Foundation Courses. Ch.1 Lecture 3: Soil Assessment Methods


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Chapter 1

Lecture 3: Soil Assessment Methods

Lecture 3 focuses on choosing the right assessment tool in order to ascertain the specific information you wish to know about your soil. You will learn that some assessment methods are more effective and reliable than others. This lecture continues to explore soil chemistry and how to accurately assess and measure soil chemistry and biology; accurate measures and assessment are fundamental prerequisites to be able to prescribe appropriate remedial treatments and adjustments.

  • Above quote is from the Foundation course manual

A Video for all you Cannabis growers out there that goes over some of what is discussed here in this post. Scott is a notable Soil Food Web Graduate. Since of course Cannabis is the most popular cash crop out there.

This Lecture was very information dense. A lot of what I took notes on here was not necessarily important for passing the quiz. However, still is needed to know and important to understand when approaching future projects/ growers who depend on the information from these soil tests that are conducted. If you have been following along you will have remembered that it is all about balancing out our fungal:Bacteria levels more so than not in our soils. Or is it? I do not know lol still learning.

Choosing the right assessment tool

  • Plate Counts

  • Used to determine numbers of individuals of one or more species or genus.

    • Will not tell you total numbers of all the individuals of all the different species
    • No food resource or mixture of food resources to supply all of the micro-organisms
    • The temperature varies for each micro-organism, so not ideal
    • Humidity levels vary for each organism, not ideal
    • Oxygen levels vary once organisms rapidly multiply, also not ideal. Pathogens thrive in limited oxygen environment.
    • Shows more anerobic organisms and not aerobic organisms due to lack of oxygen
    • To determine what healthy organisms are missing or needed we need to know what aerobic organisms are missing.
    • Can still be used but use it to determine pathogens; anerobic organisms. Inappropriate for total species or activity.
    • missing 99.9999% of total micro-organisms
  • Shadow Microscopy

  • Used to determine Organism Biomass. Used for soil analysis.

    • Measure length, with or numbers of individuals separated by general or specific morphological criteria.
    • Compare values over time.
    • Compare to desired ranges based crops/ living systems
  • CO2 absorption

  • Used to determine Organism Activity

    • CO2 absorbing chemical with a pH indicator is used so color change can be related to CO2 taken up.
    • Other chemical reactions in soil can release CO2.
    • Sampling can alter soil biology.
    • Can not differentiate one organism from another organism
    • Typical pathogens release methane and not CO2. Will not determine amount of pathogenic micro-organisms
  • CO2 absorption + Enzymes

  • Add food or not?

    • Enzymes react with substrate, measure initial and final amounts of substrate.
    • Disturbance reduces numbers and kinds of organisms
  • Chloroform Fumigation

  • Used to determine Organism Numbers

    • Fumigation is supposed to kill all the organisms in the sample, but this will not be the case unless the sample is spread very thinly, which means severe disturbance impact on the organisms.
    • All the dead organisms are supposed to now be used by the remaining living organisms. But the chloroform killed everything so how can living organisms still be present?
    • How much of the total set of organisms we not killed?
    • Temperature, moisture amount of organic matter will affect the results as well.
    • Significant controls are needed but rarely used.
  • Haney Test

  • Used for Nutrient cycling

    • Measure soluble inorganic nitrogen levels at the start and end of an incubation period.
    • Samples incubated in sealed jar will quite likely become become anaerobic, which means inorganic N will be lost as gas when the jar is opened leading to underestimates.

Soil Quality Indicator Properties

Physical PropertiesChemical PropertiesBiological Properties
Bulk densitySoil reaction of pHOrganic matter content
Rooting depthElectrical conductivityMicrobial biomass carbon
Water infiltration rateCation exchange capacityMicrobial biomass nitrogen
Aggregate stabilityOrganic matterEarthworms
Surface and sub-surface hardnessMineralizable nitrogenEnzymes
-Exchangeable potassiumDisease suppressiveness
-Exchangable calciumActive Carbon
  • There is no one value listed above that determines/ describes soil quality.
  • Depends on the type of plant you want to grow.
  • What does mineralizable mean?
    • Means taking organic form of a nutrient to a mineral form
    • Converting from an organic form to an inorganic form
    • Understanding the biology is key. Mistakes are often made because of this.

Soil Chemistry Definitions

  • pH is the negative log of the H+ concentration
    • pH is not the amount of calcium but rather hydrogen ions
    • Neutral pH or pH occurs at H+ = OH- where both are at a concentration of 10 to the -7(log number) power
  • Cation Exchange Capacity (CEC) is a measure of the ability of all surfaces such as but not just sand, silt, clay and organic matter surfaces to hold and release cations.

    • Base saturation is also another word for CEC
  • Ability of a soil to hold and exchange cations

    • ions are atoms with an electrical charge
    • Negatively charged colloids (organic matter and clay) attract and hold cations.
  • Is the total amount of cations that a soil can retain

  • The higher the soil CEC the greater ability it has to store plant nutrients.

  • Soil CEC increases as the amount of clay increases, amount of organic matter increases and when the soil pH increase.

    • the more organic matter that is added to clay the less concerned we are with our CEC in clay.
  • Proteins (organic matter) have CEC. Can hold nutrients.

    • Clay usually has the highest capacity
    • Sometimes only one Clay or thousands of different minerals. So measuring all is important.
    • Only positively charged ions looked at. Really only four of the positively charged ions, Calcium. Magnesium, Potassium and Sodium. Other positive ions are in the soil so not best way to measure soil.
    • Negatively charged colloids (organic matter and clay) attract and hold cations.
    • Biology examination is a easier way to interpret samples.
    • Better development of microscopes helped measure soil eventually
    • We needed shadowing microscope. Bright field microscopy was previous method
    • Bright field microscopy was not effective because the density of bacteria and fungi is the same as water. Was not able to see organisms.
    • The shadow allows for us to see organisms
  • Electrical Conductivity is the ability of a volume of material to transmit electrical current.
    • Expressed as Siemens per cubic meter or milliSiemans per cubic cm.
    • Be careful about the units of measurements. Measures volume.
    • When taking samples you mix the samples to make uniform. Destroys the variability of soil conditions.
    • Measures the current not the difference between - and +
    • Mis reading of actual salts in sample can happen.
  • Acids, Alkalis, and the pH Scale
  • pH is Hydrogen and Hydroxide ion concentration

    • Alkaline = higher concentration of hydroxide

    • Acidic = higher concentration of hydrogen

  • As you add more hydroxide that hydroxide binds with the hydrogen ion and takes hydrogen ion out of solution so now you might have water instead.

Base Saturation

  • is the Percentage of the soil exchange sites (CEC) occupied by the four particular cations, potassium (K+), Magnesium (Mg to the +2 power), calcium (Ca to the +2 power) and Sodium (Na+)

  • Ca:Mg affects the way Clay platelets arrange themselves: collapsed, flocculated, dispersed.

    • A clay soil with too much Ca acts like dust, repels water
    • A clay soil with too little Ca collapses and compacts
    • 6:1 ratio is desirable for most clay soils in North America
    • If ammonium is low then be sure to increase the fungi in soil so the nitrates can be converted to ammonium
    • High iron can tell you that your soil many many years ago was anerobic. Will need enzymes to help convert to plant available form.
    • Need a organic matter level of 3% to have a healthy biology in the soil.

This Lecture was extremely frustrating. But fortunately the Quiz was not that hard. Watching the lecture over and over again was very very helpful!

Let's see how I did with the Quiz. I do not expect to do well with this lecture quiz.



3.3 REFERENCES - FURTHER READING- These links are taken directly from the Foundation Course manual. If you are able to read and understand the information below than you are the less than 1% who has as most do not read this information.

Amor, M., Busigny, V., Francois, G. & Komeili, A. (2018). Using iron isotopes for identification of magnetotactic bacteria fossils. American Geophysical Union, Fall Meeting 2018.

Amor, M., Mathon, F.P., Monteil, C.L., Busigny, V. & Lefevre, C.T. (2020). Iron‐biomineralizing organelle in magnetotactic bacteria: function, synthesis and preservation in ancient rock samples. Environmental Microbiology, 22(9), 3611-3632.

Bhandari, K.B., Longing, S.D. & West, C.P. (2020). Soil Microbial Communities in Corn Fields Treated with Atoxigenic Aspergillus flavus. Soil Systems. 4(2), 1-9.

Britannica. (n.d.). Ion-exchange reaction. Chemistry Libretexts. (2019, June 5). 5.6 The pH Scale.

Conrad, R. (2020). Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation. Microorganisms, 8(6), 881.

Corwin, D.L. & Yemoto, K. (2019). Measurement of Soil Salinity: Electrical Conductivity and Total Dissolved Solids. Soil Science Society of America Journal. 83(1), 1-2.

Essington, M.E. (2015). Soil and Water Chemistry: An Integrative Approach (2nd ed.). CRC Press.

Freeman, S. (n.d.). What is pH? [Image].

Jesus, E.D.C., Liang, C., Quensen, J.F., Susilawati, E., Jackson, R.D., Balser, T.C. & Tiedje, J.M. (2016). Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. GCB Bioenergy. 8(2016), 481-494.

Khan Academy. (n.d.). Definition of pH. [Video].
Levett, A., Gagen, E.J., Rintoul, L. Guagliardo, P., Diao, H., Vasconcelos, P.M. & Southam, G. (2020). Characterisation of iron oxide encrusted microbial fossils. Scientific Reports, 10, 9889.

Lin, Y., Tang, D., Shi, X., Zhou, X. & Huang, K. (2019). Shallow-marine ironstones formed by microaerophilic iron-oxidizing bacteria in terminal Paleoproterozoic. Gondwana Research, 76, 1-18.

Melo, C., Fialho, C., Faria, A., Neto, M., Saraiva, D., Costa, M., Ferreira, L. & Ferreira, F.A. (2014). Microbial activity of soil cultivated with corn in association with weeds under different fertility management systems. Chilean Journal of Agricultural Research. 74(4), 477-484.

Paul, E. (2006). Soil Microbiology, Ecology and Biochemistry. Elsevier.

Pepper, I.L., Gerba, C.P., Gentry, T.J. & Maier, R.M. (2011). Environmental Microbiology (2nd ed.). Academic Press.

Pepper, I.L., Gerba, C.P. & Gentry, T.J. (2014). Environmental Microbiology (3rd ed.). Elsevier.

Perry Stillerman, K. & DeLonge, M. (2019). Safeguarding Soil: A Smart Way to Protect Farmers, Taxpayers, and the Future of Our Food. Union of Concerned Scientists. 2019, 1-6.

Preat, A., De Ridder, C. & Gillan, D. (2018). Bacterial origin of the red pigmentation of Phanerozoic carbonate rocks: an integrated study of geology-biology-chemistry (Ernest Van den Broeck medallist lecture 2017), Geologica Belgica, 21 (3-4), 167-175.

Rao, D.L.N., Aparna, K. & Mohanty, S.R. (2019). Microbiology and Biochemistry of Soil Organic Matter, Carbon Sequestration and Soil Health. Indian Journal of Fertilisers 15(2), 124-138.

ScienceDirect. (n.d.). Soil Organic Matter.

Sleep, N.H. (2018). Geological and Geochemical Constraints on the Origin and Evolution of Life. Astrobiology, 18(9), 1199-1219.

Sparks, D.L. (2019). Advances in Agronomy. Academic Press.

Spencer, J.N., Bodner, G.M., & Rickard, L.H. (2010). Chemistry: Structure & Dynamics (5 ed.). John Wiley & Sons.

Starr, M.P., Stolp, H., Trüper, H.G., Balows, A. & Schlegel, H.G. (2013). The Prokaryotes: A Handbook on Habitats, Isolation and Identification of Bacteria. Springer Science & Business Media.

Sustainable Agriculture Research and Education. (n.d.). Building Soils for Better Crops, Third Edition. Why Soil Organic Matter Is So Important.

University of Minnesota Extension. (n.d.). Soil organic matter in cropping systems.

Wiesmeier, M., Urbanski, L., Hobley, E., Lang, B., von Lützow, M., Marin-Spiotta, E., van Wesemael, B., Rabot, E., Ließ, M., Garcia-Franco, N., Wollschläger, U., Vogel, H.J. & Kögel-Knabner, I. (2019). Soil organic carbon storage as a key function of soils - A review of drivers and indicators at various scales.

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