The Islamic University of Gaza- Environmental Engineering Department

Environmental Microbiology (EENV-2321)

Lecture 5: Earth Environment

Prepared by
Husam Al-Najar

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Earth Living Skin:
• The complexity of the soil is driven by two components: Abiotic
soil architecture and biotic diversity.
Abiotic factors: in an environment include such items as
sunlight, temperature, wind patterns, and precipitation.
The biotic factors: in an environment include the organisms
themselves as well as such items as predation ‫االفتراس‬, competition
for food resources, and symbiotic ‫ التكافلية‬relationships
Beneath the soil layer is the subsurface that includes the
unsaturated or vadose zone, and the saturated zone including
aquifer.
The subsurface contains microorganisms, but microbial
communities are lower than in the surface soil.

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 Cross section of the subsurface

1. Soil
2. Vadose Zone
3. Saturated Zone (fringe water)
4. Saturated Zone (aqifer)
• Shallow Table aquifer
• Intermediate aquifer
• Deep aquifer
5. Saturated Zone (Wetlands)

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 Ground water flow system- Unconfined

Unsaturated zone

Pond Pond wetland

saturated zone Permeable sediments sand

and gravel

Bedrock

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Saturated Zone- Aquifers

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 Soil Formation and Composition

Soil formation is a physical and biochemical process. It has to be formed from

something and that would be the parent material. Climate and topography are
factors that don’t change easily. Then we have organisms interacting with the
environment and over time, soil is formed.
Factors of soil formation
Organisms: A teaspoon of productive soil generally contains between 100
million and 1 billion bacteria. Organisms play an important role in redoximorphic
formation, reducing oxygen, nitrogen, iron, and other minerals to complete their
life cycle.
Earthworms mix soil and create large pores which help transmit water and
oxygen.
Humans use soil for building houses and obtaining the raw materials needed for
building things.
Climate: how a rain forest soil would differ from a desert soil.
Temperature and moisture amounts cause different patterns of weathering and
leaching
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Time: The start of soil formation (time zero) generally occurs following a
major geologic event such as a volcanic eruption, deposition of material
from a flood, landslide, or a glacial period

Parent material: While some soils develop by weathering of the

underlying bedrock (residual soils), many soils form from material that
has been transported from a different area

Topography: The most important factor for hydric soil formation is

landscape position.

A hydric soil is a soil that formed under conditions of saturation, flooding, or

ponding long enough during the growing season to develop anaerobic
conditions in the upper part

The first thing we learn about hydrology is that water moves downhill.
Hydric soils are most often found in depressions, along drainage ways,
and on level or concave slopes

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The effect of topography

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Soil is frequently less than one meter thick, making it as thin
and fragile as an egg shell. 50% of it are pore spaces (which are
filled with either air or water), 45% minerals (Si, Fe, Al, Ca, K, Mg,
Na) and 5% organic matter.

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 Soil Architecture
Spaces between aggregates are
called inter-aggregate pores

spaces within the aggregates

intra-aggregate pores

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Bacteria, and viruses size is larger than the fine pore canals in the soil

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Soil Architecture: Usually, microbial gums, polysaccharides and other
secondary metabolites can bind soil particles together to form
aggregates,

somewhat like a lump of various particles.

Spaces between aggregates are called inter-aggregate pores,

and spaces within the aggregates intra-aggregate pores.

The phenomenon to note here is micropore exclusion, where molecules

enter pores so fine that excludes bacteria.

If the molecules happen to be pollutants it would be a bioremediation

challenge as the micropores provide a sink from which the pollutants can
slowly seep out in the future.

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Soil Texture: The relative proportions of sand, silt and clay particles
in a mass of soil (material less than 2 mm in size)

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Soil profile

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O horizons: are soil layers with a high percentage of organic matter

A horizon: Dark color is due to the mixing of humus with mineral

E horizon: is a mineral horizon in the upper part of the soil. Typically

present only in forested areas it underlies an O or A horizon. It is a light
colored, leached horizon

B horizons: are commonly referred to as the subsoil. They are a zone of

accumulation where rain water percolating through the soil has leached
material from above and it has precipitated within the B horizons or the
material may have weathered in place. Well drained soils typically have
the brightest color development within the B horizons.

C-horizons are glacial or post-glacial material

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Various soil profiles

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 Importance of CEC
• Chemical behavior in soils
• Fertility
• Pesticides
• Contaminants 17
 Principles of Ionic Exchange

Clay minerals and organic

matter influence CEC most
substantially
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Attachment of a bacterial cell to clay particles via cation bridging

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 Soil Organic Matter

• Soil organic matter

– all living organisms (microorganisms, earthworms, etc),
– fresh residues (old plant roots, crop residues, recently added
manures),
– well-decomposed residues (humus).
• The SOM content of agricultural topsoil is usually in the range of
1 to 6%.
• This amount is the result of all additions and losses of SOM that
have occurred over the years.

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Soil Organic matter encompasses all organic components of a soil

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 Decomposition

Organic Residue

Decomposers Catabolism Nutrient Release

Heat NH4, PO4, SO4
Bacteria
CO2
Fungi Anabolism

humification

Humus

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• Soil quality is the capacity of soils within landscapes to sustain biological
productivity, maintain environmental quality, and promote plant and
animal health.
• Protecting soil quality like protecting air quality and water quality
should be fundamental goal of our Nation’s Environmental Policy
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Soil Atmosphere

Soil and atmosphere are in direct contact, therefore the soil atmosphere
has basic composition as air: nitrogen, oxygen and carbon dioxide.
Plant and microbial activity can affect the relative proportion of oxygen and
carbon dioxide in soils that are not well aerated.

Location Composition (% volume basis)

Nitrogen (N2) Oxygen (O2) Carbon dioxide (CO2)

Atmosphere 78.1 20.9 0.03

Well-aerated surface soil 78.1 18- 20.5 0.3- 3

Fine clay or saturated soil > 79 0- 10 Up to 10

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 Soil as A microbial Environment

Biotic Stress: Soil microbes are in competition with one another.

Competition can be for: Substrate, Water, Growth factors
Microbes secrete allelopathic substance (inhibitory or toxic),
including antibiotics that harm other organisms.
Many organisms are predatory or parasitic on neighboring
microbes.
Example:
• Protozoa graze on bacteria
• Viruses infect both bacteria and fungi

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Abiotic Stresses: Including the physical and chemical
characteristics of the environment.
Light: Phototrophic microorganisms are limited to the top few centimeters
of soil.
Soil Moisture: The availability of water is critical for microbial activity.
Fungi are most desiccation resistant followed by actinomycetes and
bacteria.
Soil Temperature:
• Heat stress: Denaturing of enzymes

• Cold stress
– Decrease in fluidity of cellular membranes
– Ice nucleation

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 Soil Structure and role of microorganisms:

• Aggregates determine structure, porosity, aeration, water

retention, pore space and sizes

• Soil particles and organic matter are negatively charged

• Compounds produced by microorganisms are attracted to soil

particles
– Enzymes, Polysaccharides, Wastes, Fragments

• Bacteria and fungi negatively charged – should be repelled from

soil surfaces

• Can bind to soil particles and organic matter through

intermediates
– Divalent cations
– Adsorbed organic compounds
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 Soil pH:

• Soil organisms have optimal soil pH range

– Nutrient acquisition
– Extracellular enzyme activity
– Regulate cytoplasmic pH from that of soil solution

• Fungi are acid tolerant (pH 4 to 6.5)

• Bacteria prefer neutral conditions (6.0 to 7.5)

• Organisms have ability to alter soil pH

– Ammonium oxidizing bacteria acidify soil by producing NO3-
from NH4+

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 Microorganisms in surface soils
Bacteria:
• Are the most abundant organisms in the surface soil in terms of number
• Cultural bacteria can be 107 to 108 cells per gram soil
• The total population including non-cultrable) can exceed 1010 cells per gram soil.
• Diversity is indicated by the number of Operational Taxonomy Units (OTUs)
• each OUT represents a different bacterial population in the community.
• Diversity ranging up to 6300 OTUs per gram soil.

Actinomycetes
• are procaryotic organisms that are classified as bacteria
• unique enough to be discussed as individual group.
• can tolerate high pH, high temperature, or water stress.
• Morphologically, resemble fungi because of their elongate cells that branch into
filaments or hyphae.
• They are able to utilize great variety of substrates found in the soil. 31
 Dominant Culturable Soil bacteria

Arthrobacter (+) Nutrient cycle and biodegredation

Streptomyces (+) Nutrient cycling and biodegredation, antibiotic
Pseudomonas (-) Nutrient cycling and biodegredation, biocontrol agent
Bacillus (+) Nutrient cycling and biodegredation, biocontrol agent

Important Autotrophic soil bacteria

Nitrosomonas (-) Convert NH4 to NO2

Nitrobacter (-) Convert NO2 to NO3
Acidothiobacillus (-) oxidizes S to SO4
Acidothiobacillus dinitroficans (-) oxidizes S to SO4, function as a denitrifier
Acidothiobacillus lerrooxidans (-) oxidizes Fe2+ to Fe3+

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Fungi:
• Number of fungi usually range from 105 to 106 per gram soil
• Despite their lower number compared to bacteria, fungi contribute to higher
proportion of biomass in the soil.
• yeast are found at population up to 103 per gram of soil.
• Fungal population are greatest in the surface O and A horizon and numbers
decrease rabidly with increasing soil depth.
• Soil fungal are normally found associated with soil particles or within plant
rhizospheres.
• Fungi are important components of soil with respect to nutrient cycling and
decomposition of organic matter.
• Fungi is important in development of soil structure because they physically entrap
soil particles with fungal hyphae.
• Fungi can degrade a Varity of pollutant molecules, white-red fungus
phanerochaete chrysosporium is the best known example.
• Finally, mycorrhizal fungi are critical for establishing plant-fungal interactions that
acts as extension of the root system of almost all higher plants.
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Algae:
• Algal cells predominantly in areas where sunlight penetrate, the very surface of soil.
• Algae can found to 1 m depth because some algae, can grow heterotrophically as well
as photoautrophically.
• Typical algal populations close to the soil surface can range from 5000 to 10,000 per
gram soil, but where a visible algal bloom has developed there can be millions of algal
cells per gram of soil.
• Algae is important in establishing soil formation process, especially in volcanic area,
desert soils and rock faces.
• Algal metabolism is critical to soil formation in two ways:
1. Algae provide a carbon input through photosynthesis, and as they metabolize, they
produce and release carbonic acid, which weathering the surrounding mineral
particles.
2. Algae produce large amounts of extracellular polysaccharides, which cause the
aggregation of soil particles.
• In soils the relative abundance of the major algal groups are green algae> diatoms>
cyanobacteria> yellow-green algae.
• In tropical soils the cyanobacteria predominate
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 Protozoa:
• Most of protozoa are heterotrophic and survive by consuming bacteria,
yeast, fungi and algae.
• Protozoa are found mainly in the top 15 to 20 cm of the soil.
• Protozoa are usually concentrated near root surfaces that have high
densities of bacteria
• Soil protozoa are flatter and move flexible than aquatic protozoa, which
makes it easier to move around in the thin films of water that surround soil
particle surface.
• Number of protozoa range from 30,000 per gram soil from a
nonagricultural soil to 350,000 per gram soil from maize field.

Most of microorganisms in the earth environment are attached.

Approximately 80 to 90% of the cells are sorbed to solid
surfaces and the remainder are free- living.
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Distribution of Microorganisms in the Soil

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In surface soils, microbial distribution is also dependent on soil texture and
structure.

As soils form, microbes attach to a site that is favorable for replication.

As growth and colony formation take place, exopolysaccharides are

formed, creating a "pseudo glue" that helps in orienting adjacent clay
particles and cementing them together to form a micro aggregate.

Although the factors that govern whether a given site is favorable for
colonization are not completely understood, several possible factors have
been identified that may play a role, including nutrient availability and
surface properties.

In addition, in surface soils, pore space seems to be an important factor.

Pore spaces in microaggregates with neck diameters less than 6 µm have
more activity than pore spaces with larger diameters, because the small
pore necks protect resident bacteria from protozoal predation.

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Pore space also controls water content to some extent.
Larger pores drain more quickly than smaller pores, and therefore the
interior of a small pore is generally wetter and more conducive to microbial
activity.
It has further been suggested that gram-negative bacteria prefer the interior
of microaggregate pore space because of the increased moisture, whereas
gram-positive bacteria, which are better adapted to withstand dry
conditions, tend to occupy the microaggregate exteriors

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It must be emphasized that, although microbes are present in deep vadose zones,
rates of metabolic activity is much lower than rates in the surface soils.
In the figure, compares metabolic activity in a range of surface and subsurface
environment. Metabolic activity is expressed as the rate of CO2 production.

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Samples taken from deep cores have
shown that:
• There are lower numbers and a
more limited diversity of
microorganisms in deep saturated
zones than in the surface soils.
• The types of organisms detected
included wide range of aerobic, and
facultative anaerobic
chemoheterotrophs, denitrifies,
methanogens, sulfate reducers,
sulfate oxidizers, nitrifies and
nitrogen fixing bacteria.

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