Summer on a Shoestring

Root Identification – It’s Messy!
August 13, 2014, 4:24 pm
Filed under: Roots

By: Michael Grentzer – REU Miami University, Oxford OH

White Ash Roots

White Ash Roots

    So you want to know how to identify roots do ya?  It’s a messy business.  No, literally!  Prepare to get your hand caked in soil and to strain your eyes squinting at root cross-sections.  Identifying the roots out here in NH is not an easy task.  There are around seven species of trees and gob loads of herbaceous plants.  For the scientists out there, it only makes it more interesting and painstaking.  The roots come in all sorts of shapes, sizes, tastes, and smells.  You might be asking yourself about the last two adjectives, and you read that right.  Some the plants out here are distinguished best by their smell or taste.  This involves sinking you teeth deep into the root or scratching and sniffing the surface of the root.  You are rewarded with a sweet wintergreen taste/smell, a bitter smell/taste of bad medicine, or just plain ole’ nothing.  The tree and herb roots, while virtually the same and insignificant to the average person, are a treasure trove of information about the forest.  At the moment we are trying to distinguish the differences between the soil just millimeters away from the root, what we call rhizosphere, and the rest of the soil.  We’re testing for differences in microbial activity, nitrogen mineralization or the transformation of the nitrogen in the air to soluble compounds used for many life functions, and not but least moisture content. 

Red Maple Roots

Red Maple Roots

     Before we could do all this though, we needed to identify what root belonged to which species and this involved looking at the tips of the itty bity fine roots, the root’s curviness, the cross-section, color, smell, and taste.  Maple roots were predominantly loaded with these small beaded fine root tips.  Pin cherries tended to give off a sour smell and medicine-like taste.  The birch roots smelled and sometimes tasted like wintergreen, and the beech roots looked wiry and had a white star-shaped cross-section.  Sadly, determining the exact species could be done in areas that had only one species of a genus.  The roots tended to look too similar in most cases within a genus and made it nearly impossible to determine species without molecular data.  It’s tough and time-consuming, but in the end, we were able to accomplish this tough task. 

American Beech Roots

American Beech Roots

Pin Cherry Roots

Pin Cherry Roots

White Birch Roots

White Birch Roots

~ Michael 

Soil core installation, summer 2013
July 23, 2013, 4:17 pm
Filed under: Roots

By Brannon Barr


Question:  How do you determine if a particular soil component has an effect on root growth?

Answer: Soil coring.


After working under the direction of Melany Fisk and Shinjini Goswami, I got all the inside dirt on this procedure.  It is done by removing and amending a column of soil, reinserting it, waiting a specified length of time, and re-extracting the column to evaluate whether the amendment encouraged root growth.  We are interested in the conditions under which a mineral called apatite (Ca5(PO4)3(OH,F,Cl)) may serve as a source of calcium and/or phosphorus to plants, and so our amendment was the addition of apatite.  For the materials in apatite to be accessible to plants it must be chemically weathered, which plants cannot do on their own.  This task is performed by symbiotic fungi that colonize plant roots (known as mycorrhizal fungi).  In addition to being able to chemically weather rock, these fungi increase the water and mineral absorption capabilities of the plant roots.  In exchange for these services, plants supply the fungi with photosynthetically derived carbohydrates such as glucose and sucrose.  It may be predicted that when calcium and phosphorus are scarce in mineral soil plants will put more effort into mechanisms for acquiring these nutrients, such as the production of enzymes that break down phosphorus containing compounds in the soil and the growth of root structures to provide more area for mycorrhizal fungi to colonize.  If calcium and phosphorus are freely available in the soil, it is more advantageous for plants to invest their effort elsewhere.

Melany installing a soil core using a high tech "pusher outer."

Melany installing a soil core using a high tech “pusher outer.”

We collected soil by driving PVC pipes 20 centimeters into the mineral soil and then pulling them back out.  The soil was then pushed out of the PVC pipe with a smaller piece of PVC pipe (an “extruder,” to use the fancy term, or a “pusher-outer,” to use the really fancy term).  Forest floor was collected off the top, and the 0-10 and 10-20 centimeter depth portions were separated.  These were then sifted to remove rocks and roots.  In order to assure that the cores were all the same except for the addition of apatite, for each experimental plot all the 10-20 cm soil was combined and homogenized, as was all of the 0-10 cm soil and all of the forest floor.  The soil was reinstalled by adding 5 cm of the 10-20 fraction, lightly pressing with the extruder and adding a little water, another 5 cm, another light pressing and adding a little water, repeating with the 0-10 cm fraction, and topping it off with some forest floor.

Freshly extracted forest soil.  The upper half of the sample is noticeably darker due to higher organic matter content.

Freshly extracted forest soil. The upper half of the sample is noticeably darker due to higher organic matter content.

For every site in which we installed cores, two were enriched with apatite and two were left untreated to give us a baseline for root growth.  We installed cores in our calcium treated plots and their corresponding control plots (no treatment).  We will re-extract the cores in a year to evaluate the extent to which new roots colonized the soil we inserted.  Using a full factorial design, Melany and Shinjini will attempt to tease out to what extent and under what conditions apatite serves as a source of calcium, phosphorus, or both together.

Shinjini giving the soil a thorough mixing.

Shinjini giving the soil a thorough mixing.

This process was certainly not without its challenges.  I’m glad I did this before joining the rest of the crew with fertilizing, because fertilizing was a breeze in comparison.  It requires finding just the right spot; sometimes we would drive the PVC pipe in part way and it would come up against a root or a rock that is a complete impasse, so we would have to use the extruder to push it back into place, find another spot, and try again.  Of course, a power corer could cut right through these impediments, but for this study we would not want to cut through rock because it could alter the mineral content of the soil.  So we had to just do it manually, by pounding the PVC pipe corers into the ground with mallets.  About half the time, the pipes were very difficult to pull back out.  We could only twist them to loosen; side to side action would have distorted the hole.  At times I felt like I was trying to pull Excalibur out of the stone.  Also, there was no consistency with how much force it took to push the soil out.  If it was rather loose, the soil was liable to fly out into a big pile and getting all mixed up.  More often, though, it was very hard to push out, and sometimes we had to pound on the end of the extruder with a mallet, taking care to keep the other end still.  Great pains had to be taken to disturb the forest floor as little as possible, or we risked drawing Melany’s wrath (JK Melanie, you were quite pleasant to work with).  The humidity was intense on those days, and the mosquitoes were so awful it was like getting attacked by flying piranhas.  I’ve experienced some vicious mosquitoes in my life, but only in our C8 plot have I encountered mosquitoes that can bite me right through my jeans.  No joke, I had bites all over my lower half.  So I came out of the field feeling like I needed a transfusion, and I could have stuck my clothes to the wall.  The things we do for science!  I look forward to seeing the results.




Roots, Rhizotrons, and Root Beer by Craig See
June 25, 2011, 10:39 pm
Filed under: Cooking in the white house, Fertilization, Minirhizotrons, Roots

When the last of our plots were fertilized at Hubbard and Jeffer’s Brooks, the shoestring crew let out a great collective sigh of relief.  Everyone was full of the sense of accomplishment that comes only after the most arduous of tasks has been completed. If the shakers of phosphorus had contained parmasian cheese instead, we could easily have coated what is left of Mannattan’s Little Italy.  If the nitrogen prills had been grains of dry sticky rice, we could have gotten most of Chinatown (These are metaphors that come to mind when you’re hungry, and caked in a layer of sweat, DEET, and monosodium phosphate with nothing to look forward to but a soggy PB&J.)  There was a sense that we had done the impossible.  And no one need worry about doing it again for six weeks!

Lin and Amos celbrating the end of fertilization

With fertilization Leviathan vanquished, everyone was looking forward to a few lab days.  The decision to postpone the summer inventory however, quickly turned this into a few weeks.  This year’s summer lab work consists mainly of sorting through root cores pulled from our plots last year.  Each core has been separated by depth (0-10 cm, and 10-30 cm).  It has been the crew’s charge to cleanly remove the tree roots from these piles of sand, rocks and humus, and sort them into two categories based on diameter.  As the vast majority of these roots fall into the “less than one millimeter diameter” class, the job has proved much more tedious than it sounds.  (Think thousands of very small, hair-like, fragile needles in a sometimes sandy, always thoroughly decomposed haystack.)  The blackfly bites on Lin’s arms had hardly finished scabbing over before she was asking about when she could get back out in the field.

Shinjini pickin’ roots

It was at this low point in moral that Neal came through like a glimmering patronus in the night with all seven Harry Potter novels on his computer.  Most of the crew was at least familiar with the storyline from the movies, but like most novels put on the big screen, the Hollywood portrayal is little more than a bastardized version of the real thing.  Harry’s adventures have helped everyone through what would have otherwise been another daunting task.  The sinister doings of Lord Voldemort’s Death Eaters have become a frequent topic of dinner conversation (along with nutrient co-limitation and resource optimization theory of course), and many a work day has continued past the normal 4:30 quit time in order to finish a root core (and a chapter).  And so the rest of June has passed with the crew huddled around a table in the lab like a bunch of eager and willing house elves peering over piles of roots on wet paper towels with forceps in hands.  As there is still the better part of a freezer full of root cores left, we have been recently assured that reinforcements will be helping us out from Tim Fahey’s lab at Cornell (similar to the arrival of the Order of the Phoenix swooping in to assist Dumbledore’s army in the Department of Mysteries).


The grad students, while often picking roots, have been struggling though trials and tribulations of their own.  Kikang has been having her own root problems, with the shorting out of her minirhizotron (a camera designed to gauge root growth at different soil depths over time).  The power cord on the camera had to be twisted back and forth with every measurement, until what was going on below ground was eventually illuminated on the laptop screen, and a photo series could be taken.  This could take several minutes, and worsened with each progressing site.  Eventually the poor machine gave out altogether.  She is currently en route to California for rehabilitation (the minirhizotron, not Kikang).  Meanwhile, Shinjini and Craig were trying to sort out inventory files and organize two years of litter collections in the lab, so that the occasional mutterings from behind their computer screens were the only thing punctuating the amazingly versatile voice of Jim Dale (narrator of the Harry Potter series).

The minirhizotron inaction: Lin twists the wire attempting get an image

Mealtimes at the white house have offered well needed and deserved repose from the daily goings on at Bartlett.  With a field crew hailing from places as far as China, Malaysia, Korea, India, and Hawaii, (as well as Oregon, Vermont, New York, and Minnesota), dinner has been a delightful mixture of pan-Asian, and US cuisine, replete with deserts.  Highlights have been some amazing fried rice and stir-fries, seaweed soups, curries, and every form of potatoes imaginable.  Russell, our newest addition from Hawaii, has promised us something with Spam soon, although Craig pointed out that to be fair, Spam is produced by the good people at Hormel located in the beautiful state of Minnesota.  In keeping with the recent theme of belowground biomass, all of the international students recently experienced root beer for the first time (in float form, of course).


In an attempt to cut down on the food budget, and be a little more sustainable, Lin and Craig have planted a small garden inthe back yard, although the only things that seem to be thriving thus far are the radishes.  The point has recently been raised that we still have a half ton of fertilizer on hand in the lab, and maybe we should do our own backyard experiment on nutrient co-limitation in a common root vegetable of the Brassicaceae family.  Unfortunately, our sample size is too small for a full factorial design.

the garden

The past week has included the added stress of handing in proposals for summer projects.  With the Hubbard Brook annual cooperator’s meeting less than two weeks away, projects are on everyone’s mind.  It is common knowledge that Matt Vadeboncoeur is an encyclopedia of all things relating to the Bartlett stands and the Shoestring project as a whole.  Since his arrival 48 hours ago, he has been bombarded with questions about the sites from every direction.  Undoubtedly Microsoft PowerPoint will be open on every laptop in Bartlett over the next week and a half.  Half of the crew will spend Monday through Thursday camping at Sleeper’s River measuring tree DBH’s during the day, and probably making slides while listening to Harry Potter in their tents at night.

Everyone is looking forward to the meeting with anticipation.  When it’s over we will be back in the field for the second fertilization, meticulously shaking out enough sugar to cover every cup coffee being slurped in SoHo, and throwing down enough rock salt to cover every square inch of the wound that is Wall Street.  Plans for a day long near-marathon (25 mile) hike across the peaks of the Presidential range are also in the works.  That’s all for now.