chapter 8 soil micro Flashcards
soil layer and distribution of nutrients and microorganisms:
-layers: 1. topsoil 2. subsoil 3. bedrock
-organic nurtients: decrease woth depth
number of mos: decrease with depth but still present in bedrock
Environmental factors affecting microbial abundance in soils
Moisture content Moist soils support microbial growth better than dry soils Oxygen Moist soils are lower in oxygen than dry soils Oxygen dissolves poorly in water pH Highly acidic and highly basic soils favor fungi Temperature Most soil organisms are mesophiles Nutrient availability Microbial community size determined by how much organic material is available
Based on their size, the organisms living in soil may be
categorized into 3 groups:
1.
Microbiota: viruses, bacteria, fungi, protozoa, algae
2.
Mesobiota (0.2 2mm): nematodes, mites, snails, …
3.
Macrobiota 2mm): rodents, earthworms, large
insects
Microbes perform a number of
functions
Cycle elements and convert them to usable form
Degrade dead organisms
Produce compounds with potential human uses
Characteristics of Soil Microorganisms
A
Bacteria:
Constitute the basic mass of all soil microorganisms
Most soil bacteria have the ability to adhere to surfaces of the
mineral molecules and to the soil colloids
Actinomycetes
Aerobic, Grow @40ºC 50 ºC
Degrade steroids, chitin, hydrocarbons, fatty acids
Many types produce antibiotics Erythromycin, Neomycin, Tetracycline,
Streptomycin
Rod coccus bacteria
2 60% of soil microflora
Highly resistant to environmental factors during the vegetative stage
Capable of surviving in dry soil for few months
They can utilize a wide spectrum of organic compounds as a food
substrate.
fungi
Eukaryotes, Heterotrophs
Grow strongly in acidic soils and have crucial influence on
changing of pH reaction
They get into symbiotic relationships with algae, insects, and
higher plants
They occur mostly in the upper layers of soil, however they
can be found as deep as 1 m
Most common: Penicillium , Aspergillus , Rhizopus
What habitats are provided by soil?
Naked rocks provide a very inhospitable habitat
These rocks can be colonized by Cyanobacteria that are
nitrogen fixating photolitotrophs : require only light and
inorganic nutrients to grow
Cyanobacteria
Cyanobacteria can provide both fixed nitrogen and
carbon compounds that can be used by other organisms
The action of Cyanobacteria initiates the biological
process that lead to soil formation and to nutrient cycling
The colonization of rocks by Cyanobacteria is the first
step in the transformation of naked rocks into soil suitable
for the support of plant and animal life
The microbes present in the soil are responsible for
The microbes present in the soil are responsible for re
cycling organic and inorganic material and play an
important part in the dynamic regeneration of soil
sandy soils
cannot retain water very well
and drain very quickly this may lead to the formation of
arid soils
clays
can retain water and also tend
not to be porous so as a result of water retention they also
tend to form anaerobic environments
Plants
are the major producers of organic material to befound in soil and plant matter accumulates as debris then
the animal feces and the decomposing bodies of dead
animals complement this organic supply
Artificially added fertilizers , herbicides and pesticides
all affect
the biological component and then the
organic contents of soil
-
Microbes play a central role in re cycling such
material and besides recycling of naturally occurring
organic compounds , soil microbes are responsible
for the chemical degradation of pesticides but not
all pesticides are easily broken down.
Biogeochemical cycles
Processes by which organisms convert elements from one form
to another
Elements often converted between oxidized and reduced
forms
Involve the recycling of elements by organisms
Biogeochemical cycling entails three processes
Production Inorganic compounds converted into organic compounds Consumption Organisms feed on producers and other consumers Decomposition Organic compounds in dead organisms converted into inorganic compounds
Photoautotrophs
such as cyanobacteria, green plants, algae,
and green and purple sulfur bacteria fix (incorporate) carbon
dioxide into organic matter using energy from sunlight
Chemoautprotrophs
form also organic matter by using other
source of energy like H 2 S
Chemoheterotrophs
such as animals and protozoa eat autotrophs
and may in turn be eaten by other animals.
Chemoheterotrophs , including animals, use some of the organic
molecules to satisfy their energy requirements.
When this energy is released through respiration, CO 2 immediately
becomes available to start the cycle over again
Much of the carbon remains within the organisms until they excrete
it as wastes or die.
carbon cycle
When plants and animals die, these organic
compounds are decomposed by bacteria and fungi.
During decomposition, the organic compounds are
oxidized, and CO 2 is returned to the cycle.
Carbon is stored in rocks, such as limestone (CaCO 3 ),
and is dissolved as carbonate ions (CO 3
2 –) in
Vast deposits of fossil organic matter exist in the
form of fossil fuels, such as coal and petroleum.
Burning these fossil fuels releases CO 2 , increasing
the amount of CO 2 in the atmosphere global
warming of the Earth
Carbon Cycle
Methane (CH4) gas.
Sediments on the ocean floor contain an estimated 10 trillion tons of
methane (about twice as much as the Earth’s deposits of fossil fuels
such as coal and petroleum).
Furthermore, methanogenic bacteria in the ocean’s depths are
constantly producing more
Methane is much more potent as a greenhouse gas than is carbon
dioxide, and the Earth’s environment would be dangerously altered if
all this gas escaped to the atmosphere.
Fortunately, the majority of sea dwelling (home) bacteria use escaping
CH 4 gas as energy source so it disappears before reaching the surface of
the water
Nitrogen Cycle
Nitrogen is needed by all organisms for the synthesis of proteins,
nucleic acids, and other compounds
Molecular Nitrogen N 2 makes up about 80 % of the Earth’s
atmosphere
For assimilation and use by plants nitrogen must be fixed and
transformed to organic compounds
The activities of specific microorganisms are important to the
conversion of nitrogen to usable forms
A
Ammonification
When an organism dies, the process of microbial decomposition
results in the hydrolytic breakdown of Proteins into amino acids
Deamination :Ammonification
Deamination : the amino groups of amino acids are removed and
converted into ammonia (NH 3
This release of ammonia is called Ammonification which can be
carried by numerous bacteria and fungi
ammonification in soils
1 Dry Soil: Ammonia rapidly disappears 2 Moist soil: it becomes solubilized in water, and ammonium ions (NH 4 ++) are formed: N.B. Ammonium ions from this sequence of reactions are used by bacteria and plants for amino acid synthesis.
Nitrification :
the oxidation of the nitrogen in the
ammonium ion to produce nitrate
-
Plants tend to use nitrate as their source of nitrogen for Protein
synthesis because nitrate is highly mobile in soil
NH4+ would actually make a more efficient source of nitrogen
because they require less energy to incorporate into proteins
These positively charged ions are usually bound to negatively
charged clays in the soil, whereas the negatively charged nitrate
ions are not bound
C
Denitrification
The form of nitrogen resulting from nitrification is fully oxidized
and no longer contains any biologically usable energy
However, it can be used as an electron acceptor by microbes
metabolizing other organic energy sources in the absence of
atmospheric Oxygen
Denitrification can lead to a loss of N 2 to the atmosphere especially
as N 2 Gas
NO
3
NO 2
N 2 O (Nitrous oxide) N 2
Pseudomonas appear to be the most important group of bacteria in
denitrification in soils that occurs in water logged soils where little
O 2 is available
D
Nitrogen fixation
The air we breathe is about 79 80 % of Nitrogen
Few bacterial species including Cyanobacteria can use
atmospheric Nitrogen directly as nitrogen source
Nitrogen fixation: The process by which bacteria convert nitrogen
gas to ammonia ( Nitrogenase
Nitrogen fixation is brought about by two types of
microorganisms: free living and symbiotic.
Free Living Nitrogen Fixing bacteria are found in the rhizosphere
(region roughly 2 mm from the plant root). Ex: A zotobacter ,
Clostridium pasteurianum
Symbiotic Nitrogen Fixing Bacteria: play an even more important
role in plant growth for crop production. Ex: members of the genera
Rhizobium, Bradyrhizobium
P.S.
Agricultural fertilizers are made up of nitrogen that
has been fixed by industrial physical chemical processes
Sulfur Cycle
H 2 S represents a source of energy for autotrophic bacteria
These bacteria convert the reduced sulfur in H 2 S into elemental sulfur
granules and fully oxidized sulfates (SO 4
2
Several phototrophic bacteria, such as the green and purple sulfur
bacteria also oxidize H 2 S
Hydrogen sulfide can be used as an energy source by Thiobacillus to
produce sulfate ions & sulfuric acid.
Plants and certain microbes can use SO 4
2 to make amino acids
As proteins are decomposed, in a process called dissimilation, the sulfur is
released as hydrogen sulfide to reenter the cycle
Sulfur Cycle (cont’d)
Burning fossils fuels that contain sulfur from the remainings of dead
organisms release sulfur in the form of SO 2 (sulfur dioxide ) Natural
phenomena like volcanic eruption also release large amounts of SO 2
This SO 2 will react with H 2 O to form H 2 SO 3 the acid rain
Acid deposition often impairs the growth of trees, reacts with metals,
marble, ….
The acidification of lakes and streams affect the pH of water to levels
that are very acid to forbid the growth of fish or essential units of their
food chain
Moreover, NO 2 (nitrogen oxide) from vehicles, a large component of
urban smog enter waters and will be transformed to acid
Phosphorus Cycle
Environmental phosphorus undergoes little change in
oxidation state
Phosphorus converted from insoluble to soluble forms ,
becomes available for uptake by organisms
Conversion of phosphorus from organic to inorganic
forms Occurs by pH dependent processes
Samples Collection
As soils have discontinuous + heterogeneous
(MO )= necessity to obtain a representative sample
•
As such, sampling strategy should be designed to
ensure a quality assurance plan
Soils samples collection (cont’d)
In general a quality assurance plan include the followings
Sampling strategies (number type of samples locations,
depths)
Sampling methods (specific techniques + needed
equipment)
Sample storage (type of containers+ preservation
methods + holding times)
I Sampling strategies
Soil samples can be obtained by shovel or auger (more
precise and can be used to depths up to 180 cm)
Several samples should be collected from a site to have a
representative sample
It’s better to analyze all samples b ut due to time and
financial resources a composite sample can be done
