Abstract

Purpose

Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level.

Methods

The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase.

Results

De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalogenase IIB family hydrolase and haloacid dehalogenase type II), suggesting that these enzymes can participate in the catabolism of halogenated organic acids. The mapping identified seven Na+/H+ antiporter subunits that are vital for adaptation of the bacterium to an alkaline environment. Apart from a pairwise analysis to the well-established L-2-haloacid dehalogenases, whole-cell analysis strongly suggested that the haloacid dehalogenase type II might act stereospecifically on L-2-chloropropionic acid, D,L-2-chloropropionic acid, and 2,2-dichloropropionic acid. Whole-cell studies confirmed the utilization of these three substrates and the gene’s role in dehalogenation.

Conclusions

To our knowledge, this is the first report of the full genome sequence for strain BHS1, which enabled the characterization of selected genes having specific metabolic activities and their roles in the biodegradation of halogenated compounds.

Details

Title
Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey)
Author
Wahhab, Batool Hazim Abdul 1 ; Samsulrizal, Nurul Hidayah 2 ; Edbeib, Mohamed Faraj 3 ; Wahab, Roswanira Ab. 4 ; Al-Nimer, Marwan S. M. 5 ; Hamid, Azzmer Azzar Abdul 6 ; Oyewusi, Habeebat Adekilekun 7 ; Kaya, Yilmaz 8 ; Notarte, Kin Israel R. 9 ; Shariff, Amir Husni Mohd 10 ; Huyop, Fahrul 7   VIAFID ORCID Logo 

1  Faculty of Medicine, Al-Mustansiriyah University, Department of Microbiology, Baghdad, Iraq (GRID:grid.411309.e); Universiti Teknologi Malaysia, Department of Biosciences, Faculty of Science, Johor Bahru, Malaysia (GRID:grid.410877.d) (ISNI:0000 0001 2296 1505) 
2  International Islamic University Malaysia, Department of Plant Science, Kulliyah of Science, Kuantan, Malaysia (GRID:grid.440422.4) (ISNI:0000 0001 0807 5654) 
3  Bani Walid University, Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid, Libya (GRID:grid.440422.4) 
4  Universiti Teknologi Malaysia, Department of Chemistry, Faculty of Science, Johor Bahru, Malaysia (GRID:grid.410877.d) (ISNI:0000 0001 2296 1505) 
5  University Medical Hawler, Department of Pharmacology, Faculty of Pharmacy, Erbil, Iraq (GRID:grid.410877.d) 
6  International Islamic University Malaysia, Department of Biotechnology, Kulliyah of Science, Kuantan, Malaysia (GRID:grid.440422.4) (ISNI:0000 0001 0807 5654) 
7  Universiti Teknologi Malaysia, Department of Biosciences, Faculty of Science, Johor Bahru, Malaysia (GRID:grid.410877.d) (ISNI:0000 0001 2296 1505) 
8  Kyrgyz-Turkish Manas University, Department of Biology, Faculty of Science, Bishkek, Kyrgyzstan (GRID:grid.444269.9); Ondokuz Mayis University, Department of Agricultural Biotechnology, Faculty of Agriculture, Samsun, Turkey (GRID:grid.411049.9) (ISNI:0000 0004 0574 2310) 
9  University of Santo Tomas España, Faculty of Medicine and Surgery, Manila, Philippines (GRID:grid.412775.2) (ISNI:0000 0004 1937 1119) 
10  Universiti Malaysia Sabah, Faculty of Food Science and Nutrition, Kota Kinabalu, Malaysia (GRID:grid.265727.3) (ISNI:0000 0001 0417 0814) 
Publication year
2021
Publication date
Dec 2021
Publisher
Springer Nature B.V.
ISSN
15904261
e-ISSN
18692044
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1186/s13213-021-01625-9
ProQuest document ID
2670510568
Copyright
© The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.