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Posts from the ‘Soil moisture sensors’ Category

Oct 31

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Mesh Wireless Sensor Networks: Will Their Potential Ever Be Realized?

Although the idea of mesh wireless sensor networks is not new, the realization of their many benefits have gone largely unrealized. The low success rate of most wireless systems makes the accomplishments of this Johns Hopkins group unique.

Image of bright orange, yellow, and red colored trees in autumn

Soil moisture and temperature are major drivers of seasonal dynamics, soil respiration, carbon cycling, biogeochemical functions, and even the types of species living in a certain area.

The ability to measure soil moisture and temperature is vital to ecologists who work in heterogeneous environments because these parameters are major drivers of seasonal dynamics, soil respiration, carbon cycling, biogeochemical functions, and even the types of species living in a certain area.  But ecologists’ scientific understanding of environmental conditions is hindered when soil moisture measurements disturb the research site, or when field measurements are not collected at biologically significant spatial or temporal granularities. Soil ecologist Dr. Kathy Szlavecz and her husband and computer scientist, Dr. Alex Szalay, both at Johns Hopkins University, are working to solve this dilemma by testing a wireless sensor network (WSN; Mesh Sensor Network), developed by Dr. Szalay, his colleague, computer scientist Dr. Andreas Terzis, and their graduate students. These generate thousands of measurements monthly from wireless sensors. The husband/wife team says that WSN’s have the potential to revolutionize soil ecology by generating a previously impossible spatial resolution.

Diagram of a mesh network data system for soil moisture

Architecture of an end-to-end mesh network data collection system. (Image: lifeunderyourfeet.org)

What is a Mesh Network?

In a mesh wireless sensor network, specially designed radio units (nodes) use proprietary or open communications protocols to self-organize and can pass measurement information back to central units called gateways. Different from star networks where each node communicates directly to the gateway, mesh networks pass data to each other, acting as repeater for other nodes when necessary.

Image of 37 sampling locations at the Smithsonian Environmental Research Center

These are the 37 sampling locations at the Smithsonian Environmental Research Center (SERC) in Edgewater, MD. Data from this deployment is aimed at understanding the effect of forest age, leaf litter input, and earthworm abundance on soil carbon cycling. (Image: lifeunderyourfeet.org)

With low power and reliability as their goal, they are deployed in dense networks to automatically measure conditions such as temperature and soil moisture. These node measurements are taken every few hours over several months. The data are then uploaded onto computers, where it can be maintained and searched. Kathy explains “Without an autonomous sensor system, experiments in need of accurate information about a multitude of environmental parameters on various spatial and temporal scales require a superhuman effort. The inexpensive nature of these sensors enable scientists to place a high-resolution grid of sensors in the field, and get frequent readouts.  This provides an extremely rich data set about the correlations and subtle differences among many parameters, allowing ecologists to design experiments that study not only the gross effects of environmental variables, but also the subtle relations between gradients and small temporal changes.”

Sunlight shining through trees in a forest

Without an autonomous sensor system, experiments in need of accurate information about a multitude of environmental parameters on various spatial and temporal scales require a superhuman effort.

Landscape Studies Benefit from Mesh Networks

Kathy and Alex have deployed mesh wireless sensor networks at several study areas around the state of Maryland.  Kathy says, “Once we record the measurements, we can combine that information with observations of soil organisms to better understand how soil organisms and the soil environment interact. This means we can make better predictions about how human activities will affect the soil environment.” In one urban landscape study, Kathy and her team deployed over 100 nodes around a CO2 flux tower looking at the two major landscape covers in an urban environment: grass and forest.  She explains, “We collected data from nodes connected to soil moisture and temperature sensors for over two years at these sites, and the system worked quite well. We collected about 180 million data points, and that’s no small feat.”

Next week: Learn the results of this research group’s mesh network testing and what Kathy thinks the future holds for this technology.

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Oct 24

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Unraveling the Effects of Dams in Costa Rica (Part 2)

Dr. Rafael Muñoz-Carpena, Professor and University of Florida Water Institute Faculty Fellow and his research team are performing environmental studies on the Palo Verde National Park wetlands, trying to unravel the effects of the dams and how to revert some of the damage (see part one).  This week, find out how the researchers established connectivity in such a remote area,  some of the problems associated with the research, and how the team has addressed some unusual research issues.

ATMOS 41 Weather Station in Palo Verde National Park Wetlands

Surface water elevation gauge station at the Bebedero river. Photo credit: Marco Pazmino Antonio

The Data Challenges of Remote Locations

The team began collecting data, as part of a joint effort with the Organization of Tropical Studies (OTS) research station. However, typical sensors require constant supervision and frequent visits, which imposed a burden on the station staff. There was also the risk of losing data if a sensor malfunction went undetected between monthly visits.  Rafael says, “Sometimes access was not possible due to floods or scheduling issues, so there was a high risk of losing information. To fix the problem (thanks to a National Science Foundation grant awarded to OTS) we integrated the sensors into a system that gives us remote access on a daily basis. This allows us to see the status of the instrumentation in near real-time, and thus coordinate with OTS to replace sensors if needed.”

Fauna in Palo Verde

Glimpse of the fauna in Palo Verde. Photo credit: Alice Alonso

Connectivity Issues

The team had a difficult time finding internet connectivity because the area is so remote. After trying several solutions, they finally built their own cell towers. The stations are now outfitted with cellular-enabled data loggers in conjunction with rain gauges and soil moisture and salinity sensors. The stations also include a standing well to measure surface and river water levels and monitor flooding stages. These are coupled with shallow water table wells, installed below the surface at 3-5 meters.  Rafael says, “These are tidal rivers, so we get a lot of activity up and down. We look at river data in conjunction with inland responses to try and get an idea of the influence of the river on the shallow groundwater nearby. All these data feed into a database that researchers and stakeholders can look at.”

Composite image contrasting the Palo Verde wetland in the 1986 and the wetland in recent days (2012) during the wet seasons. It highlights the encroachment of vegetation and Typha domingensis (cattail), closing the patches of open water and reducing biodiversity and sites for birds feeding and nesting.

Composite image contrasting the Palo Verde wetland in the 1986 and the wetland in recent days (2012) during the wet seasons. It highlights the encroachment of vegetation and Typha domingensis (cattail), closing the patches of open water and reducing biodiversity and sites for birds feeding and nesting.

Internal Drivers

Dr. Muñoz-Carpena says because of the lag in the environmental response, it is not immediately clear to the general public that the wetland behavior is the result of what is happening upstream. People fail to see a connection. Therefore unraveling the data in a way that is clear is the first challenge of the project. He adds, “There are also internal drivers such as park management changes that compound the effects of the dams. Originally park managers tried invasive plant control with fire and cattle. Now they control the invasive with blade-rigged tractors that mow the cattail. But this is a highly expensive and temporary measure with recurrent costs, which provides no definitive solution to the cattail invasion. It’s important to understand the changes are not just the result of what’s happening locally. We need to find permanent solutions by tracking down the root of the problem.”

Endangered Jabiru birds in the trees in Palo Verde National Park

Endangered Jabiru in the Palo Verde National Park. Photo credit: Alice Alonso

Plants are Not the Only Invasives

Cattails are not the only invaders that plague the wetlands. Rafael explains, “The other problem is that there is trafficking going on in the park. The men see these data logger boxes with silver antennas, and they think it’s a camera, so they break off the antennas. We are now putting up signs that say, ‘This is not the government watching you. This is research to protect your environment,’ but we are afraid the next time they will break the boxes and everything that goes with them. We won’t have the manpower or the financial resources to go down there and fix the data loggers for another six months.”

Image of a typical monitoring station set up in a more dry area

Example of a typical monitoring station: Surface and subsurface water elevation and EC monitoring wells, and soil moisture and EC at 30 and 60 cm depths. Sensors connected to a wireless cellular data logger for near-real-time data access. Photo taken during the dry season. Photo credit: Alice Alonso

What’s Next?

Over the last three years the team has collected a high-resolution database of fifteen to thirty minute timed steps, with over 100 sensors deployed in twelve spatially-distributed monitoring stations around the park. With that data, Rafael’s team is conducting exploratory types of analysis to study not only potential drivers of change, but also the cause of the drivers. They want to understand potential initiatives they could introduce to make the system more sustainable. Rafael says, “Once we develop integrated hydrological models and test them for the conditions in Costa Rica, hopefully we can understand the behavior in the past and forecast some different scenarios for the future.” Because many regions in the world suffer the impacts of interbasin water transfer, this research can inform future research policy at a broader scale.

Monkeys hang from a tree branch in Palo Verde National park

Glimpse of the fauna in Palo Verde. Photo credit: Alice Alonso

See a map of the instrumentation network within the Palo Verde National Park.

Conceptual representation of the Palo Verde National Park in the context of the Tempisque watershed system.

Conceptual representation of the Palo Verde National Park in the context of the Tempisque watershed system.

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Oct 17

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Unraveling the Effects of Dams in Costa Rica

Thirty years ago, in Costa Rica’s Palo Verde National Park, the wetlands flooded regularly and eco-tourists could view thousands of waterfowl. Today, invasive cattail plants cover portions of the wetland which has subsequently dried up and become colonized by hardwoods. Consequently, the number of birds has fallen dramatically.

Flocks of birds flying against a sunset

The number of birds on Palo Verde National Park has fallen dramatically. (Image: anywherecostarica.com)

Some people blame the dams built in the 1970s which introduced hydrological power and created a large irrigation district in the remote region. Dr. Rafael Muñoz-Carpena, Professor and University of Florida Water Institute Faculty Fellow and his research team are performing environmental studies on the wetlands, trying to unravel the effects of the dams and how to revert some of the damage. Rafael explains, “We have a situation where modern engineering brought about social improvements, helpful renewable resources, and irrigation for abundant food production. But the resulting environmental degradation threatens a natural region in a country that depends on eco-tourism.”

Birds in a river at Palo Verde National Park

“A vast network of mangrove-rich swamp, lagoons, marshes, grassland, limestone outcrops, and forests comprise the 32,266 acre Palo Verde National Park.” (Image and text: anywherecostarica.com)

Are The Dams Responsible?

Dr. Muñoz-Carpena says because of lack of historical data it’s difficult to untangle and separate all the factors that have caused the environmental degradation. He adds, “Thirty years ago Palo Verde National Park was part of a large wetland system which was important to all of Central America because it contained many endangered species and was a wintering ground for migratory birds from North America. The Palo Verde field station on the edge of the wetland, operated by the Organization of Tropical Studies (OTS), attracted birdwatchers and wetland scientists from all over the world.”

In the 1970’s, with international funding, a dam was built in the mountains to collect water from the humid side of Costa Rica in order to generate hydroelectric power. It was clean, abundant, and strategically important.  With the water transferred to the dry side of the country, a large irrigation district was created to not only produce important crops to the region like rice and beans, but to distribute the land among small parcel settlers.

Flock of birds in the grasslands at Palo Verde National Park

“Birding is the principal draw of visitors to the park.” (Image and text: anywherecostarica.com)

Over the years, however, the wetland area slowly degraded to the point where its Ramsar Convention wetland classification is under question. Rafael says that understanding the causes of the degradation, the impacts of the human system, and how the natural and human systems are linked, is the big question of his research, and there are many factors to consider. “The release of the water, ground and surface water (over)use, agriculture, human development, and a larger population are all factors that could contribute to this degradation. Everything compounds in the downstream coastal wetlands. In collaboration with OTS and other partner organizations and universities, we are trying to disentangle these different drivers.”

Grasslands and swamps with mountains in the background

Understanding the causes of the degradation, the impacts of the human system, and how the natural and human systems are linked, is the big question of this research. (Image: anywherecostarica.com)

A Lack of Historical Data

One of the challenges the researchers face is to gather a sufficient amount of temporal and spatial information about what happened in the past forty years.  There are no public repositories of data to tap, and the information is spotty and hard to access. Rafael says, “Thanks to the collaboration of many local partners, we have been able to gather enough information to stitch together a large database out of a collection of non-systematic studies. The biggest challenge is to harmonize data that has been collected by different people in non-consistent ways.” This large database now contains the best long-term record possible for key hydrologic variables: river flow, groundwater stage, precipitation, and evapotranspiration.

The team is also using remote sensing sources to try to obtain time-series data for land-use and vegetation change, and will have those data ground-truthed through instruments that are collecting similar time-series data. Rafael says, “The idea is to build a network that will allow us to overlap some of the previous data sources with our own, validate and upscale the ground data with remote sensing sources, enabling us to put together a detailed picture of what happened.”

Next Week:  Find out how the researchers established connectivity in such a remote area,  some of the problems associated with the research, and how the team has addressed those issues.

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Aug 22

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Do Soil Microbes Influence Plant Response to Heat Waves? (Part II)

Rachel Rubin, PhD candidate at Northern Arizona University and her team at Northern Arizona University are investigating the role soil microbes play in plant response to heat waves, including associated impacts to microbial-available and plant-available water (see part 1). Because heat waves threaten plant productivity, they present a growing challenge for agriculture, rangeland management, and restoration. Below are the results of Rachel’s experiments, some of the challenges the team faced, and the future of this research.

A herd of cows grazing in a pasture

Heat waves present a growing challenge for agriculture, rangeland management, and restoration.

Challenges

Rachel says the experiment was not without its difficulties. After devoting weeks towards custom wiring the electrical array, the team had to splice heat-resistant romex wire leading from the lamps to the dimmer switches, because the wires inside the lamp fixtures kept melting. Also, automation was not possible with this system. She explains, “We were out there multiple times a day, checking the treatment, making sure the lamps were still on, and repairing lamps with our multi-tools. We used an infrared camera and an infrared thermometer in the field, so we could constantly see how the heating footprint was being applied to keep it consistent across all the plots.”

Arizona Fescue plant

Arizona Fescue (image: wickipedia.com)

Some Grass was Heat Resistant

Rachel says her biggest finding was that all of the C4 grasses survived the field heat wave, whereas only a third of the Arizona Fescue plants survived. She adds that the initially strong inoculum effects in the greenhouse diminished after outplanting, with no differences between intact, heat-primed inoculum or sterilized inoculum for either plant species in the field. “It may be related to inoculum fatigue,” she explains, “the microbes in the intact treatment may have become exhausted by the time the plants were placed in the field, or maybe they became replaced, consumed, or outcompeted by other microbes within the field site”. Rachel emphasizes that it’s important to conduct more field experiments on plant-microbe interactions. She says, “Field experiments can be more difficult than greenhouse studies, because less is under our control, but we need to embrace this complexity. In practice, inoculants will have to contend with whatever is already present in the field. It’s an exciting time to be in microbial ecology because we are just starting to address how microbes influence each other in real soil communities.”

Grass going to seed in an open-air field

Diminished effects may be related to inoculum fatigue.

What’s In Store?

Now that the team has collected data from the greenhouse and from the heat wave itself, they have started looking at mycorrhizal colonization of plant roots, as well as sequencing of bacterial and archaeal communities from the greenhouse study. Rachel says, “It’s quite an endeavor to link ‘ruler science’ plant restoration to bacterial communities at the cellular level. I’m curious to see if heat waves simply reduce all taxa equally or if there is a re-sorting of the community, favoring genera or species that are really good at handling harsh conditions.”

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Aug 15

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Do Soil Microbes Influence Plant Response to Heat Waves?

Rachel Rubin, PhD candidate at Northern Arizona University, is interested in the intersection of extreme climate events and disturbance, which together have a much greater impact on plant communities. She and her team at Northern Arizona University are investigating the role soil microbes play in plant response to heat waves, including associated impacts to microbial-available and plant-available water.

Wheat with sun shining through it

Plants have a tight co-evolutionary history with soil microbes. It has been said that there is no microbe-free plant on earth.

Because heat waves threaten plant productivity, they present a growing challenge for agriculture, rangeland management, and restoration.

Can Soil Microbes Increase Heat Resistance?

Many plants maintain mutualistic associations with a diverse microbiome found within the rhizosphere, the region of soil that directly surrounds plant roots. These “plant growth-promoting rhizobacteria” and arbuscular mycorrhizal fungi provision limiting resources including water, phosphorus and nitrogen in exchange for photosynthetically derived sugars. However, we understand very little about whether extreme events can disrupt these interactions.

Tubes of layered dirt

Fig. 1. Fine roots exploring the inoculum that was added as a band between layers of potting mixture.

Rachel and her team exposed rhizosphere communities to heat stress and evaluated the performance of native grasses both in the greenhouse, and transplanted under an artificial heat wave. They hypothesized that locally-sourced inoculum (a sample of local soil containing the right microbes) or even heat-primed inoculum would help alleviate water stress and improve survival of native grasses.

The Experiments

Rubin started in the greenhouse by planting Blue Grama (Bouteloua gracilis, C4 grass) and Arizona Fescue (Festuca arizonica, C3 grass) and assessed their responsiveness to locally collected soil inoculum that had either been left intact, pre-heated or sterilized (Fig. 1). Rubin says, “We expected that our plants would benefit the most from having intact soil microbe communities. But, we were surprised to find very large differences between plant species. Blue Grama performed the best with intact inoculum, whereas Arizona Fescue performed better with pre-heated or sterilized soil”. This could mean that Blue Grama is more dependent on its microbiome, whereas Arizona Fescue engineers a rhizosphere that contains more parasitic microbes rather than mutualistic microbes. Rachel says that understanding this relationship is important for tailoring plant restoration projects to local conditions. Plants that exhibit high levels of mutualisms with their rhizosphere might require an extra inoculum “boost” in order to successfully establish in highly degraded soil, whereas we should not bother to inoculate plants that tend to harbor parasites within their rhizosphere.

Research plot using infrared sensors and METER soil water content and soil water potential sensors

Fig. 2. A heated plot in the foreground connected to infrared lamps, water content and matric potential sensors, and EM50 data loggers.

After the team studied these responses, they planted the grasses into a degraded section of a grassland and installed an array of 1000-Watt ceramic infrared lamps mounted on steel frames (Fig. 2) to address whether inoculation influenced plant performance and survival. With help from a savvy undergraduate electrical engineering major (Rebecca Valencia), Rubin simulated a two-week heat wave while monitoring soil temperature and moisture using water content and water potential sensors.  She also measured plant performance (height, leaf number and chlorophyll content) before, during, and after the event. Control plots had aluminum “dummy lamps” to account for shading.

An infrared photo of the expirement

An infrared photo, which is how Rachel determined that the heating footprint was evenly distributed on all the plants. The scale bar on the right is in degrees C.

Data obtained from soil sensors helped Rachel to measure heating treatment effects as well as rule out a potential cause for plant mortality: soil moisture. “Soil temperature was on average 10 degrees hotter in heated plots than control plots, but matric potential and soil water content were completely unaffected by heating. This tells us that the grasses died from reasons other than water stress– perhaps a top-kill effect.” Although growing concern over heat waves in agriculture is centered around accompanying droughts, this experiment demonstrates that heating can produce negative effects on some species even when water is in plentiful supply.

Next week:  Learn the results of Rachel’s experiments, some of the challenges the team faced, and the future of this research.

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Jul 25

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Which Factors Make Rain Gardens More Effective? (Part 2)

Scientists often evaluate Low Impact Development (LID) design by quantifying how much stormwater rain garden systems (cells) can divert from the sewer system.  But Dr. Amanda Cording and her research team want to understand what’s happening inside the cell in order to improve the effectiveness of rain garden design (see part 1).  Below are the results of their research.

Picture of yellow flowers

Deep rooted systems were found to have a much better ability to hold the soil in place and remove nutrients.

Key Findings

Cording says that some of her key findings were that the soil media and vegetation selection is absolutely crucial to the performance of these systems. Cording’s team looked at the root layering perspective in three dimensions and found that deep rooted systems were found to have a much better ability to hold the soil in place and remove nutrients throughout the life cycle of the cell. The more surface area the roots covered, the more pollutants the cell would remove.  She adds, “Cells with deep-rooted plants were found to be resilient during increased precipitation due to climate change, did well at retaining peak flow rates, and performed well at removing total suspended solids and nutrients predominantly associated with particulates.”  Labile nutrients, Cording says, were a completely different story. She says the bioretention systems have to be specifically designed to remove  those nutrients through sorption (P) and denitrification (N).

Researcher holding dirt in cupped hand

Compost was found to have a negative effect on water quality.

Compost, which is often used as an organic amendment in the soil media to help remove heavy metals and provide nutrients for the plants, was found to have a negative effect on water quality overall, due to the high pre-existing labile N and P content. She says, “It’s intuitive, but at the same time, a lot of these systems are designed based on bloom time and color, and not necessarily on the physical and chemical pollutant removal mechanisms at work.”

Green algal bloom in a freshwater lake

Green algal bloom in a small freshwater lake in New Zealand. (Image: Massey University)

What Lies Ahead?

Cording also tested a proprietary bioengineered media in two of her cells which was designed to remove the phosphorous that causes algal blooms in the rivers and streams.  She says, “It did a phenomenal job. There was very little phosphorous coming out compared to the traditionally-designed retention cells.  Cording, who is now based in Honolulu and works for an ecological engineering company called EcoSolutions, is looking at how to use natural, highly-leached iron rich soils, to get a similar amount of phosphorous removal, and how bioretention can be designed with anoxic storage zones to remove nitrate via denitrification. She says, “These nutrients can be easily removed from stormwater with a little conscious design effort and a splash of chemistry.”

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Jul 15

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Which Factors Make Rain Gardens More Effective?

Low Impact Development (LID) is an approach to development (or re-development) that mimics pre-development hydrology and uses ecological engineering to remove pollutants in stormwater and wastewater so it can be reused or replenish groundwater supplies. Examples of LID features include porous pavement, constructed wetlands, green roofs, and rain gardens. LID stormwater bioretention systems such as rain gardens have been proven to work, but are they designed as effectively as they could be?  Dr. Amanda Cording (formerly at the University of Vermont) and her team wanted to understand which design factors would make rain gardens more resilient, increase phosphorus adsorption, and reduce nitrates.

Rain Garden aerial view

Cording and her team wanted to understand what was happening inside bioretention cells.

What’s Happening Inside?

Scientists often evaluate LID design by quantifying how much stormwater the systems (cells) can divert from the sewer system.  But Cording and her team wanted to understand what was happening inside the cell.  They wondered which types of soil media and infrastructure would optimize a stormwater bioretention system’s ability to improve water quality.  She says, “We wanted to gather water quality information coming in and going out of the system. I designed inflow and outflow monitoring infrastructure to measure nutrient and sediment pollution.”   The system monitored pollution by sampling stormwater runoff from a paved road surface before and after it went through bioretention cells. Each cell was constructed with different features to test the influence of vegetation and soil media on pollutant removal capabilities.

Bioretention cells diagram

Bioretention cells at the newly constructed Bioretention Laboratory at the University of Vermont.

Methods Used

To understand what was happening within eight bioretention cells at the newly constructed Bioretention Laboratory at the University of Vermont, Dr. Cording and her team investigated the mechanisms influencing greenhouse gas emissions and nutrient transformations at various depths in engineered soil media. In addition to using her own monitoring infrastructure, Dr. Cording used soil moisture sensors to measure water content within the soil media. She says, “I was comparing different vegetation treatments while simulating increased precipitation due to climate change in the Northeast.  I put the soil probes in at 5 cm and 61cm, one on top of the other.  Then I looked at the way the EC and the volumetric water content (VWC) changed prior to a storm event, during a storm event, and after a storm event.”

Garden in bloom in the rain

One of the team’s bioretention cells at the University of Vermont.

Cording says the EC and VWC sensors allowed them to get a general sense of what was happening inside the cell over time.  She adds, “I used the data when I needed to know more of the story, such as how the conductivity at the surface compared to other depths so we could see if the nutrients in the soil were migrating, and how much was moving down.  We were also able to use the sensors to compare the VWC around the roots of different vegetation types. It provided a lot of insight into the dynamic world that exists below the soil surface.”

Next Week:  Read about the team’s key findings and what lies ahead for this research.

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Jul 8

Improving Drought Tolerance in Soybean

Limited water availability is a significant issue threatening the agricultural productivity of soybean, reducing yields by as much as 40 percent. Due to climate change, varieties with improved drought tolerance are needed, but phenotyping drought tolerance in the field is challenging, mainly because field drought conditions are unpredictable both spatially and temporally.  This has led to the genetic mechanisms governing drought tolerance traits to be poorly understood. Researcher Clinton Steketee at the University of Georgia is trying to improve soybean drought tolerance by using improved screening techniques for drought tolerance traits, identifying new drought tolerant soybean germplasm, and clarifying which genomic regions are responsible for traits that help soybeans cope with water deficit.

Seedlings sprouting

Researchers are trying to improve soybean drought tolerance by using better screening techniques for drought tolerance traits.

Which Traits Are Important?

Clinton and his colleagues are evaluating a genetically diverse panel of 211 soybean lines in two different states, Kansas and Georgia, for over two years to help him accomplish his research objectives. These 211 lines come from 30 countries and were selected from geographical areas with low annual precipitation and newly developed soybean lines with enhanced drought-related traits, along with drought susceptible checks. The researchers are looking at traits such as canopy wilting.  Some plants will take a few days longer to wilt, allowing these plants to continue their photosynthetic ability to produce biomass for seed production. Other traits that he is interested in evaluating are stomatal conductance, canopy temperature with thermal imaging, relative water content, and carbon isotope discrimination.

Beans growing on a stalk

The scientists want to monitor traits such as canopy wilting.

Use of Microclimate Stations to Monitor Environmental Conditions

Clinton says to make selection of drought-tolerant lines easier and more predictable, knowledge of field environmental conditions is critical. He says, “You can phenotype all you want, but you need the true phenotype of the plant to be observed under real drought conditions so you can discover the genes for drought tolerance and improve resistance down the line in a breeding program.”

In addition to soil moisture sensors, the team used microclimate weather stations to help monitor water inputs at their two field research sites and determine ideal time periods for phenotyping drought-related traits.  Steketee says, “We put microenvironment monitors in the field next to where we were growing our experimental materials.  Both locations use those monitors to keep an eye on weather conditions throughout the growing season, measuring temperature, humidity, and precipitation. Since we could access the data remotely, we used that information to help us determine when it was time to go out to the field and look at the plots. We wanted to see big differences between soybean plants if possible, especially in drought conditions. By monitoring the conditions we could just go back to our weather data to show we didn’t get rain for 3 weeks before we took this measurement, proving that we were actually experiencing drought conditions.”

Soybeans

The team identified some lines that performed well.

Results So Far

Though 2015 wasn’t a great year for drought in Georgia, Clinton says there was a period in late July when he was able to measure canopy wilting, and they identified some lines that performed well.  He says, “We compared our data to the data collected by our collaborator in Kansas, and there are a few lines that did well in both locations.  Hopefully, another year of data will confirm that these plants have advantageous drought tolerance traits, and we’ll be able to probe the advantageous traits out of those lines and integrate them into our breeding program.”

Future Plans

The team will use what’s called a genome-wide association study approach to identify genomic regions responsible for drought tolerance traits of interest. This approach uses phenotypic information collected from the field experiments along with DNA markers throughout the soybean genome to see if that marker is associated with the trait they are interested in.  If the scientists find the spot in the genome that is associated with the desired trait, they will then develop genomic tools to be used for selection, integrate that trait into elite germplasm, and ultimately improve the drought tolerance of soybeans.

See weather sensor performance data for the ATMOS 41 weather station.

Explore which weather station is right for you.

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May 27

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Are Biodegradable Mulches Actually Better for the Environment?

Henry Sintim, PhD student at Washington State University, is investigating whether biodegradable mulches are, in fact, what they claim to be.

Plant row farm with dirt between each row

Application of plastic mulches conserves water, and helps in weed, pest, and disease control.

He and his research team want to understand what leaches into the soil as the mulches degrade and which ones perform as well as polyethylene-made plastic mulches (PEs) at weed, pest, and disease control.

Plastic Mulch

Application of plastic mulches in agriculture is a common practice by specialty crop producers worldwide. It conserves water, and helps in weed, pest, and disease control, subsequently improving crop yield and quality. Because PE is durable and does not degrade in the soil, you cannot leave it in the field, which ultimately leads to the question of disposal.  When PE is buried in the field, it becomes contaminated with soil and can’t be recycled but instead requires transport to a landfill, increasing production costs. Another problem arises when landfill facilities are not available. When this is the case, growers stockpile PE on their farm, where the rain can wash the mulch down to streams and water bodies. Henry Sintim and his team are investigating whether or not biodegradable plastic mulches (BDMs) could be a viable alternative.

Researchers digging a site up for installation

The team installs a lysimeter beneath the mulches.

Biodegradable Alternatives

Substituting PE with BDM could alleviate the need for disposal. However, Sintim says the potential impact on agricultural soil ecosystems needs to be assessed before adopting biodegradable mulch for field use. For instance, do biodegradable mulches really degrade?  Sintim explains, “By BDM, we mean it is plastic mulch, but it has been made from pure or partial biobased materials. Though there are plastic mulches advertised as biodegradable, none have actually been proven to biodegrade, so the team is examining degradation of different commercial BDM types over time. They have also included an experimental BDM, in which the constituents were specified by the team.”

Sintim is monitoring the degradation of BDM by assessing the material properties and measuring the particle size and surface area via photography: digitizing and analyzing them using Image J software.

Researchers standing at an installation getting data

There are indications that some of the BDMs are performing well.

How Well Do the Mulches Compare?

Sintim also wants to find out how well BDMs maintain microclimate in comparison to PE. Since soil temperature and moisture content are important parameters that govern chemical reaction rates and microbial activity, and are likely to vary among the different BDM treatments, he is monitoring soil moisture dynamics using soil moisture and temperature sensors installed at 10 cm and 20 cm depths. In addition, the team has installed sensors directly underneath the mulches to measure surface temperature and light penetration. Reduction of light penetration is the attribute that helps plastic mulches to control weeds. The team is also assessing soil quality using the USDA Soil Quality Test Kit.  

Sintim says so far one of the commercial BDMs and the experimental BDM had the same yield performance as PE.  He adds, “We don’t have final results yet, and there are a lot of variables that could come into the picture. But I will say there is an indication that some of the BDMs are performing well.”

Next week:  Find out how Sintim will determine what’s leaching into the soil and another alternative for polyethylene plastic mulch.

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Apr 18

Climate Change, Genetics, and the Future World

Climate change scientists face a particular challenge— how to simulate climate change without contributing to it. Paul Heinrich, a Research Informatics Officer associated with the Southwest Experimental Garden Array (SEGA) remembers looking at the numbers for a DOE project that would have used fossil fuel to measure forests’ response to temperature change. “It would have been very, very expensive in fossils fuels to heat a hectare of forest,” he says.

The alternative is, “to use elevation change as a surrogate for climate change so we could do climate change manipulations without the large energy costs.”

SEGA Vegetation Zones diagrams

An overview of the SEGA sites using elevation change as a surrogate for climate change. For more information on these sites, visit http://www.sega.nau.edu/. Photo credit Paul Heinrich

By monitoring organisms across a temperature gradient it is possible to identify genetic variation and traits within a species that could contribute to a species survival under projected future climates.

Control and Monitoring Infrastructure

SEGA is an infrastructure project started in 2012 after researchers at Northern Arizona University’s Merriam-Powell Center for Environmental Research were awarded a $2.8 million dollar NSF grant with a $1 million match from NAU. Consisting of ten fenced garden sites for genetics-based climate change research, SEGA is set on an elevation gradient from 4000 to 9000 feet in the Southwestern United States. Each SEGA site has an elaborate data collection and control system with meteorological stations and site-specific weather information. Custom-engineered Wireless Sensing Actuating and Relay Nodes (WiSARDs) send data packets to a hub which then send the data back to a centralized server.

Because there is inherent moisture content variability from site to site, volumetric water content and soil water potential sensors have been installed to monitor and maintain moisture levels. If there is a change in soil moisture at one site, soil sensors will detect the difference. Software on the server notes the difference and sends a signal to the other sites, turning on irrigation until the soil moisture matches across sites.

SEGA Cyberinfrastructure Major Components diagram

An illustration of SEGA’s cyberinfrastructure and data management system. Photo credit Paul Heinrich.

Having such an elaborate infrastructure creates an opportunity for researchers looking to conduct climate change research. By offering access to the pre-permitted SEGA sites, the hope is that research will generate much-needed data for climate projections and land management decisions.

When asked if the data stream was overwhelming to manage Heinrich said, “Well, not yet. We are just getting started. The system is designed for what SEGA is expected to look like in ten years, where we expect to have 50 billion data points.”

Research Considerations

Climate change projections show temperatures increasing rapidly over the next 50 to 100 years, bringing drought with it. The impact of these changes will be dramatic. Temperature and drought tolerant species will survive, those that are not will die, drastically changing the landscape in areas that are currently water stressed. Pests like the pine beetle and invasive species like cheatgrass will do well in a drier environment where water-stressed natural species will not be able to compete.

Red canyon called Soap Creek AZ from an Aerial view

Soap Creek, AZ from above. With climate change projections it is likely that more land will become marginal. Photo credit Paul Heinrich.

“Foundational species,” or species that have a disproportionate impact on the ecosystem, are the primary focus of the research efforts at SEGA sites. These are the species that drive productivity, herbivore habitat, and carbon fixation in the ecosystem. Unlike forests in other parts of the United States, forests in the Southwest can be dominated by one or two species, which makes potential research subjects easier to identify.

Genetic Variance

Amy Whipple, an Assistant Professor in Biology and the Director of the Merriam-Powell Research Station who oversees the day-to-day activities at SEGA, has been conducting some of her own research at the garden sites. Whipple has studied Piñon Pine, Southwestern White Pine, and has a proposal to study Cottonwood in process.

Whipple says that models currently suggest that Piñon Pine will be gone from Arizona within the next 50 years, adding that the models do not take into account possibilities for evolution or genetic variance that might help the Piñon survive. Her research is largely asking, will trees from hotter, drier locations have a better chance of surviving climate change? “We’re trying to do that with a number of different species to look for ways to mitigate the effects of climate change in the Southwest.”

Researchers documenting a Piñon Pine

Researchers documenting a Piñon Pine. Photo credit Paul Heinrich.

In some of her research on Piñon Pine, it was discovered that four different species were grouped morphologically and geographically from southern Arizona to Central Mexico. While this suggests that the divergence of species has occurred, it also suggests a low migration rate for these tree species. Migration rates of drought and temperature tolerant species is an important consideration when modeling for a future climate. If the migration of genetically adapted species cannot keep up with climate, the land could become marginal as a foundational species dies off.

Climate Change Predictions and Considerations

In the Southwest, there are entire forests that could become grassland in 50 years because the genetic characteristics of the foundational species currently in those regions will not adapt to higher temperatures and drought stress. But what does this mean from a land management perspective?

Ponderosa pine tree hanging off the side of a rocky cliff in the desert

Ponderosa pine trees, a foundational species in some area of the Southwestern United States.

Environmental conservationists maintain that we should protect the unique species that are in a place and that introducing other organisms or genetic material would be an ethical violation. Environmental interventionists make the argument that climate change has been caused by humans, so we have lost the option of remaining bystanders.

Research, Land Management and Policy

Paul Heinrich says that the route we take to manage the land will depend on our end goals. “Places that have trees now, if you want them to have trees 50 years from now, you are going to have to do something about it. The trees that are on the landscape right now are locally adapted to the past climate. They are not necessarily adapted to the future climate. They are probably maladapted to the future climate.”

To be clear, SEGA’s goal is not to promote or implement assisted migration. Instead, Amy Whipple says, SEGA can test what the effects of assisted migration might be. “In a smaller experimental context, we’re asking: how will these plants do if we move them around? What will happen to them if we don’t move them around?’” The goal is to provide decision makers with the data they need to make informed decisions about how to manage the land.

Image of a Meadow with trees in the distance and a set of mountains

The Arboretum Meadow in Flagstaff, AZ. Home of one of the SEGA research sites. Photo credit Paul Heinrich.

Whipple’s own view is that we may no longer have the option of doing nothing. “Unless major changes are made for the carbon balance of the planet, keeping things the same is not a viable option. Managing for a static past condition is not viable anymore.”

Remaining Questions

Both Heinrich and Whipple acknowledge that these are inherently difficult questions. Ultimately the public and land managers must make these decisions. In the meantime, data from SEGA research may help ensure better predictions, better decisions, and better outcomes.

To find out more about conducting your own climate change research using SEGA go to: http://www.sega.nau.edu/use-sega. 

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