Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential
Abstract
1. Introduction
2. Results
2.1. Antagonistic Activity and Nutritional Preferences Test In Vitro
2.2. Genetic Characteristics
2.3. Horizontal Gene Transfer
3. Discussion
4. Materials and Methods
4.1. Microorganisms
4.2. Antagonism Evaluation In Vitro
4.3. Nutritional Preferences Test In Vitro
4.4. Genomic DNA Extraction, Whole-Genome Sequencing, Annotation
4.5. Comparative Genomic and Phylogenetic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Strain | Bil-LT1_1 | Bil-LT1_2 | Cran-LT1_8 | Ling-NOR4_15 |
---|---|---|---|---|
Antifungal Activity, Growth Suppression (%) | ||||
B. cinerea T11B_BRA_189 | 52.4 ± 1.7 | 69.1 ± 1.5 | 79.7 ± 1.1 | 48.5 ± 0.6 |
F. culmorum LT_1V23b | 23.3 ± 0.7 | 19.2 ± 0.7 | 26.9 ± 0.5 | 29.7 ± 0.9 |
M. fructicola CBS 101512 | 50.6 ± 1.5 | 56.2 ± 0.3 | 59.4 ± 1.7 | 56.4 ± 0.8 |
M. frutigena MFS01 | 68.7 ± 1.8 | 99.1 ± 0.0 | 91.7 ± 0.3 | 77.5 ± 0.6 |
M. laxa CBS 489.50 | 61.2 ± 1.0 | 59.7 ± 1.1 | 84.8 ± 0.5 | 68.8 ± 1.5 |
Antibacterial Activity, Inhibition Zone (mm) | ||||
B. cereus ATCC 11778 | 10.0 ± 0.1 | 10.0 ± 0.1 | 16.0 ± 0.1 | 16.0 ± 0.1 |
E. coli ATCC 25922 | N/A | N/A | 12.0 ± 0.1 | N/A |
L. monocytogenes ATCC 13932 | 11.0 ± 0.2 | 12.0 ± 0.2 | 16.0 ± 0.1 | 16.0 ± 0.1 |
S. enterica subsp. enterica serovar Typhimurium ATCC 13932 | N/A | N/A | 14.0 ± 0.1 | 11.0 ± 0.0 |
S. aureus subsp. Aureus ATCC 25923 | 14.0 ± 0.3 | 11.0 ± 0.1 | 18.0 ± 0.3 | 14.0 ± 0.1 |
Growth on media * | Good on all tested media (LB, PCA, TSA, NA, MYP) | Dense colonies on PCA; good on other media | Large, slightly mucoid colonies on PCA; low density on TSA; poor on NA | Uniform growth on NA; pink hue on MYP |
Hemolysis on SBA | Beta | Beta | Alpha/Beta | Beta |
Mannitol fermentation on MYP | Positive (orange/yellow shift) | Positive (orange/yellow shift) | Weak/partial (yellowish; inhibited growth) | Negative (pink hue) |
Pigment production | Yellow on TSA | None observed | None observed | None observed |
Isolated B. halotolerans | Isolated B. velezensis | |||
---|---|---|---|---|
Bil-LT1_1 | Bil-LT1_2 | Cran-LT1_8 | Ling-NOR4_15 | |
SAMN36292479 | SAMN36292480 | SAMN36292481 | SAMN36292482 | |
Statistics of Sequencing Data | ||||
Raw reads | 4,383,886 | 4,967,478 | 4,499,288 | 4,914,838 |
Raw data (G) | 1.1 | 1.2 | 1.1 | 1.2 |
Clean data (G) | 1 | 1 | 1 | 1.1 |
Effective (%)/Error (%) | 91.01/0.04 | 85.39/0.03 | 85.18/0.04 | 86.38/0.04 |
GC (%) | 43.3 | 43.3 | 46.3 | 46.3 |
Assembly Information | ||||
Total reads | 4,259,074 | 4,261,465 | 4,170,815 | 4,593,628 |
Number of contigs | 39 | 34 | 28 | 21 |
Largest contig (bp) | 646,884 | 646,885 | 940,386 | 941,931 |
Mapping Statistics to the Reference Genomes | ||||
CP029364 (NCBI) | CP119675 (NCBI) | |||
Average nucleotide identity (ANI), % | 99.50 | 99.82 | 98.01 | 97.95 |
Annotation Information | ||||
Bakta annotation | 4472 | 4472 | 3962 | 4025 |
CDSs | 4313 | 4313 | 3805 | 3897 |
tRNAs; tmRNAs; rRNAs | 62; 1; 4 | 62; 1; 4 | 73; 1; 3 | 77; 1; 3 |
ncRNAs | 28 | 28 | 19 | 21 |
ncRNA regions | 62 | 62 | 59 | 60 |
Proteins with KEGG pathway assignments | 2457 | 2458 | 2315 | 2317 |
Specialty Genes | ||||
Antibiotic resistance (CARD) | 13 | 13 | 7 | 7 |
Virulence factors (VFBDs) | 39 | 39 | 38 | 38 |
Biosynthetic gene clusters (BGCs) | 14 | 14 | 20 | 21 |
Biosynthesis of antibiotics | 5 | 5 | 3 | 2 |
Bacterial Pathogenic Capacity Prediction | ||||
Mean (std) | 0.0942 (0.0204) | 0.0825 (0.0181) | 0.0514 (0.0163) | 0.0511 (0.0191) |
Bacteria Strain | Clusters for Secondary Metabolites Synthesis |
---|---|
Bil-LT1_1, Bil-LT1_2 Cran-LT1_8, Ling-NOR 4_15 | plipastatin, bacillaene, teichuronic acid, chejuenolide A/chejuenolide B, K53 capsular polysaccharide, bacillomycin D, surfactin, dipeptide aldehydes, fengycin, bacillibactin, bacilysin |
Bil-LT1_1, Bil-LT1_2 | thailanstatin A, subtilosin A |
Cran-LT1_8, Ling-NOR 4_15 | butirosin A/butirosin B, molybdenum cofactor, difficidin, macrolactin H |
Ling-NOR 4_15 | plantazolicin |
Cran-LT1_8 | mersacidin, rhizomide A/rhizomide B/rhizomide C |
Function | B. halotolerans | B. velezensis | ||
---|---|---|---|---|
Bil-LT1_1 | Bil-LT1_2 | Cran-LT1_8 | Ling-NOR 4_15 | |
Genes | ||||
Phosphate metabolism | pstB3, pstA | |||
pstS | - | pstS | pstS | |
Nitrogen metabolism | nasE, nasD, rocG | |||
Nitrogen fixation | nifS, salA, sufU | |||
Siderophore | fhuD, pchA | |||
- | fhuG | - | - | |
Phytohormone production | trpA, trpB, trpF, trpC, trpD, trpE, amiE, aldH | |||
Hydrolase | amyE, eglS, gmuD, ganB | |||
Chitinase activity | sleL, ydhD | |||
Biofilm | tasA, bslA | |||
bslB | bslB | - | bslB | |
2,3-butanediol | alsD, ilvK, ilvE, ilvA, ilvD, ilvC, ilvH, ilvB |
Access. No. in NCBI and Strain Name | HGTEs Size Range bp | No of HGTEs | Information About Isolate | Genome Size, bp | |
---|---|---|---|---|---|
Bacillus halotolerans | |||||
SAMN36292479 | Bil-LT1_1 | 5000–37,501 | 123 | Bilberry leaves, Lithuania | 4,259,074 |
SAMN36292480 | Bil-LT1_2 | 5000–52,501 | 107 | Bilberry leaves, Lithuania | 4,261,465 |
CP029364 | ZB201702 | 5131–63,099 | 61 | Drought and salt rhizosphere soil of maize, China: Inner Mongolia | 4,154,245 |
CP126100 | LN2 | 4055–128,846 | 58 | Rhizosphere soil, China: Longnan, Gansu Province | 4,252,134 |
CP110264 | HMB20199 | 4640–47,395 | 54 | Plant, against Pseudoperonospora cubensis Rostow, China: Baoding | 4,175,808 |
CP098738 | XE48 | 6651–66,933 | 62 | Marine low temperature surface sediment, West Indian Ocean | 4,140,100 |
CP138201 | DY299 | 5023–74,450 | 46 | Soil, China: Inner Mongolia | 4,208,811 |
CP136430 | Q2H2 | 5970–56,767 | 49 | Endophytic bacteria of potato root with strong antagonisticactivity, China: Inner Mongolia | 4,155,130 |
CP041357 | F41-3 | 5001–50,720 | 55 | Flower of Chiness redbud, South Korea: Jeon-buk | 4,144,458 |
Bacillus velezensis | |||||
SAMN36292481 | Cran-LT1_8 | 5001–35,001 | 50 | Cranberry leaves, Lithuania | 3,958,789 |
SAMN36292482 | Ling-NOR 4_15 | 5001–35,001 | 56 | Lingonberry leaves, Norway | 3,987,686 |
CP009679 | JS25R | 3864–33,478 | 41 | Spikelet of wheat heads, with biocontrol activity China: Beijing | 4,006,002 |
CP119675 | 160 | 5156–135,917 | 28 | Rhizosphere soil of corn crops, control agent of corn head smut, Mexico | 4,296,610 |
CP011937 | CBMB205 | 4737–36,609 | 48 | Rice rhizosphere soil, South Korea: Cheongwon | 3,929,792 |
CP026610 | CGMCC 11640 | 5090–142,965 | 50 | Bamboo forest soil, against Botryosphaeria dothidea, China:Tianmu Mountain | 4,322,979 |
CP168028 | CM5 | 3808–140,634 | 56 | Peat casing layer, biocontrol in the mushroom microcosm Spain: Rioja | 4,240,819 |
CP049904 | GB03 | 4777–34,819 | 33 | Biological Control Product Kodiak TM, Korea | 3,894,540 |
CP034203 | 83 | 3879–36,447 | 35 | Biological Control Product Fungifree AB™, Korea | 3,997,902 |
List Strains | Total Number of CDS | Number of Annotated Genes | Antibiotic Resistance Genes | Virulence Factors | |
Bil-LT1_1 | 1155 | 682 | satA_Bs, rphC | 14 * | |
Bil-LT1_2 | 1095 | 598 | satA_Bs, rphC | 13 ** | |
Cran-LT1_8 | 525 | 236 | rphC, tet(L), satA_Bs | cheY | |
Ling-NOR4_15 | 605 | 248 | satA_Bs, tet(L), clbA, rphC | dhbF, mbtH |
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Mažeikienė, I.; Frercks, B.; Kurgonaitė, M.; Rasiukevičiūtė, N.; Mačionienė, I. Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential. Int. J. Mol. Sci. 2025, 26, 6677. https://doi.org/10.3390/ijms26146677
Mažeikienė I, Frercks B, Kurgonaitė M, Rasiukevičiūtė N, Mačionienė I. Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential. International Journal of Molecular Sciences. 2025; 26(14):6677. https://doi.org/10.3390/ijms26146677
Chicago/Turabian StyleMažeikienė, Ingrida, Birutė Frercks, Monika Kurgonaitė, Neringa Rasiukevičiūtė, and Irena Mačionienė. 2025. "Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential" International Journal of Molecular Sciences 26, no. 14: 6677. https://doi.org/10.3390/ijms26146677
APA StyleMažeikienė, I., Frercks, B., Kurgonaitė, M., Rasiukevičiūtė, N., & Mačionienė, I. (2025). Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential. International Journal of Molecular Sciences, 26(14), 6677. https://doi.org/10.3390/ijms26146677