Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific

Lingqi Ma; Yuqi Bai; Weili Wang; Shengxiang Pei; Gaiyun Zhang

doi:10.3389/fgene.2024.1356956

Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific

Front Genet. 2024 Mar 14:15:1356956. doi: 10.3389/fgene.2024.1356956. eCollection 2024.

Authors

Lingqi Ma^#^{1

2

3}, Yuqi Bai^#³, Weili Wang⁴, Shengxiang Pei¹, Gaiyun Zhang¹

Affiliations

¹ Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China.
² Department of Environmental Sciences, College of the Coast & Environment, Louisiana State University, Baton Rouge, LA, United States.
³ State Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Science, Xiamen University, Xiamen, Fujian, China.
⁴ Hainan Observation and Research Station of Ecological Environment and Fishery Resource in Yazhou Bay, Hainan Institute of Zhejiang University, Sanya, Hainan, China.

^# Contributed equally.

Abstract

Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The presence of rich categories related to catalytic activity, membrane part and metabolic process highlights their involvement in cellular component, biological process, and molecular function. The genome sequence of strain R16 also revealed the presence of 13 putative biosynthetic gene clusters for secondary metabolites, including those for ε-Poly-L-lysine, ectoine, heterobactin, isorenieratene and corynecin, suggesting its potential for antibiotic production and warranting further exploration.

Keywords: Prescottella; biotechnological applications; extreme environments; phylogenetic analysis; whole-genome sequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by the National Natural Science Foundation of China through grant 42206140, the China Postdoctoral Science Foundation through grant 2021M702728, the Cross-Strait Postdoctoral Fellowship Plan through grant 2021B001, and the Outstanding Postdoctoral Scholarship, State Key Laboratory of Marine Environmental Science at Xiamen University.