Dataset Information

Comprehensive Genomic Analysis of the Endophytic Bacillus altitudinis Strain GLB197, a Potential Biocontrol Agent of Grape Downy Mildew.

ABSTRACT: Bacillus has been extensively studied for agricultural application as a biocontrol agent. B. altitudinis GLB197, an endophytic bacterium isolated from grape leaves, exhibits distinctive inhibition to grape downy mildew based on unknown mechanisms. To determine the genetic traits involved in the mechanism of biocontrol and host-interaction traits, the genome sequence of GLB197 was obtained and further analyzed. The genome of B. altitudinis GLB197 consisted of one plasmid and a 3,733,835-bp circular chromosome with 41.56% G + C content, containing 3,770 protein-coding genes. Phylogenetic analysis of 17 Bacillus strains using the concatenated 1,226 single-copy core genes divided into different clusters was conducted. In addition, average nucleotide identity (ANI) values indicate that the current taxonomy of some B. pumilus group strains is incorrect. Comparative analysis of B. altitudinis GLB197 proteins with other B. altitudinis strains identified 3,157 core genes. Furthermore, we found that the pan-genome of B. altitudinis is open. The genome of B. altitudinis GLB197 contains one nonribosomal peptide synthetase (NRPS) gene cluster which was annotated as lichenysin. Interestingly, the cluster in B. altitudinis has two more genes than other Bacillus strains (lgrD and lgrB). The two genes were probably obtained via horizontal gene transfer (HGT) during the evolutionary process from Brevibacillus. Taken together, these observations enable the future application of B. altitudinis GLB197 as a biocontrol agent for control of grape downy mildew and promote our understanding of the beneficial interactions between B. altitudinis GLB197 and plants.

SUBMITTER: Zeng Q

PROVIDER: S-EPMC8502975 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundAs one of the main pathogens causing tea anthracnose disease, Colletotrichum gloeosporioides has brought immeasurable impact on the sustainable development of agriculture. Given the adverse effects of chemical pesticides to the environment and human health, biological control has been a focus of the research on this pathogen. Bacillus altitudinis GS-16, which was isolated from healthy tea leaves, had exhibited strong antagonistic activity against tea anthracnose disease.MethodsThe antifungal mechanism of the endophytic bacterium GS-16 against C. gloeosporioides 1-F was determined by dual-culture assays, pot experiments, cell membrane permeability, cellular contents, cell metabolism, and the activities of the key defense enzymes.ResultsWe investigated the possible mechanism of strain GS-16 inhibiting 1-F. In vitro, the dual-culture assays revealed that strain GS-16 had significant antagonistic activity (92.03%) against 1-F and broad-spectrum antifungal activity in all tested plant pathogens. In pot experiments, the disease index decreased to 6.12 after treatment with GS-16, indicating that strain GS-16 had a good biocontrol effect against tea anthracnose disease (89.06%). When the PE extract of GS-16 treated mycelial of 1-F, the mycelial appeared deformities, distortions, and swelling by SEM observations. Besides that, compared with the negative control, the contents of nucleic acids, protein, and total soluble sugar of GS-16 group were increased significantly, indicating that the PE extract of GS-16 could cause damage to integrity of 1-F. We also found that GS-16 obviously destroyed cellular metabolism and the normal synthesis of cellular contents. Additionally, treatment with GS-16 induced plant resistance by increasing the activities of the key defense enzymes PPO, SOD, CAT, PAL, and POD.ConclusionsWe concluded that GS-16 could damage cell permeability and integrity, destroy the normal synthesis of cellular contents, and induce plant resistance, which contributed to its antagonistic activity. These findings indicated that strain GS-16 could be used as an efficient microorganism for tea anthracnose disease caused by C. gloeosporioides.

Project description:This article introduces a dataset of high-resolution colour images of grapevines. It contains 99 images acquired in the vineyard from a cruising tractor. Each image includes the full foliage of a grapevine plant. These images display a diverse range of symptoms caused by the grapevine downy mildew (Plasmopara viticola), a major fungal disease. The dataset also includes various confounding factors, i.e. anomalies that are not related to the disease. These anomalies are the natural and common phenomena affecting vineyards such as results of mechanical wounds, necroses, chemical burns or yellowing and discolorations due to nutritional or hydric deficiencies. Images were acquired in-situ on "Le Domaine de la Grande Ferrade" a public experimental facility of INRAE, in the area of Bordeaux. Acquisitions took place at early fruiting stages (BBCH 75-79) corresponding to the main sanitary pressure during growth. The acquisition device, embedded on a vine tractor, is composed of an industrial colour camera synchronised with powerful flashes. The purpose of this device is to produce a "day for night" effect that mitigates the variation of sunlight. It enables to homogenise images acquired during different weathers and time of the day and to ensure that the foreground (containing foliage) displays appropriate brightness, with minimum shadows while the background is darker. The images of the dataset were annotated manually by photo-interpretation with a careful review of expertise regarding phytopathology and physiological disorders. The annotation process consists in associating pixels with a class that defines its membership to a type of organ and its physiological state. Pixels from healthy, symptomatic or abnormal grapevine tissues were labelled into seven classes: "Limbus", "Leaf edges", "Berries", "Stems", "Foliar mildew", "Berries mildew" and "Anomalies". The annotation is achieved with the GIMP2 software as mask images where the value attributed to each pixel corresponds to one of the seven considered classes.

Dataset Information

Comprehensive Genomic Analysis of the Endophytic Bacillus altitudinis Strain GLB197, a Potential Biocontrol Agent of Grape Downy Mildew.

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