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Soil BiotaSoil Biota

Actinomycetes: Features Belong to the order Actinomycetales

Single celled and produced slender, branched filamentswhich develop into a mycelium in all soil genera except for the

genusActinomyces.

Actinomycetes: Features Individual filaments or hyphae are similar to fungal filament

but are less broad, usuallyy 0.5 to 1.0 mm in diameter.

Produce single ,pairs or chains of asexaul spores known as

conidia on the hyphae .

Few of the soil inhabitants bear their spores in a specializedstructure known as asporangium

Actinomycetes: Features Usually saprophytes

Competitive advantage seems to be in dry soil, high pH,

warm

Temperatures and high organic matter environments.

LikeBacillus tend to exist in spores.

Have aerial mycelium

Actinomycetes: Features Have extensive branching

Growth in liquid culture merely results in turbidity.

Common Actinomycetes in Soil 1. Streptomyces

Long chains of spores formed on filaments growing above

the medium

Species very numerous in soil and many produce antibiotics.

Streptomyces are G+ and are oxidative organotrophs.

Common Actinomycetes in Soil They make up about 90% of the actinomycete isolations from soil.


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They produce well developed compact branched mycelium and

compact colonies on agar plates.

Mycelium does not divide into segments but gives rise to conidia

Reproduction is by production of aerial spores and by mycelial

fragmentation.

Common Actinomycetes in Soil Colonies on agar media tend to be tough and have a leathery

consistency, and resist destruction by mechanical force.

They are the causal organisms of of potato scab, S. scabies

Many streptomyces produce antibiotics, variously

antibacterial, antifungal, anti-algal or anti-tumor.

Common Actinomycetes in Soil The also produce geosmin which is responsible for the smellof freshly plowed soil.

Chitin hydrolysis is often frequently encountered among

many species ofStreptomyces

Common Actinomycetes in Soil 2. Nocardia

Second most abundant, about 10 to 30%

They are aerobic and gram-positive. Mesophilic actinomycetes

Filaments unstable, fragmenting into bacteria-like units;

filaments do not usually grow above medium and spores are rarely

produced.

Common Actinomycetes in Soil The colonies ofNocardia and true bacteria bear a marked

resemblance to one another in general features and in consistency.

Some species are well documented for the metabolism of

paraffins, phenols, steriods and pyrimidines.

Common Actinomycetes in Soil 3. Micromonospora


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Third most frequently encountered, and forms less than 1-

15% of actinomycetes growing on solid media.

Filaments do not grow above medium; single spores

produced in and on surface of medium

Colonies are slow growing in most media

Common Actinomycetes in Soil Each hyphae is between 0.3-0.8 mm in diameter, while the

spores are oval to round and are produced at the terminus of the

specialized conidiophores.

Micromonospora strains decompose chitin, cellulose,

glucoides and hemicelluloses

Common Actinomycetes in Soil 4. Thermoactinomyces

Very similar to micromonospora

Single spores formed on filaments above and within medium.

Spores resistant; all species thermophilic

Very common in heating compost heaps

Common Actinomycetes in Soil 5. Streptosporangium

Spores formed in sporagia or in chains on the filament above

the media

Colony appearance similar to Streptomyces

Activity and Function

The develop far more leisurely than most fungi and bacteria. Not effective competitors and are not prominent when

nutrient levels is high and the pressure of competition is great.

Actinomycetes are heterotrophic feeders, and their presence

is therefore conditioned by the availability of organic substrates.


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Activity and Function Activity and Function Utilization of carbon sources include simple and highly complex

organic molecules from organic acids,and sugars to polysaccharides

proteins, lipids and aliphatic hydrocarbons.

Cellulose is decomposed by many species in pure culture, but rate ofdecomposition is slow.

Many strains have the capacity to synthesize toxic metabolites.

Activity and Function

They participate in a number of processes which include

a. Decomposition of certain resistant components of plant and

animal tissues. They are usually effective competitors only when

resistant compounds remain

b. Formation of humus through the conversion of plantremains and leaf litter into the types of compounds native to the soil

organic fraction.

Activity and Function c. Transformation at high temperature particularly in the rotting

and heating of green manures, hay, compost piles, and animal

manures.

d. Cause of certain soil-borne disease of plants ; for example,

potato scab and sweet potato pox, for which the causal agents are

S.scabies and S. ipomoeae, respectively.

Activity and Function e. Cause of infections of humans and animals ; for example,

Nocardia asteroides andN otitidis-caviarum..

f. Possible importance in microbial antagonism and in

regulating the composition of the soil community.- This role may be a result of the ability of many actinomycetes to excrete

antibiotics or their capacity to produce enzymes that are responsible for lysis of fungi and

bacteria.


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Bacteria: Features 1.One-celled organisms, whose genetic material are not enclosed in a

special nuclear material. About 4-5 mm (0.004-0.005mm)

2. Lack nuclear membrane and thus are termed prokaryotic.

3. Nucleoplasms not separated from cytoplasm. 4. Cell walls composed principally of peptidoglycans.

5. Reproduction of binary fission. 6. Genetic exchange accomplished by conjugation and transduction. 7. Appendages called flagella. Many swim by means of whiplike

Conjugation involves large transfer of genetic materials between donor and

recipient cells in mating. Transduction involves direct genetic exchange of DNA by virus attacking bacteria

(bacteriophage).

Groupings 1 Energy Source

a.Light as energy source -phototrophic

b. Chemicalas energy source-chemotrohic

2. Carbon Sources.

a. CO2 as C source- Lithotrophic (autothrophic) b. Organic substrate as C source- Organotrophic (hterrotropjic)

Groupings Photolitotrophs - Higher plants, algae, cyanobacteria, green sulfur

bacteria. (Photoautotroph).

Chemoorganotrophs - Require preformed organic nutrients as their

energy and carbon sources (Heterotrophs).

Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-,

S2O32-(Chemoautotrophs).

Groupings Photolitotrophs - Higher plants, algae, cyanobacteria, green sulfur

bacteria. (Photoautotroph).

Chemoorganotrophs - Require preformed organic nutrients as their

energy and carbon sources (Heterotrophs).


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Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-,

S2O32-(Chemoautotrophs).

Groupings 3. Ecological Groupings

i. Autochthonous (indegenous)- grow slowly in soils containingno easily oxidizable substrates. Humus degraders.

Indeginous populations may have resistant stages and endure long

periods without being active metabolically, but at some time these natives

proliferate and participate in the biochemical functions of the community.

Groupings ii. Zymogenous grow very fast on fresh residues in soil.

Opportunists.

a. K-Selected Species - Adapted to livng under conditions

of bountiful supply of energy. b. R-Selected Species -Live in uncrowded but physically

restrictive environments.

iii. Invaders or Allochthonous- These do not participate in

community.

Groupings activities. They enter with precipitation, disesed tissues, animal

manure , or sewage sludge, and they may persist for some time in a

resting form. They never contribute significantly to the various ecological

transformations and interaction. Not widely used now

New terms are now Oligotrophy and Copiothropy respectively

Groupings 4. Morphological

a. Cocci- Usually round, but may also be oval, elongated or

flattened on one side.

b. Bacillus

c. Spirillum- Have distinctive helical shape like a corkscrew, their

cell bodies are fairly rigid.

d. Pleomorpism -Have may shapes, not just one in a life- time

Groupings 5. Aeration Status

a. Aerobes -O2 required


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b. Anaerobes -O2 not required

c. Facultative -Grows in the presence or

absence of O2.

Groupings 6. Cell Wall Chracteristics

Gram-Positive:

Plasma membrane is surrounded but thick cell wall

Cells have peptidoglycan and teichoic acids

Gram negative:

Have thinner cell wall which is surrounded by outer cell membrane.

Has peptidoglycan but lack teichoic acids.

Conventional Taxonomy and GC ratios Guanine + Cytosine content of DNA

G +C/A+T + G + C x 100%

GC ratio vary over wide range from 20 to 80 %

Generating Phylogenetic Trees from RNA

sequences 1. Pure Culture

2. Amplify genes encoding 16S ribosomal RNA from

genomic DNA using PCR

3. Sequence PCR product

4. Analyze data by computer analysis


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Steps In Biodiversity Analysis of Microbial

Community 1. Extract DNA

2. Ribosomal DNA obtained by PCR

3. Run Gel

4. Sequence and compare clones

Importance of Soil Bacteria 1. Higher amount in soil than counted in plate.

2. Most important group in soil.

3. Contain members that grow rapidly. 4. Cannot readily degrade lignin.

5. Important in reduction of inorganic compounds.

6. Most important in the degradation of synthetic

biodegradable compounds

7. Most soil bacteria are heterotrophs. Few are autotrophs.

Importance of Soil Bacteria Common Soil Bacteria.

1. Arthrobacter -lot of unusual shapes; K strategist.

2. Bacillus -spore formers; R-strategists

3. Pseudomonas -tend to degrade a lot of things; R-strategists

4. Agrobacterium

5. Alcaligens

6. Corynebacterium -K-strategist, non-sporeforming

7. Micrococcus -Highly underestimated


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8. Staphylococcus

9. Xanthomonas

10. Mycobacterium Acid fast, less common and small significance

11. Sarcina

Common Bacteria in Soils

1. Pseudomonas G- , straight or curves rods with polar flagellata.

Aerobic except denitrifying groups

Organotrophic (most), few lithotrophic

Some are pathogenic

Attack a wide range of organic substrates including sugars,

amino acids, alcohols, and synthetic pesticides.

Many species produce pigments in media especially ironmedia.

Yield 3-15 % of colonies on agar

Involved in may soil transformations

Common Bacteria in Soils 2. Arthrobacter

Members of this genus are the numerically predominant

bacteria in the soil as determined by plate counts

Account for 5-60% of plate counts Numerically predominate in soil ( as determined by plate

count) 40% of the total plate count .

Characterized by pleomorphism and Gram variability

Slender, gram negative (G-) rod in early stage of growth.

Very short gram positive (G+) rods and coccoid at later stage of

growth

Slow growers and poor competitors in the early stages of residue

decomposition; K-strategist.

Common Bacteria in Soils 3. Bacillus:

7-67% , About 5-20 of the total bacterial count as determined

by plate counting.


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Numbers quite high, about 106 to 107 or more/gram soil

Gram negative (G-) to Gram positive (G+) variable rods

Most species are motile

Common Bacteria in Soils Heat resistant endospores are placed and sporulation is not

repressed by exposure to air.

Most are vigorous organothrophs

Metabolism is strictly respiratory, strictly fermentative or

both.

Some species are facultative litotrophs that use H2 as energy

source in

Common Bacteria in Soils the absence of carbon. B. polyxyxa fixes N2

B. thuringiensis is pathogenic to some insect larvae and is

widely used as a biological control agent.

B.anthacis highly virulent animal pathogen -causes anthrax

Common Bacteria in Soils B macerans used for netting flax Temp tolerance ranges from 5-70oC

Tolerance to acid ranges from pH 2-8

Salt tolerance is as high as 25% NaCl

Common Bacteria in Soils 4. Clostridium

Sporogenic species Most species are strict anaerobes

Few are microaerophilic

Plate counts show 103 to 107 cells/g soil


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Genus of economic importance; its species are used

commercially for the production of alcohols and commercial

solvents.

Several species, C. butyricum and C. pasteurianum are

known to fix N2.

Genus is widely distributed in soils, marine, and freshwater

sediments; manures, and animal intestinal tract.

Pathogenic forms in this genus include C..tetani and C.

botulinum.

Part 15 Bergey's manual

Common Bacteria in Soils 5. Xanthomonas

Uses O2 as the only electron acceptor

Nitrates are not reduced

Xanthomonas species are pathogenic to plants.

Common Bacteria in Soils 6. Other Soil Bacteria

a. Azotobacter -aerobic organotrophic capable of fixing

N2 symbiotically.

b. Agrobacterium- Induces galls or other hypertrophies,

such as hairy roots, on plants but does not fix N2.

Common Bacteria in Soils c. Nitrobacter and Nitrosomonas are chemolititrophic

general which cause nitrification in soil.

NH4+ NO2-

NO2 NO3-

d. Thiobacillus: sulfur compounds to SO42-


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S + 11/2O2 + H2O H2SO4\

AIR,WATER & TEMP

Soil Temperature: Processes I. Importance:

Affects physical, biological and chemical processes occurring

in soil.

II. Processes Affected

1. Microbial ActivitySoil Temperature: Processes 2. Seed Germination

Germination of seeds stop between 0-5oC

3. Root growth

4. Physical Weathering

Factors Affecting Soil Temperature 1. Energy Received

30 to 45% of heat is reflected back

3% is used for photosynthesis

Remainder is used to evaporate water

3 to 5% is stored as heat in soil and plant cover

Factors Affecting Soil Temperature Absorbs heat is lost by 1. Radiation into atmosphere

2. Heating of air above soil

3. Evaporation of water

4. Heating of soil


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2. Slope and Gradient

Factors Affecting Soil Temperature 3. Soil Cover

Color affects heat absorbed.

Dark colored soil absorbs about 80% of heat

Light color soil absorbs only about 30%

Factors Affecting Soil Temperature 4. Water Content

Mineral soil require small amount of heat to raise their temp.

The Heat capacity of soil is the heat required to raise 1 gram

of soil 1oC

Specific heat of water is 1.0 cal/gram

The heat capacity of soil is 1/5 that of water, i.e. specific heat

of soil is 0.2 cal/gram

Factors Affecting Soil Temperature

Thus moisture content is important in determining soiltemperature

Drainage is thus an important influence on soil temperature.

Control of Soil Temperature IV. Control Of Soil Temperature

1. Removal of Excess Water

2. Use of mulches and various shading devices


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I. pH Concept Water neutral pH 7

HOH H+ + OH-

At 25oC 1 liter of water weighs 997 gm

1 mole of water weighs 18 gm

Therefore 1 liter of water contains 55.4 moles of water

I. pH Concept In a liter of water 55.339,999,8 moles exist as H2O

0.000,000,1 is in H+ form and 0.000,000,1 is in the OH -

form

I. pH ConceptpH = -log [H+] or

pH = 1/[H+]

If [H+] = 10-7 moles/L

pH = -log [10-7] = 7

III. Developmento f Soil Acidity 1.1. Strongly Acid Soil.Strongly Acid Soil.

Much H+ under very acid soils because Al becomessoluble and is present in the form of Al3+ or Al hydroxyl cations.

These become preferentially absorbed in preference to H

+

bythe permanent charges on soil colloids.

III. Developmento f Soil Acidity The adsorbed Al is in equilibrium with Al3+ ions in the soil

solution. H+ released as Al3+ hydrolysis results in the soil acidity in

strongly acid soils


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Adsorbed H+ ions is the second major source of H+

concentration under these conditions.

III. Development o f Soil Acidity 2.2. Moderately Acid Soils.Moderately Acid Soils. Al compounds and H + ions account for H+ ions in these soils

but the mechanism is different .

These soils also have higher percent base saturation and pH

values.

Al3+ is converted to aluminum ions by reactions such as:

III. Developmento f Soil AcidityAl3+.6H20 Al (OH)2.5H2O + H+

Al(OH)2+.5H2O Al( OH)2+.4H20 + H+

Some Al hydroxy ions are absorbed as exchangeable cations

III. Developmento f Soil Acidity In moderately acid soils absorbed H

+

ions makes acontribution to the soil solution H+ concentration.

As pH rises, some H+ held strongly by clay are now subject

to release.

These are associated with pH -dependent groups.

III. Developmento f Soil Acidity 3.3. Neutral to Alkaline Soils.Neutral to Alkaline Soils. Soils that are neutral and Alkaline are no longer dominated

by H+ and Al3+ ions.

Permanent charge sites are now occupied by exchangeable

bases and both Al and H are largely replaced by cations such as

Ca2+, Mg2+, K+.


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III. Developmento f Soil Acidity H+ ion is released more into soil solution and react with OH-

ions to form H2O.

Overall pH in soil is a balance between Al3+ and H+ in soil

and OH- produces by basic cations.

The ion which predominates determine the soil pH. The right

balance yields a pH of 7

pH is between 6.5 and 7

III. Developmento f Soil Acidity

5.5. Calcareous SoilsCalcareous Soils Contain CaCO3 which is relatively insoluble.

Calcareous soils are 100% base saturated and pH is

controlled by the hydrolysis of CaCO3 as follows:

III. Developmento f Soil Acidity

6. Sodic Soils6. Sodic Soils These are soils are dominated by sodium.

Occurs when soil is 15% or more saturated with Na or

Na2(CO3). Hydrolysis of Na2 (CO3) release NaOH. Organic matter is highly dispersed in these soils.

Soils contain small amounts of Ca2+ and Mg2+ but larger amounts of

Na+.

Energy Concept - Water Potential. Free Energy :

Free Energy - Summation of all forms of energy available to

do work, e.g. potential, electrical and mechanical (kinetic).


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t= total soil water potential

g= gravitational potential

m= matric potential

o = osmotic potential

Gravitational Potential This is the component due to the position of the soil water in

a gravitational field.

The gravitational potential is important in saturated soils and

is shown by the tendency of water to flow to a lower elevation.Matric Potential: This is the result of the adhesive and cohesive forces

associated with the particle network of the soil or the soil matrix.

The potential is expressed relative to pure water; thus, as

soils dry and the energy content of water decrease, the matric

potential decreases

Matric Potential: The matric potential is the controlling factor in water

movement in unsaturated soils.

It is also important in movement of water from soil into plant

roots and microbes.

Osmotic Potential: This is due mainly to the attraction of water molecules for

ions produced by soluble salt.

Normally in leached soils the osmotic potential is small and

is a minor factors in water absorption.


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The osmotic potential of saline soils, by contrast, reduces the

ease that water moves into plant roots and microbes.

Plant - Soil Water Relations :

1. Maximum rententive Capacity Matric potential - 0.

2. Field Capacity : Following rain or irrigation water

moves rapidly down due to gravity or hydraulic gradient.

The point at which rapid movement becomes negligible is

called the field capacity.


At this time water has moved out of the macropores and havebeen replaced by air.

Micropores are still filled with water and will supply with

water.

The matric tension will vary slightly from soil to soil but is

generally between 0.1 - 0.3 bars.

SMT at field capacity generally set at 1/3atm (equivalent to

11ft high of water).

At field capacity SMT is low and plants root can easilyabsorb water.

Plant - Soil Water Relations : 3. Permanent Wilting Percentage:

As plants absorb water they lose most of it at leaf surface

through evapo-transpiration.

Water also lost by evaporation.

Loss occur simultaneously.

As soil dries, plants regain vigor at night.Plant - Soil Water Relations : Ultimately, the rate of water supply is so

slow that plants will remain wilted both day and night.

Although not dead, the plants are in a permanent wilted

condition and will die if water is not added.


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Matric potential at this time will be about 15 bars (kpa) for

most crop.


Soil moisture content at this point is called the permanentwilting percentage.

Water remaining in soil is found in the smallest of

micropores.

A considerable amount of water is not available to plants.


4. Hygroscopic Coefficient : If water is kept at anatmosphere that is essentially completely saturated with water

vapor (48% relative humidity), it will lose liquid held even in the

smallest micropores.

The remaining water will be associated with the surfaces of

soil particles, particular colloids, as adsorbed moisture.

Plant - Soil Water Relations : It is held so tightly that it is considered nonliquid and can

only move in vapor phase. Water content at this point is termed hygroscopic coefficient.

Tension at this point is 31 bars.

Soils high in colloidal materials hold more water under this

condition than sandy soils.

Plant - Soil Water Relations : 1. Gravitational Water: Water in excess of field capacity

(0.1 - 0.3 bars).

Under saturated conditions water in macropores have positivepotential determined by distance below surface of saturated zone.

This water will flow freely from regions of higher pressure to

lower pressure (higher elevation to lower elevation).


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Physical Classification The water that "freely flows or drains out of soil is called

gravitational water.

1. Exist in micro pores. 2. Is either free or under very low tension.

3. Moves freely through macropore space in response to

very small water pressure diffusion or gravitation.

Physical Classification of Soil Water 2. Capillary - Water held in capillary pore (0.1 - 31 bars).

3. Hygroscopic water - Water held in tension values greater

than 31 bars.

BiologicalClassification of

Soil Water 1. Available water :

Water retained in soil between field capacity (0.1 - 0.3

bars) and permanent wilting percentage (15 bars) is said to be

usable by plants and said available.

2. Unavailable water : Water held at tension greater than 15 bars.

Soil Water Determination 1. Gravimetric. a. Per Cent By Weight

- Pw= X 100

b. Per Cent by volume- Pv= Pw x Db

Soil Aeration Soil Aeration : Soil aeration is the mechanism of gas exchange in

soils that prevents O2 deficiency and CO2 toxicity.


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Well-aerated soil : This is a soil in which gas exchange between the

soil air and the atmosphere is sufficiently rapid to prevent a deficiency of O2

or CO2 toxicity and thereby permits normal functioning of plant roots and

aerobic organisms.

Soil Aeration Conditions for Satisfactory :

1. Sufficient spaces free of solids and water should be

present.

2. Ample opportunity for easy movement of air.

Soil Aeration Soil Atmosphere Vs Atmosphere :Atmosphere = 79% N, 21%, O2, 0.03% CO2Soil Atmosphere =10-100% CO2 concentration

Slightly less O2 concentration

N remains about the same.

O2 can drop to 5% or even zero in subsoils.

Soil AerationUnder actual field conditions two conditions may result in poor aerationof soil.

1. Moisture content excessively high.

2. Gaseous exchange not sufficiently rapid.

1. Excess Moisture: Waterlogging

poorly grained, fine-textured soils

small macropores.

ell-drained soil - compaction.

Soil Aeration 1. Low-lying areas - water tends to stand.

Consequences : Root growth hampered.

Prevention: Rapid removal of excess water either by

land drainage or controlled runoff.


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Artificial drainage of heavy soils.

Soil Aeration 2) Gaseous Interchange : Dependent on two factors:

a. Rate of biochemical reactions.

b. Actual rate at which gas is moving into and out ofsoil.- a. More rapid oxygen use leads to carbon dioxide. Factors : - Temperature, Organic residues

Soil Aeration b. Air Exchange :

Two mechanisms: (i) Mass flow (ii) Diffusion.

(i) Mass flow due to pressure difference between atmosphere

and soil air.

Very small thus not very important in determining the total exchange that occurs. (ii) Diffusion : Most gaseous exchange occurs by diffusion. Gas tends to move in direction determined by partial pressure.

Soil Aeration Heavy-texture top soils, especially those with poor structure,

and in compact sub soils, rate of oxygen movement is very slow.

Such soils also allow only slow oxygen penetration and thus

prevent rapid escape of carbon dioxide.Factors Affecting Aeration a. Air space available, biochemical rates and gaseous

exchange.

Total porosity determined by bulk density.

This in turn is related to texture and structure and soil organic

matter.

Also macropore to micropores is important.

In poor drained soils high proportion of soil is occupied bywater.

Factors Affecting Aeration (ii) Carbon dioxide content related to biological activity in soil.

Microbial decomposition of organic residues accounts for major

portion of carbon dioxide evolved.


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Incorporation of large quantities of organic matter, manure, sewage

sludge will alter soil air composition considerably if soil moisture and

temperature is adequate.

Factors Affecting Aeration Respiration by higher plants and contribution of their roots to organicmass by sloughage are also significant processes.

b. Subsoil Vs Topsoil :

Subsoils more deficient in oxygen than topsoil.

Total pore space as well as average size of pores is generally less in

deeper horizons.

Oxygen percent in soil air decreases with depth, the rate of decrease is

much rapid in heavy soils.

Factors Affecting Aeration c. Soil heterogeneity : Considerable variation exists in the aerationstatus of soil.

Thus poorly aerated zones may be found in an otherwise well drained

soil.

d. Seasonal differences : This has marked effect on in the

composition of soil air.

Most of this variation is accounted for by soil moisture and soil

temperature differences.

High soil moisture tends to favor low oxygen and high carbon dioxide

levels in soil air e.g. in winter and spring.Effects of Soil Aeration on

Biological Activities a. Effects on higher plants :

High plants adversely affected in at least four ways by poor aeration.

(i) The growth of the plant, particularly the roots, is curtailed.

(ii) The absorption of nutrients is decreased.

(iii) The absorption of water is decreased.

(iv) The formation of toxic inorganic compounds.

Effects of Soil Aeration on

Biological Activities

b. Effect on Microbes:

Slow decay of organic matter in surveying areas.

Transformation of nutrients.


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Class of microbes.

Reduced compounds Mn2+, Fe2+ leading to toxicity.

Effects of Soil Aeration on Biological Activities c. Other Effects

Anaerobic decomposition of organic matter much slower than that

occurring when oxygen is available.

C6H12O6 ----------> 3CO2 + 3CH4 Organic acid production ------> toxicity.

C2H4 affects plant roots.

A not subject to nitrification.

Effects of Soil Aeration on Biological Activities Carbon CO2 CH4

N NO3- N2, NH4+

Sulfur SO42- H2S, S2-

Fe Fe 3+ (ferric ) Fe2+(ferrous)

Mn Mn 4+ Mn2+

ARCHAEASoil Biota

Reading AssignmentReading Assignment

Soil Microbiology:Soil Microbiology:An exploratoryAn exploratory

ApproachApproach

Chapters 10 & 11Chapters 10 & 11


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Archaea Separable from bacteria both by their molecular phylogenyand phenology.

Cell membranes are unique.

Basic structure of cell membrane is 5-C isoprene unit

These are linked to form up to 20 chains

Chains are ether linked to glycerol, not ester as in bacteria

and eucaerya.

Halophiles have glycerol diether units;

Methanogens have mixed glycerol-diether and diglycerol-

tetraether units

In thermophilic archaea, tetraether membrane are

predominant

Archaea Divisions: 3 major Kingdoms

1. Crenarcheota

2. Euryarcahaeota

3. Karorcaeota

Archaea 1. Kingdom Euryarchaeota- Representative Groups

1. Extreme Halophiles e.g Halobacterium

2. Methanogens e.g.Methanobacterium,

Methanococcus, Methanospirillum

3. Extreme thermophiles e.g.

Thermococcus, Thermoplasma


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Archaea 2. Kingdom Crenarchaeota

- Representative groups:

1. Thermoacidophiles e.g. Sulfolobus

2. Strictly anaerobic Crenarcahaeotes e.g.

Pyrodictum

Archaea Extreme Halophiles

Require High NaCl concentrations

Most grow best at 3-4 M Can go as a high as 5.2 M

Few can grow at 1.5 M

Counterbalance external NaCl concentration by accumulating

high concentration of KCl

Archaea Many produce red carotenoid pigment which gives them protection

from sunlight.

They are mainly aerobic and organotrophs Many use light drive cellular metabolism.

In cellular metabolism, cells use the pigment retinal, the lack the plant

and bacterial chlorophylls.

Archaea Metahnogens Strict anaerobes

Produce CH4 as metabolic products

Methane emissions occur in marshes, swamps, marine sediments;

from intestines and rumens of animals; and from sludge digesters and insewage plants.

Do not use sugars as a source of cell C.

Archaea CO2 is the major C source.


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The C atom is reduced to CH4 by electrons derived from

hydrogen.

Normally uses C with no C-C bond e.g. formate, methanol.

Major source of natural methane emissions.

Archaea Extreme Thermophiles

Constitute a diverse group of archaea

Has four genera:

1. Archaeoglobus,

2. Thermoplasma,

3. Thermococcus, and

4. Pyrococcus

Archaea Archaeoglobus

Strictly anaerobic and chemorganotrophic

Catabolizes sugars and simple peptides, using sulfate as

electron at the electron acceptor

Archaea Thermoplasma

Facultatively anaerobic

Grows best at pH 1.5 and 60oC

Genus does not have a cell wall external to the cell

membrane

Archaea Thermococcus and Pyrococcus

Two very similar except for differences in their growth

temperature

Thermococcus grows optimally at 83oC andPyrococcus at

100oC


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Both are obligate anaerobes and chemorganotrophs.

Archaea Significance in Soil.

1. Serve to regulate soil bacterial population

2. May also function by allowing different competing bacteriato coexist in soil.

3. They may participate in the decomposition of plant

materials.

4. Some are pathogenic e.gEntamoeba histolytica which cases

amoebic dysentry

Viruses The are submicroscopic agents

Consist of DNA or RNA molecules within protein coats. Viral particles are metabolically inert and do not carry out

respiratory or bio-synthetic functions.

They induce a living host cell to produce the necessary viral

components

Viruses After assembly, the replicated viruses escape from the cell

with the capability of attacking new cells.

Viruses infect all categories of animal and plants, fromhumans to microbes.

Those parasitizing bacterial cells commonly are called

bacteriophages, or simply phages

Viruses Significance in Soil

Little is known about the field ecology of viruses that infect soil

organisms except that they persist in soil as dormant units that retain

parasitic activities.

The ability of viral particles pathogenic to plants or animals to survivein soil and move into the water table is of major concern to people.


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ECSC 590 soil microbiologyProblems Set 2

Use these problem set as a guide for your revision.

The questions in bold are assignment to be turned in on Thursday , 30 November

1. Chapter 4 Questions 3 and 5

2. Chapter 6. Questions 4 and 6

3. Chapter 7: Questions: 1, 2 and 4

4. Chapter 8: Questions 1, 2, and 5

5. Chapter 9. Questions 1, 2, 3, 4, and 8


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6. Cahpter 10 Questions 1, 5, 7, and 10

7. Chapter 11 Question 11

7. Chapter 5 What major roles do nematodes play in soils?