SOIL BIOLOGICAL

PROPERTIES
SSE 100-Principles of Soil Science & Ecology
–Dr Nezomba
Dept of Soil Science & Agricultural Engineering
The Living Soil
Objectives
 List the main components of soil biota
 Distinguish between phenetic & phylogenetic
classification of soil organisms
 State the importance of bacteria, fungi,
actinomycetes, algae, & small animals in the
soil
 Explain the effect of microbial activity on the
soil’s capacity to support plant growth
Why study soil biota?
 Soil biota are the biologically active powerhouse
of the soil comprising an incredible number of
organisms – ranging from microorganisms and
soil animals
 Concentrated in the litter layer, upper few cm of
the soil profile and along roots
 Some species can be pests
 The activities of soil animals can affect rates of
OM decomposition
 Act as primary decomposers
 To quantify the structure of soil faunal activities
(abundance & biomass of taxonomic and
functional groups) with emphasis on land use
patterns on this structure
 To describe & quantify the role of soil biota in
the major soil processes
 To be able to manipulate soil faunal
communities to improve soil fertility
 Soil biota may have dramatic effect on
transfers & transformations of plant residues
and SOM
The soil habitat

Essentially, all life depends

upon the soil…There can be
no life without the soil and no
soil without life; they have
evolved together”

C.E. Kellogg, 1938

The living soil
 Soil is one of the most diverse habitats on
earth
 A gram of soil may contain may contain
millions of microorganisms. Biota includes:
1. archaea; bacteria; protists; nematodes; acari;
colembola; worms; macroarthropods; and
barrowing mammals
2. Plant roots; fungi and lichens
Root exudates attract a variety of organisms that
wither feed directly on the secretions or
Graze on microorganisms concentrated near roots
The living soil
 Other soil organisms include:
Beetle larvae, flies and butterflies that use
the soil as a temporary habitat to reproduce
or spend parts of their life cycles
The soil organisms are diverse in both size
and numbers
 Soil biota presents one of the most
poorly understood topic worldwide,
though attempts have been made to
classify them
Determinants of organisms
 Populations differ from one soil to the next
because of:
complex physical and chemical nature
Porous structure
Immense surface area
Variable supply of organic matter, food , water,
nutrients
 Externally, because of:
Climate (temperature; moisture)
Vegetation
Physico-chemical conditions (Acidity; nutrients
etc).
Classification of soil biota
1: Phenetic vs phylogenetic
 PHENETIC
Based on similarities of observable traits e.g.
○ morphology;
Physiology (phenetic characteristics) e.g.
○ Size
1. Microorganisms: <0.2 mm
2. Meso- organisms : 0.2 – 10 mm
3. Macro organisms: >10 mm, visible with the
naked eye
 Basis for the 5-Kingdom classification (Plant, Animal;
Fungi; Protozoa; & Protista)
 Phenetics
 1) Phenetics – based on
differences in morphology
(appearances) between
species.

 This method judges

taxonomic affinities on
measurable similarities ad
differences by comparing as
many characteristics as
possible.
2. PHYLOGENETIC CLASSIFICATION
 Based on genetic relatedness e.g.
16S ribosomal RNA (more stable RNA, does not mutate
readily)
 Reveals ancestral relationships – if 2 organisms
have similar or identical nucleotides, they are related
BUT……
 Organisms may be wrongly classified using
phenotypic classification since these may be
modified by the environment
 Organisms of one species may end up looking
different because of environment even if their
genetic make up is the same
Phylogenetic classification
 Based on analysis of 16S ribosomal RNA
gene sequence, all living things fall into 3
broad categories
 Basis of 3 kingdom classification
1. Archaebacteria (ancient, primitive bacteria)
2. Eubacteria (true prokaryotes, includes all
ordinary bacteria)
3. Eukaryotes (plants, animals, fungi, protozoa)
Phylogenetic classif…

Example of a Phylogenetic tree

3. Classification according to source of
Energy and Carbon
Autotrophic vs heterotrophic
 AUTOTROPHS
Obtain their energy from inorganic sources other
than breakdown of organic materials e.g.
i. Solar energy &CO2 as C source
(photoautotrophs)
ii. Oxidation of chemical elements e.g. N, S, Fe
(chemoautotrophs) e.g.
○ Iron bacteria: Fe2+ -------Fe3+
○ Sulphur bacteria – Thiobacillus : S ---- SO42-
○ Nitrosomonas use NH4+, & Nitrobacter (NO2-)
 HETEROTROPHS
Obtain E & C from the breakdown of organic
material
Utilize a diverse array if compounds including
carbohydrates, proteins, lipids
Responsible for most of the decay processes in
nature
Include soil fauna, most bacteria, fungi,
actinomycetes
4. Classification according to oxygen
requirements

Aerobes
Require oxygen for respiration
Facultative anaerobes
 Normally require oxygen, but are able to adapt to
oxygen-free conditions by using nitrate or other
inorganic compounds in respiration
Obligate anaerobes
 Only grow in the absence of oxygen, as it is toxic to
them
Determining activities of organisms
 Activities of soil organisms can easily be
identified by:
a. Their numbers in soil

b. Their weight per unit volume or area of soil

c. Their metabolic activity

Methods of studying soil organisms
 Ecologists / agronomists need to know what is happening
in the field of interest
 Operate at molecular, microbiological, whole plant & field
measurements
 Need to estimate kinds, numbers & metabolic activities of
organism
 Also need to understand soil – plant – microbial
associations & interactions
 Soil samples should be accompanied by information on
site characterization
Should also be composite & replicated
 Sample processing & preparation (sieving, subsampling,
dilution, etc.)
 EARLY


CLASSIFICATION
Animals & Plants
With the discovery of the MICROSCOPE in the
1600’s many new organisms were discovered
 This was the basis for the change in the
classification system
BINOMIAL NOMENCLATURE
 Carolus Linneaus (Carl Linnaeus) (1707-1778)
– a Swedish botanist/zoologist/ physician
devised binomial nomenclature
 (2 names in Latin) Genus-Species
ex. scientific name of humans .....
Homo sapiens
Homo is the genus name .... sapiens is the
species name
Both have to be printed in italics or underlined
-Genus is ALWAYS capitalized
TAXONOMY
 Taxa (taxon) – taxonomic category
designed to show degrees of similarities
among organisms. (Groups based on
similarity)
 Higher taxa – very general
 Lower taxa – more restricted
Classification
 KINGDOM
 PHYLLUM
 CLASS
 ORDER
 FAMILY
 GENUS
 SPECIES

KING PHILIP CAME OVER FOR GOOD SADZA

Types of soil organisms
1. Archaebacteria
KINGDOM Archaea
 1most primitive and often live in extreme
environments
 LIVE IN UNUSUALLY HARSH ENVIRONMENTS
 unicellular
 Do not have a nucleus
 Include:
○ Salt-loving: Halophiles
○ heat-loving: Thermophiles
○ methane-loving: Methanogens
○ Acid-loving : Acidophiles
○ Alkaline-loving : Alaliphiles
Bacteria…
 Use a wide range of substrates
 Live in water films around soil particles
 Mostly heterotrophic & chemoautotrphs
 There are three major subgroups:
1. Unicellular Eubacteria most common
(could be autotrophic or heterotrophic)
2. Branched Eubacteria (actinomycetes) –
some of the most resistant organic C
materials (lignin) are degraded by this
competitive group.
2. Kingdom Monera
Bacteria & the Blue-green algae
(Cyanobacteria)
 Most abundant in soils
 Prokaryotic -& are unicellular with simple
internal structure
 Bacterial shapes include:
 Bacilli – straight and rod shaped (A)
 Cocci – spherical (B)
 Spirilla – spirally coiled (E)
Bacteria…
 They exhibit mycelial growth and are aerobic
heterotrophs.
 Biomass of 105 to 108 g soil-1 = 0.01% of soil
bacteria Streptomyces and Nocardia which
produce antibiotics fall under this group.
3. Myxobacteria (slime bacteria) - unicellular
organismsdiffer from Eubacteria in flexibility of
their cell wall (degrade cellulose & chitin)
 Size range: 0.5- 1.5 μm (width) by 1.0-3.0 μm
(length)
 Reproduce asexually (by simple cell division), and
very rapidly (8-24 hrs) if conditions are favourable
Bacteria …
 Practical significance includes role in natural
cycling of elements which contributes to soil
fertility
 Bacterial population runs into billions per gram of
soil, exhibiting the most diversity in comparison
with other soil organisms (aerobes, anaerobes,
sulphur digesters, cellulose digesters etc.
 This diversity also offers them limitless diversity in
terms of their metabolism hence the range of
substances they are able to decompose
 Note that bacteria also cause diseases in plants &
animals
. Actinomycetes
 Filamentous bacteria that resemble
molds, often profusely branched
 Often produce antibiotics, common
examples are Streptomyces & Norcadia
 Heterotrophic
 Aerobic metabolism but some
anaerobic
 105 – 108 g soil-1
 Actinomycetes
 Often form mycelium (massive
branching hyphae) with conidia (or
conidiospores – asexual, thin-walled
spores)
Streptomyces
 Not heat-resistant, but adaptive. Not
motile
 Located primarily in soil or aquatic
environments; widely distributed
 Can degrade numerous organic
compounds or mineralize organic
materials, produce most of the
medically useful antibiotics, and some
exist as pathogens
 Ecological and Medical Importance
 Not very good competitors but can utilize a
variety of organic matter compounds
 Degrade more recalcitrant carbon
compounds e.g. lignin
Mineralization
Aerobically degrades multiple resistant
substances
Synthesis of antibiotics
mainly non-pathogenic
KINGDOM FUNGI
 examples include yeasts, molds,
and mushrooms
 cells are usually organized into branched,
multinucleate filaments which absorb
digested food from the external environment
 Mushrooms are made up of a network of
tubes called HYPHAE
 Fungi
 Fungi are eucaryotic organisms
 Some are unicellular (e.g. yeasts)
but majority (the molds) are
multicellular
 have many distinctive structural
features
 Produce long filamentous hyphae.
 Hyphae can be 1-10 μm in diameter
and ~ 10 000 to 1 000 000 g soil-1
 All fungi are aerobic heterotrophs
 More tolerant to acid conditions
than bacteria
Fungi …
 Intolerant of anaerobic conditions
 Less numerous than bacteria
because their growth is filamentous
but biomass can be comparable to
bacteria
 are superior in their ability to
decompose lignin
 Superior ability to decompose lignin
 Can occur as soil inhabitants
feeding on dead organic matter
(saprophytes)
 Spores germinate and grow living
tissue
 Kingdom Protista
 Predominately unicellular organisms with plant or
animal-like characteristics
 examples include protozoa and all algae except
the blue-green
 have a true nucleus and nuclear membrane
 Most protozoa are motile (CAN MOVE) and are
divided into phyla based on their means of
LOCOMOTION
Animal-like Protists
 Often animal like Protists are called
PROTOZOA
 They can live in fresh or salt water, in the soil, or
in the bodies of other organisms

Plant-like Protists:
 Plant-like Protists are commonly called ALGAE
 They contain chloroplasts and are therefore
AUTOTROPHIC
Protozoa
 Are Eucaryotic unicellular organisms
some of which are intracellular
parasites
 Smallest of the soil animals – live in
the soil water.
 Size ranges between 2 – 200 µm
diameter
 Live in water films and move by
cytoplasmic streaming, cilia or
flagellae
 Euglena belongs to this group – it
contains chlorophyll & is autotrophic
 1,000,000 g-1 soil but subject to
massive fluctuations in population size.
Euglena
Protozoa …
 Biomass is comparable to earthworms
 Reproduction in this group is both sexually and
asexually
 Feed on bacteria, fungi and some nematodes,
hence controlling the numbers of such
organisms in soils.
 Feeding on bacteria is very important in the
cycling of nutrients in the BIOMASS.
 excrete NH4+ and more complex N compounds.
 A major source of food for aquatic animals
Algae
 Eukaryotic uni- and multi-celluar
organisms
 Are photosynthetic (e.g.
cynobacteria) & are therefore
restricted to the soil surface
 Usually play an important role in
the initial accumulation of soil
organic matter on barren and
eroded soils (ability to
phosynthesize)
 Very few are heterotrophic and
able to utilize simple organic
solutes in the absence of light
 Algae …
 Fix N2 e.g. Nostoc & Anabaena
 True algae are autotrophic
 NB.Blue – green algae –
Nostoc
CYANOBACTERIA are actually
bacteria – prokaryotes.
 pH range 6.0 – 9.0
 Size: 1.0 μm to many cm
 50,000 to 100,000 g soil-1
 Like protozoa, reproduction in this
group is both sexually and asexually
A film of Cyanobacteria in a
 Play a key role in the transformation
lake
of rock to soil
 Usually paves way for growth of
lichens, mosses and higher plants.
Mycorrhizae
 Symbiotic associations between fungi & plant
roots
 Mycorrhizal fungi associated with nearly all
plants -
 Two types
1. Ectomycorrhizae
 Primarily associated with trees
 Form thick (~0.05 mm) mats of mycelium around
roots, but do not penetrate root cell walls
 Aids plant phosphorus uptake while plant
supplies carbohydrates
 at least 65 fungal genera most of which are
Basidiomycetes although some are in the
Ascomycota.
 Well known genera in the Basidiomycetes
include Amanita 
 Mycorrhizae …
Endomycorrhizae
 Most important are the vesicular
abuscular mycorrhizae (VAM)
 Penetrates root cell walls, & forms
hyphal masses within cells
 Most common & widespead of all Ectomycorrhizae
mycorrhizae
 Aids plant phosphorus, zinc, copper
uptake while plant supplies
carbohydrates
 Thought to be responsible for transfer of
P from one plant to neighboring species
 Roots of common agronomic crops e.g.
maize, cotton, beans, potatoes etc.
have VA mycorrhizal associations

Endomycorrhizae
 Fungi-Plant Interaction

Mycorrhizae
(root fungus)

- extension of root system

- fungus enhances nutrient and
water intake
- plants provide carbon source

Nearly 90% of native plants have

mycorrhizae association
Viruses
 not classified in a kingdom
 contain genetic material (DNA) but lack cell
structures
 only carry on the life function of
reproduction
 They must have a host (another living
organism) to be able to reproduce
 This causes disease in the host (Ex: colds,
rabies, AIDS, flu)
Viruses …
 A virus is a small infectious agent that
can replicate only inside the living cells
of organisms.
 Most viruses are too small to be seen
directly with a light microscope.
 Viruses infect all types of organisms,
from animals and plants to bacteria TMV structure
and archaea. (above) infection
(below)
 Example: tobacco mosaic virus ;
maize streak virus
 Viruses are found in almost every
ecosystem on Earth
 Obligate parasites that require living
cells in which to reproduce
viruses…
 Cause diseases in humans and plants,
and they also infect other
microorganisms
 Spread in many ways;
 Plant viruses are often transmitted from
plant to plant by insects that feed on
sap, such as aphids,
 Animal viruses can be carried by blood-
sucking insects.
Kingdom Animalia
 multi-cellular organisms which ingest their food
– HETEROTROPHS
 Reproduce sexually
SL 101-Soil fauna presentations
 1. Earthworms (Group 1)
 2. Anthropods (Group 2)
 3. Termites (Group 3)
 4. Millipedes (Group 4)
 5. Ants (Group 5)
 6. Dung beetles (Group 6)

  For each of the above, the presentation should be on the following:

1. Genetic diversity
2. Conditions under which they exist in soils e.g. oxygen
requirements, mode of feeding, pH conditions etc
3. Contribution to soil formation (i.e. how they influence soil chemical,
biological and physical properties)
4. SUBMIT NAMES OF GROUP MEMBERS
SOIL FAUNA
1. Earthworms
 Most important group of soil
animals in the temperate regions
 Belong to the group Annelida,
18000 species worldwide
 Lumbricus terrestris, most Lumbricus terrestris
common
 Size range from a few cm to
almost 3 m long
 Ingest organic matter (major
source of food) as well as soil
 1. Earthworms…
 3 main groups
– surface
- shallow burrowers
- deep burrowers
 Importance include burrows left during their movement in soil, they
serve to aerate the soil
 Presence implies a well drained soil
 Mix & granulate soil
 Prefer a well aerated & moist habitat
 Prefer soils with a not too low pH
 Optimum temperature around 10ºC, reason for deep burrowers (1-
2 m below)
 Numbers may range between 30 – 300 per m-2 within a 15 cm
profile
Earthworm casts and faeces
 Higher pH than surrounding soil
 More exchangeable calcium, available P and N
 More microorganisms especially bacteria than
surrounding soil
 Digestive process is inefficient
< 10% chemical breakdown
digestive tracts contain many bacteria & fungi
presence of cellulases due to the microbes
2. Arthropods - Arthropoda
 Organisms with an exoskeleton and
jointed legs
 Most abundant detritus feeders: e.g.
Spingtails (Collembola) – possess a
springing organ, live in pores and
cannot burrow. Collembola
Mites (Acarina) – commonest reps of
woodland fauna;
○ breakup and decomposition of litter
○ maintain soil pore spaces

  

House dust mite

Arthropoda…
Saprophagous and herbivorous species
 Millipedes (Myriapoda)
 Woodlice (Isopoda)
 Beetles & insect larvae (also
coprophagous species e,g Dung beetle)
Carnivores
 Centipedes (Myriapoda)
 Ants and termites - very abundant;
important comminuters
 Spiders (Arachnida)
 Termites play the role of the earthworm
in the tropics
Termites
 Play the role of the earthworm in the tropics
 Ecologically, termites are important in:
 nutrient recycling through the transport,
shredding and digestion of organic matter.
habitat creation, 
soil formation,
soil quality and,
particularly the winged reproductives, as food for
countless predators.
 Can be major agricultural pests, particularly in
Africa and Asia, where crop losses can be severe.
Termites
 Counterbalancing this is the greatly improved
water infiltration where termite tunnels in the soil
allow rainwater to soak in deeply and help reduce
runoff and consequent soil erosion.
 As detrivores, they clear away leaf and woody
litter, as well as crop residues
 But considered to be a major source of CH4, one
of the prime greenhouse gases.
Termites and Ants
 Important in OM breakdown & soil manipulation
• Turnover 10s to 100+ t/ha/y of soil
• ~2000 species of termites found mostly in tropics & subtropics
 Termites build extensive & large mounds up to 6 m in
height and >6 m deep.
 Mounds abandoned after 10-20 years
 Effects of termites variable; may disrupt crop production
soil less fertile, but aid in soil formation in the tropics.
 Ants have less widespread & more local influence on soils.
 Some species have exceptional ability to breakdown woody
materials.
Millipedes
 Millipedes (and centipedes) belong to the group
Myriapoda
 are found:
 on the soil surface,
 in the litter layers,
under tree stumps and
decaying logs
 where they can find food and humidity.
 Most have a limited ability to penetrate the soil.
 They move through it by displacing it in all directions.
Millipedes
 Millipedes generally
feed on plant debris
(decomposed wood or
leaf materials), leaving
behind their numerous
droppings that
contribute to humus
and soil formation
Macrofauna
 Mice, moles
 Rabbits ,squirrels, hare
 Badgers, deer,
 Pangolin,
 Birds
Faecal matter as a resource
 faecal matter high in both aquatic and terrestrial
environments
 millipedes feed on their own faecal matter and perform
best
 some invertebrates feed on one another’s faeces
 a carnivore dung is attacked mainly by microbes
 poor quality because of the high efficiency of the
digestive system
 less common in nature than herbivores and their faeces
may not support the large specialist detritivore fauna
 herbivore dung contain abundant
organic matter e.g. cowdung;
elephant dung
 during the wet season, the The Dung beetle
dungbeetle rolls it up before burying it
several m from original pile
 uses the rolled up dung for laying
eggs
 after hatching, there is available food
for the larva as well as its own faeces
 in dry seasons, few beetles colonize
the dung
 rewetting stimulates microbial activity
but beetles do not exploit old dung
 dung deposited during the dry season
may last >2 yrs compared to 24 hrs
for the wet season dung
 A typical fertile agricultural soil has approx. (g -1)
Bacteria -------------2.5 billion
Actinomycetes---700 thousand
Fungi-------------400 thousand
Algae-------------50 thousand
Protozoa-------
30 thousand
Major groups & common occurrence in
soil
macro Live mainly on Small mammals,
plant materials insects, millipedes,
mites, slugs, snails,
earthworms
Mostly predatory Moles, insects, mites,
Animals centipedes, spiders
micro Predatory, parasitic Nematodes; Protozoa
or live plant tissue Rotifers

Roots of higher plants

Algae Green, Cyanobacteria, diatoms
Fungi Mushrooms, yeasts, molds
Plants Actinomycetes
Bacteria Aerobic Autotrophic
The soil biomass
 Refers to the mass of organisms in the soil
 kg ha-1 live-weight for macro- & meso- fauna
(may range between 2 – 5 t ha-1)
 Microorganisms intimately mixed with organic
matter in soil , so difficult to count & weigh
 Measured indirectly e.g. CO2 evolution &/ or
microbial biomass quantification
 Microbial biomass C ranges from 500 – 2,000
kg ha-1 in top 15 cm of soil
  2 – 4% of total soil C
SL 101-Soil fauna presentations
The presentation will be assessed on the basis of
1. Slide quality
2. Content
3. Use of diagrammatic illustrations
4. Audibility of the presenter (s)
5. Ability to answer questions
6. Time keeping

 Each presentation will be 10 minutes long, and 5

minutes for questions