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Roadblocks and Rocks:  How to Measure Soils in Forest Ecosystems

by Karla Jarecke and Adrian Gallo (HJ Andrews Experimental Forest)

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Fig.1 Dave Frey scouts location for a quantitative soil pit in Watershed 2 by taking a tree core in one of the younger trees in the old growth stand to date the age of the most recent landslide. Photo credit: Adrian Gallo

Standing in a meter deep hole at the HJ Andrews Experimental Forest (HJA), Adrian arranged his soil tools on the mossy surface where I stood. Knife, check. Trowel, check. Meter tape, check. I stood above him, waiting patiently to record his observations. “Subangular blocky”, he announced. Clipboard in hand, I took note. For nearly two hours Adrian stood belowground, meticulously describing the soil profile. He noted how they clumped together, how they smeared in his hand, their color, the quantity of roots or rocks, and other details that soil scientists across the U.S. have used to standardize and compare soils of different regions. I looked up at the old growth canopy thinking about the water that moves from the roots at Adrian’s feet to the leaves 90 m above us.

When he finished, we switched places. I sat on the edge of the wall and lowered my feet to the bottom of the hole. The moist and cool temperatures of the deep soil was a relief from the hot July air. I used a small trowel to scoop soil from the horizons that Adrian had identified and marked with a golf tee. I placed the soil into quart-sized plastic bags labeled with our location, the date, and the soil depth. The samples would make their way to Oregon State University for lab analysis—information that would become publically available through the HJA database.

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Fig.2 Soil profiles from three different watersheds with increasing rock content from 15% to >35% from left to right.

HJA, located in the western Cascades of Oregon, is a Long-term Ecological Research (LTER) site. Elevation ranges from 410 to 1630 m creating diverse microclimates and steep slopes. HJA is unique from other LTER sites in that it has one of the highest rates of biomass production with ~40% of the 15,800 acre basin covered in huge old-growth that sometimes exceed 700 years of age. The need for a systematic soil-sampling program sprouted from hydrologists, stream ecologists, and other scientists asking “uphill” questions without many answers. The questions that developed over the decades (HJA was a charter member of the LTER program in 1980) of ecosystem monitoring began narrowing to terrestrial-hydrologic connections and nutrient inputs to streams. However, that’s where we lacked any representative data to inform these questions.

Jeff Hatten, a professor at Oregon State University, spearheaded this field intensive soil sampling project in 2015 to quantify soils across HJA. The analysis continues to this day because we’ve moved over 45,000 kg of material and acquired more than 600 samples that are currently being analyzed for their chemical (e.g., C:N and micronutrients) and physical characteristics (e.g., rock density and soil texture). One of the main objectives of the soil sampling program was to understand belowground carbon and nutrient stocks at HJA. The majority of terrestrial organic carbon that cycles on human timescales is stored belowground in soils (Stockman et. al, 2013). To know how much carbon is stored in soil and how this is changing over time requires precise estimates of belowground bulk density, or the mass of soil in a known volume. Bulk density is a crucial scaling factor when converting the elemental-percent of soil carbon and nutrients to its storage capacity across the landscape.

Forest ecosystems are often more difficult areas to quantify bulk density because large rocks and roots prohibit the standard sampling methodology often used in grasslands or agricultural fields. In areas with minimal rocks, soil scientists pound a 300 cm3 metal cylinder into the soil and carefully weigh the mass of soil inside. These tools are small, easily transportable in the field, and simple to operate. However, rocks or roots >5 cm diameter do not fit in the cylinders and larger diameter cylinders have too much friction against the soil that pounding them into the ground is nearly impossible. To accurately measure bulk density in forests (where rocks and roots are abundant) we need a larger sampling volume! More space allows us to remove any biases we may introduce by avoiding large rocks with the cylinder method. Hence we dig, and weigh, a perfectly square cubic-meter worth of material—a method known as quantitative soil-pit.

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Fig.3 Chris So separates large rocks from soil and root material. Photo credit:  Jeff Hatten

Digging these quantitative soil pits is no small task. A single pit could take up to 8 hours of physical labor depending on the size of the crew and the amount of rocks. The process involves filling 5-gallon buckets with excavated soil, weighing each bucket and sieving the bucket’s material into three categories:  rocks, roots, and soil. These categories were weighed and subsampled for future lab analysis. Once the cubic-meter is excavated, we take high-resolution photographs and spend hours describing the color, structure, and texture of the soil horizons. By sorting and weighing an entire cubic-meter of soil, by all its component parts—rocks, roots, and soil—we’re able to obtain far more precise and accurate estimates of bulk density, rock content, large roots, water storage, and nutrient storage.  While rocks sometimes occupied over half of the volume of the cubic meter pit, the soil bulk density at HJA is relatively low due to high organic matter input, large macropore structure, and volcanic mineralogy.

Since 2015, we’ve excavated and quantified materials from 18 cubic-meter soil pits starting in low elevation watersheds. Now that the soil sampling program has a plethora of samples, we’re beginning to piece together datasets that are more representative of the spatial variability of soil properties within and among watersheds. This all sounds great for researchers who focus on soils, but the benefits of these data and sample collection will help other scientists as well. Some data include clay content for individual horizons that can be used to predict nutrient holding capacity and soil-water retention and infiltration; the former can inform ecophysiologists and the latter can inform hydrologists (Rasmussen et al., 2018). How quickly streams respond to rainfall events could be related to the size and distribution of macropores in the soil. Tree productivity could be explained by rock content allocating more space for soil that holds more nutrients than rocks or by organic matter content, which holds far more water by weight compared to mineral soil.

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Fig.4 Karla takes a traditional bulk density sample at 100 cm. Photo credit: Adrian Gallo

Factors that influence soil bulk density, and by extension, soil carbon and water storage are complex. Our hope is that these soils data can be integrated not only at the hillslope scale, but across the watershed so other researchers can turn to soils as a way to explain ecological and physical processes. The Long-term Soil Measurement Program will continue to add knowledge of soils at HJA by routinely adding quantitative soil pits each summer. It will also allow for resampling on a multi-decadal time step to assess long-term changes in soil properties. Linking soil data to long-term monitoring of water, carbon, and nutrients in streams and hillslopes will further our understanding of ecological connectivity in forests and raise the alarm if we see imbalances.

Readers can learn more about HJA Long-term Soil Measurement Program and the Oregon State Forest Soil group at:  HJA Website and OSU Forest Soils Homepage.


Rasmussen, et al., 2018 – Beyond clay: towards an improved set of variables for predicting soil organic matter content. Biogeochemical Letters.

Stockman et al., 2013 – The knowns, known unknowns, and unknowns of sequestration of soil organic carbon. Agriculture, Ecosystems and Environment. 164:80-99.

Authors’ biography:

Karla Jarecke (below, left) is a PhD candidate at Oregon State University in the Forest Ecohydrology and Watershed Science Lab. She studies soil hydrology and plant water availability at HJA. Karla collected soil samples for lab analysis of soil hydraulic properties and installed a network of soil moisture sensors at HJA. She is currently planning a study to look at carbon isotopes in tree rings to identify signs of tree water stress.

Adrian Gallo (below, right) is a PhD student who initially focused on forest floor controls of biophysical factors in soil within the Oregon Cascades, but has since expanded to carbon cycling in soil across North American wildland ecosystems through the NEON project.




Ironing out the arctic carbon cycle

by Adrianna Trusiak

Location: Toolik Field Station, Alaskan Arctic

Red and orange across the Arctic

In the environment iron is easy to identify due to its color.  Specifically, on the surface iron is exposed to oxygen in the atmosphere and oxidized, forming red-orange precipitates visible to the naked eye.  Across the arctic landscape, these red-orange precipitates can be found near rivers and streams, in soils, and even on the snow banks.  When iron is below the surface, in an oxygen poor environment, iron is reduced and it is actually invisible.  The interplay between iron in its invisible, reduced form and red-orange, oxidized form plays a role in the production of carbon dioxide (CO2) in arctic soils and soil waters.

Figure 1.  Red-orange oxidized iron precipitates across the arctic landscapes. 

In the general chemistry when learning about redox, we are taught that the reduced iron oxidation produces oxidized iron.  However, in addition to oxidized iron, highly reactive oxidants are produced.  Those highly reactive oxidant are capable of oxidizing organic carbon to CO2.  Across the Arctic there are many waterlogged, standing water areas, creating low oxygen condition in the soils.  Low oxygen conditions in the soils lead to the accumulation of reduced iron.  However, once those soils (and reduced iron in them) are exposed to oxygen due to disturbance, for example rain or someone (or some animal) stepping on the soils; that reduced iron is oxidized to oxidized iron.  In my Ph.D. research I found that during iron oxidation in arctic soil, reactive oxidants oxidize organic carbon to produce CO2.[1]  This previously unrecognized pathway of CO2 production from iron oxidation in arctic soils and soil water, can produce as much CO2 produced through microbial respiration in arctic surface waters.[2]

To study the iron oxidation and consequent production of CO2, together with colleagues from the University of Michigan, I spent three summers in the Arctic collecting and analyzing soil waters.  In the mornings out team would go out to the field to collect soil waters, either walking, driving a truck, or on special days flying in a helicopter to more remote locations far from Toolik Field Station (where the Arctic LTER in based out of).  The sample collection for this study involved sampling water without introducing oxygen from the atmosphere into the water sample- let me just say it involved a lot of patience and slow manipulations of sample syringes.  In addition to collecting water for analysis and experiments back in lab at the field station, we measured pH, conductivity, and temperature of the soil water to better understand soil water chemistry.  Sometimes in the field we also quickly checked for presence of reduced iron in soil water by mixing some of the soil water with ferrozine- a reagent that turns purple if reduced iron is present!

Back in the lab, the experiments would start!  Majority of the work needed to be done in a glove bag where there is no oxygen in the atmosphere, and thus no oxygen is introduced to the soil waters.  First thing after getting back from the field, we filtered the soil waters to remove any microbes that could produce CO2 through respiration.  Filtered soil waters were split for measurements (iron, reactive oxidants, and CO2) and treatments (no oxygen added and oxygen added).  We simulated oxidation of the soil water by introducing controlled amount of oxygen to the water and measuring changes in iron, and reactive oxidant, and CO2 production from that oxidation.  After a long day of sampling in the field and measurements back in the lab, we would still get some sunlight after a long day of work thanks to 24 hours of sunlight during summer in the Arctic!

Figure 3.  Soil waters had to be filtered in a oxygen-free glove bag back in the lab at Toolik Field Station to avoid oxidation of reduced iron before the start of experiments.

The Arctic is red hot

Human activity is increasing the amount of CO2, a heat-trapping gas in the atmosphere, leading to the warming of our planet.  The Arctic is warming twice as fast as the rest of the planet and, as a result, tremendous amounts of organic carbon that have been frozen for thousands of years are thawing[3].  Thawed organic carbon can be converted to CO2 through biological processes like microbial respiration, and through chemical processes including sunlight oxidation of organic carbon[4].  The conversion of the dissolved form of organic carbon to CO2 in soil and surface waters is up to 40% of the net global carbon land-atmosphere exchange in the Arctic[5].  Thus, CO2 production from the newly thawed organic carbon could have a large impact on the carbon cycle and accelerate climate change[6].  Understanding the processes controlling CO2 production in arctic soils is crucial for predicting the influence of arctic warming on the future climate.

Figure 4.  The Arctic is warming twice as fast as the rest of the planet.  Image source: NASA.


[1] Trusiak et al. 2018, GCA

[2] Page et al. 2013, ES&T

[3] Osborner et al. 2018. Arctic Report Card.

[4] Cory et al. 2014, Science.

[5] McGuire et al. 2009. Ecological Monographs. 79: 523–555.

[6] MacDougall et al. 2012. Nature Geoscience. 5:719-721.


Author Biography:  Adrianna Trusiak is a doctorate candidate in Professor Rose Cory’s lab in the Department of Earth and Environmental Science at the University of Michigan.  Adrianna spent four field seasons in the Alaskan Arctic collecting soils and soil waters and running experiments and sample analysis at Toolik Field Station.  Outside of the lab, Adrianna enjoys volunteering with animals, exploring nature areas, and watching movies.


Illustrating three unexpected lessons we learned whilst studying diurnal patterns of light transmittance of leaves

by Santa Neimane (University of Helsinki & University of Latvia)

Location: 02(b) Alps, France

Before we go ahead with the countdown of the new insights that we learned, but didn’t expect, first let me introduce you to the research project. We wanted to determine which part of the light spectrum is used as a cue for plants to alter UV transmittance of leaf epidermis, which in turn may act as a protection mechanism under excessive irradiance. Hence the name for the project: Sun-Signal. Additionally, led by plant physiologists Beatriz Fernandez-Marin and Jose Ignacio Garcia Plazaola, we looked at plant acclimation across a snow gradient which is particularly important considering climate change induced differences in snow cover. We set out to complete this study at the Station Alpine Joseph Fourier in the French Alps at an altitude of 2100 m which provided us with a quite unique environment, not only climatically! We had the opportunity to examine both the plants surrounding the research station and access the Lautaret Alpine Garden right next to it. If you wish to see the results from this project, keep track of @CanopySEE on twitter and visit the CanSEE Group Website.

The first conclusion from our time in the Alps – sometimes it can be fun to stumble around in the midnight with a UV flashlight. Encouraged by Pedro J. Aphalo, who also took photos of the flowers showing their reflectance in UV, we headed out to the botanical garden in the middle of the night and looked at the UV reflectance of everything we could get hold of (as most of the plants were not flowering yet, this was difficult enough). To our surprise, we found one of the most interesting sights on a rock, in UV light reflectance hid the typically invisible world.



Fig 1. The left-hand photo shows lichens on the rock in the research station under visible light conditions, whilst for the picture on the right the light source is a UV flashlight. These photos and more taken by P.J. Aphalo can be found here on his blog.

Second observation. Cover images for albums can be made by taking a bunch of people, letting them do measurements throughout the day for two weeks, preferably with the smallest curliest leaves possible and under the widest set of weather conditions. And then encouraging them to go for a hike up a mountain.

Fig 2. The Album Cover shot. Photo taken by P.J. Aphalo of all other field work group members on the last day of the project – after taking A LOT of measurements, hence those deep stares into the distance!

The last and probably the most important lesson (at least until the results of the study have been analyzed) is – wear sunscreen! In alpine environments, the amount of UV is higher and, also, as we measured, almost all of the light from the snow is reflected. Even the most educated ones, may sometimes underestimate the damaging effects of UV light and end up with irritated skin and strangely shaped tattoos from their hats and t-shirts.

Fig 3. The upper photo shows the main study area and the team members. The lower photos are of some of the plant species included in the study (Gentiana acaulis & Primula involucrata) and team leaders Matthew Robson and Pedro J. Aphalo taking snow reflectance measurements with a spectrometer.

We enjoyed our visit to the Alps and luckily enough the weather was better than expected for the time-of-year, so we had plenty of sunny days as well (as you can guess, that can be very important for photobiologists). By the end of this project we had data about the light spectral quality at the field site, changes in plant pigments and fluorescence at different points in the day, leaf optical properties of multiple alpine plant species, and even more will be found out from later analysis of the frozen samples. We wish to express our gratitude to everyone who made this project possible.

Image_of_author.jpgAuthor biography: Santa was a master degree student at the University of Latvia who spent 2017 with Canopy spectral ecology and ecophysiology (CanSEE) research group at the University of Helsinki.

Southwest Regional Student Meetup – Grasslands, Deserts, and Cities

by Megan Wheeler, Brian Kim, and Alesia Hallmark

Last October at the LTER All Scientists’ Meeting in Monterey, California the graduate student committee identified between-site relationships as a key component of our mission statement. Building on the momentum from the October meeting, graduate students from the Sevilleta and Jornada Basin LTERs joined the CAP LTER in Scottsdale, Arizona for a regional meetup in conjunction with CAP’s annual All Scientists’ Meeting (ASM).

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CAP and Sevilleta students at South Mountain Preserve, with the city of Phoenix in the background.

The ASM started out with a captivating presentation by Marc Johnson from University of Toronto discussing urban evolution and the story of a ubiquitous weed, white clover. This unassuming plant is capable of cyanogenesis, the production of hydrogen cyanide, in response to herbivory. Work in Johnson’s lab has shown that the genetically-coded ability to perform cyanogenesis varies along an urban to rural gradient, and he unfolded the story of how temperature, region, and snow removal are related to the presence of responsible genes.

The plenary talk was followed by short presentations of different themes within CAP research, ranging from Governance & Institutions with a strong social focus to Water & Fluxes with a biogeochemical lens. Students, faculty, and staff then shared their research in two poster sessions, which started out with each presenter giving a brief 1 minute overview of their poster to the room. For the many first-time poster presenters, this was probably the most nerve-wracking moment of the day! During the poster session, some overlapping research interests between the two sites became apparent. Several Sevilleta students presented work on arid grass- and shrubland pollinators, while CAP students presented about the roles and perceptions of pollinators in the urban environment.

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SESE graduate student Marisol Juarez Rivera describes her poster, “Is oxygen supersaturation in Tempe Town Lake mainly driven by abiotic processes?”

Visiting students said the urban focus of the meeting was totally different that the ecology they were used to seeing presented. One student suggested that it made her think about how work at the Sevilleta could be expanded out to urban sites in Albuquerque, where most Sevilleta LTER students live.

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Students present posters at the CAP ASM. Presenters: top left – Tim Ohlert, top right – Aaron Grade, bottom left – Nich Weller, bottom right – Kate Weiss.
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Poster presentations.

The next day, CAP students led a tour to one of CAP’s long term experimental sites at an urban desert preserve. After hiking around and taking lots of photos, Sevilleta students found the vegetation of our Sonoran Desert sites wasn’t totally different from what was found on the Sevilleta grassland. Several genera and some species could be found in both sites. Despite the urban focus of CAP, the ecological context of Phoenix and the Sevilleta were not all that different.

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CAP and Sevilleta students explore Sonoran Desert vegetation while hiking at South Mountain Preserve, a CAP long-term research site.
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Wildflowers in bloom at South Mountain Preserve.

We enjoyed this opportunity to engage with other students across sites and learn a little more about where our research intersects and where there might be possibilities for collaboration. In the future, the Graduate Student Committee plans to support similar events at different groups of sites with the goal of continuing to build and strengthen graduate student connections within the LTER network.

The Small Island of Braila

By Jen Holzer, Technion Socio-Ecological Research Group

After three days in and around Tulcea, we journeyed by car to the City of Braila, a city of about 200,000, famous as a node for the textile, shipbuilding, and shipping trades, and a surprisingly underdeveloped tourism industry. When our hosts told us this was not a travel destination, we were incredulous and inquired with the hotel reception. But the hotel proprietor confirmed that most hotel patrons are businessmen, mostly people from the Netherlands and England involved in the textile and shipping trades; they advised us to vacation in Brașov, the mountainous, “most beautiful part of Romania”7

After a tour of the University of Bucharest’s beautifully refurbished laboratory facilities in the city, we toured the Faculty’s pontoon on the Danube, complete with laboratories and sleeping quarters, and sat with local environmental managers and scientists for interviews and discussions.8

The next day, we drove to Stăncuţa to meet with the mayor of this communa, a collection of local villages bordering the protected Small Island of Braila, a LTSER platform. Interviewing the mayor and his colleagues at the Town Hall was illuminating for understanding the interplay of stakeholder interests – from EU funding requirements and opportunities to the situation of the veterinary technician who moved back to the hometown of his grandparents but was struggling to make ends meet, to wide local opposition to limits on grazing in the protected area on the Small Island of Braila.9

We were generously hosted for a fantastic lunch by the Mayor at a new research facility on the shores of the Danube, and set out on a short boat tour of Braila Island.

Coming from Israel, I am no stranger to a dynamic and fraught history of political conflict and transition, nor to a reality of contested natural resources. While the purpose of our trip was to understand the progress and barriers made by socio-ecological research in Romania, I was hardly expecting the depth of cultural exchange that took place on every level. I want to express my gratitude to our hosts, not only for their thoughtful hospitality down to the last detail, but also for their incredible patience in answering our questions – from the role of macrophytes in the Danube Delta ecosystem to the residual effects of the Communist period on environmental management to the role of ecologists as educators. As social ecologists, the social context of science is always relevant, on every level, including the personal.


Jen is a PhD student in the Technion Socio-Ecological Research Group in Haifa, Israel and is affiliated with the Israeli LTSER network, with whom she is currently writing an article about applying transdisciplinary action research at the Negev Desert platform. Her research evaluates impacts of the transition in ecological research toward transdisciplinary socio-ecological research in Europe. Her trip to Romania was funded by an eLTER Transnational Access research exchange grant. She is happy to receive your comments, feedback, and suggestions for trivia questions about Romania at