1
|
Ara I, Moriuchi R, Dohra H, Kimbara K, Ogawa N, Shintani M. Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil. Microorganisms 2023; 11:1684. [PMID: 37512857 PMCID: PMC10383586 DOI: 10.3390/microorganisms11071684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h-1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20-28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation.
Collapse
Affiliation(s)
- Ifat Ara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Ryota Moriuchi
- Functional Genomics Section, Shizuoka Instrumental Analysis Center, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka City 422-8529, Japan
| | - Hideo Dohra
- Functional Genomics Section, Shizuoka Instrumental Analysis Center, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka City 422-8529, Japan
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka City 422-8529, Japan
| | - Kazuhide Kimbara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Naoto Ogawa
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka City 422-8529, Japan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| |
Collapse
|
2
|
Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
Collapse
Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
| |
Collapse
|
3
|
Iijima S, Shimomura Y, Haba Y, Kawai F, Tani A, Kimbara K. Flow cytometry-based method for isolating live bacteria with meta-cleavage activity on dihydroxy compounds of biphenyl. J Biosci Bioeng 2010; 109:645-51. [DOI: 10.1016/j.jbiosc.2009.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 11/19/2009] [Accepted: 11/30/2009] [Indexed: 11/29/2022]
|
4
|
Ito N, Itakura M, Eda S, Saeki K, Oomori H, Yokoyama T, Kaneko T, Tabata S, Ohwada T, Tajima S, Uchiumi T, Masai E, Tsuda M, Mitsui H, Minamisawa K. Global Gene Expression in Bradyrhizobium japonicum Cultured with Vanillin, Vanillate, 4-Hydroxybenzoate and Protocatechuate. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.240] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Naofumi Ito
- Graduate School of Life Sciences, Tohoku University
| | | | - Shima Eda
- Graduate School of Life Sciences, Tohoku University
| | - Kazuhiko Saeki
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Hirofumi Oomori
- Department of Biology Graduate School of Science, Osaka University
| | | | | | | | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine
| | | | - Toshiki Uchiumi
- Department of Chemistry and BioScience, Faculty of Science, Kagoshima University
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology
| | | | | | | |
Collapse
|
5
|
Saito M, Ikunaga Y, Ohta H, Kurusu Y. Genetic Transformation System for Members of the Genera, Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|