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  • A microbial survey of the International Space Station (ISS)

    Abstract

    Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration and colonization of the solar system come to fruition.

    Results: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for 1) the Wildlife of Our Homes project and 2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both Earth homes and data from the Human Microbiome Project.

    Conclusions: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1036-4294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

    Introduction

    There is a growing appreciation of the importance of microbial communities found in diverse environments from the oceans, to soil, to the insides and outsides of plants and animals. Recently, there has been an expanding focus on the microbial ecology of the "built environment" - human constructed entities like buildings, cars, and trains - places where humans spend a large fraction of their time. One relatively unexplored type of built environment is that found in space. As humans expand their reach into the solar system, with renewed interest in space travel, and with the possibility of the colonization of other planets and moons, it is of critical importance to understand the microbial ecology of the built environments being utilized for such endeavors.

    Interest in the microbial occupants of spacecraft long precedes the launch of the International Space Station (ISS) (Trexler 1964)(Silverman 1971). Early work primarily focused on ensuring that the surfaces of spacecraft were free of microbial contaminants in an effort to avoid inadvertent panspermia (seeding other planets with microbes from Earth) (Pierson 2007). Work on human-occupied spacecraft such as Mir, Space Shuttles, and Skylab focused more on microbes with possible human health effects. With the launch of the ISS, it was understood that this new built environment would be permanently housing microbes as well as humans. Calls were made for a better understanding of microbial ecology and human-microbe interactions during extended stays in space (Pierson 2007) (Roberts 2004) (Ott 2004). Efforts were made to establish a baseline microbial census. For example, Novikova et al (Novikova 2006) obtained more than 500 samples from the air, potable water, and surfaces of the ISS, over the course of 6 years.

    These early studies were unavoidably limited by their reliance on culturing to identify microbial species. Culture-independent approaches were eventually implemented, including some small-scale 16S rDNA PCR surveys (Castro 2004),(Moissl 2007) and the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS) (Maule ), which allows astronauts to test surfaces for lipopolysaccharide (LPS - a marker for Gram negative bacteria). Originally launched in 2006, the capability of the LOCAD-PTS was expanded in 2009 to include an assay for fungi (beta-glucan, a fungal cell wall component) and Gram positive bacteria (lipoteichoic acid, a component of the cell wall of Gram positive bacteria.) The first large-scale, culture-independent 16S rDNA PCR survey was published only in 2014 using the Roche 454 platform (pyrosequencing), looking at dust on the ISS (Venkateswaran 2014). A more recent study examined several samples collected on the Japanese module of the ISS over a period of four years, also sequenced with pyrosequencing (Ichijo 2016). We report here on a further effort involving 16S rDNA PCR and sequencing, using the Illumina platform, to examine the microbial communities found on 15 surfaces inside the ISS.

    The 15 surfaces sampled on the ISS were chosen by the Project MERCCURI team in an effort to make them analogous to 1) the surfaces sampled for the "Wildlife of Our Homes" project (http://homes.yourwildlife.org) (Dunn 2013a) (Barberán 2015), which asked citizen scientists to swab nine surfaces in their homes, and 2) cell phone and shoe swab samples that were also being collected via Project MERCCURI. The motivation for choosing the sites in this way was both to increase public awareness of the microbiology of the built environment, as well as to begin to compare the microbial ecology of homes on Earth with the only current human home in space. We also present a comparison of the ISS swab results with data from 13 human body sites sampled via the Human Microbiome Project. This comparison was done to example the potential human contribution to the microbial life on the ISS.

    We have also compiled a collection of papers on space microbiology in an online resource to provide a more comprehensive historical perspective of this kind of work (see http://www.mendeley.com/groups/844031/microbiology-of-the-built-environment/papers/added/0/tag/space/).

    Methods

    Surfaces swabbed:

    Astronauts were asked to swab 15 surfaces on the International Space Station. Below are their verbatim instructions.

    1. Audio Terminal Unit (telephone) hand held push-to-talk microphone located in the forward portion of the US Lab Module

    2. Audio Terminal Unit (telephone) hand held push-to-talk microphone located in the aft portion of the US Lab Module

    3. US Lab Robotic Work Station laptop PC keyboard used to control the robotic arm

    4. US Lab Robotic Work Station hand controller used to control the movement of the robotic arm

    5. US Lab Robotic Work Station foothold, left side

    6. US Lab Robotic Work Station foothold, right side

    7. One of the main laptop keyboards in the US Lab used to control science experiments and the systems of the space station

    8. One of the vertical handrails on the equipment racks inside the US Lab

    9. Air vent in the front portion of the US Lab

    10. Air vent in the aft portion of the US Lab

    11. Air vent located on the right crew sleep compartment

    12. Tab used to open, close, and secure the Nomex privacy panel located on the starboard crew sleep compartment

    13. Air vent located on the port crew sleep compartment

    14. Tab used to open, close, and secure the Nomex privacy panel located on the port crew sleep compartment

    15. Crew Choice Surface: Audio Terminal Unit (telephone) hand held push-to-talk microphone located in the starboard portion of the Harmony module (Node 2).

    Swabbing instructions as given to astronauts:

    1. Setup Node-2 Camcorder to capture NanoRacks surface swab Ops throughout the US LAB.
    2. Retrieve a clean NanoRacks Swab Kit. Move to ISS location listed on NanoRacks Swab Kit label.
    3. Remove cotton swab from NanoRacks Swab Kit, being careful not to touch the cotton swab tip to avoid contamination.
    4. Rub cotton swab vigorously against designated surface. Spin and turn the swab to ensure maximum sample collection.
    5. Return cotton swab to NanoRacks Swab Kit and press to close (squeeze excess air out of bag before sealing). Circle number of location swabbed and label with GMT (dd/hh:mm). If swab is contaminated by touching a surface other than the designated location on the label, Label NanoRacks Swab Kit with a large, "X" and move on to the next location. Notify POIC of NanoRacks Swab Kit S/N that was contaminated
    6. Repeat step 2 to step 6 for all 15 locations listed on the NanoRacks Swab Kit label.

    NOTE: An additional large Ziplock Bag is provided (stowed inside the same bag as the NanoRacks Swab Kits) to use per crew preference to separate the used NanoRacks Swab Kits from the clean (unused) NanoRacks Swab Kits for crew efficiency during sampling.

    ISS Crew

    Swabbing was conducted during Expedition 39 (http://www.nasa.gov/mission_pages/station/expeditions/expedition39/index.html). The crew included NASA astronauts Steve Swanson and Rick Mastracchio and Russian cosmonauts Oleg Artemyev, Alexander Skvortsov, and Mikhail Tyurin. Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata was the commander for this expedition, and is the astronaut who performed the swabbing.

    Sampling site choice

    These surfaces were chosen in an attempt to sample surfaces analogous to those sampled in the pilot study for the Wildlife of Our Homes project (Dunn 2013). For this study, involving 40 homes, volunteers swabbed nine surfaces in their homes: kitchen cutting board, kitchen counter, a shelf inside a refrigerator, toilet seat, pillowcase, exterior handle of the main door into the house, television screen, the upper door trim on the outside surface of an exterior door, and the upper doo