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Posts from the ‘Plant Genetics’ Category

Top Five Blog Posts in 2016

In case you missed them the first time around, here are the most popular Environmental Biophysics.org blog posts in 2016.

Lysimeters Determine if Human Waste Composting can be More Efficient

Top five blog posts Environmental biophysics

In Haiti, untreated human waste contaminating urban areas and water sources has led to widespread waterborne illness.  Sustainable Organic Integrated Livelihoods (SOIL) has been working to turn human waste into a resource for nutrient management by turning solid waste into compost.  Read more

Estimating Relative Humidity in Soil: How to Stop Doing it Wrong

Top five blog posts Environmental biophysics

Estimating the relative humidity in soil?  Most people do it wrong…every time.  Dr. Gaylon S. Campbell shares a lesson on how to correctly estimate soil relative humidity from his new book, Soil Physics with Python, which he recently co-authored with Dr. Marco Bittelli.  Read more.

How Many Soil Moisture Sensors Do You Need?

Top five blog posts Environmental biophysics

“How many soil moisture sensors do I need?” is a question that we get from time to time. Fortunately, this is a topic that has received substantial attention by the research community over the past several years. So, we decided to consult the recent literature for insights. Here is what we learned.

Data loggers: To Bury, or Not To Bury

Top five blog posts Environmental biophysics

Globally, the number one reason for data loggers to fail is flooding. Yet, scientists continue to try to find ways to bury their data loggers to avoid constantly removing them for cultivation, spraying, and harvest.  Chris Chambers, head of Sales and Support at Decagon Devices always advises against it. Read more

Founders of Environmental Biophysics:  Champ Tanner

Top five blog posts Environmental biophysics

Image: http://soils.wisc.edu/people/history/champ-tanner/

We interviewed Gaylon Campbell, Ph.D. about his association with one of the founders of environmental biophysics, Champ Tanner.  Read more

And our three most popular blogs of all time:

Do the Standards for Field Capacity and Permanent Wilting Point Need to Be Reexamined?

Top five blog posts Environmental biophysics

We asked scientist, Dr. Gaylon S. Campbell, which scientific idea he thinks impedes progress.  Here’s what he had to say about the standards for field capacity and permanent wilting point.  Read more

Environmental Biophysics Lectures

Top five blog posts Environmental biophysics

During a recent semester at Washington State University, a film crew recorded all of the lectures given in the Environmental Biophysics course. The videos from each Environmental Biophysics lecture are posted here for your viewing and educational pleasure.  Read more

Soil Moisture Sensors In a Tree?

Top five blog posts Environmental biophysics

Soil moisture sensors belong in the soil. Unless, of course, you are feeling creative, curious, or bored. Then maybe the crazy idea strikes you that if soil moisture sensors measure water content in the soil, why couldn’t they be used to measure water content in a tree?  Read more

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How to Measure Water Potential

In the conclusion of our 3-part water potential  series (see part 1), we discuss how to measure water potential—different methods, their strengths, and their limitations.

How to measure water potential

Vapor pressure methods work in the dry range.

How to measure water potential

Essentially, there are only two primary measurement methods for water potential—tensiometers and vapor pressure methods. Tensiometers work in the wet range—special tensiometers that retard the boiling point of water (UMS) have a range from 0 to about -0.2 MPa. Vapor pressure methods work in the dry range—from about -0.1 MPa to -300 MPa (0.1 MPa is 99.93% RH; -300 MPa is 11%).

Historically, these ranges did not overlap, but recent advances in tensiometer and temperature sensing technology have changed that. Now, a skilled user with excellent methods and the best equipment can measure the full water potential range in the lab.   

There are reasons to look at secondary measurement methods, though. Vapor pressure methods are not useful in situ, and the accuracy of the tensiometer must be paid for with constant, careful maintenance (although a self-filling version of the tensiometer is available).

Here, we briefly cover the strengths and limitations of each method.

Vapor Pressure Methods:

The WP4C Dew Point Hygrometer is one of the few commercially available instruments that currently uses this technique. Like traditional thermocouple psychrometers, the dew point hygrometer equilibrates a sample in a sealed chamber.

How to Measure Water Potential

WP4C Dew Point Hygrometer

A small mirror in the chamber is chilled until dew just starts to form on it. At the dew point, the WP4C measures both mirror and sample temperatures with 0.001◦C accuracy to determine the relative humidity of the vapor above the sample.

Advantages

The most current version of this dew point hygrometer has an accuracy of ±1% from -5 to -300 MPa and is also relatively easy to use. Many sample types can be analyzed in five to ten minutes, although wet samples take longer.

Limitations

At high water potentials, the temperature differences between saturated vapor pressure and the vapor pressure inside the sample chamber become vanishingly small.

Limitations to the resolution of the temperature measurement mean that vapor pressure methods will probably never supplant tensiometers.

The dew point hygrometer has a range of -0.1 to -300 MPa, though readings can be made beyond -0.1 MPa using special techniques. Tensiometers remain the best option for readings in the 0 to-0.1 MPa range.

Secondary Methods

Water content tends to be easier to measure than water potential, and since the two values are related, it’s possible to use a water content measurement to find water potential.

A graph showing how water potential changes as water is adsorbed into and desorbed from a specific soil matrix is called a moisture characteristic or a moisture release curve.

download

Example of a moisture release curve.

Every matrix that can hold water has a unique moisture characteristic, as unique and distinctive as a fingerprint. In soils, even small differences in composition and texture have a significant effect on the moisture characteristic.

Some researchers develop a moisture characteristic for a specific soil type and use that characteristic to determine water potential from water content readings. Matric potential sensors take a simpler approach by taking advantage of the second law of thermodynamics.

Matric Potential Sensors

Matric potential sensors use a porous material with known moisture characteristic. Because all energy systems tend toward equilibrium, the porous material will come to water potential equilibrium with the soil around it.

Using the moisture characteristic for the porous material, you can then measure the water content of the porous material and determine the water potential of both the porous material and the surrounding soil. Matric potential sensors use a variety of porous materials and several different methods for determining water content.

Accuracy Depends on Custom Calibration

At its best, matric potential sensors have good but not excellent accuracy. At its worst, the method can only tell you whether the soil is getting wetter or drier. A sensor’s accuracy depends on the quality of the moisture characteristic developed for the porous material and the uniformity of the material used. For good accuracy, the specific material used should be calibrated using a primary measurement method. The sensitivity of this method depends on how fast water content changes as water potential changes. Precision is determined by the quality of the moisture content measurement.

Accuracy can also be affected by temperature sensitivity. This method relies on isothermal conditions, which can be difficult to achieve. Differences in temperature between the sensor and the soil can cause significant errors.

Limited Range

All matric potential sensors are limited by hydraulic conductivity: as the soil gets drier, the porous material takes longer to equilibrate. The change in water content also becomes small and difficult to measure. On the wet end, the sensor’s range is limited by the air entry potential of the porous material being used.

How to Measure Water Potential

TS1 Smart Tensiometer

Tensiometers and Traditional Methods

Read about the strengths and limitations of tensiometers and other traditional methods such as gypsum blocks, pressure plates, and filter paper here.

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Water Potential: The Science Behind the Measurement (Part 2)

In the second part of this month’s water potential  series (see part 1), we discuss the separate components of a water potential measurementThe total water potential is the sum of four components: matric potential, osmotic potential, gravitational potential, and pressure potential.  Below is a description of each component.

Matric Potential

Matric potential arises because water is attracted to most surfaces through hydrogen bonding and van der Waals forces. This water droplet is pure but no longer free. The matric forces that bind it to the plastic have lowered its potential and you would have to use some energy to remove it from the surface and take it to a pool of pure, free water.

Soil is made up of small particles, providing lots of surfaces that will bind water. This binding is highly dependent on soil type. For example, sandy soil has large particles which provide less surface binding sites, while a silt loam has smaller particles and more surface binding sites.

The following figure showing moisture release curves for three different types of soil demonstrates the effect of surface area. Sand containing 10% water has a high matric potential, and the water is readily available to organisms and plants. Silt loam containing 10% water will have a much lower matric potential, and the water will be significantly less available.

Matric potential is always negative or zero, and is the most significant component of soil water potential in unsaturated conditions.

matric potential

Osmotic Potential

Osmotic potential describes the dilution and binding of water by solutes that are dissolved in the water. This potential is also always negative.

Osmotic potential only affects the system if there is a semi-permeable barrier that blocks the passage of solutes. This is actually quite common in nature. For example, plant roots allow water to pass but block most solutes. Cell membranes also form a semi-permeable barrier. A less obvious example is the air-water interface, where water can pass into air in the vapor phase, but salts are left behind.

You can calculate osmotic potential from the following equation if you know the concentration of solute in the water.

Ψ_0=CΦVRT    

 

Where C is the concentration of solute (mol/kg), ɸ is the osmotic coefficient (-0.9 to 1 for most solutes), v is the number of ions per mol (NaCl = 2, CaCl2 = 3, sucrose = 1), R is the gas constant, and T is the Kelvin temperature.

Osmotic potential is always negative or zero, and is significant in plants and some salt-affected soils.

Gravitational Potential

Gravitational potential arises because of water’s location in a gravitational field. It can be positive or negative depending on where you are in relation to the specified reference of pure, free water at the soil surface. Gravitational potential is then:

Ψ_G=GH

 

Where G is the gravitational constant (9.8 m s-2) and H is the vertical distance from the reference height to the soil surface (the specified height).

matric potential

You can feel positive pressure as you swim down into a lake or pool.

Pressure Potential

Pressure potential is a hydrostatic or pneumatic pressure being applied to or pulled on the water.  It is a more macroscopic effect acting throughout a larger region of the system.

There are several examples of positive pressure potential in the natural environment.

For example, there is a positive pressure present below the surface of any groundwater. You can feel this pressure yourself as you swim down into a lake or pool. Similarly, a pressure head or positive pressure potential develops as you move below the water table.

Turgor pressure in plants and blood pressure in animals are two more examples of positive pressure potential.

Pressure potential can be calculated from:

Ψ_P=P/Ρ_W

 

Where P is the pressure (Pa) and P_W is the density of water.

Though pressure potential is usually positive, there are important cases where it is not. One is found in plants, where a negative pressure potential in the xylem draws water from the soil up through the roots and into the leaves.

Next Week: Learn the different methods for measuring water potential and their strengths and limitations.

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Secrets of Water Potential: Learn the Science Behind the Measurement

This month in a 3 part series, we will explore water potential —the science behind it and how to measure it effectively.

water potential

To understand water potential, compare the water in a soil sample to water in a drinking glass.

Definition of Water Potential

Water potential is the energy required, per quantity of water, to transport an infinitesimal quantity of water from the sample to a reference pool of pure free water. To understand what that means, compare the water in a soil sample to water in a drinking glass. The water in the glass is relatively free and available; the water in the soil is bound to surfaces, diluted by solutes, and under pressure or tension. In fact, the soil water has a different energy state from “free” water. The free water can be accessed without exerting any energy. The soil water can only be extracted by expending energy. Water potential expresses how much energy you would need to expend to pull that water out of the soil sample.

Water potential is a differential property. For the measurement to have meaning, a reference must be specified. The reference typically specified is pure, free water at the soil surface. The water potential of this reference is zero. Water potential in the environment is almost always less than zero, because you have to add energy to get the water out.

water potential

You can’t tell by measuring heat content whether or not heat will be transferred to another object if the two touch each other.

Extensive vs. Intensive Variables

Water movement in the environment is really a physics problem, and to understand it, we have to distinguish between intensive and extensive variables. The extensive variable describes the extent or amount of matter or energy. The intensive variable describes the intensity or quality of matter or energy. For example, the thermal state of a substance can be described in terms of both heat content and temperature.

The two variables are related, but they are not the same. Heat content depends on mass, specific heat, and temperature. You can’t tell by measuring heat content whether or not heat will be transferred to another object if the two touch each other. So you also don’t know if the object is hot or cold, or whether it will be safe to touch.

These questions are much easier to answer if you know the intensive variable—temperature. In fact, though it can be important to measure both intensive and extensive variables, often the intensive variable gives you more useful information.

In terms of water, the extensive variable is water content, and it tells you the extent, or amount, of water in plant tissue or soil. The intensive variable is water potential, and it describes the intensity or quality of water in plant tissue or soil.  Water content can only tell you how much water you have. If you want to know how fast it can move, you need to measure hydraulic conductivity. If you want to know whether it will move and where it’s going to go, you need water potential.

water potential

If you want to know whether water will move and where it’s going to go, you need water potential.

Two Key Water Potential Questions:

1. Where will water move? Water will always flow from high potential to low potential. This is the second law of thermodynamics—energy flows along the gradient of the intensive variable.

2. What is the availability of water to plants? Liquid water moves from soil to and through roots, through the xylem of plants, to the leaves, and eventually evaporates in the substomatal cavities of the leaf. The driving force for this flow is a water potential gradient. In order for water to flow, therefore, the leaf water potential must be lower than the soil water potential.

Next week learn about the four components of water potential—osmotic potential, gravitational potential, matric potential, and pressure potential.

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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.

drought tolerance

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.

drought tolerance

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.”

drought tolerance

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.

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Screening for Drought Tolerance

Screening for drought tolerance in wheat species is harder than it seems.  Many greenhouse drought screenings suffer from confounding issues such as soil type and the resulting soil moisture content, bulk density, and genetic differences for traits like root mass, rooting depth, and plant size. In addition, because it’s so hard to isolate drought stress, some scientists think finding a repeatable screening method is next to impossible. However, a recent pilot study done by researcher Andrew Green may prove them wrong.

drought tolerance

Automatic Irrigation Setup

The Quest for Repeatability

Green says, “There have been attempts before of intensively studying drought stress, but it’s hard to isolate drought stress from heat, diseases, and other things.”  Green and his advisors, Dr. Gerard Kluitenberg and Dr. Allan Fritz, think monitoring water potential in the soil is the only quantifiable way to impose a consistent and repeatable treatment. With the development of a soil-moisture retention curve for a homogeneous growth media, they feel the moisture treatment could be maintained in order to isolate drought stress.  Green says, “Our goal is to develop a repeatable screening system that will allow us to be confident that what we’re seeing is an actual drought response before the work of integrating those genes takes place, since that’s a very long and tedious process.”

Why Hasn’t This Been Done Before?

Andrew Green, as a plant breeder, thinks the problem lies in the fact that most geneticists aren’t soil scientists. He says, “In past experiments, the most sophisticated drought screening was to grow the plants up to a certain point, stop watering them, and see which ones lived the longest. There’s never been a collaborative approach where physiologists and soil scientists have been involved.  So researchers have imposed this harsh, biologically irrelevant stress where it’s basically been an attrition study.” Green says he hopes in his research to use the soil as a feedback mechanism to maintain a stress level that mimics what exists in nature.

drought tolerance

Data Acquisition Cabinet setup for Green’s expanded experiment.

The Pilot Study

Green used volumetric water content sensors, matric potential sensors, as well as column tensiometers to monitor soil moisture conditions in a greenhouse experiment using 182 cm tall polyvinyl chloride (PVC) growth tubes and homogenous growth media. Measurements were taken four times a day to determine volumetric water content, soil water potential, senescence, biomass, shoot, root ratio, rooting traits, yield components, leaf water potential, leaf relative water content, and other physiological observations between moisture limited and control treatments.  

Soil Media:  Advantages and Disadvantages

To solve the problem of differing soil types, Andrew and his team chose a homogeneous soil amendment media called Profile Greens Grade, which has been extensively studied for use in space and other applications.  Green says, “It’s a very porous material with a large particle size.  It’s a great growth media because at the end of the experiment you can separate the roots of the plant from the soil media, and those roots can be measured, imaged, and studied in conjunction with the data that is collected.”   Green adds, however, that working with soil media isn’t perfect: there have been hydraulic conductivity issues, and the media must be closely monitored.

What’s Unique About this Study?

Green believes that because the substrate was very specific and his water content and water potential sensors were co-located, it allowed him to determine if all of his moisture release curves were consistent.  He says, “We try to pack these columns to a uniform bulk density and keep an eye on things when we’re watering, hoping it’s going to stay consistent at every depth.  So far it’s been working pretty well: the water content and the water potential are repeatable in the different columns.”

drought tolerance

Entire Irrigation setup for the expanded study.

Plans for the Future

Green’s pilot study was completed in the spring, and he’s getting ready for the expanded version of the project:  a replicated trial with wild relatives of wheat. He’s hoping to use soil moisture sensors to make automatic irrigation decisions: i.e. the water potential of the columns will activate twelve solenoid valves which will disperse water to keep the materials in their target stress zone, or ideal water potential.

The Ultimate Goal

The ultimate goal of Green’s research is to breed wild species of wheat into productive forms that can be used as farmer-grown varieties. He is optimistic about the results of his pilot study.  He says, “Based on the very small unreplicated data that we have so far, I think it is going to be possible to develop a repeatable method to screen these materials.  With the data that we’re seeing now, and the information that we’re capturing about what’s going on below ground, I think being able to hold these things in a biologically relevant stress zone is going to be possible.”

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