Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

Victor G. Stepanov,Ganesh Babu Malli Mohan,Jason M. Wood,Camilla Urbaniak,Daniel McDonald,Jeremiah Minich,Quyen Tran,George E. Fox,Rob Knight,Aleksandra Checinska Sielaff,Kasthuri Venkateswaran,Teresa Mayer,Fathi Karouia

doi:10.1186/s40168-019-0666-x

Abstract

BackgroundThe International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring and observational studies of spacecraft and space stations have been conducted by traditional culture methods, although it is known that many microbes cannot be cultured with standard techniques. To fully appreciate the true number and diversity of microbes that survive in the ISS, molecular and culture-based methods were used to assess microbial communities on ISS surfaces. Samples were taken at eight pre-defined locations during three flight missions spanning 14 months and analyzed upon return to Earth.ResultsThe cultivable bacterial and fungal population ranged from 104 to 109 CFU/m2 depending on location and consisted of various bacterial (Actinobacteria, Firmicutes, and Proteobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Amplicon sequencing detected more bacterial phyla when compared to the culture-based analyses, but both methods identified similar numbers of fungal phyla. Changes in bacterial and fungal load (by culture and qPCR) were observed over time but not across locations. Bacterial community composition changed over time, but not across locations, while fungal community remained the same between samplings and locations. There were no significant differences in community composition and richness after propidium monoazide sample treatment, suggesting that the analyzed DNA was extracted from intact/viable organisms. Moreover, approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured.ConclusionsThe results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.

Highlights

The International Space Station (ISS) is the largest human space platform in low Earth orbit (~ 400 km above Earth’s surface) and for the last 17 years it has been continuously inhabited by an international community of astronauts performing space research
Molecular methods, such as quantitative polymerase chain reaction and targeted amplicon sequencing, which can identify and quantify both culturable and unculturable organisms provide a more thorough assessment of what is present and in what amounts [5]. While it has been recently shown as a proof of concept that PCR [6] and amplicon sequencing can be performed on the ISS [7, 8], microbial monitoring of the ISS with molecular-based methods is not routinely used because of the lack of simple, compact, and reliable sample processing instruments onboard the ISS
The average number of bacteria cultured on blood agar (BA) and R2A plates was similar between Flight 1 (F1) and Flight 2 (F2) but higher at F3 (Fig. 2a)

Summary

Introduction

The International Space Station (ISS) is the largest human space platform in low Earth orbit (~ 400 km above Earth’s surface) and for the last 17 years it has been continuously inhabited by an international community of astronauts performing space research. Culture-based analysis limits our understanding of the diversity of microbes that grow and thrive on the ISS because only a small fraction of organisms in a given environment can be cultured under standard laboratory conditions [4] Molecular methods, such as quantitative polymerase chain reaction (qPCR) and targeted amplicon sequencing, which can identify and quantify both culturable and unculturable organisms provide a more thorough assessment of what is present and in what amounts [5]. Approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured

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Conclusion