Falling forward

As the tree canopies that line your streets are beginning their transitions to scarlet reds, gamboge yellows, and amber oranges — us humans are not far behind, following the cues of the seasons. In "Autumn," poet Emily Dickinson shares the same sentiments regarding our relationship with the changing landscape and how that influences our behaviors:

The morns are meeker than they were,

The nuts are getting brown;

The berry's cheek is plumper,

The rose is out of town.

The maple wears a gayer scarf,

The field a scarlet gown.

Lest I should be old-fashioned,

I'll put a trinket on.

What changes can we see in the root lab? Marvin has officially broken out his fall beanies, and I, my winter coats. Sarah is in good spirits due to the absence of her stinger-equipped nemeses (the cold nights kill most wasps and sends the rest into hibernation). Keep reading for an update on our last waterlogging harvest, an introduction to root harvesting in the wild, and a quick look at some flavorful fungi.

We bid you adieu, maples

This week's final maple harvest wasn't too dissimilar from last week's outro with the magnolias. Don't get me wrong, every tree is special in our eyes, but the harvesting protocol and types of tissues we were targeting for collection (fine roots, coarse roots, and stem) remained the same. What was different was the abundance, or lack thereof, of certain root age classes.

Maple roots are much smaller than magnolia roots, and overall we had less fine root material to work with. This resulted in some of our age class harvests coming up short of the 60 milligram (mg) minimum we had set for the stress and NSC tests we will be running in October. For example: one sugar maple tree may have had over 60 mg for age classes one and two, and 20 mg for age three, 10 mg for age four, and 40 mg for age five. To solve this issue, we will be grouping age classes one and two into the category of "pre-waterlogging roots" and classes three, four, and five into "post-waterlogging roots." This will give us over 60 mg for both categories and allow the lipid oxidative damage and peroxidase tests to run without any worries about shortages of tissue materials. Take a look below to see the comparisons of the sugar and silver maples and check in next week for an update on where we're at with the waterlogging project now that the harvesting portion of the experiment is complete.

Lexikon Blogion

Scarlet: now commonly used to describe the deep red of fall leaves, or the color of the robes worn by characters on The Haindmaid's Tale, scarlet was initially a Persian word defining a type of high quality cloth. Persia's saqalat was translated to the Anglo-French escarlet and often associated with red, as that was the common dye used on the fabric.

Gamboge: derived from the Portugese name for the country of Cambodia, Camboja, gamboge describes the vivid yellow colors produced by tree resin of species that are native to southeast Asia. When pulverized, the resin becomes bright yellow and is used in art and medicine.

Amber: fossilized tree resin, dark yellowish-orange in color. The term has Arabic origins, anbar, or ambergenesis, referred to perfumes made by sperm whale secretions. The modern use of the word began around 1400 AD when fossil resins were found at the Baltic Sea.

Here you can see two images comparing control (grown in normal conditions) and treated maples (waterlogged). The first image depicts the sugar maple species (Acer saccharum) and the second shows the silver maples (Acer saccharinum). Looking at the above pictures compared to last week's images of the magnolias (if you wouldn't mind, scroll down a little and take a peak to refresh your memory), can you spot any differences? You are correct, the silver maples are indeed retaining larger root systems regardless of being waterlogged or not (I knew you were observant). This is pointing towards the silver maples using a different root strategy that allows their roots to withstand and/or avoid the stress induced damage that occurs when trees are in waterlogged soils. Stick around to see if our upcoming stress tests provide us with answers to the rooty resistance of the silver maple.

A brief foray

Can one even call themselves a root scientist if they've never harvested roots from a mature tree in situ? I'm not a gatekeeper of the mysterious undergound, but all I know is — this week, with mud in my fingernails and a grin on my face, I felt as if I had been initiated into the belowground band of misfits. I'm using the term "misfits" in an endearing fashion, by the way. It serves multiple meanings here, as the Root Lab's very own Dr. McCormack once told me (and right about now, is regretting having told me) that he played in a misfits cover band. All this is to say that root people are super cool and if you ever want to join the lineup just stick your hands in the ground and ... dig up her bones?

Why were we harvesting roots in the first place and what is the typical protocol for this sort of thing? On a mission to help out fellow arboretum employee and research coordinator for oak biodiversity projects, Mira, we trekked out to a particular bur oak (Quercus macrocarpa) to cover the root portion of her current genome project. Some general rules to follow when looking for fine roots include (1) tree root systems extend out 2–3 times the dripline, (2) most roots are in the top foot (30.5 cm) of soil, (3) roots extend out about 1.5 times the height of the tree, and (4) more than 60 percent of the absorbing root system is beyond the dripline. The methods you use to store your samples will depend on what you're doing with them. In this case, Mira was extracting RNA from these roots, which is highly degradable, so we immediately froze and stored them in liquid nitrogen to preserve the tissue. To find out more about what we currently know regarding root distribution, check out this helpful document that provided the tips I listed above.

Lexikon Blogion

In situ: from the Latin word situs meaning a place or situation, this term is commonly used in science to refer to an organism or observation in its original place. For example, sampling tree roots in situ would mean sampling them from their natural environment.

Dripline: located directly under a tree's outermost reaching branches and canopy, the dripline is where excess water drips down after it rains. Think of it like an umbrella, the outer rim would be comparable to the tree's outer canopy, and whatever your umbrella is dripping on would be akin to the tree's dripline.

RNA: an abbreviation for ribonucleic acid. Like DNA, RNA carries genetic material that gets translated into proteins. Unlike DNA, it is single stranded and therefore more easily degradable.

Above you can see the hands of Dr. McCormack, Marvin, and Mira, all collecting and cleaning roots. Mira is storing the roots in falcon tubes that will then be thrown into a dewar containing liquid nitrogen for safe keeping.

Tasty saprobes

Up until now, all the fungi documented on the blog have been mushrooms we have foraged from the forests. They were found in situ. Humans have been on the hunt for these flavorful, nutrient dense sources of food since prehistorical times. Fossil remains from the stone age show 19,000 year old mushroom spores on human teeth. Many cultures and societies, including the Egyptians, early Japanese and Chinese civilizations, and Greek and Roman empires, considered mushrooms to be "food of the gods" and placed a lot of value on their healing and mystical properties. Unfortunately, it was nearly impossible to harness the god-like power of these fungi, because they aren't as easily cultivated as some of our typical plant crops. Fungi are finicky, they require specific environmental conditions and are very particular about what trees and other substrates they decide to grow on.

I have to restrain myself from falling into a deep rabbit hole on the history of mushroom cultivation (and dragging you all down with me). That is an avenue I will explore on a future post. For an introduction, I think the most important takeaways are: there have been three key innovations in mushroom cultivation that have proven fruitful (pun intended), BUT it continues to be a tricky business and there's still so much we don't know and many species we haven't been able to cultivate.

The first cultivation method, inoculating tree logs, was discovered in the forests of Asia where growers placed freshly cut logs next to patches of wild growing shiitake mushrooms. The spores from those mushrooms would eventually spread to the artificially placed logs and bam! Growers now had a forest farm of fungi that could produce mushrooms for years to come. This method was later improved by drilling holes in the new logs and filling them with shiitake spores. This also happens to be one of the methods we use in the Root Lab and you can see the successful results below. The downside of this method is that your mushroom crop is very much at the mercy of environmental conditions and any other critters who may enjoy munching on mushrooms.

To the left you can see the chestnut mushrooms that were cultivated using a cookie method. Imagine a huge coaster the circumference of a tree trunk, that's how these logs were sliced. Patty-caked between these coasters was a substrate of wood chips inoculated with chestnut mushroom spores. Think of an Oreo cookie with a fungi infused filling. The logs to the right were inoculated with shiitake spores using the drilling method described above.

Indoor sterile procedures and filter patch bags are the two other innovations that revolutionized the mushroom cultivation game. Our desired mushrooms are competing with various other fungi and bacteria to utilize whatever substrate they are growing on. What does that mean for fungi farmers? Contamination. Indoor inoculation and tissue culture methods first allowed growers to sterilize their environment around the late 1960's. These practices were responsible for the spike in oyster mushroom cultivation. Later in the 1980's, filter patch bags served a similar function by allowing adequate airflow to the desired fungi within the bag, while also keeping out competing organisms. With that being said, nothing is promised in the mysterious world of mycelium, and contamination still happens. Stay on the look out for future posts on the history of mushroom cultivation and a more detailed look into tissue culture and filter bag procedures. In the meantime, check out our harvest from this week below.

Shiitake mushroom (Lentinula edodes)
This one is a classic. I will return to the shiitake's history in a future post because it deserves at least a couple of paragraphs to flesh out its influence and uses. Shiitake might be a difficult species for first time growers, as they take longer incubation periods and have less aggressive mycelium compared to species like the oyster mushroom. Don't let this deter you! One of my logs that I inoculated earlier this year (with the help of Dr. McCormack and Marvin) already yielded some crops. Known for their earthy umami flavor, they are my favorite tasting mushroom.

Chestnut mushroom (Pholiota adiposa)
Native to Europe and first described by German naturalist August Batsch in 1786, this mushroom was found to grow both saprophytically and as a weak parasite on European beech trees (
Fagus sylvatica). According to online growing guides, this fun guy isn't as easy to cultivate as the tolerant and fast growing oyster mushroom. However, it isn't too picky, and if you're a first time grower you should give this species a shot. They are tasty as well, with the classic nutty/umami flavor that many mushrooms gift us with.