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The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress

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Abstract

Background

Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of Enterobacter species under acidic stress remains poorly understood.

Objective

This study aimed to investigate the survival of an environmental isolate Enterobacter sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes.

Methods

We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions.

Results

A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that Enterobacter reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress.

Conclusions

The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of Enterobacter bacterium.

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Acknowledgements

RPS acknowledges the Department of Biotechnology, Government of India for providing the Ramalingswami Re-entry Fellowship. The author acknowledges the Dept. of Bioengineering and Biotechnology, BIT Mesra for providing the infrastructure.

Funding

The work was supported by the Ramalingswami Re-entry Grant provided by Government of India.

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Authors and Affiliations

  1. Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India

    Kiran Kumari

  2. Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA

    Parva Kumar Sharma

  3. Department of Biotechnlogy, Jaypee Insttute of Information Technology, Noida, 201309, India

    Rajnish Prakash Singh

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  1. Kiran Kumari
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Correspondence to Rajnish Prakash Singh.

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The RNA sequence of S-33 was submitted to NCBI under BioProject No. PRJNA953758.

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Kumari, K., Sharma, P.K. & Singh, R.P. The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress. Genes Genom 46, 671–687 (2024). https://doi.org/10.1007/s13258-024-01513-x

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