Abstract
Alkalihalobacillus okhensis is a halo-alkaliphile with optimal growth at pH 10 and 5% NaCl. Phylogenetic analysis revealed habitat-dependent segregation of Bacilli, with all the alkalihalophiles forming a separate clade. It uses acidification of the external medium and pH-dependent cell wall reinforcement to survive sodic environments. Interestingly, comparative genome analysis revealed the genome encodes surface proteins with a high proportion of acidic amino acids compared to their orthologs of B. subtilis, a piece of direct evidence for adaptive evolution. It has a relatively higher number of genes involved in the metabolism of osmolytes and sodium-dependent transporters when compared to B. subtilis. Growth of Alkalihalobacillus okhensis strain Kh10-101 T (hereafter A. okhensis) is Na+ dependent, with a minimum of 4% NaCl at neutral pH, but 0.5% NaCl is enough at pH 10. It tolerated a sudden increase in salt concentration and exhibited an elongated phenotype but could not tolerate a sudden pH shift from 7 to 11. The cell envelope got damaged, confirming that the pH regulation through cell wall reinforcement is key to survival at a high-pH condition. We report for the first time a comprehensive genome analysis of Bacilli to delineate the mechanisms evolved for adaptation to halo-alkaline conditions.
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source glucose (filled circle) and non-fermentable carbon source malate (unfilled circle), similar results were obtained in two individual experiments and data represented is the mean
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The datasets used and/or analyzed during the current study are available in the manuscript and supplementary information. All data generated or analyzed during this study are also available from the corresponding author on reasonable request.
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All the codes written and used during this study are also available from the corresponding author on reasonable request.
Abbreviations
- NaCl:
-
Sodium chloride
- NaOH:
-
Sodium hydroxide
- Na+ :
-
Sodium ion
- OH− :
-
Hydroxyl ion
- SEM:
-
Scanning electron microscopy
- EDX:
-
Energy-dispersive X-ray spectroscopy
- SD:
-
Standard deviation
- D:
-
Aspartic acid
- E:
-
Glutamic acid
- H:
-
Histidine
- K:
-
Lysine
- R:
-
Arginine
- G:
-
Glycine
- A:
-
Alanine
- S:
-
Serine
- V:
-
Valine
- I:
-
Iso-leucine
- N:
-
Aspargine
- ANI:
-
Average nucleotide identity
- RAST:
-
Rapid annotations using subsystems technology
- pI:
-
Iso electric point
- CMB:
-
Nutrient medium (1% d-glucose, 0.5% KH2PO4, 0.5% peptone, 0.5% yeast extract)
- NhaA-D:
-
Sodium/hydrogen antiporters A-D
- Kef:
-
Potassium efflux protein
- Ktr:
-
Potassium transporter
- MFS:
-
Major facilitator super family protein
- MurJ:
-
Murein biosynthesis integral membrane protein
- YfcH:
-
Cell division inhibitor protein
- Mot complex:
-
Flagellar motor protein complex
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Acknowledgements
We thank Dr. Catriona MA Thompson, Department of Molecular Microbiology, John Innes Center, Norwich, UK for critical reading of the manuscript. We gratefully acknowledge the Department of Science and Technology, Government of India, Funds for Infrastructure in Science and Technology, Level I and UGC Special Assistance Programme support to the Department of Biotechnology and Bioinformatics. We thank the Department of Biotechnology, Govt. of India, Centre for Research and Education in Biology and Biotechnology for providing Genomics facility and support of DST Promotion of University Research and Scientific Excellence to the School of Life Sciences, University of Hyderabad.
Funding
This work was supported by a grant from UGC ISF research project 6 6/2017(IC) and DBT funded project (BT/PR12661/NDB/39/518/2015) to J.S.S.P.
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PSK and JSSP designed and coordinated the study; PSK and JSSP wrote the manuscript; PSK, SR and JSSP performed bioinformatics analyses and edited the manuscript; PSK carried out laboratory work. All authors have contributed and approved the final manuscript.
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Krishna, P.S., Raghunathan, S. & Prakash, J.S.S. Comparative genome analysis of Alkalihalobacillus okhensis Kh10-101 T reveals insights into adaptive mechanisms for halo-alkali tolerance. 3 Biotech 11, 392 (2021). https://doi.org/10.1007/s13205-021-02938-x
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DOI: https://doi.org/10.1007/s13205-021-02938-x