Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil

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.

Paraburkholderia largidicola sp. nov., a gut symbiont of the bordered plant bug Physopelta gutta

“…Cell morphology, motility, and spore formation were observed under phase-contrast microscopy (BX50, Olympus). Growth at different temperatures (4,10,15,20,25,30,35,37, and 40 °C), NaCl concentrations 0-1.5 % (w/v; at intervals of 0.5 % unit), and pH 3.5-8.0 (at intervals of 0.5 pH unit) was assessed in TSB liquid medium with shaking (150 r.p.m.). The media were buffered with 25 mM of MES (pH 5.5-6.5), MOPS (pH 6.5-7.5), and HEPES (pH 7.5-8.0), and adjusted to varying pH by adding NaOH.…”

“…The analysis with GTDB-tk version 2.1.1 and reference database R207_v2 [28] of the complete genome of strain F2 T assigned it to the same species as strain PGU16. In the Genome Taxonomy Database (GTDB; R214) [29], the genome of strain PGU16 belonged to ‘a species cluster ( Paraburkholderia sp013426895 )’ that consisted of the genomes of the following three conspecific strains: 19C8 deposited as P. terrae [30], PCAR477 deposited as P. caribensis , and 19CS9-1 deposited as P. hospita [30].…”