The Microscopic soul of soil Week 14 part 2 Soil microbiology introduction

Function of soil Provide nutrients to roots Provide air to roots Anchor plant roots Supply water and water soluble nutrients for biomass production

How much life is really in soil? Think of something teeming with life? Ever have sea Monkeys? But think about the ecosystem of soil Essentially more living organisms in 1 teaspoon of soil than there are people On EARTH!

Who calls that 1 teaspoon of soil home?

The Soil food web

Soil organism Diversity Soil organisms can be grouped by Size Species Function/job

The Category of size Macro or large (>2mm) can easily see these with your naked eye Worms Plant roots

The Category of size Meso or Middle (2-0.2mm) Can still see some of these with eye Mites: often not seen with naked eye. But their trails can be seen on agar plate lids in the moisture. Silverfish

The Category of size Micro or small (<0.2mm) Not seen with naked eye Yeast Bacteria virus

Categorize by Species and function Categorize soil life by how they are related Animals Vertebrates: mice, gophers, moles, voles, snakes, salamanders Arthropods: spiders, ants, beetles, etc Annelids: earthworms Mollusks: snails, slugs Nematodes: (really nasty little worms)

Categorize by Species and function Categorize soil life by how they are related Plants Primary producers, take up nutrients, deposit nutrients in rhizosphere, become residue for decomposition. Algae Produce nutrients, have water holding qualities in soil

Algae in soil What cell part is this?

plants What N fixing plant is in our field plots for research? Is this an infection? If yes is it bad or good? Explain.

Rhizosphere The zone that is affected by living roots in the soil. Roughly 2mm around the root in all directions. Area rich in organic matter because of root exudates and sloughing cells from the root. ~10 more microbially active than the bulk soil.

Species and Function

Bacteria Capture energy thru photosynthesis Break down residue Enhance plant growth through nutrient cycling and protecting roots from disease-causing organisms https://www.youtube.com/watch?v=_C9RlhylY0w

actinomycetes Organic matter decomposition Maintain microbial populations Produce antibiotics Produce the earthy smell Weave a network of hyphae like fungi, but are more like bacteria, can shuttle nutrients in hyphae to plants.

fungi Break down residue Enhance plant growth through nutrient cycling and protecting roots from disease-causing organisms https://www.youtube.com/watch?v=xySygBVLsbM

Macroorganisms: Promote disease Consume plant residues and roots Graze-eat other macrorganisms and plant material Shred material Control populations. https://www.youtube.com/watch?v=nS4dHlwhick https://www.youtube.com/watch?v=ZrogAKO3dhI https://www.youtube.com/watch?v=iOakParsq34

Healthy soil A person looking at soil should expect to see Many species of vertebrate animals Earthworms 20-30species of mites 50+insect species Many nematodes 100+ fungi 1000+bacteria and actinomycetes

Factors that affect microbial growth Aeration Organic matter Moisture and temperatures Soil fertility and ph Management practices

Management practices on soil microbes Increased tillage decreases microbial diversity and biomass. Application of fertilizer to infertile soil will increase activity and biomass. Can depress activity if soil is fertile Addition of organic materials also increases activity and biomass of microbes. Keeping high SOM and residue supports activity and biomass. Pesticide use and have variable effects.

Healthy soil A health soil ecosystem is diverse Many functions, many organisms When it is diverse it is stable and resilient Soil organisms have created many working networks to improve ag soil functions. Soil management activities greatly affect the life of our soil.

Benefits of biodiversity in soil Ecosystem plasticity or resilience: Soil bounces back after trauma or severe disturbance. Ecosystem stability: Since the system is diverse the soil can accomplish many functions in different ways.

How do identify microbes after plating soil on agar Mainly we will look at bacteria and fungi Bacteria grow on agar as a colony Colony: a visible mass of microorganisms all originating from a single mother cell. Fungi grow all over agar. Much of the identification is based on the way the colony looks or it’s morphology

Whole shape of colony Varies from round to irregular to filamentous and rhizoid (root-like)

Colony size Can vary from large colonies to tiny colonies less than 1mm = punctiform (pin- point). Measure with a millimeter rule. We won’t do this.

Edge or margin of colony Magnified edge shape (use a dissecting microscope to see the margin edge well)

Chromogenesis…What color is it? Color of colonies, pigmentation: white, buff, red, purple, etc. Some pigments are water-soluble, others are not. If you take a large inoculum and place it in a tube of water or saline, do you see color? Do you see any pigment if the organism is growing in a broth medium? Does incubation temperature affect the color? Does the entire colony have the color, or is it more like a bull’s eye?

Opacity of Colony Is the colony transparent (clear), opaque (not transparent or clear), translucent (almost clear, but distorted vision–like looking through frosted glass), iridescent (changing colors in reflected light)?

Elevation of colony How much does the colony rise above the agar (turn the plate on end to determine height)?

Surface of colony Smooth, glistening, rough, dull (opposite of glistening), rugose (wrinkled)

Colony counting Grab your plate and a sharpie On the bottom of the plate dot each colony and count it. Only count a quarter of the plate and multiply by 4. If two colonies are grown together count as one. Count as one.

If plate is a lawn Put down too many to count TMC.

Fungi Identification Great rule of thumb….they are fuzzy! Can be green, white, black, gray, etc. Can be powdery looking Under a microscope you can see the hyphae

Tasks Count colonies on your plates Assess the morphology of the colonies. Fill in datasheet.