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6. Biological Characteristics of SoilENVS 334: Applied Soil Science and Land ManagementINSTR.: R.M. Bajracharya

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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.

Animals

MacroLive mainly on plant materials

Small mamals; insects; millipedes; mites; slugs; snails; earthworms

Mostly predatory

Moles; Insects; mites; centipedes; spiders

Micro Predatory, parasitic or live on plant tissue

NematodesProtozoaRotifers

Plants

Roots of higher plants

Algae Green; Blue-green; Diatoms

Fungi Mushrooms; Yeasts; Molds

Actinomycetes of many kinds

Bacteria AerobicAnaerobic

AutotrophicHeterotrophic

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Group of Organisms

Biomass (g/m2)Grassland Oak Forest Spruce Forest

Herbivores 17.4 11.2 11.3

Detritivores: LargeSmall

137.5 66.0 1.025.0 1.8 1.6

Predators 9.6 0.9 1.2TOTAL 189.5 79.9 15.1

OrganismsValues commonly found in surface soil

No./sq. meter No. per gram Biomass (kg/HFS)Microflora: Bacteria

ActinomycetesFungiAlage

1013 --1014

1012 --1013

1010 --1011

109 --1010

108 --109

107 --108

105 --106

104 --105

440—4400440—4400550—550055—550

Microfauna: ProtozoaNematodaEarthwormsOthers

109 --1010

106 --107

30—300103 –105

104 --105

10 – 102

16—16011—11016—160

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:

(L)—Rotaria rotatorial; (R)—Philodina acuticornus

Ciliated protozoan (Glaucoma scintillaus)

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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 active even under low moisture conditions.

Actinomycete threads

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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

Detritus Primary consumers

Detritivores Carnivores

Secondary consumers

Tertiary consumers

Soil humus

Microphytic feeders

Feces and dead bodies

Soil microflora

Energy and CO2 Input

Energy and CO2 loss

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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

75% 25%

Water Dry matter5%

10%

60%

25%

Fats, waxesProteinsCarbohydratesLignins

8%8%

44%

40%HAshCO

Sugars and Starches: 1-5%

Hemicelluloses: 10-30%

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

Grassland soil

0

2

4

6

8

10

12

0 20 40 60 80

Soil depth (cm)

Soil

OM

(%)

Well drained Poorly drained

Forest soil

02468

101214

0 10 20 30 40 50 60 70 80

Soil depth (cm)

Soil

OM

(%)

Well drained Poorly drained

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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 residues added

Low C:N residues remain

Organism activity

Soil N level

Compounds in original tissue

Synthesized by organisms Soil humus

New soil humus level

TIME

IncreaseN-depression

period