soil flora, microbial interaction, biogeocycle

1. D H A R M E S H S H E R A T H I A
A S S I S T A N T P R O F E S S O R
C C S I T , J U N A G A D H
D H A R M E S H . M I C R O B I O @ G M A I L . C O M
T.Y B.Sc Sem 5
Soil microbiology

2. 1.1 Physical and chemical properties of soil

3. What is soil ?
 Outer most covering of earth
 Component:
 Particles, inorganic & organic constituents.
 Definition:
“Soil is the region on the earth crust where
geology and biology meet”
 Pioneer work in soil microbiology was done by Sergei
Winogradsky & Martinus Beijerinck
 Father of soil microbiology Sergei Winogradsky
 The characteristics vary from locate and climate.
 Soil formed after several process of weathering

4.  Soil provide substratum for plant and animal
 Soil consist mainly mineral, organic matter,
water and gaseous phase
 Soil has a layer called profile
 Soil profile have a two or more layer called
horizon
 Soil horizon may vary in thickness, mineral
composition and structure

5. Soil horizon
 Soil mainly divides into five horizon according to
their characteristics
 Horizon O, Horizon A, Horizon B, Horizon C,
Horizon R


6. Horizon O
 Top most layer of the soil contain plant litter, humas
at various levels of decomposition

7. Horizon A
 Below horizon O
 Composed of primarily silicate clay particle, minerals,
humas (minerals + humas + sillcate )
 Two basic characteristics of this horizon is
1. Humas and organic matter mix with mineral
particals
2. Zone of translocation where eluviation(downward
movement) has removed fine particle and soluble
substances deposited at lower level (illuviation)
 Horizon is dark, porous and light in texture

8. Horizon B
 Strongly influence by illuviation process
 Accumulation of salts, minerals and organic matters
 High bulk density due to clay particle
 Coloured by oxidised irons, aluminium and calcium
carbonate
 Note: Illuviation: deposition of colloids, soluble salts,
suspended minerals in lower soil horizon through the
process of eluviation

9. Horizon C
 Weathered parental rock
 Particle size vary from clay to boulders
 This zone is not influence by illuviation, pedogenesis,
translocation and organic modification


11. Chemical characteristics
 Mineral properties:
Macro molecules:
Silica, aluminium, and iron
Micromolecules:
Minerals (Ca, Mg, K, P, S, Ti, etc)
 Size: clay particles(0.002 to less) to large pebbles and
gravel
 Water holding capacity, bulk density and nutrients are
determine by proportion of these particles

12.  Organic residue:
 Plants and animal remain deposited in soil
 Latter stage of decomposition is formed humas
 “Humas” is dark coloured, amorphous sub stances
composed of residual organic matter not readily
decomposed by microorganisms
 Microbial population both dead and living cells
significantly determine the organic matter of soil

13.  Humas- agriculturally important properties of
humas due to its provide buffering capacity and
water holding capacity of soil.

14. water
 Amount of water is relative to amount of
precipitation, climatic condition, drainage and soil
composition
 Water retain in space
 Organic and inorganic mole dissolve in water and
absorbed by plants and consumed by animal

15. Gases
 Nitrogen, oxygen and carbon dioxide
 Except nitrogen O2 and Co2 dissolve in water
 Amount of gases present in soil is related to moisture
present in soil

16. Soil temperature
Influence by
 Intensity of light
 Day length
 Season variation
 Plantation
 Colour and texture
 Altitude
 Place

17. Soil pH
 Acidic, basic or neutral
 Optimum pH is require for the growth of plants and
microorganisms
 Acidity of soil- (Al, Fe,Mn,Cu,Zn)
 Neutral and basic soil(Na2Co3, NaHCo3)


18. Bulk density and porosity
 Nearness of particle is called bulk density
 Distance between the particle is porosity

19. 1.2 Rhizosphere & Microbial flora off Soil
What is rhizospere?
Rhizo- root , sphere- influenced area
the narrow region of soil that is directly influenced
by root secretions(exudates) and associated soil microorganisms

20.  In another way
 The region where soil and root make contact and
designated rhizosphere
 The zone around roots are divides into two parts
1. Rhizoplane- root surface where microbes adhere
2. Rhizosphere- narrow region of soil around rood(20um)

21.  Hiltner (1904) introduce this term first time
 Thickness of this region is 1-2mm
Note: (Information only)
Two sphere endorhizosphere and ectorhizosphere
 1 um- 120 organisms
 20 um- 13 organisms (1:10)

22. Characteristics of the rhizosphere
 Microbial population around the roots are attracted
through the secretion of the plants (exudates)
 Plants root secreted some amino acids, organic acids,
sugars , vitamins, enzymes, inorganic ions etc that is
called exudates
 The growth of microbes enhanced by exudates which
is released by plants
 And hence the microbial population of this area is
higher than the bulk soil

23.  Exudates provide nutrients to microorganism and
hence microbiota of rhizosphere is more active than
the bulk soil.
 The organisms which was observed around
rhizosphere is called PGPR(plant growth promoting
rhizobacteria)
 Microbial interaction in rhizosphere can be
pathogenic, symbiotic, harmful, saprophytic or
neutral

24. Microbial flora of soil
 What is microbial flora:
Flora: the bacteria and other microorganisms in
an ecosystem (e.g., some part of the body of
an animal host)

25.  Any fertile soil inhabited by root system of plants,
animals and tremendous numbers of
microorganisms
 Microbial population:
Large difference in microbial population both in total
numbers and kinds due to soil composition, physical
properties of soil, agricultural practices

26.  There are some factors responsible for the growth of
the Mo
1. Amount and types of nutrient
2. Availability of moisture
3. Degree of aeration
4. Temperature
5. pH
6. Practices

27.  Great microbial diversity make it difficult to
determine total number of microbes
 Only culturable can be count and determine
characteristics(physiological and nutritional)
 Using direct microscopy count total no
 Enumeration techniques are suitable for specific
types of the org
 Metagenomics

28. Bacteria
 Bacterial population is large compare to another group in
soil
 Most diverse in number and variety
1.Direct microscopy : billions of cells countable
(650million/gm soil)
2. Plate count method: limited organisms
 PCT yield only fraction of this number

29.  Due to great variety of nutritional and physiological types of
bacteria in soil
1. Autotrophs or heterotrophs
2. Meso, thermo and psychrophiles
3. Aerobic and anaerobic
4. Cellulose digester
5. Sulphur oxidiser
6. Nitrogen fixer
7. Protein digester
8. Many more

30.  Actinomycetes predominant bacteria in soil
 Billions in number/gm of soil
 Predominant genera are micromonospora, nocardia,
Streptomyces
 Give musty or freshly ploughed soil
Bacterial Activity in soil
1. Degrade organic matter and improve soil
fertility
2. Antibiotic production maintain soil population

31. 2. Fungi
 There are hundreds of fungi inhabit the soil
 They are mostly abundant near surface area where
aerobic condition is prevail
 They exist in both state mycelia and spore
 Its difficult to enumerate
 Martin’s rose bangal agar with streptomycin medium
most commonly used for enumeration
 Fungi are two types
1. Mold
2. Yeast

32. Mold
 Majority of the soil fungi are mold
 Saprophytic hence mainly present inside decaying
material
 Mold in soil are mycelial, thread spong like structure
 Slime mold and mushrooms are also fungi

33.  There are importance for the following reason
1. Fungi are actively participating in decomposition of
major constituents of plant tissue namely
cellulose, lignin, pectin, hemi cellulose,
starch
2. Physical structure of soil is improved by the
accumulation of mold mycelia within it
3. Play important role in humus formation

34. Yeast
 Inhabit the soil where sugar is available
 Yeast are prevailing in soil are
1. Vineyards
2. Orchards(vegetable, fruits yard )
3. Apiaries (honeybee)

35. Useful for plants
 Fungi release plant hormones while other produce
antibiotics, while some are harmful for
plants(fusarium, phytophthora, verticillium)
 The mycorhiza are fungi that are live in or on the
root surface and increase the uptake of water and
nutrients from rhizosphere
 Produce hormones for plant growth and antibiotics
for disease

36. Industrially important fungi
 yeast for alcohol production
 Mold for enzymes and secondary metabolites
production

37. 3. Algae
 Population of algae is smaller than fungi and bacteria
group
 Algae is photosynthetic in nature, they account for their
predominance on the surface of soil and just below layer
of soil
 In reach fertile soil the biochemical properties of algae is
dwarfed by the extra amount of bacteria and fungi
 Fine soil particles bounded strongly together and form
water soluble aggregate by slimy material produced by
algae

38. Role in soil formation
 Due to photosynthetic nature and other biochemical
activity algal involved in soil formation
 A photosynthetic cyanobacteria grow on the surface of
freshly exposed rock and accumulate organic matter will
support the growth of another microbes like acid
generating lichen than mosses and than higher plants
 This will result into the reach organic soil
 Barred and eroded lands converted into organic rich soil

39. 4. Protozoa
 The presence of protozoans in soil is important since
ingest bacteria for their nutrients
 Not all microbial community is suitable as a food for
protozoa
 These will maintain population of microbes in soil
 Most soil protozoa are amoeba and flagellattes
 by eating and digesting bacteria, protozoa speed up
the cycling of nitrogen from bacteria, making it
available for plants.

40. 5. Viruses

41.  Symbiosis: An association of two or more
different species
 Ectosymbisis: One organism can be located on
the surface of another, as an ectosymbiont.
 Endosymbiosis: one organism can be located
within another organism as an endosymbiont
 Ecto/ endosymbiosis: microorganisms live on
both the inside and the outside of another
organism

42. Interaction among soil microorganisms
 In terrestrial ecosystem variety of relationship exists
between microorganism or animal or plant
 Microbial flora composition of soil or any ecosystem can
equilibrate by biological activities(microbial interaction)
 There are three types of interaction in nature
1. Neutral
2. Beneficial
3. Harmful

43. Neutral relationship
 Lack of interaction between two species create neutral
relationship
 Neutral relationship arise when there is no relationship
between two community
 Lack of nutrients create this condition like marine microbes
 Finally the two different species occupy same area without
affecting each other and utilize different nutrient from
same or different object without interfering another's life
 E.g soil microorganisms, cyst and spore,
 Relationship are strictly unobligatory
 As condition change, relationship will change

44. Beneficial interaction
Beneficial relationship can be divide on the basis of
types of interaction
 Mutualisms
 Commensalisms
 Proto-cooperation

46. Mutualism(symbiosis)
 In this kind of relationship both the partners getting
benefit from each other
 Relationship obligatory
 Both are dependent on each other
 When relationship are in terms of exchange of nutrients
then the relationship called Syntrophism; “syn”- Mutual,
“Trophe” Nourishment
 Example
1. Lichen
2. Rhizobium
3. Anabaena-azolla
 Sometime symbiosis word is also used for mutualistic
relationship

47. lichen
 Lichens are the association between specific ascomycetes (the
fungus “my-cobiont”) and either green algae or cyanobacteria
“phycobiont “..
 The phycobiont is a photoautotroph dependent only on light, carbon
dioxide, and certain mineral nutrients,the fungus can get its organic carbon
directly from the alga or cyanobacterium.
 The fungus protects the phycobiont from excess light intensities, provides
water and minerals to it, and creates a firm substratum within which the
phycobiont can grow protected from environmental stress.

49. legume
 Symbiotic Nitrogen Fixating bacteria
 MOS also interacting with some legume plants
symbiotically
 some bacteria (Rhizobium species) grow on the roots of leguminous
plants (alfalfa, clover, vetch, peas, beans, etc.) --> root nodules
 Bacteria provide ammonia by nitrogen fixation. Plants provide
nutrients and shelter and anaerobic microenvironments
 Allows growth in nitrogen-poor soils

51. Anabaena-azolla
 Association between water fern azolla and
cyanobacteria
 Important for paddy plant; nitrogen is fixed by
Anabaena Azollae
 Here azolla is water fern
 Anabaena azollae is cyanobacteria

53. Commensalisms
 Commensalism [Latin com, together, and mensa, table]
 One organism depends on the table scraps of other
 In this association one organism/partner get benefit
from another partner without affecting it.
 Does not get benefit nor negatively affected by the action
of second population
 Not obligate

54. Examples:
1. Many fungi can degrade cellulose to glucose which can
utilised by bacteria
2. Lignin of woody plant degrade by basidiomycetes fungi
and degraded product utilized by other fungi and bacteria
3. Many microbes uses oxygen for their metabolism and
create anaerobic environment for another organisms
 E.coli(facultative)- Bacteroides(anaerobes) in human
intestine

55.  Some produced growth factor like vitamin,
aminoacids can be used by another organisms
 E.g baggiatoa detoxicate H2S that benefit the H2S
sensitive organisms

56. Proto-cooperation(synergism)
Beneficial association between two species
Synergism mean both of the species got benefit from the
relationship
 A positive (not obligate) symbiosis which involves
syntrophic (both organism lives off the byproducts of
another) relationships
 Both get benefit
 In same habitat one organism create favourable
environment for another organism. Like toxic area removed
by some microbes

57.  e.g Nocardia supplies cyclohexane degradation products to
pseudomonas which supply biotin to nocardia
 Nutritional protocooperation between bacteria and fungi

60. E. Faecalis
arginine
Ornithine
decarboxylase
E.coli
Agmatine(dead
end product)
 E.coli
putrescine

61. Negative interaction

62. C. harmful/detrimental/negative interactions
Antagonism/Ammensalism
 Product of one species inhibited or adversely affect on
another's life e.g antibiotics
 When org. produce substance that is inhibitory to the
other population the interpopulation relationship is
ammensalism
 antibiosis and allelopathy is classical example of
ammensalism
 Some bacillus sp. In soil produced antifungal agent

63. 1. Several sp of streptomyces produced antibacterial and
antifungal compounds e.g Strepyomycin,
chloramphenicol, tetracyclin, cyclohexamide, etc.
 Staphylococcus aureus and pseudomonas aeruginosa are
antagonistic towards aspergillus niger
 Antibiotic production in lab and in soil is entirely different
 Cyanide production by some fungi and bacteria
 Fatty-acids production by some skin flora

64.  Some are produced alcohol e.g yeast
 Acetobacter produced acetic acid in the presence
of oxygen from ethanol

65. Competition
 Microbes exist in soil with compaction among them for
space and nutrients(growth limiting substance)
 Competition arises when different microorganisms
within a population or community try to acquire the
same resource
 Clamydospore of fusarium and oospores of aphanomyces
required nutrients in large amount for germination but
bacteria deplete nutrients limiting the population of
fungi

66. Parasitism
 Parasitism is defined as relationship between organisms
in which one organism lives in or on another organisms
 The parasites derived its food from the host
 Parasite feeds on the cells, tissue or fluid of another
organisms
 Usually but not always parasites are smaller than the
host
 Two types of the parasite; ecto and endoparasites


67.  Example:
 Gram negative bacterium Bdellovibrio, A
Bacteriovorus motile small bacterium attached on
host cell(gram negative bacteria) at special region
and causes lysis of cell
 Bacteriophage virus are obligate intracellular
parasites
 Host cell also some fungal cells or algal cells

68. Predation
 Distinction between parasitism and predation is very
sharp
 In predation, predator directly engulfs and digests
the another organisms
 Predation is association in which predator organisms
directly feed on and kill the pray organisms
 Always cyclic fluctuation in predator; prey

69.  Its one of the most dramatically inter relationship
 Nematophagous fungi –Arthrobotrytis and dactylella
 Protozoa and slime mold also feed on bacteria;
 (tetrahymena pyriformis protozoa predator and
klebsiella pneumoniae a prey bacterium)
 Bacteriophage

70. 1.4 Mineralization and immobilization of
elements
 Immobilization in soil science is the conversion of
inorganic compounds to organic compounds
by micro-organisms or plants
 Immobilization is the opposite of mineralization.

72.  The complex substrates listed in table contain only
carbon, hydrogen, and oxygen. If microorganisms
are to grow by using these substrates, they must
acquire the remaining nutrients they need for
biomass synthesis from the environment.
 Those nutrients that are converted into biomass
become temporarily “tied up” from nutrient cycling;
this is sometimes called nutrient immobilization.

73.  immobilization The incorporation of a simple,
soluble substance into the body of an organism,
making it unavailable for use by other organisms.

74.  Mineralization in soil
science is decomposition or oxidation of the chemical
compounds in organic matter into plant-accessible
forms(inorganic form)
 Mineralization is the opposite of immobilization.

76.  Organic matter varies in terms of elemental
composition, structure of basic repeating units,
linkages between repeating units,
 microorganisms require each macronutrient, if an
environment is enriched in one nutrient but
relatively deficient in another, the nutrients may not
be completely recycled into living biomass.

77.  chitin, protein, and nucleic acids contain nitrogen in
large amounts. If these substrates are used for
growth, the excess nitrogen and other minerals that
are not used in the formation of new microbial
biomass are released to the environment in the
process of mineralization. This is the process by
which organic matter is decomposed to release
simpler, inorganic compounds (e.g., CO 2 , NH 3 ,
CH 4 , H 2 ).

78. Nitrogen cycle
 Major and main element of life and constituent of air
(78%)
 It is an basic component of Amino acids , proteins and
nucleic acid
 Life cant exist without nitrogen
 Play major role in respiration and animal metabolism
 Sequence of change in oxidation state of nitrogen in
nitrogen move from atmosphere to biota
 Plant utilize inorganic state of nitrogen like
NH3,No2,No3-

79. Proteolysis
 The nitrogen in protein is locked
 This organically bound nitrogen became free for
reuse by the process of enzymatic hydrolysis of
protein that is called proteolysis.
Proteinase peptidase
Protein Peptide Aminoacid

80. Ammonification:
 The end product of proteolysis is amino acids and
utilized as a nutrient by microbes or degraded by
microbial attack
 The process in which nitrogen atom or amino group
is liberated from the amino acid is called as
deamination.
 Some variation of deamination reactions are also
exhibited by microbes, one of the end product is
always ammonia.

81. CH3CHNH2COOH + ½ O2 CH3COCOOH + NH3
Alanine Pyruvic acid + Ammonia
Ammonia is volatile But if NH3 is dissolved in water,
ammonium (NH4+) is formed and utilized by plants
and microorganisms.
Than under favorable condition it is oxidized to
nitrates.

82. Nitrification
 Conversion of………to………is called…
 Charactristics of nitrifiers:
 gram negative & chemolithotrophs
 soil, sewage and aquatic environments
 Grow on ammonium salt like NH4
 slow growing and require large inoculums
 Rod, spherical, spiral or vibrio shaped.

83.  Group of organisms oxidize ammonia
1. Nitrosomonas europaea
2. Nitrosococcus oceanus
3. Nitrosovibrio tenuis
4. Nitrosococcus nitrosus
5. Nitrosospira spp.
 Only a few species are recognized as nitrite oxidizer:
1. Nitrobacter winogradskii,
2. Nitrospina gracilis
 Nitrifications process was discovered by Schloesing and Muntz
in 1877
 Bacteria were isolated by Winogradsky in 1890.

84. Nitrate reduction
 It’s a reversible process of nitrification
 heterotrophic bacteria are capable of converting
nitrates into nitrites or ammonia
 under anaerobic conditions, oxygen of the
nitrate serves as an electron acceptor for electrons
and hydrogen

85. Dinitrification
 nitrates to gaseous nitrogen by the microorganisms
in a series of biochemical reaction, this process is
known as denirification
 Achromobacter, Agrobacterium
 Alkaligens, Bacillus
 Psudomonas, Flavobacterium,Vibrio

86.  Certain environmental factors affect microbial
denitrification
1. Increased organic matter(C/N ratio)
2. Increased temperature ( 25-60˚C)
3. Neutral or alkaline pH
4. Availability of Oxygen
5.

87. Nitrogen fixation
 Natural ability of microorganisms to convert
atmospheric nitrogen into ammonia.
 Aerobic -free-living Azotobacter, Azospirillum
 Anaerobic –free living- genus Clostridium.
 Cyanobacteria- Anabaena, Nostoc, Oscillatoria
 In addition, nitrogen fixation can occur through
symbiotic associated microbes like Rhizobium &
Bradyrhizobium.

88. Cyanobacteria heterocysts
Heterocyst

89. Symbiotic N2-fixation: Azolla - Anabena
S. Navie

90. Symbiotic N2-fixation: Azolla - Anabena

91. Rice-Azolla-Fish, China
Azolla to feed cows,
Thailand
Rice-Azolla-Ducks, Korea
Takao Furuno
Symbiotic N2-fixation: Azolla - Anabena

92. © Paul Cox
Cycas micronesica

93. Cycad root nodules

94. Cyanobacteria
 Photosynthetic and dinitrogen
fixing
 heterocysts separate the two
functions
Anabaena
Microcystis
Nostoc
Free-living

95. Cyanobacteria
 Oldest known fossils
 3.5 bybp (oldest rocks are 3.8 bypb)
filamentous Palaeolyngbya
colonial chroococcalean

96.  Haber-Bosch method for chemically conversion of ammonia
 For nitrogen fixation required several component part
 nitrogenase enzyme
 nitrogenase reductase
 ferrodoxin: strong reducing agents
 ATP
 a regulating system for NH3 production and utilization
 a system that protect the nitrogen fixing system from
inhibition by molecular oxygen.

97.  Nitrogenase enzyme(MoFe protein):
Made up of four polypeptide chains in form of two
identical dimer: α2 & β2

98.  Nitrogenase reductase(Fe subunit):
 two polypeptide chains: γ2
 ATP molecules binding sites
 Provide reduced hydrogen to reduce nitrogen and
convert in ammonia
 H2 evolved as by product utilize by rhizobium
 Nitrogenase enzyme is oxygen sensitive hence
leghemoglobin synthesized by bacteria and plant
 Leghemoglobin has a high affinity for oxygen ten times
higher than hemoglobin

99. Redrawn from www.asahi-net.or.jp/~it6i-wtnb/BNF.html
Nitrogenase enzyme complex
Physical association of nif genes in Klebsiella pneumoniae
Nitrogenase
MoFe protein
Fe protein
Electron transport
Assembling
Fe-Mo-Cofactor
Regulator
H D K T Y E NX U SVWZM F L A B QJ
  


100. Gene function
nif h: codes for subunit of Fe protein (nitrogenase reductase).
nif d & nif k: code for two polypeptide chains of nitrogenase enzyme.
nif b, nif q, nif v & nif e: synthesis of FeMo cofactor.
nif m, nif s, nif v: maturation of complete functional nitrogenase complex.
nif f & nif j: Invoved in electron transfer.
nif a & nif c: regulation of other nif genes.
nif u, nif x & nif Y: Unknown

104. Sulfur cycle
 Most of the earth's sulphur is tied up in rocks and salts or
buried deep in the ocean in oceanic sediments
 It enters the atmosphere through both natural and human
sources
 industrial processes where sulphur dioxide (SO2) and
hydrogen sulphide (H2S) gases are emitted on a wide scale
 it will react with oxygen to produce sulphur trioxide gas (SO3)
 Sulphur dioxide may also react with water to produce
sulphuric acid (H2SO4)
 dimethylsulphide, which is emitted to the atmosphere by
plankton specie

105.  Biogeochemical cycle of sulfur are also important for
life because sulfur is an essential element, being a
constituent of many proteins (amino-acids: Cysteine,
cystine & methionine) and cofactors
 There are some sequence of events of oxidation-
reduction of sulfur called sulfur cycle

107. Four step reaction/Step 1
 Plants or organisms can not be utilize/immobilize
elemental sulfur
 Bacteria are capable to oxidize sulfur to sulphates.
 E.g Thiobacillus thiooxidans,
obligate aerobe and chemolithotroph
 2S +2H2O + 3O2 2H2SO4

108. Step 2
 Utilized by plants and is incorporated into sulfur
containing amino acid/protein.
 These proteins are uptake by animals and various life
forms and ultimately dumped on the soil in form of
waste debris or dead tissues.
 proteolysis process, sulfur containig amino-acids are
liberated from which sulfur is released in form of
hydrogen sulfide by enzymatic activity of
heterotrophic microorganisms.

109.  Ammonia release from reaction

110. Step 3
 Sulphate reduced to hydrogen sulfide (H2S) by soil
microbes e.g. genus Desulfotomacculum. spp.
 At the end of this reaction, H2S remains either in the
soil or liberated out in the environment.
 H2O is also one byproduct in this reaction that
dissolves H2S.
 4H2 + CaSO4 H2S + Ca(OH)2 + 2H2O

111. Step 4
 This H2S is oxidized to elemental sulfur
 Photosynthetic purple or green sulfur bacteria and
 Which fix CO2 and release elemental sulfur back to
the first reaction.
 Co2+ 2H2S (CH2O)n + H2O + 2S

112. Winogradsky column
 Sergei Winogradsky- Investigate the organisms in
complex biofilm communities from pond
 Winogradsky isolated organisms from nature by
preparing a miniature model pond cross section --
Winogradsky column
 Column contain mud, CaSO4, plant tissue and
water
 Source of carbon and sulfur

113.  Soil is layered in column and add some water and
than covered to retard evaporation rate
 Put under light and allow to grow some phototrophs
 The resulting growth of microoraganisms can be
quite spectacular and colorful

117. Step 1
 A variety of heterotrophic organisms oxidize various
substrates. This organisms decrease the level of O2
into the column and create an anaerobic condition
Organic matter + O2 organic acids + CO2

118. Step 2
 Organic acid serve as the electron donors for the
reduction of sulfates and sulfites to hydrogen sulfide
by anaerobic sulfate reducing bacteria, for e.g.
Desulfotomaculum, desilfovibrio
 Organic acids + So4 H2S + CO2

119. Step 3
 Photosynthetic microbes like purple and green sulfur
bacteria use H2S as an electron donor to reduce CO2
 CO2 + H2S (CH2O)X + S

120. Step 4
 The aerobic sulfur metabolizing bacteria, for e.g.
Thiobacillus spp., develop in the upper portion of the
column and it can oxidize reduced sulfur compounds
to SO4
2-,S°,SO3-
 sulfur sulfur compounds S + SO4
2-

121. Step 5
 The non sulfur purple bacteria for e.g.
Rhodospirrillum, Rhodomicrobium are facultative
phototrops and are capable to convert hydrogen gas
as an electron donor in photosynthesis.
 CO2 + H2S (CH2O)x + S
light
 CO2 + 2H2 (CH2O)x + H2O

122. Carbon cycle
 Carbon is essential element on earth
 Plants and microbial cells contain large amount of
carbon approx 40 to 50 % on the dry weight
 Due to photosynthesis atmospheric carbon fix in
green plant by photosynthesis and bacteria help to
maintain the balance(carbon: nitrogen)
 Food is formed by them(plant, bacteria) serve as a
source of energy for other animals or organisms

123.  Plants such as trees and crops are often thought of as the
principal CO 2 -fi xing organisms, but at least half the
carbon on Earth is fixed by microbes, particularly marine
photosynthetic procaryotes and protists (e.g., the
cyanobacteria Prochlorococcus and Synechococcus, and
diatoms, respectively).
 Carbon is also fixed by chemolithoautotrophic microbes.
All fixed
 carbon enters a common pool of organic matter that can
then be oxidized back to CO 2 through aerobic or
anaerobic respiration

124. Carbon dioxide fixation

127. Degradation of complex organic compound
 Cellulose degradation:
 unbranched polymer of 1000 to 1 million D-glucose
units, linked together with beta-1,4 glycosidic bonds
 In acidic soil around 4 pH many predominant fungi
trichoderma, aspergillus, panicillium attack on cellulose
 In less acid or neutral condition bacteria actively attack
on cellulose and hemi cellulose
 Cellulose converted into lactic, butyric and acetic acids,
Methane, hydrogen gas, ammonia

129. Cellulose cellobiose
Cellobiose glucose
Glucose CO2
Similarly hemicelluloses, lignin, and pectin
b-1,4 glucanase
B gluconase

130. Starch
 Presence in particular part tubers, bulbs, rhizomes,
seeds
 Alpha 1-4 glycosidic linkage
And alpha 1-6 glycosidic linkage
 Alpha linkage easily hydrolyse by enzymes
 Aerobically utilize starch and produced organic acids
and carbon dioxide
 More microbes having enzyme to break this link

131. Lignin Decomposition:
 important structural materials in the support tissues
of vascular plants
 Lignin fills the spaces in
the cellwall between cellulose, hemicellulose,
and pectin components, especially
in xylem tracheids, vessel elements and sclereid cells
 White and brown rots are mainly basidiomycetes

132.  Lignin decomposition is difficult
 Peroxidise activity of certain bacteria and fungi make
change in methyl group or ring structure

133. petroleum
 Petroleum is a natural product resulting from the
anaerobic conversion of organic matter under high
temperature and pressure
 principle factors limiting petroleum metabolism
1. The resistant and toxic components in the material
itself :
2. Low temperature ; few nutrients ; limited O2
availability
3. The scarcity of hydrocarbon metobolizers.

134. Humus formation and its important:
 organic matter derived from decomposition of plants and
animals tissue by the action of various soil microbes.
 Importance of humas:
1. Improve physical condition of soil like bettering texture
and water holding capacity and forming reservoir of
mineral nutrients
2. encourages the formation of air and water pore spaces
hence maintain appropriate air and moisture
composition

135. 3. Maintain food chain and food web
4. warm up cold soils in the spring
5. During humification process, microbes secrete
sticky gum-like mucilages; hold particles together
and allowing greater aeration of the soil.