Celebrating botanical discoveries

Dumbing Down a Scientific Paper and Relating it to Mushrooms


By Abby Ayling


“Plant secondary metabolites altering root microbiome composition and function.” (Koprivova & Kopriva 2022) –  That’s a technical title 😬. Let’s unpack it.

Plant secondary metabolites – what the hell does that mean? Unless you’re really into the science of plants and soil, you’ve probably never heard of plant secondary metabolites (PSMs). They sound and are complicated on a technical level, but let’s try to make them a little less-so.

Metabolites are a broad group of molecules involved in an organism’s metabolism. Primary metabolites function in essential development, growth, and reproduction. What differentiates PSMs from primary metabolites is that PSMs technically aren’t essential for plants to live. 

Though technically non-essential, these metabolites often determine the survival of a plant in its present environment.They are metabolites like lignin, chlorophyll, and carotenoids, which are important in the differentiation and function of most plants. For example – If a carrot didn’t have carotenoids to make it orange, would it really be a carrot?

Now, there’s another half of the paper title that we haven’t addressed: “root microbiome composition and function.” This may seem a little more familiar to those not engaged in biology; you may have even heard about your gut microbiome, and how it relates to probiotics. If you haven’t, you probably should look into it 🫄👀.

The root and soil microbiome is the sum of microorganisms interacting with the roots of a plant and its surrounding soil. This almost always consists of a variety of bacteria and fungi, and may also consist of some protists. These microorganisms play different roles that affect the function of a plant, ranging from bad-neutral-good. Microorganisms that are bad for the plant will cause the release of defensive PSMs, and good microorganisms will cause the release of PSMs related to communication and nutrient transfer.

So, why are PSMs important? They’re important for a number of reasons. PSMs affect soil quality, the crop yields of future plant generations, and are indicators of environmental changes. Beyond the soil microbiome, they impact how we and other organisms metabolize plants: nutritionally, medicinally, and even recreationally (if you know you know 🌿). PSMs are everywhere. They’re important.

Now that we have an inkling of what the title means, let me share what “Plant secondary metabolites altering root microbiome composition and function” actually has to say, and what I have to say about it.


Our subject paper is informational in nature and describes recent discoveries on PSMs. It’s a short and easy read, thankfully for me, but is also a good beginner’s guide to PSMs. The paper gives an overview of what’s been discovered in recent years, and of what is being researched now. It also gives good examples of when certain PSMs are present in plants, and of what environmental factors trigger their presence.

My really, truly, very limited knowledge of plant secondary metabolites outside of this blog stems from their relation to fungi. There is a group of plant-symbiont fungi, or fungi that are friends with plants, referred to as mycorrhizal fungi. Their symbioses (friendships) are largely facilitated by secondary metabolites (SMs). Both organisms use SMs to communicate their needs to one another, primarily their need for nutrients. The ability to communicate with one another isn’t limited to the original symbionts, either – some mycorrhizae can facilitate connections between multiple plants, including those outside of the host species. In fungus-nerd communities, this is referred to as the ‘Wood-Wide Web’. 

The subject paper doesn’t delve into mycorrhizae, but its relation to them is what originally attracted me to the paper. This led me to explore more about PSMs in relation to mycorrhizal symbioses. So, I read ANOTHER scientific paper. Imagine that.

This second paper, “Arbuscular Mycorrhizal Fungi and Changes in Primary and Secondary Metabolites” (Amani Machiani et al. 2022) also had some good information. The variety of plants that they studied are referred to as medicinal and aromatic plants (MAPs), so they’re super-PSM producers. Off the bat, it stated that arbuscular mycorrhizal fungi (AMFs, just a different type of mycorrhizal fungi) can help to stimulate nutrient and water uptake in plants, and they boost photosynthetic capacity. Their production of signaling molecules, which are part of the fungi-plant communication that I mentioned earlier, can also stimulate increased PSM production. Beyond helping in these aspects, AMFs can reprogram metabolic pathways for both primary and secondary metabolites in plants. To what extent AMFs are capable of changing plant function and metabolism is, however, highly dependent on its species, the plant species, and the environment – so they aren’t always capable of awesome changes. 

When AMFs are making awesome changes to plants, they can increase their productivity of PSMs like terpenoids (essential oils; hope an essential oil mom is reading this), a defensive type of PSM called an alkaloid, an aromatic type of PSM also involved in defense called a phenol, and a PSM involved in medicine called a saponin. Increasing the amount of these PSMs in plants can help to reduce pesticide use (shoutout to the organic moms) and reduce the amount of plants that we need to grow. 


So, now you know all about PSMs, mycorrhizal fungi, and my meme obsession. Hooray! Hopefully you got more out of this paper than realizing that I am a witty genius. If not, here’s where I’ll tell you what I really want you to know.

Both of the papers cited in this blog were fairly well-written and comprehensive. From them, we learned that PSMs alone are significant due to their prevalence in plants, medicine, and day-to-day life. Mycorrhizal fungi are important due to their ability to enhance plants’ ability to uptake nutrients, perform regular functions, and produce metabolites – both primary and secondary. There are a few particular PSMs that AMFs are particularly good at enhancing, and their overall enhancement of plants can help to reduce pesticide use. 

If you’d like to learn more about mycorrhizal fungi, I’ve included some other work that I’ve done on the topic. If that’s not enough, or if you have any questions, feel free to reach out!

Thanks for reading : )

Helpful links: A paper I wrote that goes further in-depth on mycorrhizal fungi, if you’re interested : ) More mycorrhizal fungi papers!!!

Literature Cited:

Koprivova, A, and S. Kopriva. 2022. Plant secondary metabolites altering root microbiome composition and function. Current Opinion in Plant Biology. 67: 102227.

Amani Machiani M, Javanmard A, Habibi Machiani R, Sadeghpour A. Arbuscular mycorrhizal Fungi and Changes in Primary and Secondary Metabolites. Plants. 2022; 11(17):2183.

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