Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain Isolation and Cultivation
2.2. Reconstruction of the Complete Genomes
2.3. Screening of the Virulence Genes
Accession | Size | G + C | Genes | Sample | GTDB | Collection | ||||
---|---|---|---|---|---|---|---|---|---|---|
bp | % | Coding | RNA | Name | Genomospecies | Plant | Organ | Site | Date | |
CP085501.1 | 5,268,018 | 35.7 | 5533 | 149 | A24 | B. cereus ssp. A | black pepper | root | Vietnam | 24 May 2018 |
CP085506.1 | 5,183,312 | 34.9 | 5450 | 154 | HD2.4B | B. cereus ssp. A | tomato plants | rhizosphere | Vietnam, Hoai Duc, Ha Noi | 23 April 2019 |
CP085510.1 | 5,183,870 | 34.9 | 5450 | 157 | HD1.4B | B. cereus ssp. A | tomato plant | rhizosphere | Vietnam, Hoai Duc, Ha Noi | 23 April 2019 |
JABSVB000000000.1 | 5,796,358 | 34.8 | 5664 | 80 | HB3.1 | B. cereus ssp. A | orange tree | rhizosphere | Vietnam, Cao Phong, Hoa Binh | 17 April 2019 |
VDDR00000000.1 | 5,071,716 | 35.4 | 5619 | 63 | A8 | B. cereus ssp. A | coffee tree | root | Vietnam | 9 May 2018 |
VEPT00000000.1 | 5,319,678 | 35.3 | 5332 | 63 | A31 | B. cereus ssp. A | black pepper | root | Vietnam | 22 May 2018 |
VEPS00000000.2 | 6,195,299 | 34.7 | 6254 | 78 | TK1 | B. cereus ssp. B | black pepper | rhizosphere | Vietnam | 9 May 2018 |
CP085498.1 | 5,310,791 | 35.2 | 5640 | 143 | A22 | B. cereus ssp. B | coffee tree | root | Vietnam | 9 May 2018 |
JABSVF000000000.1 | 5,869,336 | 34.8 | 5640 | 80 | M2.1B | B. cereus ssp. B | maize | rhizosphere | Vietnam, Phu An, Thanh Da | 6 December 2019 |
VEPQ00000000.1 | 5,604,011 | 35.6 | 5466 | 63 | A42 | B. cereus ssp. B | black pepper | root | Vietnam | 12 May 2018 |
VEPR00000000.1 | 5,594,617 | 35.6 | 5480 | 67 | SN4-3 | B. cereus ssp. B | maize | dead insect | Vietnam | 28 May 2018 |
VEPV00000000.1 | 5,335,513 | 35.2 | 5339 | 58 | SN1 | B. tropicus ssp. B | Ostrinia nubilalis | Vietnam | 28 May 2018 | |
VEPW00000000.1 | 5,958,606 | 35.8 | 5843 | 93 | CD3-2 | B. tropicus ssp. | brown mustard | rhizosphere | Vietnam | 28 May 2018 |
VEPU00000000.1 | 5,443,801 | 35.2 | 5389 | 72 | SN4.1 | B. pacificus ssp. B | Ostrinia nubilalis | Vietnam | 28 May 2018 | |
JABSVD000000000.1 | 5,695,940 | 35.1 | 5534 | 87 | HD1.3 | Bacillus sp. | tomato plant | rhizosphere | Vietnam, Hoai Duc, Ha Noi | 23 April 2019 |
VEPX00000000.1 | 5,695,940 | 35.3 | 5136 | 65 | CD3-5 | Bacillus sp. | brown mustard | rhizosphere | Vietnam | 28 May 2018 |
VEPY00000000.1 | 5,150,560 | 35.2 | 5175 | 61 | CD3-1a | Bacillus sp. | brown mustard | rhizosphere | Vietnam | 28 May 2018 |
2.4. Genotypic and Phenotypic Characterization of the Isolate B. cereus CD3-1a
2.5. Taxonomical Phylogeny Assessment
2.6. Genome Mining
2.7. Sample Preparation and Mass-Spectrometric Detection of the Bioactive Peptides
2.8. Antifungal, Nematocidal, and Plant-Growth-Promoting Activity Assays
2.9. Data Analysis
2.10. Gene Bank Accession Numbers of the Complete Genome Sequences
3. Results and Discussion
3.1. Comparative Genome Analysis of the Isolates from Vietnamese Crop Plants Representing the Bacillus cereus s.l. Complex
3.1.1. Genome-Based Species and Subspecies Delineation of the Plant-Associated Isolates Belonging to the B. cereus Group
3.1.2. Occurrence of Virulence Genes Might Restrict the Application of B. cereus s.l. Isolates
3.1.3. Genes Encoding Insecticidal Proteins in B. cereus subsp. Bombysepticus TK1
3.1.4. Plasmid-Encoded Virulence Genes and Biosynthetic Gene Clusters in B. cereus Isolates A22, A24, HD1.4B, and HD2.4
3.2. Genome Mining for Biosynthetic Gene Clusters (BGCs) Encoding Secondary Metabolites
3.2.1. Non-Ribosomally Synthesized Antimicrobial Peptides (NRPs) and Polyketides (PKs)
3.2.2. Gene Clusters Representing RiPPs and Bacteriocins
- Class I: post-translationally modified peptides smaller than 10 kDa.
- Class II: small (<10 Da), unmodified peptides with or without a leader sequence.
- Class III: peptides larger than 10 kDa.
3.2.3. Other Antimicrobial Secondary Metabolites
3.3. Detection of Bioactive Peptides by MALDI-TOF Mass Spectrometry
bn₋H2O (found) | - | 280.123 | 337.149 | 408.107 | 495.159 | 632.284 | 760.445 | - |
bn (found) | 197.030 | 298.133 | 355.112 | - | - | - | 778.446 | 906.504 |
bn (calc.) | 197.190 | 298.238 | 355.259 | 426.296 | 513.328 | 650.387 | 778.446 | 906.504 |
C13-FA | Thr (1) | Gly (2) | Ala (3) | Ser (4) | His (5) | Gln (6) | Gln (7) | |
yn (calc.) | 906.502 | 710.322 | 609.275 | 552.253 | 481.216 | 394.184 | 257.125 | 129.066 |
yn (found) | 906.504 | 710.266 | 609.163 | 552.133 | 481.106 | 394.084 | 257.050 | 129.066 |
yn₋H2O (found) | - | 692.185 | - | - | 463.103 | - | - | - |
(A) Dipeptide fragments | m/z | m/z |
Calc. | found | |
C13-FA-Thr | 298.238 | 298.141/280.129 |
Thr-Gly | 159.077 | 159.007/141.022 |
Gly-Ala | 129.066 | 129.016 |
Ala-Ser | 159.077 | 159.007/141.022 |
Ser-His | 225.099 | 225.034/207.019 |
His-Gln | 266.125 | 266.060 |
Gln-Gln | 257.125 | 257.050 |
(B) Tripeptide fragments | ||
C13-FA-Thr-Gly | 341.244 | 341.170/323.167 |
Thr-Gly-Ala | 230.114 | 230.026/212.025 |
Gly-Ala-Ser | 216.098 | 216.024/198.022 |
Ala-Ser-His | 296.136 | -/278.050 |
Ser-His-Gln | 353.157 | 353.084/335.070 |
His-Gln-Gln | 394.184 | 394.101/335.070 |
(C) Tetrapeptide fragments | ||
C13-FA-Thr-Gly-Ala | 426.296 | -/408.121 |
Thr-Gly-Ala-Ser | 317.146 | 317.057/299.070 |
Gly-Ala-Ser-His | 353.157 | 353.084/335.070 |
Ala-Ser-His-Gln | 424.194 | - |
Ser-His-Gln-Gln | 481.216 | 481.120/463.120 |
3.4. B. cereus s.l. Strains Suppressed Plant Pathogens and Promoted Plant Growth
3.4.1. Antifungal and Nematocidal Activity
3.4.2. Plant Growth Promotion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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b ions → | |||||
bn (found) | - | 216.17 | 328.25 | 457.38 | (p)?? |
bn (calc.) | 115.09 | 216.14 | 329.22 | 457.28 | (P)570.36 |
Orn (1) | Thr (2) | Ile (3) | Gln (4) | Leu (5) | |
yn (calc.) | (p)570.36 | 456.28 | 355.24 | 242.15 | 114.09 |
yn (found) | (p)?? | 456.39 | 355.25 | 242.17 | - |
<-- y ions |
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Vater, J.; Tam, L.T.T.; Jähne, J.; Herfort, S.; Blumenscheit, C.; Schneider, A.; Luong, P.T.; Thao, L.T.P.; Blom, J.; Klee, S.R.; et al. Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds. Microorganisms 2023, 11, 2677. https://doi.org/10.3390/microorganisms11112677
Vater J, Tam LTT, Jähne J, Herfort S, Blumenscheit C, Schneider A, Luong PT, Thao LTP, Blom J, Klee SR, et al. Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds. Microorganisms. 2023; 11(11):2677. https://doi.org/10.3390/microorganisms11112677
Chicago/Turabian StyleVater, Joachim, Le Thi Thanh Tam, Jennifer Jähne, Stefanie Herfort, Christian Blumenscheit, Andy Schneider, Pham Thi Luong, Le Thi Phuong Thao, Jochen Blom, Silke R. Klee, and et al. 2023. "Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds" Microorganisms 11, no. 11: 2677. https://doi.org/10.3390/microorganisms11112677