Uncovering genomic features and biosynthetic gene clusters in endophytic bacteria from roots of the medicinal plant Alkanna tinctoria Tausch as a strategy to identify novel biocontrol bacteria
- Author
- Henry David Naranjo Benavides (UGent) , Angélique Rat (UGent) , Noémie De Zutter (UGent) , Emmelie De Ridder (UGent) , Liesbeth Lebbe (UGent) , Kris Audenaert (UGent) and Anne Willems (UGent)
- Organization
- Project
-
- MICROMETABOLITE (MICROMETABOLITE: Research Training Network on the Microbial Enhancement of Bioactive Secondary Metabolite Production in Plants)
- Micrometabolite/Isolation and functional characterization of root endophytic bacteria from Boraginaceae that promote growth and affect plant secondary metabolism.
- Genomic and functional molecular characterization of root endophytic bacteria from Boraginaceae that promote growth and affect plant secondary metabolism.
- The Flemish contribution to the European Marine Biological Resource Centre (EMBRC-ERIC)
- Multidimensional hyperspectral imaging to determine and quantify plant phenotypes in agri- and horticulture
- Abstract
- Phytopathogenic fungi are a major threat to global food production. The most common management practice to prevent plant infections involves the intensive use of fungicides. The world's population is increasing at a rate not seen in the past. Agriculture, providing food for this increasing population, is reaching its boundaries of space and natural resources. In addition, changing legislation and increased ecological awareness are forcing agriculture to reduce its environmental impact. This entails the replacement of agrochemicals with nature-based solutions. In this regard, the search for effective biocontrol agents that protect crops from pathogens is in the spotlight. In this study, we have investigated the biocontrol activity of endophytic bacteria isolated from the medicinal plant Alkanna tinctoria Tausch. To do so, an extensive collection of bacterial strains was initially genome sequenced and in silico screened for features related to plant stimulation and biocontrol. Based on this information, a selection of bacteria was tested in vitro for antifungal activity using direct antagonism in a plate assay and in planta with a detached-leaf assay. Bacterial strains were tested individually and in combinations to assess the best-performing treatments. The results revealed that many bacteria could produce metabolites that efficiently inhibit the proliferation of several fungi, especially Fusarium graminearum. Among these, Pseudomonas sp. strain R-71838 showed a strong antifungal effect, in both dual-culture and in planta assays, making it the most promising candidate for biocontrol application. Using microbes from medicinal plants, this study highlights the opportunities of using genomic information to speed up the screening of a taxonomically diverse set of bacteria with biocontrol properties.IMPORTANCE Phytopathogenic fungi are a major threat to global food production. The most common management practice to prevent plant infections involves the intensive use of fungicides. However, with the growing awareness of the ecological and human impacts of chemicals, there is a need for alternative strategies, such as the use of bacterial biocontrol agents. Limitations in the design of bacterial biocontrol included the need for labor-intensive and time-consuming experiments to test a wide diversity of strains and the lack of reproducibility of their activity against pathogens. Here, we show that genomic information is an effective tool to select bacteria of interest quickly. Also, we highlight that the strain Pseudomonas sp. R-71838 produced a reproducible antifungal effect both in vitro and in planta. These findings build a foundation for designing a biocontrol strategy based on Pseudomonas sp. R-71838.
- Keywords
- bacterial genomics, biocontrol, secondary metabolites, IRON ACQUISITION, PSEUDOMONAS, VIRULENCE, SYRINGOMYCIN, PYOVERDINE, DISEASES, SYSTEM
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HA9XA9V6F6CYDN14KZ900D62
- MLA
- Naranjo Benavides, Henry David, et al. “Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna Tinctoria Tausch as a Strategy to Identify Novel Biocontrol Bacteria.” MICROBIOLOGY SPECTRUM, vol. 11, no. 4, 2023, doi:10.1128/spectrum.00747-23.
- APA
- Naranjo Benavides, H. D., Rat, A., De Zutter, N., De Ridder, E., Lebbe, L., Audenaert, K., & Willems, A. (2023). Uncovering genomic features and biosynthetic gene clusters in endophytic bacteria from roots of the medicinal plant Alkanna tinctoria Tausch as a strategy to identify novel biocontrol bacteria. MICROBIOLOGY SPECTRUM, 11(4). https://doi.org/10.1128/spectrum.00747-23
- Chicago author-date
- Naranjo Benavides, Henry David, Angélique Rat, Noémie De Zutter, Emmelie De Ridder, Liesbeth Lebbe, Kris Audenaert, and Anne Willems. 2023. “Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna Tinctoria Tausch as a Strategy to Identify Novel Biocontrol Bacteria.” MICROBIOLOGY SPECTRUM 11 (4). https://doi.org/10.1128/spectrum.00747-23.
- Chicago author-date (all authors)
- Naranjo Benavides, Henry David, Angélique Rat, Noémie De Zutter, Emmelie De Ridder, Liesbeth Lebbe, Kris Audenaert, and Anne Willems. 2023. “Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna Tinctoria Tausch as a Strategy to Identify Novel Biocontrol Bacteria.” MICROBIOLOGY SPECTRUM 11 (4). doi:10.1128/spectrum.00747-23.
- Vancouver
- 1.Naranjo Benavides HD, Rat A, De Zutter N, De Ridder E, Lebbe L, Audenaert K, et al. Uncovering genomic features and biosynthetic gene clusters in endophytic bacteria from roots of the medicinal plant Alkanna tinctoria Tausch as a strategy to identify novel biocontrol bacteria. MICROBIOLOGY SPECTRUM. 2023;11(4).
- IEEE
- [1]H. D. Naranjo Benavides et al., “Uncovering genomic features and biosynthetic gene clusters in endophytic bacteria from roots of the medicinal plant Alkanna tinctoria Tausch as a strategy to identify novel biocontrol bacteria,” MICROBIOLOGY SPECTRUM, vol. 11, no. 4, 2023.
@article{01HA9XA9V6F6CYDN14KZ900D62, abstract = {{Phytopathogenic fungi are a major threat to global food production. The most common management practice to prevent plant infections involves the intensive use of fungicides. The world's population is increasing at a rate not seen in the past. Agriculture, providing food for this increasing population, is reaching its boundaries of space and natural resources. In addition, changing legislation and increased ecological awareness are forcing agriculture to reduce its environmental impact. This entails the replacement of agrochemicals with nature-based solutions. In this regard, the search for effective biocontrol agents that protect crops from pathogens is in the spotlight. In this study, we have investigated the biocontrol activity of endophytic bacteria isolated from the medicinal plant Alkanna tinctoria Tausch. To do so, an extensive collection of bacterial strains was initially genome sequenced and in silico screened for features related to plant stimulation and biocontrol. Based on this information, a selection of bacteria was tested in vitro for antifungal activity using direct antagonism in a plate assay and in planta with a detached-leaf assay. Bacterial strains were tested individually and in combinations to assess the best-performing treatments. The results revealed that many bacteria could produce metabolites that efficiently inhibit the proliferation of several fungi, especially Fusarium graminearum. Among these, Pseudomonas sp. strain R-71838 showed a strong antifungal effect, in both dual-culture and in planta assays, making it the most promising candidate for biocontrol application. Using microbes from medicinal plants, this study highlights the opportunities of using genomic information to speed up the screening of a taxonomically diverse set of bacteria with biocontrol properties.IMPORTANCE Phytopathogenic fungi are a major threat to global food production. The most common management practice to prevent plant infections involves the intensive use of fungicides. However, with the growing awareness of the ecological and human impacts of chemicals, there is a need for alternative strategies, such as the use of bacterial biocontrol agents. Limitations in the design of bacterial biocontrol included the need for labor-intensive and time-consuming experiments to test a wide diversity of strains and the lack of reproducibility of their activity against pathogens. Here, we show that genomic information is an effective tool to select bacteria of interest quickly. Also, we highlight that the strain Pseudomonas sp. R-71838 produced a reproducible antifungal effect both in vitro and in planta. These findings build a foundation for designing a biocontrol strategy based on Pseudomonas sp. R-71838.}}, articleno = {{e00747-23}}, author = {{Naranjo Benavides, Henry David and Rat, Angélique and De Zutter, Noémie and De Ridder, Emmelie and Lebbe, Liesbeth and Audenaert, Kris and Willems, Anne}}, issn = {{2165-0497}}, journal = {{MICROBIOLOGY SPECTRUM}}, keywords = {{bacterial genomics,biocontrol,secondary metabolites,IRON ACQUISITION,PSEUDOMONAS,VIRULENCE,SYRINGOMYCIN,PYOVERDINE,DISEASES,SYSTEM}}, language = {{eng}}, number = {{4}}, pages = {{16}}, title = {{Uncovering genomic features and biosynthetic gene clusters in endophytic bacteria from roots of the medicinal plant Alkanna tinctoria Tausch as a strategy to identify novel biocontrol bacteria}}, url = {{http://doi.org/10.1128/spectrum.00747-23}}, volume = {{11}}, year = {{2023}}, }
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