More than 80% of all land plants partner with fungi to help extract nutrients from the soil in exchange for carbon-rich sugars produced through photosynthesis. Recent research reveals that these fungi, known as mycorrhizae, store more carbon than previously thought, equal to a third of all fossil fuel emissions annually. When these fungi die, they leave behind "necromass" – dead organic material full of carbon that remains in the soil for decades before being released back into the atmosphere. The pigment melanin, present in many kinds of fungi and fungal necromass, has been found to slow down decomposition, keeping more carbon in the ground for longer. To help us better understand the role dead fungal cells may play in climate change, we reached out to ecologist Katie Beidler to learn more about her research into fungal necromass and its important carbon-stashing properties.
Will: Thanks again for speaking with us, Katie! We are excited to learn more about the hidden relationships between plants and fungi and what they have to do with a changing climate. What drew you to work with fungi in the first place?
Katie: I found fungi through plants. After college I got a job working for a lab that studied tree roots and while rooting around for my work, I would trace the white or yellow threads growing off of the root tips and out into the surrounding soil. The pine roots I was sampling formed partnerships with ectomycorrhizal fungi, and seeing this symbiosis in action made me want to learn more about fungi. In my PhD, I studied how these mycorrhizal partnerships impact soil carbon and nutrient cycling, mostly from the plant perspective. Now I am in a fully fungal lab, working as a post-doctoral researcher for Peter Kennedy (a trained mycologist and known fun guy) studying the microbes that live off of decaying fungi. I feel lucky to have landed in a fungal ecology lab and the more I learn, the more I am amazed by how so much chemical and functional diversity is held in fungal hyphae, these hidden threads that support ecosystems.
Hyphae growing off of mycorrhizal root tips of Loblolly pine (Pinus taeda)
“Soils are like a safety deposit box for carbon. Soils both store and release carbon, and in temperate forests, they currently store or lock in more carbon than they release.”
Will: That’s wild! Your career has literally traced a fungal thread from trees to fungi to the microbes that feed off their dead bodies, all happening in the soil beneath our feet. So to zoom out a bit, how do these fungal threads relate to climate change?
Katie: This is a clumsy analogy, but soils are like a safety deposit box for carbon. Soils both store and release carbon, and in temperate forests, they currently store or lock in more carbon than they release. This is important because the burning of fossil fuels has increased the amount of carbon dioxide in the atmosphere beyond what can be taken up by plants during photosynthesis. This carbon imbalance is exasperating the natural greenhouse effect and causing shifts in temperature and weather patterns which might ultimately lead to more carbon loss from soils. The idea is that soils can be managed or conserved to lock in more carbon, which in turn can help mitigate or lessen climate change.
Will: We don’t tend to think about it very much, but our every exhale contributes to the planetary carbon cycle coursing through Earth’s air, land, and oceans. The vast majority (85%) of planetary carbon is found in the ocean, while 2% is in air and roughly 5% is stored in the land. What role does fungi play in storing this land-based carbon?
Katie: Fungal hyphae grow extensively through soils in the pursuit of resources (food and water). When hyphae die, they become woven into the soil fabric, leaving behind carbon and nutrients that can then be recycled by other soil microorganisms (more on this below). Fungal necromass refers to these dead fungal cells or residues. By tracking the fate of fungal remains or necromass we can learn about the nutrients that help sustain the soil food web and the forms of carbon that endure in the soil environment. Not all soil carbon is created equally, and the soil carbon that is the slowest cycling (or able to persist for centuries to millennia) is made from dead microbes (necromass) bound to clays and other types of soil minerals. We know this because necromass has been visualized on soil mineral surfaces and the carbon that is bound to minerals is chemically similar to that of microbial cells. These microbial-mineral interactions protect soil carbon from further decomposition.
| Key Words |
| Ectomycorrhizal fungi: a symbiotic association of fungi with the roots of higher plants in which both the partners are mutually benefited. In this partnership, the fungi grow around the outside of the plant roots, helping the plant absorb water and nutrients, especially phosphorus, from the soil in return for sugars produced during photosynthesis. |
| Fungal hyphae: the long, branching, filamentous structures that make up the vegetative body of a fungus. |
| Greenhouse effect: a natural process that warms the Earth's surface by trapping heat from the sun in the atmosphere. |
Will: Ok, so the presence of dead soil microbes (necromass) slows down the process of decomposition. Can you say more about these organisms? I believe you referred to them as a decomposer community?
Katie: A decomposer community refers to the group of organisms that get their energy from breaking down dead or decaying plants, animal, and microbial matter into simpler materials, helping to return nutrients to the soil. In the process of breaking down organic matter, microorganisms release carbon dioxide, contributing to soil carbon loss. So, the growth and activity of microbial communities can determine how much carbon is stored in soils.
Will: Ok, I think I get it now–decomposition releases carbon dioxide into the atmosphere–as if the soil itself is exhaling. So is it possible to measure this decomposition in the soils you study?
Scanning Electron Microscope (SEM) image of lab grown fungal necromass
Katie: As I mentioned previously, hyphae are abundant in soil but unfortunately, they are also microscopic and diffuse. To generate enough necromass to measure decomposition we have to grow fungal biomass in the lab using methods developed by Chris Fernandez, the original Kennedy lab Necromasser and now a professor at Syracuse University. Simply put, we grow fungi in liquid culture either in large batches or many glass flasks. We break up the biomass in mortar and pestles, freeze dry it and pack it into mesh bags. To measure decomposition in the field we bury the bags of necromass, collect the bags at different time points and weigh the bags to see how much of the initial necromass was lost or decomposed. We can also look at the microbes (both fungi and bacteria) living on the necromass and the remaining necromass chemistry to see how it might be changing through time.
Will: That’s interesting! So you compare the weight of the necromass before and after in order to measure decomposition. I’ve also read that compounds like melanin can influence decomposition rate. What is melanin and how is it important to your work?
Katie: Melanin is a pigment found in many different organisms and it has a protective function in fungi. Just like in humans, it can protect hyphae from ultraviolet radiation. It is usually found embedded in fungal cell walls and it can help stop water from leaking out of hyphae or it can keep pathogens from getting in. I am interested in how melanin influences decomposition, because as you can imagine, the same properties that make melanin protective also make it harder for other microbes to break down.
Will: Being harder for microbes to break down should have an influence on decomposition rates, right?
Katie: Indeed, we found that fungi with more melanin in their cell walls decay more slowly.
Necrobags (mesh bags containing fungal necromass) ready for burying in the field
“I am interested in how melanin influences decomposition, because as you can imagine, the same properties that make melanin protective also make it harder for other microbes to break down.”
Will: Ok, so melanin helps to slow decomposition, which helps store carbon in the ground for longer. This is helping me better understand how forests could be better managed to mitigate climate change, as it was recently estimated that about 36% of current annual CO2 emissions from fossil fuels are stored in mycorrhizal mycelium. On a related note, we grow a variety of edible/medicinal mushrooms like oyster, shiitake, and lion's mane at North Spore. Where does the fungal necromass you grow for research come from?
Katie: I mainly work with microfungi, but I did successfully grow a maitake mushroom once (shout out to Lu Hook of @themycokid for providing me with the maitake culture). The necromass we produce mainly comes from Hyaloscypha bicolor (previously Meliniomyces bicolor), an ascomycetous fungus that can form both melanized and non-melanized (hyaline) hyphae depending on how you grow it, hence the bicolor part of its name. The photo of the flask below shows this process in action. When H. bicolor hyphae is exposed to more oxygen it melanizes faster. By submerging the fungus in more or less media or by shaking it at slower or faster speeds we can generate melanized and non-melanized versions of H. bicolor necromass (also see video of larger batch culture where we bubble in oxygen).
Flask containing Hyaloscypha bicolor hyphae (melanized hyphae on top and hyaline hyphae on bottom).
Melanized hyphae in a mortar and pestle during necromass production.
Flask containing Hyaloscypha bicolor hyphae (melanized hyphae on top and hyaline hyphae on bottom)
Melanized hyphae in a mortar and pestle during necromass production
| Key Words |
| Microfungi: a group of fungi and fungi-like organisms that produce microscopic fruiting bodies and include molds, mildews and rusts. |
| Ascomycetous fungus: one of the largest groups of fungi that produces sexual spores inside sac-like structures called asci. This group contains yeasts used in baking, brewing, and wine fermentation, plus delicacies such as truffles and morels. |
| Mycenoid fungi: formerly grouped in the genus "Mycena," these extremely small mushrooms are saprotrophic, meaning they consume dead or dying organic matter, and are rarely more than a few centimeters in width. |
In addition to growing fungi for necromass production, we also maintain fungal cultures to measure how different fungal species (alone and in combination) influence decomposition. Luckily for me the previous PostDoc in the lab François Maillard, another fantastic fungal scientist, isolated fungal species that were growing on necromass buried out in a pine forest. Some of the genera of fungi I grow from this culture collection include: Chaetomium, Metrahizium, Mortierella, Phialocephala, and Trichoderma.
Will: It surprised me to read that Trichoderma, while nightmarish for indoor mushroom growers, is quite beneficial to plants; promoting growth, inducing defense responses, and acting as a natural biocontrol against plant pathogens. What aspects of your work have surprised or challenged you?
Katie: One aspect of my work that is surprisingly challenging is working in the opaque and highly variable belowground world! Soils are heterogenous mixes of living and dead things that span multiple scientific disciplines (chemistry, biology, geology and hydrology) and contain processes that occur over both short and long-time scales (minutes to millennia).
Metrahizium culture
Trying to understand what microbes are doing on their small scale (see SEM image below) and how this influences carbon cycling at the larger ecosystem scale is tricky and we are still in the process of developing good methodology to try to account for all of this variability. Beyond my work belowground, I have had a wonderful and highly knowledgeable mycology mentor, Anna Gerenday who is teaching me how to identify mushrooms and prepare fungal specimens for herbaria.
SEM image of soil minerals and fungal hyphae-complex mixtures on the smallest of scales
Working with Anna has taught me how hard it is to identify most mushrooms to a species level and how we are still very much in an observational and organizational phase of fungal taxonomy. This surprised me a bit coming from the plant world.
Will: What you just said about how you are still in an observational and organizational phase of the science reminds me why we’ve only identified about 150,000 fungi out of an estimated 2 to 4 million total species! I imagine your team discovering new decomposer fungi in the future. As you continue in your career studying these microbes, what kinds of questions would you like to try and answer?
Katie: I am increasingly interested in cross-kingdom interactions. Recently we started collaborating with an awesome viral ecologist, Joanne Emmerson and though we are in the early days of this work, we are interested in the role viruses might be playing in necromass decomposition, through their effects on bacterial or fungal decomposers. Also, in the future I would like to return to my roots and do more work in the rhizosphere (or soil directly surrounding the root), looking at how root activities shape decomposer communities.
Will: I can’t even begin to wrap my head around the number and diversity of viruses out there, but science often leads to more questions than answers. So, we have arrived at my final and favorite question: If you were a fungi, what kind would you be and why?
Katie: Hmm that is a good question…I don’t fully know why, but I am drawn to Mycenoid fungi. I think their mushrooms are charming and it would be fun to be one of these little saprobes on the front lines of decomposition. Either that or I would like to be a nematophagous fungi, lassoing nematodes before they parasitize plants. I guess I just like all of the small things.
Will: I think it's the small things that make the biggest impact! Thanks again for your important work! I appreciate you taking the time to speak with us today.
Katie: Absolutely! Thanks for giving me this opportunity to share my work, I had fun answering your questions.
Anna Gerenday, Katie, and Katie's son Morris out hunting for mushrooms