Abstract
Background
PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions.
Objective
To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition.
Methods
We evaluated the activity of three Klebsiella spp. in two different conditions, specific nitrogen-deficient MS media and greenhouse experiment. Applying comparative genomics, genes encoding for PGP traits were identified from the whole-genome sequencing of the three strains. With the help of the RAST tool kit and functional annotation, a total number of genes encoding for cell wall capsule, nitrogen metabolism, sulfur genes and many other functional groups were identified. With the help of blast circular genome, similarity between GC content, pseudogene and tRNA was represented. The percentage of gene similarity of SSN1 was generated against BLAST with M5a1 and SGM81. Other methods like synteny alignment and orthologous gene clusters were applied to understand the homologous present in three strains.
Results
SSN1 was actively producing the maximum amount of ammonia 10.97 ± 0.29 µmol/mL compared to the other two strains. K. oxytoca M5a1 was considered negative for all PGP traits except ammonia production. The activity of SSN1 was showing a consistent pattern both the conditions whereas M5a1 was only active in vitro condition. Gene encoding for allantoin metabolism allD, allC, allB, allA, allE, allR, allH were identified in SSN1 and M5a1 but was absent in SGM81. The highest COG was shared between SGM81 and SSN1 predicting a maximum number of similar genes. The nif gene cluster was 98 % identical to the M5a1 strain.
Conclusions
Comparatively, SSN1 expressed the additional gene for various PGP traits which suggest higher efficiency of strain in nitrogen deficiency stress.
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Abbreviations
- PGPB:
-
Plant growth promoting bacteria
- PGP:
-
Plant growth promoting
- WGS:
-
Whole genome sequencing
- RAST:
-
Rapid annotation using subsystem technology
- PEG:
-
Protein encoding gene
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Acknowledgements
This work was supported by the Department of Science and Technology UK India Education Research (DST/INT/UK/P-156/2017). The research at the Department of Microbiology and Biotechnology, Gujarat University, School Of Sciences and Imperial College London was funded by British Council [P72898]. We thank Mr. Naman Mangukia, Research Scholar (Gujarat University) for his contribution in data submission at NCBI. DST-FIST “Fund for Improvement of S&T Infrastructure (FIST)” of the Department of Science & Technology (DST), Government of India for providing basic infrastructure grant to facilitate R&D work.
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Sharma, S., Gang, S., Schumacher, J. et al. Genomic appraisal of Klebsiella PGPB isolated from soil to enhance the growth of barley . Genes Genom 43, 869–883 (2021). https://doi.org/10.1007/s13258-021-01099-8
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DOI: https://doi.org/10.1007/s13258-021-01099-8