Dr. Priyanka Kushwaha
Hello, and welcome to Ask a Scientist, the podcast for both kids, and adults too, to ask scientists questions about anything they want to know. There are so many scientists out there doing a lot of cool scientific research. We are constantly hearing their new ideas and where those ideas are going to take us in the future. But just who are these scientists? In this podcast, we will learn a little more about who they are and what inspires them as scientists.
I’m your host, Victoria. Every other week, I’ll sit down with a different scientist and ask them questions written by you, the listeners, and by students from classrooms throughout the country.
Thank you so much for listening to Ask a Scientist and all of the support you’ve given the podcast since it started in March of 2020. We are about to hit our 50th episode of season one. And so we are going to go on a hiatus between season one and season two. I hope you’ve enjoyed listening to all of the episodes in season one as much as I have enjoyed making and producing the episodes of season one.
Victoria:
Our guest this week is Dr. Priyanka Kushwaha. She is a is a Postdoctoral Research Associate
at the University of Arizona, Tucson. She studies what kind of microbes are present in a soil
and what role they play in providing nutrients to the plants. She also studies soils that are contaminated by toxic metals.
Priyanka. Thank you so much for being here.
Dr. Kushwaha:
It’s my pleasure. Thank you, Victoria, for inviting me on your podcast.
Victoria:
Is there anything that I didn’t cover that you want to add to that very brief introduction?
Dr. Kushwaha:
No, that was great.
Victoria:
(What are soil microbes?)
Awesome. So in that case, we can just jump right into the questions. And all of these questions come from listeners that were submitted via social media or emails.
So the first question here comes from Della. What are soil microbes?
Dr. Kushwaha:
So basically, soil microbes are invisible living organisms that live beneath the soil or below ground. Diversity of the soil comprises of microbes and they can be different kinds of microbes. So it could be bacteria, archaea, fungi, viruses, and then nematodes and protozoa as well sometimes are considered in the microorganism or microbes realm, but I basically focused on bacteria, archaea, and fungi in my research.
Victoria:
(How do you study microbes? Do you use microscopes?)
Awesome. Very cool.
And this is a good follow-up question to that from Max. How do you study microbes? Do you use microscopes?
Dr. Kushwaha:
I don’t use microscopes, but I have used microscopes to look up to bacteria growing back to when I was growing bacteria on previous missions, then I would use my microscopes to look at them. But the way I study microbes is I extract DNA from soil and then use that’s the DNA markers to sequence the DNA of the microbes or bacteria in my case. And then, identify them based on their DNA qualities or DNA sequences.
Victoria:
That is so cool. How, this is not a listener question, but something I just thought of, how do you extract the DNA?
Dr. Kushwaha:
So luckily now a bit technology has given us kits that you can buy commercially. So these kits are designed that specifically to extract DNA from soil because soils have a lot of organic matter and humic acids that inhibit the processes drive downstream. So for example, you want to, when I say DNA markers, what I mean is that you’re trying to take a small piece of your DNA and make multiple copies of it, so you can study. Because in the copy number that is present in the bacteria, it wouldn’t be enough for us to study it downstream. So we want to make multiple copies and then if our DNA is not, if the DNA that extract does not clean, that will inhibit the processes downstream. So, yes.
Do I translate your question? In short, there are commercial kits available that have optimized the methodology, and we just buy them and follow the protocol. Sometimes we do have to modify that commercial protocol to suit our soil samples that we are using.
Victoria:
Oh, cool. Is that, so I recently just, this is again, just a me question. So I recently registered to on one of those websites for being a bone marrow donor and they sent me a kit and I just had to swab the inside of my cheek. So, is that similar? Is the soil kit similar? Do you just like swab the soil?
Dr. Kushwaha:
No, it’s not. In the case of soil, we don’t swab. So in the case of soils, as we take out the kit that I use, I have to take half a gram of soil that I put in a tube, and then we add some reagents to it. And then we use something called a bead-beater where it will shake the tubes. So the idea is with the buffer that you add, some enzymes that will help break open the cell walls, so you can get the DNA out of the cell walls of the microbes.
Victoria:
(What kinds of microbes are present in the soil? Are there good microbes and bad microbes?)
Oh, okay. Cool.
All right. Now back to the listener questions. The next listener question is from Melanie. What kinds of microbes are present in the soil? Are there good microbes and bad migraines?
Dr. Kushwaha:
Sure. Yes. So I briefly said, what are the microbes, so there’re bacteria, archaea, fungi, viruses, nematodes, and protozoa that are present in the soil.
And yes, there are good and bad microbes. But we have to remember the bad microbes are not necessarily trying to be evil. It’s a competition between the good and the bad and competition for nutrients. In that results, sometimes, when there’re not enough nutrients, some of the bacteria can be bad. And as a result of that, they can cause plant diseases. And some of the bacteria in soil can also cause health problems for humans. So there, yeah, there’s a combination of good and bad.
And the good ones mostly are helpful for the plant growth because they cycle nutrients, change the form of nutrient from one to the other and make it more accessible for the plants to obtain.
Victoria:
(Do you name the new microbes you find?)
Okay, cool. And speaking of the microbes, Amber wants to know, do you name the new microbes you find?
Dr. Kushwaha:
Well in the microbiology world, yes. People do name the microbes that they find, but I don’t do that kind of research where I have found a new micro, but if you find one, then you have to go through the set of rules that are established by the International Code of Nomenclature of prokaryotes. And if your new found microbe matches those set of rules, then you have for the additional steps and paperwork to submit to have that microbe named.
Victoria:
(Are there different types of microbes in different types of soils?)
Okay. That makes sense.
All right. And getting into some questions about the diversity of microbes. Lucy wants to know, are there different types of microbes in different types of soils?
Dr. Kushwaha:
Yes, there are. So depending on what kind of nutrients you will find in your soil, there will be different sets of microbes that will be present.
So for example, the deserts soil are more diverse in a group of bacteria called Actinobacteria. And one of the reasons why they are more present in deserts is because they have more stress coping mechanisms, so they can withstand heat, they can withstand drought. So that’s why they are more present in the desert. Whereas acetobacteria and verrucomicrobia these are the two that are present in forest and grasslands.
So the diversity or abundance varies across different soil types.
Victoria:
(Is it really bad to eat dirt? Will the microbes or the toxins make you sick?)
Okay. That makes sense. Cool.
And this next question comes from Chris. Is it really bad to eat dirt? Will the microbes or the toxins make you sick?
Dr. Kushwaha:
Yes, I would say it’s not a good idea to eat dirt, but there are reasons why we crave to eat dirt because of the nice smell it has, and also it has calcium. So we need calcium as a micronutrient in our body. So we tend to gravitate towards eating dirt. But we do have to remember that there are microbes are good in the soil, but they might not be good for our body. So our digestive system might not like them and our own microbiota might not appreciate new microbes because then there’s competition, right, for nutrients.
So not a good idea to eat dirt. And in addition to the bacteria, that can be some parasites that you can ingest. And if the soil has any toxins, then you can ingest that too. So because of all of these things that you can ingest that your body shouldn’t and can have harmful effects, one should avoid eating dirt I would say.
Victoria:
That’s good. And I suppose for calcium, drink dairy products or something, instead of eating dirt?
Dr. Kushwaha:
Yeah, I get calcium tablets.
Victoria:
Yeah.
Dr. Kushwaha:
And be a little bit more out in the sun. So you can get the vitamin D and calcium is used for making vitamin D or vice versa.
Victoria:
(What kind of toxins have you found in soil?)
All right.
And now we can move on to a bunch of questions here about all of the toxins in the soil. So this first question in that group comes from Jane. What kind of toxins have you found in the soil?
Dr. Kushwaha:
So basically, what I study is a mining waste, which is coal mining, sorry, mine tailings. And they are basically fine ground up powder-like material that covers acres of lands. And one of the reasons why we have such a large amount of waste is because the technology in the past wasn’t as good to not create so much waste. So technologies have improved over time, but they’re legacy signs that remain across US that have large amount of toxins that have been disposed in the environment. So the tailings that are studied, they have high heavy metal contamination, and they are particularly high in their arsenic.
Victoria:
(How do toxins get in the soil?)
Oh, man. Okay.
And you answered this a little bit already, but if you have anything to add to it. Anna wants to know how do toxins get in the soil.
Dr. Kushwaha:
So yes. As I said it can be result of mining practices or any other industry waste, which can be airport industry waste at air pollutants, or water pollutants. So if you have pollutants or any toxins in water or runoff from the water could result in the positing those toxins in the soil. And would the air pollutants, once they settle down, then those toxins can get deposited in the soil.
Victoria:
Oh man, it sounds like there’s a lot of ways that things get into the soil.
Dr. Kushwaha:
Yeah.
Victoria:
(When the microbes take up toxins from soil, where do they go? Are they passed on to whatever eats the plant?)
Yikes.
Okay. And then this next question is from Angelique. When the microbes take up toxins from the soil, where do they go? Are they passed onto whatever eats the plants?
Dr. Kushwaha:
That is a good question. So technically when we, so microbes can do different things. They can, obviously they are not expecting to uptake the toxin, but because they have different ways of taking the nutrients, they might use their nutrient uptake mechanisms to accidentally take metal. And then as a result of that, either they will get killed because the metal is toxic for them, or because this has such a small reproductive cycle that as they reproduce, they might try to change their genes so that they can make that metal not toxic for them. So there are different mechanisms. There’s a lot that goes on in microbes, right? So that is one thing that they will do.
And sometimes they are not able to particularly help the plants from stopping the plants to uptake the metals, but what they do is they will have some other compounds that they released that helps alleviate the stress for the plant. The plant is less stressed and healthy even though it’s growing in the metal contaminated area or in the soil that has toxins.
The other part of the question was if the toxins get passed to whatever eats the plant. So the answer is yes and no, because it depends on the properties of the plants. So some plants, they are able to fight those stabilize, that term means that you basically take the metals and then sort of capture them in an area. So the plants have some compounds that they release and then the metals will bind to them. And then just the metal, the metal stays in their roots, okay, doesn’t get uptake into the above ground parts of the plants.
But there are some plants which are called hyper accumulators. They are the ones who have the capability of transporting that metal from the soil to the root, and from the roots to the shoot and some leaves. And when that happens, then it becomes a problem for people who are going to eat those plants, because if the levels are too high, and animals grazing on it, or if it’s a food product, then people who are consuming it, they can get sick from those toxins.
Victoria:
Yikes. And what are those toxins? If, I mean, I don’t think this is when you study, but what do they do to people or other animals that eat them.
Dr. Kushwaha:
So I think it depends on what they have ingested. So there are different some metals, or over time accumulation of those metals in your body can result in cancers, for some, it could be a respiratory illness. So they’re like, varied health hazards that are associated with having that.
Victoria:
(Is there something that we can do to stop toxins from getting in the soil?)
Okay. Yikes.
And this next question about the toxins comes from Zoe. Is there something that we can do to stop toxins from getting in the soil?
Dr. Kushwaha:
Yes, not we have an individual side thing, but I think we need better science policy and regulations for the industry. We are aware of what waste are creating and in what amounts they are being disposed in the environment. We have gotten better from like the last 50, 60 years in having better regulations, but there are remnants of the ways that still remained from the when things were not regulated in the same manner.
So, and usually these toxins have a really long life wherever they are. So it does cause, as it’s more of a chronic exposure that happens over time to people who are living in these areas. So you might not see the health hazards or people getting sick soon. It might be a result of living in an area where they’re exposed to toxins for a couple of years before they realized what the. Sometimes the effects can be short term and you can see them right away. But in most cases, it takes a little bit longer before people even realize why that is happening.
So I would want on having better regulations. And one way we can help that is we talk to our Congress, men and women, and try to make sure that if there is an issue in your community, you bring that up and ask for better regulations in the area.
Victoria:
(Has the quality of nutrients in our soil deteriorated over the last, say, fifty years?)
Yeah. That, that makes sense.
And speaking of, you mentioned kind of things that have happened in the past. This next question from Joe is about the past and soils of the past. Joe wants to know has the quality of nutrients in our soil deteriorated over the last, say, 50 years.
Dr. Kushwaha:
Yes, it has. So there are different reasons for that.
One of the major ones, since the farming practices that we have to. So, just to give a brief summary of the plants and agriculture crops. So basically, with the soil, it’s the top soil that is the most nutrient rich for the plants to grow in. So with the different kinds of farming practices, what has happened is that it has allowed for the top soil to get eroded by wind and water. So we have lost most of the top soil. And once you don’t have the top soil, it’s harder for plants to grow because they wouldn’t get all the nutrients they want. So that is one of the reasons.
And then with the other climate changes, with either too much rainfall or no rainfall that affects the way the soil is. And also the nutrient imbalance, because we are interfering with a natural land. So that happens to you and fertilization helps, but then fertilization has other issues which are problematic.
So I think our future agriculture practices issue focused on how we can do it sustainably because there are reports where we are talking about losing more and more soil and also more of desertification, which means that there will be more soils which won’t be able to grow anything naturally.
Victoria:
Yikes.
Dr. Kushwaha:
Yeah. I feel like I’m making this sound so grim. Our future is so grim.
Victoria:
No, I mean, it’s important to talk about these things.
Dr. Kushwaha:
Yeah.
Victoria:
(What is excessive fertilizing of agricultural crops done to soil quality and microbe availability in soil?)
And this next question, since we were talking about agriculture, so good that this question comes next. This is a question from Tremaine. What is excessive fertilizing of agricultural crops done to soil quality and microbe availability in soil?
Dr. Kushwaha:
So I was saying before, quality in terms of providing for the plants has been or growing agricultural crops has been good. But what it has led to a lot of environmental problems, as I said before.
So one of the things is we have to keep in mind, the amount of fertilizer that is applied is not all that it’s used up by plants. So there are leftovers or leftover of different forms because plants take up a form and some remain in different forms. And these leftover fertilizers then become a problem as a runoff. So with the water runoff, these, so basically nitrogen phosphorus and potassium that it’s used as fertilizer in different combinations. So there will be runoffs and water and lakes, it can go into your groundwater. So that affects the drinking water for people in the neighboring communities. And then having excess of these fertilizers, again will cause health hazards. So that happens.
And in terms of the microbe availability in soil, I think with the fertilizers, because it does allow more nutrients to be available, it has microbes, but the dynamics or the diversity or the abundance of the microbes changes because of the availability of different kinds of nutrients. So one example that I would like to give is that is causing a problem because microorganisms, which transform nitrogen in from the soil, they can convert that nitrogen into nitric oxide, which is a greenhouse gas. So because there’s more availability of nitrogen for these microbes in the soil, that is happening. So that is a negative effect from having fertilizers in the soil because of adding to a greenhouse gas emissions.
Victoria:
Wow. I never thought of that before.
Dr. Kushwaha:
Yeah. Microbes are cool, not really knowing what they’re doing, well, they know for themselves, but yeah.
Victoria:
(Are there soil microbes that can produce plants with high concentrations of nutrients that animals and humans need? Such as, can microbes create a high protein grass for beef cattle consumption?)
Yeah. Oh, wow.
Yeah. And speaking of nutrients in the soil and soil quality, Joe wants to know, are there soil microbes that can produce plants with high concentrations of nutrients that animals and humans need? Such as can microbes create a high protein grass for beef cattle consumption.
Dr. Kushwaha:
That is a very good question from Joe. I think based on my knowledge, the answer is no. But if it can be done or cannot be done, I’m not a hundred percent sure about it. But what I would like to add to this question is that basically what microbes are doing is they are only providing the raw material for the plants. So they are giving the basic nutrients that plants need. And in order to provide that they sometimes form symbiotic relationship with plants. So plants provide certain nutrients to the microbes and then micros writes something to the plants. So in terms to create high protein grass for beef cattle, we will have to modify the plants. So it’s able to make more of protein, versus expecting the microbe, because microbe, as I said, is only providing the raw materials. If that makes sense.
Victoria:
Yeah. Yeah. That does. It’s not so much a microbe process, but a plant process.
Dr. Kushwaha:
Yeah. But it would be cool if we could do that. I’m sure we can modify a little bit with different kinds of microbes, so that they give, like they’re able to provide more of the nutrient. But if the plant does not using it by itself as a means to produce more than we have to modify the gene to express more and make more proteins.
Victoria:
(Are there microbes that can be added to water to increase hydroponic production of food crops?)
Okay. Yeah, that makes sense.
All right. And then another interesting question about plants and food crops. Anna wants to know, are there microbes that can be added to water to increase hydroponic production of food crop?
Dr. Kushwaha:
I would think no. The reason being microbes are raised specifically to where they grow. Like if they are growing in soils, they’re used to that environment. So taking them out of that complex, in most cases, nutrient-rich environment for the microbes. If you’re putting them in a hydroponic submission, they won’t have that holistic nutrients that they need. So they probably won’t survive.
But the way the hydroponics work says hydroponics is trying to target the role of the microbes in a water medium. So what they do is they try to use as many as nutrients the microbes in the soil are providing to the plants. So sort of mimicking what microbes would do, but by providing artificial nutrients in the hydroponics medium. So I don’t think necessarily they need microbes in that case.
Victoria:
Okay. Interesting. So did they just put, like, they’re essentially just putting fertilizer in water?
Dr. Kushwaha:
Yes. Yeah, yeah.
Victoria:
Okay.
Dr. Kushwaha:
And one thing that you could do is because it’s hydroponics can be more green. So what they do is they use different, one example that I have in mind, obviously hydroponics is not my field of study, is where you can use fish tank to use the, like the excrement that fish have because that’s nitrogen rich and it has urea, right. So you can use that for your plants. And then whatever the plants make can be used for. So it’s like establishing an artificial symbiotic relationship in the hydroponics environment. So that is one way it was done. Or you could have just fertilizers in the water.
Victoria:
Oh, that’s really cool. When a friend of mine used to have a fish tank and then the plants just kind of took over growing in the fish tank. So I guess that makes sense. Cause there was all of the nutrients from the fish excrement.
Dr. Kushwaha:
Yes.
Victoria:
Cool. Oh, I love, I love it when science like can answer, you know, questions, like make an observation about a fish tank. Oh, and then there’s the answer.
Dr. Kushwaha:
Yeah.
Victoria:
(How do you study plant genetics?)
All right. So we’ll switch gears a little bit. In the bio that you provided about your work and yourself, you mentioned plant genetics. And so we’ve got a couple of questions coming up about that. So Lucy wants to know how do you study plant genetics?
Dr. Kushwaha:
For plant genetics, similar to what I did with microbes in the soil. You extract DNA. So in the case of plants, too, you can extract the DNA or you can extract RNA. And then do the same process, use specific markers, which will help you target certain regions of the DNA. And you know, what functions these particular genes have, and then you can look at their expressions and you can look at how they have, if you have multiple plants or, you know, this probably this plant is an ancestor of the other one, you can study the evolutionary relationship using those DNA markers.
Victoria:
(How do you change the genetics of the plant?)
Okay. Cool.
And a good follow-up to that from Max. How do you change the genetics of the plant?
Dr. Kushwaha:
In order to change the genetics of the plant, you will have to modify the genes. So it’s basically genetically modifying organisms or there’s some other technologies called CRISPR now where you can do gene editing. So basically, you are changing the DNA sequence for those particular genes.
But I don’t do t hat. I don’t modify anything, but rather what I study is if I put plants under certain conditions, I left the, like, I naturally see the progression of plants, what they’re doing. If they’re under stressed environment, in my case, so metal toxins, then how do they respond in different levels of metal contamination. So once I have that experiment set up in a greenhouse, after few months of the plants growing, I will harvest the plants, and then extract DNA or RNA of the plants. If to study gene expression, I will extract RNA out of the plant, and then look at those gene expression changes from one level of metal contamination to the other.
Victoria:
(What is the coolest microbe you’ve found?)
Okay. Very cool. Awesome.
And now we’ve got two questions that are very fun questions. This first one is from Della. What is the coolest microbe you found?
Dr. Kushwaha:
Coolest microbe I have found. I would say that I don’t have a single microbe that I’m particularly fond of, but I would say that I find Actinobacteria, group of bacteria in desert, very fascinating. As I previously mentioned, they have capability of tolerating extreme heat and drought, and they have mechanics where they go dormant for a while when the conditions are not favorable. And then once they have rain and they have nutrients moving in the soil, then they become active. So I think they are really cool that they can do that. They can live in, live outside in the desert. They are pretty cool.
Victoria:
That is pretty cool.
Dr. Kushwaha:
Yeah. All right.
Victoria:
(What is your favorite microbe and why?)
And then our last question here is from Melanie. What is your favorite microbe and why?
Dr. Kushwaha:
My favorite bacteria is again from the group of Actinobacteria, it is called streptomyces. And the reason why I really liked this microbe is, because it produces a compound called geosmin, and we all have smelled geosmin. So that nice sweet smell of rain, that is just been. So the reason why we smell that is streptomyces when they don’t have favorable environmental conditions. So they’re not, if they don’t grow because they don’t have the nutrients they need and the right water availability. So they will make spores, they go dormant, make spores, and then they want those spores to be spread out. So they can find favorable conditions to grow back again. So geosmin is produced when the spores are made so that the insects in water breeds and the soil get attracted to it. And as they move around, they take the spores with them. And then hoping as a result of the insects and invertebrates taking it around, they will find a favorable environmental condition, and then they can grow and reproduce. And the reason why we only smelled geosmin when it rains is because geosmin sits on the soil, but when it rains, geosmin gets released into the air, and then we can smell it.
Victoria:
Oh, wow. That’s awesome!
Dr. Kushwaha:
And since I live in the desert, I wait for the monsoon. So it just fits perfectly to where I live. So that’s why I love it.
Victoria:
Oh, that’s awesome. Yeah. It must be pretty hot down in Arizona right now.
Dr. Kushwaha:
Yeah. I think that this week has been a little bit nicer because we got drizzles of rain, but yeah, it’s pretty hot. Colorado is hot too relative to other years, right?
Victoria:
Yeah. It’s been hot here this week, similar to you, it’s been raining. So lots of chances to smell it this week. But I think next week we’re supposed to get back up into the really hot, dry, … (33:30)
Dr. Kushwaha:
Oh, no.
Victoria:
Yeah.
Dr. Kushwaha:
Stay hydrated.
Victoria:
Yeah, you too.
All right. And that technically was not quite our last question. So I always end every episode by, you know, I’ve sat here asking you questions from the listeners, but do you have any questions that you’d like to ask the listeners?
Dr. Kushwaha:
I think my question to the listeners would be, what is one thing that they learned from the podcast that blew their mind away?
Victoria:
Yeah. That’s a good one. Do you have any professional social media accounts that the listeners can follow you on if they’re interested?
Dr. Kushwaha:
Sure. So yes, I use my Twitter account for science communication, which I’ve been a little slow, but yeah, they can definitely go there.
Victoria:
I’ll make sure to have a link to that in the description of the episode so they can follow you.
Dr. Kushwaha:
Great. This has been fun. Thank you.
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