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Moriuchi R, Sano R, Fujii S, Suzuki Y, Makita M, Kawashima Y, Shirakawa T, Shindo R, Shinkai T, Miura K, Hirose M, Nakajima M, Kurokawa A, Chetia R, Hirokawa C, Suzuki T, Ito Y, Murano H, Dohra H, Ogawa N, Kanesaki Y. Complete genome sequence of Paraburkholderia sp. strain 22B1P capable of utilizing 3-chlorobenzoate as a carbon source. Microbiol Resour Announc 2024; 13:e0123523. [PMID: 38488372 PMCID: PMC11008179 DOI: 10.1128/mra.01235-23] [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: 12/15/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Paraburkholderia sp. strain 22B1P utilizes 3-chlorobenzoate as a carbon source. Complete genome sequencing of strain 22B1P revealed two chromosomes and two plasmids. The genes involved in the conversion of 3-chlorobenzoate to 3-chlorocatechol and those involved in the conversion of 3-chlorocatechol to 3-oxoadipate were located on chromosomes 2 and 1, respectively.
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Affiliation(s)
- Ryota Moriuchi
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Rion Sano
- Shizuoka Prefectural Fujinomiya-Kita High School, Fujinomiya, Shizuoka, Japan
| | - Shuma Fujii
- OISCA Hamamatsu Kokusai High School, Hamamatsu, Shizuoka, Japan
| | - Yuito Suzuki
- Shizuoka Prefectural Shimada Senior High School, Shimada, Shizuoka, Japan
| | - Miyune Makita
- Shizuoka Prefectural Shimada Senior High School, Shimada, Shizuoka, Japan
| | - Yo Kawashima
- Hamamatsu Gakugei High School, Hamamatsu, Shizuoka, Japan
| | | | - Renki Shindo
- Shizuoka Prefectural Shizuoka Higashi High School, Aoi-ku, Shizuoka, Japan
| | - Tatsumi Shinkai
- Shizuoka Prefectural Shizuoka Higashi High School, Aoi-ku, Shizuoka, Japan
| | - Kaede Miura
- Fuji Sacred Heart School, Susono, Shizuoka, Japan
| | - Moka Hirose
- Fuji Sacred Heart School, Susono, Shizuoka, Japan
| | - Momiji Nakajima
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Asahi Kurokawa
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Rituparna Chetia
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Chiharu Hirokawa
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Tomoko Suzuki
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Yukiko Ito
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Hiroki Murano
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Hideo Dohra
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Naoto Ogawa
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Yu Kanesaki
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
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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.
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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
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Alviz-Gazitua P, Durán RE, Millacura FA, Cárdenas F, Rojas LA, Seeger M. Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium. Microorganisms 2022; 10:microorganisms10020484. [PMID: 35208938 PMCID: PMC8879955 DOI: 10.3390/microorganisms10020484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II).
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Affiliation(s)
- Pablo Alviz-Gazitua
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5311890, Chile
| | - Roberto E. Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
| | - Felipe A. Millacura
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK
| | - Franco Cárdenas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Centro Regional de Estudios en Alimentos Saludables (CREAS), Avenida Universidad 330, Curauma, Valparaíso 2373223, Chile
| | - Luis A. Rojas
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte, Avenida Angamos 610, Antofagasta 1270709, Chile;
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Correspondence: or
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