Microbiologist, Astrobiologist

Jet Propulsion Laboratory – NASA


UntitledDr. Parag Vaishampayan is a scientist in the Biotechnology and Planetary Protection Group at NASA’s Jet Propulsion Laboratory (JPL), California Institute of Technology (Caltech), in Pasadena, California. In this role, he is responsible for the characterization of the microbial diversity associated with spacecrafts outbound from Earth and the clean-room facilities in which they are assembled. Being the key bioinformatician of his group, he is also involved in the generation and curation of a comprehensive microbial sequence database at JPL. Dr. Vaishampayan has over 15 years of research experience in microbial ecology of diverse and extreme environmental niches, encompassing spacecraft assembly clean rooms, ocean, stratospheric air samples, high altitude caves, hydrothermal vents, and the human gut to name a few. His research has been showcased in more than 35 peer-reviewed publications, a book chapter and multiple presentations. A complete list of his publications can be found here.

Interviewed by Dr. Preeti Nema

Research Scientist, Blue Marble Space Institute of Science


Welcome to Astrobiology India, Dr. Parag. We are really happy to have you with us today. Could you please tell us a little about your educational background and career path to astrobiology? 


Hi, I was born and brought up in Mumbai, Maharashtra, India. I did my master’s in microbiology at Haffkine Research Institute, Mumbai. My first research experience was as an MSc trainee at an HIV lab at the Cancer Research Institute, where, I worked on the development of HIV detection ELISA Kit. At that time, all the ELISA kits were imported either from US or Europe. HIV viruses are highly mutable and there is a lot of variation from strain to strain. Strains from Indian patients are very different from those coming from European or US patients. Consequently, while testing Indian samples, we used to get many false positives and false negatives. Therefore, we worked on standardization of the kit using proteins (GP36) from Indian HIV patients. I feel fortunate that this kit, which I worked on, later became the first – HIV Detection ELISA kit, exclusively designed for Indian patients. It was also commercially launched by a company based in Delhi named J. Mitra & Co Pvt. Ltd. I had started my research career in virology and thought that I would be a virologist all my life but then, I got an opportunity to work in the field of oceanography and I moved to the National Institute of Oceanography (NIO), Mumbai.

Did you continue working in virology or microbiology at NIO?


No, the fact is once you are on a ship, you cannot be restricted to a single field and say ‘I am a microbiologist’. They train you in all scientific aspects involved in ocean research starting from botany, zoology and chemistry. We used to collect and analyze samples for everything. I also learned about wind patterns, and sea current patterns. India has 3-4 big research vessels. I spent a lot of time on one of them called the Sagar Pashmi. Our travels covered western coastal area including Goa, Ratnagiri all the way to Pakistan borders.

Then, I got a PhD position at Agharkar Research Institute in Pune. It was an Indo-Swiss collaborative project and my topic was Phytoremediation of an Organochlorine Herbicide Atrazine from Soil using Plant Microbe Interaction. For this project, I spent some time in Zurich, Switzerland. I finished writing my thesis and started looking for postdoctoral positions abroad. While I was waiting for my PhD viva, I wrote a research proposal and got funding from Department of Biotechnology (India) for one year. I joined Dr. Yogesh Shouche’s lab at National Centre for Cell Science (NCCS) in Pune. Here, I worked on microbe host interaction, studying bacteria from skin and body of insects and animals from Western Ghats of India. Interestingly, during my tenure at NCCS, I got an opportunity to work on an Indian Space Research Organization (ISRO) project too. Dr. Jayant Narlikar from the Inter-University Centre for Astronomy and Astrophysics (IUCAA), Pune headed this project and they collaborated with Dr. S. Shivaji from Centre for Cellular & Molecular Biology (CCMB) and Dr. Shouche from NCCS for study of microorganisms from stratospheric air samples using a hot air balloon setup. These experiments resulted in the isolation and identification of novel bacterial species from the stratospheric air samples. These novel species were named as Janibacter hoyle (in honor of Sir Fred Hoyle), Bacillus isronensis and Bacillus aryabhata.

So, this was your first research experience in the field of astrobiology, how did it lead you to where you are today, a NASA scientist?


Yes, this was the first time my interest was inculcated in space sciences. I was really fascinated by panspermia, lithanospermia and other similar topics. Probably, every kid wants to be an astronaut at NASA, but as a kid I always wanted to be a scientist. However, after participating in ISRO’s hot air balloon experiment, I, too, was inspired to work at NASA. But back then, we had a perception that one has to be in that field for long or at least be a US citizen. It was my dream but I never thought that I would get an opportunity so soon. In fact, the study of human gut microflora and host interaction, which was a very active research field in US at that time, and I was well aware of that, captivated my interest and led me to apply for postdoctoral positions there. I obtained my first postdoctoral research opportunity at the Lawrence Berkeley National Laboratory to work on a human gut microbiome project. I worked at the Joint Genome Institute, which is one of the largest sequencing facilities in US and was involved in the human genome sequencing project. The project involved collecting samples from a mother-baby pair, right from birth up to one year. We, for the first time, showed that the mother actually contributes to the gut flora development of the baby. We published two papers on this work, which were very well accepted by the scientific community. This is where I picked up bioinformatics and learnt next generation sequencing. And, that’s how I became a bioinformatician. Now, I mostly work on the bioinformatics side of my projects. Though I am a trained microbiologist and microbial ecologist, this experience in next generation sequencing helped me a lot in my career. When I was working at Dr. Shouche’s lab, many of the bugs from extreme environments from Western Ghats exhibited close sequence match with some of the isolates from the spacecraft building facility. I wrote a letter about my observation to one of the scientists working at JPL where they build spacecrafts and in a reply, he sent me all his relevant publications. That helped me get a better understanding of the clean room microbiology. While I was working at the Lawrence Berkeley National Laboratory, I came to know about a postdoctoral opportunity in the field of planetary protection at JPL. As I had an extensive research background in microbial ecology and bioinformatics, I felt I was an ideal candidate for this position. I applied for it, and I was offered a postdoctoral position to work at JPL. I ended up joining JPL as a scientist in 2011 and currently, I manage a multifunctional, multidisciplinary, biotechnology–based laboratory. I have partnered with several academic institutions to develop bioinformatics tools such as Megraft, STITCH and V-REVCOMP, which are commonly used by microbial ecologists worldwide. My current research focuses on the development and implementation of advance molecular techniques to characterize the microbial diversity of a spacecraft and associated clean room environments.

What is the significance of monitoring bacterial load during spacecraft assembly?


Study of bacterial load or bio-burden on a spacecraft is essential to ensure planetary protection. Planetary protection efforts are meant for protecting celestial bodies against biological contamination from Earth and vice-versa. This is very important, because we want to study other planetary bodies in their natural or unaltered state. We have to be careful in avoiding backward contamination, i.e. any life form, if existent on other planetary bodies should not be carried back to Earth while bringing samples from space. There is an international body called the Committee on Space Research (COSPAR), which dictates the rules and regulations for all the space faring nations who are going to other planetary bodies. There is an international agreement of not contaminating other planetary bodies during space travel and following planetary protection guidelines recommended by COSPAR. According to these guidelines, space missions are categorized into 5 levels of stringency depending upon the type of mission e.g. a flyby, orbiter, or lander mission; the nature of its destination e.g. a planet, moon, comet, or an asteroid and on the planetary bodies that may be encountered during the mission. Category 1 is least stringent and involves celestial bodies, which are not of direct interest for chemical evolution or the origin of life, such as the Sun or Mercury. While category 5 is the most stringent category, which involves celestial bodies with a possibility of life, such as Mars. There are also ‘special regions’ on Mars where microbes from Earth may be able to propagate or there is a possibility of the existence of extant Martian organisms. That is why any mission for the red planet falls under category 5. Following planetary protection protocols, you have to collect samples from each and every component of spacecraft while it is being assembled. You have to make sure that total microbial burden on spacecraft is below a certain threshold so that probability of contamination is close to zero or below zero. The planetary protection officer has to sign a document saying that the spacecraft is clean enough to be launched in space.

What kind of microbes do you frequently encounter in clean rooms? Is there anything peculiar about them?


The most common ones are spore-forming bacteria like Bacillus. Spore forming microbes are the hardiest microbes you can imagine. They have highest chances of interplanetary space travel and potential for survival on other planets. This is the reason NASA and other space agencies use spores as a proxy for the total bio-burden. NASA’s standard spore assay is a standardized technique, which looks for number of spores in a given sample. The logic is, if you can get rid of spores, there is a high likelihood that you have eradicated maximum number of vegetative cells. But, if you still have spores, you may have some vegetative cells remaining. Spore formers are the dominant ones, but we have found some extreme radiation resistant non-spore formers too. The most recent one reported this year is novel bacterial species named as Deinococcus phoenicis. It was isolated from a clean room at the Kennedy Space Center, where the Phoenix spacecraft was assembled. Other than that, we have also reported presence of some species of fungi, archea and anaerobes too. So, there is quite a diversity of microbes out there. But one thing I would like to mention here is that, it is not a random microbial community. Clean rooms have extreme conditions like high desiccation, very low nutrients, and strong cleaning agents. Therefore, only specialized microbes, which are extremophilic in nature, exist in the clean room. We keep getting queries from all over the world by researchers who are finding microbes from extreme natural environments like Atacama desert, deep hydrothermal vents, and high altitude caves from Venezuela that have genetic sequences that match the genetic sequences of microbes from the clean room environment. The only reason for this match is starvation – a very important ecological factor that is common between them. They all are inhabitants of environments with very low availability of nutrients, scientifically known as oligotrophy.

Now, the question may arise that Earth is the most habitable body of our solar system and the conditions for life are rare elsewhere. Then, why are we concerned about contaminating other planetary bodies? We have bacteria who can survive in clean rooms but how could we say that they can survive in space or during interplanetary transfer? To test this, we did two experiments, first one was three years back, in collaboration with European Space Agency (ESA) named EXPOSE. We selected Bacilluspumillus SAFR 032; this is the hardiest microorganism we have ever isolated from the clean room facility at JPL. It is the most radiation resistant microorganism on Earth. We placed its spores on aluminum metal discs, which were kept on spacecraft hardware. Subsequently, it was flown to the International Space Station (ISS) and it was mounted outside ISS for 18 months. These bugs were directly exposed to actual space conditions including radiations like galactic rays, cosmic rays high-energy particles, UV, microgravity and extreme temperature fluctuations. The reason we selected the time period of a year and half is that this is the amount of time they will be exposed to radiation during an interplanetary travel of eight and half months from Earth to Mars and back. As a control, a parallel experiment was conducted on Earth called as the Mission Ground Reference (MGR) with identical samples but under simulated conditions. When we got the samples back, we tried to revive them and to our surprise we were able to get 19 survivors from 107 spores coated on those aluminum discs. We did several studies on these space-surviving spores including proteomic analysis, and whole genome sequencing. All our results were published in a special issue of Journal Astrobiology in 2012. The take home message from those experiments was that if microbes can find optimal conditions on a spacecraft, they can survive both interplanetary travel and conditions on other planets. Recently, we started a similar experiment named PROTECT. This time, another extremophilic microorganism Bacillus hornecki, named in honor of German astrobiologist Gerda Hornecki, has been used. She has done a lot of pioneering work in space microbiology. As we speak, Bacillus hornecki is being exposed to real space conditions on the ISS. Data generated by these experiments will help us understand the probability of forward contamination by terrestrial microorganisms. We are also concerned about backward contamination. Currently, I am working on two more Mars missions: InSight 2016 and MARS 2020. The latter mission will collect samples of Martian rocks and soil in a sealed container to be available for a possible follow-up mission to bring back to Earth. We are working on techniques to ensure that there is not even a single dust particle from Mars that is stuck to the sample containers to prevent backward contamination, which is also referred to asbreaking the chain.

Do you think these super-bugs could have any biotechnological applications, especially in space missions?


We are doing some experiments on how we can use microorganisms for long duration sustenance of humans in space or human habitation in extreme conditions. Also, lots of experiments are being done where microbes can be used for energy production. Astronauts in space can use these microbial fuel cells. Extremophiles have many applications not only in space science but in day-to-day life as well. The best example is DNA polymerases.

You are involved in science communication, education and outreach activities as well, please tell us something about that.


I love teaching; I am an adjunct faculty in two local universities where I teach microbiology. This also gives me an opportunity to introduce students to the research we do at NASA. I am involved in some NASA science outreach programs. One of them is NASA Spaceward Bound, where we go to Mojave Desert in California every year and work in a makeshift research lab for four days.

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We train teachers, students, who are taking credential courses to be teachers, and students from an array of scientific backgrounds including biology, physics, chemistry, mathematics, engineering and others. We take them on field, teach them how sample collection is done and how we perform astrobiology experiments. I have been going there for past four years and it t has been a fantastic experience throughout. Couple of years back, NASA astrobiology started a national level competition for astrobiology science communication, called NASA FameLab, where participants talk on any topic about astrobiology for three minutes and the best orator gets a prize. I was very fortunate to be one of the 10 national finalists, at the first NASA FameLab competition in USA.


You are involved in so many scientific activities; in this busy schedule, what do you do for fun? What are your hobbies?


I am an avid hiker; I do rock climbing, back packing, and hiking. Being in California is a blessing; we have huge deserts, Death Valley, Yosemite, so many beaches. I like to spend time with friends and family. I am also involved with many social organizations.

What advice would you give to young students who want to work at NASA as an astrobiologist?


My advice is to be passionate, only your passion can drive you. More than your expertise, I think your passion will help you reach where you want to be. Expertise can be acquired over time, but if you run out of passion, you cannot reach where you want to be. Science is changing so fast. Things you learnt two years back, may be obsolete now. So, keep the passion alive and keep learning new things as they come along.

What are your thoughts on our initiative to promote astrobiology through Astrobiology India?


I came to know about Astrobiology India community through Dr. Sanjoy Som of NASA Ames Research Centre. Astrobiology is a great field and I am very happy that something like this has been started for Indian students. I will be more than happy to contribute in any way I can. I wish all the very best for this initiative.

Well, we definitely need your valuable insights to enhance the utility of Astrobiology India initiative. Thank you so much indeed, Dr. Parag, for sharing the outstanding features of your profound scientific career.