ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Terrestrial Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1626161
This article is part of the Research TopicMicrobial Solutions for Restoring Depleted SoilsView all 6 articles
Multiple-omics analysis of three novel haloalkaliphilic species of Kocuria revealed the phenolic acids-degrading abilities are ubiquitous in the genus
Provisionally accepted
- 1Nanjing Agricultural University, Nanjing, China
- 2Inner Mongolia University, Hohhot, China
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Phenolic acids (PAs), which can exert toxic effects on seed germination and plant growth, are the most common allelopathic substances in soils. To better understand the degradation fates of PAs in the rhizosphere of halophyte, five haloalkaliphilic PA-degrading bacteria, which were identified as three novel species of Kocuria (namely Kocuria rhizosphaerae sp. nov., Kocuria kalidii sp. nov., and Kocuria rhizosphaericola sp. nov.), were obtained from the rhizosphere and bulk soil of the halophyte Kalidium cuspidatum. All the five Kocuria strains could efficiently degrade ferulic acid (FA) and cinnamic acid (CA) under saline alkaline conditions. Genomic and transcriptomic analyses revealed that the acrylic groups of FA and CA was first converted to a carboxyl via the CoA-dependent non-β-oxidation pathway by the five Kocuria strains. However, the five Kocuria strains selected different aromatic ring-cleavage ways for the degradation of the benzoic-derivates intermediates of the two compounds. The protocatechuate result from FA was then thoroughly degraded with aromatic ring-opening reaction catalyzed by protocatechuate 3,4-dioxygenase (PcaGH), and the β-ketoadipic acid pathway; while the yield benzoate originated from CA was subsequently converted to catechol by the benzoate 1,2-dioxygenase system (BenABCD) or phenylacetyl-CoA epoxidase (PaaABCD) and further completed the ring-cleavage by catechol 1,2-dioxygenase or catechol 2,3-dioxygenase (two non-PcaGH dioxygenases). The comparative genomic analysis revealed that the genes for phenolic acids hydroxylation, protocatechuate 3,4-dioxygenation, and those involved in the β-ketoadipic acid pathways are universal in the Kocuria strains. It is also demonstrated that the Kocuria strains maintain their osmotic balance by accumulation potassium, but not by biosynthesizing organic osmoprotectants under hypersaline conditions.
Keywords: phenolic acids, Biodegradation, Kocuria, Comparative genomic analysis, osmotic stress, polyphasic taxonomy
Received: 10 May 2025; Accepted: 08 Jul 2025.
Copyright: © 2025 Xu, Sun, Zeng, Wei, Shen and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ji-Quan Sun, Inner Mongolia University, Hohhot, China
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