Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi

Lefort, François; Calmin, Gautier; Pelleteret, Pegah; Farinelli, Laurent; Østerås, Magne; Crovadore, Julien

doi:10.1128/genomea.00016-14

Cited by 7 publications

(4 citation statements)

References 13 publications

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“…The genome size of B. amyloliquefaciens (UASWS BA1), an antifungal strain isolated from sycamore tree tissues, was found to be 3.944 Mb, with a GC content of 46.6%. Consistent with our results, previous research revealed that plant growth-promoting B. amyloliquefaciens includes subspecies with highly varied whole-genome sequence sizes, ranging from 3.86 to 4.24 Mb, with GC contents ranging from 45.7 to 46.6 percent [51]. The sequencing results of the current study are similar to those of the previous investigation, in which the genome of B. aryabhattai (SQU-R12) isolated from date palm saplings was found to be 5.584 Mb in size and to have a GC content of 37.74% [52].…”

Section: Discussionsupporting

confidence: 93%

Whole-Genome Sequencing of Two Potentially Allelopathic Strains of Bacillus from the Roots of C. equisetifolia and Identification of Genes Related to Synthesis of Secondary Metabolites

Wang,

Chen,

Lin

et al. 2024

Microorganisms

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The coastal Casuarina equisetifolia is the most common tree species in Hainan’s coastal protection forests. Sequencing the genomes of its allelopathic endophytes can allow the protective effects of these bacteria to be effectively implemented in protected forests. The goal of this study was to sequence the whole genomes of the endophytes Bacillus amyloliquefaciens and Bacillus aryabhattai isolated from C. equisetifolia root tissues. The results showed that the genome sizes of B. amyloliquefaciens and B. aryabhattai were 3.854 Mb and 5.508 Mb, respectively. The two strains shared 2514 common gene families while having 1055 and 2406 distinct gene families, respectively. The two strains had 283 and 298 allelochemical synthesis-associated genes, respectively, 255 of which were shared by both strains and 28 and 43 of which were unique to each strain, respectively. The genes were putatively involved in 11 functional pathways, including secondary metabolite biosynthesis, terpene carbon skeleton biosynthesis, biosynthesis of ubiquinone and other terpene quinones, tropane/piperidine and piperidine alkaloids biosynthesis, and phenylpropanoid biosynthesis. NQO1 and entC are known to be involved in the biosynthesis of ubiquinone and other terpenoid quinones, and rfbC/rmlC, rfbA/rmlA/rffH, and rfbB/rmlB/rffG are involved in the biosynthesis of polyketide glycan units. Among the B. aryabhattai-specific allelochemical synthesis-related genes, STE24 is involved in terpene carbon skeleton production, atzF and gdhA in arginine biosynthesis, and TYR in isoquinoline alkaloid biosynthesis. B. amyloliquefaciens and B. aryabhattai share the genes aspB, yhdR, trpA, trpB, and GGPS, which are known to be involved in the synthesis of carotenoids, indole, momilactones, and other allelochemicals. Additionally, these bacteria are involved in allelochemical synthesis via routes such as polyketide sugar unit biosynthesis and isoquinoline alkaloid biosynthesis. This study sheds light on the genetic basis of allelopathy in Bacillus strains associated with C. equisetifolia, highlighting the possible use of these bacteria in sustainable agricultural strategies for weed management and crop protection.

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Section: Discussionsupporting

confidence: 93%

Whole-Genome Sequencing of Two Potentially Allelopathic Strains of Bacillus from the Roots of C. equisetifolia and Identification of Genes Related to Synthesis of Secondary Metabolites

Wang,

Chen,

Lin

et al. 2024

Microorganisms

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“…A second phylogenomic analysis was conducted using the core genome of all published or released B. siamensis (Jeong et al ., 2012), B. methylotrophicus and B. amyloliquefaciens genomes (Blom et al ., 2012; Cai et al ., 2014; Dunlap et al ., 2013; Geng et al ., 2011; Hao et al ., 2012; Lefort et al ., 2014; Manzoor et al ., 2013; Nelson et al ., 2014; Niazi et al ., 2014a, b; Yang et al ., 2011; Zhang et al ., 2011, 2014). The core genome for the group was 2948 genes.…”

Section: Resultsmentioning

confidence: 99%

“…plantarum strains as biological control agents and plant growth promoters (Ongena & Jacques, 2008; Pérez-García et al ., 2011; Shan et al ., 2013; Sharma & Satyanarayana, 2013; Shi et al ., 2014). In recent years, interest in understanding the mode of action of these strains has led to many genomes being published for these strains (Blom et al ., 2012; Cai et al ., 2014; Dunlap et al ., 2013; Geng et al ., 2011; Hao et al ., 2012; Lefort et al ., 2014; Manzoor et al ., 2013; Nelson et al ., 2014; Niazi et al ., 2014a, b; Yang et al ., 2011; Zhang et al ., 2011, 2014). At the time of writing, 28 genome assemblies had been reported for B. amyloliquefaciens and two had been reported for B. methylotrophicus.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

Dunlap

Kim

Kwon

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus. INTRODUCTIONBacillus methylotrophicus, isolated from rice rhizosphere soil (Korea), was recently described by Madhaiyan et al. (2010). The type strain, KACC 13105 T (5CBMB205 T ), was found to be closely related to members of the Bacillus subtilis species complex (see Rooney et al., 2009, for a recent review of this species complex), and showed 16S rRNA gene sequence similarity values ranging from 98.2 to 99.2 %. The strain was also shown to be a methylotrophic organism capable of utilizing methanol, triethylamine and ethanol as a sole carbon source.Bacillus amyloliquefaciens was recognized as a distinct species in 1987 and was originally described as a producer of extracellular enzymes (Priest et al., 1987). The species was recently divided into two subspecies, Bacillus amyloliquefaciens subsp. amyloliquefaciens and Bacillus amyloliquefaciens subsp. plantarum, based on complete genome comparisons . Strains of the B. amyloliquefaciens subsp. plantarum clade are plant-associated isolates and typically isolated from the soil or rhizosphere of plants Madhaiyan et al., 2010;Palazzini et al., 2007; Rückert et al., 2011;Schisler et al., 2002). These strains were typically isolated as biological control agents or plant growth promoters.Over the past decade, considerable interest has been shown in developing B. methylotrophicus and B. amyloliquefaciens subsp. plantarum strains as biological control agents and plant growth promoters (Ongena & Jacques, 2008; Pérez-García et al., 2011;Shan et al., 2013;Sharma & Satyanarayana, 2013;Shi et al., 2014). In recent years, interest in understanding the mode of action of these strains has led to many genomes being published for these strains (Blom et al., 2012;Cai et al., 2014;Dunlap et al., 2013;Geng et al., 2011; Hao et al., 2012; Lefort et al., 2014; Manzoor et al., 2013;Nelson et al., 2014;Niazi et al., 2014a T was cultured in tryptone-glucose-yeast extract media to early stationary phase (*24 h) and harvested by centrifugation. DNA extraction was performed on the pelleted bacterial biomass using a QIAcube instrument with a QIAmp DNA mini QIAcube kit (QIAGEN). The total genomic DNA extraction was subsequently fragmented to 400 bp using a bioruptor (Diagenode) and size-selected using an E-gel apparatus (Life Technologies). Sequencing adapters were ligated using an Ion Express Plus Fragment Library kit (Life Technologies). Emulsion PCR to incorporate the DNA fragment library to the sequencing beads was performed using the Ion OneTouch instrument with an Ion OneTouch System Template kit (Life Technologies). The library sample was finally sequenced on an Ion Torrent Personal Genome Machine using an Ion 318 chip and t...

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“…Suspensions were made in 0.02% Tween 20 in ultrapure water (Siemens, Switzerland) and then spread on PGA medium at different dilutions to adjust the concentration of viable propagules at a final concentration of 10 7 cfu/ml. Bacterial aqueous suspensions were obtained from 2 day-old B. amyloliquefaciens strain UASWS BA1 (Lefort et al, 2014) grown in fresh Luria Bertani broth (LBB; Carl Roth, Switzerland) at room temperature in the dark under shaking at 150 rpm. Bacteria concentration of the liquid culture was first assessed with a Thoma haemocytometer.…”

Section: Biological Treatmentmentioning

confidence: 99%

Growth of Populus tremula on CO2-enriched soil at a natural mofette site

Pasche¹,

Crovadore²,

Pelleteret³

et al. 2016

Dendrobiology

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A search for endophytes in Castanea sativa Miller (Fagales: Fagaceae) grafting scions showed that a latent pathogenic fungus Gnomoniopsis smithogilvyi (Diaporthales: Gnomoniaceae) was present as the major component of the endophytic flora. Initially, the goal of this study was to develop a biological control method of Cryphonectria parasitica (Diaporthales: Valsaceae), the chestnut blight agent, by soaking chestnut scions before grafting in antagonists suspension. However, the healthy chestnut material used in in vitro and glasshouse experiments turned out to be naturally infected by a pathogen. At first view, the symptoms looked very similar to those caused by C. parasitica but some differences were noticed. DNA sequencing and application of Koch's postulates revealed that G. smithogilvyi was the agent responsible of those symptoms. Preventive biocontrol experiments were carried out with chestnut tree scions soaked overnight in a liquid suspension of Bacillus amyloliquefaciens (Bacillales: Bacillaceae). This bacterium was then frequently found in the lower parts of scions (CF of 100% between 3.1 and 6 cm) and up to a height of 18 cm. It was observed that when B. amyloliquefaciens was present, the endophytic and opportunistic pathogenic fungus G. smithogilvyi was not present. Conversely, the parts not colonized by the bacteria were always naturally infected by the endophytic fungus. This would indicate that the endophytic behavior of B. amyloliquefaciens inhibited the growth of G. smithogilvyi and reduced its presence in scions. A similar experiment, carried out with the Trichoderma atroviride (Hypocreales: Hypocreaceae), led to similar observations. Trichoderma atroviride was frequently isolated in the lower parts of scions (CF of 100% until 6 cm) and up to a height of 27 cm. Inoculating B. amyloliquefaciens and T. atroviride as part of a preventive biocontrol treatment would allow these biological control agents to colonize the plant as endophytes and prevent the development of G. smithogilvyi.

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Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi

Cited by 7 publications

References 13 publications

Whole-Genome Sequencing of Two Potentially Allelopathic Strains of Bacillus from the Roots of C. equisetifolia and Identification of Genes Related to Synthesis of Secondary Metabolites

Whole-Genome Sequencing of Two Potentially Allelopathic Strains of Bacillus from the Roots of C. equisetifolia and Identification of Genes Related to Synthesis of Secondary Metabolites

Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

Growth of Populus tremula on CO2-enriched soil at a natural mofette site

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