The Basic Science Research Concept

“So are you trying to make plants more defended?”

This is often the first question I encounter when I share my research questions with anyone that does not spend their work life thinking about plants. Before the conversation can get much further, I find it helps to introduce the difference between basic science research and applied research.

Both are important, but it is easier for people to connect with applied research: research designed to improve the way humans live. However, many of the solutions we use today came as a result of discoveries from basic science research: research designed to understand the way something works for the sake of understanding.

Like what?

PCR: the technology that lets us duplicate tiny amounts of DNA, was only possible because a scientist was curious about how acidic and hot Yellowstone hot springs could be for bacteria to survive. Bacteria flourishing at high temperatures have DNA too, and the enzymes that could replicate DNA despite the heat were eventually extracted and were able to withstand the hot temperatures in PCR.

Efficient building design: scientists were curious about the structure of termite mounds, which can maintain a constant temperature despite the heat of the desert. The results from these studies were used to construct a building in Zimbabwe (The Eastgate Centre) that uses 90% less energy.

Velcro, the ubiquitous adhesive found on light-up shoes, was inspired by plant hook-shaped hairs.

And the list goes on. The moral of the story is that technology gets along well with natural selection, but first we have to understand how it all works.

My research goal is to understand how plant-insect interactions change as a result of the chemistry within the plants that have a symbiotic relationship with nitrogen-fixing bacteria. I spend my time at my desk wondering about how and when plants will use their resources to make the stuff that protect them- either directly by making poisonous chemicals, or indirectly, by sending volatile compounds into the air to communicate with the predators of their attackers.

Instead of trying to get plants to do anything, my goal is to understand what they actually do on their own- to understand the unknown aspects of their biology.

Do these bacteria play an important role in the food web by altering plant-insect interactions? My research will let you know.

Plants with Benefits

Maintaining relationships, even great ones, can be challenging.

Some plants juggle multiple relationships ALL of the time.

Think of an organism that does something helpful for a plant. Bees, hummingbirds, and other pollinators may come to mind. But plants also recruit toucans, black bears, and other seed dispersers as well as predatory insects such as ants and wasps for defense.

And then there are microbes.

My goal for this research paper was to show how one microbe in particular, nitrogen-fixing bacteria called rhizobia, can alter a plants’ entire network of relationships—from the bottom-up.

Rhizobia live inside nodules on plant roots in a tight-knit symbiotic relationship, exchanging fertilizer for sugars from photosynthesis. Plants that form this relationship benefit immensely from the nitrogen, but providing sugar in return can tax the plant.

Plants like dip n' dots too. #rhizobia #nitrogenfixation #biopsu

A post shared by Adrienne Godschalx (@agodschalx) on

Plants also use their homemade sugar to secrete extrafloral nectar. Nectar typically attracts pollinators, but in the case of extrafloral nectar, plants produce nectar to attract ants, which patrol their sugar source like bodyguards. By evicting intruding bugs attempting to feed on the host plant, extrafloral nectar can be an effective indirect plant defense…

…as long as the ants show up to do their part.

But the key result from our paper is that ants are less attracted to plants that have nitrogen-fixing rhizobia in root nodules belowground. Keep in mind- the ants and bacteria do not interact directly. What connects ant to bacteria?

The plant between them.

Plant chemistry changes when plants form symbiosis with rhizobia. Plants with nitrogen-fixers make more of the nitrogen-based traits, protein and cyanogenesis. Surprise. But these plants also secrete less sugary nectar, therefore attracting fewer ants.

Even in the plant world, some relationships can be more demanding than others.

How do rhizobia cause plants to compromise their ant relationships?

It could be that rhizobia demand so much sugar to keep the nitrogen flowing that the plant’s excess sugar supply is exhausted, leaving little to serve as ant lures. Alternatively, why would plants that get a constant supply of nitrogen to make cyanide need to attract ants anyways?

Either way, we now know rhizobia can change plant relationships with ants.

But why would that matter?
Ants are everywhere- so are rhizobia. Both play important roles in how ecosystems function, but the fact that they can indirectly affect one another may have strong and widely overlooked impacts on plant ecology.

© Adrienne Godschalx (adrg@pdx.edu) August 19, 2015

The Crazy Things Plants do for Nitrogen

What’s the big deal with nitrogen, you ask? Nitrogen is the key ingredient in proteins. In biology, if our DNA does the talkin’, proteins do the walkin’. Proteins can be enzymes that help reactions happen. In plants, the sugar-making part of photosynthesis, (aka the dark cycle) is run by an enzyme called RuBisCO, which also happens to be the most abundant enzyme on earth. The remarkable thing about this super important enzyme, responsible for turning CO2 into sugars, is that it is a super slow, clunky enzyme. Plants often compensate for its slowness by making more of it. More enzyme=more protein. Plants need nitrogen to make proteins.

I thought about naming this post: “Nodules, photosynthetic pathways, and carnivorous plants, oh my!” But the number of syllables got in my way. Still, these three evolutionary wonders all help plants deal with limited nitrogen, and deserve to show up in a blog post together.

But why are plants so nitrogen-limited in nature?

The answer includes a terrifying word from Intro to Chemistry: stoichiometry. (Which I recently learned from this fantastic paper: Nitrogen and Nature.)

The number of nitrogen molecules in plants is small among all of the carbon molecules, which drives the ratio of carbon to nitrogen molecules the leaf litter, overwhelming the soil with carbon and making nitrogen hard to come by. Further, nitrogen is typically stuck directly to carbon in a covalent bond, which is harder to break off than ionic bonds that work like magnets. Even when nitrogen is in this “magnetic” form, these ions are negatively charged—just like soil particles—and easily leech from the soil with rainwater.

Yes, that is why nitrogen is limited in the soil, but most of the nitrogen in the world is in the air; isn’t there plenty of it in the air that plants could use? The atmosphere is made up of roughly 79% nitrogen. Unfortunately, that nitrogen is not accessible to plants. Each nitrogen is tightly bound to a second nitrogen atom like this: N≡N, and triple bonds are especially tough to break, even for a plant.

But some bacteria can break all three bonds!! Microbes have crazy metabolic pathways, many of which are crucial to the chemical balance of the world existing as we know it. By turning N≡N into fertilizer in a process called nitrogen fixation, the nitrogen cycle is driven by microbes.

Evolutionary wonder #1: Some plants figured this out (over evolutionary time), and formed a symbiotic relationship with nitrogen-fixing bacteria. These groups of bacteria: rhizobia, Frankia, and cyanobacteria, live in nodules on their plant hosts’ roots and provide a source of house-made fertilizer in exchange for sugars. Plants, which do photosynthesis, that have nitrogen-fixing bacteria in their roots represent the interface of two important geochemical cycles: the nitrogen and carbon cycles.

Not only are plants solar-powered sugar factories, but some plants can make sugars through several different metabolic pathways: C3, C4, and CAM. For perspective- we don’t even have one carbon assimilating pathway, but the plant kingdom has three.

Evolutionary Wonder #2: In “normal photosynthesis”, or C3 photosynthesis, plants lose water through pores called stomata when they take in carbon to turn into sugars. Some plants reduce the amount of water they lose by either opening their stomata at night when the air is cooler (Crassulacean Acid Metabolism or CAM), or by concentrating the CO2 in a separate compartment with those super slow enzymes (C4). Why are these nitrogen-limited adaptations? Because making enzymes more efficient helps plants with the initial problem of needing nitrogen to churn out tons of slow, clunky enzymes.

Yet some plants carry out old fashioned C3 photosynthesis without any N-fixing bacteria in root nodules and are able to live in extremely nitrogen-poor soil. Their secret? Eat the tiny packets of nitrogen buzzing and crawling everywhere around them.

Evolutionary wonder #3: Carnivorous plants are exciting because they deviate from our basic understanding of what plants do. When my mom let me buy a $4.99 Venus fly trap at City Market, my mind was blown. I wrote songs and recorded one too many home videos about the plant that eats flies!

Even Darwin himself was excited by this menacing behavior and laid some groundwork for research on how Venus flytraps close in on their prey.

Despite the diversity of strategy, ranging from pitcher plants that collect bugs that slip into the plants’ digestive juices to sticky plants that catch bugs with glandular hairs, carnivorous plants evolved to deal with stressful environments lacking that not-so-secret ingredient in all proteins:

Nitrogen.

Feliz día: International Women’s Day

Many creative and brave women shaped the way we understand the world, including many women scientists.

Recently I bought a new computer, and I decided to name it after a groundbreaking woman scientist. Marie Curie, who pioneered radioactivity came to mind, as did Rosalind Franklin, who, independent of Watson and Crick, determined the structure of DNA using x-ray crystallography. But then… I was stumped.

Even as a scientist I could only name two famous women scientists who shaped my understanding of science. I was astonished I could not name more without a google search. I admire many women currently working on cutting-edge science, but I knew many lady scientists significantly contributed to developing the ideas that we teach in intro-level courses.

Luckily, as a teaching assistant, I get to learn introductory biology all over again. One day in principles of biology lecture, my advisor described the concept of how mitochondria and chloroplasts came to exists as organelles inside of a cell- and that Lynn Margulis, despite grief from her male colleagues, solidified the endosymbiotic theory—a way of thinking that is essential to our current understanding of biology.

Here is why endosymbiosis is so cool:

Remember learning about all of the organelles inside of a cell? And about how the mitochondria is the “powerhouse of the cell”? Plants have a “make-your-own-food-from-sunlight” organelle: chloroplasts. Both mitochondria and chloroplasts are surrounded by a second membrane and contain their own circular DNA, which led Lynn Margulis to propose the idea that these organelles were originally prokaryotes, like bacteria, which were engulfed by another cell! While inside the cell, this prokaryote/ organelle ancestor paid enough “rent” by producing ATP or creating sugars from sunlight, so the landlord cell kept its tenants around.

An entire domain of life began- eukaryotes. (We belong to this domain…so does your cat.)

Yet, as I hinted earlier, this theory explaining the origin of eukaryotes and the organelles providing the energy was not accepted with open arms. I am not sure if the theory would be equally as contested if a man proposed it, but as a woman, Lynn’s publication On the Origin of Mitosing Cells was rejected 15 times, and even after it was accepted and printed in 1967, she still was not widely accepted by her male colleagues who thought her idea was ridiculous.

But with sheer courage she persisted, and now overwhelming evidence supports the endosymbiotic origin for the mitochondria and chloroplast. First, if you take all of the mitochondria or chloroplasts out of a cell, the cell cannot make more, which implies the ancestor cell took it in to begin with. Not only do both organelles have their own DNA resembling that of bacteria, but when scientists look at the DNA sequences, the base pairs line up well with current prokaryotes. Cyanobacteria is the chloroplast’s closest relative, even though chloroplasts are found in plants!

I can’t even imagine what we would teach students about how eukaryotes gained extra organelles, which gave this domain of life access to energy that enabled the crazy diversity we see today.

Lynn continued in her career by showing how symbiotic interactions—organisms interacting with one another—can act as a major evolutionary force.  My own research depends on this concept, and involves a form of endosymbiosis: bean plants take up bacteria into their roots that turn atmospheric nitrogen into a form the plant can use. This cooperation between plants and bacteria enables both to flourish.

This weekend I was honored to participate as a mentor for a Women in Science day event: girls 12-18 years old toured Genentech, a leading biotech company and talked with a wide variety of scientists to learn about possible careers. I was struck by the momentum behind encouraging girls to pursue science, and the confidence that there is power in women’s perspectives in creating innovative science.

“Life did not take over the globe by combat, but by networking”- Lynn Margulis (and Dorion Sagan)

Santa Claus is Comin’ to Town!

In the spirit of Christmas, a time for giving, I find it fascinating that one concept perplexing many scientists is the number of species that help each other. This is called a mutualism in science speak, and is confusing to many scientists because the underlying rules of natural selection (Darwin, 1859) intuitively work against spending energy or valuable resources helping others. Remember, fitness= grow and reproduce (although this kind of fitness is also fun). Any trait involved in spending the currency on an unrelated organism that would otherwise go towards kids theoretically would not last for many generations (because it takes having kids to make a new generation with those traits). But mutualistic traits do last, even when other organisms evolve ways to cheat and take more than they provide, further baffling evolutionary ecologists.

Which is why I think this paper is so cool.

The scientists used a creative strategy to assess how plants deal with the extra loss of sugars without any return of nitrogen when the symbiotic bacteria in their root nodules cheat. The creative part is forcing bacteria to cheat: rhizobia, which take the inaccessible, triple-bonded nitrogen from the air and turn it into a useful, organic molecule for the plant are not able to provide this service when there is no nitrogen in the air! Dr. E. Toby Kiers and her team kicked out all of the nitrogen by flooding chambers with roots and nodules with oxygen, 20% (rhizobia need oxygen too), and argon, 80% – a stable gas that is heavier than nitrogen.

Plants with “cheating” rhizobia on their roots cut off the oxygen supply to those nodules!

This concept of punishing cheaters (aka host sanctioning) to maintain a fitness benefit from the relationship is a huge help in solving the evolutionary questions about two-way beneficial relationships (mutualisms!) in nature.

It’s kind of like how Santa keeps you on your best behavior so you don’t get coal in your stocking.

Merry Christmas (or whatever you celebrate)!

-A