Abstract
Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3− uptake and interconversion, and anaplerotic HCO3− fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.
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Data availability
This whole-genome shotgun project for Youngimonas vesicularis CC-AMW-ET has been deposited at DDBJ/ENA/GenBank under BioProject no. PRJNA531816, and the accession no. is SSMD00000000. The version described in this paper is the first version.
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Authors would like to thank Yu-Ting Hseih for her technical assistance.
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This work was financially supported by the National Science and Technology Council (Taiwan) under Grant No. 111–2313-B-005–050 and by the “Innovation and Development Center of Sustainable Agriculture” from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan.
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CCY and AH conceptualized the work. AH drafted the manuscript. AH, SKV and PS performed genomic data mining, annotation and comparative genomics. AH analyzed the data and restructured the manuscript with scientific input from all the authors. SYL performed AAI, UBCG and microscopic analysis. All the authors discussed the results and revised the manuscript.
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Hameed, A., Suchithra, K.V., Lin, SY. et al. Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-ET affiliated to family Paracoccaceae. Antonie van Leeuwenhoek 116, 1247–1259 (2023). https://doi.org/10.1007/s10482-023-01881-6
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DOI: https://doi.org/10.1007/s10482-023-01881-6