II. SOIL ENVIRONMENT

 

Before studying the organisms themselves, first must understand at the environments in which these organisms function. The environment affects the soil microfauna and flora, both quantitatively and qualitatively.

 

A. Regolith vs Soil

What is regolith?

 

 

 

What is soil?

 

 

 

 

What is the difference?

 

 

 

 

 

 

B. Topsoil

What is "topsoil"?

 

 

 

 

 

 

C. Subsoil

What is "subsoil"?

 

 

D. Influences on Soil Microorganisms

Soil effects can be soil organisms can be divided into two categories:

(1) Direct

 

 

 

 

 

 

 

(2) Indirect

 

 

 

 

 

 

 

1. Water

Soil microorganisms must be in a water environment or in a water film to be active.

What factors affect soil water contents?

a. Climate -

 

 

 

 

 

b. Texture -

What is soil texture?

 

 

What is the size of soil bacteria?

 

Table - Miller et al.

Soil texture affects pore size

 

 

 

 

 

Table - Available water (Tennessee)

 

 

 

Pore size can be categorized into three general groups:

 

(1) Macropore -

 

 

 

 

 

 

 

 

 

 

(2) Micropore -

 

 

 

 

 

 

 

(3) Biopore -

 

 

 

 

 

 

Water movement through the soil - "piping"

 

 

 

 

 

 

 

 

 

 

 

 

 

As H2O content goes down, water films become thinner; until reach permanent wilting point. What is the permanent wilting point?

 

 

 

 

 

 

Is the PWP meaningful for soil organisms?

 

 

 

 

 

 

2. Oxygen

Microorganisms can be divided by oxygen requirements:

 

 

 

 

 

 

 

 

 

What factors affect soil O2 levels?

 

(1) Soil water content

How?

 

 

 

 

 

 

 

 

 

 

 

(2) Soil depth

How does soil depth affect soil O2 levels?

 

 

 

 

 

 

 

 

 

 

(3) CO2 effects

 

 

 

 

 

 

 

 

 

 

 

3. Temperature

Soils temperature affects growth of soil organisms. They can be divided by temperature requirements:

 

 

 

 

 

 

 

 

 

 

 

Q-10 factor - what is it?

 

 

 

 

 

 

4. Nutrients

Soil nutrients can be categorized by "availability" classes

1) Unavailable

 

 

 

 

 

 

2) Exchangeable

 

 

 

 

 

 

 

What is Cation exchange capacity (CEC)?

 

 

 

 

 

 

 

 

What factors control soil CEC levels?

 

 

 

 

 

 

 

3) Solution

 

 

 

Table

 

 

 

Compare to plants, how important are soil nutrients in controlling the growth of soil organisms? If add N-P-K fertilizer to soil, would you expect a response in microbial populations?

 

 

 

 

 

5. pH

What is pH?

 

How average pH values??

a. Factors affecting soil pH

 

 

 

 

 

 

 

b. Effects on soil organisms

Soil acidity has a major impact on the numbers, types, and activity of soil organisms. How??

 

(1) Availability of nutrients

 

Figure

 

 

 

 

 

 

 

 

(2) Direct effect of H or Al on microorganisms

 

 

 

 

 

 

 

 

 

 

 

Effect of fire on soil pH

Will soil pH go up, down, or stay the same after a forest fire?

6. Organic Matter

Property of the soil which most often limits the soil microflora. Why?

 

 

 

 

 

 

 

 

 

a. Heterotrophic microorganisms

 

 

 

 

 

 

 

 

 

 

 

b. Autotrophic Microorganisms

 

 

 

 

 

 

 

 

 

 

 

c. Soil Horizons

Distribution of organic matter in a soil profile greatly affects the distribution and activity of soil organisms.

 

(1) Surface organic layers

Oi horizon -

 

 

 

 

 

 

 

Oe horizon -

 

 

 

 

 

 

 

Oa horizon -

 

 

 

 

 

 

 

(2) Mineral horizons

A horizon -

 

 

 

 

 

 

E horizon -

 

 

 

 

B horizons

Bh

 

 

Bs

 

 

Bhs

 

 

 

 

 

3. What is humus?

 

 

 

 

 

 

 

 

 

 

 

4. Factors affecting soil organic matter levels

 

 

 

 

 

 

 

 

 

 

 

 

 

E. Microbial Movement

Many soil processes involve movement of microorganisms in the soil. This is becoming especially important as soil is becoming more "managed"!!

 

 

 

 

 

1. Movement through soil

How do microorganisms move through soil?

(a) Active -

 

 

 

 

 

 

 

(b) Mass flow of water -

 

 

 

 

 

 

 

(c) Diffusion in water films -

 

 

 

 

 

(d) Roots -

 

 

 

 

(e) Soil animals -

 

 

 

 

 

 

 

(f) Growth -

 

 

 

 

 

 

2. Soil factors affecting movement

Microorganisms being held in soil and not washing through. Two possible causes:

(a) Filtering (entrapment) -

 

 

 

 

 

 

(b) Adsorption -

 

 

 

 

 

3. Isoelectric point (pI) of microbial cell

What is pI?

 

 

 

 

 

Would the soil attract or repel soil microorganisms?

 

 

 

 

 

 

4. Cation Effect

The greater the amount of di and trivalent cations in the soil, the greater the adsorption.

 

 

 

 

 

 

 

 

 

5. Microbial Specificity

Different organisms have different adsorption rates in the same soil. Why?

 

 

III. BACTERIA.

One of the five major soil groups. Most abundant group by far, but because of small size, account for less than half of the microbiological mass in the soil. Rarely are larger than several microns in length and one u in diameter.

 

A. Abundance and Distribution

1. Numbers - depends on method used.

Several 1,000 to several billion, depending on the method used (plate count, direct count) and the type of soil

 

 

Which soil would likely have high, medium, or low bacteria populations:

sand dunes

 

prairie soils

 

agricultural soils

 

forest soil

 

 

 

2. Distribution Pattern

Bacteria (and other soil microorganisms) are not uniformly distributed throughout soil profile. Where would you expect to find the highest numbers?

 

Handout

 

 

 

 

 

B. Environmental Influences

Only mention the factors which are important or unique for this microbial group.

 

1. Water and O2

Excess water reduced infiltration rate of O2 into soil and CO2 out. Generally increase numbers of anaerobic organisms in wet soils.

 

Which microbial groups would be favored in anaerobic soils or microhabitats?

 

 

 

Where in the soil would you expect higher numbers of anaerobic bacteria?

 

Handout

 

 

 

2. pH

The soil bacteria as a group can tolerate wide range - normal pH 4-10. Population size is strongly affected!! The optimum is normally (6.5 - 7.5) slightly alkaline. However, certain genera or species within genera sometimes show very restricted tolerances (e.g., Azotobacter will not grow below pH 6.0), Nitrosomonas below 5.5.

 

 

Thiobacillus thio-oxidans -

 

 

 

Urease bacteria

 

 

 

 

 

 

 

 

C. Bacterial Groupings

Various ways by which the soil bacteria can be described.

1. Taxonomically

Classical system grouping the bacterial into genus and species.

 

"Bergey's Manual" (1957 edition) - 190 genera listed and 51 percent could be broadly considered as soil associated.

 

What criteria are used to separate various genera and species?

 

 

 

 

How effective is this classification system?

 

 

 

 

 

2. Morphologically

Categorize soil bacteria by morphological groups. What does this entail?

 

 

 

 

 

 

 

Two systems are shown in Handout

 

 

 

 

 

 

Any problems with using this classification system?

 

 

 

3. Nutritionally

Two approaches have been used to classify or categorize soil bacteria (and other soil microorganisms) based on their nutritional requirements or transformations:

 

a. Nutrient transformation (physiological groups)

The soil bacteria is grouped by the nutrient or chemical change they cause.

 

Handout # 7

 

 

 

 

This approach does not differentiate among diverse groups: fungi, bacteria, etc.

 

 

b. Nutrient requirements

Soil bacteria are classified according to their nutritional requirements.

 

Handout # 8.

 

 

 

This is one of the most complex and more recent systems that have reduced the number of groups. Generally, large numbers of soil bacteria require the presence of some growth factor.

 

 

 

 

Where would these bacteria obtain these growth factors??

 

 

 

 

 

 

Ecological significance of this?

 

There is very little correlation between the morphological and nutritional schemes.

 

 

Handout

 

 

 

Tendency for gram (-), nonspore forming rods (Pseudomonds) to have simpler requirements and the pleomorphic bacteria to have more complex requirements.

 

 

 

 

4. Ecologically

Divides the soil microflora into three main groups based on ecological role in the soil:

 

Autochthonous (indigenous) - soil population is normally not subject to great fluctuations.

 

 

These organisms as feeding on the stable soil organic matter fractions - lignin, humic acids, etc.

 

 

 

Characteristics:

(Slow growth rate

( not dependant directly on outside energy source

(Arthrobacter group - many authors, but not all)

 

 

 

Zymogenous flora - show very rapid increases in population

 

Use simple carbon sources are exhausted and drop.

 

 

Characteristics:

(Fast grower, pioneer organisms)

(Rapid population fluctuations)

(Directly dependent on outside carbon sources)

 

 

 

Allochthonous (invaders) - do not actively participate in soil biochemical processes.

 

Characteristics:

Present in litter, manure, roots, rain, etc.

(isolated by culturing the soil.)

 

 

 

 

System conceptually good, but difficulty comes when trying to assign specific organisms to each group. Probably best to think of the soil flora as three general groups:

(resting, active, and transient.)

 

D. Methods

1. Qualitative

See what is there, but no accurate estimate of populations.

 

Rossi - Cholodny buried slide -

 

 

Capillary tubes -

 

 

Electron Microscope -

 

 

lmmunofluorescent technique -

 

 

 

2. Elective Culture (Perfusion or enrichment culture)

Altering conditions to the advantage of desired organisms. Allows one to isolate organisms normally present in fewer numbers in soil or a strain having a particular metabolic property.

Examples??

 

 

 

 

 

 

 

3. Quantitative (population size)

a. Direct Counts - Count numbers of microorganisms with microscope. Take soil suspension and place on slide, stain and count based on the area of microscope. Use also with "vital" stains such as acridine dye.

 

Problems??

 

 

b. Plate Counts - dispersal and dilution of soil sample, followed by plating on an agar medium. Here you know you are getting live cells.

Assumptions??

 

 

 

 

 

 

 

 

Vary the media depending on which group of organisms you want.

 

Examples???

 

 

 

 

 

 

 

Populations are much higher when estimated by direct counting techniques (1-9 billion)

Handout Number # 9

 

Why??

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Differences between plate and direct often 50 - 100 times (over 1,000 on handout). This gap narrows greatly immediately after some organic material is added to soil.

Why?

 

 

 

 

 

 

 

 

 

c. Most Probable Number (Extinction Dilution): This technique can also be used for estimating total populations of bacteria in soil. Not as accurate as plate counts for normal counting.

 

Best for the estimation of specific groups which would be difficult to determine on conventional plate counts.

Examples:

Nitrifiers - Procedure consists of placing aliquots of soil dilution into a series of tubes containing liquid NH4 medium (usually five or ten/dilution). The presence of the desired organism is indicated by growth or treatment with suitable chemicals.

If NO3 is present when an indicator is added, turns solution red. The numbers of + and - tubes at each dilution are then compared to most probable number tables to get an estimate of soil populations.

 

Handout # 10

 

 

 

 

Desulfovibrio - Produce FeS which forms black precipitate.

 

 

 

 

Nitrogen - fixing bacteria

B. Distribution and Alumdance

Population estimates have ranged from 10,000=s to millions. Table is Alexander #12. 1-50% of the total population. Populations are much lower in acid soils & in wet, waterlogged areas. Plate counts have generally been used, with specialized media - chitin, ?? one problem here is the apparent waxy surface of the conidia. These conidia will not wet and so float on the surface giving lower counts (Russell 1960) slide techniques indicate very few actinomycates hyphae, so most investigators think the high plate counts are due to spores. Counts are strongly effected by climate and type of soils (see Table). Similar problems exist as found in bacteria as to what is active or not more so than with bacteria-comdiea.