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Diaminopimelic acid metabolism by Pseudomonadota in the ocean


Zheng, L-Y and Liu, N-H and Zhong, S and Yu, Y and Zhang, X-Y and Qin, Q-L and Song, X-Y and Zhang, Y-Z and Fu, H and Wang, M and McMinn, A and Chen, X-L and Li, P-Y, Diaminopimelic acid metabolism by Pseudomonadota in the ocean, Microbiology Spectrum, 10, (5) pp. 1-15. ISSN 2165-0497 (2022) [Refereed Article]

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© 2022 Zheng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) license (

DOI: doi:10.1128/spectrum.00691-22


Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world’s oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 μM and 0.96 μM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota, which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria.

Item Details

Item Type:Refereed Article
Keywords:diaminopimelic acid, Pseudomonadota, seawater
Research Division:Biological Sciences
Research Group:Microbiology
Research Field:Microbial ecology
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Marine biodiversity
UTAS Author:McMinn, A (Professor Andrew McMinn)
ID Code:154131
Year Published:2022
Deposited By:Ecology and Biodiversity
Deposited On:2022-11-02
Last Modified:2022-12-02
Downloads:3 View Download Statistics

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