Follow-Up to the Interview with Sarah Hargreaves on Soil Microbes in Prairies

Back in March, I posted an interview with Sarah Hargreaves, who recently completed her PhD studying soil microbial ecology at Iowa State University.  She gave us some great information about how we should be thinking about soil communities in prairies.  Some of you provided some excellent questions in the comments section (I had a few too), so Sarah graciously agreed to answer a few of them in this follow-up post.  I edited both the questions and her responses, so my apologies if I changed the context or meaning of either.  Questions from readers are in italics, and Sarah’s answers are below each question.  …A big thank you to Sarah for taking the considerable time needed to answer these.

How much are prairie plant communities driven by soil microbes?  How much can/should we be manipulating those soil communities?  There are way more questions than answers at this point, but the field or research is advancing rapidly.

How much are prairie plant communities driven by soil microbes? How much can/should we be manipulating those soil communities? There are way more questions than answers at this point, but the field of research is advancing rapidly.

Are archaea really a part of soil microfauna in prairies around here, or are we really talking about bacteria and fungi only? – Chris H

A survey of the dominant groups of archaea across a latitudinal gradient of native tallgrass prairie sites within the United States revealed that majority of sites have archaea, but in small abundance relative to other microbial groups (<5% total). We still don’t know about the functional significance of their presence, but I think it is fair to focus on fungi and bacteria when thinking about restoration.


What are the things land managers should be doing right now to help advance research in this critical field of studies?  I’d love to know what I should be doing before we begin our restoration projects to best track progress in microbes as we reestablish native grasses. Is this as simple as just taking soil samples? -Rachael R

My suggestion would be to take soil samples for the following purposes. First, you can use the soil samples for microscope counts of diversity (using the Soil Food Web method, for example). This is coarse, but is easy and can tell you something. I think the best approach would be to freeze a sub-sample of the soil for Phospholipid Fatty Acid (PLFA) analysis, which is a great tool for measuring fungal: bacterial ratios. The soil is stable at -20°C so it can sit frozen until you are ready to compare to your restored soils. If you are really keen, you could also track aggregate stability and total organic carbon as a measure of soil structure and carbon storage, which are both intimately connected with microbial activity.


I have thought several times about the possibility of transplanting small amounts of soil (say, a few 5-gallon buckets worth) from a remnant prairie into a prairie restoration to help re-diversify the soil organisms in these ecological restorations. What are your thoughts on this?  – Danelle H

I think the idea is a promising one, and one that farmers are starting to think about as a way to restore soil health for crop productivity. In fact, this is the premise behind compost teas (see Rodale Institute). When made properly, the idea of a compost tea is to have a substance ripe with good microbes and enough nutrients to get them started and that can be sprayed across larger areas. Unfortunately, there isn’t a lot of scientific data on this type of approach, including information on application rates and frequency, or the potential for amelioration in different soil/management types. I am sorry I don’t have a more definitive answer for you – it is a rapidly growing field and I think data on the efficacy of this type of inoculation is a high priority because of its relative ease. I also agree with Jonathan’s comment (below) about inoculating nurse plants if you are doing transplants.

…This was a response to Danelle’s question (above) when she posted it in the comments section of the initial blog post on this topic…

This paper might be helpful:
Many of the micro-organisms that are likely to improve restoration outcomes (e.g. mycorrhizae) depend on plants. So, how you introduce those microbes to a restoration will matter. The study in the paper I linked to inoculated “nurse plants” and raised these seedlings before transplanting them, along with at least some components of the soil community. There’s lots of work left to do, but this approach seems really promising. It also doesn’t require a lot of soil, so damage to remnants can be minimal.  – Jonathan B


When most of us do prairie restoration (reconstruction), we focus mainly on harvesting and planting seeds.  We think a little about soils in terms of getting good seed-soil contact and the seed bank of weed species.  Should we be thinking much more about the soil microbial community and potentially adding to it?

When most of us do prairie restoration (reconstruction), we focus mainly on harvesting and planting seeds. We think a little about soils in terms of getting good seed-soil contact and the seed bank of weed species. Should we be thinking much more about the soil microbial community and potentially adding to it?

Can soil distribution of microbes be very abrupt in composition – for example, when we see a very distinct “vegetated wall” that seems to resist an invasive species that has consumed other areas of the prairie? – David

How quickly do soil organisms expand into former cropland habitat? – James M

In regards to boundaries and expansion of soil microbes: soil microbes disperse and lay dormant (i.e. are present, to a certain extent), so the rate limiting step affecting visible boundaries and lags with restoration is more likely attributable to the soil conditions not yet being good enough to promote a fully functional microbial community. It is like a positive feedback between soil structure, plant-microbe interactions (like symbiosis) and soil microbial community function, and it takes time (decades).


I’m especially interested in your comment that ‘prairie burns help maintain a good fungal to bacterial ratio by promoting fungal abundance’. Can you explain how prairie burns help promote fungi? – Teresa

Great question! A recent meta-analysis of data on fire effects on microbial communities suggests that microbial communities in grasslands are better adapted to respond positively to fire than those from other ecotypes (e.g. boreal and temporal forests). However, it is really not known why this is – perhaps due to release of nutrients that fungi are able to capture or indirectly through plant response, etc.?

We still have a lot to learn about how fires affect the soil microbes in prairies.

We still have a lot to learn about how fires affect the soil microbes in prairies.

Would you be able to make some suggestions to me for potential science fair projects in this area? It looks like a fertile area for research! – Novalene T

How great would it be to see microbe and prairie-related projects in a science fair! The low hanging fruit is probably to sample soil from different types of ecosystems, like a prairie and a lawn for example, and examine the microbial community under a microscope and try to count the number of different types of organisms as an index of diversity (you may look at Soil Food Web microscope guides for this). Or look for mycorrhizal infection rates in the roots from different ecosystems. You could also consider the “tea bag index of decomposition”, which is a method used to measure different rates of decomposition (i.e. microbial activity). If done according to the instructions in this link, data can be added to a global network!


A Primer on Soil Microbes – An Interview with Sarah Hargreaves

Most of us who work in prairies think mostly about what we see aboveground.  I guess that’s understandable, but to ignore the complex and critical functioning of the soil and its inhabitants is to ignore much of what really drives grassland ecology.  Of course if we DID want to focus belowground, what would we actually focus on?  How much do you know about soil fungi or bacteria?

Exactly.  Me too.

This is why I was excited that Sarah Hargreaves agreed to an interview about the mysterious world of soil microbes.  Sarah is finishing up her PhD in microbial ecology at Iowa State University.  That means she’s not only up to speed on what’s known about soil microbes in the scientific literature, she’s also been studying them herself for the last several years.  A perfect person to throw hard questions at.

What do you know the little creatures that live underground in prairies?  And no, prairie dogs don't count.

What do you know the little creatures that live belowground in prairies? And no, prairie dogs don’t count.

So, here are my initial questions for Sarah, followed by her answers.  As you’ll see, she’s an excellent writer, and can communicate complex ideas in a very accessible way.  Because of that, I’ve also asked her if she’d be willing to answer follow up questions from both me and you – and she agreed (though she asked if she could wait until she finishes her dissertation, which I think is due TODAY!)

So, after you read this post, leave any questions you have in the comments section, and we’ll see if Sarah can answer a few of them in a future post.

What is a soil microbe?  What broad taxa are we really talking about?

Soil microbes span all three domains of life and include bacteria, archaea, fungi. They are the most diverse group of organisms, comprising the vast majority of living organisms on earth! Bacterial and archaea are single-celled and not visible to the naked eye unless clumped together in biofilms. Although bacteria and archaea are similar in many ways, archaea often live in extreme environments, like hot springs or salt lakes, and perform more obscure functions, like transforming methane. Fungi, in contrast, are multicellular organisms. Because of the visible fruiting bodies (“mushrooms”) of some fungi, it may seem odd that they are “microorganisms”. The vast majority of a soil fungus, however, lives below the soil surface in the form of mycelia, which consist of root-like structures called hyphae.

Now and then we get a look at soil fungi

Now and then we get a look at soil fungi, but only when they pop up above ground.

What roles do microbes play in prairie soils?

By releasing digestive enzymes into the soil environment, microbes break down dead plants, animals, and other microbes. This process of recycling makes nutrients available to living plants, soil microfauna and microbes. Decomposition by microbes also builds soil organic matter, which gives prairie soil its beautiful dark color, provides rich texture, and stores nutrients, carbon, and water. All of these factors combine to create a healthy environment for the web of life to thrive: for plants to grow, soil microfauna to explore, and animals to burrow. Soil microbes are also important partners to plants. In exchange for carbon from the plant, symbiotic bacteria (e.g. nitrogen fixers associated with legumes) and fungi (i.e. mycorrhizae associated with prairie plants) greatly enhance plant nutrient uptake.

Is it fair to compare our ability to describe the world of soil microbes to looking into a room through the keyhole? 

Microbes are the most diverse type of organism on earth and soil is arguably the most complex matrix, so for microbes, it’s more like looking into a room through a pinhole – this means the field of soil microbiology is a very exciting place to be! While we have cultured (grown) some microbes in the laboratory for over a century, soil microbiology was previously limited by our ability to isolate and cultivate the vast majority of them. Largely as a result of the human genome and human microbiome projects, new sequencing technologies now make it possible to sequence the immense diversity of the soil microbiome directly from DNA extracted from soil. From these studies, we have learned that microbes are far more diverse and ecologically important than we previously thought. Sequencing has also put pressure on culturing techniques, and we are becoming much better at growing microbes in the lab. My hope is that future advances in soil microbiology will couple sequencing with culturing in order to understand the ecology of specific microbes and identify keystone microbes that can be targeted in restoration.

What else would you want someone interested in prairie ecology to understand or think about in terms of soil microbes?

Microorganisms, and microbial communities, are not all equal. For example, fungal-to-bacterial ratios are critical to soil health and sustainability. This is because soils with more fungi relative to bacteria (higher fungal to bacterial ratios) regain structure faster, retain more nitrogen and are more resilient to drought and floods.  In addition, all bacterial and fungi aren’t equal. Ideally, a prairie soil has a mix of fast and slow growing bacteria and a diversity of symbiotic fungi so that prairie plants can find an ideal match. Finally, while microbes are the foundation of a healthy soil, they are part of a larger soil food web that must be intact in order to sustain the microbial community.

As prairie managers and ecologists, we think a lot about the relative abundance of plants, but not necessarily fungi or bacteria...

As prairie managers and ecologists, we think a lot about the relative abundance of plants, but not necessarily fungi or bacteria…

So, is there an optimal ratio of fungi to bacteria in soils?

“Healthier” soils generally have a fungal-dominated community. Given variability in the measurements we use and differences across sites, it is hard to pinpoint an optimal ratio; it is fairer to say that the ratio should increase with restoration.

The fungal to bacterial ratio is important because of the different lifestyles of bacteria and fungi. Bacteria have faster turnover rates (i.e. short life cycles), such that bacterial-dominated communities are linked to faster rates of nitrogen cycling and subsequent N losses from soil. In contrast, fungi have slower life cycles, which result in greater retention of nitrogen in the soil.  Due to their extensive hyphal networks, fungi are also thought to be larger contributors to both the production of enzymes involved in decomposition and aggregate formation, and resistant to drought. On a community-level, fungal hyphae are the “internet of the soil” – they facilitate connections among other microbes and plants, helping plants to acquire nutrients and alleviate plant water stress. This doesn’t mean bacteria aren’t good! It is the balance between bacteria and fungi that seems to be most important.

What’s known about how prairie restoration and management can impact soil microbial communities? 

First, diversity begets diversity, so it’s important to start with a diverse mixture of native prairie plants.  There is also some evidence to show that prairie burns help maintain
a good fungal to bacterial ratio by promoting fungal abundance.

However, while we know some groups of microbes are very important in prairie soils – like Verrucomicrobia bacteria that dominate native prairie soils and arbuscular mycorrhizal fungi that form symbiotic relationships with plants – there is still a lot of work to be done to understand how to manage restoration for these and other specific groups of microbes. Even more, past land use has a legacy that will determine what might be needed to restore a rich diversity of soil microbes. Nitrogen fertilization, pesticides and tillage can all have lasting impacts on the types of organisms that are active in a soil. That said, the microbes are there, often in a dormant state, so they do have the capacity to come back and improve soil health when and if the conditions are right.

When we convert cropland to prairie, we just broadcast seeds on top of the ground, but ultimate establishment success depends upon soil microbes we usually don't even think about.

When we convert cropland to prairie, we just broadcast seeds on top of the ground, but what’s belowground has a huge impact on what kind of plant community is formed.

There is certainly lots to learn…  Speaking of that, what story is emerging from your particular research on soil microbes in agricultural systems?

My graduate research contrasts soil microbial communities in conventional corn-based agricultural systems with alternative agricultural systems that incorporate perennial plants. The idea is that, by providing microbes with perennial root systems, they have a richer “buffet” of food that they can use to restore soil health. What I am finding is that newly established perennial cropping systems improve the function of the microbial communities but I have not yet seen dramatic changes in the diversity of the microbial communities. The perennial cropping system that I work with is a switchgrass monoculture and my results are mirrored by work in a diverse prairie cropping system. Overall, these results tell me that perennial plants in agricultural ecosystems can restore soil microbes, but practices such as fertilization and harvesting likely limit the rate and extent of restoration.

(THANK YOU to Sarah for taking time away from her dissertation writing to help us understand more about soil microbes!)