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

2021 ◽  
Vol 12 ◽  
Author(s):  
Qingchao Zeng ◽  
Jianbo Xie ◽  
Yan Li ◽  
Tantan Gao ◽  
Xun Zhang ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Biocontrol Agent ◽  
Evolutionary Process ◽  
Genomic Analysis ◽  
Endophytic Bacterium ◽  
Future Application ◽  
Circular Chromosome ◽  
Genetic Traits ◽  
Grape Downy Mildew ◽  
Core Genes

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.

scholarly journals Isolation and Characterization of a Cold-Tolerant Strain of Fusarium proliferatum, a Biocontrol Agent of Grape Downy Mildew

2001 ◽  
Vol 91 (11) ◽  
pp. 1062-1068 ◽  
Author(s):  
Shlomo Bakshi ◽  
Abraham Sztejnberg ◽  
Oded Yarden
Keyword(s):  
Downy Mildew ◽  
Radial Growth ◽  
Biocontrol Agent ◽  
Plasmopara Viticola ◽  
Fusarium Proliferatum ◽  
Tolerant Strain ◽  
Gus Reporter ◽  
Isolation And Characterization ◽  
Cold Tolerant ◽  
Grape Downy Mildew

A cold-tolerant strain of the mycoparasite Fusarium proliferatum was isolated following UV mutagenesis of the G6 strain, which is a biocontrol agent of grape downy mildew. The isolated strain (designated 1505) exhibited radial growth two to threefold that of the parent strain when grown at 13°C, which is generally suboptimal for growth of Fusarium spp., but desirable for its host, Plasmopara viticola. This rapid growth was correlated with improved biological control of P. viticola, determined by a detached-leaf assay. Even though radial growth of strain 1505 at higher temperatures was slower than that of G6 and the strain failed to conidiate, there was no reduction in biocontrol efficacy. Significantly higher levels of extracellular β-glucosidase and endo-1,4-β-glucanase activity were measured in the culture filtrate of strain 1505 relative to that of strain G6. A DNA-mediated transformation procedure that included the introduction of antibiotic resistance and a GUS reporter gene system was adapted for F. proliferatum. Using the GUS-engineered strains, we demonstrated that both G6 and 1505 exhibit the characteristic coiling and penetration of host structures.

scholarly journals Genomic Analysis of a Newly Isolated Acidithiobacillus ferridurans JAGS Strain Reveals Its Adaptation to Acid Mine Drainage

Minerals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 74
Author(s):  
Jinjin Chen ◽  
Yilan Liu ◽  
Patrick Diep ◽  
Radhakrishnan Mahadevan
Keyword(s):  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Genomic Structure ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Protein Coding ◽  
Acid Mine ◽  
Inorganic Ion ◽  
Unique Genes ◽  
Core Genes

Acidithiobacillus ferridurans JAGS is a newly isolated acidophile from an acid mine drainage (AMD). The genome of isolate JAGS was sequenced and compared with eight other published genomes of Acidithiobacillus. The pairwise mutation distance (Mash) and average nucleotide identity (ANI) revealed that isolate JAGS had a close evolutionary relationship with A. ferridurans JCM18981, but whole-genome alignment showed that it had higher similarity in genomic structure with A. ferrooxidans species. Pan-genome analysis revealed that nine genomes were comprised of 4601 protein coding sequences, of which 43% were core genes (1982) and 23% were unique genes (1064). A. ferridurans species had more unique genes (205–246) than A. ferrooxidans species (21–234). Functional gene categorizations showed that A. ferridurans strains had a higher portion of genes involved in energy production and conversion while A. ferrooxidans had more for inorganic ion transport and metabolism. A high abundance of kdp, mer and ars genes, as well as mobile genetic elements, was found in isolate JAGS, which might contribute to its resistance to harsh environments. These findings expand our understanding of the evolutionary adaptation of Acidithiobacillus and indicate that A. ferridurans JAGS is a promising candidate for biomining and AMD biotreatment applications.

scholarly journals Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 54 ◽  
Author(s):  
Yoyeon Cha ◽  
Jihwan Chun ◽  
Bokyung Son ◽  
Sangryeol Ryu
Keyword(s):  
Staphylococcus Aureus ◽  
Biocontrol Agent ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Experimental Setting ◽  
Human Pathogens ◽  
Bacteriophage Therapy ◽  
Chromosomal Structure ◽  
Inhibition Effect ◽  
Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

scholarly journals Timing of Grape Downy Mildew Onset in Bordeaux Vineyards

2019 ◽  
Vol 109 (5) ◽  
pp. 787-795 ◽  
Author(s):  
Mathilde Chen ◽  
François Brun ◽  
Marc Raynal ◽  
David Makowski
Keyword(s):  
Downy Mildew ◽  
Severe Disease ◽  
Survival Analyses ◽  
Fungicide Treatment ◽  
Grapevine Downy Mildew ◽  
Local Characteristics ◽  
South West ◽  
Disease Surveys ◽  
Grape Downy Mildew ◽  
Regional Disease

Grapevine downy mildew (GDM) is a severe disease of grapevines. Because of the lack of reliable information about the dates of GDM symptom onset, many vine growers begin fungicide treatments early in the season. We evaluate the extent to which such preventive treatments are justified. Observational data for 266 untreated sites for the years between 2010 and 2017 were used to estimate the timing of GDM onset on vines and bunches of grapes in South West France (Bordeaux region) through survival analyses. The onset of GDM was not apparent on vines and bunches before early to mid-May, and the rate of GDM symptom appearance was highly variable across years. Depending on the year, 50% of the plots displayed symptoms between mid-May and late June for vines. For several years, our statistical analysis revealed that the proportion of plots with no symptoms was high in early August on vines (27.5 and 43.7% in 2013 and 2016) and on bunches (between 23 and 79% in 2011, 2013, and 2016). We found a significant effect of the amount of rainfall in spring on the date of symptom appearance. These results indicate that preventive fungicide application is unjustified in many vineyards, and that regional disease surveys should be used to adjust fungicide treatment dates according to local characteristics, in particular according to rainfall conditions in spring.

scholarly journals Evaluation of a Disease Warning System for Downy Mildew of Grapes

Plant Disease ◽  
2000 ◽  
Vol 84 (5) ◽  
pp. 549-554 ◽  
Author(s):  
L. V. Madden ◽  
M. A. Ellis ◽  
N. Lalancette ◽  
G. Hughes ◽  
L. L. Wilson
Keyword(s):  
Linear Model ◽  
Downy Mildew ◽  
Environmental Conditions ◽  
Generalized Linear Model ◽  
Disease Incidence ◽  
Warning System ◽  
Plasmopara Viticola ◽  
Effective Control ◽  
Subsequent Infection ◽  
Grape Downy Mildew

An electronic warning system for grape downy mildew— based on models for the infection of leaves of Vitis lambrusca, production of sporangia by Plasmopara viticola in lesions, and sporangial survival—was tested over 7 years in Ohio. Grapevines were sprayed with metalaxyl plus mancozeb (Ridomil MZ58) when the warning system indicated that environmental conditions were favorable for sporulation and subsequent infection. Over the 7 years, plots were sprayed from one to four times according to the warning system, and from four to 10 times according to the standard calendar-based schedule (depending on the date of the initiation of the experiment). The warning system resulted in yearly reductions of one to six sprays (with median of three sprays). Disease incidence (i.e., proportion of leaves with symptoms) in unsprayed plots at the end of the season ranged from 0 to 86%, with a median of 68%. Incidence generally was very similar for the warning-system and standard-schedule treatments (median of 7% of the leaves with symptoms), and both of these incidence values were significantly lower (P < 0.05) than that found for the unsprayed control, based on a generalized-linear-model analysis. Simplifications of the disease warning system, where sprays were applied based only on the infection or sporulation components of the system, were also effective in controlling the disease, although more fungicide applications sometimes were applied. Effective control of downy mildew, therefore, can be achieved with the use of the warning system with fewer sprays than a with a standard schedule.

Occidiofungin is the key metabolite for antifungal activity of the endophytic bacterium Burkholderia sp. MS455 against Aspergillus flavus

2021 ◽  
Author(s):  
Jiayuan Jia ◽  
Emerald Ford ◽  
Sarah Hobbs ◽  
Sonya Baird ◽  
Shien Lu
Keyword(s):  
Antifungal Activity ◽  
Aspergillus Flavus ◽  
Safety Concern ◽  
Regulatory Gene ◽  
Genomic Analysis ◽  
Endophytic Bacterium ◽  
Aflatoxin Contamination ◽  
Plant Production ◽  
Antifungal Compound ◽  
Buffer Control

Aflatoxin is a secondary metabolite produced by Aspergillus fungi and presents a major food safety concern globally. Among the available methods for prevention and control of aflatoxin, the application of antifungal bacteria has gained favorability in recent years. An endophytic bacterium MS455, isolated from soybean, exhibited broad-spectrum antifungal activity against economically important pathogens, including Aspergillus flavus. MS455 was identified as a strain of Burkholderia based on genomic analysis. Random and site-specific mutations were employed in discovery of the genes that share high homology to the ocf gene cluster of Burkholderia contaminans strain MS14, which is responsible for production of the antifungal compound occidiofungin. RNA-seq analysis demonstrated ORF1, a homolog to the ambR1 LuxR-type regulatory gene, regulates occidiofungin biosynthesis in MS455. Additionally, a total of 284 differentially expressed genes, including 138 up-regulated, and 146 down-regulated genes, suggesting that, in addition to its role in occidiofungin production, ORF1 is involved in expression of multiple genes, especially those involved in ornibactin biosynthesis. Plate bioassays showed the growth of A. flavus was significantly inhibited by the wild-type strain MS455 as compared with the ORF1 mutant. Similarly, corn kernel assays showed that growth of A. flavus and aflatoxin production were reduced significantly by MS455 as compared with buffer control and the ORF1 mutant. Collectively, the results demonstrated that production of occidiofungin is essential for antifungal activity of the endophytic bacterium MS455. This research has provided insights to understanding antifungal mechanisms of MS455 and development of biological approaches to prevent aflatoxin contamination in plant production.

Use of probabilistic expert elicitation for assessing risk of appearance of grape downy mildew

2019 ◽  
Vol 126 ◽  
pp. 104926
Author(s):  
M. Chen ◽  
F. Brun ◽  
M. Raynal ◽  
C. Debord ◽  
D. Makowski
Keyword(s):  
Downy Mildew ◽  
Expert Elicitation ◽  
Grape Downy Mildew
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