Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

Anna C Simpson; V V Ramprasad Eedara; Nitin K Singh; Namita Damle; Ceth W Parker; Fathi Karouia; Christopher E Mason; Kasthuri Venkateswaran

doi:10.3389/fmicb.2023.1166013

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

Front Microbiol. 2023 Jun 15:14:1166013. doi: 10.3389/fmicb.2023.1166013. eCollection 2023.

Authors

Anna C Simpson¹, V V Ramprasad Eedara², Nitin K Singh¹, Namita Damle³, Ceth W Parker¹, Fathi Karouia⁴, Christopher E Mason³, Kasthuri Venkateswaran¹

Affiliations

¹ California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States.
² Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India.
³ Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States.
⁴ NASA Ames, Moffet Field, CA, United States.

Abstract

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1^T. The 16S sequence of the F6_2S_P_1^T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1^T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1^T are anteiso-C_15:0 (51.7%), iso-C_16:0 (23.1%), and iso-C_15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1^T (=NRRL B-65657^T and DSMZ 115098^T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1^T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1^T and other members of this clade.

Keywords: Cohnella; International Space Station (ISS); novel bacteria; pangenome analysis; space biology.

Grants and funding

Part of the research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with National Aeronautics and Space Administration. This research was funded by a 2012 Space Biology NNH12ZTT001N grant no. 19-12829-26 under Task Order NNN13D111T award to KV, which also funded the post-doctoral fellowship for CP. The funders had no role in study design, data collection and interpretation, the writing of the manuscript, or the decision to submit the study for publication.