Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species

Mullins, Alex J.; Li, Yinshui; Qin, Lü; Hu, Xiaojia; Xie, Lin; Gu, Chunhao; Mahenthiralingam, Eshwar; Xing, Lixin; Webster, Gordon

doi:10.1099/mic.0.000986

Cited by 12 publications

(6 citation statements)

References 38 publications

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“…Our own results and data of other researchers [ 29 , 47 , 48 , 49 , 64 , 67 , 74 , 75 , 76 , 77 ] demonstrated a strong antagonistic activity of B. velezensis to the pathogenic fungi Fusarium graminearum , F. oxysporum and R. solani, thus confirming this species as a very promising biocontrol agents [ 24 , 78 , 79 ]. Practical value of this antagonism has been proved by the use of B. velezensis in BioYield commercial formulation applied in management of soil-born pathogens and M. incognita on tomato [ 11 ].…”

Section: Discussionsupporting

confidence: 82%

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

et al. 2021

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Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops.

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Section: Discussionsupporting

confidence: 82%

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

et al. 2021

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“…Our results showed that the co-culture of E. amstelodami and Bacillus species significantly improves the inhibitory effect against S. aureus and different co-culture combination showed different improvement effects. Many studies have demonstrated that B. amyloliquefaciens can produce a wide variety of SMs with desirable antibacterial activity ( Shahzad et al, 2018 ; Mullins et al, 2020 ). Here, we observed that B. amyloliquefaciens pure cultures exhibited excellent inhibition of S. aureus , which was consistent with previous reports ( Arguelles-Arias et al, 2009 ; Du et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

Wang

Chen²,

Xin³

et al. 2023

Front. Microbiol.

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As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.

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“…The natural product capacity of individual Burkholderia species has been previously explored to understand BGC distributions and facilitate discovery of uncharacterized metabolites ( Mullins et al, 2019 ; Jones et al, 2021 ); similar to species of other genera, such as Bacillus velezensis ( Mullins et al, 2020 ). However, despite a successful history of natural product discovery in Burkholderia , considerably more genome mining analyses have been performed at the broader genus-level in other genera.…”

Section: Discussionmentioning

confidence: 99%

The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato

Mullins

Mahenthiralingam

2021

Front. Microbiol.

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Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.

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Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species

Cited by 12 publications

References 38 publications

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato

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