1.20.25

Microbes facing tough times

Jennifer sampling soil before the shelters were set up. Here you can see the control (left) and carbon addition (right) plots.

The activities are as follows:

As the climate changes, Michigan is expected to experience more drought. Droughts are periods of low rainfall when water becomes limiting to organisms. This is a challenge for our agricultural food system. Farmers in Michigan will be planting crops into conditions that make it harder for corn, soybean, and wheat to grow and survive.

Scientists are looking into how crop interactions with other organisms may help. Microbes are microscopic organisms that live in soils everywhere. Some microbes can help crops get through time times. These beneficial microbes are called mutualists. They give plants nutrients and water in exchange for carbon from the plant. Microbes use the carbon they get from plants as food. If plants are stressed and don’t have any carbon to give, microbes get carbon from dead plant material in the soil.

Jennifer is a biologist studying the role of microbes in agriculture. She has always been interested in a career that would help people. As a student, Jennifer thought she would have a career in politics. Along the way, she learned that a career in science is a great way to study questions that may lead to solutions for the challenges we are facing today. Jennifer was drawn to the Kellogg Biological Station, where she joined a team of scientists studying the impacts of climate change and drought on agriculture.

Jennifer and other scientists set out to test ways that we can give mutualists in the soil a boost. She thought, perhaps if we were to give microbes more food, they would be less stressed during a drought and would be able to help out crops growing in these stressful conditions.

To test this idea, Jennifer needed to test how well microbes were doing under different carbon and drought conditions. First, she set up treatments in soybean fields to manipulate the amount of carbon in the soil. She set up control plots where she left the soil alone. She also set up carbon treatment plots where dead plant litter was added to the soil to increase the carbon available to microbes.

Next, Jennifer manipulated the availability of water in her plots to test the microbes under stress. To do this, she set up her plots under shelters that kept out rain. The shelters had sprinklers, which were automated to add specific amounts of water to the plots. This design allowed Jennifer to control the watering schedule for each plot. One shelter treatment was a control, where water was added to the plots every week. This is similar to the schedules of local farmers who add water through irrigation. The other shelter treatment was drought, where plots received no water for six weeks. This experiment was replicated 4 times, meaning there were 4 shelters on the control watering schedule and 4 shelters that were under drought conditions.

A view of one of the shelters used in Jennifer’s experiment.

Finally, Jennifer had to measure how the microbes were doing in each treatment. She did this by measuring their enzyme activity. Enzyme activity is a measure of how active the microbes are. The higher the enzyme activity, the happier the microbes are. To measure this, Jennifer collected soil samples from each plot throughout the growing season and took them to the lab to measure enzyme levels in the soil samples. These enzymes are made by microbes when they are active. She then calculated the mean of all her samples for each treatment combination.

Jennifer predicted two things. First, if drought is harmful to microbes, then she would expect to see lower enzyme activity in the drought treatment compared to the irrigated treatment. Second, if adding carbon to the soil is a way to help microbes overcome the challenge of drought, she expected higher enzyme activity in the plots with plant litter added compared to the control treatment. Both of these taken together would indicate that drought is stressful for microbes, but we can help them out by adding resources like plant litter to soils.

Featured scientist: Jennifer Jones (she/her) from the Kellogg Biological Station Long Term Ecological Research Site. Written with Melissa Frost and Liz Schultheis.

Flesch–Kincaid Reading Grade Level = 8.2

Additional teacher resources related to this Data Nugget:

To introduce this Data Nuggets activity, students can watch a talk by Jennifer when she made a classroom visit to share her background and research interests. This video is a great way to introduce students to scientist role models and learn more about what a career in science looks like, as well as get an introduction to the themes in the research.

There is also a video of Jennifer and her scientist colleague, Grant Falvo, out in the field talking about their research under the rainout shelters.

For more information about the rainout shelter experiment, students can watch this short video featuring Jennifer Jones and another scientist on the team, Grant Falvo:

  • https://youtu.be/1lDUQIxwRaM

These data are part of the Kellogg Biological Station Long Term Ecological Research Program (KBS LTER). To learn more about the KBS LTER, visit their website:

  • https://lter.kbs.msu.edu
6.17.22

Going underground to investigate carbon locked in soils 

Mineral-associated organic matter (MAOM) at the bottom of a test tube in a salt solution.

The activities are as follows:

Soil is an important part of the carbon cycle because it traps carbon, keeping it out of the atmosphere and locked underground. At a global level, the amount of carbon stored by soil is more than is found in all of the plants and the atmosphere combined. Carbon trapped underground does not contribute to the rising carbon dioxide concentration in our atmosphere that leads to climate change. For decades, scientists have been researching how much carbon our soils can store to understand its role in slowing the pace of climate change.

Carbon enters the soil when plants and animals die, and their organic matter is decomposed by soil bacteria and fungi. Sometimes it is broken down into very small molecules. These molecules become attached to minerals in the soil, like clay particles. We call this mineral-associated organic matter (MAOM). The carbon is connected to minerals with very strong chemical bonds. Because these bonds are hard to break, the carbon stays in the soil for long periods of time and accumulates on clay minerals. 

Some studies have shown that the carbon in MAOM can be trapped in soils for thousands of years! When more of the carbon in the soil is attached to minerals and locked in the soil for longer time periods, the ecosystem is serving an important role in keeping carbon out of the atmosphere. 

Ashley in the lab, using a saltwater solution to isolate mineral-associated organic matter (MAOM) from soil samples.

Ashley is working to understand how much stable carbon there is in soils, and the role of climate. Microbes work faster in warmer and wetter conditions, which results in quicker decomposition. Ashley thought this rapid decomposition would cause organic matter to be broken down into smaller particles sooner. Therefore, she thought that in warmer or wetter environments, more soil carbon would attach to minerals and become stable MAOM. In colder or drier environments, she expected this process to happen more slowly, leading to a smaller amount of MAOM in the soil.

To test these ideas, Ashley used soil samples from forests with different climates throughout the Eastern United States. Soil samples were collected from New Hampshire to Alabama by teams of researchers using the same sampling protocol. The samples were mailed to Ashley’s lab at Indiana University for analysis. Ashley measured the amount of MAOM in each soil sample by taking advantage of a key feature: MOAM is heavy! Ashley submerged each soil sample in a saltwater solution, and the parts that floated were discarded, while the parts that sunk to the bottom were classified as MAOM. She then rinsed the salt off and measured the amount of carbon in the MAOM with an instrument called an elemental analyzer. She compared this number to the amount of carbon in the whole soil sample to calculate what percentage of the total soil carbon was attached to minerals.

Featured scientist: Ashley Lang from Indiana University

Flesch–Kincaid Reading Grade Level = 10.8

Additional teacher resources related to this Data Nugget:

3.31.22

Salty sediments? What bacteria have to say about chloride pollution

Lexi taking water quality measurements at Cedar Creek in Cedarburg, WI.

The activities are as follows:

In snowy climates, salt is applied to roads to help keep them safe during the winter. Over time, salt – in the form of chloride – accumulates in snowbanks. Once temperatures begin to warm in the spring, the snow melts and carries chloride to freshwater lakes, streams, and rivers. This runoff can quickly increase the salt concentration in a body of water. 

In large amounts, salt in the water is harmful to aquatic organisms like fish, frogs, and invertebrates. However, there are some species that thrive with lots of salt. Salt-loving bacteria, also known as halophiles, grow in extreme salty environments, like the ocean. Unlike other bacteria and organisms that cannot tolerate high salinity, halophiles use the salt in the environment for their day-to-day cellular activities. 

Lexi is a freshwater scientist who is interested in learning more about how ecosystems respond to this seasonal surge of chloride in road salts. She thought that there may be enough chloride from the road salt after snowmelt to change the bacteria community living in the sediment. More salt would support halophiles and likely harm the species that cannot tolerate a lot of salt. 

By taking a water sample and measuring the chloride concentration, we can see a snapshot in time of how toxic the levels are to organisms. However, the types of bacteria in sediments take a while to change. Halophiles may be able to tell us a long-term story of how aquatic organisms respond to chloride pollution. Lexi’s main goal is to use the presence of halophiles as a measure of how much chloride has impacted the health and water quality of river or stream ecosystems. This biological tool could also help cities identify areas that may be getting salted beyond what is necessary to keep roads safe.

Lexi expected that there would be few, or maybe no, halophiles in rural areas where there are not many roads. She also thought halophiles would be widespread in urban environments where there are many roads. Because salt impacts the streams year after year, she expected that halophiles would become permanent members of the microbial community and increase in winter and spring. Therefore, she also wanted to track whether halophiles remain in the sediment throughout the year, increasing in numbers when salt levels become high. 

She began to sample sediments from two different rivers in Southeastern Wisconsin. The urban Kinnickinnic River site is in Milwaukee, WI, and the Menomonee River site is in a rural environment outside of the city. She selected these sites because they offer a good comparison. Because there are more roads, and thus saltier snowmelt, the Kinnickinnic site in the city should have higher chloride concentrations than the Menomonee site. 

When visiting her sites throughout the year, Lexi collected multiple water and sediment samples. Every time she visited, she also recorded important water quality characteristics such as pH, conductivity, and temperature of the water. She then brought the samples to the laboratory and analyzed each for its chloride concentration. To measure the quantity of halophiles in the sediment, Lexi used a process where the sediment is shaken in water to separate the bacteria from the sediment and suspend them in the water. Samples from the water were then plated on a growth medium that contained a very high salt concentration. Because the growth medium was so salty, Lexi knew that if bacteria colonies grew on the plate, they would most likely be halophiles because most bacteria do not thrive in salty environments. Lexi counted the number of bacteria colonies that grew on the plates for each sample she had collected.

Featured scientist: Lexi Passante from the University of Wisconsin-Milwaukee

Flesch–Kincaid Reading Grade Level = 12.0

Some videos about Lexi and her research:

Additional teacher resources related to this Data Nugget:

1.8.21

Fertilizer and fire change microbes in prairie soil

Christine collecting samples from the experimental plots to measure root growth.
Christine collecting samples from the experimental plots to measure root growth.

The activities are as follows:

Stepping out into a prairie feels like looking at a sea of grass, with the horizon evoking a sense of eternity. Grasses and other prairie plants provide important benefits, such as creating habitat for many unique plants, mammals, insects, and microbes. They also help keep our water clean by using nutrients from the soil to grow. When plants take up these nutrients, they prevent them from going into streams. High levels of plant growth also keeps carbon bound up in the bodies of plants instead of in the atmosphere.  

Prairies grow where three environmental conditions come together – a variable climate, frequent fires, and large herbivores roaming the landscape. However, prairies are experiencing many changes. For example, people now work to prevent fires, which allows forest species to establish and eventually take over the prairie. In addition, a lot of land previously covered in prairie is now being used for agriculture. When land is used for agriculture, farmers add nutrients through fertilizer. With all these changes, prairie ecosystems have been declining globally. Scientists are concerned that as they disappear so will the benefits they provide. 

Lydia and Christine are two scientists contributing to the effort to learn more about how to preserve prairies. They both became interested in studying soil because of their appreciation for prairies at a young age. For Lydia, she lived in an area that was covered by trees and farmland, but knew at one time it used to be prairie. This made her want to learn more about prairie environments and how places like where she grew up have changed through history. For Christine, she grew up surrounded by prairies where she developed a passion and curiosity for the natural world. Especially for the organisms living in the soil that you cannot see, called microbes. 

These are two different experimental plots within the large field experiment at Konza Prairie Biological Station. The one with lots of trees is an unburned plot, the one with lots of grass is a burned plot.
These are two different experimental plots within the large field experiment at Konza Prairie Biological Station. The one with lots of trees is an unburned plot, the one with lots of grass is a burned plot.

Lydia and Christine read about how grassland scientists have been doing research to learn more about what happens when fire is stopped and excess nutrients are added. These changes reduce biodiversity and affect which species of plants can grow in the prairie. However, Lydia and Christine noticed that the research had been mostly focused on what happens aboveground.  Lydia and Christine had a hunch that the aboveground communities were not the only things changing. They thought that belowground components would be changed by fire and fertilizer too. They turned their focus to microbes in the soil, because they also use nutrients. In addition, they thought these microorganism would be affected by the changes in aboveground plant biodiversity. 

To see if this was true, they used data that they and other scientists collected at Konza Prairie Biological Station from a large field experiment. The experiment was set up in 1986 and the treatments were applied at the field site every year until 2017! Lydia and Christine focused on the fertilizer (nitrogen) addition and prescribed burning treatments to answer their questions. The nitrogen treatment had eight plots where nitrogen had been added and eight with no nitrogen as a control. Similarly, the prescribed burn treatment was applied to eight plots, while eight plots had no burning as a control. These two treatments were also crossed with each other, meaning that some plots were burned and nitrogen was added.

Lydia and Christine expected the types of microbes in the soil to change in response to the nitrogen and burning treatments because of the different aboveground plant communities and difference in soil nutrients. Soil microbial communities can change in multiple ways. First, the number of unique species can increase or decrease, measured as richness. The other way is how many individuals of each species there are in the community, measured as evenness. Taken together, richness and evenness give a measure of diversity, which can be summarized using the Shannon-Wiener index. The value will get bigger if either richness or evenness increases because it incorporates both. For example, a community with five species that has equal abundance of each will have a larger Shannon-Wiener index than a community with five species where one species has a lot more individuals than the other four.  

Featured Scientists: Lydia Zeglin and Christine Carson from the Konza Prairie Biological Station. Written By: Jaide Allenbrand

Flesch–Kincaid Reading Grade Level = 10.4

9.4.18

Alien life on Mars – caught in crystals?

Magnesium sulfate crystals trapping liquid water.

The activities are as follows:

Is there life on other planets besides Earth? This question is not just for science fiction. Scientists are actively exploring the possibility of life beyond Earth. The field of astrobiology seeks to understand how life in the universe began and evolved, and whether life exists elsewhere. Our own solar system contains a variety of planets and moons. In recent years scientists have also discovered thousands of planets around stars other than our Sun. So far, none of these places are exactly like Earth. Many planets have environments that would be very difficult for life as we know it to survive. However, there are life forms that exist in extreme environments that we can learn from. On Earth there are extremely hot or acidic environments like volcanic hot springs. Organisms also live in extremely cold places like Antarctic glacier ice. Environments with extremely high pressure, like hydrothermal vents on the ocean floor, also support life. If life can inhabit these extreme environments here on Earth, might extreme life forms exist elsewhere in the universe as well?

A view of the astrobiology lab.

Charles is an astrobiologist from Great Britain who is interested in finding life on other planets. The list of places that we might look for life grows longer every day. Charles thinks that a good place to start is right next door, on our neighboring planet, Mars. We know that Mars currently is cold, dry, and has a very thin atmosphere. Charles is curious to know whether there might still be places on Mars where life could exist, despite its extreme conditions.While there is no liquid water on the surface of Mars anymore, Mars once had a saltwater ocean covering much of its surface. The conditions on Mars used to be much more like Earth. Liquid water is essential for life as we know it. If there are places on Mars that still hold water, these could be great places to look for evidence of life. Charles thought that perhaps salt crystals, formed when these Martian oceans were evaporating, could trap pockets of liquid water.

Charles and his fellow researcher Nikki knew that there are a number of kinds of salts found in Martian soils, including chlorides, sulfates, perchlorates and others. They wanted to test their idea that water could get trapped when saltwater with these salts evaporate. They decided to compare the rate of evaporation for solutions with magnesium sulfate (MgSO4) with another commonsalt solution: sodium chloride, or table salt (NaCl). They chose to investigate these two salts because they are less toxic to life as we know it than many of the other chloride, perchlorate, or sulfate salts. Also, from reading the work of other scientists, Charles knows the Martian surface is particularly rich in magnesium sulfate.

Charles and Nikki measured precise quantities of saturated solutions of magnesium sulfate and sodium chloride and placed them into small containers. Plain water was used as a control. There were three replicate containers for each treatment – nine containers in total. They left the containers open to evaporate and recorded their mass daily. They kept collecting data until the mass stopped changing. At this point all of the liquid had evaporated or a salt crust had formed that was impermeable to evaporation. They then compared the final mass of the control containers to the other solutions. They also checked the resulting crusts for the presence or absence of permanent water-containing pockets. Charles and Nikki used these data to determine if either saltmakes crystals that can trap water in pockets when it evaporates.

Featured scientists: Charles Cockell, UK Centre for Astrobiology, University of Edinburgh, & Nikki Chambers, Astrobiology Teacher, West High School, Torrance, CA

Flesch–Kincaid Reading Grade Level = 8.7

Additional teacher resource related to this Data Nugget: