Soil Organisms and Biochemical Processes in Soil

Presenter: Ruby Sarapanan, MSc, R. Agr.
Position: Assistant Professor IV, Mindanao State University-General Santos

Soil Animals

  • Most soils harbor a large number and great variety of soil animals which play an important role in soil processes and organic matter decomposition.

A. Protozoa

  • Protozoa are the simplest and most abundant of the soil animals.

  • Soil protozoa primarily consist of:

    • Ciliates

    • Flagellates

    • Testacea

  • Soil protozoa are largely heterotrophic, feeding on:

    • Soluble substrates

    • Sometimes insoluble substances

    • The most common food source is bacteria.

B. Nematodes

  • Soil nematodes are small round worms.

  • Over 2,000 species inhabit the soil; approximately half are plant root parasites.

  • Key points about nematodes:

    • They do not directly participate in the decomposition of organic residues.

    • Their ecological importance lies in their effect on total microbial activity through the destruction of species they consume.

Nematodes in Ecology

  • Types of Nematodes:

    • Bacteria-feeding nematodes

    • Predatory nematodes

    • Role: Feed on primary decomposers (bacteria, fungi, actinomycetes) and release nutrients (e.g., nitrogen) contained in the bodies of these decomposers.

C. Earthworms

  • Approximately 1,800 known species of earthworms exist.

    • Their passage of organic debris and mineral soil aids:

    • Organic matter decomposition

    • Solubilization of nutrient elements

    • Increase in water-stable aggregates.

D. Arthropods

  • Arthropods include:

    • Woodlice

    • Scorpions

    • Spiders

    • Millipedes

  • Their feeding habits accelerate degradation of surface litter, particularly in non-cultivated soils.

Soil Microorganisms and Nutritional Classification

A. Soil Bacteria

  • Bacteria are small, single-celled prokaryotic organisms with no distinct nucleus.

  • Common shapes of bacteria:

    • Cocci (nearly round)

    • Bacilli (rod-like)

    • Spirilla (spiral)

  • Nutritional Classification Based on Carbon and Energy Utilization:

    1. Autotrophs

    • Obtain energy from oxidation of simple inorganic substances (e.g., S, H2S, NH4^+, NO2^-, Fe^2+, Mn^2+).

    • Obtain carbon from CO2 and hydrogen from water.

    1. Heterotrophs

    • Require preformed organic substances for carbon and energy, relying on organic matter.

Bacterial Growth and Oxygen Requirements

  • Classifications based on oxygen presence/absence:

    1. Aerobic Bacteria

    • Can live only in the presence of oxygen.

    1. Anaerobic Bacteria

    • Thrive in complete absence of oxygen.

    1. Facultative Bacteria

    • Can survive in both the presence or absence of oxygen.

Role in Soil Chemistry

  • Bacteria play crucial roles in the oxidation or reduction of specific chemical elements in soils.

  • Common genera of soil bacteria:

    • Pseudomonas

    • Rhizobium

    • Bacillus

    • Clostridium

    • Arthrobacter

B. Actinomycetes

  • Actinomycetes are unicellular aerobic microorganisms that form branched mycelia and reproduce through fragmentation or asexual spore formation.

  • Typically, actinomycetes are aerobic heterotrophs residing in decaying organic matter.

  • Many species produce antibiotic compounds, such as:

    • Actinomycin

    • Neomycin

    • Streptomycin

  • They are vital for decomposing soil organic matter and liberating nutrients, even decomposing resistant compounds like:

    • Cellulose

    • Chitin

    • Phospholipids.

  • Dominant in later decay stages when easily metabolized substrates have been exhausted.

  • Typical genera of soil actinomycetes:

    • Nocardia

    • Streptomyces

C. Fungi

  • Fungi are eukaryotes with nuclear membranes and cell walls, categorized as heterotrophic organisms.

  • They depend on living or dead organic materials for both carbon and energy.

  • Fungal characteristics:

    • Primarily aerobic

    • Filamentous fungi consist of long, threadlike chains of cells (hyphae) often twisted into mycelia.

  • Fungi are versatile decomposers capable of breaking down:

    • Cellulose

    • Starch gums

    • Lignin

    • Easily metabolized proteins and sugars.

  • Common genera:

    • Penicillium

    • Mucor

    • Fusarium

    • Aspergillus

D. Algae

  • Algae are the most abundant photosynthetic microorganisms in the soil, classified as photoautotrophic.

  • Mostly found in the upper 2-4 cm of soils.

Functions of Soil Algae

  • Important functions include:

    1. Nitrogen fixation

    2. Colonization of new rock or barren surfaces

    3. Supply of organic matter and nitrogen for humus formation

    4. Weathering of rocks and minerals

    5. Binding of soil surfaces to aid in soil erosion control.

  • Examples:

    • Chlorella

    • Heterococcus

    • Plectonema

Microbial Growth Phases

  1. Lag Phase

    • Occurs under appropriate conditions but with a delay in measurable population density changes.

    • Organisms adjust to new substances and physical conditions.

  2. Exponential or Logarithmic Growth Phase

    • The population adjusts to new conditions, and rapid division occurs, leading to observable population increase.

  3. Stationary Phase

    • Cell multiplication equals cell death; primary mode of existence for most microbial species.

    • Multiplication is controlled by the release of limiting nutrients from biomass due to cell death and decomposition.

  4. Decline or Death Phase

    • More cells die than new cells are synthesized.

    • Causes include nutrient limitation or increased concentrations of toxic by-products.

Growth Curve of Bacteria

  • Idealized bacterial growth curve:

    • Phases:

    1. Lag Phase

    2. Exponential Phase

    3. Stationary Phase

    4. Decline/Death Phase

    • Visualization of phases:

    • Number of cells plotted against time (in hours).

Estimation of Soil Microbial Populations

  1. Dilution Plate Method

    • Procedure for estimating microbial populations on a petri plate with solid medium (agar, mineral salts, organic substrate).

    • Involves introducing a known weight of soil into sterile water to create dilutions.

    • A series of dilutions is prepared, indicating concentrations (e.g., 10^-1 to 10^-7).

    • Inoculation of sterile petri plates with diluted soil shows colony growth from the original sample.

    • Results are reported as colony-forming units (CFUs) per gram of soil.

  2. Direct Microscopic Examination

    • Involves weighing soil into melted agar, adding drops to a hemocytometer, staining, and examining under a microscope to quantify bacterial numbers.

  3. Rossi-Cholodny Buried Slide Technique

    • A microscope slide is buried in soil, left for a time, and then examined to study microbial film adhering to the slide after staining.

Process of Decomposition in Soils

  • Composition of Plant Residues:

    • Primary materials undergoing decomposition include:

    1. Cellulose: 15-60%

    2. Hemi-cellulose: 10-30%

    3. Lignin: 5-30%

    4. Water-soluble fraction: 5-30% (simple sugars, amino acids)

    5. Ether/alcohol-soluble constituents: fats, oils, waxes, etc.

    6. Proteins: 8-10%

    7. Ash: 8-10%

Rate of Decomposition

  • The decomposition rate varies:

    1. Rapid decomposition occurs in sugars and simple proteins.

    2. Moderate decomposition: crude proteins.

    3. Slow decomposition: hemicellulose, cellulose, fats, waxes, lignins, and other phenolic compounds.

Stage of Decomposition

  • Decomposition within soils converts complex organic materials into simpler compounds (e.g., CO2, NH4^+).

  • Rapid colonization of dying plant material occurs due to fast-growing bacteria and fungi.

  • Humus: A blend of colloidal organic decay products that accumulate due to slow decay rates.

Transformation of Nitrogen Compounds (Nitrogen Cycle)

  • Definition:

    • The nitrogen cycle refers to the sequence of chemical and biological changes undergone by nitrogen as it transitions from the atmosphere to water, soil, living organisms, and back into the environment upon the death of these organisms.

A. Nitrogen Mineralization

  • Definition:

    • The conversion of organic nitrogen to inorganic nitrogen, primarily producing ammonia or ammonium, referred to as ammonification.

    • Mineralization is carried out by diverse groups of bacteria, fungi, and actinomycetes that can live in aerobic or anaerobic conditions across a wide temperature range.

Factors Affecting Rate of Mineralization

  1. Residue Size:

    • Smaller particle sizes lead to more rapid decomposition due to increased surface area exposure and easier access to decomposable tissues.

  2. C/N Ratio of Organic Materials:

    • Soil microbes require a balance of nutrients, with most relying on carbonaceous materials while also needing nitrogen for various cellular components.

  3. pH of the Environment:

    • Neutral pH promotes greater production of inorganic nitrogen compared to acidic soils, where mineralization is depressed.

    • Liming acidic soils can encourage mineralization by raising pH to favorable levels for microbial activity.

  4. Moisture and Aeration:

    • Poorly drained and waterlogged soils reduce microbial metabolism, lowering mineralization. Ideal conditions fall between 50-75% water holding capacity.

B. Nitrogen Immobilization

  • Definition:

    • The conversion of nitrogen from inorganic to organic forms within microbial or plant tissues, rendering it unavailable to other organisms.

  • This process is essentially the reverse of mineralization where microbial and plant nutrients are returned to the inorganic state.

C. Nitrification

  • Definition:

    • The biological formation of nitrate or nitrite from reduced nitrogen compounds.

  • The process involves two main steps:

    1. Conversion of ammonium to nitrite by autotrophic bacteria (e.g., Nitrosomonas).

    2. Conversion of nitrite to nitrate by another group of autotrophs (e.g., Nitrobacter).

D. Denitrification

  • Definition:

    • The conversion of nitrate ions into gaseous forms of nitrogen by mainly facultative anaerobic bacteria (e.g., Thiobacillus denitrificans).

E. Volatilization of Ammonia (NH3)

  • Definition:

    • The conversion of ammonium (NH4^+) into ammonia (NH3) in alkaline aqueous conditions.

F. Biological Nitrogen Fixation

  • Definition:

    • The biological conversion of elemental nitrogen into forms that can be used in biological processes.

1. Symbiotic Nitrogen Fixation

  • a. Symbiotic fixation with legumes

    • Beneficial relationship between legumes and genera such as Rhizobium and Bradyrhizobium that provide the major source of fixed nitrogen in agriculture.

    • Rhizobium bacteria interact with root hairs to form root nodules, serving as sites for nitrogen fixation, whereby the plant provides carbohydrates in exchange for fixed nitrogen compounds.

Classification of Rhizobia Bacteria and Associated Legumes

  • Examples:

    • Rhizobium leguminosae with peas, vetch, lentils.

    • Rhizobium meliloti with Medicago (alfalfa).

    • Bradyrhizobium japonicum with Glycine sp. (soybeans).

b. Symbiotic Fixation with Non-legumes

  • Involving cyanobacteria, particularly the Azolla-Anabaena complex, which fixes nitrogen comparably to the Rhizobium-legume system.

  • Some grasses and other non-legume plants also engage in nitrogen-fixing through root exudates providing energy to bacteria like Spirillum and Azotobacter.

2. Non-symbiotic Nitrogen Fixation (Free-Living)

  • Conducted mainly by aerobic bacteria species such as Azotobacter and Beijerinkia in upland mineral soils, which are less efficient than symbiotic nitrogen fixers.

G. Industrial Nitrogen Fixation (Chemical N-fixation)

  • Ammonia is synthesized from a 3:1 volume mixture of hydrogen and nitrogen using an iron catalyst.

  • Hydrogen sources include water, natural gas, oil, or coal, while nitrogen is sourced from the atmosphere.

Transformation of Phosphorus Compounds

  1. Mineralization:

    • Biochemical conversion of organic phosphorus to inorganic phosphorus.

  2. Immobilization:

    • Conversion of inorganic phosphorus into organic phosphorus, driven by factors such as C:P ratio, temperature, soil moisture, aeration, and soil pH.

  3. Phosphate Solubilization:

    • Mobilization of insoluble phosphorus by organic acids, converting Ca3(PO4) into di- and monobasic phosphates, enhancing availability to plants.

Transformation of Sulfur Compounds

  1. Mineralization:

    • Biochemical conversion of organic sulfur into inorganic sulfur.

  2. Immobilization:

    • Similar mechanism as nitrogen immobilization where inorganic sulfate is assimilated into microbial tissues.

  3. Sulfur Oxidation and Reduction:

    • Oxidation is facilitated by autotrophic bacteria (e.g., Thiobacillus).

    • Reduction transforms sulfate ions into sulfide by genera such as Desulfovibrio and Desulfotomaculum.

Ecological Relationships Among Soil Organisms

  • Mutualistic Associations:

    • Occur between plant roots and soil organisms, and between microorganisms (e.g., lichens).

  • Competition:

    • Microbial competition can involve toxin production for resources.

Production of Toxins

  • Types of biological inhibitors produced by soil microorganisms:

  1. Effective at high concentration:

    • Organic acids, chelators.

  2. Effective at low concentration:

    • Antibiotics (e.g., streptomycin from Streptomyces griseus).

    • Siderophores, which transport iron under limited availability conditions (e.g., produced by Pseudomonas fluorescens).

Mitigation Strategies for Toxin Impact

  • Strategies include maintaining neutral pH through liming, better soil drainage, heavy phosphorus application, and avoiding specific crops in contaminated soils.

Pesticide Degradation

  • Definition:

    • Pesticides are substances designed to control or eradicate specific pests. Their ecological effects vary widely.

Types of Pesticides

  1. Insecticides:

    • Used to eliminate insects (e.g., organophosphates, carbamates).

  2. Fungicides:

    • Control plant diseases (e.g., pyraclostrobin, mancozeb).

  3. Herbicides:

    • Mainly for weed control (e.g., glyphosate, paraquat).

  4. Rodenticides:

    • Target rodents (e.g., Coumatetralyl).

  5. Nematocides:

    • Specific for nematodes (e.g., Carbofuran).

Beneficial Properties and Functions of Soil Organic Matter

  1. Reservoir of nitrogen (N), phosphorus (P), and sulfur (S) released slowly.

  2. Enhances soil structure through granulation in clay and sandy soils.

  3. Improves micronutrient utilization by plants.

  4. Organic acids solubilize nutrients in soil minerals, making them available to plants.

  5. Increases cation exchange capacity (CEC) in various soil types.

  6. Enhances buffering and water holding capacity.

  7. Forms complexes that reduce toxicity of metals like aluminum, manganese, etc.

  8. Promotes microbial biodiversity and fosters biological control.

Effect of Organic Matter on Soil Properties

  1. Improves soil fertility and microbial activity.

  2. Increases cation exchange capacity and micronutrient utilization.

  3. Enhances buffering capacity and root respiration.

  4. Promotes aggregation, water holding, favorable aeration, and lowers bulk density.