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: https://cce.lternet.edu/blogs/201908/.



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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!

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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.

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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)


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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.

Citations

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.

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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.

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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!

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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.

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

References

[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.


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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.

 

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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.

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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.

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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.

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).


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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?

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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.

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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.

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HOW TO MEASURE SOIL MOISTURE IN THE DESERT WITH COSMIC-RAY NEUTRONS?

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.

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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.

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

E-Mail: stereite@gmail.com

Light and conversation advance the work of the Cairngorms LTSER

Author: Jen Holzer

Cairngorms LTSER

Israeli musicians Ehud Banai and the Refugees muse in the 1987 song, “Magic of the Galil”:

 

“…I imagined Scotland as Tavor Mountain

one dark night when I froze from cold

a guitar helped me

the fire helped me

the morning of renewing light helped me….”

 

While longing for landscapes of the Holy Land throughout the ages is incomparable, nostalgia of Israeli pop songs longing for landscapes abroad is also a noteworthy modern theme. As an Israeli researcher on my first trip to Scotland — in December 2016 – I was inspired by the bucolic and rugged landscapes of Cairngorms National Park, but I was also unduly influenced by the brief daylight, and cold and grey of solstice in the Highlands. To the contrary, when I returned this June 2018 at peak daylength, sunny days seeming to brighten every interaction.

In December 2016, Dr. Jan Dick, a Scottish scientist based at the Center for Ecology and Hydrology, helped to coordinate an interview tour of Edinburgh, Aberdeen, Perth, and the Cairngorms National Park that would comprise a case study of the Cairngorms LTSER, part of a cross-platform study that also includes LTSER platforms in Romania and Spain. During that first visit, we conducted 23 in-depth stakeholder interviews in nine days.

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Cairngorms LTSER stakeholders interviewed in December 2016.

This June, I returned to present our findings, based on those interviews, about how the Cairngorms Long-Term Socio-Ecological Research (LTSER) platform is measuring up to its goals, as well as by comparing it to other LTSER platforms I had visited in Romania and Spain. Days were long and sunny, with Scots seeming to revel in the specialness of these bright but short-lived weeks on the calendar. While I had noticed the Scotch sociability and penchant for storytelling on my last visit, on this visit nearly everyone we met seemed to be taking the opportunity of our meeting to visit a special natural spot or go for a lunchtime jog on the grounds of a nearby estate.

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Presenting interview findings to geologist ‘Ness Kirkbride, on the grounds of Scottish Natural Heritage’s Battleby Conference Centre campus.

Besides the long days and beautiful weather, another particularly special aspect of my experience was the nature of the trip itself. I will explain. My host, Dr. Jan Dick, often refers to her leadership of the EU-sponsored OPENness project by saying something like: “It’s the most fantastic thing. I got paid to take the results of our research back to the stakeholders and ask them if they thought it was useful – or to tell us that it’s rubbish. I don’t care if they do think it’s rubbish – I just want to know whether it was useful!” This was also the mandate of my second trip to Scotland. My PhD research is an evaluation of LTSER platforms in Europe; in particular, the following questions:

 

  • Are social questions being integrated into ecological science?
  • Is it stakeholder-driven science?
  • Is there evidence of impacts?
  • Is there added value to this approach?
  • What are the challenges?

 

One of the novel aspects of this project is that it evaluates research that aims to be transdisciplinary, which means that it attempts to integrate different disciplines, diverse researchers and practitioners, and their varied types of knowledge, and then to make that research directly applicable to the policy and practice of environmental management. So, as outlined in our evaluation approach (Holzer et al. 2018), we believe an essential part of evaluating transdisciplinary research (or research that aims to be transdisciplinary) is to take the evaluation results back to the potential end-users of that knowledge (before publishing) and getting their validation and/or criticism, and to incorporate that into the final results.

 

For the most part, the co-directors of the Cairngorms LTSER did validate our findings, which was affirming in that it meant that our interviewees had corroborated perceptions of local experts, and that on the whole, we had synthesized the interview material to accurately represent the big picture. However, what was perhaps more interesting came up when Dr. Jan Dick turned to me on the way to the LTSER co-directors’ meeting and said, “I’m using you as a boundary object!” A boundary object is any tangible thing – usually a map, graphic, or document — that a group of people, especially people with varied backgrounds and interests, can use as a focal point for their meeting, and to help keep the conversation constructive despite different points of view and reasons for being at the meeting. I realized that while I had been focused on getting feedback on my results, if another important goal was to contribute something to the platform itself, then my visit did inherently give something back in that it provided a clear focus – and perhaps even inspiration — at the LTSER co-directors’ meeting, which was convened because of my visit. To put it bluntly, bringing a visitor from abroad may create an excuse for doing certain things!

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My trip provided an opportunity for Dr. Jan Dick to catch up with her Environmental Change Network colleague ‘Ness Kirkbride.

I have read many accounts of scientists and creatives getting their best ideas while walking, swimming, or sleeping. On this trip, ideas really came together for the paper we hope to co-author with LTSER co-directors when we brought a laptop along to an outdoor café for lunch. If I had to be honest, I would tell you that I’m an introvert, and spending many of my hours manning the helm of my computer is a perk of doing a PhD. But I will also be the first to say that while good ideas may start with a solitary stroll or laps in the pool, they get developed in conversation, all the better if that conversation can take place somewhere beautiful.

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Outlining a manuscript at the café in Pentland Hills Regional Park.
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A morning jog on the Muir Way near Holyrood Park in Edinburgh.

It was a productive and engaging trip, with perks like staying minutes from Edinburgh’s Holyrood Park, getting to work outdoors, and opportunities to socialize with scientists – like at the ESCom Conference  where I had the opportunity to present a flash talk. Now that I’m back in Israel, I’m ready to write the great next pop song longing for another summer in Scotland.


About the Author:

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Jen is a PhD candidate in the Technion Socio-Ecological Research Group in Haifa, Israel. Her research evaluates impacts of the transition in ecological research toward transdisciplinary socio-ecological research. Her trip to Scotland was funded by an eLTER Transnational Access research exchange grant. She is happy to receive your comments, questions, and feedback at jholzer@technion.ac.il.

If you would like to be interviewed by Jen’s colleague Yael Teff-Seker, who will be conducting walking interviews in the Cairngorms National Park in July 2018, please be in touch.

Adventures in the stoichiometry of Braila Island, Research Center in Systems Ecology and Sustainability

Author: Shabnam G.Farahani

Braila eLTER

My scientific trip to Romania started on September 2nd, 2017. On the following day, I visited the Faculty of Biology, of the University of Bucharest where I met  the intimate staff of Biogeochemical Circuits laboratory.

On Monday morning after meeting the team from the Research Center in Systems Ecology and Sustainability, we headed to the Braila Research Station. The Research Centre in Systems Ecology and Sustainability (RCSES) of the University of Bucharest was established in 1999. RCSES coordinates the national Long Term Ecological Research Network and contributes to large scale and long-term research in Europe (e.g. LTER Europe, ILTER, LifeWatch Europe).

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During the three days of my stay in Braila, I was accompanied by a friendly and well organized team who assisted with the sampling and field experiments for my research.

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Braila city is located in the flat plain of Baragan.  On the east side there is the Danube, which forms an island – The Great Braila Island surrounded by the Macin channel, Cremenea channel and Valciu channel. On the northern side there is the Siret river and on the north-western side there is the Buzau River.

Braila took  me back in time as a lively and amazing city. I was genuinely impressed by the city’s past and how it became a cosmopolitan economical center of the previous century, it is really worth seeing for those who want to admire the sights of the Danube and Braila Island. In my PhD thesis at National Academy of Science of Belarus, I am examining the elemental composition of zooplankton and seston communities as it varies seasonally in the littoral and pelagic zones of temperate lakes. As such during my field trip in Braila Island, I focused on spatial differences in seston community as a limiting factor for food quality of freshwater consumers and their C:N ratios in 7 different stations along the Danube river.

After finishing the field trip, we visited the Pontoon of the Small Braila Island Natural Park administration and got acquainted with its staff.

On September 7th, we made a farewell to the beautiful city of Braila and departed for Bucharest in order to carry on the elemental analysis, at the University.

“ KUFTEH “in a foil

Kufteh is a Persian, also middle eastern yummy food which is a kind of herb meat ball in tomato plum sauce which was so similar to what I did in sample preparation for CN machine at Bucharest University . I divided each filter into four pieces, roll them as a ball and packed them in foil, then weighed them by micro scale to place them in machine.

To tell the truth, this trip was a unique opportunity for me not only for learning new things in stoichiometry at the LTSER  site, but also for having so much fun, going with the boat on the Danube, sightseeing in Braila City, cooking steak for the team by my own recipe and 3 nights living in pontoon on beautiful Danube river.

This project would have been really impossible without the support of all my colleagues from the Faculty of Biology.

I am using this opportunity to express them my gratitude for providing the facilities of such exciting exploratory trip.


About the Author:

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Shabnam is a PhD student at Belarus National Academy of Science

CaveGIS – bringing location analysis to the underground

Author: Vojkan Gavojić

eLTER TA site: Postojna Planina Cave System (PPSC)

Postojna-Planina cave systems’ consists of more than 30 km long passages of Postojnska and Planinska jama caves. Their passages collect and conduct surface and underground waters from Pivka and Cerknica and release them to Planinsko polje. It also represents the most biologically diverse cave in the world with more known species of stygobionts (obligate, permanent resident of aquatic subterranean habitats) than any other subterranean site in the world. Such complex system allows researchers to conduct long-term interdisciplinary karstological research that combines knowledge from chemistry, hydrology, physics, geology, geomorphology, meteorology, ecology, zoology etc.  Large amount of different data have been collected through years and decades, often with redundancy, which resulted in multiple data collections for same phenomenon at the same time window and in same space. Intention of this research is to consolidate such data so they can be presented through geographic information system (GIS) within same time-space window, providing all the researchers unified basis for further research. Such basis would consist of spatial, numerical and spatio-temporal data, which all together will allow location analysis in such complex systems such caves are.

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Figure 1: Fixed cave survey point – the basis for determination of location

But, first things first! Where do data come from? And when? Usually, researchers focus on space and time frame that is proposed by their research objectives. The phenomenon that they are tracking is located in space. Corridor type spaces that caves are represented by are plotted on survey maps by speleologists using different methods and tools. Postojnska jama cave, for example, has fixed cave survey points that have been used to determine exact location of points where data about different phenomenon are being collected by automatic monitoring stations or by manual collections.

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Figure 2: Postojnska jama cave corridors with locations of monitoring stations

Data acquisition is dependent on time frame defined by researcher. Intervals can vary from seconds to days within defined time frame. There is variety of phenomenon that can be monitored: cave meteorological data (temperature, humidity, air flow, gases…), hydrological data (pH, water flow, conductivity …), chemical data (presence of metallic elements or solutions), cave species, rock movements, speleothem formation, limestone dissolution etc. So, it is variety of data that can be changes over time.

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Figure 3: One of monitoring stations for cave meteorological data

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Figure 4: Stalagmite formation in Postojnska jama cave

When we determine location of monitoring stations we can present such data in spatio-temporal visualization. For example, using space-time cubes we can visualize the space-time frame of collected data, and determine whether they can be used for our own research. By providing such data from one central place, e.g. GIS database, we can ease researchers in process of data acquisition, and enable them to perform spatio-temporal and location analysis within their frame or research.

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Figure 5: Space-time cube visualization of conductivity values (left) and species number (right) on locations in time


About the Author:

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Vojkan is PhD student of Karstology at University of Nova Gorica, whose research focuses on using GIS and Remote Sensing in Karstology researches.