Microbial Control of Crop Diseases: Limitations and Optimizations

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 19924

Special Issue Editor

Unit of Environment Chemistry and Interactions with Living Organisms, University of the Littoral Opal Coast, France
Interests: biological control of fungal diseases; resistance inducers; plant pathology; plant-fungi interactions; arbuscular mycorrhizal fungi; bacterial biocontrol agents

Special Issue Information

Dear Colleagues,

The world’s population is expected to reach 9.8 billion in 2050. This increase will require the intensification of crops and make their exploitation more sustainable. Intensive agriculture, as practiced over the last 50 years, has depleted natural resources and compromised the sustainability of this mode of production. The announced challenge will require producing twice as much while responding to the emergence of unprecedented constraints: climate change, the energy transition, and increased competition for non-renewable natural resources (soil and water).

The number of studies on the development of alternative solutions, such as the use of microbial biological control agents (MBCAs), to suppress or manage pathogen development has significantly grown over the past 30 years. Despite their effectiveness in the lab, their effectiveness under greenhouse or field conditions is often disappointing. Moreover, effective solutions for controlling diseases remain insufficiently proposed to farmers.

This Special Issue will focus on “Microbial Control of Crop Diseases: Limitations and Optimizations”. We welcome original research articles, reviews, and opinion pieces on any related topic, including the development of new agent screening methods; the factors involved in the erosion of biocontrol effectiveness; biocontrol mechanisms and their modulation with regard to plant physiology, plant genotype, or the growing conditions of MCBAs; implications of the combination of various modes of action for biocontrol effectiveness; population modeling of applied MBCAs; and possible risks of MBCAs and their secondary metabolites for humans or non-targeted organisms.

Dr. Maryline Magnin-Robert
Guest Editor

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Keywords

  • Microbial biological control agents
  • Plant diseases
  • Novel screening approaches
  • Indirect mechanisms and direct action on pathogens
  • Mixed modes of action
  • Factors influencing protection effectiveness

Published Papers (7 papers)

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Research

17 pages, 3599 KiB  
Article
Potential of Pseudomonas and Trichoderma from the Brazilian Amazon as Biocontrol Agents against the Wheat Blast Disease
by Maikon Richer de Azambuja Pereira, Silvino Intra Moreira, Abimael Gomes da Silva, Tiago Calves Nunes, Samara Nunes Campos Vicentini, Davi Prata da Silva, Patrícia Ricardino da Silveira, Tamiris Yoshie Kiyama de Oliveira, Tatiane Carla Silva, Deila Magna dos Santos Botelho, Mario Lúcio Vilela Resende and Paulo Cezar Ceresini
Agronomy 2022, 12(9), 2003; https://doi.org/10.3390/agronomy12092003 - 25 Aug 2022
Viewed by 2000
Abstract
Blast is one of the most significant wheat diseases, causing high yield losses in susceptible varieties under favorable conditions in Latin America, Southeastern Asia and Eastern Africa. The disease is caused by the ascomycetous fungal pathogen Pyricularia oryzae Triticum lineage (PoTl). [...] Read more.
Blast is one of the most significant wheat diseases, causing high yield losses in susceptible varieties under favorable conditions in Latin America, Southeastern Asia and Eastern Africa. The disease is caused by the ascomycetous fungal pathogen Pyricularia oryzae Triticum lineage (PoTl). Chemical control with fungicides has been used as a management strategy; however, the effectiveness of the major classes of high-risk site-specific systemic fungicides has been reduced due to the widespread prevalence of resistance, especially in Brazil. Biological control is seen as a highly important and sustainable strategy to minimize the impact of yield losses associated with wheat blast in areas where fungicides are ineffective. In our study, we specifically aimed to determine the biological control potential of the three isolates of fluorescent Pseudomonas and three of Trichoderma as the antagonists of PoTl, both in in vitro and under greenhouse conditions. Additionally, we aimed to describe the ultrastructural interactions among the biocontrol agents and the pathogen in vitro by means of scanning electron microscopy (SEM). Fluorescent P. wayambapalatensis ‘Amana’ or Pseudomonas sp. nov. ‘Yara’, both from the P. putida group, and Trichoderma koningiopsis ‘Cachara’ significantly reduced PoTl in vitro mycelial growth and the blast disease severity on wheat plants. The SEM analyses revealed ultrastructural antagonistic mechanisms: biofilm formation, direct antagonism and mycoparasitism. Further research on the topic should include the development of stable formulations of the Pseudomonas- and Trichoderma-based biocontrol agents selected in our study for managing the wheat blast disease and the field tests of the biofungicide formulations obtained thereafter. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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15 pages, 2629 KiB  
Article
Bioprospecting Fluorescent Pseudomonas from the Brazilian Amazon for the Biocontrol of Signal Grass Foliar Blight
by Samara Nunes Campos Vicentini, Giselle de Carvalho, Loane Dantas Krug, Tiago Calves Nunes, Abimael Gomes da Silva, Silvino Intra Moreira, Lucas Matheus de Deus Paes Gonçalves, Tatiane Carla Silva and Paulo Cezar Ceresini
Agronomy 2022, 12(6), 1395; https://doi.org/10.3390/agronomy12061395 - 10 Jun 2022
Cited by 3 | Viewed by 2056
Abstract
Biological control is considered the only viable integrated disease management practice for controlling the widely distributed and destructive foliar blight and sudden death disease caused by the fungus Rhizoctonia solani AG-1 IA on signal grass (Urochloa brizantha) pastures. Since major signal [...] Read more.
Biological control is considered the only viable integrated disease management practice for controlling the widely distributed and destructive foliar blight and sudden death disease caused by the fungus Rhizoctonia solani AG-1 IA on signal grass (Urochloa brizantha) pastures. Since major signal grass varieties are highly susceptible and fungicide sprays are not labeled for grass pasture cropping systems, biological control is sought as an alternative for managing this fungal disease. In this study, 24 fluorescent Pseudomonas isolates obtained from naturally suppressive soils from the Amazon biome were bio-prospected for their role as biocontrol agents against R. solani AG-1 IA. Based on in vitro antagonism, three isolates (Amana, Poti, and Yara) were selected for further in vivo assays. Multilocus phylogenetic analysis indicated that Amana and Yara were grouped into the Pseudomonas putida group while Poti was grouped into the Pseudomonas asplenii group, and could well constitute a new Pseudomonas species. For in vivo biocontrol assays, the biocontrol agents were applied either via seed-treatment or via foliar spray. All three isolates produced siderophores and solubilized phosphate, while Amana and Poti showed protease and chitinase in vitro activity. Foliar application of P. putida Amana from Amazonian suppressive soils resulted in a significant reduction of the foliar blight disease severity on signal grass. We discuss further steps for the development and labeling of Pseudomonas-based biofungicides for managing the foliar blight disease on signal grass pastures in Brazil. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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10 pages, 2487 KiB  
Communication
Antagonism of Bacillus velezensis Isolate from Anaerobically Digested Dairy Slurry against Fusarium Wilt of Spinach
by Tomomi Sugiyama, Keiko T. Natsuaki, Naoto Tanaka, Yuh Shiwa and Mami Irie
Agronomy 2022, 12(5), 1058; https://doi.org/10.3390/agronomy12051058 - 28 Apr 2022
Cited by 1 | Viewed by 1540
Abstract
This study was designed to assess the suppressive effects of various anaerobically digested slurries (ADSs), and the microorganisms inhabiting them, against Fusarium wilt in spinach. We used five different ADSs from a range of source materials (dairy cow manure, sewage sludge, food garbage, [...] Read more.
This study was designed to assess the suppressive effects of various anaerobically digested slurries (ADSs), and the microorganisms inhabiting them, against Fusarium wilt in spinach. We used five different ADSs from a range of source materials (dairy cow manure, sewage sludge, food garbage, pig manure, night soil sludge), combined in different proportions. All five raw ADSs suppressed the growth of Fusarium oxysporum f. sp. spinaciae (Fos) on agar plates using a co-culture test. In contrast, filtrate ADSs did not suppress the growth of Fos. In total, 32 bacterial strains were isolated from five ADSs, and eight isolates showed antagonistic activities against Fos. Based on 16S rDNA sequences, the strain AD-3 isolated from ADS from dairy cow manure belonged to Bacillus velezensis. Genome analysis revealed that AD-3 had two kinds of genes related to the production of the non-ribosomal lipopeptides, fengycin/plipastatin (pps genes), and surfactin (srf genes). In pot assays, inoculation of AD-3 (1.0 × 106 CFU·g−1 dry soil) into Fos-infected soil (1.0 × 105 bud-cells·g−1 dry soil) significantly reduced the severity of Fusarium wilt disease at 28 d after seedling. The percentage reductions in disease severity in two replicates were 64.3% and 44.3%, respectively. Thus, bacterial strain AD-3 could be applied to reduce Fusarium wilt in spinach. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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15 pages, 3388 KiB  
Article
Effect of the Combined Treatments with LC2017 and Trichoderma atroviride Strain I-1237 on Disease Development and Defense Responses in Vines Infected by Lasiodiplodia theobromae
by Pedro Reis, Vincenzo Mondello, Inês Diniz, Artur Alves, Cecília Rego and Florence Fontaine
Agronomy 2022, 12(5), 996; https://doi.org/10.3390/agronomy12050996 - 21 Apr 2022
Cited by 4 | Viewed by 3836
Abstract
Grapevine trunk diseases constitute one of the major problems for viticulture worldwide, with Botryosphaeria dieback considered as one of the most important of these diseases. In this work, we aimed to (i) evaluate the effect of the combination of two products, Esquive® [...] Read more.
Grapevine trunk diseases constitute one of the major problems for viticulture worldwide, with Botryosphaeria dieback considered as one of the most important of these diseases. In this work, we aimed to (i) evaluate the effect of the combination of two products, Esquive® (a Trichoderma-based product) and LC2017 (a low-copper-based product), in the control of Lasiodiplodia theobromae, by evaluating the internal lesion length caused by inoculation of this pathogen on greenhouse kept grapevines of cvs Cabernet Sauvignon and Touriga Nacional and, (ii) investigating their elicitor effect on plant defense responses, through the analysis of the expression of a set of genes. The pathogen was always re-isolated from the infected tissues and was able to cause wood discoloration. Touriga Nacional exhibited longer lesions than Cabernet Sauvignon, and the application of both products did not appear to reduce lesion length when compared to LC2017 applied alone. The elicitor effect of LC2017 on plant defense was confirmed by gene expression analysis, and no significant differences were found between plants treated with LC2017 and with both products. Moreover, a specific response related to the cultivar was verified, but this apparently unique interaction between product, cultivar and pathogen remains to be further investigated. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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11 pages, 1313 KiB  
Article
Isolation and Identification of Lipopeptide-Producing Bacillus velezensis Strains from Wheat Phyllosphere with Antifungal Activity against the Wheat Pathogen Zymoseptoria tritici
by Rémi Platel, Mélodie Sawicki, Qassim Esmaeel, Béatrice Randoux, Pauline Trapet, Mohammed El Guilli, Noureddine Chtaina, Ségolène Arnauld, Alexandre Bricout, Alice Rochex, Natacha Bourdon, Patrice Halama, Cédric Jacquard, Essaid Ait Barka, Philippe Reignault, Maryline Magnin-Robert and Ali Siah
Agronomy 2022, 12(1), 95; https://doi.org/10.3390/agronomy12010095 - 31 Dec 2021
Cited by 11 | Viewed by 2611
Abstract
Septoria tritici blotch, caused by the fungal pathogen Zymoseptoria tritici, is a highly significant disease on wheat crops worldwide. The objective of the present study was to find out new bacterial strains with bio-antimicrobial activity against Z. tritici. Two phyllospheric bacteria [...] Read more.
Septoria tritici blotch, caused by the fungal pathogen Zymoseptoria tritici, is a highly significant disease on wheat crops worldwide. The objective of the present study was to find out new bacterial strains with bio-antimicrobial activity against Z. tritici. Two phyllospheric bacteria (S1 and S6) were isolated from wheat ears and identified as Bacillus velezensis strains according to 16S rRNA Sanger sequencing. Antagonistic assays performed with either living strains or cell-free culture filtrates showed significant in vitro antifungal activities against Z. tritici. For the culture filtrates, the half-maximal inhibitory dilution and the minimal inhibitory dilution were 1.4% and 3.7% for the strain S1, and 7.4% and 15% for the strain S6, respectively. MALDI—ToF analysis revealed that both strains synthesize cyclic lipopeptides but from different families. Interestingly, only strain S1 produces putative bacillomycin D. Such differential lipopeptide production patterns might explain the difference observed between the antifungal activity of the culture filtrates of the two strains. This study allows the identification of new lipopeptide-producing strains of B. velezensis with a high potential of application for the biocontrol of Z. tritici. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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17 pages, 3879 KiB  
Article
Unraveling the Association between Metabolic Changes in Inter-Genus and Intra-Genus Bacteria to Mitigate Clubroot Disease of Chinese Cabbage
by Lanfang Wei, Jun Yang, Waqar Ahmed, Xinying Xiong, Qi Liu, Qiong Huang and Guanghai Ji
Agronomy 2021, 11(12), 2424; https://doi.org/10.3390/agronomy11122424 - 28 Nov 2021
Cited by 14 | Viewed by 2090
Abstract
Clubroot disease caused by the obligate parasite Plasmodiophora brassicae is a serious threat to cabbage production worldwide. Current clubroot control primarily relies on a fungicide, but this has a negative impact on the environment and the use of a single biocontrol agent cannot [...] Read more.
Clubroot disease caused by the obligate parasite Plasmodiophora brassicae is a serious threat to cabbage production worldwide. Current clubroot control primarily relies on a fungicide, but this has a negative impact on the environment and the use of a single biocontrol agent cannot efficiently control the disease. Thus, the combined application of different biocontrol agents has been proposed as a promising alternative. In this study, we used bacterial biocontrol agents as a co-culture (inter-genus and intra-genus) and mono-culture to mitigate the clubroot disease of Chinese cabbage. We evaluated their biocontrol effect and plant growth promoter (PGP) traits in in vitro and in vivo experiments. This study revealed that the inter-genus bacterial co-culture significantly suppresses the incidence of clubroot disease and enhances plant growth compared with intra-genus and mono-culture. In pairwise interaction, we observed that Bacillus cereus BT-23 promotes the growth of Lysobacter antibioticus 13-6 (inter-genus bacterial co-culture), whereas L. capsici ZST1-2 and L. antibioticus 13-6 (intra-genus microbial co-culture) are antagonists to each other. Furthermore, a total of 5575 metabolites, 732 differentially expressed metabolites (DEMs), and 510 unique metabolites were detected through the LC-MS/MS technique in the bacterial co-culture. The number of unique metabolites in inter-genus bacterial co-culture (393 metabolites) was significantly higher than in the intra-genus bacterial co-culture (117 metabolites). Further analysis of DEMs showed that the DEMs were mainly involved in four kinds of metabolism pathways, i.e., carbohydrate metabolism, amino metabolism, nucleotide metabolism, and metabolism of cofactors and vitamins. The contents of some secondary metabolites with biocontrol activity and plant growth-promoting functions were increased in inter-genus bacterial co-culture, indicating that inter-genus bacterial co-culture has a solid potential to suppress clubroot disease. We conclude that the inter-genus bacterial interaction changes the community metabolism and improves several secondary metabolites functions with respect to disease control and PGP ability. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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18 pages, 2558 KiB  
Article
The Influence of Temperature on the Growth, Sporulation, Colonization, and Survival of Trichoderma spp. in Grapevine Pruning Wounds
by Guzmán Carro-Huerga, Sara Mayo-Prieto, Álvaro Rodríguez-González, Samuel Álvarez-García, Santiago Gutiérrez and Pedro A. Casquero
Agronomy 2021, 11(9), 1771; https://doi.org/10.3390/agronomy11091771 - 03 Sep 2021
Cited by 8 | Viewed by 4733
Abstract
Trichoderma is a genus of fungi used for the biological control of plant diseases and a large number of its bio-formulates are available in the market. However, its efficacy under field conditions remains unclear, especially for the protection of grapevine plants against Grapevine [...] Read more.
Trichoderma is a genus of fungi used for the biological control of plant diseases and a large number of its bio-formulates are available in the market. However, its efficacy under field conditions remains unclear, especially for the protection of grapevine plants against Grapevine Trunk Diseases (GTDs). These diseases are caused by a complex of fungal pathogens whose main point of entrance into the affected plants is through pruning wounds. In this research, different Trichoderma native strains have been evaluated according to their ability to grow at different temperatures and their capacity to colonize pruning wounds in adverse climatic conditions. Strains from section Trichoderma have adapted to cooler conditions. On the other hand, strains from clade Harzianum/Virens grow at higher temperatures. However, differences can also be found between strains inside the same clade/section. Native strains were able to colonize more than 70% of vine pruning wounds in winter conditions. The Trichoderma strain T154 showed a significantly higher re-isolation degree from vine plants and its concentration was optimized for spraying onto vine plants. In conclusion, Trichoderma native strains are better adapted to survive in a changing environment, and they could give better protection to grapevine plants in co-evolution with each specific vineyard. Full article
(This article belongs to the Special Issue Microbial Control of Crop Diseases: Limitations and Optimizations)
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