GRAZER-microbiome interactions at soil to landscape scales

Yes, microbes are everywhere, have a huge diversity of ways of getting energy from their environments, and through these metabolic activities control the levels and forms of organic and inorganic chemicals in every habitat, including animal host environments. This means animal - including human - health and nutrition is affected by microbes, in analog to microbes' importance for plant, soil and ecosystem health and fertility. Society benefits from the microbial and ecosystem services that we study.

At the landscape scale, large grazing ungulates may have an active effect on soil microbial structure and function. For example, grazers can move nutrients and microorganisms long distances across the landscape, and concurrently make nitrogen more available for plant growth through their digestion products. Our lab has been investigating soil microbial distribution, diversity, and soil fertility responses to bison grazing for several years (see left & short YouTube video) through support from NSF (CAREER.pdf).

One goal of this research is to broaden our geographic perspective and understanding of the redundancy of bison and cattle grazing effects on soil, by sampling rangelands across the Flint Hills. See this flyer for more detail on the search parameters for private lands participants, and see this example report on bison grazing data for site managers. Contact Lydia Zeglin with any questions.

What is a grassland without grazers and fire? Pre-European colonization, bison ranged the North American Great Plains, and fire was frequent due to active Indigenous use and lack of fire suppression. Today, cattle are common, and are managed in a  different ways. However, some grassland areas have been left unmanaged, as a lack of grazing or prescribed fire. These management effects on microbial biodiversity, and soil health in general, are the focus of another current study, supported by the USDA-NRCS Soil Survey.

We are also embarking upon a new project that will help understand how microbial biodiversity responds to different cropping and irrigation systems across the midwest (FFAR/Bayer press release). By working to define which attributes of microbial biodiversity are associated with both crop production and soil health, we can support best outcomes for producers and sustainable soil fertility.

When it comes to soil health and water quality, who's really in charge, the microbes, or the humans? All of our work on management effects is about understanding human-microbe interactions. Through a better understanding of these interactions, we gain the ability to nurture positive relationships, and strive to live and work better, together.

Stream ecosystem function
and microbial diversity

From pole to pole across our planet, stream ecosystems are perhaps the most dynamic, heterogeneous and biogeochemically active components of the landscape, and carry integrated signals of the watershed upstream. A large portion of the balance between stream nutrient uptake and export, thus water quality, is mediated by microbiota, but little is understood about the links between microbial diversity and stream function. More work is needed to measure and identify the active components of microbial diversity in streams, the mechanistic links between diversity and function, and to address how population-, community-level or physiological responses of stream microbiota to global change drivers affect stream function.

Does microbial structure and function correlate more with rainfall, or land-use? How well do genetic attributes of microbial communities predict lotic ecosystem function? Many streams across the USA are intermittent or ephemeral, and these real waters are critical locations of nutrient processing and removal in their watersheds. We're using observational data, manipulative experiments, and biogeochemical, target gene and metagenomics approaches to parse out the effects of microbiome vs. water chemistry on C and N-cycling function. Two large collaborative grants support this work: the Watershed Dynamics and Evolution SFA, and Aquatic Intermittency effects on Microbiomes in Streams (AIMS.pdf). Our lab's role in these interdisciplinary projects is to investigate how local stream bacteria, algae, and protists survive and thrive through extreme drying and re-wetting cycles, and in turn how this biological resilience controls stream water chemistry and quality. The topic is of increasing concern as extreme drought threatens the stability and productivity of ecosystems globally.

We investigate the same questions in streams across the McMurdo Dry Valleys (MDVs) in Antarctica. The MDVs are both cold and an extreme desert, receiving under 4 inches of mean annual precipitation. As a consequence, the novel diversity in MDVs streams is a reservoir of biological capacity for drought tolerance, and is also vulnerable to loss under warmer and wetter future environmental conditions. Our research is part of another large interdisciplinary project, McMurdo Dry Valleys Long-Term Ecological Research (MCM-LTER), which has been funded by the National Science Foundation since 1992. Together, this group studies how physical, chemical, and biological processes interact to shape ecosystem structure and function in one of the most extreme and dynamic environments on the planet.

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Kasatochi Island before and after; a patch of Leymus mollis that has vegetatively recovered (supporting a much higher abundance, diversity and activity of soil microbes in the ash below, and more organic matter); lhz and CC working at the reference site on Adak Island. Thanks to the Alaska Maritime National Wildlife Refuge for being so supportive of young scientists who carry as much soil away with them as possible! The Aleutians are stark and beautiful.

Recovery of soil microbial structure and function post-volcanic eruption

Kasatochi Volcano erupted in 2008, burying previously lush Kasatochi Island, Alaska in pyroclastic material. Since, communities of plants, animals and microbes have re-established on certain areas of this new surface, and a multi-disciplinary team of USGS, USFWS and academic scientists is studying this recovery. Volcanism shaped the Aleutian Islands, and results to date suggest the regional biota is resilient to this high- magnitude disturbance.

Microbial colonization of the new surface is directly linked to organic matter inputs - seabird deposition, plant regrowth, aeolian redistribution of pre-eruptive soil. "Recovery" of the soil microbial structure and function has been rapid (~5y), but slower accumulation of organic matter may limit whole system recovery.

​It is still not clear whether these recovery responses represent regional microbial dynamics, or are uniquely localized patterns. The Aleutian Islands have a mild climate, highly productive vegetation (it's a temperate rain-grassland!)... this creates potential for rapid soil organic matter accumulation though plant growth and high regional microbial dispersal potential due to big weather and seabird populations.

Past projects

BGPE (top): guess which treatment hasn't been burned for >30y?
Other pics show CC and a root ingrowth core, Priscilla and the LiCor for belowground CO2 flux, Matt working to isolate bacteria from the soil.

Grassland ecosystem
sensitivity and recovery
from chronic fertilization

As part of the Konza Prairie Long-Term Ecological Research program, after 30 years, we stopped fertilizing the soil at the Belowground Plots Experiment (BGPE), and are measuring the subsequent changes in soils, microbes, and plants. This will allow us to understand the mechanisms that regulate the time it takes the ecosystem to recover from chronic nitrogen fertilization. The BGPE also includes a long-term factorial fire treatment, so we can learn how fire management affects fertilization sensitivity and recovery.

So far, we have learned that plant production is more sensitive to fertilization in annually burned conditions, soil bacterial and archaeal community composition is more sensitive to fertilization in unburned conditions, and soil fungal and plant community composition is sensitive to both long-term fertilization and the lack of fire. These differential responses are related to the role of fire cessation in causing higher ambient soil nitrogen (N) availability and allowing woody encroachment.

We are in the process of learning how sensitive the key soil microbial activities of nitrification and denitrification were to chronic fertilization, and estimating how these rates of nitrogen loss from the ecosystem might compare to losses driven by fire. These results have major implications for understanding if the added N will stay in the soil, or will leach from the soil into groundwaters as nitrate, or will be returned to the atmosphere as either greenhouse gases, or inert, harmless gases.

From 1986-2016, a total of 300 g of N per square meter of land was added to the prairie (close to 3000 lbs. per acre, at a rate of just under 100 lbs. per acre per year). Where did and where will all of this nitrogen go? Results from this work are showing the extent to which, and how, soil microbial responses to changes in land management affect important ecosystem properties (soil N availability, soil C accumulation, greenhouse gas emission, N loss potential). Check out the Data Nugget (lesson for high school students) that Jaide put together on our work here!

woody encroachment effects on soil carbon cycling

Woody plants are replacing grasses across the Great Plains, and in many other grassy ecosystems globally. The deeper-rooted shrubs deliver new carbon into the soil profile. (1) Will this input stimulate decomposition or carbon storage? (2) Will the whole ecosystem carbon balance change?

Our collaborative project (DOE.pdf) will answer these questions using new empirical data of soil C stocks and cycling activity profiles in native tallgrass prairie and woody-invaded prairie (picture to right), experiments to assess priming potential in these soils, including at depth, and most exciting, use of these data in updated earth systems models that include plant cover change and drought impacts in their predictive capacity.

Drought is increasing across the globe, and woody plants also pull more water from depth. This could have important feedbacks on both vegetation change and carbon storage, particularly in high-clay soils of this region (note color change at depth in the pictured core).

In the late 1970's, these watersheds (above) looked the same. Since then, one was burned annually (left) and one was burned twice (right). The consequent woody encroachment could change soil carbon dynamics (1-m core below, top to right of rotated picture), and the whole ecosystem carbon balance.

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Microbial turnover & stress responses to intensified drought in Grassland soils

Global change models predict that Great Plains soils will experience longer periods of drying and larger re-wetting events in the future. While altered precipitation does impact microbial function, many prairie soil microbiota are tolerant to the stress of drought. Understanding the mechanisms driving stress tolerance, and the prevalence of these traits in native and agricultural soils, will help in predicting and preparing for the future.

We ran lab experiments that showed greater taxon-specific sensitivity (death) through dry-down/re-wet cycles in soils with a history of less drought, which was also associated with more soil C loss. Also, we evlauated how a simulated "megadrought" affects microbiota in situ in soils with different drought histories.

This work was done in collaboration with investigators on the Rainfall Manipulation Plots (RaMPs, at right).

Konza Prairie at top. This is Nature Conservancy land managed by the K-State Konza Prairie Biological Station, that hosts many projects, including some of ours. Thanks to Dr. Hartnett for letting us use his Jeep Liberty (and to Sean and Victoria for sieving)!

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​Updated September 2026