Kia Pākiki Canterbury – plant molecular biology

In this Kia Pākiki Canterbury podcast, Science Communicator Tom Goulter and Associate Professor Adrian Paterson from Lincoln University interview Dr Samarth from Canterbury University.

They discuss Samarth’s work in plant molecular biology and the ways in which plants can sense, communicate and respond to their environment.

Kia Pākiki Canterbury is a monthly podcast presented by the Canterbury branch of the Royal Society Te Apārangi.

Transcript

Tom Goulter

I’m here with Adrian and Samarth. Samarth is a postdoctoral fellow at Canterbury University’s School of Biological Sciences. He’s a plant molecular biologist working to develop solutions for sustainable agriculture and biodiversity conservation, and in 2024, he received the Illumina Emerging Researcher Award for his exceptional use of molecular biology tools. Samarth, you’re looking into how plants sense, integrate and remember environmental cues. Is that right?

Dr Samarth

Yes. It’s been long that we all have believed that plants are quite passive organisms and they are quite unaware. But through my research, we are trying to show how much they can perceive environmental signals. In particular, I’m looking at how they can hear different sound vibrations, how they are able to sense those vibrations from the environment and translate those physical signals into biomolecular signatures and convert that into biological processes and how they respond differently. Moreover, I’m looking at how plants or trees can detect summer solstice and initiate their reproductive or developmental transitions, which is interesting seeing that such a small change in a day length could initiate something really important for those trees. And I’m also looking at how plants can remember flooding signals and how they are able to remember those signals in terms of whether they can produce specific metabolites that can help them overcome the flooding stress, yeah.

Tom Goulter

So plants do feel stress as people do.

Dr Samarth

Yeah.

Tom Goulter

But it seems like they might be better than people at dealing with it. Is that right?

Dr Samarth

Absolutely. Since they don’t have to go away anywhere, they have to almost develop some sort of strategy to be able to cope with it. So they have multiple layers of mechanisms underneath them in ways that they could remember them. So whenever there’s a specific stress coming in or there’s stress applied in the form of – it could be man-made or it could be natural – they would remember a certain type of transcription factor, certain genes that they induce and that provide resilience against those stresses in the plants.

Associate Professor Adrian Paterson

So what does memory mean in this sense for you?

Dr Samarth

So memory is essentially, I think it’s very much an anthropomorphic term. So they do remember in case if there is a stress applied for a very short term. So they would perceive it that, “OK, I am in this condition. I now need to activate this gene or this protein to help me counteract the stress.” OK.

Associate Professor Adrian Paterson

So you get into a drought or dry conditions, you’re feeling dry, you do some things to get through it.

Dr Samarth

OK. This is for the short term. Now, what happens if that stress is applied for a very long term, let’s say a week instead of one day? Now, when it starts happening, the plants would automatically start to transcribe those genes and activate those proteins automatically. So they have some fixed signatures of memory, which means they remember the memory signatures. In scientific terms, we say they have specific epigenetic marks that are there on the plant genome that stay there, and as soon as the stress comes back again, it starts activating those genes.

Associate Professor Adrian Paterson

It might be good to explain epigenetics.

Dr Samarth

That’s a really good question. Yes, so epigenetics is – in a very crude way, I would say that these are specific marks or addition of some chemical groups in the DNA that allows the plant to carry that information through time or through spatial-temporal manner. So for example, if I have –

Associate Professor Adrian Paterson

Sort of a non-genetic information that can get passed along for some period of time.

Dr Samarth

Yes. For example, if I remember to brush every day in the morning, the plants would remember every day to wake up and activate certain genes that do the morning business for them. So that’s kind of like an epigenetic mark, as you can say, yeah.

Associate Professor Adrian Paterson

So in terms of flowering and masting of seeds and so on, what’s your main interest?

Dr Samarth

Yes. So we were looking at masting from a point of view of how plants initiate flowering firstly, and how do they actually remember those signals to initiate flowering or to initiate masting over multiple years. So over –

Associate Professor Adrian Paterson

So what is the main difference between masting and flowering? Or is it just a certain type?

Tom Goulter

Can I – yeah, I’d like to get a basic definition of what masting is for a start.

Dr Samarth

So masting is when a tree produces enormous amounts of seed but in a very sporadic and intermittent fashion, and this is produced by a population of trees over a huge geographical area. So, for example, we have beech masting.

Associate Professor Adrian Paterson

Beech trees, yeah.

Dr Samarth

Yep, which goes all across South Island, and it creates havoc in terms of our conservation efforts because it leads to a massive explosion in rats, stoats and possums numbers.

Associate Professor Adrian Paterson

Because there’s suddenly all this food.

Dr Samarth

Absolutely. And that leads to, when the food runs out, they tend to go and eat our native birds, killing about 50 million birds supposedly every year. So it’s still a big number, and Department of Conservation spends millions of dollars each mast year to drive conservation efforts to protect our native fauna. So to do that, we need to know when exactly masting is going to happen.

Associate Professor Adrian Paterson

When it’s coming.

Dr Samarth

Yep, exactly. So this sort of higher synchronisation is driven by a weather cue, and it’s been postulated that, a lot of times, these weather cues could be correlated with these masting patterns. For example, currently Department of Conservation uses a delta T model, which is basically the temperature difference between the successive summers, which is if the summer temperature of the previous year is significantly higher than the year before, that means you’re going to have a masting year in the following year. So somehow now plants are able to remember the temperatures for over 2 years and coordinate it in a fashion to actually drive flowering and to drive masting.

Associate Professor Adrian Paterson

And so this is why it’s usually unpredictable because, well, if we don’t know that fact, we just see that some years, and it’s not just it’s a hot year, it’s got to be hotter than the previous year.

Dr Samarth

Yes, so that’s one aspect of it. That’s one correlation. There’s new studies coming up stating that there’s also a role of resources. So how inside the plant, how much resources are available, how much carbon they have stored – that also plays a role in driving that masting effort – along with what specific temperatures are going to be important. We have some idea but not very clear idea what exact temperatures are going to form or what exact temperatures are going to be important for these masting.

Associate Professor Adrian Paterson

And so you are interested in the genetics of the masting itself or how they remember the temperature from the year before or both of those things?

Dr Samarth

Actually, both of those. So in my PhD, I think we started with understanding how that happens at the genetic level, and then following on, how do they actually remember it. So how do they remember or which gene is responsible for remembering those specific marks that are there to remember those temperatures where they start to get integrate. So coming from a molecular biologist perspective, I was asked to answer these questions in a very ecological phenomenon, so merging two or three different fields together.

Tom Goulter

Let’s go back to sound. My dear mother used to believe that, if she played classical music to her plants, they would grow more healthy. But I imagine that your research is somewhat more sophisticated than this.

Dr Samarth

I think the basis is the same.

Tom Goulter

OK. Go ahead, tell me more.

Dr Samarth

So the idea is that plants respond to sounds, and they have different frequencies that they’re responding to it. Scientifically, people have shown plants respond to from 50 hertz to 5 kilohertz. Some sounds help them grow, some sounds act as sort of a deterrent in growing. So it really depends on which crop or which plant you are talking about, and they all have different frequencies they respond to. But the ultimate challenge that comes on to is how are they actually detecting it and how are they responding to it? We really don’t know yet, and that’s where my research comes in, where I recently was awarded with a Marsden Fast-Start grant where I’m looking at whether trichomes, which are small protrusions on the leaf surface, whether they can act as mechanoreceptors to absorb that pressure wave from sound, because sound is nothing but a mechanical pressure wave, and it can absorb that, and it can translate that physical signal into a biochemical cue and initiate the downstream gene expressions and changes in biological processes.

Associate Professor Adrian Paterson

So why would they need to worry about sound in the evolutionary past?

Dr Samarth

There are different evolutionary constraints that I believe or have been published which shows that sound is really important. For example, in one of the papers, it was shown that garden pea roots actually use sound to find out where the roots are, where the water is, and they move towards where the water source is. It’s also related to herbivory, where in 2014 by Appel and Cocroft, if I remember it correctly, they showed that plants which was exposed to sounds made by herbivores, particularly caterpillar chewing, they produce more defence metabolites or they activated defence metabolisms, so they were more resistant to herbivory. There’s also a study where they showed that plants having actually – if you expose them to pollinator sound, they produced more sugar or more nectar in the flowers, which promotes pollinator attractions and increasing pollination efficiency. And very recently in 2019, I think, it was shown that, by Khait et al., it was shown that plants actually also produce sound, ultrasound waves that tell them which stress they are going through. So if it’s a drought stress, they would have different sound. If they’re going to something like a biotic stress or something like a cut or a herbivory, they would produce a different sound.

Associate Professor Adrian Paterson

And so potentially the other plants can pick that up and they can tell themselves, “I’m being eaten by caterpillars, you maybe need to watch out.”

Dr Samarth

We believe that would happen, but it’s not scientifically shown yet. But I think it’s still in the process.

Associate Professor Adrian Paterson

But it’s possible.

Dr Samarth

It’s possible.

Associate Professor Adrian Paterson

More possible than it potentially was thought 10 years ago.

Dr Samarth

Yes, absolutely. That being said, the neighbouring plants do hear the same sound. Not sound, same chemical signal. So if a plant is being eaten by one insect, it releases chemicals called volatile organic compounds, and that can be sensed by the neighbouring plants, and they can also induce or sort of upregulate their defence mechanisms. So somehow they are communicating with each other. Yeah, so they can talk as well.

Tom Goulter

How does all of this help us to develop novel solutions for sustainable agriculture?

Dr Samarth

That’s a really good question. So if we do understand how plants are interacting with the environment, we would have our ways where we can find novel strategies, for example, to eliminate or to make the plants sort of less susceptible to diseases, make them more resilient towards abiotic stresses with climate warming coming in the picture. You have, because of the climate warming, the winter temperatures are going – sort of not coming to that point where they receive enough cold, which affects their reproduction, which affects the flowering as well. So knowing how plants interact with their environment would help us make sure that we can fine-tune those molecular processes happening behind those biological processes, and we can help our farmers to develop those kind of varieties which can sustain those climate changes.

Associate Professor Adrian Paterson

How did you get into this research area?

Dr Samarth

This is what exactly happened, and I’m not kidding about this. So in 2013, before I was supposed to do a master’s in biopharmaceuticals and proteins. So that was my main interest. But what happened was I went on a pilgrimage with my parents and my family, and there was a flash flood in the mountains, and we got stuck there. We were stuck in the mountain, in cold air in the Himalayas at 14,000 feet with no shelter, no food, nothing. And we had to just survive on what we could find around each other. And that sort of sparked my interest and curiosity, how well the plants supported us and how much important they are for us. And from there on, I got the curiosity to start looking around and understanding their physiology, which made me go into doing my master’s in plant biotechnology. And from there on, that really piqued my interest, and I just was completely hooked onto plants from there on. And from there on, I developed certain characteristics of learning about metabolism or more about computational side of biology, genomes and DNA, and then molecular biology. So yeah, that’s how it all started, it all began.

Associate Professor Adrian Paterson

So do you have a favourite plant, favourite flower?

Dr Samarth

I do like antirrhinums. They’re very cool. Snapdragons. And they come in different colours, and they have different mutants. They look really pretty, and I’m really fascinated by the different colours and variations that they have.

Tom Goulter

This is getting to be a bit like the Proust Questionnaire. Where do you hope that your research might take you Samarth?

Dr Samarth

To a Nobel Prize. One day.

Tom Goulter

Wonderful. Aim high.

Dr Samarth

One day. Yes. My father always told me that, dream big enough such that, what if you can’t fail? So why not?

Associate Professor Adrian Paterson

Ideally, what would you find with your research? What would your ideal result be?

Dr Samarth

So ideally, I’m looking into (a) understanding how plants interact with the environment through sound vibrations. That’s the main goal. But I also want to understand how sound vibrations or acoustic energy can affect biomolecular sort of structures. For example, proteins or your DNA or protein-DNA interactions. So my main goal is to use acoustic energy, or sound frequency of specific wavelength, and use them to actually either promote or repress protein concentrations inside the cell. So if we could do that, we could achieve a lot of processes, industrial applications that is there, but also we could prevent so much damage done by biotic attacks or build resilience among plants against abiotic stress, because we would be able to just apply sound waves which can allow the plants to promote their defence mechanisms. We don’t have to put any pesticides, we don’t have to put any herbicides. We don’t have to treat them with anything. You just have some mechanism, a sound wave-based mechanism that can help plants to do that. And that would be my ideal achievement.

Associate Professor Adrian Paterson

I guess we’re in an increasingly noisy world as well. I think of all those plantings they put along motorways and so on and the sheer noise.

Dr Samarth

Absolutely. And I think they are more towards rhythm-based. So if there’s a continuous rhythm of noise, that might decrease the detrimental effects. But potentially, if it’s a one block of sharp sound, that might have a different effect.

Associate Professor Adrian Paterson

I remember for, I think it was bird species, if you have a river, like a really raging river, like a canyon or something like that, seems to have much less effect than, like you say, just the occasional really loud noise. They kind of get used to it.

Dr Samarth

Yeah.

Associate Professor Adrian Paterson

Just strikes me that we often monitor birds now. We can use acoustic recorders, and you set them out in the environment for a month, and then you find out what they’ve been listening to, and you can use AI models now to basically say it’s this bird. Strikes me when you say that the plants are generating noise, that maybe you have invasive plants coming in and they’re going to make a sound, and if we could actually identify the particular sounds to particular species, we could actually search for them maybe a lot easier. Is that possible in the future do you think?

Dr Samarth

Why not? If we have the right tools and if we can identify specific acoustic signatures with each species and how they’re responding, we might be able to detect it, and it could be one non-chemical and non-genetic way of detecting which species it is. Definitely, it’s a possibility in the future. It would be an ideal scenario.

Associate Professor Adrian Paterson

It does strike me, how far away can you hear a plant?

Dr Samarth

About 20 centimetres. You have to put a microphone and you would be able to listen to it. Where the signatures are coming, what acoustic, which frequency they are vibrating. And they’re producing those sound waves.

Associate Professor Adrian Paterson

Amazing.

Tom Goulter

You’re also interested in science communication as well, aren’t you? How does that play into your work?

Dr Samarth

So I do like to present my science in front of a general audience and like to do outreach programmes as well. For example, in my previous postdoc, I did a lot of school events where we were presenting our science. I was presenting for general awareness about CRISPR-Cas9 gene editing and how that’s going to affect, and more so just talking about plant biology in general, how aware the plants are and how much we know now from an environmental point of view. So that helped generate that curiosity among students. And a lot of my students had come up with really interesting questions, and that’s the way forward that I have kept also in my teaching. Whenever I do that at Canterbury University, I try to push towards more giving general examples and more examples with where they are related, so it helps the students bring out that curiosity and help them generate that imaginative capability where they can find solutions for those complex problems.

Tom Goulter

Blowing people’s minds for a job of work. That’s wonderful.

Associate Professor Adrian Paterson

So you’re at University of Canterbury.

Dr Samarth

The department, it’s such a family-like environment, and I absolutely love it because it’s so easy to talk to professors and researchers and discuss science, and they have morning coffees. So it’s always a very relaxed and chill environment where you can come and work and enjoy the work.

Associate Professor Adrian Paterson

The thing that really struck me recently was going to see the corpse flower flowering away in the Botanic Gardens. Crazy looking thing.

Tom Goulter

Crazy smelling thing.

Associate Professor Adrian Paterson

Definitely crazy smelling thing. But yeah, it doesn’t look real. Kind of looks like a prop from a Doctor Who 1970s polystyrene sort of thing. But it’s got interesting colours and obviously smell, and just huge. So is that something – you probably haven’t worked on corpse flowers, but what are the key things about flowering and the colour of the flowers and so on from a genetic point of view?

Dr Samarth

I think that plant in particular sort of flowers after a long time or something, right? And when the temperature is right, that’s when –

Associate Professor Adrian Paterson

Yeah, and then it raises its temperature, and that’s what helps create the smell or something.

Dr Samarth

Yeah. It smells like rotten meat or something, right?

Associate Professor Adrian Paterson

It definitely does.

Dr Samarth

And it does that actually because the plant, where it is from originally, it sort of tries to attract insects that are meat-eating, and that can help them for increasing pollination.

Associate Professor Adrian Paterson

Pollination, yeah.

Dr Samarth

And that’s why we have, that plant has developed that smell, just to increase their pollination efficiency. In terms of beautiful looking flowers, once a plant has decided to, or I would say committed to induce flowering or to initiate flowering, it also initiates production of a lot of polyphenolic compounds – those secondary metabolites we call flavonoids. And these flavonoids are the ones that give colour, particularly anthocyanins. I think we all have read and talked about anthocyanins and how good they are from antioxidant perspective. But those beautiful colours also act as pollinator attractants, and different plants produces different colours, anthocyanins or 3-deoxyanthocyanins, apigeninidin, to have those acting as pollinator attractants so that the pollinators would come, jump in and get the pollens and – yep.

Associate Professor Adrian Paterson

So what was your research angle on looking at flowers?

Dr Samarth

So, from a flowering point of view, I was more interested in what the genetic side of it. How the plants initiate flowering. But from a colour point of view, I was looking at how colours actually evolved. So I was studying plants that are close to the ancestral land plants, so like plants that came here at 400 million years ago. A group called hornworts, and I was looking at why they don’t have specific flavonoids or how do they produce colours actually. So what are the different type of compounds that are in there? What is the genetic regulation of those colours?

Associate Professor Adrian Paterson

And so this gives you an idea about how it all might have started.

Dr Samarth

Yes. How that have evolved over time, because colours, as I said, is really important because it protects, you can say it act as a sunscreen for plants, and it protects them against the high UVB radiation that, when you come to land, you experience, and it allows the plant to save themselves. And that’s believed to be the main reason why plants have evolved these colours in them, along with some other additional processes that, over the time, these genes and their different metabolites that came up and started producing, they would be different colours. So predominantly, it used to be red colour, but now you could see a lot of different colours as well.

Tom Goulter

We just have one question that we like to ask every participant on our podcast Samarth, which is what’s the last thing that made you curious?

Dr Samarth

So one of the things that I got really curious today was about understanding how sound waves or acoustic energy can be made from a protein sequence. So if you have a protein sequence of amino acids or if you have DNA bases, can you turn it into a music? Can you turn it into a musical note and you can play it? How would that sound like? I think it’s been done, but it’s very curious.

Tom Goulter

That is wild. What a great answer. Thank you. Thank you so much for your time Samarth.

Associate Professor Adrian Paterson

Yeah, thanks Samarth.

Dr Samarth

Thank you for having me here.

Acknowledgements

Tom Goulter
Associate Professor Adrian Paterson, Lincoln University
Dr Samarth, University of Canterbury

Kia Pākiki Canterbury logo, © Plains Media/Royal Society Te Apārangi (Canterbury Branch)
Images of Tom Goulter and Adrian Paterson, © Royal Society Te Apārangi (Canterbury Branch)
Image of Samarth, © Samarth
New Zealand native iris (Libertia) and narrow-leaved plantain (Plantago lanceolata), The University of Waikato Te Whare Wānanga o Waikato
Mountain beech (Fuscospora cliffortioides), Krzysztof Ziarnek, CC-BY 4.0
Flowers in Himalayas, Ansul24Sharma, CC-BY-SA 4.0
River and plants beside New Zealand highway, Maksym Kozlenko, CC-BY-SA 4.0
Corpse flower (Amorphophallus titanum), © Tom Goulter