Genomic characterization of plant-growth promoting features of Sphingomonas strains isolated from the International Space Station, with an emphasis on phytohormone production

AbstractIn an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Phylogenetic analysis, based on the 16S rRNA gene sequence, identified the ISS strains as S. sanguinis (n=2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as S. paucimobilis. Metagenomic sequence analyses of various ISS locations identified 23 Sphingomonas species, with an abundance of shotgun metagenomic reads detected for S. sanguinis in the location from where the ISS isolates were sampled. A complete genome was assembled from the metagenome and its comparison with the whole genome sequences (WGS) of the ISS isolates revealed that they were highly similar to S. sanguinis. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well characterized Sphingomonas sp. LK11, a desert arid strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, Indole 3-acetic acid, was further confirmed in the ISS strains using metabolomics. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, oxidative and osmotic stress resistance, appear to be present in these space related S. sanguinis and S. paucimobilis strains. Characterization of these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future.ImportanceSphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the International Space Station, which are capable of producing the phytohormone indole 3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology -related applications.