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Long-read sequencing reveals increased occurrence of genomic variants and adenosine methylation in Bacillus pumilus SAFR-032 after long-duration flight exposure onboard the International Space Station

Published online by Cambridge University Press:  16 November 2021

Samantha M. Waters Open the ORCID record for Samantha M. Waters [Opens in a new window] ,
S. Marshall Ledford ,
Amanda Wacker ,
Sonali Verma ,
Bianca Serda ,
Jordan McKaig Open the ORCID record for Jordan McKaig [Opens in a new window] ,
Joseph Varelas ,
Patrick M. Nicoll ,
Kasthuri Venkateswaran  and
David J. Smith
Samantha M. Waters*
Affiliation:
Universities Space Research Association, Columbia, CA, USA NASA Ames Research Center, Space Biosciences Research Division, Moffett Field, CA, USA
S. Marshall Ledford
Affiliation:
Vassar College, Poughkeepsie, NY, USA
Amanda Wacker
Affiliation:
University of California San Diego, La Jolla, CA, USA
Sonali Verma
Affiliation:
NASA Ames Research Center, Space Biosciences Research Division, Moffett Field, CA, USA
Bianca Serda
Affiliation:
Department of Biology, University of New Mexico, Albuquerque, NM, USA Current: Department of Biochemistry and Molecular Biology, MSU-DOE Plant Research Laboratory Michigan State University, East Lansing, MI, USA
Jordan McKaig
Affiliation:
Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
Joseph Varelas
Affiliation:
Universities Space Research Association, Columbia, CA, USA
Patrick M. Nicoll
Affiliation:
NASA Ames Research Center, Space Biosciences Research Division, Moffett Field, CA, USA Blue Marble Space Institute of Science, Moffett Field, CA, USA Current: Department of Psychology, University of Victoria, Victoria, BC, Canada
Kasthuri Venkateswaran
Affiliation:
Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, USA
David J. Smith
Affiliation:
NASA Ames Research Center, Space Biosciences Research Division, Moffett Field, CA, USA
*
Author for correspondence: Samantha M. Waters, E-mail: [email protected]
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Abstract

Bacillus pumilus SAFR-032, an endospore-forming bacterial strain, was investigated to determine its methylation pattern (methylome) change, compared to ground control, after direct exposure to space conditions onboard the International Space Station (ISS) for 1.5 years. The resulting ISS-flown and non-flown strains were sequenced using the Nanopore MinION and an in-house method and pipeline to identify methylated positions in the genome. Our analysis indicated genomic variants and m6A methylation increased in the ISS-flown SAFR-032. To complement the broader omics investigation and explore phenotypic changes, ISS-flown and non-flown strains were compared in a series of laboratory-based chamber experiments using an X-ray irradiation source (doses applied at 250, 500, 750, 1000 and 1250 Gy); results show a potentially higher survival fraction of ISS-flown DS2 at the two highest exposures. Taken together, results from this study document lasting changes to the genome by methylation, potentially triggered by conditions in spaceflight, with functional consequences for the resistance of bacteria to stressors expected on long-duration missions beyond low Earth orbit.

Keywords

Bacillusionizing radiationISSmethylationsequencing
Type
Research Article
Information
International Journal of Astrobiology , Volume 20 , Issue 6 , December 2021 , pp. 435 - 444
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Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press

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