ENVIRONMENTENVIRONMENT & &

MICROORGANISMSMICROORGANISMS

Doç.Dr.Hrisi BAHARDoç.Dr.Hrisi BAHAR

MICROORGANISMSMICROORGANISMS

The word microorganism is used to describe an organism that is so small that can not be seen without the use of a microscope.

Viruses, bacteria, fungi, protozoa and some

algae are all included in this category.

Microorganisms are responsible for many of the Microorganisms are responsible for many of the changes observed in organic and inorganic changes observed in organic and inorganic matter (e.g., fermentation and the carbon, matter (e.g., fermentation and the carbon, nitrogen and sulfur cycles that occurred in nitrogen and sulfur cycles that occurred in naturenature))..

Microorganisms in our livesMicroorganisms in our lives

► Microorganisms as Disease Agents

► Microorganisms and Agriculture

► Microorganisms and the Food Industry

► Microorganisms, Energy, and the Environment

► Microorganisms and the Future

Microorganisms in our livesMicroorganisms in our lives

They generate at least half the oxygen we breathe.

They are roots of life's family tree. An understanding of their genomes will help us understand how more complex genomes developed.

Microorganisms (microbes)Microorganisms (microbes)

Microbiology is the study of microorganisms also known as microbes.

MicrobesMicrobes are single-celled microorganisms that can are single-celled microorganisms that can perform the basic functions of life: metabolism, perform the basic functions of life: metabolism, reproduction, and adaptation.reproduction, and adaptation.

Except virusesExcept viruses.. Viruses can’t metabolize nutrients, Viruses can’t metabolize nutrients, can’t produce and excrete wastes, can’t move can’t produce and excrete wastes, can’t move around on their own, or even can’t reproduce unless around on their own, or even can’t reproduce unless they are inside another organism’s cells.they are inside another organism’s cells.

Medical microbiologyMedical microbiology

Medical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings.

MıcroorganismsMıcroorganisms

Microorganisms are similar to more complex Microorganisms are similar to more complex organisms in that they need a variety of organisms in that they need a variety of materials from their environment to function materials from their environment to function and accomplishand accomplish two two primary goalsprimary goals . .

11--ToTo supply enough energy to manage their supply enough energy to manage their processesprocesses

22-To e-To extractxtract building blocksbuilding blocks to repairto repair themselves or procreatethemselves or procreate..

Environmental factorsEnvironmental factorsaffecting the growth of affecting the growth of

microorganismsmicroorganisms

Mıcroorganisms haveMıcroorganisms have

Physical RequirementsPhysical Requirements Chemical RequirementsChemical Requirements from the environment where they live.

Physical RequirementsPhysical Requirements

1.1. TemperatureTemperature:: Microbes are Microbes are looselyloosely classified into several groups based on their classified into several groups based on their preferred temperature ranges.preferred temperature ranges.

Physical RequirementsPhysical Requirements --TemperatureTemperature --

A-A-PsychrophilesPsychrophiles: : “Cold-loving”. Can grow at 0“Cold-loving”. Can grow at 0ooC. C.

Two groups:Two groups: True PsychrophilesTrue Psychrophiles: Sensitive to temperatures over : Sensitive to temperatures over

2020ooC. Optimum growth at 15C. Optimum growth at 15ooC or below. C or below.

Found in very cold environments (North pole, ocean Found in very cold environments (North pole, ocean depths). Seldom cause disease or food spoilage.depths). Seldom cause disease or food spoilage.

PsychrotrophsPsychrotrophs: Optimum growth at 20 to 30: Optimum growth at 20 to 30ooC. C. Responsible for most low temperatureResponsible for most low temperature food spoilagefood spoilage..

Physical RequirementsPhysical Requirements - - TemperatureTemperature - -

B.B. MesophilesMesophiles: : ““Middle loving”. Most bacteria.Middle loving”. Most bacteria. Include most pathogens and common Include most pathogens and common

spoilage organisms.spoilage organisms. Best growth between 25 to 40Best growth between 25 to 40ooC. C. Optimum temperature commonly 37Optimum temperature commonly 37ooC.C. Many have adapted to live in the bodies of Many have adapted to live in the bodies of

animals.animals.

Physical RequirementsPhysical Requirements -- TemperatureTemperature - -

C-C- ThermophilesThermophiles: : “Heat loving”.“Heat loving”. Optimum growth between 50 to 60Optimum growth between 50 to 60ooC. C. Many cannot grow below 45Many cannot grow below 45ooC.C. Adapted to live in sunlit soil, compost piles, and hot Adapted to live in sunlit soil, compost piles, and hot

springs. springs. Some thermophiles form extremely heat resistant Some thermophiles form extremely heat resistant

endospores.endospores. ExtremeExtreme ThermophilesThermophiles (Hyperthermophiles):(Hyperthermophiles):

Optimum growth at 80Optimum growth at 80ooC or higher. Archaebacteria. C or higher. Archaebacteria. Most live in volcanic and ocean vents.Most live in volcanic and ocean vents.

Physical RequirementsPhysical Requirements - - pH pH --

Most Most bacteriabacteria prefer neutralprefer neutral pH (6.5-7.5).pH (6.5-7.5). MoldsMolds andand yeastyeast grow in wider pH range, but grow in wider pH range, but

prefer pHprefer pH between 5 and 6.between 5 and 6. AcidityAcidity inhibits most microbial growth and is used inhibits most microbial growth and is used

frequently for food preservation (e.g.: pickling).frequently for food preservation (e.g.: pickling). AlkalinityAlkalinity inhibits microbial growth, but not inhibits microbial growth, but not

commonly used for food preservation.commonly used for food preservation. Acidic products of bacterial metabolism interfere Acidic products of bacterial metabolism interfere

with growth. Buffers can be used to stabilize pH.with growth. Buffers can be used to stabilize pH.

Physical RequirementsPhysical Requirements - - pH pH --

Organisms can be classified as: Organisms can be classified as: A. A. AcidophilesAcidophiles:: “Acid loving”.“Acid loving”.

Grow at very low pH (0.1 to 5.4)Grow at very low pH (0.1 to 5.4) LactobacillusLactobacillus produces lactic acid, tolerates mild produces lactic acid, tolerates mild acidity.acidity.

B. B. NeutrophilesNeutrophiles:: Grow at pH 5.4 to 8.5.Grow at pH 5.4 to 8.5. Includes most human pathogens.Includes most human pathogens.

C. C. AlkaliphilesAlkaliphiles:: “ “Alkali loving”.Alkali loving”. Grow at alkaline or high pH (7 to 12 or higher)Grow at alkaline or high pH (7 to 12 or higher) Vibrio choleraeVibrio cholerae and and Alkaligenes faecalisAlkaligenes faecalis optimal pH 9.optimal pH 9. Soil bacterium Soil bacterium AgrobacteriumAgrobacterium grows at pH 12. grows at pH 12.

Physical RequirementsPhysical Requirements - Osmotic pressure -- Osmotic pressure -

Cells are 80 to 90% water.Cells are 80 to 90% water.

A. A. Hypertonic solutionsHypertonic solutions: High osmotic pressure removes : High osmotic pressure removes water from cell, causing shrinkage of cell membrane water from cell, causing shrinkage of cell membrane (plasmolysis).(plasmolysis).

Used to control spoilage and microbial growth.Used to control spoilage and microbial growth. Sugar in jelly.Sugar in jelly. Salt on meat.Salt on meat.

B. B. Hypotonic solutionsHypotonic solutions:: Low osmotic pressure causes water Low osmotic pressure causes water to enter the cell. In most cases cell wall prevents excessive to enter the cell. In most cases cell wall prevents excessive entry of water. Microbe may lyse or burst if cell wall is entry of water. Microbe may lyse or burst if cell wall is weak.weak.

Physical RequirementsPhysical Requirements - Osmotic pressure-- Osmotic pressure-

Halophiles: Require moderate to large salt concentrations. Ocean water contains 3.5% salt.

Most bacteria in oceans.

Extreme or Obligate Halophiles: Require very high salt concentrations (20 to 30%).

Bacteria in Dead Sea

Facultative Halophiles: Do not require high salt concentrations for growth, but tolerate 2% salt or more.

Chemical RequirementsChemical Requirements--Carbon-Carbon-

Makes up 50% of dry weight of cell.Makes up 50% of dry weight of cell.

Structural backbone of all organic compounds.Structural backbone of all organic compounds.

ChemoheterotrophsChemoheterotrophs:: Obtain carbon from Obtain carbon from their energy source: lipids, proteins, and their energy source: lipids, proteins, and carbohydrates.carbohydrates.

Chemoautotrophs and PhotoautotrophsChemoautotrophs and Photoautotrophs: : Obtain carbon from carbon dioxide.Obtain carbon from carbon dioxide.

Chemical RequirementsChemical Requirements- - Nitrogen, Sulfur, and PhosphorusNitrogen, Sulfur, and Phosphorus --

► NitrogenNitrogen:: Makes up 14% of dry cell weight. Used to Makes up 14% of dry cell weight. Used to form amino acids, DNA, and RNA. form amino acids, DNA, and RNA.

► SulfurSulfur:: Used to form proteins and some vitamins Used to form proteins and some vitamins (thiamin and biotin). (thiamin and biotin).

► PhosphorusPhosphorus:: Used to form DNA, RNA, ATP, and Used to form DNA, RNA, ATP, and

phospholipids.phospholipids.

Chemical RequirementsChemical Requirements - - Other ElementsOther Elements & & Trace ElementsTrace Elements - -

Other ElementsOther Elements Potassium, magnesium, and calcium are often required as Potassium, magnesium, and calcium are often required as

enzyme cofactors. enzyme cofactors. CalciumCalcium is required for cell wall is required for cell wall synthesis in Gram positive bacteriasynthesis in Gram positive bacteria

Trace ElementsTrace ElementsMany are used as enzyme cofactors. Commonly found in tap water. Iron Copper Molybdenum Zinc

Chemical RequirementsChemical Requirements --OxygenOxygen--

Organisms that use molecular oxygen (O2), produce more energy from nutrients than anaerobes.

Microorganisms can be classified based on their oxygen requirements:

AA..Obligate AerobesObligate Aerobes:: Require oxygen to live. Require oxygen to live. DisadvantageDisadvantage:: Oxygen dissolves poorly in water. Oxygen dissolves poorly in water.

ExampleExample:: PseudomonasPseudomonas, common nosocomial , common nosocomial pathogen.pathogen.

Chemical RequirementsChemical Requirements --OxygenOxygen--

B. Facultative AnaerobesB. Facultative Anaerobes: Can use oxygen, but : Can use oxygen, but can grow in its absence. Have complex set of can grow in its absence. Have complex set of enzymes. enzymes.

ExamplesExamples:: E. coli, StaphylococcusE. coli, Staphylococcus, yeasts, and , yeasts, and many intestinal bacteria.many intestinal bacteria.

C. Obligate AnaerobesC. Obligate Anaerobes:: Cannot use oxygen and Cannot use oxygen and are harmed by the presence of toxic forms of are harmed by the presence of toxic forms of oxygen.oxygen.ExamplesExamples: : ClostridiumClostridium bacteria that cause bacteria that cause tetanus and botulism.tetanus and botulism.

Chemical RequirementsChemical Requirements --OxygenOxygen--

D. Aerotolerant AnaerobesD. Aerotolerant Anaerobes:: Can’t use oxygen, but Can’t use oxygen, but tolerate its presence. Can break down toxic forms tolerate its presence. Can break down toxic forms of oxygen.of oxygen.

ExampleExample:: LactobacillusLactobacillus carries out fermentation carries out fermentation regardless of oxygen presence.regardless of oxygen presence.

E. Microaerophiles:E. Microaerophiles: Require oxygen, but at low Require oxygen, but at low concentrations. Sensitive to toxic forms of oxygen.concentrations. Sensitive to toxic forms of oxygen.

ExampleExample:: CampylobacterCampylobacter

Toxic Forms ofToxic Forms of OxygenOxygen1. 1. Singlet OxygenSinglet Oxygen:: Extremely reactive form of oxygen, Extremely reactive form of oxygen,

present in phagocytic cells.present in phagocytic cells.

2. 2. Superoxide Free Radicals Superoxide Free Radicals (O(O22-.-.):): Extremely toxic and Extremely toxic and

reactive form of oxygen. All organisms growing in reactive form of oxygen. All organisms growing in atmospheric oxygen must produce an enzyme atmospheric oxygen must produce an enzyme superoxide dismutase (SOD)superoxide dismutase (SOD),, to get rid of them. to get rid of them. SOD is made by aerobes, facultative anaerobes, and SOD is made by aerobes, facultative anaerobes, and aerotolerant anaerobes, aerotolerant anaerobes, but notbut not by anaerobes or by anaerobes or microaerophiles.microaerophiles.ReactionReaction: : SODSODOO22

-.-. + + OO22-.-. + + 2H2H++ -----> H-----> H22OO22 + O + O22

SuperoxideSuperoxide HydrogenHydrogenfree radicalsfree radicals peroxideperoxide

Chemical RequirementsChemical Requirements - -Hydrogen PeroxideHydrogen Peroxide--

Hydrogen PeroxideHydrogen Peroxide (H(H22OO22):): Peroxide ion is toxic and the Peroxide ion is toxic and the

active ingredient of several antimicrobials (e.g.: benzoyl active ingredient of several antimicrobials (e.g.: benzoyl peroxide). There are two different enzymes that break peroxide). There are two different enzymes that break down hydrogen peroxide:down hydrogen peroxide:

A. CatalaseA. Catalase: : Breaks hydrogen peroxide into water and OBreaks hydrogen peroxide into water and O22. . Common. Produced by humans, as well as many bacteria.Common. Produced by humans, as well as many bacteria.

B. PeroxidaseB. Peroxidase: : Converts hydrogen peroxide into waterConverts hydrogen peroxide into water

Chemical RequirementsChemical Requirements - -Hydrogen PeroxideHydrogen Peroxide-- CatalaseCatalase

2 H2 H22OO22----------> 2H----------> 2H22O + OO + O22 HydrogenHydrogen Gas Gas peroxideperoxide Bubbles Bubbles

PeroxidasePeroxidase HH22OO2 2 + 2H + 2H++----------> H----------> H22OO HydrogenHydrogen peroxideperoxide

Microbial Stress ResponseMicrobial Stress Response

A changing environment creates conditions that can be stressful for microorganisms.

Microbes have physiological acclimation mechanisms to survive and remain active in the face of stress.

They have to appropriately respond to have to appropriately respond to numerous adverse conditions in order to numerous adverse conditions in order to proliferate or at least surviveproliferate or at least survive

Stress response in pathogensStress response in pathogens

Human pathogens infecting humans respond to stress situations encountered during transition from natural environment to the host.

1-Temperature stress The first signal to an invading bacteria on entry

into the host is an increase in temperature from that of the environment to the physiological temperature of the human body (37°C).

Response: * Induction of virulence genes * Induction of heat shock genes

http://www.ias.ac.in/jarch/jbiosci/21/149-160.pdf

Stress response in pathogensStress response in pathogens

2-2-Oxygen stress The expression of adherence and invasion factors

of several pathogenic bacteria is regulated by oxygen concentration. High oxygen usually represses whereas low

oxygen induces invasiveness Response:Induction and repression of some

genes . One regulatory network is the Fnr (fumerate-

nitrate reductase)-dependent control in response to anaerobiosis

Stress response in pathogensStress response in pathogens3-Osmotic stress For a pathogenic bacterium which passes from environmental

waters to the human body for infection, osmolarity is an important criterion to

distinguish between the external and host associated environments.

Osmolarity of an aqueous environment is thought to be no greater than that equivalent to 0·06 M NaCl while in the intestinal lumen the osmolarity is much higher (equivalent to 0·3 M NaCl) and in the blood stream the bacteria encounters an osmolarity equivalent to about 0·15 M NaCl.

Response. Increase in osmolarity is associated with expression of virulence factors in many pathogenic organisms.

Stress response in pathogensStress response in pathogens

4-4-Metal ion stress

Iron is an essential element for bacterial growth and many pathogenic bacteria

have evolved highly efficient iron scavenging systems which are regulated in response to the iron status of the environment.

Response: Ex: Low iron concentration leads to the increased synthesis of virulence determinants in several pathogenic bacteria.

Stress response in pathogensStress response in pathogens

5-Presence of Antibiotic as a stress for bacteria5-Presence of Antibiotic as a stress for bacteria An untreated microbe maintained under optimal

growth conditions will not be stressed. *Similarly, the same cell when exposed to an

antibiotic to which it is fully resistant will also not be stressed.

*When exposed to a lethal concentration of an antibiotic to which it is susceptible, the cell will be highly stressed in its quest to survive.

ResponseResponse:Antibiotic resistance:Antibiotic resistance

Stress response in pathogensStress response in pathogens

ACTIVEDRUG

Days

GROWTHINHIBITION(CELL DIVISION)

ACTIVEDRUG

Minutes

STRESS RESPONSE

Bacterial response to Bacterial response to environmentenvironment

Rapid response crucial for survivalRapid response crucial for survival– Simultaneous transcription and translationSimultaneous transcription and translation– Coordinate regulation in operons and regulonsCoordinate regulation in operons and regulons– Global genetic control through modulonsGlobal genetic control through modulons

Bacteria respond toBacteria respond to– Change from aerobic to anaerobicChange from aerobic to anaerobic– Presence/absence of glucosePresence/absence of glucose– Amount of nutrients in generalAmount of nutrients in general– Presence of specific nutrientsPresence of specific nutrients– Population sizePopulation size

Quorum SensingQuorum Sensing

Bacteria monitor their own population sizeBacteria monitor their own population size– Pathogenesis: do not produce important molecules too Pathogenesis: do not produce important molecules too

soon to tip off the immune system.soon to tip off the immune system.– Light production: a few bacteria make feeble glow, but Light production: a few bacteria make feeble glow, but

ATP cost per cell remains high.ATP cost per cell remains high.– Bacteria form spores when in high numbers, avoid Bacteria form spores when in high numbers, avoid

competition between each other.competition between each other. System requirementsSystem requirements

– A signaling molecule that increases in concentration as A signaling molecule that increases in concentration as the population increases; LMWthe population increases; LMW

– A receptor; activation of a set of genesA receptor; activation of a set of genes

Quorum SensingQuorum Sensing

New peptide communication factor enabling bacteria to 'talk to each other' discovered

http://phys.org/news112885276.html

Chemotaxis and other taxesChemotaxis and other taxes

Movement in response to environmental Movement in response to environmental stimulusstimulus– Positive chemotaxis, attraction towards nutrientsPositive chemotaxis, attraction towards nutrients– Negative: away from harmful chemicalsNegative: away from harmful chemicals– Aerotaxis: motility in response to oxygenAerotaxis: motility in response to oxygen– Phototaxis: motility to certain wavelengths of lightPhototaxis: motility to certain wavelengths of light– Magnetotaxis: response to magnetic fieldsMagnetotaxis: response to magnetic fields

Taxis is movementTaxis is movement– Includes swimming through liquid using flagellaIncludes swimming through liquid using flagella– Swarming over surfaces with flagellaSwarming over surfaces with flagella– Gliding motility, requiring a surface to move overGliding motility, requiring a surface to move over

Starvation ResponsesStarvation Responses

Bacteria frequently on Bacteria frequently on the bord the bord of starvation of starvation– Rapid utilization of nutrients by community keeps Rapid utilization of nutrients by community keeps

nutrient supply lownutrient supply low– Normal life typical of stationary phaseNormal life typical of stationary phase– Bacteria monitor nutritional status and adjust through Bacteria monitor nutritional status and adjust through

global genetic mechanismsglobal genetic mechanisms Types of responsesTypes of responses

– Lower metabolic rates, smaller size Lower metabolic rates, smaller size ..– Release of extracellular enzymes, scavenging Release of extracellular enzymes, scavenging

moleculesmolecules– Production of resting cells, sporesProduction of resting cells, spores..

Microganisms leaving a stressful environment