Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

Abstract

BackgroundThe International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutrient-availability due to cleaning, and an increased radiation level. We hypothesized that the microbial community inside the ISS is modified by adapting to these stresses.For this reason, we analyzed 8–12 years old dust samples from Russian ISS modules with major focus on the long-time surviving portion of the microbial community. We consequently assessed the cultivable microbiota of these samples in order to analyze their extremotolerant potential against desiccation, heat-shock, and clinically relevant antibiotics. In addition, we studied the bacterial and archaeal communities from the stored Russian dust samples via molecular methods (next-generation sequencing, NGS) and compared our new data with previously derived information from the US American ISS dust microbiome.ResultsWe cultivated and identified in total 85 bacterial, non-pathogenic isolates (17 different species) and 1 fungal isolate from the 8–12 year old dust samples collected in the Russian segment of the ISS. Most of these isolates exhibited robust resistance against heat-shock and clinically relevant antibiotics. Microbial 16S rRNA gene and archaeal 16S rRNA gene targeting Next Generation Sequencing showed signatures of human-associated microorganisms (Corynebacterium, Staphylococcus, Coprococcus etc.), but also specifically adapted extremotolerant microorganisms. Besides bacteria, the detection of archaeal signatures in higher abundance was striking.ConclusionsOur findings reveal (i) the occurrence of living, hardy microorganisms in archived Russian ISS dust samples, (ii) a profound resistance capacity of ISS microorganisms against environmental stresses, and (iii) the presence of archaeal signatures on board. In addition, we found indications that the microbial community in the Russian segment dust samples was different to recently reported US American ISS microbiota.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0217-7) contains supplementary material, which is available to authorized users.

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“…These genera in the air may come from the human gut with the crewmembers stay in LP1 for long time. Mora et al (2016a) also confirmed the composition of the ISS microbiota was a typical human-associated community. This observation appears logical due to the tremendous impact of the human microbiota on the environment and the severe restriction of other potential microbe sources.…”

“…For example, several microbiota monitoring experiments on the ISS have been launched (i.e., NASA's ‘Microbial Observatory’ project (Venkateswaran et al ., ), JAXA's ‘Microbe’ experiment series (Kazuo et al ., ) and ESA's ARBEX/Extremophiles project (Moissleichinger et al ., ). Mora and Checinska (Mora et al ., ; Be et al ., ) found that specific human skin‐associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth‐based cleanrooms. During the Mars500 project, despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal (Schwendner et al ., ).…”

“…The maintenance of human health has been focused on as a crucial issue for realizing manned deep-space exploration (Mora et al, 2016a;Kuda et al, 2017;White, 2017). The gut microbiota is essential to health; it plays a vital role in host physiology, metabolism, nutrition and immune system development (Dore and Blottiere, 2015;Greenhalgh et al, 2016;Lv et al, 2016); dysbiosis of the gut microbiota is associated with illness and infection (Liu, 2016;Schwendner et al, 2017).…”

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“…Spaceflight could affect the drug resistance phenotype of bacteria and a profound drug resistance capacity of ISS microorganisms against environmental stresses was detected during these years (Mora et al, ; Singh et al, ; Urbaniak et al, ). It has been demonstrated that the increased antibiotic tolerance of Escherichia coli in human spaceflight environment might be attributed to the upregulation of genes related to oxidative stress response (Aunins et al, ).…”

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“…It is isolated from different metal-contaminated environments (Diels & Mergeay 1990;Brim et al 1999;Goris et al 2001) as well as volcanic basalt (Kelly et al 2010) and granite rock (Sahl et al 2008). In addition, C. metallidurans strains have been recovered from other anthropogenic environments including medically-relevant sources (Langevin et al 2011;Van Houdt et al 2012) and space habitats (Mijnendonckx et al 2013;Mora et al 2016). Its interaction with basalt as well as its response to spaceflight conditions has previously been studied Mergeay & Van Houdt 2015;Bryce et al 2016).…”