Soil Science class spring 2023

Relief! I'm finally signed up and can access the class content in Moodle.
It looks to be a challenging course.

Here's the main textbook, I think:

https://www.sare.org/wp-content/uploads/Building-Soils-for-Better-Crops.pdf

Building Soils for Better Crops

The class is 16 people, some names I recognize from the Weeds class.
We meet MWF, 12:40 to 2:30, and there is a soils lab too.

Off we go....

https://www.youtube.com/watch?v=vDL6F6GkAzI&list=PLZVYohuIygMqtilTezSHbzveYU...

Reflection Questions:
In your own words, try to define soil. What is it made of? What makes soil different from something that is not soil? What makes soil soil?
Consider the following list of materials and identify whether they are soil or not, and why each is or isn’t soil: Sediments on the surface of the moon, Peat-based potting “soil”, stuff in the cracks of pavement with plants growing out of them, compost, beach sand, materials following a mudslide,
Consider your previous impression of soil. What aspects of the definition of soil do you find surprising or confusing? What questions do you have?
Think of 5 or 6 jobs/services/roles that soil plays in terms of human life or planetary system/function? Which of these are provisioning services and which of these are regulating services?
Think about how soil functions interact - for example, some soil functions make others possible, whereas some might impede other functions. Pick 2 sets of 2 soil functions and describe how they might interact with one another.
Contribute Edit section
Ideas for contributions to this page:

Think of a specific example of a soil function and why it is important and write a case example (i.e. a specific road that washed out, or an example of water purification). The key for this is to have a specific place/time/event that demonstrates soil function.

Prep for lab: physical characteristics
(note to self: bring a Sharpie)

Soil Bulk Density test

Field Sampling
transect the field and take five samples per transect.

Soil colors

Munsell Color Charts
Hue pages
start on 10YR page
Y=yellow
R=red
value vs chroma on each page

Resources for writing lab reports
If you choose to write a lab report for this course, it needs to contain the following:

Title
Introduction
Methods
Results
Discussion
Below are some good resources for writing lab report

https://writingcenter.unc.edu/tips-and-tools/scientific-reports/

https://www.monash.edu/rlo/assignment-samples/science/science-writing-a-lab-repo...

Lab Report (50 pts total)
Purpose: Lab reports are a standard component of many science classes and you may not understand why you
have to write them, or feel like they are not very fun to write, however they do have specific purposes. First off, lab
reports are written in the style of scientific research papers and if you have any interest in pursuing science beyond
the bachelor’s level, you will find that they are good practice for writing scientific research papers. However even if
you are not planning on pursuing science beyond Berea, you will find that writing lab reports will help you read
research papers later. In many aspects of agriculture, forestry and engineering you will find it good to be able to
read research papers.
More importantly for me, I find that writing lab reports helps students synthesize the information you have learned
in this unit, analyze data, use quantitative reasoning to think about how numerical data relate to concepts we have
discussed in class and then apply these results to bigger issues facing the world. Lab results have many standard
components that you see below. I expect each of these sections to be present in your final lab report.
I will grade your lab report on completeness, and how well you address the specific tasks listed in each section. I also
expect you to follow standard grammar, punctuation and writing conventions. Despite the work you do in class, this
is the only thing you turn in for a grade, so make sure to spend time on this. Example lab reports with the grades
they received can be found on Moodle. Note that lab reports should be written in very factual, straight-forward
language. Figurative language and metaphors are not standard practice in writing scientific papers and should not
be used here. See the moodle folder for good and bad examples.
Introduction (8 pts)
Your introduction is 1-2 paragraphs that introduce the important concepts of what was studied in the lab. For
example, in this lab you will need to explain what the three phases of soil are, why they are important in terms of
the function of the soil, and what types of ways they can be measured (think of the questions that I listed on the lab
handout.) You could also talk about how soils in different places, that are used differently have different relative
amounts of the different phases. Please cite the text book when you describe these things.
NOTE: This is NOT a hypothesis based lab. We did not have a hypothesis to begin with that we are trying to test,
this is a "descriptive" lab report - where we went out and took measurements and are then describing what we
observed. However, we did have an objective, so please include an objective statement at the end of the
introduction (“The objective of this lab was to…”)
Methods (6 pts)
You don't need to go into extreme detail here, some measurements like core bulk density, clod bulk density and
moisture content are standard and the details of "putting them into the oven and then taking them out" are not
important. But this is what you DO need to mention:
1. Where you took your soil samples from
2. How many samples were taken at each place (4 for 4 groups!)
3. What measurements you took - for example, bulk density in the lab, by packing wet soil into cylinders.
4. What type of statistical analysis you performed – we will do this together on Monday, Sep 3
Things you SHOULD NOT include in your methods
1. Who did what (this includes phrases like "our group" or "the other groups"
2. Results (save this for the results section!)
3. Discussion (save for discussion section)
4. Irrelevant details that have no bearing on the experiment.
Results (15 pts)
Required components:
1. At least 2 figures (graph or table), Graphs must be labeled appropriately and include error bars and p-values.
2. A paragraph that includes or describes data, trends and/or other observations - including qualitative
observations like soil texture and structure.
3. All data presented has been aggregated some way - it is the mean of 4 measurements and/or the result of a ttest or ANOVA analysis
This is where you deliver your results! This includes the ANALYZED numerical data You can and should include
graphs and/or tables of ANALYZED data - this means you should run an ANOVA analysis on at least 2 of your
calculated variables, and then graph them if it seems reasonable.
Things you MUST discuss in your results:
1) What was the bulk density of your different locations? Was there a difference? Why?
2) You measured bulk density in 2 different ways. Were they different from each other? Why do you think
this was?
3) What was the different soil texture of the different locations?
4) What was the different soil colors of the different locations?
5) What were the water contents? Were they significantly different from each other? Why do you think this
is or isn’t the case?
Discussion (15 pts)
This is where you get to show me what you learned in the lab/Unit. This is the most important part of the lab
report. The discussion consist of 3 - 4 paragraphs and does 2 things,
1. It digs into the data and explains why you think you found what you found. Discuss any significant
differences between different fields, or any correlations between measurements. Also, if you had erroneous
or weird data, you can mention it (for example, bulk density usually falls between 1.1 g/cm3
and 1.5 g/cm3
; if
your data fell outside this range you might want to mention that and explain why you thought this was)
2. Relate the measurements and observations you made to the larger world of soil science. Talk about why
forests have a different bulk density than a tilled field - why soils have air pockets and why this is important,
why soil structures were different (or not) between the three sites and what this has to do with soil water
movement etc. Make inferences or hypotheses that you might want to test further.
Things to address in THIS lab report:
1. Which soils had the most pore space? What might have caused this increase in pore space compared to
the other soils? What function might this pore space serve for the function of the soil?
2. How did your bulk density measurements compare to general measuremnets of bulk density you have
come across in your readings?
3. What types of soil structures did you observe in these three soils? How does different soil structures relate
to other measurements such as pore space, water content, bulk density and texture?
4. What environmental factors and/or observations relate to what you found regarding your water content?
For all these questions, use and cite your textbook, and/or other sources to back up what you are saying.
Include a source list (it just might be your text book) at the end of your lab report. (3 pts)
The remaining 3 pts are for writing style, conventions, professionality, etc.

I bought a copy of the 3rd edition of Better Soils for Better Crops. It’s the 2010 publication and the 4th edition, online is published in 2020.
I just prefer having a hard copy and hope the revisions are minor. But I can always double-check.

The classroom I thought was Soil Science had a piece of paper on it that said Plant Science. Turns out they are just sharing the room this term, so we are cautioned to clean our messes when made.
There are 16 of us, and three others from the Weeds class. Multiple students are highly energized about the subject.
Prof. Parr seems organized and interesting.
I appreciated that she had handouts, not just relying on Moodle.
The theme of the class will be soil function.

We spent a while trying to define what soil is; which was surprisingly complex. Less physical definitions (though they are there) than an understanding of ecosystem.

Mineral particles - sand, silt, clay >2mm
Includes air gaps, liquids and organics.

I was taught that soil is everything from bedrock up. The functional definition is 200cm, mostly because soil scientists don’t want to dig further than 6½ feet.

Then we discussed the six functions, some of which are regulating and some are provisioning; some are both.
We worked by table group. I met Joseph, who is from Jackson County (where my ridgetop property is) and Simon, from Pittsburgh (where I grew up.)

I need to read up on “bulk density” which we will measure soon. Never heard of it.

A question was “Is beach sand soil?” I proposed a field trip to immediately test the question. Favorable reaction.

The bulk density of soil depends greatly on the mineral make up of soil and the degree of compaction.3 The density of quartz is around 2.65 g/cm3 but the (dry) bulk density of a mineral soil is normally about half that density, between 1.0 and 1.6 g/cm3. In contrast, soils rich in soil organic carbon and some friable clays tend to have lower bulk densities (4

Bulk density of soil is usually determined from a core sample which is taken by driving a metal corer into the soil at the desired depth and horizon.5 This gives a soil sample of known total volume, Vt. From this sample the wet bulk density and the dry bulk density can be determined.6

For the wet bulk density (total bulk density) this sample is weighed, giving the mass Mt. For the dry bulk density, the sample is oven dried and weighed, giving the mass of soil solids, Ms. The relationship between these two masses is Mt = Ms + Ml, where Ml is the mass of substances lost on oven drying (often, mostly water). The dry and wet bulk densities are calculated as

Dry bulk density = mass of soil/ volume as a whole

ρ
b
=
M
s
V
t
\rho_b = \frac{M_s}{V_t}
Wet bulk density = mass of soil plus liquids/ volume as a whole

ρ
t
=
M
t
V
t
\rho_t = \frac{M_t}{V_t}
The dry bulk density of a soil is inversely related to the porosity of the same soil: the more pore space in a soil the lower the value for bulk density.

So, perhaps, a roundabout way to measure organic matter?

We worked on the math of bulk density. First a refresher on geometry and algebra. Columnar volumes was most important for our purposes, needing to know the size of the samples we take using a probe. So reacquainting myself with pi.

I do recall that we did not have calculators when I first learned this stuff. I remembered fairly swiftly and did not struggle like a few in the class did. Simon and I compared answers and he offered a fist bump.

There are three phases to soil: solids, liquid and air. Porosity helps to determine density. A typical soil is half solids and a quarter water and a quarter air; subject to fluctuations of water.

The symbol most often used for density is ρ (rho). Particle densities hover near the density of the parent material - quartz, in most cases. p =2.65g/cm3

So bulk density ranges from 1 (undisturbed, high organic) to 1.9 (very compacted). High organic, like peat land, can be less than 1. We will see 1.2 to 1.4 typically. So, it’s the digits to the right of the decimal that make the difference.

Next week we will go take some samples and then measure mass wet and then dry.

We also ran calculations to find soil water content. (Theta) The volumetric soil water content, Θ, is expressed in cm3 water per cm3 of soil. In terrestrial soils values of Θ suitable for crop growth are in the range of 0.1 to 0.5 cm3 cm−3.

Before class I chatted with Levi. He’s from northern Virginia.

It was obvious today that I’ve been too sedentary the past few months. We hiked out to the woods, hayfield and grassland to take soil samples. I worked with Simon and Joseph. Joseph says he did some land competition in high school, but it doesn’t seem to have been extensive.
We took measured volume samples for drying to determine bulk density. We brought back random sized clods for a water measurement. We took soil temperature and tried to determine soil color in the Munsell tables. That is surprisingly difficult to determine with one’s own eyes, much less come to a group consensus.
I chatted with Jordan on the way back to the vans. She’s from Lexington, but her family is from Huntington, WV.

The hiking was a bit strenuous and getting up from kneeling - I waited till no one was looking, as I wasn’t springing upright as easily as I’d like. My back needed a rest when I got home.

I was reminded of this nice area nearby for nature walks though. Daughter took me there once I believe. Scenic, charming.

When you don’t see the leaves, you don’t think of the presence of poison ivy in a location. I must have found some roots in the woods site.

I took a Benadryl on Friday, for the itch, and I was a bit numb and brain-fuzzed.

Texture
Sand and silt are roundish particles.
Clay is molecularly different. It’s substance has been dissolved and recrystalized to plate or sheet structure. (Must explore this!)
The differences in surface area are vast.
One gram of
Sand - 30cm2
Silt - 1500cm2
Clay - 3,000,000cm2

Loam is the idealized soil, where the influence of sand silt and clay are equal.
This does not mean amounts are equal.

Silt is fine for crops, but is structurally unsound as a foundation.

We played with the numbers to examine surface areas of various soils.
Gritty
Smooth-slick
Sticky

Pore space

Soil structure - changeable based on management.

Surface crusting - bare earth and rain
Columns - high salt content

The lab part of the class we handled the samples we took on Wednesday. Elaine joined our group. She had missed the bus Wednesday.

Our core samples were dry. So we measured volume and weighed them, comparing them to their wet weight.
We took clods of earth, dipped them in paraffin and measured their displacement in water. Those will dry in a low oven during the weekend.
We took clumps of soil, wet them and tried to ribbon them. The woods sample was the stickiest.
I caught two errors made by the group, one math, the other a logic error.
I might have made errors too, but I was not leading the work, just struggling to follow.

Monday we discussed Soil Water.
I’m going to need to read the materials again, as my notes are scant.
Retention -
adhesion - water attracted to surfaces - not all available to plants
cohesion - water molecules like to stay together

Field capacity
Wilting point - lack of available water causes plant death

Water potential
Pressure potential
Diffusion gradient

Roots have protein channels that absorb water and nutrients. The channels are specialized for each.

Evapotranspiration is what primes the pump for water movement up the plant. Generally happens during daytime; stops at night.

Capillary fringe - micropore in soil

Preferential flow

We did some calculations which I can’t recall.

Prof Parr brought in two soils, one from local, which was almost pure clay. I was able to ribbon it several inches.
The other was from her parents place in Georgia. It must have been coastal. It had a nice loam content, but no clay and you could feel the sand content.

An aside to Hallie as we were leaving I said I wished I still had my textbook from the 1970s. I don’t recall being exposed to any of this technical information. Her reply - She just keeps in mind that farmers have raised crops successfully for millennia without knowing this stuff.

Wednesday’s class was cancelled. Prof Parr’s daughter had a medical emergency. I hope it was just normal little kid stuff. I didn’t get the notice, though I had checked Moodle that morning. I found four classmates huddled over their laptops anyway, working on lab reports.
Hallie said she would text me if cancellations happen again.

I had brought an old mounted photo in to give away. It was a professional photo of a dairy cow barn interior from the 20s or 30s. Simon took it. I knew someone would.☺️

In Parr’s written materials for next class (Soil temperature), she had said to pay less attention to the formulas than the general concepts. I mentioned that I liked that. A couple said they liked the formulae! And Hallie said she liked them because Parr is a weak lecturer, and doing the math helped her understand. Hmm. I think I have to agree with the first part of that statement.

Haven’t decided whether I will produce reports for grade yet. It’s all intimidating.

Friday we did a slake test on our three soils. I was amazed at how much soil stayed clumped in the very open wire baskets when submerged in water. The clarity of the water differed as well, with the higher organic content clearer than the others.

We had a short lecture on soil temperature, but I’ve misplaced my notes! Been looking for them all weekend, as I’m preparing my end of unit review. There are nearly 30 questions to answer, and due today.

Soil Minerals
We have discussed the phases of soil - the solid, liquid, and gas phases. Let's zoom in on the molecular level in those phases—starting with the mineral portion of the solid phase.

Most of the solid phase is made of minerals. Where do those minerals come from? What are they?

ROCKS! - the answer is the soil mineral phase comes from rocks that weather in various ways (physical, chemical, biological) to form soil minerals.

- Go to this lesson in the Plant and Soil Sciences eLibrary to learn about the rocks and minerals that make up soils. (This lesson is several pages long, so make sure to read all the pages.)

Soil Genesis and Development Lesson 1 - Rocks, Minerals and Soils
https://passel2.unl.edu/view/lesson/e378a6ea538f

The weathering - or breakdown of the structure of rocks and minerals to form other minerals and substances - is the key to soil formation. The second lesson is about weathering. Make sure to go through this whole lesson as well:

Soil Genesis and Development Lesson 2 - Processes of Weathering
https://passel2.unl.edu/view/lesson/edd25385ca3d

So what is clay? Is it just really really little pieces of sand and silt? Actually no. Clay is chemically different from sand and silt in that it is formed by the chemical dissolution of aluminum and silicate molecules from rocks that re-form into specific patterns called aluminum phyllosilicates. There are several different types of aluminum phyllosilicates, each with different properties. Below you will find a video with more descriptions on how this clay is formed. After watching the video you can look at the several links to clay minerals from the Virtual Museum of Minerals and Molecules. And finally read the extension hand-out that describes how these different clay structures properties can affect the function of clay in important use-aspects of soil.

To learn more about how clay forms from minerals read this page here:

Weathering and Clay Minerals
https://www2.tulane.edu/~sanelson/eens211/weathering&clayminerals.htm

Watch this video with good descriptions I made during the pandemic (10 min)

Clay Formation
Clay Formation

Clay Formation

to see more clearly the structure of minerals look at this:
Links to minerals: - when you get to this site, you can drag the mineral to turn it in different ways. It makes it much easier to see the layers if you shift the image around.

Kaolinite
https://virtual-museum.soils.wisc.edu/display/kaolinite/
Smectite
https://virtual-museum.soils.wisc.edu/display/soil-smectite/
Vermiculite
https://virtual-museum.soils.wisc.edu/display/vermiculite/
Chlorite
https://virtual-museum.soils.wisc.edu/display/chlorite/
Hematite (This is an iron oxide clay, that is only present in our temperate soils I'm a small amount, but oxide clays are very abundant in warm, tropical locations)
https://virtual-museum.soils.wisc.edu/display/hematite/

Extension Handout: Swelling Clays and Septic Systems (PDF)
https://www.extension.purdue.edu/extmedia/RW/RW-3-W.pdf

Saw this over at Popular Science and thought you needed to know (ICYMI): Scientists designed the free-to-play game 'Dirty Matters' to help us appreciate this overlooked substance.

That sounds great! Sad the article doesn’t provide a link.
Off to search…

https://soilgame.wixsite.com/free2print/items

Soil pH - U of Nebraska

https://passel2.unl.edu/view/lesson/d2b52174b1a7

Sorry I haven't posted on the last few classes.
I might grab my notes and do it later. We've been on the chemical attributes of soil.

Today we start organic aspects.

Soils are amassing the cumulative carbon and nutrient capture from plant production, and the largest amount of carbon present on the land is not in the living plants but is instead stored in soil organic matter. It has taken a while, but that understanding is now finding its way into discussions of the carbon cycle. More carbon is stored in soils than in all plants, all animals and the atmosphere combined. Soil organic matter contains an estimated four times as much carbon as living plants, and in fact carbon stored in all the world’s soils is two to three times the amount in the atmosphere.

https://www.sare.org/publications/building-soils-for-better-crops/what-is-organi...

Chemistry textbook

https://open.umn.edu/opentextbooks/textbooks/918

What organisms are involved?
What is the nature of the interaction- what does each side give/get?
Where does the interaction happen?
How does the plant encourage the interaction?
What does the microbe do for the plant?

Ectomycorrhiza
using EMF in temperate and boreal forests restoration programs

https://www.frontiersin.org/articles/10.3389/ffgc.2020.00097/full

M -Mycorrizae
NM - no mycorrizae
C - contaminated soils heavy metals
NC - no contamination

Phyla of the kingdom fungi (Basidiomycota, Ascomycota and Zygomycota)

Ectomycorrhizal fungi: exploring the mycelial frontier

measuring and observing

https://academic.oup.com/femsre/article/31/4/388/2398987?login=false


Mycelial systems of ectomycorrhizal fungi. (a) A typical microcosm system demonstrating the mycelium of Suillus variegatus growing from a Scots pine seedling (photo taken by P.M.A. Fransson). (b) Russula sp. fruiting body and associated mycelium. (c) A close-up of (b) showing the base of the fruiting-body stipe, the associated white mycelium, and ECM root tips (arrows) colonized by this fungus. (d) A dense mycelial mat that has been lifted from a rock surface in a native Scots pine forest. Patches of brown, pink, white and yellow mycelium of different fungal species are visible (photo taken by C.D. Campbell).

Teacher declared a Zoom class yesterday as her 3 year old had Strep. That part was fine; but then we split into groups remotely and researched and produced a PowerPoint production in the last half hour. Luckily, Joseph took me on and quickly did the tech part that I had no idea how to start. And finish, as it had to be submitted on Moodle.

Great topic though. Precisely the material I wanted to know more about when I signed up for the class.
Morels and truffles are the fruiting bodies of ectomycorrhizae

We watched this film in class today:

Under Cover Farmers
https://m.youtube.com/watch?v=nWXCLVCJWTU

UK lime and nutrient recommendations

http://www2.ca.uky.edu/agcomm/pubs/agr/agr1/agr1.pdf

https://www.uky.edu/KGS/foundation/index.php

Foundation Engineering
Pyrite oxidation and expansion in the New Albany black shale have caused serious foundation problems in numerous buildings and structures constructed in the black shale soil horizons in various parts of Kentucky. Pyrite oxidizes, causing various secondary sulfates to form when excavated shale or shale fill is exposed to the atmosphere, water, and humidity; these shales can therefore cause serious problems when used in foundations. These secondary sulfates are sensitive to water and humidity and can form when only minor amounts of water are present in foundation materials. In addition to heaving, these sulfate minerals can also create a mild sulfuric acid in foundation soils. These sulfates form by crystal growth and expansion by volume change, which cause subsequent soil expansion and heaving of any foundation materials when confined. Several structures—schools, hospitals, commercial buildings, water plants, and factories—have had expensive remediation to repair damaged sidewalks, floors, walls, utility conduits, and foundations. One home was condemned and others have severe damage. Repairing these conditions is sometimes more expensive that the original cost of building.

Monday: Soil Forming Factors
Back during the first weeks of class we dug up and looked at some different soils. You may have noticed that they had different colors and different patterns. Some were dark on the surface, while others changed colors as you dug deeper. You may have traveled to other places and seen soils that were of different colors, including reds, oranges, yellows, and greys. Some soils are very shallow, while others go down for meters. The way soils look is referred to as their morphology - soil morphology includes things like soil color, texture, depth, and horizons. The way soils end up with different morphologies is as a result of their formation. Today's topic is on soil formation: how different soils end up with different soil properties.

Soils are formed by the process of weathering. We have talked about weathering before, but please check out this quick Lesson (seriously, it is very short) to give you a refresher on weathering:
How much and which types of weathering are governed by soil-forming factors. There are generally 5 recognized factors in soil formation. These are alliteratively called the Five Soil Forming Factors: Climate, Organisms, Relief*, Parent Material, Time - You can remember this as CLORPT
* Relief can also be referred to as Topography or Landscape

Webinars

https://instagram.com/soilfoodwebschool?igshid=YmMyMTA2M2Y=

Iron enhanced sand filter to catch phosphorus run-off before it enters water.

https://www.instagram.com/reel/CrzZ0_4A6Uu/?igshid=NTc4MTIwNjQ2YQ==