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Genomic characterization and molecular dating of the novel bacterium Permianibacter aggregans HW001T, which originated from Permian ground water

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Abstract

The Permian Basin is a unique ecosystem located in the southwest of the USA. An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater. In our previous study, a novel bacterial strain, Permianibacter aggregans HW001T, was isolated from microalgae cultures incubated with Permian Basin waters, and was shown to originate from the Permian Ocean. In this study, strain HW001T was shown to be the representative strain of a novel family, classified as ‘Permianibacteraceae’. The results of molecular dating suggested that the strain HW001T diverged ~ 447 million years ago (mya), which is the early Permian period (~ 250 mya). Genome analysis was used to access its potential energy utilization and biosynthesis capacity. A large number of transporters, carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T. In addition, a series of important metabolic pathways, such as peptidoglycan biosynthesis, osmotic stress response system and multifunctional quorum sensing were annotated, which may confer the ability to adapt to various unfavorable environmental conditions. Finally, the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted, indicating that the adaptation of P. aggregans to a changing marine environment depends on the evolution of their metabolic capabilities, especially in signal transmission. In conclusion, the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.

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Data availability

The genome sequence has been submitted to the GenBank database under BioProject PRJNA526813 and accession number CP037953.

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Acknowledgements

Funding for this study was provided by the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0606), National Natural Science Foundation of China (92051118), Guangdong Science and Technology Department (2019A1515011139), and 2020 Li Ka Shing Foundation (LKSF) Cross-Disciplinary Research Grant (2020LKSFG07A).

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Authors and Affiliations

  1. Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China

    Shuangfei Zhang & Hui Wang

  2. Biology Department, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China

    Shuangfei Zhang & Hui Wang

  3. Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, 21201, USA

    Russell T. Hill

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HW and RTH conceived and designed the experiments; SZ performed the experiments and drafted the manuscript; HW, RTH, and SZ revised the manuscript; HW supervised the project. The final manuscript was approved by all of the authors.

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Correspondence to Hui Wang.

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Zhang, S., Hill, R.T. & Wang, H. Genomic characterization and molecular dating of the novel bacterium Permianibacter aggregans HW001T, which originated from Permian ground water. Mar Life Sci Technol 5, 12–27 (2023). https://doi.org/10.1007/s42995-023-00164-3

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