Application of

Soil and Rhizospheric Bacteria

in Biotechnology

Dr. Fathia Mubeen

PS
 Development of Soil Microbiology
Soil Microbiology
Branch of science dealing with the microorganisms and
activities of the microorganisms inhabiting in the soil is known
as soil microbiology. The microorganisms in the soil can be
classified in to bacteria, actinomycetes, fungi algae and
protozoa.

J. B. Boussingault, 1838/
Chemist/farmer
Legume can get nitrogen from air when grown in a soil which
was not heated.
 Development of Soil Microbiology --conti

In 1888
M. W. Beijerinck
Isolated bacteria from nodule on legume roots.
(1838-1888)
-Robert Koch , Louis Pasteur Germ theory of disease

Antony Van Leeuwenhoek 1632-1723, Drawing of microorganism.

Joseph Lister, 1878 Pure culture of bacteria by serial dilution in liquid
media.
S. N. Winogradsky (1856- 1953) Autotophic mode of life among bacteria.
Beiijerinck and Winogradsky Enrichment culture technique for isolation of
sparsely occuring organisms
 Development of Soil Microbiology-- conti

Omeliansky, 1902 Cellulose degradation/ anaerobic soil bacteria

Lipman and Brown, 1903 Ammonification of organic

nitrogenous substances/ soil bacteria
Work on Rhizosphere
Hiltner 1904 Germany
Starkey 1929 USA
Lochhead 1940 Canada
Katznelson 1946 Canada
Rovira 1956 Australia
Matcura and associates 1961 Czechoslovakia.
Russel and Hutchinson 1909 England Role of protozoa in controlling the
bacterial population and activity in soil.
 Development of Soil Microbiology-- conti
Rayner and Melin 1921-1927 Mycorrhiza
Garrett 1936 UK Established a school in U. K. on soil fungi and their
classification
Alexander Fleming 1929 Pencillin
Waksman 1944 Streptomycin
Gerresten and Mulder The Netherland, Phosphate solubilizing/ soil bacteria
Ruinen 1956 in Indonesia concept of Phyllosphere
Van Niel 1931 USA Studies on soil bacteria, Chemo-autotrophic bacteria/
bacterial photosynthesis.
Umbreit 1947, Problems of autotrophy,
Baker anaerobic fermentation by methane bacteria
Starkey 1945 Iorn bacteria
Allen and Allen 1940 soil bacteria / root nodule bacteria
Fred and co-workers 1932 On nodule bacteria/
Alexander 1961 UK School of soil microbiology/ pesticide degradation
Fritsch, Fogg and Stewart UK and Lyengar /india Algae and microalgae
Dobereiner 1959 Brazeel Associative nitrogen fixation in grasses
 Rhizosphere and Rhizosphere Fractions
Rhizosphere

It is the area around the plant roots where Exo rhizosphere

the microbial population is affected by
root exudation.
Endo rhizosphere

Rhizosphere Fractions
Rhizoplane

a. Endorhizosphere Histoplane
b. Exorhizosphere Rhizosphere (soil)
Rhizoplane
Non Rhizosphere soil, NRS
Phyllosphere. Phylloplane leaf surface
 Rhizosphere Bacteria
• Pseuomonas -Nitrogen fixing
• Arthrobacter -Phosphate solubilizing
• Agrobacterium
• Azotobacter -acid requiring
• Mycobacterim, -vitamin requiring
• Flavobacteriu
• Cellulomonas -Root colonization 4-10 root area
• Micrococcus and -Colonization site junction of
• Azospirillum -Epidermal cells (root exudation area)
Rhizobium -Root excretions/ root derived organic
Nitrosomonas matter is growth substrate
Nitrococcus
Nitrobacter
Sulphur oxidizer Thiobacillus sp/
 Nitrogen Fixing Bacteria
• Azotobacteriaceae,
• Spirillaceae,
• Enterobacteriaceae
• Bacillaceae
• Pseudomonadaceae
• Achromobacteriaceae

• Azotobacter soil/less on roots (Acidity)

• Azospirillum good root colonizer with intrusion in root tissue
• Frankia
• Azotobacter chroococcum/ True colonizer of grasses rhizosphere
• Azotobacter paspali
• Pseudomobnas
 Root Exudates
a. Plants secrete a variety of substances from the roots to the
rhizosphere soil, called root exudates.
b. Root exudates contains the great variety of organic
substances which influence the quality and quantity
of microorganisms in the root region.
a. Aminoacids, organic acids, vitamies, nucleotides etc.
b. The nature and amount of substances exuded depends upon
plant species, age, and environmental condition.
c. Root cap and area of active growth are primary region of root
oxidation.
d. One major site of carbon release is the zone of root elongation
(wheat).
e. The root exudation is either from root tip or regions of lateral
root emergence from the main root.
Organic compounds in plant Root exudates.

a. Sugars.
b. Amino Compounds.
c. Organic acids.
d. Fatty acids and steroles.
e. Growth factors.
f. Nucleotide, favonones and enzymes.
g. Miscellaneous.
Organic compounds in plant Root exudates.

Sugars.

-Glucose, fructose,
-sucrose , maltose,
-galactose, rhamnose,
-ribose, xylose,
-arabinose, raffinose,
-oligosaccharide.
Organic compounds in plant Root
exudates.
Amino Compounds.

-Asparagine, a-alanine, glutamine,

-aspartic acid, leucine/ isoleucine,
-serine, aminobutyric acid,glycine,
-cysteine/cystine, methionine,
-phenylalanine, tyrosine, threonine,
-lysine, proline, tryptophan, B-alanine,
- arginine, homoserine, cystathionine.
Organic compounds in plant Root exudates.

Organic acids.
-Tartaric, oxalic, citric,
-malic, acetic, propionic,
-butyric, succinic, fumaric,
-glycolic, valeric, malonic.
Organic compounds in plant Root exudates.

Fatty acids and steroles.

-Palmitic, stearic,
-oleic, linoleic, linolenic acid,
-cholesterol, campesterol,
-stigmasterol, sitosterol.
Organic compounds in plant Root
exudates.
Growth factors.
-Biotin, thiamine,
-niacin, pantothenate,
-choline, inositol,
-pyridoxine,
-p-aminobenzoic acid,
 Organic compounds in plant Root
exudates.
Nucleotide, flavonones and enzymes.
-Flavonone, adenine,
-guanine, uridine/ cytinine,
-Phosphatase,
-invertase, amylase,
- proteinase,
-polygalacturonase,
Organic compounds in plant Root exudates.

Miscellaneous.
-Auxins, scopoletin,
-fluorescent substances,
-hydrocyanic acid, glycosides,
-saponine, (glucoside) organic P compounds,
-nematode cyst or egg hatching factors,
-nematode attractant,
fungal mycelial growth stimulants and inhibitors,
-zoospore attractants,
-spore and seclerotium germination stimulants and inhibitors,
-bacterial stimulants and inhibitors,
-parasitic weed germination stimulators
 Organic compounds in plant Root exudates.
Sugars. Glucose, fructose, sucrose , maltose, galactose,rhamnose,ribose, xylose,
arabinose, raffinose, oligosaccharide.
Amino Compounds. Asparagine, a-alanine, glutamine, aspartic acid, leucine/
isoleucine, serine, aminobutyric acid,glycine, cysteine/cystine, methionine,
phenylalanine, tyrosine, threonine, lysine, proline, tryptophan, B-alanine,
arginine, homoserine, cystathionine.
Organic acids. Tartaric, oxalic, citric, malic, acetic, propionic, butyric, succinic,
fumaric, glycolic, valeric, malonic.
Fatty acids and steroles. Palmitic, stearic, oleic, linoleic, linolenic acid,
cholesterol, campesterol, stigmasterol, sitosterol.
Growth factors. Biotin, thiamine, niacin, pantothenate, choline, inositol,
pyridoxine, p-aminobenzoic acid,
Nucleotide, favonones and enzymes. Flavonone,adenine, guanine, uridine/
cytinine, Phosphatase, invertase, amylase, proteinase, polygalacturonase,
Miscellaneous. Auxins, scopoletin, fluorescent substances, hydrocyanic acid,
glycosides, saponine, (glucoside) organic P compounds, nematode cyst or egg
hatching factors, nematode attractant, fungal mycelial growth stimulants and
inhibitors, zoospore attractants, spore and seclerotium germination stimulants
and inhibitors, bacterial stimulants and inhibitors, parasitic weed germination
stimulators
 Nitrogen fixing systems
• Symbiotic Nitrogen Fixation
-Rhizobium Legume Symbiosis Nodules formation,
Rhizobium, Azorhizobium, Bradyrhizobium,
Sinorhizobium
-Azolla –Anabaena Sybmiosis Heterocyst formation
Algae/cynobacteria
-Actinorhizal symbiosis Nodule/ group of small, nodules, Actinomycetes,
Frankia, Casuarina
• Non-symbiotic nitrogen fixation
(Associative nitrogen fixation) Lose association, Live on soil /root
surfaces/ Intrude inside root surface cells. Azospirillum,
Pseudomonas, Herba spirillum, Acetobacter. Azoarcus,
Free Fixer live freely in soil. Klebsiella, Azotobacter
Nutrients for microbes in the rhizosphere
Rhizosphere Colonization
Fixed C 5-21 % in root exudates
Bacteria no. 10 – 1000 times RS > NRS

Pseudomonas fluorescence/Tomato
Root base 106 c.f.u/cm
Root tip 102 – 103 c.f. u/cm

Colonization site Junction of epidermal cells and

site of lateral root emergence
 Nutrients For Microbes in Rhizosphere

Effect of Exudate Composition

organic acids , sugars

Bacterial mutants -ive organic acid Poor colonizer

Bacterial mutants -ive sugar Good colonizer

 Tomato root exudates (Citrate and glucose ) allow/ support the growth of
tomato root pathogen (Fusarium oxysporum)
 Pseudomonas fluorescence delays this process.