Exploring the Microbiome on the International Space Station (ISS)

Exploring the Microbiome on the International Space Station (ISS)

Author: Vera KoesterORCID iD, Kasthuri Venkateswaran, Nitin Kumar SinghORCID iD

Dr. Kasthuri Venkateswaran (Venkat) and Dr. Nitin Kumar Singh, both of NASA’s Jet Propulsion Laboratory (JPL) in Southern California, USA, are part of JPL’s planetary protection group. The team ensures that spacecraft meet stringent cleanliness requirements to prevent forward contamination (i.e., microbial contamination of extraterrestrial bodies by spacecraft launched from Earth) and backward contamination (i.e., extraterrestrial contamination of Earth and the Moon by sample return missions).

Here they talk with Dr. Vera Koester of ChemistryViews about their search for extremophiles, bacteria on the space station, and how bacteria support plant growth.


You found four strains of bacteria on the International Space Station (ISS), three of which were previously unknown. What are your motivations for studying bacteria on the ISS?

Kasthuri Venkateswaran: We are a planetary protection group, which means we seek to protect all planets all the time. Whenever you explore other planets, there is a possibility to take microbes along with you as “hitchhikers”. We are developing a lot of cleaning and microbial reduction technologies for the crew system as well as the spacecraft system to get a handle on the level of microbes that are hitching rides with us.

The inspiration for our research is mainly to look for extreme microbes in places from the deep sea to deep space and everywhere in between to see which extremophiles are likely to survive on another planet, so we can develop an appropriate cleaning and microbial reduction procedure as a countermeasure to minimize such contamination. In this regard, the space station is one of the most extreme closed environments. The big difference between the space station and your home or office is that the space station is hermetically sealed. Nothing comes in from the outside other than the cargo vehicle and the human transport vehicle.

Microbes have been around for about 3.4 billion years, and they are able to withstand a wide variety of conditions. That is a fascinating story in itself. Most likely, the microbes that will survive on other planets may be radiation-resistant and also potentially show high tolerance to desiccation. So that is the inspiration behind this study: to get an overview of these things. What exactly are these microbes that could withstand a microgravity environment and that could withstand both elevated CO2 and elevated radiation? What are the microbes that astronauts need to coexist with?

Under space conditions, even benign microbes or opportunistic pathogens could be problematic for space-induced immunocompromised hosts—in this case, the crew. Very healthy, very capable people are selected to serve on the space station, but due to the gravity of space, their immune systems are weakened, so they become immunosuppressed. So opportunistic pathogens might become problematic. These are the kinds of things we are investigating to prepare for permanent life in space and a presence there for an extended period.


So it is normal to constantly check the space station for bacteria or microorganisms?

Kasthuri Venkateswaran: Yes.


What is special about the newly discovered bacteria?

Nitin Kumar Singh: We are doing plant growth experiments on the International Space Station and have found that these organisms have a genetic makeup that may support plant growth. They belong to the Methylobacteriaceae family.


What kind of plants are you growing on the space station right now?

Nitin Kumar Singh: Right now, scientists have been successfully growing wheat, lettuce, radish, and Arabidopsis, or thale cress.


Is it possible to grow any plant on the space station?

Kasthuri Venkateswaran: That is one thing we want to test. So far, we have not tried a number of things like rice. The space station is only 20 years old, and it is only within the past five years that NASA has been growing plants in space. So there is still a long way to go.

You also do not have a lot of room for things like a greenhouse and gardening. So we have a very small space where we grow, as Nitin said, radishes. Also ornamentals are easy to germinate and grow.


Why do you grow ornamental plants?

Kasthuri Venkateswaran: To make it more vibrant in the space station. People live there for a long time. If you have a plant in your office or home, you know it makes you feel different, right? So the plant may not be suitable for you to eat, but it is good for your well-being. Also, it can reduce the CO2 in the atmosphere. So it has many benefits.


And how can the bacteria now help the plants?

Nitin Kumar Singh: In general, they help in two ways. One is nitrogen fixation. The best-known bacterium is Rhizobium, which gets into the root modules of plants and helps fix nitrogen from the soil.

The second way that these bacteria help is by producing growth-promoting hormones. A plant has hormones like auxins, gibberellins, cytokinins, and abscisic acid. For example, auxin is important for root growth, gibberellin is important for shoot growth, and so forth. So when a bacterium produces auxins, it helps the root growth of the plant. When a bacterium produces gibberellins, it may help the shoot growth of the plant.

Bacteria are also important for germination. A combination of auxin and gibberellin helps in seed germination.
Also, when symbiotic microbe accumulate on the root, they increase the surface area of the root. This allows the plants to absorb more nutrients.


What is the aim of your research? Would you like to use special microorganisms in space to grow plants in the future?

Nitin Kumar Singh: We want to see how the novel organisms will help plants grow when we go to the Moon or to other planets. For sustained life and a long-term presence in space, we should be able to grow plants using in situ resources, such as the soil. Since these organisms are adapted to space, they would be more successful in surviving in those extraterrestrial conditions.

Kasthuri Venkateswaran: The microorganisms will form natural microbial consortia because they work together in a community like a machine. You have to find a suitable combination, otherwise, you won’t get everything right. So we want to find out what are the consortia that work under these conditions? Lunar soils, for example, have fewer nutrients.

For example, radishes, which can grow in healthy soil, cannot grow in the deserts of Saudi Arabia. Nor can they grow in the dry conditions of the Atacama Desert. So we are trying to figure out how it can adapt to these desert conditions, and then we take that knowledge to space because there is no water there.

Nitin Kumar Singh: Dr. Venkateswaran raises a very good point there. The idea of space research is not necessarily to grow something in outer space itself. How it can help on Earth is much more critical. For example, if this organism helps plant growth in desert soils, that is more of an Earth-based application that we are interested in. If it helps in space, of course, that is very good.


In space, it is very cold and in a desert, it is very warm, so could that be very different for the bacteria? Or is that not such a big problem?

Kasthuri Venkateswaran: That is one of the things we need to look into. Those bacteria that grow under cold conditions are the champions in the mix. Those are the polyextremophilic microbes that we are looking for.


And does that mean that you are growing new bacteria, in the sense that there are new conditions for the bacteria and therefore they change and adapt to this new environment?

Kasthuri Venkateswaran: If there is a need, and if that one species of bacteria that propagates in the arid environment accepts the cold and assimilates the genes, then those genomic characteristics could aid in genetically modifying microbes that we could use. If not, we will look for microbes that can withstand these extreme conditions, both dry and cold. There are multiple extreme or tolerant microbes out there with multiple adaptive characteristics which might help in future biotechnological applications. That is why we are constantly looking for these extremophiles.


Was it very unexpected that you found these new organisms?

Kasthuri Venkateswaran: No, not at all. They may have been taken to the space station with the cargo or a human. That is not unexpected. They could be present as rare variants somewhere on Earth, making up an undetectable percentage of the total microbe population here.

On the space station, the microbes that are labile, that are susceptible, are eradicated from the start. All the cargo is cleaned as it is unloaded. The cleaning agents do not sterilize, but they do greatly reduce the microbial load. The majority of the dominant microbes are cleaned away. So now you have no competition for bacterial species that can withstand the radiation. Those are the bacteria that are resistant to interplanetary transfer conditions. So they are desiccation-resistant and they can withstand a small amount of radiation. They form pigments that help them do that. It is not only melanin that helps to protect against radiation but also other metabolites such as carotenoid pigment that absorbs low-level radiation.

So the bacteria that we find are the ones that have survived. I am not saying it is easy to find them. You have to search for years.


How do you conduct your measurements? I mean, you cannot just go to the ISS, take your samples, and then analyze them.

Kasthuri Venkateswaran: Normally, we bring the bacteria back to Earth and then culture them in the lab. We are very careful, though, with handling and test procedures. So we are developing technologies to measure them without culturing them. For example, we collect samples, extract DNA or RNA, and then we look to determine what kind of microbial composition or function we find. NASA is also developing technologies for DNA sequencing that takes place in space.

If we see a type of problematic microbe, we can target it and ask the astronauts to use appropriate cleaning reagents. If the microbes are biotechnologically useful and space-application relevant, we will try to look for them on the ground and then take these biotech-friendly microbes to the space station in a controlled fashion to look for their applications.


Can you take these samples all the time or only when someone leaves the space station or comes back?

Kasthuri Venkateswaran: To get the samples, you do not need to have people come back. You can get them via crew resupply vehicles (CRV). You can bring the cargo back via CRV, which splashes down in the Pacific or Atlantic Oceans and is retrieved by the ISS support team. That is what we normally do.

Right now, when the crew comes back, it is not done using a space shuttle. Rather, it is done in a capsule, so they do not have a lot of room, and it is not possible to transfer frozen samples. So the crew resupply vehicles bring the samples back when they return from the space station. Then we bring them to our lab. It currently takes three months from sample collection to isolation and analysis. But, as I just mentioned, in the future, we want to do everything in space without culturing.


When the crew of the space station changes, does the composition of the microbes on the station also change? Or does that not have such a big effect?

Nitin Kumar Singh: That is the subject of a study by one of our collaborators. The idea is that it goes both ways: When a crew goes to the space station, the space station microbiome shifts with the input from the new astronauts. And then we have also seen that the space station microbiome actually changes some of the astronauts’ microbiome. So that is a question that I would say is still under study.

Kasthuri Venkateswaran: So the question is, is there an interchange between the human microbiome and the environmental microbiome? We have shown that the answer is yes.

The crew shares the environmental microbiome of the space station, which is a closed system. That is to say, the air that they breathe in and breathe out is recirculated, appropriately processed, restored, and then sent back into this closed system. With the arrival of new crew members, the microbes change dynamically because each human has a different set of microbes; they are individualistic. For example, I have a different microbiome than Nitin has and that you have.

We have done a lot of work on the skin microbiome as well as the nasal and oral microbiome, which are the exposed parts, but we have not done as much with the gut microbiome. NASA has done a twin study—with one twin in space and one on the ground—that includes the gut microbiome. They found that their gut microbiome changes over time at the phylum level. [A phylum is a level of classification or taxonomic rank below kingdom and above class.]

However, there are some fungi, some opportunistic pathogens, and some beneficial microbes that can survive over time and then successively establish a niche.


That is really interesting. Thank you very much for the insight into your work.


The paper they talked about:


Four strains among the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS). One of the strains, Methylorubrum rhodesianum, was already known. The other three rod-shaped, gram-negative bacteria were previously unknown. They are assigned to a novel species within the genus Methylobacterium; the name Methylobacterium ajmalii sp. nov. is proposed.

The genus Methylobacterium consists of 45 recognized species that are ubiquitously present in a variety of habitats including air, soil, freshwater, and sediments and can exist either in free form or in association with plant tissue. Methylobacterium species are involved in nitrogen fixation, phosphate solubilization, abiotic stress tolerance, plant growth promotion, and biocontrol activity against plant pathogens. In addition to sugars and organic acids, they can grow on methane or methanol as a carbon and energy source.

Kasthuri Venkateswaran (Venkat) studied biology at Annamalai University, Annamalainagar, India, and received his Ph.D. in 1982 in marine microbiology from there. After a research period at Hiroshima University, Japan, and employment with various Japanese companies, Venkat became a senior researcher at the University of Wisconsin-Milwaukee, USA, in 1996. In 1998, he became a senior scientist in astrobiology at the California Institute of Technology (CalTech), Pasadena, CA, USA. Since 1999, he has been a senior research scientist at the Jet Propulsion Laboratory (JPL).

Venkat’s research focuses on molecular microbial analyses to better understand the ecological aspects of microbes. He has studied microbes from various extreme environments such as the deep sea, in assembly plant cleanrooms, for spacecraft missions, and from space environments in Earth orbit (the ISS).


Nitin Kumar Singh studied biotechnology at the University of Bikaner (now known as Maharaja Ganga Singh University), India, and received his Ph.D. in microbiology in 2015 from the Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India. After a postdoc at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and another at JPL, he has been a planetary protection scientist in the Biotechnology Planetary Protection Group at JPL since 2017.

He specializes in working on pathogenic microbes found in hospital environments and clean rooms to understand how microbes adapt to become more pathogenic under anthropogenic pressure. Among other accomplishments, he has played a critical role in validly describing 14 new bacterial species from different environments and has helped narrow down the dominant microbial population on the ISS and determine its genomic identity.




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