Blog Updates

Art by Graeme Walker

The blackest box

April 2nd, 2024

Hello, my dear readers. Many of you have emailed me asking when the next blog post will be posted, what topics we'll cover next, if that cliffhanger from last season will be resolved, and why I decided to partner with a new publishing company. All of those questions will not be addressed in this post because they are made up. Instead, we will pick up the shovel where we dropped it last — the black box of fine-root ecology — and traverse into an even darker territory, fungal guilds and functional traits. 

Fungal guilds

Allow me to formally introduce you to a group who needs no introduction, kingdom Fungi! Fungi can fare without an intro because they're having a moment. Whether they're starring in Netflix documentaries and New York Times articles, or popping up in podcasts and your own back yard fungi are getting around. If you bend towards the alternative crowd and aren't impressed with fungi's recent hype in popular culture, let me try to dazzle you with numbers instead. A detailed 2021 review covering fungal diversity and conservation estimated that there are currently 6.3 million to 13.2 million fungal species sharing the planet with us (but also see Larson and co's 2017 publication which estimated an astounding 165 million fungal species). Further, if some of you refuse to be numerically charmed, let me overwhelm you with MASS. The trophy for the largest living organism on earth was awarded to a species of honey fungus, Armillaria ostoyae, in 1998. This belowground behemoth covers a landmass equal to 1600 football fields in Oregon's Blue Mountains. Whatever way you tally it, both societally and biologically, fungi are a popular and expansive bunch. 

To reach such levels of fame and species diversity demands a high degree of biological innovation. Fungi have evolved to set up shop, find resources, and reproduce in most habitats on Earth. This makes fungi fundamental in both human affairs and ecosystem processes. For example, fungi play pivotal roles in the biosynthesis of important drugs like antibiotics and statins. They also make their way into our food systems (in yummy forms like mushrooms and truffles and breads, and in not-so-yummy forms like the rusts and smuts that can wreak havoc on our crops). Switching gears, if we zoom out and look at things from an ecosystem perspective, fungi perform unique and vital functions in nature by decomposing the Earth's leaf litter, wood, soil organic matter, animals, and even themselves. In addition to decomposition, fungi uptake nutrients and water to utilize for their own growth as well as the growth and health of their various plant and bacterial symbionts. Fungi's roles as decomposers and symbionts therefore have significant effects on global biogeochemical cycles and the composition of plant, bacterial, and animal communities. 

From the oyster mushrooms popping out of the growing kit that your aunt gifted you to the Pisolithus helping out their tree hosts in pine plantations, fungi have evolved a creative repertoire of life strategies and adaptations to all kinds of habitats. This makes kingdom Fungi an endlessly fascinating taxa, but also causes researchers to scratch their heads and hold their chins when trying to understand fungal diversity and its impacts on ecosystem processes. To prevent researchers from aggravating their scalps and permanently altering the structure of their mandibles, fungi were assigned to guilds based on the types of resources they use. This began with a Berlin researcher by the name of JHF Link who categorized endophytic fungal species in 1809. From then on, guild classifications were in mycological vogue, and other guilds were described. Below, I will cover the fungi involved in fungi-plant symbioses which include pathogenic, saprotrophic, endophytic, and mycorrhizal fungi (plus a surprise guest, the lichenized fungi, who associate with algae and/or cyanobacteria). Further, we'll cover fungal function traits, with an emphasis on mycorrhizal traits, for all of us with a keen interest in our root-associated friends. 

Lexikon Blogion

Kingdom Fungi: one of the six kingdoms of life containing eukaryotic members who move via growth, and absorb nutrients by excreting enzymatic cocktails into their surrounding habitats. Members of kingdom fungi can be unicellular (e.g., yeasts), but most are multicellular and filamentous. To reproduce, fungi produce spores and undergo alternations of generations, which includes a haploid gametophyte stage and a diploid sporophyte stage.  Finally, and perhaps most interestingly, fungal cell walls are constructed with a derivative of glucose called chitin (the second most abundant polysaccharide in nature!). 

A. ostoyae is a pathogenic fungi that can be found in both hardwood and conifer forests. Photo by Walt Sturgeon.

Fungal guilds:
a grouping system of the kingdom fungi based on their lifestyles and modes of nutrient acquisition. Knowing the guild of a fungus will inform you of what substrates it grows on.

Each colored bar shows the proportion of species within a specific guild across fungal lineages. Figure from Zanne et al. 2020.

Pathogenic fungi

Pathogens are found throughout the fungal family tree, but most of the described species are in the subphylum Dikarya which includes the divisions Ascomycota and Basidiomycota. To be considered as an official pathogen and get your "blue check" on the Department of Agriculture's fungal databases, a fungi must a) infect host tissue, and b) induce disease or damage. 

The words "infect," "disease," and "damage," tend to paint a dismal picture, but pathogenic fungi serve as important regulators of biodiversity in our ecosystems. For example, fungal pathogens can prevent the dominance of competitive tree species and increase the biodiversity in some forests. In contrast, the subdivisions Pucciniomycotina (rust fungi) and Ustilaginomycotina (smut fungi) within Basidiomycota tend to love our monocropping systems, so us humans have to find inventive ways of keeping them at bay.

To make a living off of dead and dying host tissue, fungal pathogens utilize a unique suite of enzymes, morphologies, and methods for overcoming host resistance. To describe these different traits and methods, researchers further categorize fungal pathogens into three types: necrotrophs, biotrophs, and hemibiotrophs. As it turns out, most currently described pathogens seem to go the necrotrophic route. This prevalency towards necrotrophy is supported by a strong arsenal of enzymes (e.g., carbohydrate-active enzymes) that break down complex compounds found in plant cell walls.  

Ganoderma is a wide-spread fungal genus containing around 80 species of pathogenic-saprotrophic fungi. Some identifiable features include the pores on the underside of their caps (instead of gills), their shelf or bracket-like growth form, and their occurrence on dead or dying trees.

Lexikon Blogion

Necrotrophs: fungi that kill host tissue before nutrient absorption. To me, this seems like quite the empathetic approach

Biotrophs: fungi and bacteria that require living plant tissue to acquire nutrients and reproduce. However, context can alter the status of biotrophic relationships. Some conditions can cause fungal or plant partners to shift their cooperative attitudes towards a more selfish strategy. If things get really bad, some symbioses end in divorce, or even a slanderous tell-all book. 

Hemibiotrophs: fungi that function as both biotrophs and necrotrophs, absorbing nutrients from living and dying tissue as their host takes its last breaths. Once their host is officially KO'ed, hemibiotrophs will transition to a necrotrophic arsenal of enzymes and finish up the job (this is an oversimplification for comedic effect, but the process described above is hopefully somewhat correct). 

Saprotrophic fungi

Akin to their pathogenic cousins described above, saprotrophic fungi are widely dispersed amongst the fungal family tree. In fact, various unsolved murder cases have been solved by saprotrophs submitting their DNA to companies like 9andMe, which has allowed police to track down pathogenic relatives who've left their DNA at crime scenes. Just kidding, this is all nonsence. However,  according to the Evans et al., Agaricus bisporous has 9 chromosomes, so if there was in fact a company mapping fungal ancestry, it's only reasonable that it would be named "9andMe." Anyway, to make it as a saprotroph, one must live a life decomposing wood, leaf litter, soil organic matter, or the necromass of other fungi. Some may not consider this a glorious life, but we'd all be buried without them. 

Much like researchers group pathogenic fungi into categories to understand their lifecycles and absorption strategies, saprotrophic fungi are distinguished by the types of substrates they grow on. Substrates like soil, leaf litter, and wood, all contain unique communities of saprotrophs that are able to enzymatically (and in some cases, non-enzymatically) digest their tissues. Soil saprotrophs are found in all major lineages, whereas leaf litter and wood decaying saprotrophs are more closely related and a little more specialized. For example, wood decaying fungi are found in the same popular fungal divisions mentioned above (Ascomycota and Basidiomycota), and categorized based on their rot strategy. White rot fungi can degrade both lignin (i.e., compound in bark) and plant cell walls, whereas brown rot fungi leave the lignin behind. These rot strategies have important implications on how organic materials are cycled through our ecosystems. 

The above figure shows the different residues left behind by brown and white rot saprotrophic fungi: a) brown rot residue, b) brown rot fungus Fomitopsis pinicola, c) white rot residue, and d) white rot fungus Fomes fomentarius. Remembering the difference between these two rot strategies can be a little tricky, but if you see brown then you know that lignin was left behind, if you see white, then lignin was decomposed. Figure from Krah et al. 2018.

Endophytic fungi

Remember our friendly biotrophs mentioned above? Well, say hello to perhaps the most widespread fungal biotroph in the game, endophytic fungi! Endophytes are mostly within the Ascomycota division and are found in association with all living land plants. Inside living plant tissues both above- and belowground, endophytes hang around peacefully without causing disease. Other than their location on the fungal family tree, there isn't much else I can confidently share with you about this fungal group. Endophytes are a mysterious bunch, and much about their lifecycles and functions remain unknown.

Holding true with all of the previously covered fungal trophic groups, endophytic fungi are further separated into distinct groups. Rather than grouping based on nutrient absorption strategies or substrate preferences, endophytes are categorized by the way they spread to different hosts. Endophytes can spread vertically by taking a ride on seeds from parent plants, or horizontally by "jumping" to other plants in the surrounding environment. Vertically transmitted endophytes are all within the Clavicipitaceous group and associate with grasses. The horizontally transmitted endophytes, some of which are in the previously mentioned Ascomycota and Basidiomycota divisions, associate with a broad range of angiosperm and gymnosperm species. Both types can facilitate host-plant growth, tolerance to environmental stressors like drought and herbivory, and alter soil community composition.

Figures showing different growth forms of endophytic fungal mycelia between and within plant cells, and the different functional classes of endophytes proposed by Rodriguez et al. 2009. Class 1 includes those Clavicipitacious members that I mentioned earlier, whereas classes 2-4 are all nonclavicipitatious. Classes exhibit various levels of plant colonization, diversity, and benefits to their plant partners. Figure from Kusari and Spiteller 2012.

Lichenized fungi

If you're dying to see fungi in person this very second, go outside to your nearest undisturbed surface (a tree, a rock, the bumper of the car your neighbor has been working on in his driveway for the past 12 years) and feast your eyes on the quiet and confident lichen! Lichenized fungal species are mostly within the Ascomycota division, but they can also be found in Basidiomycota and Glomeromycota. Back in the early days (before the 1860's) lichen were thought to be a singular organism. It wasn't until 1867 that a Swiss botanist named Simon Schwendener made the seemingly outrageous claim that lichen were in fact a symbiosis between fungi and algae/cyanobacteria. Now we know for a fact that when you see that lichen on your neighbor's car bumber, what you are actually seeing is a fungi absorbing water and nutrients from the air and exchanging those resources for sugar from its photosynthetic partner.

Because of the complexities of the lichen symbiosis that can be seen in the figure to the right, further categorization of the fungi in this group is a bit trickier than what we saw in the previous fungal guilds. With that being said, researchers have done a lot of work to examine the morphologies of lichen, what substrates they grow on, and to identify the photobionts (i.e., the algae and cyanobacteria) in the symbiosis. Regarding morphology, microscopic analysis shows unique characteristics of the lichen body, or the thallus. Lichen also vary in color and the structure of their rhizines, which are root-like structures that can attach to trees, rocks, and other surfaces. As far as substrate preferences go, just like our saprotrophs, lichenized fungi can specialize on different substrates and in various microhabitats. To help them adapt to specific substrates and microhabitats, lichenized fungi can associate with distinct photosymbionts that are best adapted to a given environment (Del Campo et al., 2013).

Above I introduced lichen as quiet and confident, and that's because even though they look unassuming, they play extremely important roles in many ecosystems. In some biomes, like alpine and arctic tundras, lichens can be the dominant form of vegetation. They are an important food source for reindeer, caribou, deer, and other smaller mammals. Lichen can also fix nitrogen in low-nutrient habitats and sequester heavy metals in polluted areas. 

Lexikon Blogion

Photobionts: the photosynthetic symbiont found in lichen. Photobionts are typically green algae (85%), but can also be cyanobacteria (10%), or an individual lichen can host multiple photobionts (as can be seen in the figure below from Morillas et al. 2022). 

Thalli: the vegetative growth, or "body" of the lichen that is formed by the fungal partner. Another figure from Morillas shows the multiple fungal layers that make up the thallus: the upper cortex that protects the photobiont, the medulla and lower cortex that are found underneath the photobiont, and the rhizines, which are described approximately two centimeters below this line of text.

Rhizines: don't let their rhiz fool you, rhizines are not true roots, but instead fungal filaments that are specialized to attach lichens to surfaces. Much like the rhizoids found on mosses and liverworts, our current understanding suggests that rhizines don't perform nutrient or water uptake, but instead serve as anchors growing into substrate. 

The figure to the left shows lichen thalli along with different photobiont pairings. Lichens a and b have a single algal layer. Lichen c shows a tripartite symbiosis between fungi, algae, and cyanobacteria. Finally, the lichen in d shows a symbiosis between fungi and cyanobacteria where the cyanobacteria is dispersed throughout the medulla.  

Mycorrhizal fungi

We have finally reached my preferred fungal guild, the mycorrhizal fungi. Don't let my bias influence you, all of these guilds are equally important in the functioning of our ecosystems and for the entertainment of odd people like us who enjoy learning about them. Back to the fungi, mycorrhizal fungi are a diverse bunch that can be found in the Ascomycota, Basidiomycota, and Mucoromycota divisions. To further orient you, the ectomycorrhizal fungal type that forms associations with many dominant forest tree species (and produces tasty mushrooms!) are found in Ascomycota and Basidiomycota. Whereas the arbuscular mycorrhizal fungal type that associates with 80% of all vascular land plants are found within Mucoromycota in the subdivisions Glomeromycotina and Mucoromycotina. There are 10+ more types of root-associated fungi, but I will save that topic for another post. Fungi in the mycorrhizal guild make their living by trading nutrients, water, and great conversation, for sugar and a couch to sleep on (i.e., root living space) from their plant symbionts. This symbiotic strategy seems to work well for both partners, and that is one of the reasons why this fungal guild is so diverse.

As I not-so-subtly alluded to above, there are various types of mycorrhizal fungi and these types are distinguished by the species of fungus involved in the symbiosis (i.e., their phylogeny) AND the type of structural interface they form with roots (i.e., their interior or exterior design strategies). Along with the different family crests and architectural tastes that mycorrhizal fungi bring to the table, they also differ among traits, which we'll be covering in a later section of this installment. In the mean time, if you need a refresher on the differences between ecto- and arbuscular mycorrhizal fungi or mycorrhizal nutrient economies, check out these previous blog posts. 

The above images show oak roots associated with a variety of mycorrhizal fungal partners. Photo cred goes to Root Lab team members: Claire, who just had a birthday and bakes a great olive oil and lemon cake, and Bill, who is currently reading the tale of a western robber named Black Bart.  

Guild shifting: a fungal identity crisis

Before moving on to the topic of functional traits, it's important to let you know that everything you just read about fungal guild categorization is a lie. Just kidding, I would consider it more of a ... not-full truth? The thing is, scientists love to categorize. Categorizing is a pragmatic way to understand the world. In an ecological context, it allows us to understand why organisms and communities respond to certain environmental conditions, disturbances, and other organisms. However, because an unconceivable number of environmental conditions + disturbances + other organisms occur in nature, and because kingdom fungi is so diverse,  it's hard to place fungal species into definitive guilds. 

For all of the guilds covered above, there are certain environmental contexts and host-related interactions that may encourage a shift in a fungi's occupation. For example, the tranquil co-existence between an endophytic fungi and their host may turn parasitic if the host begins to decline in health because of some other factor. In some cases, something as small as the host no longer laughing at the endophyte's jokes can turn a relationship sour. In line with this heartbreaking tale of scorned roommates, mycorrhizal fungi may also shift towards parasitic relations with their hosts if nutrient conditions change and it's more beneficial to store nutrients or use it for their own growth. If you are interested in learning more about guild flexibility (also referred to as “dual niche” and “multifunctional” fungi) check out Selosse et al.’s 2018 commentary on the subject. The authors do a great job in encouraging mycologists and ecologists to think beyond their specialty fields when researching fungi, and also provide a helpful review of experiments showing the multifunctionality of many fungal taxa. 

When narrowing the focus to ectomycorrhizal fungal species, guild assignment can get even trickier. Comparatively, it's much easier to rock a rhyme that's right on time (song reference for all of you people who listen to songs out there). The trickiness arises from the diversity in the ectomycorrhizal fungal group and its evolutionary origins from various saprotrophic lineages (80+). Because of this diversity in species and phylogeny, ectomycorrhizal fungi seem to exist on a biotrophy-saprotrophy continuum where some species maintain more saprotrophic traits from their ancestors and are able to obtain carbohydrates both with- and without a plant host (Koide et al. 2008). The existence of this spectrum doesn't discount the fact that some fungal species, to our knowledge, are purely ectomycorrhizal or purely saprotrophic. However, it opens the door for more nuance, and emphasizes the importance in considering the flexibility in some fungal species' trophic habits. 

Fungal functional traits

Similar to what was emphasized in my previous post covering root functional traits, fungal functional traits are important for helping us understand not only fungal biology and ecology, but also their impacts on individual hosts and whole-ecosystem processes. Fungal traits determine what environments fungi are able to inhabit, what substrates or hosts they get their resources from, what unique structures and tissues they produce, and their reproductive strategies. For plant hosts, fungal traits can influence growth, stress tolerance, seedling establishment, and community composition. Finally, fungal traits influence whole ecosystem processes, mostly through the production of mycelia, mineralization and immobilization of soil nutrients, and their impacts on plant community composition and production. Since we gravitate towards roots here in the mysterious underground, below we'll cover some important mycorrhizal functional traits of the two main types (ectomycorrhizal and arbuscular mycorrhizal) that influence fungal communities and ecosystem processes in temperate forests. Sources for images below: 1, 2, 3, and 4

Exploration typE

For ectomycorrhizal fungi, genera and species are categorized into exploration types ranging from contact- to long-distance (seen on the left). For arbuscular mycorrhizal fungi, species are grouped based on edaphophilic or rhizophilic habits, which means that some species will grow more extensively into the soil or inside the root, respectively. Exploration types and hyphal growth are important for nutrient uptake, carbon demands on hosts, and soil nutrient cycling. 

Enzyme production

Ectomycorrhizal fungal species are generally known to produce a stronger suite of enzymes than arbuscular mycorrhizal fungi and this allows them to mine the soil for nitrogen and phosphorous in nutrient poor environments. Further, within the ectomycorrhizal fungal group, there are species who have conserved plant cell wall degrading enzymes from their saprotrophic ancestors. These fungi can decompose complex cellulose, hemicellulose, and even some lignin compounds.

Reproductive traits

Traits like spore ornamentation (seen to the left), size, abundance, and fruiting body type, size, and abundance, influence fungal dispersal and investment in reproductive tissues. In addition, some mycorrhizal fungi reproduce asexually, produce belowground fruiting structures, or spread vegetatively through hyphae and colonized root tips. These traits are important for understanding mycorrhizal fungal lifecycles, community dynamics, and ecosystem carbon and nitrogen cycles. 

melanin content

Melanin is a group of complex compounds that is deposited in fungal cell walls. Melanin compounds can increase fungal and host tolerance to environmental stressors such as heat, drought, and mycophagy. The degree of melanization in fungal tissues varies by species (and even individuals), and this variation influences decomposition rates. 


The seasonality, or phenology, of mycorrhizal fungi influences fungal lifecycles, community dynamics, and functions like the timing of nutrient uptake and transfer to hosts. In regards to fungal lifecycles, we can ask questions about the timing of organ development. For example, in ectomycorrhizal fungi, when are mantles, mycelia, and fruiting bodies produced? We can also ask how the community composition shifts over the course of the year (stay tuned for more on this).

Hurdles and opportunities in constructing a mycorrhizal trait-based framework

Now that we’re all convinced that traits are cool and can tell us stuff, let me catch you up on the exciting challenges faced by the modern mycologist. First, the lessons we can learn from plant and animal trait studies aren’t always translatable to mycorrhizal fungi and other microbial organisms. This discrepancy comes from the cryptic nature of many mycorrhizal fungal species, and traits that are difficult to measure and observe. Next, the fact that mycorrhizal traits are an emergent property arising from two organisms causes variation in trait values and context dependent results. Finally, similar to what was discussed by Selosse and co, bias of researchers coming from different backgrounds creates plant- or fungal-centric views of mycorrhizal systems and can lead to inconsistent definitions of mycorrhizal traits. 

Moving forward, one way to address these issues is to describe and study mycorrhizal traits based on location. For example, because mycorrhizal traits emerge from both the fungal and plant species engaged in the symbiosis, fungal mycorrhizal traits, plant mycorrhizal traits, and symbiotic mycorrhizal traits can all be defined and studied. Many important fungal traits were already mentioned above, but plant- and symbiotic mycorrhizal traits can be found in Chaudhary et al. 2022 (see Table 2). Until the time comes when I bury you with another blog post, check out the below figure from Chaudhary and co to get a sense of the different categories of mycorrhizal traits. 

Art by Sun-Hyuk Kim

Belowground business

April 21st, 2023

What about our experience as fleshy, thumb-bearing, humans, can be shared with a resilient patch of daisies or a sturdy, hardened, oak? Quite a lot, when you consider that we are all formed of the same materials and shaped by time and natural selection to perform the interrelated tasks of growth, survival, and reproduction. For our green friends, various adaptations coined 'plant functional traits' have been accrued, modified, and lost throughout their consistent and biosphere-shaping reign on our planet to address these primary objectives. After a brief introduction on the background of functional trait research, we'll delve below the surface to focus more closely on root functional traits, why they are important, and how they shape ecosystems. It's not a far stretch to see how our own specie's adaptations, powered by our thumbs and tools, allow us to adjust and simultaneously redesign environments across the globe, just like those belonging to our autotrophic planet-mates. 

Viewing Plants Through Trait-tinted Glasses

Before we get our hands dirty investigating belowground root traits, it would be beneficial to define plant functional traits and why some scientists have adopted a trait-based approach to ecology. Here's how ecologist Sandra Díaz defines the subject in question, “Functional traits are morphological, biochemical, physiological, structural, phenological, or behavioral characteristics that are expressed in phenotypes of individual organisms and are considered relevant to the response of such organisms to the environment and/or their effects on ecosystem properties.” I'll provide a simplified and ineffective explanation for any of you readers out there who aren't feeling Dr. Díaz's wonderful but wordy description - a plant functional trait is any measurable characteristic that impacts how a plant approaches the whole "life" thing. Are you a live-fast and die-young kinda plant, sucking up all life has to offer in the here and now. Or are you a conservative, invest in your tissues and 401k kinda plant, with long-term plans and dreams? While you ponder that philosophical enquiry, let's look at how all this talk about traits entered the plant science conversation.

Over a century ago, researchers began connecting quantitative measures of plant growth to specific leaf characteristics. One of these characteristics, or traits, if you will, would become known as specific leaf area (SLA). SLA is the ratio of leaf area to leaf dry mass, and because a larger leaf area can capture more sunlight (and therefore produce more sugars to build more tissues), it can serve as an accurate indicator of a plant's life-strategies regarding its rates and efficiencies of nutrient acquisition and growth. As the story all too often seems to go, this discovery led to plentitudes of aboveground research while inadvertently ignoring the universe below our feet. Nevertheless, leaf traits were the initiating ripple in the waters of ecological research that soon amounted to a trait-based wave of studies that shaped how we understand plant ecophysiology, biogeography, and evolutionary history today. Full disclosure: the bitterness displayed here is all a part of my online persona, and at my core I appreciate leaves just as much as roots, but what can I say - the drama really ups the blog's user engagement. 

As we now know, SLA was a big hit, and everybody was super excited about leaves and what they can tell us about plant strategies and blah blah blah. All of this foliage frenzy led to the development of the leaf economics spectrum (LES) in the late 90's, and while I was busy choreographing performances with my Spice Girls figurines in the bathtub, scientists Peter Reich, Ian Wright, and many more, were preoccupied with less urgent matters such as investigating the relationship between leaf nitrogen content, life-span, photosynthesis, respiration rates, and SLA. A worldwide analysis was organized in hopes of determining if plants fell along a global spectrum of fast (acquisitive) to slow (conservative) nutrient return on biomass investment, and ever-so-conveniently for me and the hard-hitting science journalism I'm doing at this very moment, they found evidence for such a spectrum. Further disclosure: I spent way too much time thinking about a pun that would utilize the title of a Spice Girls hit song and end this paragraph with a bang. Just imagine a world in which I pulled it off, and it was really clever, and you laughed a lot ... and it spiced up your life. 

Lexikon Blogion

Morphological: anything involving form and structure. This not only includes an organism's external structures, but also internal shapes and configurations. 

Phenotype: the observable characteristics of an organism that are driven by both genetic makeup and the environment. Genes are providing organisms with a set of traits, and the environment(s) the organism develops in will tweak some of those traits. Basically, "genotype + environment = phenotype." The below diagram provides an example of how a phenotypic trait like plant height can be impacted by elevation.

Specific leaf area (SLA): the area of a single leaf, or all leaves in a tree's canopy, divided by the dry mass of said leaf/leaves. The inverse of SLA, leaf mass per area (LMA) is also used by scientists, depending on what questions they're asking. If focusing on growth rates, SLA is the usual go-to. When focusing on leaf longevity and the investments plants make in proteins per unit of leaf area, LMA is preferred. 

Leaf economics spectrum (LES): A theory describing the aboveground trade-off in plants between resource acquisition and leaf construction costs. This trade-off can be observed in the relationships between traits such as LMA, leaf respiration rates, and leaf nitrogen and phosphorous content.

The empirical evidence supporting the LES led to further studies on other plant traits such as wood density and crown architecture, and it was shown that traits are linked within species and individuals (e.g., a plant with a fast leaf strategy will also exhibit high rates of water conduction using a fast wood strategy), and all biomes house plant communities consisting of species that exist along this 'fast-slow' gradient of nutrient acquisition and growth/life-span. If I lost ya there, I'll provide you with an example of how this impacts both individual plants and entire ecosystems. Let me introduce you to our two tree guests, the quick weeping willow and the sluggish Japanese maple. The willow, equipped with a high quantity of cheaply constructed leaves, captures tons of sunlight and uses large diameter vessels to pump the water needed to support fast photosynthetic rates and respiration. As a result of all this hurried work, the willow is rewarded with a large sum of photosynthates which are then used to support plant growth. On the other end of the spectrum, the Japanese maple invests a lot of time and carbohydrates into the construction of its tissues. Its leaves are thicker, capturing less light, and its vessels are smaller in diameter but higher in quantity. These traits lead to slower nutrient acquisition, but longer life-span, and in many cases, higher resistance to stress. 

As I mentioned earlier, ecosystems are composed of a wide variety of fast and slow species, so how do these traits factor into forest dynamics and competition? Fast tree species will have high max growth rates and a low tolerance for competition during their seedling years. In times of resource excess, the willow will most likely out-compete the neighboring Japanese maple. However, when resources are scarce, the maple will be able to hunker down with minimal amounts of stress, as the willow freaks out like a guy with low blood sugar in a Snicker's commercial. You can see how both fast and slow traits are optimal under different conditions, and most systems operate at their own unique equilibrium of fast/slow species depending on factors like successional stage, biome type, disturbance, and more. In understanding these traits on an individual, species, and community level, we can begin to grasp whole-ecosystem responses to biotic and abiotic factors, such as invasive species and climate change. If you remain confused as to what plant functional traits are or why they are important, I recommend checking out this presentation by Dr. Reich before we traverse underground and get rooty. 

Fine-root Functional Traits

Hey! Since you're on youtube already, fully immersed in my recent recommendation, why don't you make it a viewing party and watch Dr. Luke McCormack's presentation on linking root traits to ecosystem processes. That would save me the hassle of defining what class of roots we're talking about here. Plus, as per our official contract (which Luke has signed and is definitely not something I just conjured up for amusing blog material), I will receive a yearly supply of rare Chinese teas per every thumbs up on this five-year-old video. It's never too late to go viral. 

Contractual obligations aside, because there's no way for me to know if you, the reader, watch anything I have ever suggested throughout the history of this blog, I will briefly summarize the first section of Luke's talk. When we're thinking about belowground functional traits, and therefore tree water and nutrient acquisition, we have to look at a specific class of roots called fine roots. Unlike the large coarse roots that serve anchorage and storage functions for trees, fine roots are positioned on the most distal end of a tree's root system and are generally grouped as anything >2mm. Plot twist: because root diameter varies vastly amongst tree species, the >2mm cut-off isn't always sufficient in targeting absorptive roots, and when it's possible, it would be better for researchers to use an order based system that is more likely to select the fine roots responsible for absorptive functions rather than transport functions. Below you'll find an image from a  2015 publication by McCormack et al. that will hopefully aid in your absorption of this message.

Lexikon Blogion

Order based system of fine-root classification: borrowed from scientists who've studied the natural branching patterns of rivers and streams, this method of classification labels the most distal roots within a system as 1st orders.

Absorptive fine roots:
the lowest order of fine roots within a root system, responsible for acquiring soil nutrients and water.

Transport fine roots: higher order roots that result from the merging of multiple absorptive roots, responsible for transporting nutrients and water through the root system.

Okay, now we know what class of roots we're looking at, but why venture below the topsoil at all? If we know that plants land somewhere along a 'fast-slow' spectrum, and that the functional traits driving their rates of nutrient acquisition and growth line up across organs, why not just assume a tree with fast aboveground strategies is as equally fast belowground? Depending on the root scientist you ask this question, you may receive different answers, but here I will defer to Dr. Monique Weemstra and co's 2016 paper because I think they offer succinct explanations for this inquiry (and whose illustration can be seen here). 

Let's begin by admitting the obvious: roots are much more complex, dynamic, and mysterious, compared to their aboveground counterparts because of the diverse multitude of biotic and abiotic pressures they face within the soil, the numerous functions they perform, and the mycorrhizal interactions that make this whole belowground story more tangled. Soil texture and chemistry influence fine-root growth and exploration, and in addition, roots must acquire water and 15 essential nutrients from different soil types. Some root traits may enhance uptake of a specific nutrient, while impeding another, and you can see how this muddies our understanding of root functions when aiming to link them to measurable traits. The sophistication doesn't end there, as interactions with mycorrhizal fungi also influence root traits and functions. For instance, a fine root may thicken and slow down its metabolism (i.e., slow traits) in order to provide the best home for a fungal tenant to move in, but that mycorrhizal fungi could then increase that root's nutrient uptake (i.e., fast trait). Because of this complicated belowground landscape and the various adaptations roots have evolved to coexist there, a simple spectrum comparable to the LES is not applicable to roots. 

By now, I'm sure I've thoroughly convinced you that roots are a beautiful, labrinythian, disaster of a research focus that everyone should dedicate their lives to, but to satisfy the rest of the human population who seems to be so obsessed with things they can see during their afternoon walk, we can aim to address how root traits impact the aboveground world. Just like the broader category of plant functional traits covered at the start of this trait tale, root functional traits influence not only individual plants, but whole-ecosystem community structure and nutrient cycling. For us curious folk who enjoy learning for the sake of blogging or annoying their friends with information they didn't ask for, root traits can give us insight into fun topics like species biogeography, evolutionary history, and ecosystem interactions. For the more applied-minded tribe, root traits can assist us in identifying plants that can tolerate certain environments and stressors such as water and nutrient abundance or limitation. Last but not least, for all of you perplexing peeps who enjoy modeling as a past-time, root traits have significant impacts on ecosystem net primary productivity and carbon cycling. 

Trait Introductions

Hopefully I've been successful in my attempts to unearth the messages that root functional traits require a more complex spectrum than the acquisitive - conservative model typically used in aboveground ecology, and that the consideration of these traits is important when aiming to understand whole-ecosystem dynamics. Exciting research over the last 15 years has deepened our knowledge of the evolutionary forces fine-tuning fine-roots, root trait impacts on plant nutrient and water relations, and the multibranched interactions that all of these belowground traits have on one another. Before I get into the current literature, I'll give you some actual traits to hold in your conceptual root trait repertoire. 

Imagine a scenario where I've dragged you to a social function populated by hundreds of renowned root traits who are all standing around, mingling, and I've been granted the marvelous opportunity of introducing you to each of them. Instead of pawning you off on Mrs. Root-calcium-content after exclaiming that you both enjoy dairy products, maybe it's best to dig in where we left off aboveground. Earlier I explained the discovery of SLA and how this leaf functional trait led to an understanding in plant investment versus return of resources in the form of sunlight capture and subsequent photosynthate production. The closest belowground equivalent would be specific root length (SRL), which is essentially telling a similar story where resource acquisition (root length) is divided by resource investment (root dry mass). Root diameter (RD) is another important phylogenetically conserved root trait studied frequently because of its relation to SRL, nutrient foraging strategies, mycorrhizal fungi colonization, and simply because it's convenient to measure. To throw more traits at you (because you seem really adept at small talk and the root traits just adore you), there's root tissue density (RTD), root nitrogen content, root respiration, root branching intensity, root branching ratio, and over 300+ more if you want to visit the Root Trait Inventory over at Oak Ridge National Laboratory's website. 

Resources such as the Fine Root Ecology Database, cutely acronymized as 'FRED' and linked above, have worked to pool root data from all over the world and provide researches with information on hundreds of root traits spanning across a diverse range of species and biomes. To the distinguished root traits you met earlier, this is their home - The Hamptons for root traits, if you will. If you happened to take an interest in any of the traits previously mentioned, which for some odd reason I've decided to personify as affluent East Coasters (what does this say about me), you can zero in on that specific trait using the helpful categories listed on the trait inventory page: "root anatomy, architecture, chemistry, dynamics, morphology, physiology, whole-root system, and microbial associations." If you're looking for a more detailed understanding of these traits, as well as their connections to one another, you can check out this 2017 paper by McCormack and colleagues which offers a lot of cool rooty material, such as the image of EM fungi and their root hosts shown below. 

Lexikon Blogion

Specific root length (SRL): I may have defined SRL multiple times on this blog by now, so for those of you rolling your eyes at my redundancy, I apologize ... for being thorough and thoughtful! Okay, so SRL is the belowground analogue to SLA that compares acquisition potential to tissue investment. One of the first scientists to use SRL when looking at root functions and ecosystem processes was Alastair H. Fitter, who also happened to be the scientist responsible for applying the order-based system to roots. Dr. Fitter, if you see this, visit the root lab sometime. We would all enjoy picking your ear about the underground, and also, I'm eager to meet someone with the name 'Alastair.' 

Phylogenetically conserved: genes, and therefore traits, that are retained through a specie's evolutionary history with few to minor changes. Examples include the proteins cytochrome c and hemoglobin that can be found in mammals and all other organisms that depend on oxygen for respiration. These proteins serve such vital functions that any mutation acquired is typically selected against and not reproduced. This is evolution's way of communicating "if it ain't broke, don't fix it!"

Root diameter (RD): the measurement of length across the body of a root.

Root tissue density (RTD): the ratio of root dry mass to root volume. The story of this trait starts to get pretty complicated when considering the different tissue layers within a root. For example, the cortical tissue layers in the middle of the root are less dense than the inner stele tissue. 

Root nitrogen content: the mass of nitrogen per root mass. I think it is fair to say that this particular trait has caused quite the headache for some researchers, as it doesn't "behave" the same way, or tell us the same things, as leaf nitrogen content. What we do know is that it is largely driven by soil traits and nutrient availability, and impacts root litter decomposition rates as well. Fine roots with higher nitrogen content and lower carbon content decompose at faster rates. 

Root respiration: the amount of CO2 released from a given mass of roots. Roots with higher respiration rates are "breathing" or "working" harder, just like you may find yourself doing after powering your way through this long blog post. 

Root branching intensity: number of lower-order roots per centimeter length of higher-order root.

Root branching ratio: number of roots in a given order divided by the number of roots in the higher order.

Evolutionary Ties

Congratulations, you've thoroughly networked with all the traits at this made-up root gala, listening to them talk on and on about their root children, philanthropic ventures, and how much phosphorous they've absorbed this year. Let's now transport ourselves back in time to witness just how these traits have evolved. If you can recall from an earlier post that overviewed the adaptations plants refined while making their transition to land, the Cretaceous (145-65 mya) was a prolific period for plant diversification and geographical expansion into different habitats. It was like the Renaissance for trees, and you should take that simile very seriously coming from someone who knows extremely little about the historical relevance of the Renaissance and slightly more, but still not that much, about plant evolution. Anyway,  poets nor trees can escape the influence of the geologic time of their existence, and both end up being shaped by their environment while simultaneously impacting it. This 2012 publication by Comas et al. does a fantastic job explaining just that - the connection between the evolutionary forces of the Cretaceous environment, the resulting tree adaptations, and the subsequent shift in Earth's biogeochemical cycles.

All of the above images are showcasing the most ancient woody roots from lycopods that existed during the Carboniferous, which occurred between 360-300 mya (much earlier than the Cretaceous, but still a great example of how roots have evolved over time). These fossils are called stigmaria, which is a type of 'form genera,' meaning that they are grouped based on a part of the organism rather than by species. Geologists use this classification system because organisms such as large trees tend to fossilize specific parts (e.g., leaves, cones, and bark) that are found spatially separate from one another. Shout out to the geology department at Kentucky University who provided me with these pictures, and make sure to check out that link if you're interested in learning more about stigmaria - UK does a great job at explaining the specifics of the stigmaria fossilization process.

The above paper, as well as the later 2018 research conducted by Ma et al., emphasizes the importance of RD, SRL, and mycorrhizal fungi association types as three traits that show distinct changes over evolutionary timescales, high phylogenetic signals, and significant influences over nutrient uptake strategies and other interrelated root traits. As atmospheric CO2  decreased during the Cretaceous, and leaves increased their stomatal conductance and leaf vein density to maintain photosynthetic rates, roots had to increase their efficiency belowground to support these aboveground adaptations. Simultaneously, decreased CO2  caused slower decomposition rates in soils, limiting the pool of mobile soil nutrients, and we begin to see the origins of the first ectomycorrhizal fungi evolving separately in different lineages of trees. It is because of these circumstances that tree species across the globe have generally evolved lower RD, higher SRL, and less dependence on arbuscular mycorrhizal fungi over time.

These trends towards lower RD and higher SRL reduced the energy costs of root production, increased water conductance and nutrient uptake rates, and extended the available root surface area for ectomycorrhizal colonization. Species descending from more ancient lineages tell a different story. This can be seen in roots within the Magnoliaceae family, which exhibit thicker RD compared to more recently evolved tree species. Though magnolias are primitive flowering plants that have many unique characteristics, I'm mentioning their root-based differences here to provide support for the strong phylogenetic influence on some morphological root traits. For those of you who missed the definition of 'phylogenetically conserved' amongst the extremely important and fun to read vocabulary words defined above, this means that a specific region of DNA has remained mostly unchanged in many groups of related species. These segments of DNA are highly heritable, consistent, and code for genes that serve vital functions. This is all to say that the persistent evolutionary direction of fine roots seems to be leaning towards thin and nimble, but, a tree's ancestral history still has some say in the manner.

A diagram I'm borrowing from the previously mentioned Comas paper that's showing root diameter (in millimeters) of 20 tropical and subtropical angiosperm trees. I found this extremely helpful when trying to visualize how recently evolved species trend towards lower RD.

Trait Interactions with Water and Nutrients

Now that we've reviewed a brief background check on the evolutionary and phylogenetic histories of these three root traits, I'll quickly address how RD, SRL, and mycorrhizal fungi association impact water absorption and nutrient uptake. The enhancement in soil exploration strategies that a low RD and high SRL offer directly impact the access to available water and nutrients. Thin and soft roots are able to weave their way through small soil pores like nubby contortionists, and being bendy really comes in handy when in competition with other organisms or in seasonal/infertile environments where water and nutrients are sporadic. The ability of a plant's root system to quickly proliferate new growth in response to abiotic (e.g., rain and temperature) and biotic cues (e.g., herbivory and soil microbe interactions) are also linked to RD and SRL, again with lower RD and higher SRL species performing better in this area. Researches would label a plant wielding these root traits and the accompanying soil exploration strategies as a fast/acquisitive species, but we know from our tree tale at the beginning of this post that the speedy willow doesn't always win the race.

Associations with mycorhizzal fungi also influence access and uptake rates of water and nutrients. Increases in EM fungal colonization in particular greatly expand a tree's ability to explore the soil via hyphal networks, and such networks have longer life-spans than the more ephemeral AM built structures. In addition, mycorrhizal fungi participate in the formation of different 'nutrient economies' because of their impact on soil nutrient availability through decomposition. Fungi within the AM group are primarily assisting trees with phosphorus uptake. They also pass along nitrogen, which they uptake from pools of inorganic N. Their more versatile counterparts, EM fungi, are able to access organic N pools, as well as weather minerals, to offer a more diverse nutrient payment to their tree hosts. These differences are driven by each group's inventory of enzymes. The later-diverged EM fungi have evolved stronger saprotrophic capabilities (or rather, never lost them) which allows them to access organic forms of nutrients through decomposition in a manner that is not available to the AM group. Both fungal groups play a pivotal role in not only individual plant nutrient uptake, but also nutrient cycling in forests and plant and soil community structure. Despite my urge to dive deeper into this subject matter, I will stop right now, thank you very much (Spice Girls lyrics), and encourage you to take a look at the paper I linked earlier in this paragraph, which is co-authored by Morton's very own Dr. Meghan Midgley, and is also the source of the informative graphic below. 

Exploring the Connections Between Traits

There are innumerable examples of how these traits of interest inevitably end up influencing other root traits, and if I really wanted to show you my quirky hyper-fixation side, I would take over a wall in the lab and connect all 300+ root traits using newspaper clippings and strings of red yarn. For now we'll limit our focus to the impacts on root lifespan, root branching intensity, and root branching ratio. Root lifespan is positively linked to root diameter, and therefore negatively to SRL. Roots with higher diameters are investing more in tissue construction, leading to higher root longevity. This has been linked to other plant traits such as root calcium content and plant growth rate. McCormack et al. found that temperate trees with thicker roots had up to a three-fold increase in root lifespan. The exact mechanism driving this increase has yet to be fully uncovered, and it is my suspicion that thicker roots have access to an expensive anti-aging cream which they apply nightly. In actuality, explanations involving root anatomy likely influence this trait (e.g., a thick exodermis could support higher root lifespans because it prevents desiccation, herbivory, and offers a stronger barrier to plant pathogens). Kong and co. explored this further, but more research is needed to elucidate the relationships between root lifespan and other root traits. 

The complicated story involving mycorrhizal colonization and root lifespan is a little more fuzzy and requires additional exploration before making any definitive statements on how these two traits interact. In AM species, mycorrhizal colonization has been shown to increase root lifespan by enhancing tolerance to drying soils and protecting against root pathogens, but these results are dependent on the tree and fungal species involved, as well as the available resources (e.g., water, nitrogen, phosphorous, etc.). For instance, Hooker and colleagues found Populus roots colonized by AM fungi to have shorter lifespans. Studies on EM fungal colonization and root lifespan are even more sparse, but I did find an interesting study by Liese et al. reporting on a dried soil experiment. The results showed fine roots colonized by EM fungi to have shorter lifespans than those with AM fungal partners by ~50 days when in drought conditions.

Root architectural traits such as root branching intensity and branching ratio show strong relationships to mycorrhizal colonization type and weaker associations to the phylogenetic signals that influence RD and SRL. We can turn to another publication by Liese and colleagues for evidence supporting this claim. Architectural trait relations with mycorrhizal fungi show observable trends in angiosperm AM and EM species, with EM species generally showing higher root branching intensity that allows them to produce highly clustered root growth and exploit nutrient rich patches in the soils. Contrastingly, AM species show low root branching intensity, and rely more on changes in root morphological traits (specifically RD) to coordinate with their fungal partners for nutrient acquisition. These strategies can look a little different for gymnosperm EM species, who show low branching intensity due to the even distribution of sparse nutrients in the soils they are typically found growing in. Multiple studies have shown architectural traits to be less constrained by species lineage and more plastic than morphological traits such as RD, SRL, and RTD. This suggests that root branching intensity and branching ratio allows plants to adapt to a variety of environmental and nutrient conditions. 

 The Race to Uncover a Multidimensional Root Trait Spectrum ... that works

The second Liese paper linked above provides us with a smooth segue to the end of  this section, as the group also found correlations between root architectural traits and aboveground traits, which implies that some root traits may serve as increasingly accurate indicators of fast and slow species. This is not only important for figuring out a root economics spectrum (RES) that makes sense, but also for tying these traits and processes to the aboveground economy. To offer a rudimentary summarization of Liese's findings, intensive root branching leads to low C:N ratios and high SRL in fine roots (i.e., fast traits), which indirectly causes high SLA and short leaf longevity (also fast traits). Below is a diagram from the Liese et al. paper that may further confuse you or make this more digestible. Let me know in my non-existent suggestions box, or better yet, allow your virtual voices to be heard in the comment section on Luke's youtube lecture.

If my explanations of the frequently measured root traits above have painted a clear picture for you regarding a universally agreed upon RES, then you should start questioning that picture now. In the last decade alone, there has been a lot of research showing the inconsistencies of linking root traits to strategies, functions, and to each other. This is especially true when looking at morphological traits such as RD, SRL, and RTD. To return to the Weemstra paper linked earlier in this post, issues pinning down an RES that is analogous to the aboveground LES arise because of the complex functions root must perform, the multitude of environmental factors roots they face, as well as the diversity in type and function of their symbioses with soil microbiota. This has led to continuous tweaking of the axes on the root economic spectrum, as well as many unanswered questions. 

So, where are we at now? Should we bury all hopes for a cohesive RES and call it a day? Recent research by Bergmann (2020) and Yi (2023) suggests not, and through summarizing their findings maybe I can glue all of this together into somewhat of a cohesive narrative and finally set you free from this virtual entrapment. By pulling from global trait measurements of close to 2,000 species (woody and non-woody), Bergmann and colleagues were able to find evidence supporting the addition of a mycorrhizal collaboration axis to the classic conservation axis. This collaboration gradient was driven by SRL, RD, and cortex fraction, with thin rooted species (i.e., high SRL) relying on their own roots for water and nutrient acquisition, and thick rooted species (i.e., high RD and cortical space) investing in larger roots that can be colonized by more mycorrhizal fungi, therefore outsourcing their uptake needs. The diagram below depicts Bergmann's framework in addition to the classic fast-slow spectrum driven by root nitrogen and root tissue density. 

Yi and colleagues added to the complexity of the above model by emphasizing the role of root function in the RES. Researchers have been stressing the importance of measuring functional/physiological traits in addition to the frequently measured morphological ones, but as I've mentioned many times in this blog, studying roots is challenge. This is especially true when trying to measure ongoing processes like root respiration, exudation, and so on. This paper focused on measuring root nitrogen uptake rates, and found that high SRL was not associated with higher nitrogen uptake, which differs from the conventional view that a fast trait like SRL will have higher nutrient uptake rates. This finding led the authors to incorporate an 'amount-efficiency' spectrum driven by trait morphology and physiology. In addition, they found higher branching ratios caused higher mycorrhizal fungi colonization rates, therefore a 'self-symbiosis' axis was driven by root architectural traits. These discoveries aren't replacing the former model that rests on the relationship between RD and AM mycorrhizal fungi colonization rates, but rather adding to it. Imagine a model where axes of low to high branching ratio and RD run parallel alongside low to high mycorrhizal fungi colonization rates. If you can't imagine it, I don't have an image for you, and I would suggest that you work on your child-like wonder.  

Although we've reached the end of this trait tour, much like the Spice Girls, I'm not finished performing! Now that you all have been introduced to plant and root functional traits and their importance, when returning to this subject we'll take a look at how climate, soil, season, and plant functional types influence global root trait variation. There's also a lot of ground to cover regarding mycorrhizal fungi's influence in the belowground space, and I'll be sure to dig into that as well.