Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming, alkane degrading bacterium, designated DJM-14T, was isolated from oilfield alkali-saline soil in Heilongjiang, Northeast China. On the basis of 16 S rRNA gene sequencing, strain DJM-14T was shown to belong to the genus Nocardioides, and related most closely to Nocardioides terrigena KCTC 19,217T (95.53% 16 S rRNA gene sequence similarity). Strain DJM-14T was observed to grow at 25–35 °C, pH 7.0–11.0, in the presence of 0–6.0% (w/v) NaCl. The predominant respiratory quinone was MK-8 (H4) and LL-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were identified as iso-C16:0 and C18:1 ω9c. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The genome (3,722,608 bp), composed of 24 contigs, had a G + C content of 69.6 mol%. Out of the 3667 predicted genes, 3618 were protein-coding genes, and 49 were ncRNAs. Digital DNA–DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of strain DJM-14T against genomes of the type strains of related species in the same family ranged between 18.7% and 20.0%; 68.8% and 73.6%, respectively. According to phenotypic, genotypic and phylogenetic data, strain DJM-14T represents a novel species in the genus Nocardioides, for which the name Nocardioides limicola sp. nov. is proposed and the type strain is DJM-14T (= CGMCC 4.7593T, =JCM 33,692T). In addition, novel strains were able to grow with n-alkane (C24-C36) as the sole carbon source. Multiple copies of alkane 1-monooxygenase (alkB) gene, as well as alcohol dehydrogenase gene and aldehyde dehydrogenase gene involved in the alkane assimilation were annotated in the genome of type strain DJM-14T.
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Acknowledgements
We thank all the laboratory members for their critical reviews and comments on this manuscript, and we thank Sai Yang for the sample collection and Xin Zhang for the help during the experiment.
Funding
This work was financially supported by the National Natural Science Foundation of China [31770543, 41503068, 31600069], Priority Academic Program Development of Jiangsu Higher Education Institutions [PAPD-2018-87] and the Natural Science Foundation of Jiangsu Province of China [BK20150496, BK20150497].
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This study was conceived and designed by LZ and WW, BYY and WJG performed the experiments. XX and SKL provided guidance on data analysis. XYH analyzed the data and drafted the manuscript. All authors reviewed this manuscript.
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Zhu, L., Yang, B., Guo, W. et al. Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil. Antonie van Leeuwenhoek 117, 14 (2024). https://doi.org/10.1007/s10482-023-01907-z
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DOI: https://doi.org/10.1007/s10482-023-01907-z