Soil Biota Actinomycetes: Features

Belong to the order Actinomycetales Single celled and produced slender, branched filaments which develop into a mycelium in all soil genera except for the genus Actinomyces.

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 specialized structure known as a sporangium

Actinomycetes: Features
Usually saprophytes Competitive advantage seems to be in dry soil, high pH, warm Temperatures and high organic matter environments. Like Bacillus 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.

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 smell of freshly plowed soil. Chitin hydrolysis is often frequently encountered among many species of Streptomyces

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 of Nocardia 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

Third most frequently encountered, and forms less than 115% 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 5. Streptosporangium

Common Actinomycetes in Soil

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.

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 of decomposition 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 plant remains 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 ; Nocardia asteroides and N otitidis-caviarum.. f. Possible importance in microbial antagonism regulating the composition of the soil community.

for example, and in

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.

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. 6.

Reproduction of binary fission. 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

Energy Source a. Light as energy source - phototrophic b. Chemical as 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).

Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-, S2O32-(Chemoautotrophs).

Groupings
3. Ecological Groupings i. Autochthonous (indegenous)- grow slowly in soils containing no 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

b. Anaerobes c. Facultative absence of O2.

-O2 not required -Grows in the

presence or

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 RNA from

2. Amplify genes encoding 16S ribosomal genomic DNA using PCR

3. 4.

Sequence PCR product Analyze data by computer analysis

Steps In Biodiversity Analysis of Microbial Community

1. 2. 3.

Extract DNA Ribosomal DNA obtained by PCR 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 2. Bacillus 3. Pseudomonas 4. Agrobacterium 5. Alcaligens 6. Corynebacterium 7. Micrococcus

-lot of unusual shapes; K strategist. -spore formers; R-strategists -tend to degrade a lot of things; R-strategists -K-strategist, non-sporeforming -Highly underestimated

8. 9. 10. 11.

Staphylococcus Xanthomonas Mycobacterium Sarcina

Acid fast, less common and small

significance

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 iron media. 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.

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

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. a. N2 b. such as

Other Soil Bacteria Azotobacter -aerobic organotrophic capable of fixing symbiotically. Agrobacterium- Induces galls or other hypertrophies, hairy roots, on plants but does not fix N2. chemolititrophic

Common Bacteria in Soils

c. Nitrobacter and Nitrosomonas are general which cause nitrification in soil. NH4+ NO2NO2 NO3 d. Thiobacillus: sulfur compounds to

SO42-

S + 11/2O2 + H2O

H2SO4

AIR,WATER & TEMP

Soil Temperature: Processes

I. Importance: Affects physical, biological and chemical processes occurring in soil.

II. 1.

Processes Affected Microbial Activity

Soil Temperature: Processes

2.

Seed Germination

Germination of seeds stop between 0-5oC 3. 4. Root growth 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 Absorbs heat is lost by 1. Radiation into atmosphere 2. Heating of air above soil 3. Evaporation of water 4. Heating of soil

Factors Affecting Soil Temperature

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 soil temperature

Drainage is thus an important influence on soil temperature.

Control of Soil Temperature

IV. Control Of Soil Temperature 1. 2. Removal of Excess Water Use of mulches and various shading devices

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 Concept
pH = -log [H+] pH = 1/[H+] If [H+] = 10-7 moles/L pH = -log [10-7] = 7 or

III. Developmento f Soil Acidity

1.

Strongly Acid Soil. Much H+ under very acid soils because Al becomes

soluble and is present in the form of Al3+ or Al hydroxyl cations. These become preferentially absorbed in preference to H+ by the 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

Adsorbed H+ ions is the second major source of H+ concentration under these conditions.

III. Development o f Soil Acidity

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:

2.

Moderately Acid Soils.

III. Developmento f Soil Acidity

Al3+.6H20 Al (OH)2.5H2O + H+
2+ Al(OH) .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 a contribution 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.
+

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+.

III. Developmento f Soil Acidity

H+ ion is released more into soil solution and react with OHions 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. Calcareous 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 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).

Substances have a tendency to move from a state of higher to one of lower free energy.

Energy Concept - Water Potential.

Water moves from soil saturated with water (high free energy) to dry soil (low free energy).

Absolute free energy is not as important as differences in energy levels from one contiguous site to another.

Factors Affecting Free Energy :

1.

Adhesion - attraction to soil solid

(matrix)

This provides matric force responsible for capillarity and reduces the free energy of the adsorbed water and those held by cohesion.

Factors Affecting Free Energy

2. Attraction of ions and other solutes for H2O results in osmotic forces. This also tends to reduce free energy of H2O.

3. Gravity tends to pull water downwards. Free energy at given elevation higher than at lower elevation.

Total Water Potential:

This is the difference in free energy between two contiguous It ultimately determines soil water behavior.

sites.

Total soil water potential is in effect the sum of the potential resulting from various forces acting on soil H2O and is described by the relation below:

Total Water Potential:

t = g + m + o Where:

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.

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.

Plant - Soil Water Relations :

At this time water has moved out of the macropores and have been 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 easily absorb 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.

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

Plant - Soil Water Relations :

Soil moisture content at this point is called the permanent wilting percentage.

Water remaining in soil is found in the smallest of micropores.

A considerable amount of water is not available to plants.

Plant - Soil Water Relations :

4. Hygroscopic Coefficient : If water is kept at an atmosphere 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 positive potential 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).

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.

Biological Classification 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.

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% CO2 Soil Atmosphere = 10-100% CO2 concentration

Slightly less O2 concentration N remains about the same. O2 can drop to 5% or even zero in subsoils. Under actual field conditions two conditions may result in poor aeration of 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

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.

Artificial drainage of heavy soils.

2) Gaseous Interchange : Dependent on two a. Rate of biochemical reactions. b. Actual rate at which gas is moving into and
a. More rapid oxygen use leads to carbon Factors : - Temperature, Organic residues

Soil Aeration

factors: out of
dioxide.

soil.

Soil Aeration
b. Air Exchange : Two mechanisms: (i) Mass flow (ii) Diffusion. (i) Mass flow due to pressure difference between and soil air.

atmosphere diffusion.

Very small thus not very important in determining the total exchange that occurs.

(ii)

Diffusion : Most gaseous exchange occurs by

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 by water.

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.

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 organic mass 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 aeration status 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.

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 N Sulfur Fe Mn

CO2 NO3SO42-

CH4 N2, NH4+ H2S, S2Fe2+(ferrous) Mn2+

Fe 3+ (ferric ) Mn 4+

ARCHAEA

Soil Biota
Reading Assignment Soil Microbiology: An exploratory Approach Chapters 10 & 11

Archaea
Separable from bacteria both by their molecular phylogeny and 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 diglyceroltetraether units In thermophilic archaea, tetraether membrane are predominant

Archaea

Divisions: 3 major Kingdoms 1. Crenarcheota 2. 3.

1.

Euryarcahaeota Karorcaeota
Kingdom Euryarchaeota
Representative Groups

Archaea

1. Extreme Halophiles e.g Halobacterium 2. Methanogens e.g. Methanobacterium, Methanococcus, Methanospirillum 3. Extreme thermophiles e.g. Thermococcus, Thermoplasma

Archaea

2. Kingdom Crenarchaeota
Representative groups:

1.

Thermoacidophiles e.g. Sulfolobus e.g.

2. Strictly anaerobic Crenarcahaeotes 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 in sewage plants. Do not use sugars as a source of cell C.

Archaea
CO2 is the major C source.

 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 Archaeoglobus Strictly anaerobic and chemorganotrophic

Archaea

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 and Pyrococcus at 100oC

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 bacteria to coexist in soil. 3. They may participate in the decomposition of plant materials. 4. Some are pathogenic e.g Entamoeba 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, from humans 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 survive in soil and move into the water table is of major concern to people.

ECSC 590 soil microbiology Problems 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. 2. 3. 4. 5.

Chapter 4 Chapter 6. Chapter 7: Chapter 8: Chapter 9.

Questions 3 and 5 Questions 4 and 6 Questions: 1, 2 and 4 Questions 1, 2, and 5 Questions 1, 2, 3, 4, and 8

6. 7. 7.

Cahpter 10 Chapter 11 Chapter 5

Questions 1, 5, 7, and 10 Question 11 What major roles do nematodes play in soils?