Abstract—Spore-forming bacteria have a unique resistance to negative environmental conditions, including aggressive space factors, and are an excellent model for studying adaptation mechanisms and survival strategies at the molecular level. The study analyzed the genome of Bacillus velezensis, which remained viable after a 2-year exposure in outer space on the outer surface of the ISS as part of the Test space experiment. A comparative analysis of the draft genomes of the exhibit strain and the ground control did not reveal significant changes; the average nucleotide identity was 99.98%, which indicates the ability of microorganisms to maintain genome stability in space conditions, due to both increased stress resistance of bacterial spores and efficient operation of the system of repair of accumulated changes. The study of a single nucleotide polymorphism in the genome of B. velezensis revealed nine point substitutions, three of which are in intergenic regions, six in protein-coding genes, three of them are missense mutations, two nucleotide deletions leading to a shift in the reading frame, and one synonymous substitution. The profiles of the housekeeping genes were determined during MLST typing and it was found that the allelic profiles obtained for B. velezensis T15.2 and 924 strains do not correspond to any of the previously described sequence types.The presented results indicate the ability of B. velezensis bacteria to maintain the viability of spores and the integrity of the genome for a long time under extreme conditions of outer space, which is important for the problem of planetary protection, as well as the potential possibility of performing biotechnological processes based on B. velezensis during space exploration.
REFERENCES
Horneck G., Klaus D. M., Rocco L. 2010. Space Microbiology. Microbiol. Mol. Biol. Rev. 74, 121–156.
Horneck G., Bucker H., Reitz G. 1994. Long-term survival of bacteria spores in space. Adv. Space Res. 14, 41–45.
Rabbow E., Rettberg P., Barczyk S., Bohmeier M., Parpart A., Panitz C., Horneck G., Burfeindt J., Molter F., Jaramillo F. 2015. The astrobiological mission EXPOSE-R on board of the International Space Station. Int. J. Astrobiol. 14, 3–16.
Baranov I.M., Novikova N.D., Polikarpov N.A., Sychev V.N., Levinskikh M.A., Alekseev V.R., Okuda T., Sugimoto M., Gusev O.A., Grigoriev A.I. 2009. Biorisk experiment: 13-month exposition of resting forms of organisms on the outer side of the Russian Segment of the International Space Station (preliminary results). Dokl. Biochem. Biophys. 426, 206–209.
de La Torre R., Sancho L.G., Horneck G., de los Ríos A., Wierzchos J., Olsson-Francis K., Cockell C.S., Rettberg P., Berger T., de Vera J.P.P., Ott S., Frías J.M., Melendi P.G., Lucas M.M., Reina M., Pintado A., Demets R. 2010. Survival of lichens and bacteria exposed to outer space conditions—results of the Lithopanspermia experiments. Icarus. 208 (2), 735–748.
Ott E., Kawaguchi Y., Kölbl D., Rabbow E., Rettberg P., Mora M., Moissl-Eichinger C., Weckwerth W., Yamagishi A., Milojevic T. 2020. Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission. Microbiome. 8 (1), 150.
Nicholson W.L., Moeller R., Horneck G. 2012. Transcriptomic responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated martian conditions on the EXPOSE-E experiment PR-OTECT. Astrobiology. 12 (5), 469–486.
Vaishampayan P.A., Rabbow E., Horneck G., Venkateswaran K.J. 2012. Survival of Bacillus pumilus spores for a prolonged period of time in real space conditions. Astrobiology. 12 (5), 487–497.
Mastroleo F., Van Houdt R., Leroy B., Benotmane M.A., Janssen A., Mergeay M., Vanhavere F., Hendrickx L., Wattiez R., Leys N. 2009. Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight. ISME J. 3 (12), 1402–1419.
Wilson J.W., Ott C.M., Honer zu Bentrup K., Ramamurthy R., Quick L., Porwollik S., Cheng P., McClelland M., Tsaprailis G., Radabaugh T., Hunt A., Fernandez D., Richter E., Shah M., Kilcoyne M., Joshi L., Nelman-Gonzalez M., Hing S., Parra M., Dumars P., Norwood K., Bober R., Devich, J. Ruggles A., Goulart C., Rupert M., Stodieck L., Stafford P., Catella L., Schurr M.J., Buchanan K., Morici L., McCracken J., Allen P., Baker-Coleman C., Hammond T., Vogel J., Nelson R., Pierson D.L., Stefanyshyn-Piper H.M., Nickerson C.A. 2007. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. Proc. Natl. Acad. Sci. USA. 104 (41), 16299–16304.
Klaus D.M., Howard H.N. 2006. Antibiotic efficacy and microbial virulence during space flight. Trends Biotechnol. 24, 131–136.
Su L., Chang D., Liu C. 2013. The development of space microbiology in the future: The value and significance of space microbiology research. Future Microbiol. 8, 5–8.
Oshurkova V.I., Deshevaya E.A., Suzina N.E., Shubralova E.V., Shcherbakova V.A. 2021. Methanogenic archaea in space conditions. Aerospace Environ. Med. 55 (1), 63‒69.
Deshevaya E.A., Shubralova E.V., Fialkina S.V., Guridov A.A., Novikova N.D., Tsygankov O.S., Lianko P.S., Orlov O.I., Morzunov S.P., Rizvanov A.A., Nikolaeva I.V. 2020. Microbiological investigation of the space dust collected from the external surfaces of the international space station. BioNanoScience. 10, 81–88.
MagocT., Salzberg S. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27 (21), 2957–2963.
Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., Formsma K., Gerdes S., Glass E.M., Kubal M., Meyer F., Olsen G.J., Olson R., Osterman A.L., Overbeek R.A., McNeil L.K., Paarmann D., Paczian T., Parrello B., Pusch G.D., Zagnitko O. 2008. The RAST Server: Rapid annotations using subsystems technology. BMC Genomics. 9, 75.
Langdon W.B. 2015. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min. 8, 1.
Bankevich A., Nurk S., Antipov D., Gurevich A.A., Dvorkin M., Kulikov A.S., Lesin V.M., Nikolenko S.I., Pham S., Prjibelski A.D., Pyshkin A.V., Sirotkin A.V., Vyahhi N., Tesler G., Alekseyev M.A., Pevzner P.A. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19 (5), 455–477.
Liang Q., Liu C., Xu R., Song M., Zhou Z., Li H., Dai W., Yang M., Yu Y., Chen H. 2021. fIDBAC: A platform for fast bacterial genome identification and typing. Front. Microbiol. 18, 723577.
Saitou N., Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.
Tamura K., Stecher G., Kumar S. 2021. MEGA 11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 25, 3022–3027.
Jolley K.A., Bliss C.M., Bennett J.S., Bratcher H.B., Brehony C., Colles F.M., Wimalarathna H., Harrison O.B., Sheppard S.K., Cody A.J., Maiden M.C.J. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading). 158 (Pt 4), 1005–1015.
Chaumeil P.A., Mussig A.J., Hugenholtz P., Parks D.H. 2019. GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 36 (6), 1925–1927.
Ruiz-GarcíaC.,BéjarV., Martínez-ChecaF., LlamasI., QuesadaE. 2005. Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Int. J. Syst. Evol. Microbiol. 55 (Pt 1), 191–195.
Moeller R., Setlow P., Horneck G., Berger T., Reitz G., Rettberg P., Doherty A.J., Okayasu R., Nicholson W.L. 2008). Roles of the major, small, acid-soluble spore proteins and spore-specific and universal DNA repair mechanisms in resistance of Bacillus subtilis spores to ionizing radiation from X rays and high-energy charged-particle bombardment. J. Bacteriol. 190, 1134–1140.
Moeller R., Reitz G., Berger T., Okayasu R., Nicholson W.L., Horneck G. 2010. Astrobiological aspects of the mutagenesis of cosmic radiation on bacterial spores. Astrobiology. 10 (5), 509–521.
Hullo M.F., Moszer I., Danchin A., Martin-Verstraete I. 2001). CotA of Bacillus subtilis is a copper-dependent laccase. J. Bacteriol. 183, 5426–5430.
Lenhart J.S., Schroeder J.W., Walsh B.W., Simmons L.A. 2012. DNA repair and genome maintenance in Bacillus subtilis. Microbiol. Mol. Biol. Rev. 76, 530–564.
Rebeil R., Sun Y., Chooback L., Pedraza-Reyes M., Kinsland C., Begley T.P., Nicholson W.L. 1998). Spore photoproduct lyase from Bacillus subtilis spores is a novel iron-sulfur DNA repair enzyme which shares features with proteins such as class III anaerobic ribonucleotide reductases and pyruvate-formate lyases. J. Bacteriol. 180, 4879–4885.
Liu Y., Jeraldo P., Herbert W., McDonough S., Eckloff B., de Vera J.P., Cockell C., Leya T., Baqué M., Jen J., Schulze-Makuch D., Walther-Antonio M. 2022. Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions. Sci. Rep. 12 (1), 12580.
Setlow P. 2014. Spore resistance properties. Microbiol. Spectr. 2 (5), TBS-0003-2012.
Chiang A.J., Mohan G.B.M., Singh N.K., Vaishampayan P.A., Kalkum M., Venkateswaran K. 2019. Alteration of proteomes in first-generation cultures of Bacillus pumilus spores exposed to outer space. mSystems. 4 (4), e00195-19. https://doi.org/10.1128/msystems.00195-19
Peyvan K., Karouia F., Cooper J.J., Chamberlain J., Suciu D., Slota M., Pohorille A. 2019. Gene expression measurement module (GEMM) for space application: design and validation. Life Sci. Space Res. 22, 55–67.
Olsson-Francis K., Doran P.T., Ilyin V., Raulin F., Rettberg P., Kminek G., Mier M.Z., Coustenis A., Hedman N., Shehhi O.A., Ammannito E., Bernardini J., Fujimoto M., Grasset O., Groen F., Hayes A., Gallagher S., Kumar K. P., Mustin C., Nakamura A., Seasly E., Suzuki Y., Peng J., Prieto-Ballesteros O., Sinibaldi S., Xu K., Zaitsev M. 2023. The COSPAR planetary protection policy for robotic missions to Mars: A review of current scientific knowledge and future perspectives. Life Sci. Space Res. (Amst.). 36, 27–35.
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The work was carried out within the framework of the ISS (Science) (Science-1) Test_22 program and contract No. 2123730201782217000241851/22 - 12-640/(15–07001-2002)-07001/75–2022.
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Fialkina, S.V., Deshevaya, E.A., Rakitin, A.L. et al. Genome Stability of Bacillus velezensis after Two-Year Exposure in Open Space. Mol Biol 58, 33–42 (2024). https://doi.org/10.1134/S0026893324010023
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DOI: https://doi.org/10.1134/S0026893324010023