Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals and Media Components
2.2. Microorganisms
2.3. Deposition of Rosenbergiella meliponini D21B
2.4. Isolation of Microorganisms from T. carbonaria
2.5. Cultivation of Microorganisms from T. carbonaria
2.6. Genome Sequencing and Genome Assembly
2.7. Annotation of the R. meliponini D21B Genome
2.8. Genomic DNA Isolation
2.9. 16S rDNA Amplification by PCR
2.10. Phylogenetic Analysis
2.11. Physiological and Biochemical Characterization of R. meliponini D21B
2.12. Electron Microscopy of R. meliponini D21B
2.13. Fatty Acid Methyl Ester (FAME) Profile of Hydrolyzed Lipids from R. meliponini D21B
2.14. Fatty Acid Trimethylsilyl Ester Profile of Hydrolyzed Lipids from R. meliponini D21B
2.15. Spent Liquid Medium Extractions for the Detection of Lipophilic Secondary Metabolites
2.16. Collection of Volatiles from R. meliponini D21B
2.17. Quantification of 2-Phenylethanol and 2-Phenylacetic Acid
2.18. Antibiotic Resistance of the Rosenbergiella Isolates
3. Results
3.1. 16S rRNA Sequence Analysis of the Isolates from T. carbonaria
3.2. Genome of R. meliponini D21B
3.3. Phylogenetic Comparison of R. meliponini D21B and R. epipactidis 2.1A
3.4. Analysis of Secondary Metabolite Biosynthetic Gene Clusters from R. meliponini D21B
3.5. Physiological and Biochemical Characterization of R. meliponini D21B
3.6. Minimal Growth Requirements of Rosenbergiella
3.7. Electron Microscopy of R. meliponini D21B
3.8. Fatty Acid Profile of Hydrolyzed Lipids
3.9. Production of 2-Phenylethanol by the Rosenbergiella Isolates from T. carbonaria
3.10. Analysis of spent medium of R. epipactidis 2.1A and R. meliponini D21B
3.11. Quantification of 2-Phenylethanol and 2-Phenylacetic Acid Production by Rosenbergiella
3.12. Antibiotic Resistance of Rosenbergiella Strains
4. Discussion
4.1. Possible Symbiotic Benefits of Rosenbergiella for Bees
4.2. Amino Acid and Vitamin Synthesis
4.3. Digestion of Food
4.4. Ecological Role of Secondary Metabolites
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Number | % of Total | |
---|---|---|
Total number of bases | 3,042,366 | 100.00% |
Number of coding bases | 2,695,972 | 88.61% |
G/C content | 1,433,972 | 47.13% |
NG50 | 299,429 | |
L50 | 4 | |
DNA scaffolds | 21 | 100.00% |
Genes (total number) | 3023 | 100.00% |
Protein coding genes | 2924 | 96.73% |
Regulatory and miscellaneous features | 44 | 1.46% |
RNA genes | 55 | 1.82% |
rRNA genes | 5 | 0.17% |
5S rRNA | 3 | 0.10% |
16S rRNA | 1 | 0.03% |
23S rRNA | 1 | 0.03% |
tRNA genes | 47 | 1.55% |
other RNA genes | 3 | 0.10% |
Protein coding genes with predicted function | 2521 | 83.39% |
Protein without function prediction | 403 | 13.33% |
Protein coding genes with enzymes | 952 | 31.49% |
Protein coding genes connected to KEGG pathways | 1085 | 35.89% |
Protein coding genes not connected to KEGG pathways | 1839 | 60.83% |
Protein coding genes connected to KEGG orthology (KO) | 2001 | 66.19% |
Protein coding genes not connected to KEGG orthology (KO) | 923 | 30.53% |
Protein coding genes connected to MetaCyc pathways | 795 | 26.30% |
Protein coding genes not connected to MetaCyc pathways | 2129 | 70.43% |
Protein coding genes with COGs3 | 2494 | 82.50% |
with Pfam3 | 2564 | 84.82% |
with TIGRfam3 | 1249 | 41.32% |
with SMART | 560 | 18.52% |
with SUPERFam | 2409 | 79.69% |
with CATH FunFam | 2080 | 68.81% |
in internal clusters | 539 | 17.83% |
Strain | dDDH (d0, in %) | C.I. (d0, in %) | dDDH (d4, in %) | C.I. (d4, in %) | dDDH (d6, in %) | C.I. (d6, in %) | G + C Content Difference (in %) |
---|---|---|---|---|---|---|---|
Rosenbergiella epipactidis 2.1A | 78.8 | [74.8–82.3] | 61.4 | [58.6–64.2] | 78 | [74.6–81.1] | 0.46 |
Rosenbergiella nectarea 8N4 | 73.9 | [69.9–77.5] | 31.1 | [28.7–33.6] | 61.6 | [58.3–64.8] | 0.31 |
Rosenbergiella collisarenosi 8.8A | 51.3 | [47.9–54.8] | 20.7 | [18.5–23.1] | 39.8 | [36.9–42.9] | 1.04 |
Rosenbergiella australiborealis CdVSA20.1 | 47 | [43.6–50.4] | 20.2 | [18.0–22.6] | 37 | [34.1–40.1] | 1.82 |
Pantoea cypripedii LMG 2657 | 13.2 | [10.5–16.5] | 20 | [17.8–22.4] | 13.6 | [11.2–16.3] | 6.92 |
Characteristic | R. meliponini D21B1 | R. epipactidis 2.1A |
---|---|---|
Urease activity | Yes | No |
Utilization of citrate | Yes | No |
Growth at 37 °C | Poor | No |
NRPS/PKS gene cluster | Present | Absent |
Production of 2-phenylethanol | Yes | No |
Thiamine dependency | Independent | Dependent |
Pyocin encoding genes | No | Yes |
Hemolysin encoding genes | No | Yes |
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Farlow, A.J.; Rupasinghe, D.B.; Naji, K.M.; Capon, R.J.; Spiteller, D. Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria. Microorganisms 2023, 11, 1005. https://doi.org/10.3390/microorganisms11041005
Farlow AJ, Rupasinghe DB, Naji KM, Capon RJ, Spiteller D. Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria. Microorganisms. 2023; 11(4):1005. https://doi.org/10.3390/microorganisms11041005
Chicago/Turabian StyleFarlow, Anthony J., Darshani B. Rupasinghe, Khalid M. Naji, Robert J. Capon, and Dieter Spiteller. 2023. "Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria" Microorganisms 11, no. 4: 1005. https://doi.org/10.3390/microorganisms11041005
APA StyleFarlow, A. J., Rupasinghe, D. B., Naji, K. M., Capon, R. J., & Spiteller, D. (2023). Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria. Microorganisms, 11(4), 1005. https://doi.org/10.3390/microorganisms11041005