Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Light Microscopy and Transmission Electron Microscopy
2.2. Cultivable Endophytic Bacteria Isolation and Growth Conditions
2.3. Random Amplified Polymorphic DNA (RAPD) Analysis
2.4. 16S rRNA Gene Amplification and Sequencing and ARDRA Analysis
2.5. Phylogenetic Tree Construction
2.6. Antibiotic Resistance Tests
2.7. Cross-Streaking Test against Burkholderia cepacia Complex Strains
2.8. Genome Sequencing
2.9. Genome Assembly and Bioinformatic Analysis
3. Results
3.1. Electron Microscopy
3.2. Cultivable Endophytic Bacteria Isolation
3.3. Analysis of the Structure of the Seed-Associated Endophytic Community
3.4. Taxonomic Affiliation of the Endophytic Strains
3.5. Antibiotic Resistance Profiles
3.6. Cross-Streaking Test against Burkholderia cepacia Complex Strains
3.7. Genome Sequencing of Bacillus sp. OR9
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain | Species | Origin |
---|---|---|
FCF3 | B. cepacia | CF patients |
FCF23 | B. cenocepacia | |
LMG16656 | B. cenocepacia | |
LMG21462 | B. cenocepacia | |
LMG24506 | B. cenocepacia | |
K56–2 | B. cenocepacia | |
LMG13010 | B. multivorans | |
LMG19182 | B. ambifaria | Environment |
LMG1222 | B. cepacia | |
LMG19230 | B. cenocepacia | |
LMG17588 | B. multivorans |
ARDRA Profiles | RAPD Haplotypes | Isolates | Genus | Accession Number |
---|---|---|---|---|
1 | 1 | OR1 | Pseudomonas | OP522403 |
2 | 2 | OR2 | Pantoea | OP522404 |
3 | OR11 | Pantoea | - | |
3 | 4 | OR3 | Erwinia | OP522405 |
5 | OR6; OR15 | Erwinia | - | |
4 | 6 | OR4 | Paenibacillus | OP522406 |
5 | 7 | OR5 | Pseudomonas | OP522407 |
8 | OR19 | Pseudomonas | - | |
9 | OR28 | Pseudomonas | - | |
10 | OR65 | Pseudomonas | - | |
6 | 11 | OR7 | Peribacillus | OP522408 |
7 | 12 | OR8 | Bacillus | OP522409 |
13 | OR18 | Bacillus | - | |
8 | 14 | OR9 | Bacillus | OP522410 |
9 | 15 | OR12 | Peribacillus | OP522411 |
10 | 16 | OR24 | N.A. a | N.A. |
11 | 17 | OR31 | Staphylococcus | OP522412 |
12 | 18 | OR36 | Kocuria | OP522413 |
13 | 19 | OR51 | Erwinia | OP522414 |
14 | 20 | OR56 | Pseudomonas | OP522415 |
MIC (µg/mL) | |||||||
---|---|---|---|---|---|---|---|
Genus | Isolate | Str. | Tet. | Cip. | Kan. | Chl. | Rif |
Bacillus | OR9 | 50 | 0.5 | 0.5 | 50 | 2.5 | 5 |
Bacillus | OR8 | 50 | 1.25 | 0.5 | 5 | 25 | 5 |
Bacillus | OR18 | 50 | 1.25 | 0.5 | 5 | 25 | 5 |
N.A. a | OR24 | 50 | 1.25 | 5 | 5 | 5 | 5 |
Erwinia | OR3 | 10 | 12.5 | 0.5 | 10 | 5 | 25 |
Erwinia | OR6 | 10 | 5 | 0.5 | 10 | 5 | 10 |
Erwinia | OR51 | 10 | 12.5 | 0.5 | 10 | 5 | 25 |
Kocuria | OR36 | 10 | 12.5 | 5 | 50 | 5 | 10 |
Paenibacillus | OR4 | n.a. a | n.a. a | n.a. a | n.a. a | n.a. a | n.a. a |
Pantoea | OR2 | 10 | 5 | 0.5 | 50 | 2.5 | 10 |
Pantoea | OR11 | 10 | 2.5 | 0.5 | 10 | 1 | 10 |
Peribacillus | OR7 | 50 | 1.25 | 0.5 | 10 | 25 | 5 |
Peribacillus | OR12 | 50 | 1.25 | 0.5 | 5 | 25 | 5 |
Pseudomonas | OR1 | 10 | 2.5 | 0.5 | 2.5 | 25 | 5 |
Pseudomonas | OR19 | 50 | 1.25 | 2.5 | 2.5 | 5 | 5 |
Pseudomonas | OR5 | >50 | 25 | 0.5 | 10 | >50 | 25 |
Pseudomonas | OR28 | >50 | 25 | 0.5 | 10 | >50 | 25 |
Pseudomonas | OR56 | >50 | 25 | 0.5 | 10 | >50 | 25 |
Pseudomonas | OR65 | >50 | >25 | 0.5 | 10 | >50 | 25 |
Staphylococcus | OR31 | >50 | >25 | 0.5 | 5 | 2.5 | 5 |
BCG type | From (nt) | To (nt) | Most Similar Known Cluster | % Similarity |
---|---|---|---|---|
Contig 1 | ||||
Trans AT-PKS, NRPs | 495644 | 558461 | Bacillomycin D | (40%) |
Terpene | 2943693 | 2964472 | Molybdenum cofactor | (17%) |
NRPs | 3799358 | 3842588 | - | - |
RiPP-like | 3864265 | 3873890 | - | - |
RiPP-like | 3919957 | 3929781 | - | - |
Betalactone | 3978104 | 4003065 | Fengycin | (40%) |
NRPs | 4005346 | 4068767 | Puwainaphycin F/ MinutissamideA | (44%) |
NRPs-like, NRPs | 4190374 | 4235399 | Bacillibactin | (38%) |
Siderophore | 4609931 | 4624859 | Petrobactin | (100%) |
NRPs | 4685992 | 4742532 | Octapeptin C4 | (17%) |
RRE-containing, RiPP-like | 5304467 | 5324736 | - | - |
Contig 2 | ||||
RRE-containing | 150714 | 170974 | - |
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Semenzato, G.; Faddetta, T.; Falsini, S.; Del Duca, S.; Esposito, A.; Padula, A.; Greco, C.; Mucci, N.; Zaccaroni, M.; Puglia, A.M.; et al. Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds. Microorganisms 2022, 10, 2086. https://doi.org/10.3390/microorganisms10102086
Semenzato G, Faddetta T, Falsini S, Del Duca S, Esposito A, Padula A, Greco C, Mucci N, Zaccaroni M, Puglia AM, et al. Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds. Microorganisms. 2022; 10(10):2086. https://doi.org/10.3390/microorganisms10102086
Chicago/Turabian StyleSemenzato, Giulia, Teresa Faddetta, Sara Falsini, Sara Del Duca, Antonia Esposito, Anna Padula, Claudia Greco, Nadia Mucci, Marco Zaccaroni, Anna Maria Puglia, and et al. 2022. "Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds" Microorganisms 10, no. 10: 2086. https://doi.org/10.3390/microorganisms10102086