Download Soil Microbiology

Soil Microbiology
ENVIRONMENTAL MICROBIOLOGY
WHAT IS SOIL?
 Soils are excellent culture media for the growth of many
kinds of microorganism
Who is at home in the soil?
Soils are excellent culture media for
the growth of many kinds of
microorganism
Size of Soil Organisms
Macro or large
(>2 mm)
Meso or mid-size
(2–0.2 mm)
Micro or small
(<0.2mm)
Mite
Earthworm
Alfalfa root
Yeast
Springtail
Bacteria
A single teaspoon of soil contains
over 1,000,000,000
bacteria, about120,000 fungi and
25,000 algae.
Organism
Earthworms
Mites
Nematodes
Protozoa
Algae
Fungi
Actinomycetes
Bacteria
1
Number
per gram soil
(~1 tsp)
Biomass1
(lbs per
acre 6”)
–
1-10
10 – 100
up to 100 thousand
up to 100 thousand
up to 1 million
up to 100 million
up to 1 billion
100 – 1,500
5 – 150
10 – 150
20 – 200
10 – 500
1,000 – 15,000
400 – 5,000
400 – 5,000
Biomass is the weight of living organisms
 Microorganism in 1 acre of average fertility soil would
weight as a medium sized-dairy cow
 Bacteria
 Fungi
MOO!
 Actinomycetes
 Algae
 Protozoa
The world of microorganisms in soil
Bacteria
 Bacterial population of the soil exceeds other groups of





microorganisms in number and variety.
Plate count yields 1-10% of the total count (as compared
to direct microscopic counts).
Dominant genera : Arthrobacter, Pseudomonas, Agrobacterium,
Flavobacterium and Bacillus.
Animal pathogens : Clostridium, Bacillus, Coxiella and
Streptococcus
Plant pathogens : Agrobacterium, Erwinia, Corynebacterium,
Pseudomonas and Xanthomonas.
Different physiological groups are also present.
Where are the microorganisms located in
the soil?
 Usually the top 2-3 cms.
 Commonly found close to root
surfaces, in dead roots, on soil
particles or amongst aggregates
of soil particles.
 Soils that are clayey have many
bacteria because these soils
have lot of small pores.
 Sandy soil is less suitable
habitat.
Fertile Soil
Clay Soil
Infertile Soil
Sandy Soil
Soil factors that
affect
microorganism
growth
Spherical Bacteria
 Organic matter
 Aeration (oxygen)
 Moisture and temperature
 Soil fertility and pH
Rod-Shaped Bacteria
Organic matter in the soil
 Organic matter = anything
that contains carbon
compounds that were
formed by living organisms.
 Dead forms of organic
material - mostly dead plant
parts (85%)
 Living parts of plants - mostly
roots (10%)
 Living microbes and soil
animals
 Partly decayed organic matter
is called humus
Components of Soil Organic Matter
Microbial degradation or organic matter
 Involves complex processes. Chemical alteration of
organic matter, physical fragmentation and release of
mineral nutrients.
 The dead organic matter is colonized by microbes and
degraded with help of microbial enzymes.
 Macromolecules are broken down into simpler units and
further degraded into constituent elements.
Organic matter decomposition
Everyone is involved
 Bacteria
 Population increases rapidly when
organic matter is added to soil
 Quickly degrade simple compounds
- sugars, proteins, amino acids
 Have a harder time degrading
cellulose, lignin, starch
 Cannot get at easily degradable
molecules that are protected
Bacteria on fungal strands
Spiral bacteria
Rod bacteria
Effect of soil temperature
 Microorganisms have been found growing in
virtually all environments where there is
liquid water, regardless of its temperature.
 Microorganisms are found growing at the sub
zero temperatures of Antarctic soil to
temperatures as high as 115oC in deep sea
hydrothermal vents.
General response of microorganisms to temperature and
pH.
SOIL MOISTURE CONTENT
 Availability of water (aw -
known as water activity) is a
critical factor that affects
the growth of all cells.
 aw pure water = 1
 range of m.o. = aw 1 to 0.7.
 aw agricultural soils : 0.9 to
1.
Limiting aw for growth of certain procaryotes.
Soil pH
 The pH or hydrogen ion concentration of natural
environments varies from about 0.5 in the most
acidic soils to about 10.5 in the most alkaline lakes.
 Most free living prokaryotes can grow over a range
of pH.
 Depending on pH preferences microorganisms are
classified into
– acidophiles, neutrophiles and alkaliphiles.
Sources of N
 Lightning
 Inorganic fertilizers
 Nitrogen Fixation
 Animal Residues
 Crop residues
 Organic fertilizers
Forms of Nitrogen
 Urea  CO(NH2)2
 Ammonia  NH3 (gaseous)
 Ammonium  NH4
 Nitrate  NO3
 Nitrite  NO2
 Atmospheric Dinitrogen N2
 Organic N
Roles of Nitrogen
 Plants and bacteria use nitrogen in the form of
NH4+ or NO3 It serves as an electron acceptor in anaerobic
environment
 Nitrogen is often the most limiting nutrient in soil
and water.
Nitrogen is a key element for
 amino acids
 nucleic acids (purine, pyrimidine)
 cell wall components of bacteria (NAM).
NITROGEN CYCLE
 AMMONIFICATION
 NITRIFICATION
 DENITRIFICATION
 NITROGEN FIXATION
Nitrogen in
the air
nitrogen fixing plant
eg pea, clover
animal protein
plant made
protein
root nodules
(containing nitrogen
fixing bacteria)
nitrates absorbed
dead plants & animals
urine & faeces
denitrifying
bacteria
decomposition by bacteria & fungi
ammonia
nitrates
bacteria
nitrites
bacteria
(nitrifying bacteria)
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N2
N2O
NH4
NO2
R-NH2
NO
NO2
NO3
Ammonification or Mineralization
N2
N2O
NH4
NO2
R-NH2
NO
NO2
NO3
Mineralization or Ammonification
 Decomposers: earthworms, termites, slugs,
snails, bacteria, and fungi
 Uses extracellular enzymes  initiate
degradation of plant polymers
 Microorganisms uses:
 Proteases, lysozymes, nucleases to degrade
nitrogen containing molecules
 Plants die or bacterial cells lyse  release of
organic nitrogen
 Organic nitrogen is converted to inorganic
nitrogen (NH3)
 When pH<7.5, converted rapidly to NH4
 Example:
Urea
NH3 + 2 CO2
Nitrification
N2
N2O
NH4
NO2
R-NH2
NO
NO2
NO3
Nitrification
Two step reactions that occur together :
 1rst step catalyzed by Nitrosomonas
2 NH4+ + 3 O2  2 NO2- +2 H2O+ 4 H+
 2nd step catalyzed by Nitrobacter
-
 2 NO2 + O2  2 NO3
-
 Optimal pH is between 6.6-8.0
 If pH < 6.0  rate is slowed
 If pH < 4.5  reaction is inhibited
Denitrification
N2
N2O
NH4
NO2
R-NH2
NO
NO2
NO3
Denitrification
 Removes a limiting nutrient from the environment


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
4NO3
+ C6H12O6 2N2 + 6 H20
Inhibited by O2
Not inhibited by ammonia
Microbial reaction
Nitrate is the terminal electron acceptor
Nitrogen Fixation
N2
N2O
NH4
NO2
R-NH2
NO
NO2
NO3
Nitrogen Fixation
 Energy intensive process :
 N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 +
16ADP + 16 Pi
 Performed only by selected bacteria and
actinomycetes
 Performed in nitrogen fixing crops
(ex: soybeans)
Microorganisms fixing
 Azobacter
 Require the enzyme
 Beijerinckia
nitrogenase
 Inhibited by oxygen
 Inhibited by ammonia
(end product)
 Azospirillum
 Clostridium
 Cyanobacteria
The nitrogen fixing bacteria are found inlumps on the roots
called root nodules. The bacteria and the plant have a
symbiotic relationship: the bacteria benefits by having food
and shelter from the plant and the plant benefits by having
nitrates produced by the bacteria.
Roots of a legume plant (peas, beans and clover).
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