Skip to content

Posts tagged ‘Agriculture’

Sep 4

1 Comment

Examining Plant Stress using Water Potential and Hydraulic Conductivity

Many scientists rely on water potential alone to measure plant water stress.  Leo Rivera, a METER soil scientist, shows how a two-pronged approach, using hydraulic conductivity as well as water potential, can make those measurements more powerful.  

Green tomato plant with three bright red tomatoes

Measuring hydraulic conductivity in nursery plants shows why plants are stressed.

Soil moisture release curves can give you incredible detail about water movement, allowing you to understand not only that plants are stressed, but WHY they are not getting the water they need.

Recently, we ran into a mystery where this method was useful.  Growers at a Georgia nursery noticed that plants growing in a particular soilless substrate were beginning to show signs of stress at about -10 kPa water potential, which is still really wet. They wanted to know why.

We decided to create the unsaturated hydraulic conductivity and soil moisture release curves  for the substrate (using the Wind Schindler technique [HYPROP lab instrument]) and found that it had a dual porosity curve: essentially, a curve with a “stair step” in it. The source of the “stair step” can be explained by considering the substrate, which was made up of bark mixed with some other fine organic materials. In the bark material there were a lot of large and small pores, but no medium-sized pores (this is called a “gap-graded” pore size distribution).  This gap in the pore size distribution reduced the unsaturated hydraulic conductivity and caused the stress. Even though there was available water in the soil, it couldn’t flow to the plant roots.

Blue crates with lots of green nursery seedlings in each crate

Nursery seedlings

That would have been pretty hard to understand without detailed hydraulic conductivity and soil moisture release curves—curves with more detail than most traditional techniques can provide.  Our measurements showed that unsaturated hydraulic conductivity can have a major effect on how available water is to plants.  Our theory about the soilless substrate was that as the roots were taking up water, they dried the soil around them pretty quickly. In a typical mineral soil, the continuous pore size distribution would allow water to flow along a water potential gradient from the surrounding area to the soil adjacent to the roots. In the bark, the roots dried the area around them in the same way, but the gap in pore size distribution created low hydraulic conductivity and prevented water from moving into the soil adjacent to the roots. This caused plants to start stressing even though the substrate was still quite wet. 

We were pretty excited about this discovery. It shows that water potential, though critical, may not always tell the whole story. Using technology to measure the full soil moisture release curve and the hydraulic conductivity in one continuous test, we discovered the real reason plants were wilting even when surrounded by water. In the past, it took three or four different instruments and several months to take these measurements.  We can now do it in a week. For more information about creating these kinds of curves, check out the app guide:  “Tools and Tips for Measuring the Full Soil Moisture Release Curve.”

Download the “Researcher’s complete guide to water potential”—>

Download the “Researcher’s complete guide to soil moisture”—>

Get more information on applied environmental research in our

LinkedInMessengerRedditThreadsCopy

Aug 22

Author Interview: Soil Physics with Python

The new book Soil Physics with Python: Transport in the Soil-Plant-Atmosphere System written by Dr. Marco Bitteli, Dr. Gaylon S. Campbell, and Dr. Fausto Tomei presents concepts and problems in soil physics as well as solutions using original computer programs.

Picture of the cover of the book "Soil Physics with Python" by Marco Bittelli, Gaylon S. Campbell, and Fausto Tomei

Soil Physics with Python

In contrast to the majority of the literature on soil physics, this text focuses on solving, not deriving, differential equations for transport. Numerical methods convert differential equations into algebraic equations, which can be solved using conventional methods of linear algebra.  Here, Dr. Campbell interviews about this update to his classic book Soil Physics with BASIC.

Why did you write the first book, Soil Physics with BASIC?

Soil physics classes were always frustrating for me because you would spend time writing fancy equations on the chalkboard, and in the end, you couldn’t do anything with them.  You couldn’t solve any of the problems because, even though they involved difficult mathematics, the math was still so simplified that it didn’t apply to anything that went on in nature.

When I taught my first graduate soil physics class, I determined that we were going to be able to do something by the time we finished.  Luckily, in the mid-1970s, personal computers were being developed, and I realized this was the answer to my problem.  Numerical methods could solve any problem with any geometry in it.  It wasn’t limited to problems that fit the assumptions needed to derive a complex differential equation.  I could write computer programs that simplified the mathematics for the students and teach them how to solve those problems using numerical methods.  By the end of the semester, my students would have a set of tools that they could use to solve problems in the real world.  

Did this book come from class notes or some other source?  

I wrote two textbooks and they both came the same way.  When I first started teaching, I had a textbook that was inadequate, so I began writing notes of my own and handing them out to the students.   After two years, I turned these notes into An Introduction to Environmental Biophysics.  Soil Physics with BASIC came about by the same process, but I enlisted the help of my daughter, Julia, to type it up. It was in the early days of word processing so entering equations was quite difficult.  It all went well for her until chapter eight, which was a nightmare of greek symbols. After she finished slogging for days through the material, we somehow lost the chapter.  She retyped it, and we lost it again, making her type it three times!  We didn’t have spreadsheets then either, so the figures were all hand-drawn by my daughter, Karine.

Red soil in the desert with trees and brush around

Marco [Bitteli] has added two and three-dimensional flow problems, so you can model whole landscapes and water behavior in an entire terrain.

What does Soil Physics with Python add to the conversation?

First, it updates the programming language.  BASIC was a language invented at Dartmouth and intended to be a simple teaching language.  It was never supposed to be a scientific computer language.  Python (13:26.) is a newer language, and there are many open source programs for it, making it a better language to use for science.

Secondly, the old book had one-dimensional flow problems in it for the most part, but Marco [Bitteli] has added two and three-dimensional flow problems, so you can model whole landscapes and water behavior in an entire terrain.

In addition, Dr. Bitteli describes the process and analysis of soil treated as fractals as well as soil image analysis.  There are a lot of extensions and updates that weren’t in the original book.  

Will it be accessible across all disciplines?

To some extent, different disciplines speak different languages.  A soil physicist talks about water potential, and a geotechnical engineer talks about soil suction. Thus, there may be some translation of discipline-specific terms, but it’s intended to be a book that people in the plant sciences can use along with people in the soil sciences.

Dr. Marco Bitteli earned his PhD at Washington State University and was Dr. Campbell’s former student.  This book is a product of their continued collaboration. Dr. BBitteli is now a professor at University of Bologna, the oldest university in operation in the world.  Soil Physics with Python  is available at Amazon.com.

Download the “Researcher’s complete guide to water potential”—>

Download the “Researcher’s complete guide to soil moisture”—>

Get more information on applied environmental research in our

LinkedInMessengerRedditThreadsCopy

Aug 14

2 Comments

The Potential of Drones in Research

Someday soon,  multi-rotors will execute pre-programmed flight paths over several hundred research plots collecting daily data and sending it back to a computer while researchers sip their morning coffee.  Researchers and growers won’t need to know anything about flying: the drones will fly themselves.  This is the dream.

One UAV (unmanned air vehicle) industry leader at the above drone demonstration commented, “The truth is that this is where agriculture (and research) is going, and I don’t mean ‘Tomorrowland’ going–I mean it’s pretty much there.  The only thing that’s holding us back is a permit from the FAA for autonomy, and that’s because the FAA is slowly backing into this UAV piece because we have the busiest general aviation sky in the world. But really, what you should have in your mind is multiple units operating with a single operator in a control vehicle.”  The above UAV was extensively tested in California’s NAPA valley with results soon to be published online.

In this blog, a METER scientist and an instrumentation engineer give their perspectives on what needs to happen before drones reach their full research potential.  

Drone hexacopter flying against a blue sky

Drone Hexacopter

What are the advantages of drones for researchers?

Dr. Colin Campbell, research scientist-

One of the biggest challenges of work in the field is variability: low spots, high spots, sandy soil, clay soil, hard pans beneath the surface in some areas and not in others.  This results in highly variable performance in crops.  In addition to that, even when you have good homogeneity in a field, you might have differences due to irrigation or rainfall. If we want to improve agriculture, one thing that we have to do is be able to come out with better tools to be able to visualize the field in more than a single dimension. In order to do this right now, students go out and take plant measurements all day, every day, all summer long. The advantage of a drone is that you could do flyovers of a field, monitoring the traits that you’re interested in using reflectance indices that would normally take days of work.

What are the obstacles to progress?

Greg Kelley, mechanical engineer, and drone hobbyist-   

Recently, the FAA has come out with a set of guidelines for the industrial use of drones:  flying machines have to stay under a certain ceiling (500 ft; 150 m), and they have to be flown in the line of sight of the operator.  The naive thing about those policies is: how much control does the operator have over the drone anyway?  It used to be that with your remote control, you were moving the control surfaces (flaps, rudder, etc) on the aircraft, but this is changing.  The onboard computer performs things like holding a stable altitude, maintaining a GPS location, or auto-stabilization (it keeps the aircraft level, even when a gust of wind comes).  Those are degrees of control that have been taken away from the operator. Thus, according to the level of automation that the operator has built into the system, he may not be in direct control at all times. In fact, these machines are being developed so that they can fly themselves. From my perspective, the FAA regulations are going to have to evolve along with the automation of drones in order to allow the development of this technology in an appropriate way.

Drone with eight rotors sitting on a landing pad

Drone with eight rotors.

What needs to happen before drones reach their full potential?

Dr. Colin Campbell–  

Even if we get the flexibility required with drones, we’ve got to get the right sensor on the drone. On the surface, this seems relatively simple.  Sensors to measure spectral reflectance are available in a package size that should easily mount on a drone platform. But, there are still many challenges.  First, current spectral reflectance sensors make a passive reflectance measurement, meaning we’re at the mercy of the reflected sunlight.  Clouds, sun angle, and leaf orientation, among other things, will all affect the measurement. There are several groups working on this (just search “drone NDVI” on the internet), but it’s a difficult problem to solve.  Second, drones create a spectral reflectance “map” of a field that needs to be geo-referenced to features on the ground to match measurements with position.  Once data are collected, the behavior of “plot A” can only be determined by matching the location and spectral reflectance of “plot A.”  Different from the first challenge, this is more related to programming than science but is still a major hurdle.

Despite these challenges, drones promise incredible benefits as an agricultural and environmental measurement tool. As one industry leader at the drone demonstration put it, “the complexity of the problems that agriculture faces and the opportunities for efficiencies are vast.  It will require ongoing engagement, next year and the year after that. There are a lot of questions to be answered and the efficacy is yet to be determined, but it’s exciting to watch the UAV helicopter and where it’s going.”  Both Campbell and Kelley agree that significant advances will be made within the next few years.

Read about an ROI calculator that’s been created to help growers quantify whether the benefits of using a drone will exceed their costs.

Download the “Researcher’s complete guide to soil moisture”—>

Get more information on applied environmental research in our

LinkedInMessengerRedditThreadsCopy

Aug 7

New Medium Scale Soil Moisture Measurement Technique

Between dielectric soil moisture sensors with a volume of influence measured in liters and remote sensing systems which measure soil moisture on the scale of kilometers, there is a gap—a gap Dr. Larry Murdoch of Clemson University has been working to fill. In this post, read about the DELTA (Displacement Extensometer for Lysimetric Terrain Analysis), an instrument that measures water content measurements over an area with a 25 m radius.

Close up picture of cracked and dried soil

Dr. Murdoch became interested in how much water content was in the vadose zone (the unsaturated soil above the water table). He wondered if he could use a strain measuring technique to quantify it.

A New Idea:

Dr. Murdoch was a graduate student in structural geology and geomechanics in the mid-1980s, working on the mechanics of hydraulic fractures in soil.  He developed techniques for environmental “fracking” to clean up contaminated soil, long before the recent applications by the oil industry that have caused fracking to become a household word.  Fracking causes movements in soil, and Dr. Murdoch developed methods for measuring those movements in order to monitor fracture displacement. This led to work on sensitive borehole extensometers that could measure small strains in rock during well testing.

In the course of his hydrology work, Dr. Murdoch became interested in how much water content was in the vadose zone (the unsaturated soil above the water table). He wondered if he could use the strain measuring technique to quantify it.  He decided to bore a hole into the vadose zone and insert a simplified extensometer device that could measure the strain as the soil expands and contracts.  This would allow him to gauge the weight change of the overburden.  Then, because other mass changes are relatively minor compared to the water in the soil, that weight change would enable him to determine water content.

Since soil compresses more than bedrock, Dr. Murdoch developed a method where he inserted two anchors and cylinders that are pressed up against the soil borehole.  In the middle of these cylinders is a fiberglass rod held tight by the bottom anchor which is able to move inside the top anchor.  The anchors move up and down from the stress on the soil, and this movement is transferred to the rod where it can be measured with a high-resolution displacement transducer.

Diagram of the Delta (Displacement Extensometer for Lysimetric Terrain Analysis)

Diagram of the DELTA (Displacement Extensometer for Lysimetric Terrain Analysis)

Dr. Murdoch’s device is so sensitive that when it is buried 6 m, it will register clear strain signals as his student walks over it. The weight of a person causes around 50 nanometers of displacement at the Clemson Field site, but the instrument itself can resolve displacement approaching 1 nanometer. And the diameter of measurement on the surface is about 4 times the depth.  So if you install the system at 7m, you’d be measuring about a 25 m diameter circle on top.

Like almost all other water content techniques, the challenge is removing all other confounding factors that affect the measurement. It has been said that all sensors are temperature sensors first.  Not surprisingly, one thing that causes errors in the system is temperature, though Dr. Murdoch’s team has dealt with that by getting the system deep in the soil and putting the electronics near it so the temperature change is small.  Barometric pressure also produces cyclical loading of soil mass and requires correction over a range of periods. And, since the calculation of water content requires an estimate of the soil elasticity, changes in soil moisture also may affect the measurement. Considerable work has been done and significant progress has been made in dealing with these and other issues with the extensometer approach.

picture of a field with a barn in the distance and the ski orange and grey

An advantage of the system is its ability to be buried. In order to plow, for example, all you have to do is pull the sensor up, take off the top plastic casing, and cap it, and the grower can drive a plow over the top.

Strengths:

The amazing thing is that Dr. Murdoch’s system can resolve less than a millimeter of rain water falling on the soil surface, and it can match trends over time. In addition, you can easily calibrate the system by getting your 190-pound student to walk over the top of it and then checking that the compressibility of the soil matches that weight.

Another advantage of the system is its ability to be buried.  In order to plow, for example, all you have to do is pull the sensor up, take off the top plastic casing, and cap it, and the grower can drive a plow over the top. Finding the installation can be challenging, so it must be located by precision GPS or survey equipment prior to burial. But, if done correctly, the site can be monitored for long periods of time.

Though not yet a final technology, the Delta extensometer did correlate well with point measurements of water content and shows a lot of promise. The instrument was developed with funding from the National Science Foundation. Colby Thrash, a grad student at Clemson, has done much of the recent work. Dr. Murdoch’s team will publish a paper describing the technique soon in Water Resources Research.

Download the “Researcher’s complete guide to soil moisture”—>

Get more information on applied environmental research in our

LinkedInMessengerRedditThreadsCopy

Jul 11

Great Science Reads: What our Scientists are Reading

We asked our scientists to share the great science reads they’ve perused recently.  Here’s what they’ve been reading:

Open book with Highlighter and Glasses on top of it

Letters to a Young Scientist by E.O. Wilson

Edward Wilson's book "Letters To A Young Scientist"

Steve Garrity: E.O. Wilson is a leader in the science of biology. This book is a simple read. What I like most about it is that it very effectively conveys Dr. Wilson’s passion for science. His thoughts on what it takes to be a successful scientist resonated with me the most.  In describing what it takes to be a successful scientist, E.O. Wilson says that being a genius, having a high IQ, and possessing mathematical fluency are all not enough. Instead, he says that success comes from hard work and finding joy in the processes of discovery. Dr. Wilson gets specific and says that the real key to success is the ability to rapidly perform numerous experiments. “Disturb nature,” he says, “and see if she reveals a secret.” Often she doesn’t, but performing rapid, and often sloppy, experiments increases the odds of discovering something new.

Out of the Scientist’s Garden by Richard Stirzaker

Picture of the cover of "Out Of The Scientist's Garden- A Story Of Water And Food"

Lauren Crawford: “Richard Stirzaker is a scientist out of Australia committed to finding tools to make farming easier and more productive in third world countries.  I love how he talks about what happens when he uses water from his washing machine on his garden and the unanticipated effects: what does the detergent do to the fertilizers and the soil properties?  It’s a scientific view of how a garden works.”

Introduction to Water in California by David Carle

The cover of the book "Introduction To Water In California" by David Carle

Chris Lund: “This is a great introduction to California’s water resources, from where the water comes from to how it is used….particularly relevant today given California’s ongoing drought and the hard choices California faces as a result.”

The Drunkard’s Walk:  How Randomness Rules our Lives, by Leonard Mlodinow

A picture of the cover of the book "The Drunkard's Walk- How Randomness Rules Our Lives" by Leonard Mlodinow

Paolo Castiglione:  “The Drunkard’s Walk’s beginning quote perfectly reflects the author’s thesis: “In God we trust. All others bring data!”. I enjoyed the author’s discussion on how the past century was strongly influenced by ideologies, in contrast to the present one, where data seems to shape people’s actions and beliefs.”

Chapter 13 of An Introduction to Environmental Biophysics, by Gaylon Campbell

A picture of the cover of the book "An Introduction To Environmental Biophysics" by Gaylon S. Campbell and John M. Norman

Colin Campbell:  “Because of teaching Environmental Biophysics class, all my focus has been on reading An Introduction to Environmental Biophysics.  And, although I’ve read it too many times to count, I finally had a chance to study the human energy balance chapter (13) in depth, which was amazing.  The way humans interact with our environment is something we deal with at every moment of every day; often not giving it much thought. In this chapter, we are reminded of the people of Tierra del Fuego (Fuegians) who were able to survive in an environment where temperatures approached 0 C daily, wearing no more than a loincloth. Using the principles of environmental biophysics and the equations developed in the chapter, we concluded that the Fuegian metabolic rate had to continuously run near the maximum of a typical human today. The food requirements to maintain that metabolic rate would be somewhere between the equivalent of 17 and 30 hamburgers per day (their diet was high in seal fat).  You can read more about the Fuegians here.”

Download the “Researcher’s complete guide to soil moisture”—>

Get more information on applied environmental research in our

LinkedInMessengerRedditThreadsCopy
Newer Entries »