Microbes play an important role in bioremediation by using their enzymatic activity to destroy pollutants or transform them into less harmful forms. During their normal metabolic processes, microbes can break down toxic compounds and convert them into simpler, non-toxic molecules. Bioremediation harnesses microbes' natural degradation abilities to clean contaminated sites using biological rather than physical or chemical methods. This approach is often more cost-effective and environmentally friendly compared to excavating and disposing of polluted soils and water.

1. Dr. Kashif Bashir
MPhil (BioInformatics)
PhD (Biotechnology)
University of Peshawar

2. • These are found in just about every kind of habitat.
• Microbes are incredibly diverse thriving in environmentsfrom
the very cold tothe extremely hot.
• Theyare also tolerant of many other conditions such aslimited
water availability high salt content and lowoxygen levels.
• Not every microbe cansurvive in allhabitats.

3. • Only one percent of microbes that live in soil have been
identified.
• These organisms take part in the formation of soil and are
essential components of theirecosystems.
• Bacteria and fungi that live in soil feed mostly on organic
matter such asother plants andanimals.
• Thesemicrobes are very sensitive to their localenvironment.
• Factors such as the levels of carbon dioxide and oxygen the pH
moisture and temperature all affect the growth of microbes in the
soil.

4. • Microbes live in bothfresh and salt water.
• Theseorganisms include microscopic plants and animals as
well asbacteria fungi andviruses.
• Aswith other microbes the ones that live in water are adapted
to the specific conditions of their environment.
• Habitats range from ocean water with an extremely high salt
content to freshwater lakes orrivers.

5. • Microbes also live on otherorganisms.
• Aswith the ones found on people these microbes can
be harmful or beneficial tothe host.
• Example:
• Bacteria grow in nodules on the roots of pea and bean plants.
Thesemicrobes convert nitrogen from the air into aform that
the plants canuse.
• In many waysanimals and plants have evolved ashabitats
for the millions of microbes that call them home.

6. • Themicrobes living in extreme conditions arecalled
extremophiles.
• Thisliterally meansthat they love theextreme
conditions of theirhabitat.
• Theextremophiles are sowell adapted to theirown
environment.
• Somelike the ones in hot springs needextreme
temperatures to grow.

8. • The relationship in which one organism may depend on another
for its survival. Sometimes they need each other. This is called
symbiosis.
EXAMPLES
• Photosynthetic plants and microbes provide oxygen that
humans need to live.
• Trees offer shelter to other plants and animals.
• And many rely on other creatures as sources of food or
nutrients

9. • Often, especiallywith microbes, one organism livesinside another —the
host.
• Microbial symbiosisoccursbetween two microbes.Microbes, however,form
associationswith other types of organisms, including plants andanimals.
• Bacteria havealong history of symbiotic relationships, andhave evolved in
conjunction with their hosts.Other microbes,suchas fungi and protists, alsoform
symbiotic relationships with other organisms.
• HOST-usually the LARGERmember
• SYMBIONT- usually the SMALLERmember

10. MUTUALISM:-In this type of relationship, both partners benefit
E.coli synthesizes vitamin Kin theintestine
in exchangethe large intestine provides nutrientsnecessary for
survival of the microorganisms.
Example;
E.Coli
COMMENSALISM:-one organism is benefited and the otheris
unaffected by this type ofrelationship.
They bring no benefit to the host and yet the microorganisms
benefit greatly from the environment they inhabit.
Example;
Staphylococcus on skin

11. • One organism benefits at the expense of the other all
pathogens are parasites.
• EXAMPLE:-
• Human parasites (e.g. Lice).
• BACTERIAL SYMBIOSIS
• Bacteria form symbiotic relationships with many organisms,
including humans.
• One example is the bacteria that live inside the human
digestive system.
• These microbes break down food and produce vitamins that
humans need. In return, the bacteria benefit from the stable
environment inside the intestines.

12. • Fungiand plants form mutually-beneficial relationshipscalled mycorrhizal
associations.
• Thefungi increasethe absorption of water and nutrients by the plants, and
benefit from the compounds produced by the plants duringphotosynthesis.
• Thefungus alsoprotects the roots from diseases.Somefungi form extensive
networks beneath the ground, and havebeen known to transport nutrients
between plants and trees in different locations.

13. • In this mutually-beneficial relationship, the fungus forms the body of the
lichen —the thallus. Thisstructure attaches to the surfaceof arock ortree.
• The fungal cells absorb water and nutrients from the surrounding
environment. Algal cells grow inside the cells of the fungus. The algal cells
convert sunlight to chemicalenergy through photosynthesis.
• This process benefits the fungus. In return, the algal cells are protected from
theenvironment.

15. Biogeochemical Cycles or Nutrient cycles:
Is how elements, chemical compounds, and other forms of matter are
passed from one organism to another and from one part of the
biosphere to another.
Types of Biogeochemical Cycle:
• Atmospheric- carbon cycle and nitrogen cycle
• Sedimentary - phosphorus cycle and Sulphur cycle

16. • Matter canneither be created ordestroyed.
• Aconstant amount of matter in the environment must
be recycled.
• Microbes are essential in the conversion ofnutrients
into organic and usable formats.
• Microbes are essential in the conversion of nutrients into
the inorganic form.

18. Carbon is akey ingredient of living tissue.
In the atmosphere, carbon is present ascarbon dioxidegas,
CO2.
Carbon dioxide is released into the atmosphereby
volcanic activity
respiration
Human activities
the Plants take in carbon dioxide and usethe carbon tobuild
carbohydrates during photosynthesis.
The carbohydrates are passed along food webs to animals
and other consumers.
In the ocean, carbon is alsofound, along with calciumand
oxygen, in calcium carbonate, which is formed by manymarine
organism decomposition of organicmatter.

20. Microbes decompose proteins form dead cells andrelease
amino acids.
Ammonia is liberated by microbial ammonification ofamino
acids.
Ammonia is oxidized to produce nitrates forenergy by
nitrifying bacteria.
Denitrifying bacteria reduce nitrogen in nitrates tomolecular
nitrogen.
N2 is converted into ammonia by nitrogen fixing bacteria
Ammonium and nitrate are used by bacteria and plantsto
synthesize amino acids.

22. Plants and certain microbes can useSO42-to makeamino
acids.
H2Sis oxidized to form SO42-.

23. Proteinsandwasteproducts Aminoacids
Microbialdecomposition
Amino acids(–SH)
Microbialdissimilation
H2S
H2S
Thiobacillus SO4
2–(for energy,byrespiration)
SO4
2–
Microbial & plantassimilation
Aminoacids

25. Inorganic phosphorus is solubilized by microbialacids.
Made available to plants and othermicrobes
Issoluble in water
Combines with calcium in calcium phosphate.

27. • Primary producers in most ecosystemsare
photoautotroph's.
• Primary producers in deep oceanandendolithic
communities are chemoautotrophic bacteria.
H2S SO4
2– Providesenergyfor bacteria which maybeusedto fixCO2
CO2 Sugars Providescarbonfor cellgrowthCalvinCycle

28. Algae, cyanobacteria, aerobic heterotrophs
–CO2+H2O CH2O +O2
H2Ois asource of electrons
–CH2O +O2  CO2 +H2O
Aerobic respiration

29. H2Soxidizers
CO2+H2S CH2O+S+ H2O
H2Sis asource ofelectrons

30. Tremendous ecological importance in the C,Oand Ncycles.
Evolutionary relationship to plants.
Cyanobacteria have chlorophyll a, carotenoids andphycobilins
.

31. Cyanobacteria are very similar to the chloroplasts of red algae
(Rhodophyta).
Severalspecies of cyanobacteria are symbionts of liverworts,
ferns, cycads,flagellated protozoa, andalgae.
Example:
There is also an exampleof
acyanobacterium as
endosymbionts of plant cells.

33.  Intensification of agriculture and manufacturing industries has
resulted in increased release of a wide range of xenobiotic
compounds to the environment.
 Excess loading of hazardous
 waste has led to scarcity of clean water and disturbances of soil thus
limiting crop production.
 Environment is formed by the combination of air , soil, water in the
oceans, lakes etc.
 Trees play an important role in the environment.
 They may pollute or clean the environment.

34. In bioremediation, microorganisms are used to destroyor
immobilize wastematerials.
Bacteria
Fungi
Algae
Actinomycetes
(filamentous bacteria)

35.  Useof living organisms (e.g., bacteria) to clean up oil spills
or remove other pollutants fromsoil, water, and waste
water.“
Source:UnitedStates Environmental Protection Agency,Officeof Compliance andAssurance
“clean-up of pollution from soil, groundwater, surface water and
air, using biological, usually microbiologicalprocesses”
Source:Philipetal.,2001

36. Bioremediation can be defined as any process that uses microorganisms or their
enzymes to return the environment altered by contaminants to its original
condition.
Microbes play its role by the activities of their enzymes, which helps in the
destruction of pollutants or their transformation to lessharmfulforms.
Microorganisms are very important in bioremediation because they have
extraordinary metabolicdiversity.

37. • Industrial wastes
• Loss of ecosystem/habitat
• Overfishing-depressed fish stock
• Soil erosion
• Fresh water supplies
• Infectious disease

38. 1. Air pollution
2. Water pollution
3. Toxic and heavy metal pollution
4. Solid and hazardous waste

39. Major environmental problem in cities
Sources
• Vehicle emissions
• Industrial plants
• Power stations
• Oil refinery
• Domestic heating
• Cement plants

40. Gives rise to 3 other phenomena
• Acid rain
• Ozone depletion
• Global warming climatic change

41. Ozone
• A bluish reactive gas made up of 3 oxygen atoms
• 10-40km above the earth surface
• Protects life on earth from UV light
Problems ??
• Appearance of holes
• Holes created by gases CFC, halons, methyl bromide
• Effects excess UV skin burns, skin cancer, cataracts,

42. GLOBAL WARMING
• World is warming
• Cause emission of CO2 and other greenhouse gas
• Consequence Temperature change 1.1oF (0.6oC) but the effects are
quite drastic
• Tree-eating wood beetles are likely to benefit from a warmer climate
and reproduce in ever-increasing numbers

43. 2. WATER POLLUTION
Sources
• Municipal detergents / washing powder high in phosphates
• Industrial toxic wastes and organic substances
• Agriculture fertilizers esp. nitrates
PESTICIDES
Problems with pesticides
• Only 0.1 reach targets the rest - 99 affects non-target organisms
widely dispersed in the environment
• 10 of 80,000 pesticides used are carcinogenic e.g. testicular cancer
• Highly toxic to aquatic life

44. AZODYES
• Synthetic colorants
• One of the oldest man-made chemicals
• Applications in textiles, food, cosmetics, plastics, leather, paper, color
photography, pharmaceutical industries
AZODYES - Problems
• Not easily degraded
• About 10 of dyestuff does not bind to fibres during dyeing process
• ? released into the environment accumulate in the biosphere
• Some are carcinogenic

45. 3. TOXIC AND HEAVY METALS POLLUTION
What are heavy metals ???
• Metallic chemicals like mercury, lead, cadmium, arsenic, copper and zinc
that can be harmful pollutants when they enter soil and water generally toxic
in low concentrations to plants and animals persist in the environment and
bioaccumulate tend to be toxic
Heavy metal pollution
• From extensive use in agriculture, chemical and industrial processes and
waste disposal
• Electronic wastes TV and computer monitors contain between 3-5 kg of
lead

46. • Threat to human health and limit plant productivity heavy metal
poisoning

47. BIOREMEDIATION
How to remediate restore polluted environment?
• Use physical and chemical methods e.g.
• dig up contaminated soils remove it to landfills
• capping and containment
• use chemicals

48. BIOREMEDIATION
Using living organisms to decontaminate polluted systems
Living organisms
1. Bacteria
2. Fungi
3. Algae

49. BIOREMEDIATION
• Why bacteria ?
• most common bioremediation microorganisms
• Natures recyclers e.g. Carbon, Nitrogen cycle
• Can degrade a variety of compounds as a result of million of years of
evolution
• With genetic engineering, can be tailored to degrade pollutants that we
want

50. BIOREMEDIATION
• How do bacteria degrade pollutants ???
• produce enzymes
• break up toxic compounds to lesser or non-toxic
compounds

51. BIOREMEDIATION Current research
• HEAVY METALS
• PESTICIDES
• DYES
• DETERGENTS
• PLASTICS
• OILS HYDROCARBONS

52.  Phytoremediation describesthe treatment ofenvironmental
problemsthrough the useof plants that mitigate the
environmentalproblemwithout the needto excavatethe
contaminantmaterial anddisposeof itelsewhere.

53.  Rhizoremediation, which is the most evolved process of
bioremediation, involves the removal of specific contaminants
from contaminated sites by mutual interaction of plant roots and
suitable microbialflora.

54. Microorganisms usetheir enzymatic activity for thedestruction
of pollutants or their transformation to less harmful forms.
Their enzymatic action on the contaminants of environment,
break them into digestible form and there microbes get energy
by performing normalmetabolism.
Here augmentation alsoinvolves.

55. Contaminant compounds are transformed by living organisms
through reactions that take place as a part of their metabolic
processes.
Biodegradation of a compound is often a result of the actions
of multiple organisms. When microorganisms are imported to a
contaminated site to enhance degradation we have a process
known asbioaugmentation.

56. • Microbes can convert many chemicals into harmless compounds
usingcleanupreaction.
• Aerobic or anaerobically.
• Both involve oxidation and reductionreactions.
• Oxidation involves the removal of one ormore electrons.
• Reduction involves the addition of one ormore electrons.
• Oxidizing agents gain electrons and reducing agents loseelectron.
• When both reaction occursat atime, it will be redox
• reaction.

57. Petroleum Hydrocarbons
Gasoline
Diesel Fuel
Polyaromatic Hydrocarbons
Creosote
Chlorinated Hydrocarbons
Chlorinated Aliphatics: trichloroethylene
Chlorinated Aromatics : PCB’s, Pentachlorophenol
Explosives
RDX, TNT
Inorganic via Reduction to a Lower Valence Causing
Precipitation
Uranium, Technicium
Sulfur and Sulfuric Acid
Ammonia or Nitrate/Nitrite

58. Primary substrate
enough available to be the sole energysource
Secondary substrate
provides energy, not available in highenough
concentration
Co metabolicsubstrate
fortuitous transformation of acompound by amicrobe
relying on some other primarysubstrate

59. EDTA
is achemical agent which reduces the toxicity produced by the
contaminants in the environment specially inwater.
ForExample,
if the toxicity results from heavy metals, EDTAwill be added to
the waste and the effluent will be tested again to determine if
the toxicity hasbeen acceptablyreduced.

60. On the basis of removal and transportation of wastes for
treatment there are basically twomethods
Ex-situ (off-site) strategies
Excavation/pumping, followed by…
Landfill
Incineration
Chemical removal
In-situ (on-site) strategies
Immobilization (chemicals, wells, membranes)

61. • Canbe highly specific
• Lessexpensivethan excavation or incineration processes
• If mineralization occursget complete degradation and cleanup
• Does not transfer contaminants from one environment to another
• Usesanatural process
• Goodpublic acceptance
• Processis simple

62. • Not instantaneous.
• Often need to develop a system.
• Always need to test and optimize conditions empirically – not with
computer models.
• May have inhibitors present.
• Compounds may not be in a biodegradable form – polymers, plastics.

63. • We should clean the environment including land ,soil, water etc. by using
biological methods in which bioremediation is very suitable.
• In bioremediation, microbes play important role by their enzymatic activity.
• They do normal metabolism and destroy the pollutants.
• We can purify the wastewater, polluted soil, do better crop production,
better variety of fruits.
• In this way it is economically important method.

64. Bioremediation is an attractive alternative to traditional physico-chemical
techniques for remediation of contaminated sites
• Cost effective
• Selectively degrade pollutants without damaging site indigenous flora
and fauna
• Low-technology techniques
• High public acceptance

65. BUT STILL FRAUGHT WITH PROBLEMS
• Substrate and environmental variability
• Limited biodegradative potential and variability of naturally occurring
microorganisms
• HOWEVER may be overcome by biomolecular engineering enhance
bioremediation programs