[Interview] Turning to science to find innovative solutions: plant biologist E. V. Soniya

For E. V. Soniya, a scientist with the Rajiv Gandhi Centre for Biotechnology (RGCB) in Thiruvananthapuram, Kerala, science, and especially molecular biology, has been a lifelong passion. Her expertise in the basic tenets of biology has allowed her to expand her research horizons.

As the senior-most scientist of the plant biology research group, Soniya has worked on the plants black pepper and bael (Aegle marmelos). Kerala is a leading exporter of spices in India, among which black pepper is prominent for its commercial importance and medicinal properties. Bael is a tree with ethnobotanical importance; it has religious significance and is added to some Ayurvedic medicines.

Quite early in her career, Soniya discovered her deep curiosity for the molecular biology of plants and their interaction with pathogens and the environment. Her focus was on the stress biology of spice crops like black pepper, ginger, etc., and the metabolic pathways for the biosynthesis of natural compounds.

Her strong leadership skills got her the position as the Chief Scientific Officer of Molecular Forensics and DNA technologies (MFDT) at the RGCB, which provides human DNA fingerprinting services to judicial, crime investigation and law enforcement agencies as well as wildlife forensics. MFDT also provides services for the DNA barcoding of plants, animals and microbes.

Under her supervision, the team at RGCB was able to successfully undertake the challenging work of identifying unrecognisable dead bodies following the Puttingal fireworks disaster and Ockhi cyclone tragedy. She also shouldered the responsibility to create a DNA fingerprint database for captive elephants in Kerala. The fingerprinting of elephants could save the animals from illegal trade. With her molecular biology background, she found that it is easy to adapt to different samples.

Soniya has come a long way since wrapping up her Ph.D. in 1995. Towards the end of a two-year-long postdoctoral stint at the Central Tuber Crops Research Institute (CTCRI), she saw an advertisement for a project position at RGCB, which had just come into existence. When Soniya went for the interview, she was seven months pregnant.

“I did not think anyone would pick me. So I did my interview well, without any tension. But they did select me – I got the position. I worked for two more months and then took a short break. I was in the lab until two or three days before the delivery,” she shared with a laugh.

Earlier this year, Soniya travelled to Delhi to receive the Janaki Ammal – National Women Bioscientists Award – 2019, awarded by the Department of Biotechnology, Government of India. The award, which carries a cash prize of Rs. 5 lakhs (Rs. 500,000) together with a citation and a gold medal, is “in recognition for her lifetime research contributions and their application to society.”

“This is the most prestigious award I have received. It is a lifetime achievement award,” was Soniya’s simple response to her award.

“Basic research is very interesting. We feel very happy when we get new findings. But ultimately, research should be something useful to the public also,” said Soniya.

Soniya has a simple, matter-of-fact manner with bursts of animation when she speaks of a particularly exciting project. Chatting with this Mongabay-India correspondent in her cosy office space, it is easy to see that her office is always open for the research scholars in her team.

A remarkable feature of her lab is also the number of female research scholars. During our conversation, one student had to go home to take her infant to the hospital.

“I have so many girl students. Every single day something will happen,” said Soniya smilingly after asking the young mother to go home at once.

Here are excerpts from our long chat. The interview has been divided into sections and edited for clarity.

Initial career: Working with Kerala’s spice bounty

My first research project was on tomato and black pepper, mainly tissue culture and marker development. We raised a lot of tomato plants in vitro and using RAPD (Random Amplification of Polymorphic DNA) markers in the in vitro plants; we were able to study variation among the plants. This was to be expected, but I was able to prove it through the RAPD analysis. I could establish that different plant strains were genetically different.

I presented the findings at the Kerala Science Congress that year, under the Agriculture category. I won the Young Scientist Award that year (Jan 1999).

It was around this time that I started work on black pepper. The Department of Biotechnology wanted us to focus on spices like pepper and ginger because Kerala was famous for its spices. It was good to work on them from a policy point of view.

What was your main research with black pepper?

There were – and are – a lot of issues with spice cultivation. There are high chances of devastating disease, which can affect our exports. These diseases are common all over Kerala. Because of our tropical climate, the oomycete [reproductive bodies] of fungi can grow very rapidly. This creates a lot of problems. There are many species and subspecies of black pepper across Kerala, but there are no disease-resistant varieties. There is some degree of tolerance, but not resistance.

Then comes the yield. In the pepper found in the wild, the yield is typically low. Farmers obviously want high yields. After spending so much time in cultivation, low yields really affect farmer incomes.

There was a need for strategies to improve yields. Spices research and agricultural research institutes were developing their own strategies, but again the problem is there is no resistant variety. Being a biotechnology Institute, we started working on genomics and developing strategies to find solutions to this problem.

What strategy did you use to come up with resistant varieties?

We used tissue culture to develop genetically modified pepper using transgenics. At that time, that was the upcoming field. The problem with tissue culture was that the presence of endogenous bacteria [bacteria found inside plant tissue which can potentially cause infections] makes the culturing difficult. Also, some of the tissue was recalcitrant – they were not responding to tissue culture treatments. We had to overcome all these problems.

As we moved from tomato to black pepper, we had to spend a lot of time coming up with suitable tissue culture protocols. Then came the gene. Which gene is to be introduced?

Initially, when genetically modified organisms (GMO) was introduced, people were introducing bacterial genes – this also led to some controversies. Others were working to localise a gene that can break down fungal walls and provide protection from fungal disease.

We wanted to develop transgenics using genes from resistant varieties. We found certain varieties of black pepper, like Piper colubrinum from Brazil, which is resistant to certain diseases. We wanted to see what resistant genes this species had, that other species lacked. We found that it was mainly a difference in the level of expression of genes.

Over the years of your research on black pepper, have you observed any changes in the field? Have people shifted from one variety to another?

One thing I want to stress is that we are not working on pepper in the field – we are working in the lab only. Whenever we wanted to translate our findings in the field, we collaborate with agricultural university, because we always want the expertise from their field.

However, I can give you some examples. Karimunda [a popular cultivar in Kerala] is supposed to be a disease-tolerant variety. It is also a wild variety. But, the yield is low, compared to another variety called Panniyur, which gives high-quality seeds and the yield is also high. So, farmers want to use that.

One of the main constraints in black pepper production in India is Phytophthora foot rot (‘quick wilt’) caused by an oomycete [plant pathogen] called Phytophthora capsici. Unlike model organisms, there is no rapid elevation in pepper research due to the scarcity of the available genome sequence information.

Until now, there is no resistant variety. There are only tolerant varieties. Indian Institute of Spice Research (IISR) has also been developing and distributing new varieties of pepper, including both tolerant and high yielding varieties. Being a biotechnology institute, our prime aim is to pursue basic research. We focus on molecular level. Once product is ready, we tie up with ISSR or Agriculture University to take the products to the field.

Taking cues from nature and culture

Can you talk of your work with bael?

Aegle marmelos (bael in Hindi, vilvam in Tamil and koovalam in Malayalam) is a tree usually found in Shiva temples as the sthala viruksham (temple tree). It is auspicious to use bael during Shivaratri (a Hindu festival dedicated to Shiva). Bael is also used in Ayurvedic preparations – for instance, the preparation dasamularishtam contains bael.

I found that this is a wonderful plant. It produces secondary metabolites (specialised chemical compounds) like quinolones that have many anti-microbial and anti-cancer properties. Quinoline alkaloids, found abundantly in the roots of bael possess various biological activities. They are efficient drugs for the treatment of malaria and are considered as potential lead molecules for novel drug designing. For the first time in plants, we characterized a novel enzyme (a type III polyketide synthase) named Quinolone synthase (QNS) involved in quinolone biosynthesis from Bael. We demonstrated the remarkable ability of QNS to catalyze the formation of quinolone.

A full-length gene was isolated and expressed in a bacterial system. That protein has to be expressed in bacteria (like Escherichia coli) to make the protein in large amounts. We then went for in vivo and in vitrio assays. For the in vitrio assay, we had had to show that this enzyme is capable of accepting specific substrates to produce the compound. We could show that this particular compound is found at higher levels when you overexpress the quinolone synthase gene.

This work was published in the Journal of Biological Chemistry, a prestigious journal in which it is not easy for plant biologists to publish. I was very happy to publish in it.

Applying first principles to multiple problems

I have been leading the DNA fingerprinting team at RGCB from 2014 onwards. I must stress that it was just a leadership change. That doesn’t mean anything! People have always been working in the lab.

I read that your team had worked towards identifying victims of cyclone Okchi (2017) and the Puttingal fire tragedy (2016). 

There was a lot of work during those periods. At that time, we didn’t have much staff also – just four people. We somehow managed. That is our work culture, actually. I have to appreciate the dedication of the staff working in the fingerprinting centre. During times of need they dedicate themselves completely without even thinking of their families. Not only Okchi and Puttingal, but there were also other cases that were very time-bound – the staff worked night and day to produce the results.

Was it different, working with human remains after working with plants?

No. See, our work is mainly based on molecular biology. Only sample processing is different. Basically, the work and methodology remain the same. Once you have a background in molecular biology, it is easy to adapt to different samples.

Did you feel like there was a human element?

That is not a big problem. We treat it as another scientific problem and I was always confident of getting the result. I can deal with any molecular biology related problem!

What we had to do, as team leaders, was to motivate them [the team] internally and help them in case of any problems. We had to be there always. Me going home to my family and telling the team to work is not fair. We have to be there for the team. Sometimes it will get late; sometimes we have to take food from the canteen at night; when there is an emergency we need to get the work done.

I have done many such things with my kids. Similar to what happened to my lady student, my kids have fallen sick too, many times. My husband has helped a lot; he also takes leave to take care of the kids. The onus is not on me alone.

Where does your husband work?

He is a scientist at the Vikram Sarabhai Space Centre (VSSC) in Trivandrum. He understands how science works, the pressures of research. We can understand each other, and my husband has always been supportive. He never interferes with my official work; if I do something, he never says no. That’s the main thing. He never pressurised (me) for anything.

Can you talk about your work with captive elephants? 

This was an offshoot of the DNA fingerprinting lab. Each elephant needed to have a unique genetic identity that should not be found in any other elephant.

It was a different experience, with new challenges and again very interesting. With detailed knowledge, there are a lot of things that we can do. We follow the same protocols – marker development, fingerprinting. The main challenge was that we had to find out a particular region that is not repeated.

The forest department wanted us to work on captive elephants because of certain issues faced with owners, legal issues.

When asked could you do this, my response was, we will do it. We completed the work with great success. We gained a lot of confidence by trying out new projects — we gained the confidence to take up any challenge.

Any other project you found interesting?

I think the elephant project was one of my most interesting. I don’t think anyone in India has tried such a project.

The application of this fingerprinting to multiple research questions, anything at all actually, is interesting. There are cases sometimes that the Kerala government or police department asks us to work on. We get a lot of paternity cases.

We also work on wildlife forensics – for instance, cases of animal poaching. We get samples through the court and we have to identify whether it is from a wild animal or other animals. We have been getting a lot of poaching cases.

They send an animal part and the lab has to find out what animal it is?

Not just the animal part! It can even be a dish made out of a wild animal – it can be deer, for example. It can be the animal in any form!

Initially, I was a bit reluctant to accept the responsibility of the DNA fingerprinting facility. I was comfortable just doing my research. The facility takes up a lot of time and I lose the research time. But later, I understood: if I am working continuously, service to society is also important. I can be a part of the process.

We have a new project with Sharanabalyam, the state social justice department. They wanted our help to identify parentage when people come as guardians to small children – to confirm if a person is the real father/mother. This is of great help, especially in the case of custodial issues.

International collaborations

In 2017, the European Molecular Biology Organisation, EMBO, had a worldwide open competition to choose the host to conduct a global conference. EMBO would screen applicants and fund one group which they deem most suitable. It was funding to organise an international meeting, with strict guidelines: to ensure representation from across the world, maintain gender balance, have strict criteria for presentations, etc.

It was my students who were very interested and worked hard toward the application. When we got the funding, it was a pleasant surprise. We conducted the meeting, called “Micro and metabolic regulators in plants,” here in Thiruvananthapuram.

This story is supported by the Solutions Journalism Network ‘LEDE’ fellowship, aimed at spreading solutions journalism around the globe.

Banner image: Quite early in her career, Soniya discovered her deep curiosity for the molecular biology of plants and their interaction with pathogens and the environment. Photo from E.V. Soniya.