Bilogical Properties of Soil

Soil organism

Creatures that spend all part of their lives in the soil environment

Function of Soil Organisms in relation to higher plants

• Organic matter

• Nutrient cycling

• Inorganic transformations

• Nitrogen fixation

• Plant protection

• Some are pests, but most are beneficial

Classification of Soil Organisms

• Based on Size

• Based on metabolism

• Base on ecological function

• Based on hierarchy in soil food web

• Based on three domain system

Based on Size

• Megafauna

• Macrofauna

• Mesofauna

• Microfauna

Based on Metabolism

• Carbon Source

  Autottrophs

  Heterotrophs

• Energy Source

  Phototrophs

  Chemotrophs

• Electron Sources

  Lithotrophs

  Organotrophs

Some terms can be combined to classify organisms by both energy and carbon source

• Photoautotrophs

• Chemoheterotrophs

• Chemoautotrophs

• Photoheterotrophs

Megafauna

size range >20 mm upward

(E.g. Moles, rabbits, and rodents)

Macrofauna

Size range 2- 20 mm

(e.g. Earthworms, beetles, centipedes)

Mesofauna

Size range 100 um to 2 mm

(e.g. Tardigrades, mites, springtales)

Microfauna

Size range one to 100 um

CS-Autotrophs

CS-Heterotrophs

ES-Phototrophs

ES-Chemotrophs

ELS-Lithotrophs

ELS-Organotrophs

Based on Ecological Function

• Herbivores

• Detritivores

• Predators

• Parasites

Based on Hierarchy

• First Level

• Second Level

• Third Level

• Fourth Level

• Fifth Level

Based on th Three Domain system

• Eukarya

• Bacteria

• Archaea

Soil Biodiversity-Biodiversity

set of animal and vegetable species their genetic material and the ecosystem they belong to

Diversity of Soil Organisms

• Genetic Diversity

• Species Diversity

• Ecosystem Diversity

• Functional Diversity

Ecosystem Dynamics

• Functional Redunduncy

• Keystone species

Soil Organisms

• Soil Fauna

• Soil Flora

• Soil Fungi

• Prokaryotes: Bacteria & Archaea

• Actinomycetes

• Virus

Examples of Soil Fauna

• Earthworms (Oligochaetes)

• Ants

• Termites

• Nematodes

• Protozoa

• Amoeba (Testate, Naked)

• Ciliates

• Flagellatess

Types of earthworms

• Epigeic

• Endogein

• Anecic

Nematodes-Cryptobiotic State

The resting state of the nematode

Flagellates-Cyst

Resistant resting stage, forms when the soil dries and becomes food scarce

Soil Flora

• Roots

• Soil algae

Roots

• Mucigel

• Rhizosphere

• Endorrhizosphere

• Rhizoplane

• Extorhizosphere

• Rhizodeposition

• Allelopathy

• Rhizobacteria

• Plant-growth Promoting Rhizobacteria (PGPR)

Soil Algae-Lichen

Symbiotic association of fungi with algae and certain cyanobacteria

Common Soil Algal Division

A. Chlorophycophyto- green algae

B. Charophyta- stoneworts

C. Euglenophycophyta- euglenoids

D. Phaeophycophyta- brown algae

E. Chrysophycophyta- golden & yellow algae

F. Pyrrhophycophyta- dinoflagellates

G. Cryptophycophyta- cryptomonads

H. Rhodophycophyta- red algae

Soil Fungi-Hyphae

Individual fungal filament

• Septate or non-septate commonly multinucleated

Soil Fungi-Mycelia

• Woven ropes of hyphae

Soil Fungi- Mycotoxins

• Hghly toxic chemicals that are produced by fungi

Example of Soil Fungi

• White rot fungi

• Yeast

Types of Endomycorrhiza

• Abuscular Mycorrhizae (AMF)

  Arbusceles

  Vesicles

  Auxillary cells

  Glomineae

  Gigasporineae

• Erichoid Mycorrhizae

• Monotropoid Mycorrhiza

• Orchid Mycorrhiza

Prokaryotes: Bacteria & Archaea- Bacteria

• Most numerous of the microorganisms

• Cell wall is principally composed of peptidoglycan

Classification of bacteria

• Based on pH

  • Acidophile

  • Nuetrophile

  • Alkalophile

• Based of Temperature

  • Psychrophile

  • Psychrotoph

  • Mesophile

  • Thermophile

  • Hyperthermophile

• Based on Oxygen Requirement

  • Obligate aerobe

  • Facultative Anarerobe

  • Aerotolerant Anaerobe

  • Obligate Anaerobe

  • Microaerophile

Archaea

Cell membranes of archaea differ from bacteria, such as the use of isoprene derivatives instead of fatty acids

Cynobacteria

• Previously called blue-green algae

• Chlorophyll bearing

• Numerous rice paddies and other wetland environments

Actinomycetes

• Term traditionally used for bacteria in the orded actinomycetales within the phylum actinobacteria

Geosmins

Volatile derivatives of terpene, that gives the soil the earthy aroma of soils.

Streptomycetes

A genus of Actinomycetes capable of producing antibiotics (Streptomyces)

Virus

• Consist of RNA and DNA mlolecules with protein coat

• Metabolically inert and do not carry out respiratory or biosynthetic functions

Soil Characteristics that influence the activity of soil microorganisms

• Organic Resources

• Oxygen level

• Moisture and temperature condition

• Soil pH/Exchangable Calcium

Soil Organic Matter (SOM)

• Refers to the entire portion of the soil

• Surface residue is not considered to be part of SOM

Soil Organic Carbon

• Used to refer to the C component of soil organic matter

• SOM is higher in temperate areas than in tropical areas

• The SOM content of agricultural topsoil is in the range 1-6%.

Humus

• Dark colored, heterogeneous, mostly colloidal-sized mixture of bits of plants and microbial tissues, modified lignin and other plant compound

Organic Components of Soil

1. Fresh residue

   • Carbohydrates (60%)

     • Cellulose- most abundant polysaccharide

     • Cellulase- Enzyme that can break the bonds cellulose, thus catalysing the decomposition of starch

   • Lignin (25%)

   • Protein (10%)

   • Fats, waxes, tannins (5%)

2. Decomposing OM (Active Fraction)

   • 10-30% of SOM

3. Stable OM

   • Humus- Can absorb water six times its weight

4. Living Organisms- Promotes active decomposition of the fresh residue

Influence of OM on Plant Growth and Soil Function

• Biological

• Chemical

• Physical

Decomposition- Decomposition process

1. Enzymatic Oxidation

2. Release of Essential Nutrient Elements

3. Synthesis Of New Compounds

4. Protection from Further Microbial Decay

Soil Respiration

Anaerobic Decomposition

Factors affecting Organic Matter Decomposition

1. C/N ratio

2. Oxygen supply

3. Moisture

4. Temperature

5. pH, Salinity and mineral Nutrient

6. Amount of Phenolic Compounds

7. Amount of organic matter and stage of decay

Composting

• Controlled Biological aerobic decomposition of organic material into stable humus-like substance called compost

• Process by which various aerobic microorganisms decompose raw materials to obtain energy and material they needed for growth and development

Stages of Composting

1. Active stage

   • period of vigorous microbial activity

   • Readily degradable materials and compounds decomposed as well as some of the more decay resistant materials (primming effect)

   • Characterized by the rapid increase in temperature

2. Curing stage

   • Follows the active stage

   • Lower level of microbial activiyty

   • Further decomposition of the decay resistant material

   • Mineral transformations

C/N ratio

• 20:1 is the optimum ratio

• C/N ratio goes up=slower decomposition, C/N ratio goes down=faster decomposition

• C/N ratio above 30:1= Immobilization

• C/N ratio below 30:1= Mineralization

Principal Components of the compost Mix

1. Primary Substrate

2. Amendment

3. Bulking Agent

Microbial transformation of N

1. Mineralization

   • Conversion of organic N to inorganic N which renders N available for plant use

2. Immobilization

   • Conversion of inorganic N to organic N which renders N unavailable for plant use; occurs when available N is used by soil microorganisms and assimilated into their bodies

3. Ammonification

   • Process by which ammonia is produced by microbial breakdown of organic mater

4. Anammox(anaerobic ammonium oxidation)

   • Anaerobic oxidation of NH4+ in conjuction with NO2- (electron acceptor) to produce N2O gas

   • More recently discovered bacterial process

5. Nitrification

   -Microbial oxidation of ammonium to nitrite and subsequently to nitrate.

   -Carried out by autotrophs

   -Significantly increase the soil acidity by producing H+ ions (reaction 1)

   • Steps 1. Oxidation of ammonium to nitrite (carried by bacteria of the genus Nitrosomonas)

   • Step 2. Oxidation of nitrite to nitrate ( carried by bacteria in the genus Nitrobacter)

   • Step 3. The second reaction follows the first very cosely enough to prevent the accumulation of nitrite (nitrite is quite toxic the mots plants)

   • Step 4. When oxygen supply is limited, nitrifying bacteria may produce some NO and N2O which are potent greenhouse gas

Factors affecting Nitrification

1. Oxygen Supply

   • nitrification if favored by well drained soils

2. Moisture Content

   • 60% of the pore spaces is filled with water

3. Temperature

   • 20-30 degrees cetrigrade

4. Dissimilatory Nitrate reduction to Ammonium

   • anaerobic bacterial process that reduces NO3- to NO2- and then to NH4+

5. Denitrification

   • Mostly carried out by heterotrophic facultative anaerobic bacteria (Pseudomonas, Baccilus, Micococcus, Achromobactor)

6. Ammonification

   • release of ammonium ions from organic compounds

7. Biological N Fixation (BnF)

   • Next to photosynthesis, probably the most important biochemical reaction for life on earth

     • Nitrogenase- Catalyzes the reductio of N2 to ammonia

     • Leghemoglobin- binds the oxygen in such way as to protect the nitrogenase while making oxygen available for respiration in other parts of the nodule tissue

8. Symbiotic BNF

   • Occurs primarily in the plant legume family (Fabaceae)

Bacteria

“Cows of the soil”

Aerotolerant

Not oxygen requiring and does not die in the prescence of oxygen

Ammonium to nitrite

Nitrosomonas

Denitrification

Not a fate of ammonium in the soil/Not in the path of Ammonium

Nitrate

Inorganic nitrogen is a plant-available form

Cryptobiotic stage

Resting stage of nematode

Cyst

Resting stage of Protozoa

Archaea

Microorganism whose cell wall is made up of polysacchharides

Mineralization

Release of Nitrogen