UNIVERSITY OF LAGOS

FACULTY OF SCIENCE
DEPARTMENT OF MICROBIOLOGY

MIC 305/323 : MICROBIAL ECOLOGY

TOPIC: MICROORGANISMS IN THEIR NATURAL ENVIRONMENTS I

(SOIL)

DR. A.E. OMOTAYO 1

OUTLINE

Microorganisms in their natural environments I

Introduction
 Physico-chemical conditions in soil
 Types of organisms in soil, spatial & seasonal
distribution

Microorganisms in their natural environments II

 Sources of substrates in soil for microbial growth
 Energy flow in soil ecosystems
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Microorganisms in their natural environments I

3
 INTRODUCTION
Composition of the soil
Soils are a very complex natural resource, much more so
than air and water. Soil is the natural medium for
terrestrial plant growth and it governs productivity in
agriculture and forestry. It is composed of varying
proportions of inorganic and organic components which
arises as the result of interactions between many
complex processes such as weathering of rocks, the
Figure 1: Composition of the soil
decomposition of plant materials and the redistribution
of materials by water movement.
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Soil Classification
 Soil Classification concerns the grouping of soils with a similar range of properties (chemical, physical
and biological) into units that can be geo-referenced and mapped.

 Soils contain all naturally occurring chemical elements and combine simultaneously solid, liquid and
gaseous states.

 Soil can be divided into a number of major types which are associated with climatic and vegetation
zones.

 Major soil differences are also associated usually with parent material. i.e, the soils derived from chalk
tend to be shallow, light, freely drained, whereas those derived from clays tend to be heavy and liable to
waterlogging.
 Texture is an important classification feature which describes the size distribution of particles in the
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soil.
Soil classification systems make use of all these differences and can either reflect the agricultural potential of

the soil, as in Land Use Classification, or its geological and pedological properties.

There are different soil classification systems. Examples include:

 Unified Soil Classification System (USCS) in North America: The USCS has three major classification

groups: (1) coarse-grained soils (e.g. sands and gravels); (2) fine-grained soils (e.g. silts and clays); and (3)

highly organic soils (referred to as "peat’’).

 The European soil classification system (ISO 14688)

 AASHTO Soil Classification System (i.e, American Association of State Highway and Transportation

Officials Soil Classification System

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Physical Properties of Soil

Soil Texture
The particles that make up soil are categorized into three groups by size – sand, silt, and clay.

Figure 2: Types of soil: 7

 Sand particles are the largest and clay particles the smallest.

 Most soils are a combination of the three.

 The relative percentages of sand, silt, and clay are what give soil its texture.

 A clay loam texture soil, for example, has nearly equal parts of sand, slit, and clay. These textural
separates result from the weathering process.

 There are 12 soil textural classes represented on the soil texture triangle.

 This triangle is used so that terms like “clay” or “loam” always have the same meaning.

 Each texture corresponds to specific percentages of sand, silt, or clay.

 Knowing the texture helps in the management of soil.

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Figure 3: The textural classes of soil

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Soil Structure

Soil structure is the arrangement of soil particles into small clumps, called peds or aggregates.

Soil particles (sand, silt, clay and even organic matter) bind together to form peds.

Depending on the composition and on the conditions in which the peds formed (getting wet and drying

out, or freezing and thawing, foot traffic, farming, etc.), the ped has a specific shape.

They could be granular (like gardening soil), blocky, columnar, platy, massive (like modeling clay) or

single-grained (like beach sand).

Structure correlates to the pore space in the soil which influences root growth and air and water

movement.
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Soil Tilth

Soil tilth is a physical condition of soil, especially in relation to its suitability for planting or growing

a crop. The tilt of soil is closely related to its structure and it is dependent on the size distribution of

the particles.

Soil Colour

Soil color is influenced primarily by soil mineralogy – this reflects what is in a specific soil. Soils high

in iron are deep orange-brown to yellowish-brown. Those soils that are high in organic matter are dark

brown or black. Color is also an indication of how a soil “behaves” – a soil that drains well is brightly

colored and one that is often wet and soggy will have a mottled pattern of grays, reds, and yellows.
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Soil Profile

 The soil forming process give rise to distinct layers or horizons, which collectively form

the soil profile.

 The soil profile is a vertical section of the soil that depicts all of its horizons.

 The soil profile extends from the soil surface to the parent rock material.

 They can be differentiated by colour, texture, physical structure, porosity, the amount and

kind of organic matter, root growth and microbial and other organisms present.

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Figure 4: Typical soil profile.
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Soil Permeability

 This is the ability of the soil to transmit water and air.

 An impermeable soil is good for aquaculture as the water loss through seepage or infiltration is low.

 As the soil layers or horizons vary in their characteristics, the permeability also differs from one

layer to another.

 Pore size, texture, structure and the presence of impervious layers such as clay pan determines the

permeability of a soil. Clayey soils with platy structures have very low permeability.

 Permeability is measured in terms of permeability rate or coefficient of permeability (cm per hour,

cm per day, cm per sec.).

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A Good Soil

1. A soil is considered to have a good structure when it holds sufficient water to prevent moisture
deficits around plant roots during dry periods but on the other hand allows sufficient drainage to
prevent water logging during wet periods.

2. Soil structure is also important at seeding: The aggregates in the seed bed must be sufficiently large to
prevent wind erosion but must not be so large as to provide a mechanical barrier to the germinating
seed.
3. Microorganisms can contribute to the structure of soil by producing gums and cements but these can
also damage structure by blocking pores. That is microorganisms are involved in soil aggregation and
soil stabilization.
4. Tillage provides more oxygen for the soil microflora which --- synthesize polysaccharide gums but it
also induces the oxidative decomposition of the structure.
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PHYSICO-CHEMICAL CONDITIONS IN SOIL

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Soil Surfaces
Clay:
 Clay particles are colloids and potentially can interact with microorganisms.
 Kaolinite, montmorillonite and illite are the principal clay minerals found in soil and these
have been used in the study of microorganism interactions.
 Clay colloids are coated with metal hydroxides and sesquioxides and the surfaces carry
polarized but net electronegative charges.
 Microorganisms are similar in some respects to clay colloids since the macromolecules lying
on the surface of the cell wall or the capsule possess charged groups, which are again polarized
and net electronegative.
 The polarization of charges causes microorganisms to be sorbed to the clay colloids.

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Soil Surfaces
Sand and silt:

 Sand and silt particles are relatively large.

 They have surfaces which are relatively inert

 They carry little moisture or organic matter.

 There is little microbial activity on them.

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Water

 Micro-organisms are generally considered to be aquatic but there is often a restriction in

the availability of water to microorganisms in terrestrial systems.

 Water serves to bind and secure the physical particulates in soil structure.

 It is the medium by which natural chemicals and essential trace element nutrients are

transported to plants and microorganisms.

 Gas and water are contained in the voids between particles.

 Microbiologists frequently use the empirical gravimetric ‘determination and express the

water content as a percentage.

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Temperature

 Temperature is a determining factor in both the composition of the soil microflora and its

activity.

 It varies with latitude and altitude and its cyclic both diurnally and seasonally.

 There is also a great variation with depth and this is influenced by the water content.

 The presence of vegetation, plant residues or mulches reduces the variation in soil

temperature. Heat from the sun can also be reflected back by soil, the effect being greatest in

light-coloured soil.

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Acidity and alkalinity

 The composition of the soil microflora is highly dependent on the on soil pH.

 However it is very difficult to measure the pH of the soil.

 This is largely a result of the properties of the diffuse double layer, causing hydrogen ion

concentration gradient between the surface of soil particles and the surrounding soil

medium.

 The lowest pH is on the particle surface and the gradient is reduced if the electrolyte

concentration in the soil solution is increased.

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Acidity and alkalinity Cont’d

 Metabolic activity, particularly that involving redox reaction, influence the pH of soil.

 For example the reduction of nitrate to nitrogen and sulphate to sulphide takes place

under anoxic conditions will cause the pH of soil to become alkaline.

 However, the production of carbon dioxide during respiration causes the pH to become

acidic.

 The pH is influenced by the time of the year, the climate and the previous cropping

history.

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Soil atmosphere

 In a well-drained soil, many of the voids are filled with air.

 There will always be some spaces which are effectively sealed and where microbial

respiration results in a decline in the oxygen concentration with concurrent synthesis of

carbon dioxide and other gaseous metabolites.

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Soil atmosphere Cont’d

 Particle size is a governing factor in soil atmosphere:

 In wet soils, there are more ‘sealed’, voids and consequently the mean concentration of oxygen

throughout the soil is reduced, with some pockets becoming anoxic.

 This has a great influence on the soil microbial population because fungi and aerobic bacteria

require oxygen and in only rare instances, it has been reported of fungi other than yeasts acting as

anaerobes.

 Even very small crumbs are likely to be heterogeneous and whereas for example the surfaces may

be aerobic, allowing the formation of nitrate (nitrification) to occur, the centres may be anaerobic,

promoting the formation of nitrous oxide and nitrogen (denitrification).

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Soil atmosphere Cont’d
 The production of gas is promoted by substrates for microbial growth and thus cropping, farmyard
manure, crop residues and green manure increase production of carbon dioxide.
 However, these processes may also increase the air space in the soil, resulting in greater loss of the
gaseous metabolite.
 Farmers can affect soil aeration by cultivation, although in the absence of a drainage system the effects
are limited to surface layers.
 Ploughing is effective in aerating soil and might appear more effective than the modern practice of
directly drilling seeds into soil without prior cultivation.
 When oxygen has disappeared from the soil atmosphere, microbial activity can be continued by those
organisms capable of using alternative electron acceptors, such as sulphate.
 Thus the soil must be treated as a collection of microenvironments which do not remain in a constant
physical, chemical or biological state.
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THE SOIL POPULATION

Types of organisms - BACTERIA

 Bacteria are the most numerous (106 — 109 viable cells cm-3) but owing to their

small size (ca 1 µm) are not necessarily the major component of the soil biomass.

 Generally they are largely responsible for the cycling and transformation of

carbon, nitrogen, phosphorus, iron and Sulphur within the soil.

 The soil bacterial population is extremely diverse.

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THE SOIL POPULATION

Types of organisms - FUNGI

 Fungi which are larger (spores ca 20 µm), are as important as bacteria in soil.

 Their tolerance to low pH makes them particularly significant in acid soils.

 They have major roles in plant residue decomposition and in plant pathogenesis.

 Soil fungi also exhibit great species diversity in soil and identification is complicated by

the fact that their life-cycles in soil are often quite different from those in laboratory

culture.

 Soil yeasts have been implicated in increasing soil structural stability through their ability

to produce extracellular gums. 27

THE SOIL POPULATION

Types of organisms – OTHER COMPONENTS

 Actinomycetes: Streptomyces spp. have been shown to be common producers of antibiotics.

 Protozoa occur in soil as flagellates, amoebae, ciliates and sporozoa at the order of l03 g-1 wet soil

for each group. They may have a role in ecology as predators of soil bacteria.

 Another group which has received virtually no attention in soil microbial ecology is the viruses. The

activities of soil animals such as nematodes, enchytraeid worms (pot worms), lumbricid worms

(earthworms), termites, springtails and mites also contribute to the soil biomass.

 Activities of soil population are not only the result of whole organisms but can also result from the

activity of free enzymes in the soil. There is a great diversity of such activity in the soil.

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SPECIAL AND SEASONAL DISTRIBUTION

 There have been many studies of the seasonal distribution of microorganisms, particularly

fungi and there is great variation.

 Similar studies have been made of species diversity down the soil profile but few have

considered the correlation between the products of metabolism and the microbial

population. One exception is the work on denitrification of nitrate added to the soil

surface. It was demonstrated that this process increased down the profile and was

correlated with an overall increase in the number of denitrifiers.

 Populations do not always correlate with activities.

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MICROORGANISMS IN THEIR NATURAL ENVIRONMENTS II

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SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH
Inorganic sources

 Soil microorganisms are dependent on the minerals in the soil in addition to any added

fertilizers to satisfy their requirements for both major and trace elements.

 The lithotrophic population use these as a source of reducing equivalents, often coupled

with light energy.

 Amongst the phototrophs are the blue-green algae, which occur in the surface horizons and

can fix atmospheric nitrogen if there is an abundant source of light energy and surface water,

and the nitrifying bacteria.

 Plants can influence the availability of inorganic nutrients to microorganisms. 31

SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH CONT’D

Crop residues and leaf litter

 The carbon substrate for saprophytes in forest ecosystems is leaf litter and the

counterpart in agriculture is crop residues.

 The growth of heterotrophs in soil is usually considered to be limited by the

availability of a suitable carbon source.

 However, there are exceptions, for example, microbial growth on straw when N may

be the limiting nutrient.

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SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH CONT’D
 There have been many studies on the pattern of microbial, particularly fungal, succession on
crop residues and leaf litter.
 The primary colonizers are those which can use the simple soluble materials, including
monosaccharides and disaccharides, which are the first to be leached. Examples of these are the
primary saprophytic sugar fungi, such as Mucor spp. and Rhizopus spp. They grow rapidly
relative to later colonizers and it has been indicated that this may be characterized by a high
specific rate of sugar utilization.
 The secondary colonizers use the more complex material, such as polysaccharides, and
commonly produce cellulases.
 Tertiary colonizers are capable of metabolizing some of the more complex polymers such as
lignin, but as these are not readily assimilable energy sources the growth is quite slow.
 Successional groupings usually overlap. 33
SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH CONT’D

 The colonization of plant residues by fungi is of particular agronomic

significance if the colonizers are plant pathogens.

 Often the microorganisms will only show their pathogenic properties if present in

sufficient numbers.

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SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH CONT’D

Root exudates

 The movement of plant roots through the soil causes some of the root cells to slough off.

 In addition, soluble organic materials can diffuse through root cell membranes and reach the soil.

 Both of these processes produce substrates for the soil microflora and together are usually referred to as root

exudates.

 Root exudates are responsible for the ‘rhizosphere effect’ - there is a dense proliferation of microorganisms

around the root epidermis.

 Root exudate material consists usually of about 90% carbohydrate and l0% amino acids.

 Microorganisms themselves could modify the pattern of exudation.

 Contact with solids, anaerobiosis, moisture stress, low temperature, herbicides and mechanical forces all

increase exudation. 35
SOURCES OF SUBSTRATES FOR MICROBIAL GROWTH CONT’D

Soil organic matter

 When biological residues decay in soil, they become humified.

 Lignin is the more resistant woody part of decaying plant tissue left after hemicelluloses and celluloses have been

metabolized, and is composed mainly of phenolic polymers, which eventually give rise to humic acid.

 There are three main aryl aldehydes in the polymers:

 These substances in the polymeric form do not provide very favourable growth substrates for microorganisms.

 In the free state, the aryl aldelhydes can be degraded very slowly by basidiomycetes, ascomycetes, actinomycetes,

and some bacteria.

 The degradation is usually stepwise to give dihydroxyphenols followed by ring fissure. The oxidative coupling of

phenols and amino acids by microorganisms leads to the brown polymer pigment, melanin, although an additional

energy source is usually required to produce this compound. 36

ENERGY FLOW

Principles

The heterogeneous distribution of substrates in soil means that microbial activity is distributed similarly.

Generally, microbial growth in laboratory culture can be described as closed (batch) or open (continuous

flow). None of these systems describes microbial growth in the natural environment.

In the terrestrial environment there are continuing inputs of organic matter, but these occur as pulses of

varying duration with the deposition of leaf litter and crop residues. Therefore, this situation may be

considered as a succession of ‘batch cultures’, where microorganisms grow at their maximum rate until

the substrates are exhausted and they then become dormant or die.

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ENERGY FLOW CONT’D

Principles Cont’d

 In practice substrates are often poor sources of energy and high growth rates cannot be achieved.

 Also the available energy is not used by individual species, but rather by successions of

populations.

 The growth of micro-organisms in the rhizosphere is a different situation because here the input of

substrates from root exudates is a continuous process and its rate can be determined.

 However, there is no effective dilution of the rhizosphere populations by ‘washout’, as would be

the situation in ‘continuous culture but the kinetics of growth might be considered to be more

allied to ‘fed batch culture’.

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ENERGY FLOW CONT’D

Calculation of energy budget

 In many natural systems the supply of energy substrate (ds/dt) can be calculated from a

knowledge of the amounts of leaf litter, crop residues and root exudates which are added

annually.

 The soil biomass can be calculated from counting the population by direct observation and

by a knowledge of the mean cell or unit hyphal weight, as determined in the laboratory

section.

 It is most important that fungi are included with bacteria in estimates of biomass as many

investigators have found these to be the major components of that soil biomass. 39
ENERGY FLOW CONT’D

Respiration

It has been considered that as respiration is often a good index of microbial activity.

Measures of the CO2 output of soil would be a means to producing energy budgets.

Whereas many investigators have failed to show that a good correlation exist between

bacterial numbers and CO2 output of soil, however, there are exceptions.

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ENERGY FLOW CONT’D

Root exudates and the rhizosphere

 The continuing flow of organic materials from roots ensures that an active microbial

population is sustained around them.

 Microorganisms on and around the roots enhances the release of substrates, possibly

both directly, by making holes or by the production of substances which stimulate

the process, and indirectly by utilizing the exudates and preventing their build-up in

solution, thus increasing outward diffusion.

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ENERGY FLOW CONT’D

The carbon: nitrogen ration

In laboratory studies of microbial growth on defined media, it is usually clear which is the

growth—limiting nutrient and this is normally carbon or nitrogen.

There is no such certainty in the natural environment. Organic materials which are

incorporated can have widely different carbon: nitrogen (C:N) ratios. If the ratio is below 20,

this is often adequate to satisfy the nitrogen requirements of the microflora which decompose

the residues. However, ratios above this unusually result in immobilization of nitrogen in the

soil, which has to be refurbished with fertilizer nitrogen to avoid nitrogen deficiency in the

soil. 42