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Phycicoccus avicenniae sp. nov., a novel endophytic actinomycete isolated from a branch of Avicennia mariana

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Abstract

A novel endophytic actinomycete, designated strain BSK3Z-2 T, was isolated from a surface-sterilised branch of Avicennia mariana from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. Cells were observed to be Gram-stain positive, aerobic, asporogenous and rod-shaped. Strain BSK3Z-2 T was found to grow optimally at 30 °C, pH 7.0 and in the presence of 1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BSK3Z-2 T belongs to the genus Phycicoccus and has high 16S rRNA gene sequence similarity of 98.1% with Phycicoccus endophyticus IP6SC6T. Phylogenetic analysis based on the genome of strain BSK3Z-2 T was performed by extracting and aligning 39 conserved proteins and 88 housekeeping genes, which further confirmed the phylogenetic assignment of strain BSK3Z-2 T. The draft genome of strain BSK3Z-2 T is 3.54 Mbp with a DNA G + C content of 73.8%. The average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain BSK3Z-2 T and species of genus Phycicoccus were 73.8–85.6%, 64.5–75.9% and 19.5–23.8%, respectively, which are below the standard cut-off values for bacterial species delineation. Strain BSK3Z-2 T contains MK-8(H4) as the dominant menaquinone. The cell wall peptidoglycan contains meso-diaminopimelic acid. The polar lipids profile of strain BSK3Z-2 T was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The predominant fatty acids were identified as C15:0, C17:0, iso-C16:0 and C17:1ω8c. Comparing the phenotypic and phylogenetic features of the strain BSK3Z-2 T and related taxa, strain BSK3Z-2 T is concluded to represent a novel species of the genus Phycicoccus, for which the name Phycicoccus avicenniae sp. nov. is proposed. The type strain is BSK3Z-2 T (= CGMCC 1.18743 T = JCM 34335 T).

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Data availability statements

All data generated or analysed during this study are included in this published article, its supplementary information files and GenBank/EMBL/DDBJ.

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Acknowledgements

The authors thank Dr. Shao-Wei Liu for the reference strain Phycicoccus endophyticus IP6SC6T. This research was supported by the National Natural Sciences Foundation of China (NSFC, Grant no. 81960642) and Guizhou Provincial Science and Technology Foundation (No. Qian Ke He Jichu [2019]1347).

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Authors and Affiliations

  1. Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People’s Republic of China

    Ming-Sheng Chen, Xiao-Hui Chen, Zi-Hao Huang, Xiao-Rui Yan & Li Tuo

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  1. Ming-Sheng Chen
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  2. Xiao-Hui Chen
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  3. Zi-Hao Huang
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  4. Xiao-Rui Yan
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  5. Li Tuo
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Contributions

Ming-Sheng Chen was responsible for the major experiments, analyzed data and prepared the manuscript; Li Tuo, Xiao-Rui Yan and Ming-Sheng Chen isolated strain; Ming-Sheng Chen, Xiao-Hui Chen and Zi-Hao Huang were responsible for physiological and biochemical experiments; Li Tuo designed the experiments and guided the manuscript writing. All authors have read and approved the final manuscript.

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Correspondence to Li Tuo.

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Chen, MS., Chen, XH., Huang, ZH. et al. Phycicoccus avicenniae sp. nov., a novel endophytic actinomycete isolated from a branch of Avicennia mariana. Antonie van Leeuwenhoek 114, 1431–1442 (2021). https://doi.org/10.1007/s10482-021-01614-7

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  • DOI: https://doi.org/10.1007/s10482-021-01614-7

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