ENVIRONMENTAL

MICROBIOLOGY
 Topic outline
 Diversity of microorganism (extremophiles)
 Symbiosis (mycorrhizae)
 Soil Microbiology and Biogeochemical cycle
 Carbon cycle
 Nitrogen cycle
 Sulfur cycle
 Phosphorus cycle
 Degradation of synthetic chemicals in Soil and
Water.
 Microbial Diversity and Habitats

 The diversity of microbial populations indicates

that they take advantage of any niches found in
their environment.
• As aerobes uses up the
oxygen, anaerobes are
able to grow.

• If the soil is disturbed

by plowing, or by
earthworms, the
aerobes will again be
able to grow.
 EXTREMOPHILES-
live in extreme
conditions.

 They make themselves

grow under such
conditions because of
they contain enzymes
(EXTREMOZYMES)
 Thermus aquaticus-
found in hot spring in
Yellowstone National Park.

 Source of valuable Taq

Polymerase enzyme for
Polymerase chain reaction.

 The enzyme functions at

temp. as high as 95°C.
 Bacteria also found
buried deep in ice
sheets of Antarctica
and Greenland.

 They survive at temp.

as low as -40°C within a
life-giving film of water
only about three
molecules thick.
 Cyanobacteria found in
the rainless Atacama
Desert of Chile.

 lives inside salt

crystals.

 its only moisture is

absorbed from the
atmosphere each light,
and its energy is
derived from sunlight
 Lactic acid bacteria are
able to make an
environmental niche
inhospitable to competing
organisms.

 They may inhibit or

enhance the growth of
other competing microbes.
SYMBIOSIS

- is the relationship of two different organisms

living together in a close association that is
either beneficial to one or both of them.

 Ex: Ruminant, animals that have tank-like

digestive organ called rumen.

 Bacteria helps to ferment the cellulose into

compounds to be absorbed into the blood and
used for carbon and energy.

 Rumen protozoa control the bacteria by

eating them.
 Mycorrhizae
(myco = fungus, and
rhiza = roots)

 Two types:
 Endomycorrhizae
(vesicular-arbuscular
mycorrhizae)

 Ectomycorrhizae
Endomycorrhizae (vesicular-
arbuscular mycorrhizae

 The hyphae
penetrates into the
plant root and forms
two structure :
 vesicles- smooth oval
bodies for storage
structure
 arbuscules – tiny
bush-like structures
 Nutrients travel from the
soil through fungal hyphae
to these arbuscules, which
gradually break down and
release the nutrient to
the plant.

 arbuscule means “little

bush”

 As it decomposed, it
release nutrients for the
plants
Ectomycorrhizae

 These are the fungi that

form a symbiotic
relationship with a plant
forming a sheath around
the root tip of the plant.
 The fungus then forms a
Hartig Net which means
that there is an inward
growth of hyphae (fungal
cell growth form) which
penetrates the plant root
structure.
 The fungus forms mycelial mantle over the
small root of the tree which helps to the
absorption of nutrients.
Matsutake Mushroom Chanterelles Mushroom

Morel Mushroom Porcini Mushroom

Biogeochemical Cycle
 Biogeochemical cycles is the flow in
various forms from the nonliving (abiotic)
components of the biosphere to the living
(biotic) components and back
Carbon cycle
 is the primary biogeochemical cycle

 all organisms, plants, microbes, and animals contain

large amount of carbon in the form of cellulose,
starches, fats and proteins.

 Autotrophs reduces CO2 to form organic matter.

 The first step is Photosynthesis.

 Photoautotrophs like cyanobacteria, green plants,

algae, and green and purple sulfur bacteria fix
(incorporate) CO2 into organic matter using energy
from sunlight.
 Next step, chemoautotrophs like animals, and
protozoa eat autotrophs and may in turn be eaten
by other animals.

 This results to the transfer of carbon atoms from

one organism to another.

 Through respiration, CO2 immediately becomes

available to start the cycle over again.
 However, much of CO2 remains within the
organisms until they excrete or die which will be
decomposed by bacteria and fungi.

 During decomposition, the organic compounds are

oxidized and CO2 is returned to the cycle.

 Carbon is also stored in rocks, such as limestone

(CaCO3) and dissolved in C03-2 in ocean.

 Methanogens converts C02 to CH4.

Nitrogen cycle
 All organisms need nitrogen to synthesize
protein, nucleic acids, and other nitrogen
containing compounds.

 N2 makes up almost 80% of the Earth`s

atmosphere.

 4 steps:
1. Ammonification 3. Denitrification
2. Nitrification 4. Nitrogen fixation
1. Ammonification

 2 steps: deamination and ammonification

 When an organism dies, microbial decomposition

resulted to hydrolytic breakdown of proteins into
amino acids.

 Deamination
Proteins from dead Microbial decomposition Amino
cells and waste products Acids

 Ammonification
Microbial decomposition
Amino acids Ammonia (NH3)
 Because NH3 is a gas, it rapidly disappears
from the dry soil, but in moist soil, it
becomes solubilized in water and forms
NH4.

 NH3 + H2O NH4+ + OH-

2. Nitrification
 is the oxidation of the nitrogen in the ammonium ion
to produce nitrate through the help of autotrophic
nitrifying bacteria living in the soil:

Nitrosomonas – oxidizes ammonium to nitrates

Nitrosomonas

NH4+ NO2-
Ammonium ion Nitrate ion

Nitrobacter – oxidizes nitrites to nitrate

Nitrobacter

NO2- NO3-
Nitrite ion Nitrate ion
 NH4+ would make a more efficient source of
nitrogen for they require less energy to
incorporate into protein,

 however, plants tend to use NO3- for it is highly

mobile in the soil.

 This is because the positive charge of the NH4+

bound to the negative charges of the clay soil,
compared to the negative charge of NO3- that do
not bound.
3. Denitrification
 The form of N2 resulting from nitrification is fully
oxidized and no longer contains any biological usable
energy.

 But, it can be used as an electron acceptor by

microbes in the absence of oxygen.

 Denitrification is the loss of nitrogen to the

atmosphere, especially N2 gas.
NO3- NO3- N2O N2
Nitrate ion Nitrite ion Nitrous oxide N2 gas

 Denitrification occurs in waterlogged soils, where

little oxygen is available.
 4. Nitrogen Fixation

 is the process by which they convert nitrogen gas

to ammonia by some few species of bacteria, and
cyanobacteria.

 these bacteria rely on the enzyme nitrogenase

which is inactivated by oxygen.

 Nitrogen fixation is brought by either of the 2

types of microorganisms: free living and the
symbiotic
 Free- Living Nitrogen
Fixing Bacteria

- Are found in
particularly high
concentrations in the
rhizosphere ( a region
2 mm from the plant
roots
 Azotobacter
- aerobic microorganism
- they shield the
anaerobic nitrogenase
enzymes from oxygen
by using high rate of
oxygen.
 This minimizes the
diffusion of oxygen
into the interior of the
cell, where the enzyme
is located.
 Clostridium pasteurianum  Cyanobacteria
- also fix nitrogen
- Carry their nitrogenase
- anaerobic microbes enzyme in heterocysts that
provide anaerobic condition
for fixation.
• Symbiotic Nitrogen Fixing Bacteria
 Infected root nodules of Alder Tree by nitrogen
fixing bacteria Actinomycetes (Frankia)
 Lichens are also nitrogen fixing bacteria which are a
combination of fungus and an alga or cyanobacteria. This
resulted to a fixed nitrogen that eventually enriches the
forest soil.
Sulfur cycle
 H2S represents a source of energy for autotrophic
bacteria.

 These bacteria converts the reduced sulfur in H2S

into elemental sulfur granules (S2) and to fully
oxidized sulfates (SO4-).

 Several phototrophic bacteria, such as the green

and purple sulfur bacteria, also oxidizes H2S
forming colorful internal sulfur granules.
Beggiatoa
- they further oxidize the sulfur to sulfate ions.
- they also use light for energy, thus, using H2S to
reduce CO2.
 Thiobacillus
- Uses H2S as an energy source to produce SO4- and
sulfuric acid H3SO4.
- They grow well at pH as low as 2 and has practical
uses in mining.
 Plants and bacteria incorporate sulfates to
become part of the sulfur-containing amino
acids for humans and animals.

 They form disulfide links that give

structure to proteins.

 As proteins are decomposed, sulfur is

released as H2S to reenter the cycle
(dissimilation)
 Interestingly, deep-sea
caves, which is totally
isolated from sunlight,
have been discovered
that also support entire
biological communities.

 The primary producers

in these systems are
chemoautotrophs rather
than photoautotrophs.
Endoliths
- Discovered 1 km. deep within rocks which must grow in
the near absence of oxygen and with minimal nutrient
supplies.
Phosphorus cycle
 Phosphorus exists primarily as PO4-3 with little
change in oxidation state.

 There is no volatile phosphorus-containing

products to return phosphorus to the atmosphere.

 the cycle only involves changes from being soluble

to becoming insoluble forms, and from organic to
inorganic phosphates in relation to pH.

 That`s why, the availability of phosphorus may

determine whether the plant and other organisms
can grow in an area.
 Phosphates in rocks can be solubilized by an acid
produced by bacteria like Thiobacillus.

 When it rains, some Phosphorus accumulates to

the sea or remained to the soil.

 It can be retrieved by mining the above-ground

sediments or digging the sea for most deposits
of calcium phosphate Ca3(PO4)2.

 Seabirds also mine phosphorus as they eat

phosphorus-containing fishes and deposits it as
bird droppings.
Degradation of Synthetic Chemicals
in Soil and Water

 Not all material could be degraded by soil

microorganisms.

 Many chemical that do not occur in nature

(xenobiotics), like plastics, enter the soil in large
amount (1/4 of total municipal wastes).
 As a solution, researchers developed a
Polylactide (PLA) plastics produced by lactic acid
fermentation.
 When composted, PLA degrades in a few weeks.
 Aside from plastics,
synthetic chemicals are
also highly resistant to
degradation by
microbial attacks.

Ex: DDT
(Dichlorodiphenyl-
trichloroethane)
- a well-known chemical
that is so resistant that
it accumulated to
damaging levels in the
environment.
 2,4, D (2 4-dinitrophenylhydrazine)
- For lawn weed.

2,4,5-T (Trichlorophenoxyacetic acid)

- a synthetic auxin, is a
chlorophenoxy acetic acid herbicide
used to defoliate broad-leafed
plants

 Both were components of Agent Orange used to

defoliate jungles during Vietnam War.
 These chemicals is leached into groundwater of
toxic materials that are not biodegradable or that
degraded very slow.

 Among the sources includes landfills, illegal

industrial dumps, or pesticides, applied to
agricultural crops.
Bioremediation
 Is the use of microbes to detoxify or degrade
pollutants.

 ex: Oil spills from wrecked tankers. Microbes

attack the petroleum if conditions are aerobic.

 However, microbes usually obtain nutrients in

aqueous solutions, and oil-based products are
nonsoluble.

 Petroleum are also deficient in essential

elements, like N2 and P.
 Bioaugmentation

– addition of specialized microbes that have been

selected for growth on a certain pollutant or of
genetically modified bacteria that can adapt to
metabolize petroleum products.
Solid Municipal Wastes
 Composting
- conversion of plant remains into the
equivalent of natural humus through microbial
degradation.

 Thermophiliac bacteria will raise the

temperature of the compost to 55- 60°C in a
couple of days.

 As temp. declines, the piles can be turned to

renew oxygen supply.

 Over time, Thermophiliac bacteria will be

replace by mesophiliac bacteria that will continue
the conversion.