Lecture 2: The Microbial Planet 2024 MSZ Lecture Notes PDF

The Microbial Planet Lecture topics Lecturers Meet the Microbes Dr Merve Suzan The Microbial Planet Zeden A history of human-microbe Prof Vince interactions O’Flaherty Medical Microbiology Prof Gerard Wall Prokaryotic genetics Dr K...

The Microbial Planet Lecture topics Lecturers Meet the Microbes Dr Merve Suzan The Microbial Planet Zeden A history of human-microbe Prof Vince interactions O’Flaherty Medical Microbiology Prof Gerard Wall Prokaryotic genetics Dr Kate Microbial molecular Reddington diagnostics A. Prof Florence Microbiomes Abram Environmental Microbiology Dr Gavin Collins Microbes & Food Production Dr Alma Siggins Food Preservation Methods Dr Katrina Lacey Marine Microbiology Tutorials/Practicals  The Earth is approximately 4.6 billion years old Single celled microorganisms were the first organisms on Earth approximately 3.7 billion years ago, more than 3.0 billion years before the appearance of plants and animals Microorganisms can be documented through 80% of the entire history of the Earth “The role of the infinitely small in nature is infinitely large” Louis Pasteur  O2 Atmosphere Evidence of these early microorganisms is seen in the fossil record of stromatolites. Stromatolites are organo-sedimentary structures produced by sediment trapping, binding or precipitation as a result of the growth and metabolic activity of microorganisms, primarily cyanobacteria (photosynthetic bacteria). STROMATOLIES today, Shark Bay Australia  O2 Atmosphere Stromatolties developed in shallow water where there was light and CO2 to fuel phytosynthesis This photosynthetic activity on ancient Earth both consumed atmospheric CO2 and enriched it with O2 paving the way for an O2 atmosphere that supports plants and animals.  Historical 5 kingdoms of life is INCORRECT ORGANISMS WERE PLACED INTO 5 KINGDOMS BROADLY BASED ON MORPHOLOGY & NUTRITION PROKARYOTES PLACED INTO A SINGLE KINGDOM MONERA 4 EUKARYOTE KINGDOMS PROTISTA PLANTA FUNGI * ANIMALIA THIS CLASSIFICATION IS INCORRECT BACTERIAL MORPHOLOGY DOES NOT HELP WITH THEIR TAXONOMY  CLASSIFICATION IS BASED ON ANALYSIS OF GENE OR AMINO ACID SEQUENCES. BY COMPARING THE SAME GENE SEQUENCE AMONG ORGANISMS THE EVOLUTIONARY RELATEDNESS BETWEEN THEM CAN BE DETERMINED. TERMED PHYLOGENETICS USING THE RIBOSOMAL RNA GENE WHICH IS PRESENT IN ALL LIVING ORGANIMS, CARL WOESE, PRESENTED THE UNIVERSAL TREE OF LIFE  There are 3 domains of life Universal tree of life, showing the evolutionary relationship between the  Three Domains of Life ALL LIFE FALLS INTO ONE OF THREE DOMAINS - BACTERIA, ARCHAEA OR EUKARYOTES BACTERIA AND ARCHAEA ARE DISTINCT DOMAINS EUKARYOTES DOMAIN INCLUDES ALL EUKARYOTIC CELLS FROM ALGAE, SLIME MOLDS, FUNGI, PLANTS, ANIMALS AND US! EXTRAORDINARY DIVERSITY SEEN WITH THE PROKARYOTE DOMAINS THE VAST MAJOIRTY OF ALL LIVING ORGANISMS ARE PROKARYOTES (BACTERIA & ARCHAEA)  How many? *Estimated total number of prokaryotes around 4 - 6 x 1030 4 x 10 is four million, million, million, million, 30 million or 4 000000 000000 000000 000000 000000 THERE ARE APPROXIMATELY 1022 -1024 STARS IN THE UNIVERSE ABOUT 6,897,440,749 = 6 X 10 9 OR 6 BILLION PEOPLE ON EARTH *Whitman et al., 1998 MICROORGANIMS ARE THE UNSEEN MAJORITY BOTH IN TERMS OF DIVERSITY AND NUMBER There are macroscopic clues to the shear abundance and importance of microorganisms. In nutrient rich waters during summer months blooms of E. huxleyi can be observed by satellite. Biofilm inside an industrial pipe E. huxleyi bloom in the English Impact of Microbiology Microbiology impacts upon: Health Food Environment Energy Biotechnology Agriculture Climate & Global Climate Change  Microorganisms ‘Friend or Foe’ Pathogenic Friendly - microbiome Disease & Food spoilage probiotics  Health A small minority of microorganisms cause disease in humans and animals. Control of Infectious Disease has developed from the study of microbiology There has been a lot of success in reducing infectious diseases in the developed world  Antibiotics  Development of vaccines  Improved sanitation Death Rates in the USA 1990- 2000 MICROBIAL NON- MICROBIAL DISEASES DISEASES  Methicillin Resistant Staphylococcus aureus (MRSA) Microorganisms are constantly evolving and developing drug resistance e.g. MRSA MRSA is a strain of Staphylococcus aureus so called as it was first noted for its resistance to the antibiotic methicillin but is also highly resistant to a range of antibiotics. MRSA is resistant to antibiotics and can cause skin and soft tissue infections, can lead to bacteremia and spread to other Resistan Sensitive organs to cause a variety of t MSSA  Vibrio cholera Cholera: Water-borne illness caused by ingesting water or food contaminated with Vibrio cholera  Microbiology & Food Food e.g. E. coli Pathogens Spoilage O157:H7 Source: Epidemiology of Verotoxigenic E. coli in Ireland 2017. HSE  Food preservation To prevent microbial spoilage of food and extend the shelf life Canning Frozen–foods Freeze dried foods Pasteurisation Pickling Radiation Chemical Food production Yeasts: beer, wine, bread Lactic Acid Bacteria: yogurt, cheese, sour cream, buttermilk Vinegar - fermentation of ethyl alcohol to acetic acid by acetic acid bacteria. Fermented foods: Soy sauce, salami, sauerkrauts, kombucha, olives, cocoa (there is no chocolate flavor in cocoa beans without fermentation!) Mushrooms & Quorn filamentous fungus Fusarium venenatum Microbiology and Agriculture Soil health and fertility Soil microorganisms mineralise organic matter in the soil Cycle essential nutrients, making them available for plant growth e.g. Nitrogen and Sulphur Legumes (e.g. clover) have symbiotic bacteria associated with their roots that fix atmospheric N2 into bioavailable from of nitrogen the plants can use for growth Symbiotic N2 fixing bacteria associated with the roots of clover  Ruminants (e.g. cows, goats, sheep) have a rumen containing microorganisms that digest cellulose First, cellulolytic protozoa and bacteria hydrolyse cellulose to disaccharides cellobiose and glucose Secondly, the glucose is fermented by bacteria producing volatile fatty acids (VFAs) including CO2 and methane Rumen microorganisms also make essential amino acids and vitamins Cows are feeding machines for the microorganisms!  Foe - Agriculture Pathogens of crops and stocks can have devastating effects for agriculture Bovine tuberculosis caused by Mycobacterium bovis Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals Dairy cattle mastitis caused by Staphylococcus aureus Energy and Environment Energy: A lot of Natural Gas (methane) is produced by bacteria Microbial Biofuels: Use microorganisms to convert terrestrial plant biomass and waste to bioenergy to generate electricity, light, heat, motion and fuel  Biofuels Henry T Ford’s 1941 Model T- Ford ran on 100% ethanol – powered by microbes! Biofuels ‘Fuels of the Future’ Natural microbial communities can breakdown many environmental contaminants e.g. crude oil. Bioremediation – use of microorganisms to remediate contaminated environments.  Bioremediation strategies Bioattenuation: natural biological breakdown. Biostimulation: addition of nutrients or surfactants to stimulate the activity of the natural microbial community. Bioaugmentation: addition of microorganisms with the ability to breakdown the contaminant. Microorganisms, the engines of the Earth’s biosphere 50% of the worlds primary productivity occurs in the ocean by cyanobacteria Microorganis ms cycle and transform essential nutrients e.g. carbon, nitrogen, phosphorus, sulphur, oxygen.  Microorganisms and Biotechnology Enzymes for varied uses (GM enzymes); biocatalysts Engineered proteins (antibodies) Vaccines and antibiotics (secondary metabolites) Pharmaceuticals and novel chiral chemicals Biosensors (use of enzymes to specifically detect chemicals in medical, industrial and environmental settings) Emerging Biotechnology Synthetic Biology Worlds First Synthetic Organism Mycoplasma mycoides ASPIRES TO COMBINE AN ENGINEERING APPROACH TO (MICRO)BIOLOGY, TO DESIGN CELLS TO PREFORM A SPECIFIC FUNCTION e.g. Biofuel production using engineered microbes  Plastic-eating bacteria Researchers engineered bacteria to “eat” plastic waste, addressing one of the planet’s pressing environmental concerns. These modified bacteria can degrade plastics much faster than natural processes. This emerging biotechnology could shift waste management significantly reducing pollution.  Summary There are 3 domains of life: bacteria, archaea and eukarya Microbes can be beneficial and/or harmful (friend/foe) Microbiology impacts upon: Health Food Environment Energy Biotechnology Agriculture Climate & Global Climate Change