] [Indexed: 11/18/2022]
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