Research

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28 pages, 4768 KiB

Open AccessArticle

Transcriptome and Secretome Analyses of Endophyte Methylobacterium mesophilicum and Pathogen Xylella fastidiosa Interacting Show Nutrient Competition

by Manuella Nobrega Dourado, Paulo Marques Pierry, Oseias Rodrigues Feitosa-Junior, Guillermo Uceda-Campos, Deibs Barbosa, Paulo A. Zaini, Abhaya M. Dandekar, Aline Maria da Silva and Welington Luiz Araújo

Microorganisms 2023, 11(11), 2755; https://doi.org/10.3390/microorganisms11112755 - 11 Nov 2023

Viewed by 1241

Abstract

Xylella fastidiosa is the causal agent of several plant diseases affecting fruit and nut crops. Methylobacterium mesophilicum strain SR1.6/6 was isolated from Citrus sinensis and shown to promote plant growth by producing phytohormones, providing nutrients, inhibiting X. fastidiosa, and preventing Citrus Variegated [...] Read more.

Xylella fastidiosa is the causal agent of several plant diseases affecting fruit and nut crops. Methylobacterium mesophilicum strain SR1.6/6 was isolated from Citrus sinensis and shown to promote plant growth by producing phytohormones, providing nutrients, inhibiting X. fastidiosa, and preventing Citrus Variegated Chlorosis. However, the molecular mechanisms involved in the interaction among these microbes are still unclear. The present work aimed to analyze physiological and molecular aspects of M. mesophilicum SR1.6/6 and X. fastidiosa 9a5c in co-culture. The transcriptome and secretome analyses indicated that X. fastidiosa down-regulates cell division and transport genes and up-regulates stress via induction of chaperones and pathogenicity-related genes including, the lipase-esterase LesA, a protease, as well as an oligopeptidase in response to M. mesophilicum competition. On the other hand, M. mesophilicum also down-regulated transport genes, except for iron uptake, which was up-regulated. Secretome analysis identified four proteins in M. mesophilicum exclusively produced in co-culture with X. fastidiosa, among these, three are related to phosphorous uptake. These results suggest that M. mesophilicum inhibits X. fastidiosa growth mainly due to nutrient competition for iron and phosphorous, thus promoting X. fastidiosa starvation, besides producing enzymes that degrade X. fastidiosa cell wall, mainly hydrolases. The understanding of these interactions provides a direction for control and management of the phytopathogen X. fastidiosa, and consequently, helps to improve citrus growth and productivity. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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13 pages, 2642 KiB

Open AccessArticle

In Vitro Evaluation of Azoxystrobin, Boscalid, Fentin-Hydroxide, Propiconazole, Pyraclostrobin Fungicides against Alternaria alternata Pathogen Isolated from Carya illinoinensis in South Africa

by Conrad Chibunna Achilonu, Marieka Gryzenhout, Soumya Ghosh and Gert Johannes Marais

Microorganisms 2023, 11(7), 1691; https://doi.org/10.3390/microorganisms11071691 - 29 Jun 2023

Cited by 3 | Viewed by 1656

Abstract

Black spot disease or Alternaria black spot (ABS) of pecan (Carya illinoinensis) in South Africa is caused by Alternaria alternata. This fungal pathogen impedes the development of pecan trees and leads to low yield in pecan nut production. The present [...] Read more.

Black spot disease or Alternaria black spot (ABS) of pecan (Carya illinoinensis) in South Africa is caused by Alternaria alternata. This fungal pathogen impedes the development of pecan trees and leads to low yield in pecan nut production. The present study investigated the in vitro effect of six fungicides against the mycelial growth of A. alternata isolates from ABS symptoms. Fungicides tested include Tilt (propiconazole), Ortiva (azoxystrobin), AgTin (fentin hydroxide), and Bellis (boscalid + pyraclostrobin). All fungicides were applied in 3 concentrations (0.2, 1, and 5 μg mL⁻¹). Tilt and Bumper 250 EC containing propiconazole active ingredient (demethylation Inhibitors) were the most effective and inhibited all mycelial growth from up to 6 days post-incubation. The other active ingredients (succinate dehydrogenase inhibitors, organotin compounds, and quinone outside inhibitors) showed 75–85% mycelial growth inhibition. The effective concentration to inhibit mycelial growth by 50% (EC₅₀) was estimated for each isolate and fungicide. The overall mean EC₅₀ values for each fungicide on the six isolates were 1.90 μg mL⁻¹ (Tilt), 1.86 μg mL⁻¹ (Ortiva), 1.53 μg mL⁻¹ (AgTin), and 1.57 μg mL⁻¹ for (Bellis). This initial screening suggested that propiconazole fungicide was the most effective for future field trials test and how these fungicides could be used in controlling ABS disease. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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12 pages, 989 KiB

Open AccessArticle

Microbiota Assessment of Fresh-Cut Apples Packaged in Two Different Films

by Joana Madureira, Sara Gonçalves, Celestino Santos-Buelga, Fernanda M. A. Margaça, Isabel C. F. R. Ferreira, Lillian Barros and Sandra Cabo Verde

Microorganisms 2023, 11(5), 1157; https://doi.org/10.3390/microorganisms11051157 - 28 Apr 2023

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Abstract

The aim of this work was to assess the natural microbiota of packed fresh-cut apples during refrigerated storage. Two different films were tested for the package, a biodegradable (PLA) film and a conventional and commercial one (OPP). Two antioxidant additives were applied, a [...] Read more.

The aim of this work was to assess the natural microbiota of packed fresh-cut apples during refrigerated storage. Two different films were tested for the package, a biodegradable (PLA) film and a conventional and commercial one (OPP). Two antioxidant additives were applied, a natural olive pomace extract and the commercial ascorbic acid used by the industries. The results revealed lower bacteria counts in samples with olive pomace extract and PLA films than in those with ascorbic acid and OPP films after 5 and 12 days of storage. These findings suggest that the use of such natural extracts as additives in fruits could delay the growth of mesophilic bacteria. The characterization and identification of the bacterial isolates from fresh-cut apple samples showed that the most prevalent species were Citrobacter freundii, Staphylococcus warneri, Pseudomonas oryzihabitans, Alcalinogenes faecalis, Corynebacterium jeikeium, Micrococcus spp., Pantoea aglomerans and Bacillus spp. Furthermore, an increase in the microbial diversity during the storage time at refrigerated temperatures was observed, except for the sample treated with olive pomace extract and packaged in OPP film. The highest microbial diversity was found for samples with ascorbic acid as an additive. This could indicate a negative effect of ascorbic acid on the microbial inhibition of apple slices. The natural olive pomace extract demonstrated potential as an antimicrobial additive for fresh-cut apples. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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17 pages, 9784 KiB

Open AccessArticle

Differences in Soil Microbial Communities between Healthy and Diseased Lycium barbarum cv. Ningqi-5 Plants with Root Rot

by Chenbo Jia, Yingrui An, Zhongyu Du, Huihui Gao, Jianyu Su and Chunyan Xu

Microorganisms 2023, 11(3), 694; https://doi.org/10.3390/microorganisms11030694 - 08 Mar 2023

Cited by 3 | Viewed by 1777

Abstract

For a long time, the development of the Lycium barbarum industry has been seriously restricted by root rot disease. In general, the occurrence of plant root rot is considered to be closely related to the composition and diversity of the soil microbial community. [...] Read more.

For a long time, the development of the Lycium barbarum industry has been seriously restricted by root rot disease. In general, the occurrence of plant root rot is considered to be closely related to the composition and diversity of the soil microbial community. It is critical to understand the relationship between the occurrence of root rot in L. barbarum and the soil microbial composition. In this study, samples of the rhizosphere, rhizoplane, and root zone were collected from diseased and healthy plants. The V3–V4 region of bacterial 16S rDNA and the fungal ITS1 fragment of the collected samples were sequenced using Illumina MiSeq high-throughput sequencing technology. The sequencing results were first quality controlled and then aligned with the relevant databases for annotation and analysis. The richness of fungal communities in the rhizoplane and root zone of the healthy plants was significantly higher than that of the diseased plants (p < 0.05), and the community evenness and diversity of all the rhizoplane samples were significantly different from those of the rhizosphere and root zone. The richness of the bacterial communities in the rhizosphere and root zone of healthy plants was significantly greater than those of diseased plants (p < 0.05). The community composition of the rhizoplane was quite different from the other parts. The abundance of Fusarium in the rhizoplane and rhizosphere soil of diseased plants was higher than that in the corresponding parts of healthy plants. The abundances of Mortierella and Ilyonectria in the three parts of the healthy plants were correspondingly higher than those in the three parts of the diseased plants, and Plectosphaerella was the most abundant in the rhizoplane of diseased plants. There was little difference in the composition of the dominant bacteria at the phylum and genus levels between healthy plants and diseased plants, but the abundances of these dominant bacteria were different between healthy and diseased plants. Functional prediction showed that the bacterial community had the largest proportion of functional abundance belonging to metabolism. The functional abundances of the diseased plants, such as metabolism and genetic information processing, were lower than those of the healthy plants. The fungal community function prediction showed that the Animal Pathogen-Endophyte-Lichen Parasite-Plant Pathogen-Soil Saprotroph-Wood Saprotroph group had the largest functional abundance, and the corresponding fungi were Fusarium. In this study, we mainly discussed the differences in the soil microbial communities and their functions between the healthy and diseased L. barbarum cv. Ningqi-5, and predicted the functional composition of the microbial community, which is of great significance to understanding the root rot of L. barbarum. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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15 pages, 11791 KiB

Open AccessArticle

Epiphytic and Endophytic Fungi Colonizing Seeds of Two Poaceae Weed Species and Fusarium spp. Seed Degradation Potential In Vitro

by Jevgenija Ņečajeva, Anete Borodušķe, Vizma Nikolajeva, Māris Seņkovs, Ineta Kalniņa, Ance Roga, Edmunds Skinderskis and Dāvids Fridmanis

Microorganisms 2023, 11(1), 184; https://doi.org/10.3390/microorganisms11010184 - 11 Jan 2023

Cited by 3 | Viewed by 1570

Abstract

Fungi colonizing the surface and endosphere of two widespread Poaceae weed species, Avena fatua and Echinochloa crus-galli, were isolated to compare the taxonomic composition between the plant species, location, and year of the seed collection. The seed-degrading potential of Fusarium isolated from [...] Read more.

Fungi colonizing the surface and endosphere of two widespread Poaceae weed species, Avena fatua and Echinochloa crus-galli, were isolated to compare the taxonomic composition between the plant species, location, and year of the seed collection. The seed-degrading potential of Fusarium isolated from the seeds was tested by inoculating seeds of E. crus-galli with spore suspension. Molecular identification of epiphytic and endophytic fungal genera was performed by sequencing the ITS region of rDNA. Endophytes comprised of significantly lower fungal richness compared to epiphytes. A significant taxonomic overlap was observed between the endosphere and seed surface. The most abundant genera were Alternaria, Fusarium, Cladosporium, and Sarocladium. Analysis of similarities and hierarchical clustering showed that microbial communities were more dissimilar between the two plant species than between the years. Fusarium isolates with a high potential to infect and degrade E. crus-galli seeds in laboratory conditions belong to F. sporotrichioides and F. culmorum. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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16 pages, 1711 KiB

Open AccessArticle

Plant and Soil Core Mycobiomes in a Two-Year Sorghum–Legume Intercropping System of Underutilized Crops in South Africa

by Gilmore T. Pambuka, Tonjock Rosemary Kinge, Soumya Ghosh, Errol D. Cason, Martin M. Nyaga and Marieka Gryzenhout

Microorganisms 2022, 10(10), 2079; https://doi.org/10.3390/microorganisms10102079 - 20 Oct 2022

Cited by 3 | Viewed by 1781

Abstract

Fungal communities form close beneficial (mutualists) or detrimental (pathogens) associations with their plant hosts. Their diversity and abundance can be affected by agricultural practices which include cropping systems such as rotations and intercropping. Despite the importance of cropping systems in increasing productivity, knowledge [...] Read more.

Fungal communities form close beneficial (mutualists) or detrimental (pathogens) associations with their plant hosts. Their diversity and abundance can be affected by agricultural practices which include cropping systems such as rotations and intercropping. Despite the importance of cropping systems in increasing productivity, knowledge of the fungal mycobiome and the core inhabitants for under-utilised cereal and legume crops, particularly over a period, is still limited. The core mycobiomes in plant tissues and bulk soils of a cereal–legume intercrop were characterized over two years using high-throughput sequencing. The intercropping trial consisted of sorghum, Bambara groundnut, cowpea, dry bean, and soybean. A greater number of molecular operational taxonomic units (MOTUs) were found in plant tissues compared to those from the soils and between year one and year two. Principal coordinate analyses revealed that fungal communities for each year were relatively distinct, particularly for the soils. The core mycobiome was dominated by a Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Didymellaceae sp. 2 (Epicoccum), Fusarium sp. 2, Unidentified (Ascomycota), and Cryptococcus MOTUs that were present in all plant tissues and soils of year one and two. Other key MOTUs were only specific to a year, substrate, or crop. Although the mycobiome of sorghum were more distinct than the cores of the legumes, there were still MOTUs dominant across all of the crops. Characterization of this baseline core across two years provides insight into those fungi that are always present in these crops, and that could be utilized in improving crop performance and productivity. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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Review

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22 pages, 4134 KiB

Open AccessReview

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

by Magdalena Ptaszek, Loredana Canfora, Massimo Pugliese, Flavia Pinzari, Giovanna Gilardi, Paweł Trzciński and Eligio Malusà

Microorganisms 2023, 11(1), 224; https://doi.org/10.3390/microorganisms11010224 - 16 Jan 2023

Cited by 6 | Viewed by 3442

Abstract

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have [...] Read more.

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers’ point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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23 pages, 1790 KiB

Open AccessReview

Microbial Effectors: Key Determinants in Plant Health and Disease

by Jewel Nicole Anna Todd, Karla Gisel Carreón-Anguiano, Ignacio Islas-Flores and Blondy Canto-Canché

Microorganisms 2022, 10(10), 1980; https://doi.org/10.3390/microorganisms10101980 - 06 Oct 2022

Cited by 6 | Viewed by 4535

Abstract

Effectors are small, secreted molecules that alter host cell structure and function, thereby facilitating infection or triggering a defense response. Effectoromics studies have focused on effectors in plant–pathogen interactions, where their contributions to virulence are determined in the plant host, i.e., whether the [...] Read more.

Effectors are small, secreted molecules that alter host cell structure and function, thereby facilitating infection or triggering a defense response. Effectoromics studies have focused on effectors in plant–pathogen interactions, where their contributions to virulence are determined in the plant host, i.e., whether the effector induces resistance or susceptibility to plant disease. Effector molecules from plant pathogenic microorganisms such as fungi, oomycetes and bacteria are major disease determinants. Interestingly, the effectors of non-pathogenic plant organisms such as endophytes display similar functions but have different outcomes for plant health. Endophyte effectors commonly aid in the establishment of mutualistic interactions with the plant and contribute to plant health through the induction of systemic resistance against pathogens, while pathogenic effectors mainly debilitate the plant’s immune response, resulting in the establishment of disease. Effectors of plant pathogens as well as plant endophytes are tools to be considered in effectoromics for the development of novel strategies for disease management. This review aims to present effectors in their roles as promotors of health or disease for the plant host. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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