OITE Lec 6: Organisms in their Environment PDF

Lecture 6—Jan 22nd 2025 BES 108D Organisms in their environment By Dr. Benazir Alam Copyright © 2025 Pearson Canada, Inc. 27 - 1  2 Topic:1 Prokaryotes: Bacteria...

Lecture 6—Jan 22nd 2025 BES 108D Organisms in their environment By Dr. Benazir Alam Copyright © 2025 Pearson Canada, Inc. 27 - 1  2 Topic:1 Prokaryotes: Bacteria and Archaea Chapter: 27…continued Copyright © 2025 Pearson Canada, Inc. 27 - 2  Conjugation: Pilus vs mating bridge Conjugation is the process by which genetic material is unidirectionally transferred between two bacteria directly through a physical connection called a mating bridge The sex pilus is responsible for bringing the bacteria into close contact Recipient The structure through which the genetic material is transferred Donor between the bacteria is called a mating bridge 1. A donor cell attaches to a recipient by a pilus. 2. The pilus retracts bringing the cell membrane of the two bacteria in close proximity. 3. A stable mating bridge forms through which DNA usually involved in antibiotic 27 - 3 resistance or the ability toCopyright use new metabolites © 2025 transfers. Pearson Canada, Inc.  Conjugation: What decides if a 4 bacterium will be a donor or a recipient? A piece of DNA called the F or fertility factor is required for the production of pili. Cells containing the F plasmid/segment of DNA in the chromosome function as DNA donors during conjugation. Cells without the F factor function as DNA recipients during conjugation The F factor is transferable during conjugation Copyright © 2025 Pearson Canada, Inc. 27 - 4 How F factor is transferred during conjugation in E. coli Rolling circle replication Copyright © 2025 Pearson Canada, Inc. 27 - 5 R Plasmid R plasmids may carry resistance genes to upto 10 antibiotics Antibiotics kill sensitive bacteria, but not bacteria with specific R plasmids Many R plasmids, like F plasmids, have genes that encode pili and enable DNA transfer from one bacterial cell to another by conjugation Via natural selection, the fraction of bacteria with R plasmid increases rapidly in a population exposed to antibiotics Resistance genes can spread within and among bacterial species by horizontal gene transfer. Copyright © 2025 Pearson Canada, Inc. 27 - 6  The Role of Oxygen in Metabolism Prokaryotic metabolism varies with respect to O2 – Obligate aerobes require O2 for cellular respiration – Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration (by using nitrate, NO3- ions or sulphate, SO42- ions to accept electrons at the “downhill” end of electron transport chains) to generate ATP. – Facultative anaerobes can survive with or without O2 because they can switch between aerobic respiration and anaerobic respiration/fermentation depending on the presence or absence of O2 Copyright © 2025 Pearson Canada, Inc. 27 - 7  Metabolic Cooperation: Biofilms q Metabolic cooperation refers to the interaction between different prokaryotic organisms or within a single prokaryotic community, where the exchange of metabolic products benefits the involved species. E.g. biofilms q A biofilm is a complex community of microorganisms, primarily bacteria, embedded in a self-produced extracellular matrix often Pseudomonas aeruginosa containing polysaccharides and proteins that form a slime layer or forming a biofilm capsule. P. aeruginosa biofilms can cause serious q Channels in the biofilm allow nutrients to reach cells in the interior infections of human skin, and wastes to be expelled. urinary tract, and lungs that are difficult to treat with antibiotics qBiofilms are difficult to treat with antibiotics: a. because of the extracellular matrix i.e. the capsule or slime layer make the entry of antibiotics difficult. b. Bacteria in a biofilm often exist in a state of slowed growth or dormancy. Slow- growing or dormant bacteria are less susceptible to the action of antibiotics, as these drugs are less effective against non-dividing cells. This allows bacteria deep within the biofilm to survive even in the presence of antibiotics. c. The extracellular matrix of biofilms also helps bacteria evade detection and destruction by the immune Copyright system.© 2025 Pearson Canada, Inc. 27 - 8 Exploring Bacterial Diversity : beneficial bacteria 1. Cyanobacteria- 2. Gram-positive These gram- bacteria negative Streptomyces is the photoautotrophs are source of many the only antibiotics such as prokaryotes with tetracycline and plantlike, oxygen- erythromycin generating photosynthesis. Bacteria on human colon 3. The number of bacteria living on (such as skin) or within (such as gut) humans comprises microbiome. Human intestines are home to about 500–1,000 species of bacteria q It has been estimated to be 10x larger than the number of human cells q These bacterial communities live symbiotically in many locations including on the skin, in mouths, the stomach, intestines, and vagina. Copyright © 2025 Pearson Canada, Inc. 27 - 9  10 Think Disruption of the gut microbiome, which can occur through the use of antibiotics, can allow opportunistic bacteria like the diarrhea-causing Clostridium difficile to take hold. What do you think the impact of taking an antibiotic on your gut microbes? Copyright © 2025 Pearson Canada, Inc. 27 - 10 Exploring Bacterial Diversity: Pathogenic Bacteria Bacteria cause about half of all human diseases – For example, Lyme disease caused by the bacterium, Ixodes scapularis and is carried by ticks that live on deer and field mice Copyright © 2025 Pearson Canada, Inc. 27 - 11  Pathogenic Bacteria: Exo/Endo toxins Pathogenic bacteria typically cause disease by releasing exotoxins or endotoxins Exotoxins are secreted and cause disease even if prokaryote that produced them are not present: e.g. Cholera, a dangerous diarrheal disease, is caused by an exotoxin secreted by the proteobacterium Vibrio cholerae. The exotoxin stimulates intestinal cells to release chloride ions into the gut, and water follows by osmosis. Endotoxins are toxic lipopolysaccharide components of the outer membrane of certain gram-negative bacteria that are released only when bacteria dies and their cell walls break down: e.g. Salmonella typhi, which causes typhoid fever Copyright © 2025 Pearson Canada, Inc. 27 - 12  Antibiotic Resistance Since their initial use in the 1940s, antibiotics have saved many lives and reduced the incidence of disease caused by pathogenic bacteria Bacteria have developed resistance to every antibiotic currently in clinical use, often within a few years The rise of antibiotic resistance. Identify the antibiotic for which resistance appeared before the antibiotic began to be used medicinally Copyright © 2025 Pearson Canada, Inc. 27 - 13  Instead, Archaea cell wall contains polysaccharides and proteins A Comparison of Bacteria vs Archaea Copyright © 2025 Pearson Canada, Inc. 27 - 14  Archaea Some archaea live in extreme environments and are called extremophiles Extreme halophiles live in highly saline environments-e.g. the proteins and cell wall of Halobacterium have unusual features that improve function in extremely salty environments but render these organisms' incapable of survival if the salinity drops below 9%. Methanogens live in swamps, marshes or under ice in Greenland. They also live within the guts of cattle, termites, and other herbivores. They use CO2 to oxidize H2, a process that produces both energy and methane (CH4) waste Methanogens are strict anaerobes and are poisoned by O2 Extreme thermophiles thrive in very hot environments. E.g. (1) Pyrococcus furiosus lives in geothermally heated marine sediments that reach temperatures of 100°C. (2) Orange and yellow colonies of Sulfolobus grow in the sulfur rich volcanic springs of Nevada geyser. Copyright © 2025 Pearson Canada, Inc. 27 - 15  Prokaryotes in Research and Technology Experiments using prokaryotes have led to important advances in DNA technology – E. coli is used in gene cloning (transformation) – Use of DNA polymerase from Pyrococcus furiosus, an archaea in the PCR technique – Through genetic engineering, we can modify bacteria to produce vitamins, antibiotics, hormones, and other products. – Soil bacteria can produce, Malacidins, a class of antibiotics effective against CMRSA10 a highly virulent strain of methicillin-resistant Staphylococcus aureus (MRSA). – CRISPR-Cas9 system for gene knockout Copyright © 2025 Pearson Canada, Inc. 27 - 16  CRISPR-Cas9 system: a prokaryotic 17 antiviral system against viruses The genomes of many prokaryotes contain short DNA repeats, called CRISPRs (clustered regularly interspaced short palindromic repeats), that it acquired from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence CRISPR play a key role in the antiviral defense system of prokaryotes and provide a form of heritable acquired immunity for prokaryotes. CRISPR: Opening new avenues of q CRISPRs interact with endonuclease proteins research for treating HIV infection. known as Cas9 (CRISPR-associated protein 9) that cuts DNA. q Cas9 proteins, acting together with “guide RNA” made from the CRISPR region, can cut any DNA sequence to which they are complimentary. q Scientists have been able to exploit this system to target cells whose DNA they want to alter. Copyright © 2025 Pearson Canada, Inc. 27 - 17  Prokaryotes in Research and Technology: Biodegradable plastic 1. Bacteria can be used to make natural plastics. Bacteria synthesize and store a polymer called PHA (polyhydroxyalkanoate), a component of biodegradable plastics. 2. Prokaryotes are the principal agents in bioremediation, use of organisms to remove pollutants from environment such as cleaning up oil spills and precipitating radioactive material (such as uranium) out of groundwater. a. Spraying fertilizer stimulates the growth of native bacteria that metabolize oil, increasing the breakdown process up to fivefold. b. Anaerobic bacteria and archaea decompose the organic matter in sewage, converting it to material that can be used as landfill or fertilizer after chemical sterilization. Copyright © 2025 Pearson Canada, Inc. 27 - 18