Hung out to dry: conducting ecological research in grassland streams during a historic drought

by Molly Fisher and James Guinnip (Konza Prairie Biological Station)

In the spring of 2018, I began to seek out summer research opportunities during my sophomore year as an undergraduate at Simpson College. Simpson College, a small, private college located in south-central Iowa, had fostered my initial interest in ecological research and water sources found in prairie ecosystems. One position caught my eye as a tallgrass prairie stream in Kansas was the subject of the study – Kings Creek located on Konza Prairie Biological Station. Konza Prairie (Konza) is a 3,487-hectare unplowed, native tallgrass prairie located in the Flint Hills Region, KS, USA and is jointly owned by Kansas State University and The Nature Conservancy. Konza was one of the original six LTER sites funded by the National Science Foundation when the LTER program began in 1980. The research conducted on this site focuses generally on understanding how fire, grazing, and climate impact tallgrass prairie ecosystems.

 Konza Prairie Biological Station.

I applied for and accepted a position with the NSF-REU (research experience for undergraduates) program at Kansas State University working with Dr. Walter Dodds. The goal of the project was to investigate effects of woody plant expansion on nitrogen (N) cycling in grassland streams. I arrived in Kansas in late May 2018 excited to conduct research in Kings Creek, one of few remaining stream networks with its watershed consisting entirely of pristine tallgrass prairie. Tallgrass prairie streams around the United States have been largely degraded by humans through agriculture and urbanization, with more than 90% of tallgrass prairie converted to other land uses (Samson and Knopf 1994). This has important impacts on ecosystem processes such as N cycling because small streams, such as Kings Creek, are a crucial component in N retention as streams flow to downstream habitats and eventually the ocean. Without N retention in small streams, increased nutrient loads would ultimately be transported downstream where high concentrations of nutrients can cause catastrophic algal blooms resulting in low-oxygen conditions (hypoxia) and large-scale animal die-offs such as the “dead zones” commonly observed in the Gulf of Mexico.

Unfortunately, Konza was experiencing the worst drought on record since the United States Geological Survey began monitoring stream flow on Kings Creek in 1979. Streams no longer flowed through the prairie and the isolated pools that remained grew smaller each day. My excitement surrounding my intended research in Kings Creek seemed to evaporate alongside any remaining water, until I saw the optimism of my research mentors, Dr. Walter Dodds and James Guinnip (PhD candidate in the Dodds lab). Rain was not in the foreseeable future nor was conducting our research because the stream sites we planned to use were entirely dry. However, from a different perspective, the drought presented a unique opportunity to document changes in N cycling that occur when streams stop flowing and water recedes to isolated pools.

Even though weeks of planning had seemingly been lost into the depths of groundwater, we still had useful research tools that could be applied in this unexpected scenario. Specifically, isotopic tracer studies can give insight to the processes that drive N cycling by tracing the movement of rare N isotopes (15N) into various biogeochemical reservoirs. Furthermore, we could utilize portable recirculating chambers, which act as microcosms of a stream ecosystem, to enable us to increase the sample size of our research project. Therefore, rates of N cycling could still be estimated in the isolated pools of water with the assistance of recirculating chambers (microcosms) and an isotopic tracer. The potential research could be completed with relatively small amounts of stream water and biological material. Furthermore, the methodology we chose would be novel as no one had previously used recirculating chambers with the isotopic tracer method we selected (Laws 1984). Despite an extreme and unexpected disturbance to our original research plans, it was finally becoming clear we would be able to make the best out of an unfortunate situation.

An overhead view of recirculating chambers.

Our updated research objectives were clear but required a significant amount of preparation before we started to collect data. We planned to utilize recirculating chambers and a manufactured form of ammonium (NH4+) salt isotopically enriched with 15N (15NH4Cl) to investigate multiple components of the N cycle (remineralization, uptake, and nitrification) using epilithic biofilms in isolated pools. We were interested in measuring these three processes because they are important contributors to overall N retention in streams, which prevents excess N from being transported to downstream habitats. In the field, we indiscriminately selected cobbles from the stream and placed them inside recirculating chambers, which were filled with stream water we enriched with 15NH4+ by filling a bucket with a measured volume of stream water then adding a small, precisely measured amount of 15NH4+ solution. Other cobbles from the pool were placed in coolers and saved for future processing to determine background 15N content of the biofilms on cobbles.

The cobbles in recirculating chambers were incubated for several hours then taken back to the lab where I had the pleasure of scraping biofilm off the cobbles with something similar to a metal-bristled toothbrush. The biofilm scraped from the rocks became a slurry, which was filtered onto glass fiber filters to measure the isotopic enrichment of organic N in the biofilm material. N uptake by the biofilms was calculated by comparing the amount of 15N in biofilms before and after our field experiment. We used a similar approach to estimate rates of N remineralization and nitrification by comparing 15N content of dissolved NH4+ and nitrate(NO3), for each process respectively, before and after our field experiments with recirculating chambers. We utilized data from O’Brien et al. (2008) to compare our results to similar estimates conducted during normal stream flow. We found that rates of N uptake and remineralization by biofilms in isolated pools were much higher compared to periods of normal stream flow, which is likely due to increased N concentrations and deposition of organic matter in isolated pools relative to background levels of these variables when streams are flowing.

Components of the N cycle investigated by using 15NH4+ dilution method and isotopic enrichment of other N pools.

At the start of 2019 I was, once again, searching for summer research positions and accepted a second NSF-REU position with the Dodds lab. This time around, however, I would travel to Mongolia to assist doctoral candidate, Anne Schechner, with collecting river metabolism data during the month of June. In July 2019, James and I were able to sample Kings Creek during normal stream flow using the same methodology as the summer prior. We have yet to finish data analysis for 2019 but continue to work diligently to finish analyses so we can begin to draw more reliable conclusions about how the severe drought of 2018 affected N dynamics in Kings Creek.

In conclusion, what once appeared to be a lost research opportunity turned into many successes. Not only were we able to complete a novel research project examining effects of drought on prairie streams, but I have also coauthored a manuscript on broader ecological effects of the 2018 drought in Kings Creek (Hopper et al. 2019) and presented research at an international conference. Through these somewhat unpredictable research experiences I have had the opportunity to work alongside numerous graduate students at Kansas State University for the past two years. I have had the honor to contribute to their projects as well as my own, and in doing so reinforced my decision to attend graduate school.


Hopper, G.W., K.B. Gido, C.A. Pennock, S.C. Hedden, J.P. Guinnip, M.A. Fisher, C.M. Tobler, C.K. Hedden, and L.A. Bruckerhoff. 2019. Biomass loss and change in species dominance shift stream community excretion stoichiometry during severe drought. Freshwater Biology. DOI: 10.1111/fwb.13433

Laws, E. 1984. Isotope dilution models and the mystery of the vanishing 15N. Limnology and Oceanography 29(2) (1984): 379-386. DOI: 10.4319/lo.1984.29.2.0379

O’Brien, J.M. and W.K. Dodds. 2008. Ammonium uptake and mineralization in prairie streams: chamber incubation and short-term nutrient addition experiments. Freshwater Biology 53(1): 102-112. DOI: 10.1111/j.1365-2427.2007.01870.x

Samson, F and F. Knopf. 1994. Prairie conservation in North America. BioScience 44(6): 418-421. DOI: 10.2307/1312365

Author biographies:

Molly Fisher is a senior at Simpson College majoring in environmental science. She will be attending Kansas State University in the fall of 2020 as a Masters student. She will be a member of two labs Dr. Walter Dodds’ and Dr. Sonny Lee’s as she plans to study coral genomics and nutrient cycling.

James Guinnip is a PhD candidate in the Dodds lab at Kansas State University studying benthic and riparian N cycling in the Kings Creek stream network.

Understanding Coral Bleaching: Research and Lessons from Mo’orea

by Jannine Chamorro, Moorea Coral Reef LTER

Last September I had the opportunity to participate in a project studying coral bleaching in Mo’orea, French Polynesia. This was the first time I had ever worked in a remote field location. While initially the thought of flying to a place I could not see on a map made me queasy, I am forever grateful for this unforgettable experience and all it taught me.

The project, led by Professor Marie Strader at Auburn University, focused on examining how population level patterns of epigenetic marks, such as DNA methylation, shift during and after a bleaching event in the coral species Acropora hyacinthus. For those unfamiliar with epigenetics, they are modifications to DNA that do not change the DNA sequence. DNA methylation, a commonly quantified epigenetic mechanism, is the addition of a methyl group to the DNA molecule. Environmentally induced changes in methylation patterns of the genome can influence gene expression and subsequently phenotype. Therefore, understanding how DNA methylation patterns change in re­­sponse to a bleaching event is important, as it will give us insight on the role of epigenetic mechanisms in response to ecologically relevant environmental stress.

Tackling research questions such as these start in the field requiring a wide range of unconventional skills, from using a hammer and chisel underwater to gently washing tissue off of coral skeletons. It was the opportunity to use these skills that made me most excited about participating on this project. While there are tons of details I can get into, I will briefly try and summarize the field methods used in this project. First, establishing a baseline is important to track changes in these molecular mechanisms over time. Therefore, at the beginning of the bleaching event, divers tagged, photographed, and sampled coral colonies at various Mo’orea Coral Reef (MCR) LTER sites around the island. Colonies were then resurveyed and sampled at four time points over the course of the bleaching event. In total this resulted in countless hours underwater and over 1500 samples collected!

Researchers, Kelly Speare and Marie Strader, collecting coral colonies.

As the time progressed, corals showed remarkable variation in their bleaching response. While many of the corals colonies unfortunately died, many others either recovered from the bleaching event or were resilient. Determining if there are molecular differences, genetic or epigenetic, in these coral colonies will be exciting and can bring us one step closer in determining the role of molecular mechanisms in species resistance to environmental stress.

Corals demonstrated drastic differences in bleaching severity.


One of the highlights of working on this project and conducting research at a remote field location is that it allowed me to develop my skills as a field biologist. While its location makes it a place of wonder, this introduced challenges when conducting experiments due to the limited access to equipment and supplies. These limitations meant we had to be resourceful and inventive to execute our experiments. An example being our coral transporter, an essential tool for bringing colonies to and from the boat; it was a dishrack.

The greatest lesson I learned in field biology was the importance of a supportive team and good communication. Having only been diving off the coast of California, I was thrilled to dive in the warm waters of Moorea. However, I was also a bit nervous about this completely new location. It made all the difference being comfortable enough with my team and knowing that I had their support. We understood that our safety was the priority above all research. Additionally, proper communication was also important as it ensured everyone was on the same page allowing experiments to run as smoothly as possible.

The amazing team that worked on this project. (Left to right: Logan Kozal, Kelly Speare, Marie Strader, Terence Leach and Jannine Chamorro)

I am thankful to have been given the opportunity to work on this project with such a great team. Apart from conducting significant and inspiring research, waking up to chickens, swimming with humpback whales, and playing with the station dogs became my new normal for a very short but wonderful time. While some days were exhausting going from hours of diving to hours in the lab, I look back at it as one of the greatest experiences in my research career.

Penny, one of the lovely station pups.


Author Biography: Jannine is a PhD student in the Hofmann Lab at the University of California-Santa Barbara. She studies physiological and molecular mechanisms organisms employ to deal with rapid environmental change. While she is associated with the Santa Barbara Coastal LTER, she became involved in the MCR LTER coral bleaching project after working with Dr Marie Strader during her time with the Hofmann Lab.


A walk in the woods – 17 years later

by Ian Yesilonis (Baltimore Ecosystem Study LTER)

Figure 1. Ian Yesilonis by a large tulip poplar tree in Gwynns Falls/Leakin Park in Baltimore City.

Walking through the woods and observing the trees and animals is something I have always loved to do growing up in Baltimore.  Our temperate deciduous forests in the city are typically smaller patches; however, one park, the Gwynns Falls/Leakin Park (1,216 acres), is quite large and also has big trees (see Figure 1).  The trees and soils of these forest fragments, which make up 34 percent of the city’s tree canopy, provide important ecosystem services such as stormwater runoff reduction, water purification, food and habitat for animals, air temperature reduction, and carbon sequestration.  These patches are surrounded by an urban matrix comprised of roads, houses, and people.  The surrounding urban environment influences these patches many different ways, for instance, as sources of metals and nutrients, as well as invasive species.  Over time, these different influences may affect the general health of the forest.  In my project, I wanted to look at changes in soil properties over 17 years, specifically in carbon, nitrogen, pH, calcium (Ca), and magnesium (Mg) content in urban remnant forests and compare those to rural areas in Baltimore County.

Most temperate deciduous forest soil resampling studies investigate acid deposition before the 1970’s and consider the leaching of Ca and Mg through the soil profile.  Acid rain affected the entire forest ecosystem, including plants and wildlife, all over the east coast of North America.  Generally, these studies have found a decrease in Ca which is needed for a variety of living organisms such as arthropods and snails to create exoskeletons and shells. However, no retrospective studies have been done in an urban context to investigate the effects of the urban matrix.  In urban environments, the soils are not necessarily depleted in Ca. We are finding the opposite, i.e. there is excess Ca due to the abundance of cement and concrete which erodes and washes into nearby soils, or it becomes dust, deposited on the soil surface and by wind. This constant source of CaCO3 could affect soil pH which determines what plants can grow successfully.

Figure 2. Big wheel tire in the middle of our Hillsdale plot, Baltimore City.

Carbon dynamics in our forest systems are complex.  A confounding issue found in the urban forests is the presence of earthworms that mix and integrate leaf material into the upper horizon of the soil profile therefore affecting where carbon is stored.  Another difference between urban sites and rural sites is the increased temperatures in the urban area.  As temperature rises, assuming the moisture is the same, decomposition of organic matter also is accelerated which decreases the amount of organic matter in the soil.


Our hypotheses are 1) soil organic carbon will decrease in urban areas due to increased temperatures and worm activity, and 2) conversely, pH will increase because of the amount of calcium prevalent in the urban system from cement.  In order to detect change, we resampled forest fragment plots from a previous study, conducted in 2001.  One challenge was to find the same plots.  Two things helped us achieve this goal: first, we had original hand-drawn field maps with detailed descriptions of the locations and second, we were able to talk with the investigator of the 2001 sampling. This guided our interpretation of these maps and ensured that collection methods were comparable.  Remember, this was a time before GPS was readily available and the signals from satellites were scrambled for civilians.  Although it was a challenge, I learned a great deal of patience, and ultimately enjoyed finding the exact same sites.  The maps were detailed, but things change over time in forests; trees fall over in wind storms, thus trees, originally standing on the 2001 field map, were on the ground in 2018.  On the other end of the spectrum, some things didn’t change at all; for example, at one site in Hillsdale, which is surrounded by neighborhoods, we found the exact same toy big wheel tire in the center of the plot that was drawn on the field sheets.  It hadn’t moved and, being plastic, had not decomposed in 17 years (Figure 2).  In the field, I was prepared for mosquitos, dog and black-legged ticks, and poison ivy but I was not prepared for stray dogs.  At one plot in Leakin Park, we saw two large dogs barking at us on the other side of the ravine.  They started running towards us and tried to find a way to cross the ravine.  I did not want to challenge their territory so we quickly made our way to the van and ended field work for the day.  Despite some unpleasant encounters such as this, I enjoy working in the forest, digging in dirt, enjoying the shade of the trees, hearing the birds, and watching the squirrels.

Figure 4. Soils from different plots throughout Baltimore.


After our summer field work was completed, we worked in the lab to analyze the samples for nutrients, pH, and determined soil density (Figure 3).  Currently, we are examining data and look forward to exploring the results which could be used to predict future conditions and better plan for management of forest patches.

Author Biography: Ian Yesilonis is a Soil Scientist for the USDA Forest Service Northern Research Station and a PhD student at Johns Hopkins University in Dr. Szlavecz’s lab in the Department of Earth and Planetary Sciences.  He studies all aspects of urban soils including metal contamination (especially Pb), soil respiration, carbon storage, and decomposition.

Cruising the Ocean off California: Wrangling the MOCNESS monster

by Laura Lilly (CCE-LTER grad student rep)

In August, the California Current Ecosystem (CCE) LTER program undertook a 32-day Process Cruise to sample the ocean off California. We left San Diego Harbor under sunny skies and smooth sailing conditions and headed north toward Monterey, California. The goal of our month long cruise was to track water filaments that are upwelled in near-coastal waters off central California and flow out to the open ocean several hundred miles offshore. We measured various aspects of the biological production associated with filaments: viruses and bacteria, phytoplankton and zooplankton, along with the nutrients that fuel their growth. Our 2019 cruise was the 9th cruise of the CCE-LTER site, which was started in 2004. The program consists of a core body of scientists from Scripps Institution of Oceanography and collaborators from numerous other institutions, as well as visiting scientists and volunteers from around the world. Our 2019 cruise included participants from as far away as Canada, France, Luxembourg, and Ghana!

Below is one of our blog posts throughout the month. You can check out the entire cruise blog at:

Recovering MOCNESS nets can be exciting in rough seas. They really do look like creatures from the watery depths!

One of the core measurements we conduct on our Process Cruises is zooplankton net tows. We do these tows to determine which organisms associate with the various water parcels we are measuring. We expect to see differences in zooplankton communities that live in highly-productive filament waters that have just been upwelled and contain lots of nutrients and phytoplankton food for zooplankton versus ‘blue-ocean’ waters farther offshore that have much lower nutrient concentrations and may host a more subtropical zooplankton community. We also expect to see differences in the numbers and types of plankton in different depths of the ocean.

When you do zooplankton tows, you bring a lot of monstrous-looking creatures onboard. Sometimes we get Phronima hyperiid amphipods, which were the inspiration for the 1979 movie Alien; occasionally we pull up red tuna crabs, small lobster-like crustaceans with very sharp claws; and even a rare vampire squid, a small purple creature with big black eyes, Dumbo ears, and tissues between its tentacles that resemble vampire cloaks. But one of the craziest monsters we have is the net we use to capture and sample these organisms: the MOCNESS!

Phronima hyperiid amphipod curled up in a hollow salp ‘barrel’ (body case). Phronima carves a salp’s body out and uses the barrel as a house – like a slightly morbid version of a hermit crab. Photo courtesy of Pierre Chabert.

Assuming you haven’t been living under a rock for the past hundred years, you will probably recognize MOCNESS as a play on Scotland’s Loch Ness Monster. MOCNESS stands for Multiple Opening/Closing Net and Environmental Sampling System, and was developed by Peter Wiebe at Woods Hole Oceanographic Institution. If you can process that behemoth of a name, you will get clues about what the MOCNESS does. Most of our plankton nets, such as Bongo nets, have simple circular ‘mouths’ that stay open for the whole net deployment: they go down to depth open and come back up still open, so if we sample down to 200 meters we are actually collecting animals everywhere between the surface and 200 meters. That comprehensive sampling is fine for a lot of the research questions we ask (aka: “Who is present in the upper ocean off San Diego versus Monterey?”), but sometimes we want more information about which animals live at specific depths. As its name implies, the MOCNESS has multiple nets (10 on our current setup!) attached to one frame, and they can be opened and closed in sequence to sample different depths. If you want to compare the zooplankton living at 1000 meters versus 100 meters, you can program separate nets to close at each of those depths. The MOCNESS also has oceanographic instruments to measure water temperature, salinity, oxygen, and fluorescence, so we can get information about the physical water profile in addition to zooplankton specimens.

Most of our MOCNESS tows on this cruise sample down to 450 meters, although occasionally we sample to 1000 meters. Those deep tows can last over three hours, which doesn’t even include the net washdowns afterward! majority of the sample from each net filters down to a plastic jar attached to the end of the net, but once the nets come back on deck, we hose them down to make sure we collect all the animals that may have gotten stuck in the net mesh. Net washdowns sometimes feel endless, but they can be very important: one of the vampire squids we caught a couple of days ago was stuck halfway down the net, and we wouldn’t have collected it if we hadn’t done the net washdown.

Each of the ten MOCNESS nets has a plastic ‘cod end jar’ attached to the end. These jars collect most of the organisms that get caught in the nets, and bring them back to the surface for us to sample. Four cod end jars are visible here as the grey cylinders with drainage holes and duct tape bumpers. Photo courtesy of Lance Wills.

Net washing time is also essential for taking in the afternoon sun (or sometimes early morning pre-dawn night air) out on deck, and for keeping an eye and ear open for passing whales. Today we started our third cycle, and we were graced all day by the presence of fin whales. Their deep exhaling sighs and broad backs were sometimes just 50 feet away from our ship. The sound of a fellow mammal emerging from the depths of the ocean to release a breath of air never gets old. Plus, all those whales are a sure sign that there are zooplankton around to feed on!

Roadblocks and Rocks:  How to Measure Soils in Forest Ecosystems

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

fig 1.jpeg
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.

fig 2.png
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.

fig 3.jpg
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.

fig 4.jpeg
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).

wheeler et al
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.

wheeler et al 2
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.

wheeler et al 3
Students present posters at the CAP ASM. Presenters: top left – Tim Ohlert, top right – Aaron Grade, bottom left – Nich Weller, bottom right – Kate Weiss.
wheeler et al 4
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.

wheeler et al 5
CAP and Sevilleta students explore Sonoran Desert vegetation while hiking at South Mountain Preserve, a CAP long-term research site.
wheeler et al 6
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.

Understanding species’ responses to climate change

by Cliff Bueno de Mesquita, Niwot Ridge LTER

This month Cliff will be sharing some of his dissertation work from his beloved alpine field site at the Niwot Ridge LTER site in the Colorado Rocky Mountains (Fig 1).

Figure 1. View of the Niwot Ridge LTER Site in the Rocky Mountains, Colorado, USA. Photo by William D. Bowman.

Mountainous areas often experience a greater magnitude of climate change than other areas. Data collected from our long-term records at Niwot Ridge show that summer temperatures are increasing (Figure 2) and snow is melting out earlier. How will plants respond to these changes?

Figure 2. Increasing summer temperature trends at Niwot Ridge. Shown are lines from linear regression (red) and a loess function (blue). From Bueno de Mesquita et al. 2018, Arctic, Antarctic, and Alpine Research.

One way plants and other organisms can adapt to climate change is by moving into suitable habitats. As climate warms, this typically means moving either up in elevation, or poleward in latitude. To colonize new areas, plants rely on their seeds to first disperse there, after which they must successfully germinate, grow, and survive. Such distributional shifts are important because if organisms can’t track their suitable climate for growth and reproduction, they could be killed either by unfavorable conditions where they currently are, or competition from more warm-loving species that are thriving in the warmer climates.

Here at the Niwot Ridge LTER, an experiment just concluded in which we hauled pots (Fig 3) of several alpine plant species up to 3900 m elevation (12800 ft) and transplanted them into unvegetated soils beyond their current range. We manipulated when the snow melted as well as which microbes the plants were grown with to see how these two factors influenced plant performance in a new habitat. By microbes, I mean the microscopic bacteria and fungi that grow in soil and often play important roles for plants, particularly in making nutrients plants need more available. To manipulate snowpack, we spread a thin layer of black sand onto the snow to absorb more solar radiation relative to clean snow. Think about what it’s like wearing a black shirt on a sunny day compared to a white one! To manipulate the microbes, we grew plants in soil collected from different areas that we knew had different microbes.

Figure 3. Our team of strong ecologists carrying up the transplants on a stretcher! Photo by Jane G. Smith.

After two years of growth at our site on Niwot Ridge, one of the three plants were doing very well, while the other two mostly died. The one plant that had good survival had differences in growth depending on which microbes we gave it, suggesting the microbes played a role in plant growth in new habitats. We also observed the snowbed melted out earlier and earlier each summer, such that by the 2nd summer, we saw negative effects of earlier snowmelt on plant survival. Areas where snow melted out too early may experience dry conditions later in the summer. Overall, our results show that 1) not all plants will be able to colonize new habitats to track suitable climates, 2) microbes can influence plant growth in new habitats, and 3) early snowmelt may help plants colonize higher elevation areas, but too early snowmelt may be detrimental, likely due to less water availability later in the summer.

Author Biography: Cliff Bueno de Mesquita is a doctoral candidate in Katie Suding’s lab in the Department of Ecology and Evolutionary Biology at the University of Colorado Boulder. Having first been a participant in the Research Experience for Undergraduates program at Niwot Ridge, then moving on to conduct all of the field work for his dissertation on Niwot Ridge, he has worked on Niwot Ridge for six summers and enjoyed every moment (except for maybe the scary thunder hailstorms)! Outside of the lab, Cliff enjoys spending time in the mountains hiking, climbing, and skiing, as well as playing rock n roll music with his band, The Casual Ales.




Author: Stephanie Reiter

eLTER TA site: Negev

Research stay dates:      09/16 to 01/17  

The water bound in our soils, in particular soil moisture, influences plant growth, water infiltration, flood regulation and even climate patterns. Although on a global scale the overall quantity of soil moisture is small (<0.05%), it influences ecological, hydrological and meteorological processes.

Soil moisture content is an essential variable for eco-hydrological modelling or irrigation management as it provides the main water storage for plant uptake. Although the precise prediction of soil moisture over various scales is of high interest, its measurement and quantification is still challenging. Satellite remote sensing techniques are able to depict soil moisture patterns over large areas but a major drawback of these measurements is a shallow penetration depth of only a few centimeters of topsoil. Point measurement techniques using in-situ measurements can be interpolated to bigger areas but the spatial variability of soil moisture may complicate the upscaling; the vertical measurement depth of commonly used soil moisture in-situ probes is restricted to the topsoil layer as well.

Cosmic-ray neutron sensing (CRNS) is able to close the gap between large scale satellite remote sensing and point measurements, allowing soil moisture to be quantified non-invasively at the intermediate scale, e.g. for a small watershed or field site. The method uses measurements of cosmic-ray neutrons in a cosmic-ray neutron probes footprint, its horizontal (circular) and vertical measurement area. The cosmic-ray neutron particles are mainly absorbed and moderated by hydrogen. As a result, these neutrons are highly sensitive to the concentration of water in soil. This means under wet soil conditions the probe will detect less neutrons than under dry soil conditions. Especially in arid and semi-arid regions where water is scarce, it is critical to better understand soil moisture dynamics. That is why we set up a research project in a dryland region on the European Long-Term Ecosystem Research (eLTER) site in the Negev Desert, Israel.

In September 2016, I traveled from Berlin to Tel Aviv with a 32 kg heavy metal box containing a cosmic-ray neutron probe, a massive soil driller and an extra-large hammer. For normal people these things seem to be peculiar to travel with, but not so for a Geoecologist.

Not speaking any Hebrew, I had to figure out how to get from Tel Aviv to the Midreshed Sde Boker, an educational center in the middle of the Negev Desert, where I independently conducted the research on soil moisture measurements for my Master thesis. Fortunately, Israelis are extremely helpful. Several young soldiers helped me getting to Sde Boker with the neutron detector. And wow, what a place. A green oasis overviewing the Martian-like desert landscape of the Sde Zin valley, home to a small but flourishing community of about 1800 people, many of them students and researchers of the Ben-Gurion University of the Negev and its affiliated institutes there.

Desert research in the arid environment of the Negev has a long history, starting in the late 1950s with the establishment of the close-by first experimental farm near Avdat, where Michael Evenari and his colleagues were keen to investigate ancient and innovative practices to meet the challenges of Israeli agriculture. The story of Evenaris farm for runoff and desert ecology research is described in his personal and scientific narrative The Negev: The challenge of a desert, giving an idea of historical environmental research before satellite remote sensing, computer models or neutron probes were invented. When I visited the farm, dust and sand covered books in the library and piles of hand-drawn maps were scattered here and there. The old measurement instruments on the roof of the now abandoned building were fascinating to me, raising my spirits to be a desert researcher.

At the Evenari desert farm in Avdat, Israel

Basically, what I wanted to do was measure soil water in the desert with cosmic-ray neutrons. My research aimed at quantifying soil moisture over tens of hectares using a combined approach that comprised the novel physical science based CRNS and hyperspectral remote sensing of vegetation. I installed the cosmic-ray neutron probe on the eLTER field site next to the Sde Boker campus and started measuring shortly after my arrival towards the end of the dry season in mid-September.

My daily routine would include walking through the heat to the field site to check the probe and transfer data to a computer. In order to convert the neutron intensity into soil moisture, I needed to conduct three calibration campaigns that consisted of the collection of soil samples in the CRNS probes’ circular footprint area. It turned out that taking soil samples up to a depth of 40 cm is a real challenge in the concrete like, dry desert soil. Although I had helping hands from my colleagues Kristina and Haijun, and from the lab technician Alexander Goldberg, we were not able to use the special soil driller that I brought from Germany to extract the samples. We adjusted the sampling method to the field conditions and used a spade to dig holes and extract the samples by hand for the laboratory analysis.

On seven of the days during my research stay, we conducted hyperspectral measurements of soil and vegetation on the site using a heavy field spectroradiometer. The field work in the heat of the day with temperatures rising up to 40 degrees Celsius and no shade was hard but I always enjoyed the rides to the site in the electric golf cart, when we could get it.

My research at the eLTER site in Israel showed that CRNS is a reliable technique to measure soil moisture content (even in minute amounts) in a natural dryland environment with shrub vegetation. Area average soil moisture values could be derived up to a penetration depth of 46 centimeters over an area of about 28 hectares reliably. The approach to combine CRNS data with remotely sensed vegetation parameters in order to obtain comparable values of soil water content needs to be tested in further (desert) studies. By the end of my research, the vegetation grew only sporadically on the field and I was not able to detect a clear signal of vegetation in the hyperspectral data. Ideally, spectral data can provide vegetation indices such as the Normalized Difference Infrared Index (NDII), a proxy to assess root zone soil moisture which is able to visualize the natural interaction between precipitation events, soil moisture and leaf water content.

I enjoyed my research stay in Sde Boker, learned a lot about Israeli culture and hummus, and met wonderful people from all over the world. In the evenings, I would leave my air conditioned student apartment, and take a five-minute walk to the cliff where the wide view over the Zin Valley never ceased to amaze me, and where the night sky was so clear that I could see the far-far away galaxies sending out continuous streams of cosmic ultra-high-energy particles. My thoughts would drift through space and time like the cosmic-ray neutrons that hit my neutron probe.

Sampling location on the eLTER research site near the Sde Boker campus, Israel
Alexander Goldberg with the field spectrometer
The cosmic-ray neutron probe in the field – powered by the sun
Me collecting soil samples on the field
The Sde Zin valley, Israel

About the Author:

Reiter1Stephanie (26) is a graduate student with a MSc. in Geoecology. She is passionate about the importance of soils within our ecosystems. During her research at the eLTER site in Israel, she studied how to measure water in desert soils non-invasively using a novel method called cosmic-ray neutron sensing. Her research stay was supported by the eLTER H2020 Transnational Access grant. When not digging in soils or dealing with extragalactic particles, she enjoys long-distance hiking, gardening and organic food.