Isolation, Identification, and Complete Genome Assembly of an Endophytic Bacillus velezensis YB-130, Potential Biocontrol Agent Against Fusarium graminearum

Wheat scab caused by F. graminearum is a highly destructive disease that leads to yield reduction and mycotoxin contamination of grains. In this study, an endophytic bacterium of strain YB-130 was isolated from surface sterilized wheat spikes with scab symptoms and identified as Bacillus velezensis by whole genome annotation, 16S rRNA gene and average nucleotide identities analysis. The whole-genome sequence of strain YB-130 was obtained by PacBio sequencing. 88 putative Carbohydrate-Active Enzymes and 12 gene clusters encoding for secondary metabolites were identified in the YB-130 genome, including one gene cluster for the synthesis of lanthipeptide only found in strain YB-130 genome. In dual cultures, strain YB-130 significantly inhibited the growth of F. graminearum PH-1 and other eight fungal plant pathogens, indicating a broad antifungal activity. Furthermore, strain YB-130 was able to significantly inhibit spore morphology and hyphal development of F. graminearum PH-1. Strain YB-130 also reduced deoxynivalenol production by F. graminearum PH-1 in dual cultures, possibly due to its ability to suppress the expression of tri5, tri3, and tri8 that are required for deoxynivalenol production in F. graminearum. Overall, B. velezensis YB-130 is a promising biological control agent of both F. graminearum infection and mycotoxin production.

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Biocontrol of tomato bacterial wilt by a new strain Bacillus velezensis FJAT-46737 and its lipopeptides

10.21203/rs.2.17222/v1 ◽

2019 ◽

Author(s):

Meichun Chen ◽

Jieping Wang ◽

Bo Liu ◽

Yujing Zhu ◽

Rongfeng Xiao ◽

...

Keyword(s):

Bacterial Wilt ◽

Plant Pathogens ◽

Antimicrobial Agents ◽

Gene Clusters ◽

Antimicrobial Activities ◽

Whole Genome Sequence ◽

Dependent Manner ◽

Bacillus Velezensis ◽

Tomato Bacterial Wilt

Abstract Background There is an urgent need to discover alternative antimicrobial agents to control bacterial wilt. The objectives of this study were to report a new lipopeptide-producding biocontrol strain FJAT-46737 and its lipopeptides, and to investigate their antagonistic effects.Results Based on the whole genome sequence analysis, the new strain FJAT-46737 was finally identified as Bacillus velezensis and seven gene clusters that responsible for synthesis of bioactive secondary metabolite in the FJAT-46737 were predicted. Antimicrobial results demonstrated that FJAT-46737 exhibited broad-spectrum antimicrobial activities in vitro against bacteria and fungi. The pot experiments showed that the tomato bacterial wilt control efficiencies of the whole cultures, the 2-fold diluted supernatants and the crude lipopeptide of FJAT-46737 were 66.2%, 82.0%, and 96.2%, respectively. The above results suggested that one of the antagonistic mechanisms of FJAT-46737 was secretion of lipopeptides that consisted of iturins, fengycins and surfactins. The crude lipopeptides had significant antagonistic activities on several pathogen in a dosage-dependent manner, and the fengycins confirmed to play a major role in antibacterial abilities in vitro of the lipopeptides against Ralstonia solanacearum . Furthermore, it was found that the rich organic nitrogen sources (expecially yeast extracts) in the media were benificial for FJAT-46737 to produce fengycin and surfactin. The secretion of these two lipopeptides were also adjusted by the culture temperature: the content of the fengycins decreased by 96.6% and that of the surfactins ascended by 59.9% from 20 o C to 40 o C. And 20 o C~25 o C is the suitable temperature for FJAT-46737 to produce lipopeptide.Conclusions The B. velezensis strain FJAT-46737 and its lipopeptides would used as new sources of potential biocontrol agents against plant pathogens, especially the bacterial wilt pathogen R. solanacearum .

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Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

Marine Drugs ◽

10.3390/md19050243 ◽

2021 ◽

Vol 19 (5) ◽

pp. 243

Author(s):

Wael M. Abdel-Mageed ◽

Lamya H. Al-Wahaibi ◽

Burhan Lehri ◽

Muneera S. M. Al-Saleem ◽

Michael Goodfellow ◽

...

Keyword(s):

Genome Sequence ◽

Gene Clusters ◽

2D Nmr ◽

Whole Genome Sequence ◽

Rrna Gene ◽

Whole Genome ◽

Mariana Trench ◽

Chemical Structures ◽

Desferrioxamine B ◽

Challenger Deep

A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

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Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist of Fungal Plant Pathogens

Genome Announcements ◽

10.1128/genomea.00595-18 ◽

2018 ◽

Vol 6 (25) ◽

Cited By ~ 2

Author(s):

Julia Pezarini Baptista ◽

Paula Pinheiro Sanches ◽

Gustavo Manoel Teixeira ◽

Alexandre Tadachi Morey ◽

Eliandro Reis Tavares ◽

...

Keyword(s):

Biological Control ◽

Complete Genome ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Gene Clusters ◽

Bacillus Velezensis ◽

Coding Sequences ◽

Content Type ◽

Dna Coding ◽

Fungal Plant Pathogens

Bacillus velezensis strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens.

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Genome-based Classification of Streptomyces Pinistramenti sp. nov., a Novel Actinomycete Isolated From a Pine Forest Soil in Poland With a Focus on Its Biotechnological and Ecological Properties

10.21203/rs.3.rs-1173277/v1 ◽

2022 ◽

Author(s):

Magdalena Śwecimska ◽

Patrycja Golinska ◽

Michael Goodfellow

Keyword(s):

Phylogenetic Trees ◽

Plant Pathogens ◽

Draft Genome ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Housekeeping Genes ◽

Gene Clusters ◽

Diaminopimelic Acid ◽

Rrna Gene ◽

Fungal Plant Pathogens

Abstract A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28T, that was recovered from the litter layer in a polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classification in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid and glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, iso- and anteiso- fatty acids, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units and had a polar lipid pattern composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, glycophospholipids and three uncharacterized components. Phylogenetic trees prepared using 16S rRNA gene and multilocus gene sequences of conserved housekeeping genes showed that the isolate formed a branch that was loosely associated with the type strains of several validly published Streptomyces species. A draft genome generated for the isolate was rich in natural product-biosynthetic gene clusters with the potential to produce new specialised metabolites, notably antibiotics, and stress related genes which provide an insight into how they may have adapted to the harsh conditions that prevail in acidic forest soils. A phylogenomic tree based on the genomes of the isolate and its phylogenetic neighbours confirmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide index and digital DNA:DNA hybridization values with its phylogenomic neighbours and was also distinguished from them using a combination of cultural and micromorphological properties. Given this wealth of taxonomic data it is proposed that isolate SF28T (=DSM 113360T=PCM 3163T) be classified in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.

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Biocontrol of tomato bacterial wilt by a new strain Bacillus velezensis FJAT-46737 and its lipopeptides

10.21203/rs.2.17222/v2 ◽

2019 ◽

Author(s):

Meichun Chen ◽

Jieping Wang ◽

Bo Liu ◽

Yujing Zhu ◽

Rongfeng Xiao ◽

...

Keyword(s):

Bacterial Wilt ◽

Plant Pathogens ◽

Antimicrobial Agents ◽

Gene Clusters ◽

Antimicrobial Activities ◽

Whole Genome Sequence ◽

Dependent Manner ◽

Bacillus Velezensis ◽

Tomato Bacterial Wilt

Abstract Background: There is an urgent need to discover alternative antimicrobial agents to control bacterial wilt. The objectives of this study were to report a new lipopeptide-producing biocontrol strain FJAT-46737 and its lipopeptides, and to investigate their antagonistic effects. Results: Based on the whole genome sequence analysis, the new strain FJAT-46737 was finally identified as Bacillus velezensis and seven gene clusters that responsible for synthesis of bioactive secondary metabolite in the FJAT-46737 were predicted. Antimicrobial results demonstrated that FJAT-46737 exhibited broad-spectrum antimicrobial activities in vitro against bacteria and fungi . The pot experiments showed that the tomato bacterial wilt control efficiencies of the whole cultures, the 2-fold diluted supernatants and the crude lipopeptide of FJAT-46737 were 66.2%, 82.0%, and 96.2%, respectively. The above results suggested that one of the antagonistic mechanisms of FJAT-46737 was secretion of lipopeptides that consisted of iturins, fengycins and surfactins. The crude lipopeptides had significant antagonistic activities on several pathogen in a dosage-dependent manner, and the fengycins confirmed to play a major role in antibacterial abilities in vitro of the lipopeptides against Ralstonia solanacearum . Furthermore, it was found that the rich organic nitrogen sources (especially yeast extracts) in the media were beneficial for FJAT-46737 to produce fengycin and surfactin. The secretion of these two lipopeptides were also adjusted by the culture temperature: the content of the fengycins decreased by 96.6% and that of the surfactins ascended by 59.9% from 20 o C to 40 o C. The temperature of 20 o C~25 o C is the suitable temperature for FJAT-46737 to produce lipopeptide. Conclusions: The B. velezensis strain FJAT-46737 and its lipopeptides would used as new sources of potential biocontrol agents against plant pathogens, especially the bacterial wilt pathogen R. solanacearum .

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Biocontrol of tomato bacterial wilt by the new strain Bacillus velezensis FJAT-46737 and its lipopeptides

10.21203/rs.2.17222/v3 ◽

2020 ◽

Author(s):

Meichun Chen ◽

Jieping Wang(New Corresponding Author) ◽

Bo Liu(Former Corresponding Author) ◽

Yujing Zhu ◽

Rongfeng Xiao ◽

...

Keyword(s):

Bacterial Wilt ◽

Plant Pathogens ◽

Antimicrobial Agents ◽

Nitrogen Sources ◽

Gene Clusters ◽

Antimicrobial Activities ◽

Whole Genome Sequence ◽

Bacillus Velezensis ◽

Tomato Bacterial Wilt

Abstract Background: There is an urgent need to discover alternative antimicrobial agents to control bacterial wilt. This study reports on a new lipopeptide-producing biocontrol strain FJAT-46737 and explores its lipopeptidic compounds, and this study investigates the antagonistic effects of these compounds. Results: Based on a whole genome sequence analysis, the new strain FJAT-46737 was identified as Bacillus velezensis, and seven gene clusters responsible for the synthesis of bioactive secondary metabolites in FJAT-46737 were predicted. The antimicrobial results demonstrated that FJAT-46737 exhibited broad-spectrum antimicrobial activities in vitro against three bacteria and three fungi. Pot experiments showed that the control efficiencies for tomato bacterial wilt of the whole cultures, the 2-fold diluted supernatants and the crude lipopeptide of FJAT-46737 were 66.2%, 82.0%, and 96.2%, respectively. The above results suggested that one of the antagonistic mechanisms of FJAT-46737 was the secretion of lipopeptides consisting of iturins, fengycins and surfactins. The crude lipopeptides had significant antagonistic activities against several pathogens (including Ralstonia solanacearum, Escherichia coli and Fusarium oxysporum) and fengycins were the major antibacterial components of the lipopeptides against R. solanacearum in vitro. Furthermore, the rich organic nitrogen sources (especially yeast extracts) in the media promoted the production of fengycin and surfactin by FJAT-46737. The secretion of these two lipopeptides was related to temperature fluctuations, with the fengycin content decreasing by 96.6% and the surfactins content increasing by 59.9% from 20 oC to 40 oC. The optimal temperature for lipopeptide production by FJAT-46737 varied between 20 oC and 25oC. Conclusions: The B. velezensis strain FJAT-46737 and its lipopeptides represent new sources of potential biocontrol agents against plant pathogens, especially the bacterial wilt pathogen R. solanacearum.

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Whole-Genome Sequencing Reveals a New Genospecies ofMethylobacteriumsp. GXS13, Isolated fromVitis viniferaL. Xylem Sap

Genome Announcements ◽

10.1128/genomea.01695-15 ◽

2016 ◽

Vol 4 (1) ◽

Cited By ~ 1

Author(s):

Wan Xin Lai ◽

Han Ming Gan ◽

André O. Hudson ◽

Michael A. Savka

Keyword(s):

Xylem Sap ◽

Gene Clusters ◽

Homoserine Lactone ◽

Whole Genome Sequence ◽

Whole Genome ◽

Acyl Homoserine Lactone ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Cell Wall Modification ◽

Cytokinin Synthesis

The whole-genome sequence of a new genospecies ofMethylobacteriumsp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

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Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-01-20-0016-a ◽

2020 ◽

Vol 33 (8) ◽

pp. 1022-1024

Author(s):

Giovanni Cafà ◽

Thaís Regina Boufleur ◽

Renata Rebellato Linhares de Castro ◽

Nelson Sidnei Massola ◽

Riccardo Baroncelli

Keyword(s):

Comparative Genomics ◽

Genome Sequence ◽

Plant Pathogens ◽

Sequence Data ◽

Gene Prediction ◽

Whole Genome Sequence ◽

Future Research ◽

Whole Genome ◽

Genome Sequence Data ◽

Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

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Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion

AMB Express ◽

10.1186/s13568-020-01101-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Karina A. Balderas-Ruíz ◽

Patricia Bustos ◽

Rosa I. Santamaria ◽

Víctor González ◽

Sergio Andrés Cristiano-Fajardo ◽

...

Keyword(s):

Biological Control ◽

Plant Growth ◽

Biological Control Agent ◽

Gene Clusters ◽

In Vitro Assays ◽

Shoot Biomass ◽

Plant Growth Promoting Bacteria ◽

Bacillus Velezensis

Abstract Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains.

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