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Díaz-Díaz M, Antón-Domínguez BI, Raya MC, Bernal-Cabrera A, Medina-Marrero R, Trapero A, Agustí-Brisach C. Streptomyces spp. Strains as Potential Biological Control Agents against Verticillium Wilt of Olive. J Fungi (Basel) 2024; 10:138. [PMID: 38392810 PMCID: PMC10890128 DOI: 10.3390/jof10020138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Verticillium wilt of olive (VWO) caused by Verticillium dahliae is considered a major olive (Olea europaea) disease in Mediterranean-type climate regions. The lack of effective chemical products against VWO makes it necessary to search for alternatives such as biological control. The main goal of this study was to evaluate the effect of six Streptomyces spp. strains as biological control agents (BCAs) against VWO. All of them were molecularly characterized by sequencing 16S or 23S rRNA genes and via phylogenetic analysis. Their effect was evaluated in vitro on the mycelial growth of V. dahliae (isolates V004 and V323) and on microsclerotia (MS) viability using naturally infested soils. Bioassays in olive plants inoculated with V. dahliae were also conducted to evaluate their effect against disease progress. In all the experiments, the reference BCAs Fusarium oxysporum FO12 and Aureobasidium pullulans AP08 were included for comparative purposes. The six strains were identified as Streptomyces spp., and they were considered as potential new species. All the BCAs, including Streptomyces strains, showed a significant effect on mycelial growth inhibition for both V. dahliae isolates compared to the positive control, with FO12 being the most effective, followed by AP08, while the Streptomyces spp. strains showed an intermediate effect. All the BCAs tested also showed a significant effect on the inhibition of germination of V. dahliae MS compared to the untreated control, with FO12 being the most effective treatment. Irrigation treatments with Streptomyces strain CBQ-EBa-21 or FO12 were significantly more effective in reducing disease severity and disease progress in olive plants inoculated with V. dahliae compared to the remaining treatments. This study represents the first approach to elucidating the potential effect of Streptomyces strains against VWO.
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Affiliation(s)
- Miriam Díaz-Díaz
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Begoña I Antón-Domínguez
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - María Carmen Raya
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Alexander Bernal-Cabrera
- Centro de Investigaciones Agropecuarias (CIAP), Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
- Departamento de Agronomía, Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Ricardo Medina-Marrero
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Antonio Trapero
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Carlos Agustí-Brisach
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
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Cardoni M, Mercado-Blanco J. Confronting stresses affecting olive cultivation from the holobiont perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1261754. [PMID: 38023867 PMCID: PMC10661416 DOI: 10.3389/fpls.2023.1261754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
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Affiliation(s)
- Martina Cardoni
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Cardoni M, Fernández-González AJ, Valverde-Corredor A, Fernández-López M, Mercado-Blanco J. Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria. ENVIRONMENTAL MICROBIOME 2023; 18:21. [PMID: 36949520 PMCID: PMC10035242 DOI: 10.1186/s40793-023-00480-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Verticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed. RESULTS Inoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the 'Picual' root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the 'Picual' microbial community; instead, PICF7 inoculation increased the microbiota's compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected. CONCLUSION The absence of significant modifications on the structure and composition of the 'Picual' belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the 'Picual' microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.
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Affiliation(s)
- Martina Cardoni
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain
| | | | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain.
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Granada, Spain.
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Saberi Riseh R, Hassanisaadi M, Vatankhah M, Kennedy JF. Encapsulating biocontrol bacteria with starch as a safe and edible biopolymer to alleviate plant diseases: A review. Carbohydr Polym 2023; 302:120384. [PMID: 36604062 DOI: 10.1016/j.carbpol.2022.120384] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Healthy foods with few artificial additives are in high demand among consumers. Preserving conventional pesticides, frequently used as chemicals to control phytopathogens, is challenging. Therefore, we proposed an innovative approach to protect agricultural products in this review. Biocontrol bacteria are safe alternatives with low stability and low efficiency in the free-form formulation. The encapsulation technique for covering active compounds (e.g., antimicrobials) represents a more efficient protection technology because encapsulation causes the controlled release of bioactive materials and reduces the application doses. Of the biopolymers able to form a capsule, starch exhibits several advantages, such as its ready availability, cost-effectively, edible, colorless, and tasteless. Nevertheless, the poor mechanical properties of starch can be improved with other edible biopolymers. In addition, applying formulations incorporated with more than one antimicrobial material offers synergistic effects. This review presented the starch-based capsules used to enclose antimicrobial agents as effective tools against phytopathogens.
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Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran.
| | - Mohadeseh Hassanisaadi
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran; Department of Plant Protection, Faculty of Agriculture, Shahid Bahonar University of Kerman, 7618411764 Kerman, Iran
| | - Masoumeh Vatankhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran
| | - John F Kennedy
- Chembiotech Laboratories Ltd, WR15 8FF Tenbury Wells, United Kingdom.
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Saberi Riseh R, Hassanisaadi M, Vatankhah M, Soroush F, Varma RS. Nano/microencapsulation of plant biocontrol agents by chitosan, alginate, and other important biopolymers as a novel strategy for alleviating plant biotic stresses. Int J Biol Macromol 2022; 222:1589-1604. [DOI: 10.1016/j.ijbiomac.2022.09.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
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Bonaterra A, Badosa E, Daranas N, Francés J, Roselló G, Montesinos E. Bacteria as Biological Control Agents of Plant Diseases. Microorganisms 2022; 10:microorganisms10091759. [PMID: 36144361 PMCID: PMC9502092 DOI: 10.3390/microorganisms10091759] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022] Open
Abstract
Biological control is an effective and sustainable alternative or complement to conventional pesticides for fungal and bacterial plant disease management. Some of the most intensively studied biological control agents are bacteria that can use multiple mechanisms implicated in the limitation of plant disease development, and several bacterial-based products have been already registered and marketed as biopesticides. However, efforts are still required to increase the commercially available microbial biopesticides. The inconsistency in the performance of bacterial biocontrol agents in the biological control has limited their extensive use in commercial agriculture. Pathosystem factors and environmental conditions have been shown to be key factors involved in the final levels of disease control achieved by bacteria. Several biotic and abiotic factors can influence the performance of the biocontrol agents, affecting their mechanisms of action or the multitrophic interaction between the plant, the pathogen, and the bacteria. This review shows some relevant examples of known bacterial biocontrol agents, with especial emphasis on research carried out by Spanish groups. In addition, the importance of the screening process and of the key steps in the development of bacterial biocontrol agents is highlighted. Besides, some improvement approaches and future trends are considered.
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Prigigallo MI, Gómez-Lama Cabanás C, Mercado-Blanco J, Bubici G. Designing a synthetic microbial community devoted to biological control: The case study of Fusarium wilt of banana. Front Microbiol 2022; 13:967885. [PMID: 35992653 PMCID: PMC9389584 DOI: 10.3389/fmicb.2022.967885] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4) is threatening banana production because of its increasing spread. Biological control approaches have been widely studied and constitute interesting complementary measures to integrated disease management strategies. They have been based mainly on the use of single biological control agents (BCAs). In this study, we moved a step forward by designing a synthetic microbial community (SynCom) for the control of Fusarium wilt of banana (FWB). Ninety-six isolates of Pseudomonas spp., Bacillus spp., Streptomyces spp., and Trichoderma spp. were obtained from the banana rhizosphere and selected in vitro for the antagonism against Foc TR4. In pot experiments, a large community such as SynCom 1.0 (44 isolates with moderate to high antagonistic activity) or a small one such as SynCom 1.1 (seven highly effective isolates) provided similar disease control (35% symptom severity reduction). An in vitro study of the interactions among SynCom 1.1 isolates and between them and Foc revealed that beneficial microorganisms not only antagonized the pathogen but also some of the SynCom constituents. Furthermore, Foc defended itself by antagonizing the beneficial microbes. We also demonstrated that fusaric acid, known as one of the secondary metabolites of Fusarium species, might be involved in such an interaction. With this knowledge, SynCom 1.2 was then designed with three isolates: Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and Trichoderma virens T2C1.4. A non-simultaneous soil application of these isolates (to diminish cross-inhibition) delayed FWB progress over time, with significant reductions in incidence and severity. SynCom 1.2 also performed better than two commercial BCAs, BioPak® and T-Gro. Eventually, SynCom 1.2 isolates were characterized for several biocontrol traits and their genome was sequenced. Our data showed that assembling a SynCom for biocontrol is not an easy task. The mere mixtures of antagonists (e.g., SynCom 1.0 and 1.1) might provide effective biocontrol, but an accurate investigation of the interactions among beneficial microorganisms is needed to improve the results (e.g., SynCom 1.2). SynCom 1.2 is a valuable tool to be further developed for the biological control of FWB.
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Affiliation(s)
- Maria Isabella Prigigallo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
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Gómez-Lama Cabanás C, Wentzien NM, Zorrilla-Fontanesi Y, Valverde-Corredor A, Fernández-González AJ, Fernández-López M, Mercado-Blanco J. Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses. Front Microbiol 2022; 13:809126. [PMID: 35242117 PMCID: PMC8885582 DOI: 10.3389/fmicb.2022.809126] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.
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Affiliation(s)
- Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Nuria M. Wentzien
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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Montes-Osuna N, Cernava T, Gómez-Lama Cabanás C, Berg G, Mercado-Blanco J. Identification of Volatile Organic Compounds Emitted by Two Beneficial Endophytic Pseudomonas Strains from Olive Roots. PLANTS (BASEL, SWITZERLAND) 2022; 11:318. [PMID: 35161300 PMCID: PMC8840531 DOI: 10.3390/plants11030318] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta.
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Affiliation(s)
- Nuria Montes-Osuna
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Cordoba, Spain; (N.M.-O.); (C.G.-L.C.)
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Cordoba, Spain; (N.M.-O.); (C.G.-L.C.)
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria; (T.C.); (G.B.)
- Leibniz-Institute for Agricultural Engineering Potsdam, Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Cordoba, Spain; (N.M.-O.); (C.G.-L.C.)
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10
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Mukherjee A, Dechow-Seligmann G, Gallie J. Evolutionary flexibility in routes to mat formation by Pseudomonas. Mol Microbiol 2021; 117:394-410. [PMID: 34856020 DOI: 10.1111/mmi.14855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022]
Abstract
Many bacteria form mats at the air-liquid interface of static microcosms. These structures typically involve the secretion of exopolysaccharides, the production of which is often controlled by the secondary messenger c-di-GMP. Mechanisms of mat formation have been particularly well characterized in Pseudomonas fluorescens SBW25; stimuli or mutations that increase c-di-GMP production by diguanylate cyclases (WspR, AwsR, and MwsR) result in the secretion of cellulose and mat formation. Here, we characterize and compare mat formation in two close relatives of SBW25: Pseudomonas simiae PICF7 and P. fluorescens A506. We find that PICF7-the strain more closely related to SBW25-can form mats through mutations affecting the activity of the same three diguanylate cyclases as SBW25. However, instead of cellulose, these mutations activate production of the exopolysaccharide Pel. We also provide evidence for at least two further-as yet uncharacterized-routes to mat formation by PICF7. P. fluorescens A506, while retaining the same mutational routes to mat formation as SBW25 and PICF7, preferentially forms mats by a semi-heritable mechanism that culminates in Psl and Pga over-production. Our results demonstrate a high level of evolutionary flexibility in the molecular and structural routes to mat formation, even among close relatives.
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Affiliation(s)
- Anuradha Mukherjee
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Gunda Dechow-Seligmann
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Jo Y, Back CG, Kim KH, Chu H, Lee JH, Moh SH, Cho WK. Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits. Int J Mol Sci 2021; 22:6202. [PMID: 34201359 PMCID: PMC8227054 DOI: 10.3390/ijms22126202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/05/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022] Open
Abstract
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.
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Affiliation(s)
- Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
| | - Chang-Gi Back
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 55365, Korea;
| | - Kook-Hyung Kim
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
| | - Hyosub Chu
- R&D Division, BERTIS Inc., Seongnam-si 13605, Korea;
| | - Jeong Hun Lee
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (J.H.L.); (S.H.M.)
| | - Sang Hyun Moh
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (J.H.L.); (S.H.M.)
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
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Evaluation of Indigenous Olive Biocontrol Rhizobacteria as Protectants against Drought and Salt Stress. Microorganisms 2021; 9:microorganisms9061209. [PMID: 34204989 PMCID: PMC8230297 DOI: 10.3390/microorganisms9061209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022] Open
Abstract
Stress caused by drought and salinity may compromise growth and productivity of olive (Olea europaea L.) tree crops. Several studies have reported the use of beneficial rhizobacteria to alleviate symptoms produced by these stresses, which is attributed in some cases to the activity of 1-aminocyclopropane-1-carboxylic acid deaminase (ACD). A collection of beneficial olive rhizobacteria was in vitro screened for ACD activity. Pseudomonas sp. PICF6 displayed this phenotype and sequencing of its genome confirmed the presence of an acdS gene. In contrast, the well-known root endophyte and biocontrol agent Pseudomonas simiae PICF7 was defective in ACD activity, even though the presence of an ACD-coding gene was earlier predicted in its genome. In this study, an unidentified deaminase was confirmed instead. Greenhouse experiments with olive ‘Picual’ plants inoculated either with PICF6 or PICF7, or co-inoculated with both strains, and subjected to drought or salt stress were carried out. Several physiological and biochemical parameters increased in stressed plants (i.e., stomatal conductance and flavonoids content), regardless of whether or not they were previously bacterized. Results showed that neither PICF6 (ACD positive) nor PICF7 (ACD negative) lessened the negative effects caused by the abiotic stresses tested, at least under our experimental conditions.
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Gómez-Lama Cabanás C, Fernández-González AJ, Cardoni M, Valverde-Corredor A, López-Cepero J, Fernández-López M, Mercado-Blanco J. The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense. J Fungi (Basel) 2021; 7:jof7030194. [PMID: 33803181 PMCID: PMC8002102 DOI: 10.3390/jof7030194] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).
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Affiliation(s)
- Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda, 18008 Granada, Spain; (A.J.F.-G.); (M.F.-L.)
| | - Martina Cardoni
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Javier López-Cepero
- Departamento Técnico de Coplaca S.C. Organización de Productores de Plátanos, Avd. de Anaga, 11-38001 Santa Cruz de Tenerife, Spain;
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda, 18008 Granada, Spain; (A.J.F.-G.); (M.F.-L.)
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
- Correspondence: ; Tel.: +34-957-499261
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