Microbiology; soil microbiology

2. SOIL ENVIRONMENTS AND MICROBIAL DYNAMICS
SOIL – It is the outer loose material of the earth surface.
COMPOSITION
Organic and inorganic Constituents
1. Mineral matter ( < 50 % )
2. Organic matter ( 1-6%)
3. Living organisms (<1%)
4. Pore space ( Water & air ) 50%

3. Reservior ( Air, water and nutrients)- Plant growth
Bed rock – Portion of the earth beneath the soil
Fertility of soil – Chemical composition and microflora
Soil- Bacteria, fungai, virus , nematodes, algae , protozoa,
actinomycetes bring about great variety of processes

4. Soil Microbiology
It is a branch of soil science dealing with soil inhabitating microbes
and their functions and activities
Soil Microbiology has expanded to include the study of the role of
soil micro organisms in genetic engineering,
Bio control of pest and diseases, degradation of pollutants,
production and destruction of radio active gasses and its transfer –
Global science

5. Distinct phases of soil microbiology
1. Ecological phase: Quality and Quantity
2. Experimental and physiological phase:
Physiology ,Bio chemistry and utilisation of
microbes for the formation of valuable
metabolic products
3. Agronomical phase: Soil fertility and crop
production
4. Pedalogical phase: Soil formation and soil
structure

6. 1. Antony Von Leeuwenhoek (1632-1723) – Grinding lenses and
observing different things
In 1674 – Drop of Lake water through ground glass lense-
World of microbes- Drawings
History and Development of Microboilogy

7. 2. J.B . Boussingault (1838) - Legumes can obtain nitrogen from air,
when grown in soil which was not heated
3. Leishman (1858) - Nodules are formed on the roots of leguminous
plants – Bacteria
4. Woronin (1866) – Studied Nodule bacteria and found them to be
mortile and rods
5. A.B. Frank (1879) – Nodules on the roots of plants are formed as a
result of infection by micro-organisms
6. Hillriegel and Wilfarth (1885) – Legumes took nitrogen from air
through the agency of bacteria existing in the nodules of their roots
7. Beijerilck (1888) – Isolated root nodule bacteria in pure culture –
Bacillus radicicola- Foundation for development of soil microbiology

8. 8. S.N. Winogradsky (1890) – Autotrophic mode of life among
bacteria and showed microbial transformation of N and S
Beijerilck and S.N. Winogradsky - Poineers of soil microbiology
9. Omeliansky (1902)- Found out that anaerobic soil bacteria
degrade cellulose
10.Lipman and Brown (1903)- Studies on mineralisation of
organic residues and ammonification and developed tumbler/
beaker method for studying different types of transformations in
soil
11. Hiltner (1904) – Coined the term Rhizosphere
12. Rangaswamy- Studied Rhizosphere and application of
Rhizosphere microorganisms in the plant growth and biological
control of plant pathogens
13. Matcura associates ( 1961) – Rhizosphere consept
14. Russel and Hutchinson – Importance of protozoa in
controling bacterial population and activities in soil

9. 15. Conn - Direct soil examination of microbes- undisturbed soil
16. Rossi and Cholodny – Developed buried slide technique
17. Rayner and Melin, Harley, Gerdemann, Marx, Trappe and
brown – Studied mychorizal fungai
18 Alexander fleming (1929)- Penicillin antibiotic
19.S. A. Waksman (1944)- Streptomycin antibiotic
20. Van Neil – Soil bacteria and bacterial photosynthesis
21.Garret – Ecological classification of soil fungai
22. Allen and Alen – Differwnciated soil bacteria from root nodule
bacteria
23. Starkey – Studies on Iron transformation by bacteria
24. Ruinen (1956)- Phyllosphere concept
25. Alexander Martin – Started school of soil microbiology at
Cornell University and worked on cellulose decomposition, pesticide
degradation

10. Contributions of some of important scientists
1. S.N. Winogradsky (1856-1953)
➢ Role of bacteria in nitrification process and isolated two groups of
nitrifying bacteria
➢ Established role of microbes in N & S transformation process and
discovered the autotrophic mode of life among bacteria
➢ Developed enrichment culture technique making use of principle of
natural selection

11. 2. M.Beijerinck
➢Isolated Azospirillum in 1822
➢Isolated Azatobacter (1858) and obtained pure culture of A.Chroococcum and
A.agilis
➢Obtained the pure culture of root nodule bacterium- Rhizobium
➢Obtained the pure culture of Thiobacillus thioparus, T. Denitrificants and sulphur
oxidizing bacteria
➢Establishing the transformation of nitrogen
➢Developed enrichment culture technique along with Winogradsky

12. 3. Alexander Flaming –
Penicilin- Milestone in medical microbiology
Found that natural substances having antimicrobial property due to
the action of lysozyme
Worked with Staphylococcus aureus and observed the inhibition of
growth of Sa. In the plate due to the growth of penicilin
Later Florey and Chain isolated pencillium in pure culture

13. 4. S. A. Waksman
Isolated thiobacillus thioxidans
Published book on principles of soil
microbiology
Identified the soil organisms
producing antibiotics
Showed the importance of soil as a
source of antagonistic organisms
Discovered streptomicinantibiotic for
TB – Micobacterium tuberculosis
Discovered Neomycin, Actinomycin
antibiotics
Studied variety of biochemical
reactions carried out by soil micro-
organisms while decomposing
organic matter

14. Components of soil
1.Mineral matter
2.Organic matter
3.Soil air
4.Soil water
5.Soil microbes

15. Mineral matter:
• Inorganic fraction&disintigration of parent material or rocks
leads to formation of MM
• Constitutes45-49%
• Stone,sand,silt,clay-determinessoil structure&texture
Gravel(>2mm)
Coarse sand(2-0.2mm)
Fine sand(0.2-0.002mm)
Silt(0.002-0.0002mm)
Clay(<0.0002mm)
• Influence microbial growth by affecting availability of
nutrients.aeration&WHC
Soil structure:arrangement of soil particles-gummy substances-
bind soil particles
Soil texture:proportion of these particles-sandy,loam,clay

16. *Based on colour
Red&Black soil
*Based on size of soil particles
Heavy soils &Light soils
Heavy soils-Fine structured soils
Light soils-Coarse structured soils
1. Heavy soils- Clay– has large surface area because of fine particals- improves surface
area
Absorbtion capacity, exchange of ions , flacculation etc..
Clay – reserviour of an-ions( negativelycharged ) – containsmore nutrients and more
fertile encourages the growth of anaerobic microorganisms
Sandy soils – Less fertile, more aerationand supports aerobic micro-organisms
Puddled soils creates anaerobicconditionsand supports anaerobes
Good structure of soilsholds moisture, nutrients, provides good aerationand drainageto
avoidwater logging – aerobic microbes are more in number

17. Soil organic matter
Organic matter is anything which contains carbon in it.
Organic matter-1to4% in normal soils,supports growth of microbes
as it serves as Carbon&energy source&potential source of N,P,S
O M(bound nutrients) degradation Avilable form of nutrients
enter the soil solution &absorbed by the roots.
OM of soil influence –physical,chemical,biological properties ofsoil
,CEC&WHC
Depth of soil-top&deeper layers
Top-more microbes due to avilable OM-aerobes
Deeper-less microbes as OM is less-anaerobes
Bacteria are dominant organisms followed by
Fungi,Actinomycetes,protozoa

18. SOIL AIR
Soil air contains C,O,H2 etc &depends on soil pore space
Heavy soils –less air-Anaerobic microbes
Light soils-more air –Aerobic microbes
SOIL WATER
Sandy soils-WHC is low-Aerobes
Clay soils-WHC is more-Anaerobes &microaerophillic
Hygroscopicwater-water held tightly between the soil particles –
not available to mos or plants
Capillary water-water held in minute pore space between soil
particles in the form of capillaries &available to mos&plants
Gravitational water-held in larger pore space&smaller pore space
,available to microbes &plants

19. If proportionof water&air is equal Good for microbes
1 to 2% of soil,may be micro,macro-
Bacteria,Fungi,Actinomycetes,algae,Protozoaetc
All iteract among themselves to maintain
equillibrium in their population
Bacterial population is more –smaller size so
population per unit area is high&in all ecosystem
Bacteria forms major

20. Bacteria - 108 to 109 cells / gm of soil
Fungi - 103 to 105 cells / gm of soil
Actinomycetes - 104 to 105 cells / gm of soil
Nematodes - 102 cells / gm of soil
Algae - 102 to 103 cells / gm of soil
Protozoa - 102 to 103 cells / gm of soil
Papulation of Micro organisms in soil

21. Bacteria
These are the most dominant group of micro organisms in soil and
more numerous than other 4
Reason behind this is
➢Because of their small size (0.5- 1 micron)
➢Metalic and respiration rate is high
➢Generation time is very less compared to others( 24 hrs only)
➢Quick adoptability
➢Nutritional diversity
They present in all types of soil but their papulation decreases as the
depth of soil increases
In aerated soil bacteria will be dominating
In transformation process bacteria stands first due to their rapid
growth

22. Soil microbiological papulation has been divided into two broad groups by
Winogradsky
Autohcthonous Microbes
( Native flora ) ( indegenous flora)
Zymogenous ( Allochthonous )Mos
( Invaders) ( fermentative Mos)
➢Characteristics of particular
soil& which may be expected
always to be found there.
➢Papulation remains constant
➢No drastic change upon
addition of any soil amendments
/ nutrients as their nutrition is
derived from native soil organic
matter
➢eg : Arthobacter, Nocardia
➢These are not native organisms of
perticular soil but enters the soil
through precipitation , sewage, cow
dung or through diseased plant tissue
so called invaders
➢They derived nutrients from easily
available substrate as they require
specific substrates for their growth
➢They responds to soil amendments
➢Papulation increases upon addition
of soil amendments and decreases
when the added substrate get
exhausted
➢eg : pseudomonas, bacillus ,
cellulose decomposers, N- utilising
bacteria, Nitrifiers
AgriculturallyZymogenous are
important
As they respond to the carcbon source
easily

23. Transient microbes
Are those organisms, that are introduced into the soil by legume
inoculant unintentionally,
As in the case of agents producing animal and plant diseases
Based on Nutrition
Autotrophs Heterotrophs
➢These prepare their own
food material
➢Derives C from CO2 and
energy from Sunlight
Depends on prepared food for
their nutrition
Derives energy and C from
organic compounds
Eg : Rhizobium, Azatobacter,
psuedomonas

24. Energy –sun light
Carbon – CO2
Photoautotrophes - Chemoautotrophes
Chlorobium Nitrosomonas, Nitrobacter
Autotrophes
Energy –oxidation of
inorganic chemicals
Carbon – CO2

25. Based on O2 Requirement
➢Aerobic - Need O2 for their growth
eg: Azotobacter
➢An aerobic - They grow in absence of O2
eg : Clostridium, Methanobacteria
➢Facultatively an aerobic- these live in the presence or absence of O2
eg: Rhizobium
➢Microaerophillic : They require O2 in traces for their growth
eg : Azospirillum

26. Based on Structure
Bacilli – Rod shaped- Rhizobium
Cocci- Spherical shaped – Bacillus
Spirillium – Spiral shaped – Azospirillum
Vibrio – coma shaped

27. Based on temperature requirement
1. Psychrophiles- cold tolerent organisms- even temp of <
20℃
Eg : Psuedomonas
2. Mesophiles –medium temperature for their growth i.e
20 ℃ to 45 ℃
Eg: Rhizobium
3. Thermophiles : High temperature tolerant organisms
i.e. > 45 ℃ even upto 80 ℃
Eg: Bacillus, Clostridium

28. Based on position of Flagella
Monotrichus – Single flagella at one end
Lopotrichus – Tufts of flagella at one end
Amphitrichous- flagella at both the ends
Peritrichous- flagella all over the body
A trichous- No flagella

29. Actinomycetes:
Transitional group between bacteria and fungi , gm +ve
, produce branching mycelia and undergo fragmentation subdivide
to form asexual pores called conidia. As they look like fungai so
called ray fungi but chemically these are true to bacteria as they
have peptidoglycon in the cell wall and nuclear material DNA is
circular and single stranded but fungai has Chitin and cellulose in
their cell wall and also actinomycetes are sensitive to anti bacterial
compoundsbut not for anti fungal compounds
❖Similarities in cell wall composition and sensitivity to anti bacterial
compoundsbut not for antifungal compounds. So similarities in cell
wall composition and sensitivity to actibacterial compounds
true to bacteria
Eg : Streptomyces, Nocordia, Micromonospora, frankia

30. Distribution
Compost pits, river muds, lake bottoms,surface soil also in lower
horizons to considerable depths
In abundance they are second to bacteria and few species can cause
diseases to animals, human beings and plants
IMPORTANCE
Decomposition of resistant plant and animal tissues
N2 fixation – Frankia with casurina
Transformations at high temperature , perticularly in manure pits
and compostpits Eg : Thermoactinomyces
Cause certain soil borne diseases to plants eg: Potato scab of
apple, Sweet potato pox etc
Cause infectious diseases to humans and animals

31. Importance in microbial antagonism by production of antibiotics and
production of enzymes
Antibiotics is an organic molecule produced by organisms which kills other
organisms at low concentration only
Eg: Streptomyces griseus Streptomycin
Micromonospora Gentamycin
S. Erythricus Erythromycin
S. Vinezulae Chloramphinicol

32. Streptomyces : Produces MUSTY odour ( Earthy odour )
it is a odour coming out from the 1st rain – when splashes to
soil or odour in freshly turned soil
Therefore this streptomyces produces geosmin and other
volatile products ( acetates, aldehydes & alcohal)
These actinomycetes are also able to utilise organic residues
like cellulose, hemicellulose, pectin, keratin and chitin of insects