Applied and Environmental

Microbiology
(APEP1609)
‫دﺑﻠﻮم ﺗﻜﻨﻮﻟﻮﺟﯿﺎ ﺣﻤﺎﯾﺔ اﻟﺒﯿﺌﺔ‬
Lecture(3)
Reem Alghamdi
Email: ramghamdi@uqu.edu.sa
Biology Department, Faculty of Applied Science, Umm Al-Qura University
Lecture outlines
vMicrobial life in the environment
• Different Microbial Habitat
• Extreme Microbial Environments
üThermophiles
üPsychrophiles
üHalophiles
üAcidophiles
üAlkaliphiles
üBarophiles
• Biotechnological Application of Extremophiles
Microbial Habitats
• An ecosystem is a dynamic complex of plant, animal, and microbial communities and
their abiotic surroundings, all of which interact as a functional unit.
• An ecosystem contains many different habitats, parts of the ecosystem best suited to one
or a few populations.
• A Habitat a place where an organism make its home, a habitat meets all the
environmental conditions an organism need to survive.
• Microorganisms are present in any habitat containing plants and animals, many microbial
habitats are unsuitable for plants and animals. why?
• Microbes are incredibly diverse thriving in environments from the very cold to the
extremely hot.
• They are also tolerant of many other conditions such as limited water availability, high
salt content and low oxygen levels.
• Not every microbe can survive in all habitat
Terrestrial Microbial Habitats
• 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 their ecosystems.
• Bacteria and fungi that live in soil feed mostly on organic matter such
as other plants and animals .
• These microbes are very sensitive to their local environment.
• Factors such as the level of carbon dioxide and oxygen , the pH,
moisture and temperature all affect the growth of microbes in the
soil.
Aquatic Microbial Habitat
• Microbes live in both fresh and salt water
• These organisms include microscopic plants and animals as well as
bacteria ,fungi and viruses
• As with 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 or rivers.
Microbial Habitats in Other Organisms
• Microbes also live on other organisms
• As with the ones found on people these microbes can be harmful or
beneficial to the host.
• Examples:
• Bacteria grow in nodules of the root of pea and beans plants. These
microbes convert nitrogen from the air into a form that the plant can
use.
• In many ways animals and plant have evolved as a habitats for the
millions of microbes that call them host.
 Microbial Habitats in Other Organisms
• The surfaces of the human body inside
and out, for example the skin, mouth
and the intestines, are covered in
millions of individual microorganisms
that don’t do us any harm. In fact, they
help to protect us from becoming
infected with harmful microbes. They are
known as the normal body flora.
• The number of normal bacterial cells
that live on the body is in the region of
100 million. This number is 10 times
You, yourself are a habitat for billions of bacteria greater than the 10 million cells that
make up the human body!
Extreme Microbial Environment
• The microbes live in extreme
conditions are called extremophiles.
• Extremophiles thrive under
environmental conditions in which
eukaryotic organisms cannot survive
• They are adapted to their own
environment like acidic lakes to the
deepest ocean, and from frozen
environments to hydrothermal vents.
 Extreme Microbial Environment
Thermophiles:
• A thermophile is an organism—a type of extremophiles—that
thrives at relatively high temperatures, between 41°C and
122 °C (106 and 252 °F).Many thermophiles are archaea ,
though they can be bacteria or fungi.
• Thermophiles are found in various geothermally heated
regions of the earth , such as hot springs like those in
Yellowstone National Park and deep-sea hydrothermal vents,
as well as decaying plant matter.
• Thermophiles can survive at high temperatures, whereas other
bacteria or archaea would be damaged and sometimes killed if
exposed to the same temperatures.
• The enzymes in thermophiles function at high temperatures.
Some of these enzymes are used in molecular biology, for
example the Taq polymerase used in PCR. ”
• E.g. Pyrolobus fumarii
Extreme Microbial Environment
Adaptation mechanisms of thermophiles:
• Membrane lipids have ether linkage- more branched, more saturated and are of high
molecular weight. These characters increase melting temperature of membrane lipids.
• Heat shock protein- more hydrophobic interiors- prevents unfolding or denaturation at
higher temperatures.
• High GC content than AT content in nucleic acid structure.
• Reverse DNA gyrase enzyme- catalyzes positive supercoiling of closed circular DNA-
positively supercoiled DNA appears to resist degradation more than negatively
supercoiled DNA.
• DNA association with DNA binding histone like protein.
• Salts like potassium and magnesium are found at higher levels in thermophilic archaea-
protect double- stranded DNA from phosphodiester bond degradation.
• Thick pseudo-crystalline proteinaceous surface layer(s layer) surrounding cell.
 Extreme Microbial Environment
Psychrophiles
• Psychrophilic (cold-loving) microorganisms particularly bacteria ,
have a preferential temperature for growth at less than 59
Fahrenheit (-15 Celsius).
• Earth is primarily a cold marine planet:
ü 90% of the water in the oceans has temperatures of 5℃ and
20% of the terrestrial region of earth is glaciers and ice
sheets, polar sea ice- and snow-covered regions
e.g.
• Polaromonas vacuolata Subglacial stream flowing from the Glacier
du Mont Mine, Swiss Alps. The water
• Pseudomonas antarctica temperature is less than 1ºC, yet viable
and culturable microorganisms have been
isolated from this stream. Photo by S.
• Methanogens, member of archaea, are the only group known to Montross
be psychrophiles (methanococcoides burtonii)
Extreme Microbial Environment
Adaptation mechanisms of psychrophiles
• presence of unsaturated fatty acids in cell membranes which remains as liquid even at low temperature to
facilitate solute transport across the membrane
• cold shock proteins and cryoprotectants for synthesizing cold adapted enzymes: Several changes like
membrane fluidity, reduced levels of transcription and translation and structure of ribosomes contribute to
changes in cellular machinery at low temperature.
• Psychrophiles protect themselves from freezing by :
1. accumulating compatible solutes like glycine betaine, mannitol and sucrose
2. synthesizing antifreeze proteins which prevents ice crystal growth.
3. psychrophiles also induces production of exopolysaccharides as a mechanism against cryo-protection.
• These microbes also offer complex metabolic adaptations such as altered mechanisms of nutrients
transport, cold-denaturation of proteins, intracellular ice formation and protein folding.
 Adaptation
Mechanisms
of
Psychrophiles
 Extreme Microbial Environment
Halophiles
• Are organisms that live in extremely salty environments. The
name halophile means (salt-loving)
• According to the optimal salt concentration for growth- classified
in three categories:
ü Extreme halophile – grow in an environment with 3.4-5.1 M
(20%to30%) NaCl
ü Moderate halophile - grow in an environment with 0.85-3.4
M (3% to 25%) NaCl
ü Slightly halophiles – grow in an environment with 0.2-0.85 M
(1% to 5%) NaCl
• E.g. Halobacterium salinarum
Extreme Microbial Environment
Adaptation mechanisms for halophiles
• One mechanism halophiles use to survive in high concentrations of
salt is the synthesis of osmoprotectants, which are also known as
compatible solutes. These work by balancing the internal osmotic
pressure with the external osmotic pressure, making the two
solutions isotonic, or close to it.
• Compatible solutes are small-molecular weight molecules. “Some are
widespread in microorganisms, namely trehalose, glycine betaine and
α-glutamate, while others are restricted to a few organisms.”
• The use of compatible solutes is the most common mechanism of salt
resistance among halophiles.
 Extreme Microbial Environment
Acidophiles
• or acidophilic organisms are those that thrive under highly acidic
conditions (usually at pH 2.0 or bellow).
• Highly acidic environments can result naturally from
geochemical activities ( such as the production of sulfurous
gases in hydrothermal vents and some hot springs) and form the
metabolic activities of certain acidophiles themselves.
Acidophiles are also found in the debris left over from coal
mining.
• E.g. Sulfolobus acidocaldarius
Extreme Microbial Environment
Adaptation mechanisms of Acidophiles :
• Interestingly, Acidophiles cannot tolerate great acidity inside their
cells, where it would destroy important molecules as DNA, Most
acidophile organisms have evolved extremely efficient mechanisms to
pump protons out of the intracellular space in order to keep the
cytoplasm at or near neutral pH. Therefore, intracellular proteins do
not need to develop acid stability through evolution.
• However, other acidophiles, such as Acetobacter aceti, have an
acidified cytoplasm which forces nearly all proteins in the genome to
evolve acid stability.
Extreme Microbial Environment
Alkaliphiles
• are a class of extremophilic microbes capable of survival
in alkaline (pH roughly 8.5-11) environments, growing
optimally around a pH of 10.
• Soda Lakes ( saline and alkaline ecosystem) such as Lonar
Crater soda lake in India, Mono lake , Big soda lake and
Soap lake in USA, and lake Magadi in Kenya.
• To survive, alkaliphiles maintain a relatively low alkaline
level of about 8 pH inside their cells by constantly
pumping hydrogen ions in the form of hydronium ions
(H3O+) across their cell membranes and into their
cytoplasm.
• e.g. Natronobacterium gregoryi
Lonar Crater soda lake in India
Extreme Microbial Environment
Barophiles
• A barophiles is an organism that needs a high-pressure environment in order to grow.
ü Barotolerants (faculatative): grow at pressure from 100-400 Atm
ü Barophilic(obligative): grow at pressure greater than 400 Atm
ü Extreme Barophilic: grow at pressures higher than 700 Atm
• An example of a high-pressure habitat is the deep-sea environment, such as ocean floors
and deep lakes where the pressure can exceed 380 atm. Another is the subsurface rocks
with high lithostatic pressures.
• E.g. Halomonas salariaa Gram-negative proteobacterium, is an example of an extreme
barophile. It needs a pressure of 1000 atm.
• Many barophiles are sensitive to ultraviolet rays and are susceptible to UV radiation. They
lack the essential mechanisms of DNA repair to counter the effects of UV radiation. Thus,
many of them grow in darkness.
Extreme Microbial Environment
Adaptation mechanisms of barophiles:
• Lipids contain unsaturated fatty acids (PUFA)- protect from the
pressure
• Proteins coat ( omps, Outer membrane proteins) protects from the
pressure.
• Proteins/ enzymes hold the cellular structure together by allowing the
normal chemical reactions to take place.
• Pressure controlled gene expression.
Meet the most interesting extremophile!
• Boil them ..
• Deep-freeze them ..
• Crush them ..
• Dry them out ..
• Blast them into space ..
Tardigrades will survive it all and come
back for more !!
Biotechnological Application of Extremophiles
Hyper thermophiles
(sources) DNA Polymerase
(sources) Alkaline phosphatase
(sources) protease and lipases
(sources) proteases
(sources) Alcohol dehydrogenase
(sources) Xylanases
S- layer proteins and lipids
Lanthionine
Old degrading microorganisms
Sulfur oxidizing microorganisms
Hyper thermophilic consortia
Uses
DNA amplification by PCR
Diagnostics
Diary products, detergents
Baking, brewing, amino acid production from keratin
Chemical synthesis
Paper bleaching
Molecular sieves
Pharmaceutical
Surfactant for oil recovery
Bioleaching coal and waste gas desulfurization
Waste treatment and methane production.
Biotechnological Application of Extremophiles
Psychrophiles Uses
(sources) Alkaline phosphatase Molecular biology
(sources) Lipases and proteases Cheese manufacture and diary production
(sources) proteases Contact-lens cleaning solutions, meat tenderizing
(sources) polyunsaturated fatty acids Food additive, dietary supplements
(sources) proteases, lipases, cellulases and amylases Detergents
Methanogens Methane production
Various enzymes Modifying flavors
B-galactosidase Lactose hydrolysis in milk production
Ice nucleating proteins Artificial snow, ice cream, other freezing applications
in the food industry.
Various enzymes ( dehydrogenases) biotransformation
Various enzymes (oxidases) Bioremediation, environmental biosensors
 Biotechnological Application of Extremophiles
Halophoiles Uses
(sources) Bacteriorhodopsin Optical switches and photocurrent generators in bioelectronics
(sources) polyhydroxyalkanoates Medical plastics
(sources) Rheological polymers Oil recovery
(sources) Eukaryotic homologues (myc oncogene Cancer detection, screening anti-tumor drugs
product)
(sources) lipids Liposomes for drug delivery and cosmetic packaging
(sources) compatible solutes Protein and cell protectants in variety of industrial uses e.g. freezing
heating
(sources) membranes Surfactants for pharmaceuticals
Nucleases, amylases, proteases Various industrial uses e.g., flavoring agents
g-linoleic acid, b- carotene and cell extracts e.g., Health food, dietary supplements, food coloring and feedstock
spirulina and Dunaliella
Microorganisms Fermenting fish sauces and modifying food textures and flavors
Microorganisms Waste transformation and degradation, e.g., hypersaline waste brines
contaminated with a wide range of organics
Biotechnological Application of Extremophiles
Alkaliphiles Uses
Proteases Gelatin removal on X- ray film
Proteases, celluases, xylanases, lipases and pullulanases Detergents
Elastases, keritinases Hide dehairing
Cyclodextrins Foodstuffs, chemicals and pharmaceuticals

Xylanases and proteases Pulp bleaching

Pectinases Fine papers, waste treatment and degumming

Alkaliphilic halophiles Oil recovery

Biotechnological Application of Extremophiles

Acidophiles Uses
Sulfur oxidizing microorganisms Recovery of metals and desulfurization of coal
Microorganisms Organic acids and solvents
References
• Brock Biology of Microorganisms(14th Edition) by Michael T. Madigan, John M. Martinko, Kelly S. Bender,
Daniel H. Buckley
• Microbial Ecology by Diana Northup and Larry L. Barton.
Note: All the images that included descriptions in this ppt are from the above two textbooks.
• Rothschild LJ, Mancinelli RL. Life in extreme environments. Nature. 2001 Feb 22;409(6823):1092-101. doi:
10.1038/35059215. PMID: 11234023.