6.

Biological
Characteristics
of Soil
ENVS 334: Applied Soil
Science and Land
Management
INSTR.: R.M. Bajracharya

1
 Soil biological properties
• Organisms, both animals (fauna/micro-fauna) and
plants (flora/micro-flora) are important in the overall
quality, fertility and stability of soil.
• They are responsible for the formation of humus, a
product of OM degradation and synthesis.
• Moreover, organisms aid in the physical manipulation,
mixing, and formation of soil & its structural stabilisation.
• Soils contain a vast number and wide range of
organisms
• A greater proportion of these belong to the plant
family
• Organisms are important in the myriad of biochemical
reactions and intricate biological processes that take
place within the soil.
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 Soil Organisms
• Organisms (biological component) of the soil
play major roles in:
– Nutrient cycling & release (breakdown of organic
compounds)
– Biochemical weathering of minerals & soil development
– Ameliorating soil physical & chemical properties
• Without this living component, the mere accumu-
lation of the mineral fraction would not be “soil”.
• Soil organisms include plants and animals.
– Majority of soil organisms are plants (microflora), but
animals are equally important (have more physical role)
– Most are microscopic, i.e., microflora and microfauna.

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 Major groups of organisms of common
occurrence in soils.
Live mainly on Small mamals; insects; millipedes;
Macro plant materials mites; slugs; snails; earthworms
Mostly Moles; Insects; mites; centipedes;
Animals predatory spiders
Micro Predatory, Nematodes
parasitic or live Protozoa
on plant tissue Rotifers
Roots of higher plants

Algae Green; Blue-green; Diatoms

Plants Fungi Mushrooms; Yeasts; Molds

Actinomycetes of many kinds

Bacteria Aerobic Autotrophic

Anaerobic Heterotrophic 4
Group of Biomass (g/m2)
Organisms
Grassland Oak Forest Spruce Forest
Herbivores 17.4 11.2 11.3
Detritivores: Large 137.5 66.0 1.0
Small 25.0 1.8 1.6
Predators 9.6 0.9 1.2
TOTAL 189.5 79.9 15.1

Values commonly found in surface soil

Organisms No./sq. meter No. per gram Biomass (kg/HFS)
Microflora: Bacteria 1013 --1014 108 --109 440—4400
Actinomycetes 1012 --1013 107 --108 440—4400
Fungi 1010 --1011 105 --106 550—5500
Alage 109 --1010 104 --105 55—550
Microfauna: Protozoa 109 --1010 104 --105 16—160
Nematoda 106 --107 10 – 102 11—110
Earthworms 30—300 16—160
Others 103 –105 110—1100
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 Earthworms
• Earthworms are the most important of the soil
macro-animals.
• More than 1800 species known worldwide.
• Length ranges from few cm to 3 m long (topics)
• They ingest soil along with OM & create pores/
channels (improve aeration & drainage).
• Numbers range from <1/m2 to >500/m2 &
turnover as much as 250 mt/ha/year of soil.
• Casts are higher in bacteria, OM & available
plant nutrients than the soil itself.
• Hence, earthworms ameliorate soil in many
ways, physically and biochemically
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 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 (savannahs and forests).
– Termites (“white ants”) build extensive & large mounds
upto 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 break-
down woody materials.
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 Soil Microfauna
• Of the many microscopic animals that live in the soil,
3 groups are of some importance:
• Nematodes (“threadworms” or “eelworms”):
– Found in relatively large numbers in nearly all soils
– >1000 species known
– May be beneficial (saprophytic) or detrimental to crops
– Parasitic nematodes, such as Heterodera sp. infest roots
• Protozoa – among simplest form of animal life
– Most varied and numberous of the soil microfauna
– Unicellular, but much larger (5-100 μm) than bacteria
– >250 species isolated; include cilliates, flagellates, amoeba
• Rotifers – thrive under moist conditions (swampy)
– About 100 species; active mainly in organic soils or wet
areas of mineral soils.

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Microscopic soil animals

Nematode [magnified
~120 times]

Rotifers:
Ciliated protozoan
(L)—Rotaria rotatorial; (Glaucoma scintillaus)
(R)—Philodina acuticornus

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 Soil Flora – Roots of Higher Plants
• Plant roots are constantly growing & dying in soil,
thereby, supplying soil organisms w/ food+energy.
– Roots also physically modify soils by creating stresses &
strains enhancing aggregation; create channels.
– They constantly release exudates, mucilages, enzymes, as
well as, dead cells – materials leading to the formation of
humus to significant depths in the soil.
– Upon harvesting of crops, 15-40% of above ground
weight of plants is left in the ground as root mass.
• Rhizosphere – is the zone immediately surrounding
active young roots.
– Here microorganisms are ~100 time greater in number
– Organic acids solubilize plant nutrients making them
readily available for plant uptake.

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 The Rhizosphere
Bacteria associated with roots
of wheat [magnified 3900 X]
1-simple exudates; 2-secretions (from
metabolic processes); 3-plant mucilages;
4-mucigel (gelatinous mucilage-soil
mixture); 5-lyzates (cmpds released
through digestion of cells by bacteria)
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Soil Alage
• Soil algae are found near the surface of soil
(need light for photosynthesis).
• They are active mostly under wet conditions.
• Several hundred species identified; four major
groups in soils:
– Blue-green: most common; grow in grasslands and wet
soils such as paddy fields
– Green: survive under non-flooded conditions and
under low pH (acidic) soils
– Yellow-green: less common
– Diatoms: tend to occur in old gardens under drier
conditions.
• Blue-green alage growing within leaves of Azolla
(aquatic fern) in paddy fields fix nitrogen.
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 Soil Fungi
• There are over 690 species of soil fungi identified.
• Important in transforming soil constituents (all types
of organic comps – cellulose, starches, gums and lignin).
• Fungi include yeasts, molds & mushrooms:
– Yeasts are uncommon in soil habitats.
– Molds: filamentous and microscopic to semi-microscopic
• Develop in all ranges of soil pH (acidic to alkaline)
• Especially thrive in acidic surface soils (e.g., forests)
• Common genera: Penicillium, Mucor, Fusarium, Aspergillium
– Mushroom fungi: found in moist areas with high OM
• Common in forests and grasslands
• Decompose woody tissue (lignins)
• Have mass of hyphae below the ground surface
• Significant impacts locally
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 Mycorrhizae
• Symbiotic fugus-root assoc.
markedly increases avail. Of
certain essential nutrients to
plants, esp. in infertile soils.
• P, Zn, Cu, Ca, Mg, Mn & Fe
• Of economic importance in
production of wheat,
potato, beans, sugarcane,
cassava & dryland rice.
• Ectomycorrhiza: assoc.
more with tree roots (pine,
birch, oak, spruce, fir, etc.)
• Endomycorrhiza: assoc. w/
annual & perennial crops +
trees (apple, maple, poplar,
coffee, rubber, etc.) – VAM:
vesicular arbuscular
mycorrhizae (most
important)
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 Actinomycetes
• These are filamentous and
similar to molds, but mycelial
threads are smaller than
fungal hyphae.
• Unicellular and similar in size
to larger bacteria.
• Grow best in moist but well
aerated soil conditions.
• Most suitable pH is 6--7.5
(near neutral)
• Actinomycetes remain Actinomycete threads
active even under low
moisture conditions.
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 Bacteria in Soils
• Bacteria are single-celled & among the simplest
of life forms; 4-5 μm in length; approach clay-size
• Rapid reproduction & response to envir. changes
• Variable shapes: round, spiral, rod-like
• Rod-shaped most common in soils.
• May be autotrophic or heterotrophic; in soils,
most are heterotrophs (get energy & C from OM)
• Bacteria participate vigorously in all organic
transactions in the soil; they are most numerous
and often exceed both fungi & actinomycetes.
• They have nearly exclusive action in nitrification,
sulfur oxidation & N-fixation in soil.
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 General pathway of OM breakdown and
role of organisms
Energy and Energy and
CO2 Input CO2 loss

Detritivores Carnivores
Detritus
Primary Secondary Tertiary Soil
consumers consumers consumers humus

Microphytic
feeders

Feces and
dead bodies

Soil microflora 17
 OM decomposition in soil
• Detritivores (ie. Primary
consumers-micro-flora/fauna)
initiate the decomposition of
detritus (organic debris)
• They utilise the energy in plant
residues as main food source
– Microflora mainly act through
chemical decomposition
– Action of fauna is both physical
and chemical
• Secondary consumers join in:
– Mites, snails, beetles, springtails,
earthworms, etc.
– These include carnivores that
feed on animals and
microphytic feeders that
consume bacteria, fungi, algae
• Tertiary consumer further
prey upon the primary or
secondary consumers
• Even in the latter cases,
however, microflora still play
a major role – they are
active within the digestive
tract of many animals.
• Moreover, microflora are
mainly responsible for further
decomposing organic
material in animal feces and
dead bodies of animals.
• Hence, they are known as
the ultimate decomposers.
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 Composition of organic matter in soil
8%
8%
H
40% Ash
C
O
75% 25%

44%

5%
Water Dry matter 25% 10%

Fats, waxes
Proteins
Carbohydrates
Sugars and Starches: 1-5% Lignins
Hemicelluloses: 10-30%
60%
Cellulose: 20-50%
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 Rate of OM decomposition
• Much of OM undergoes enzymatic oxidation with
carbon dioxide, water and heat released as the main
products
– [C, 4H] + 2O2 CO2 + 2H2O + energy (heat)
• Essential elements (N, P, S) are released/immobilised
by series of specific reactions for each element
• Compounds resistant to microbial action are
ultimately formed through the decomposition
processes (SOM or humus)
• Rate of decomposition of different compounds:
– Sugars, starches & simple proteins rapidly decomposed
– Crude proteins
– Hemicelluloses
– Cellulose
– Lignins, fats, waxes, etc. Very slowly decomposed
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 Distribution of SOM in different soil types

Forest soil Grassland soil

Well drained Poorly drained Well drained Poorly drained
14 12
12 10
Soil OM (%)

Soil OM (%)
10
8
8
6
6
4
4
2 2
0 0
0 10 20 30 40 50 60 70 80 0 20 40 60 80
Soil depth (cm) Soil depth (cm)

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 SOM (humus) and C:N ratio of soils
• Soil organic matter is a stable, complex mixture of
dark amorphous and colloidal substances modified
from original tissue or synthesized by soil organism
called humus.
• Humus is not a single substance, but a mixture of
complex compounds.
• It is thought to consist of:
– Fulvic acid –low molecular weight; light coloured; acid &
alkali soluble
– Humic acid—medium molecular weight & colour; alkali
soluble, acid insoluble
– Humin—highest molecular weight; darkest colour; acid &
alkali insoluble

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Humus & C:N Ratios of Soils
• Humus has high CEC (150-300 cmolc/kg), low
plasticity & cohesion.
• The carbon-nitrogen ratio of soils range from
8:1 to 15:1, being most frequently between
10:1 and 12:1 compared to higher values for
plant material and slightly lower for microbes
(4:1 to 9:1).
• C:N ratio is important because of competition
for N among organisms when plant residues
are added, leading to temporary nitrate
depression; and also because N influences the
maintenance of soil OC levels (soil C:N ratios
remain relatively constant).

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Organism activity, N availability and humus formation

High C:N Organism

residues added activity
Soil N level

Low C:N residues

remain
N-depression
Increase period

Compounds in
original tissue New soil
humus level
Synthesized by
organisms Soil humus

TIME 24