MCROBIO LE 1.pdf

MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ◆ global ecosystem depends on their activities MODULE 1: INTRODUCTION...

MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ◆ global ecosystem depends on their activities MODULE 1: INTRODUCTION Decomposition role Convert nitrogen to oxygen Important in ecosystem 01 EXPLORING THE MICROBIAL WORLD ◆ influence human society in many ways Antibiotics came from microorganisms (penicillin) WHAT IS MICROBIOLOGY from fungi ➔ Old definition: study of “organisms & agents too small to be seen by the naked eye” BASIC MICROBIOLOGY ➔ New definition: The study of organisms that can ➔ Virology: viruses exists as single cells (others are acellular), ➔ Mycology: fungi contain a nucleic acid genome for at least ➔ Phycology: algae some part of their life cycle, and are capable of ➔ Protozoology: protozoa replicating that genome” ➔ Bacteriology: bacteria ◆ Viruses are included in the new definition APPLIED MICROBIOLOGY THE SCIENCE OF MICROBIOLOGY ➔ Applying our understanding of microbial life ➔ revolves around two interconnected themes: processes for the benefit of humankind and ◆ understanding the living world of planet Earth. microscopic organisms (as a basic ➔ applied microbiology fields include biological science) ◆ First three are interconnected Microorganism should be ◆ Microorganisms has different understand application due to ubiquitous in nature ◆ applying our understanding of microbial life processes for the benefit of humankind & planet Earth (as an applied biological science) Microorganisms can benefit positive and negative Majority are not harmful and does not cause disease Majority of microorganism give benefits A BRIEF HISTORY OF MICROBIOLOGY THE SCOPE & RELEVANCE OF MICROBIOLOGY ➔ Importance of microorganisms ◆ first living organisms on planet Reason why we have oxygen. ◆ live everywhere life is possible Can adapt survival ◆ more numerous than any other kind of organisms ➔ Fermented foods & beverages ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 1 MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ◆ Yeast fermentation yields Ethanol and ➔ Early Notions of Disease, Contagion, Carbon Dioxide. Containment Ethanol in the bread will be ◆ Ancient Greeks attributed disease to evaporate bad air, mal’aria, which they called ◆ A microscopic view of Saccharomyces “miasmatic odors” cerevisiae, the yeast responsible for Allowed them to practice making bread rise (left) hygiene para iwas lol. Saccharomyces is a fungi and ◆ The Romans also believed in the not bacteria “miasma” hypothesis & created a ◆ Yeast is a microorganism & its cells complex sanitation infrastructure to metabolize carbohydrates in flour deal with sewage (middle) & produce carbon dioxide, ◆ In Rome, they built aqueducts, which which causes the bread to rise (right) brought fresh water into the city, and a giant sewer, the Cloaca Maxima, which carried waste away & into the river Tiber Cloaca maxima holds the infection that prevents the infection. MODERN MICROBIOLOGY ➔ Otzi the Iceman ◆ Infected with the eggs of the parasite Trichuris trichiura, which may have caused him to have abdominal pain & anemia During their time, sick is usually term as god punishment ◆ Possible infection with Borrelia burgdorferi, a bacterium that causes Lyme Disease. ◆ Some researchers think Otzi may have been trying to treat his infections with ➔ Zaccharias Janssen The first compound the woody fruit of the Piptoporus microscope (3-10x) was invented in 1597 betulinus fungus ◆ Total magnification 1000x ◆ This fungus has both laxative and ➔ Antonie van Leeuwenhoek (1676) “wee antibiotic properties animacules” ◆ Describe as microorganisms ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 2  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ➔ Robert Hooke (1655) ◆ Discovery of cell (plant cell) Biotechnology : BT CORN, BT EGGPLANT ◆ simple compound microscope (30x) ➔ A microbial culture is a collection of cells that ◆ “cells” in cork; “elongated stalks” have been grown in or on a nutrient medium. (fungi) ◆ inoculum , you get from the culture to First one to observe the incolute to in the medium elongated stalks A medium (plural, media) is a liquid (broth) or ➔ Sample he use corks solid nutrient (agar) mixture that contains all of the nutrients required for a microorganism to 1.1 MICROORGANISMS, TINY TITANS OF grow. THE EARTH ◆ Agar has no NUTRIENT just a SOLIDIFYING agent ◆ If agar is only in the medium, no growth of microorganisms. ◆ Different type of media: Liquid to culture large number of microorganisms and easy access to nutrients Solid medium usually use to estimate number of cell CSF per meal and looking out cultural characteristic in agar plate ➔ Microorganisms (also called microbes) are life Semi solid medium usually use forms too small to be seen by the unaided to observe the motility human eye. (movement) of the ◆ Not always true microorganism - some ➔ Microorganisms typically live in complex microbes exhibit motility microbial communities and their activities are ➔ In microbiology, we use the word growth to regulated by interactions with each other, with refer to the increase in cell number as a result their environment, and with other organisms of cell division. ◆ Each color represent of microbes - ◆ Growth = cell division through fish ➔ A single microbial cell placed on a solid nutrient ➔ The science of microbiology is all about medium can grow & divide into millions or even microorganisms, who they are, how they work, billions of cells that form a visible colony. and what they do. ➔ Fungi (Molas, Yeasts, and Mushrooms) ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 3  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 GENES, GENOMES, NUCLEUS, & NUCLEOID ➔ All cells also possess a DNA genome - the full set of genes in a cell ◆ Virus has own genome as well ➔ A gene is a segment of DNA that encodes a protein or an RNA molecule Fluorescent microbes vibrio ◆ Introns and exons Technique used clock streaking or quadrant ◆ Introns segment in the genome that streaking does not encode a protein and only for ○ Purpose of this streak is to isolate the exons (Eukaryotic) colonies and gives us culture ◆ Bacteria don't have introns Isolate colonies pure culture ➔ The genomes of prokaryotic cells & eukaryotic = ONE SPECIES ex. E.coli cells are organized into structures called ○ Diluting the microorganism chromosomes ◆ Eukaryotic linear ◆ Prokaryotes circular, package STRUCTURE & ACTIVITIES OF chromosome in circular way 1.2 MICROBIAL CELLS ➔ In eukaryotic cells, DNA is present as several linear molecules within a membrane-enclosed nucleus. ELEMENTS OF MICROBIAL STRUCTURE ➔ The chromosome aggregates within the prokaryotic cell to form the nucleoid a mass Prokaryotic Cell that is visible in the electron microscope, but which not enclosed by a membrane. ◆ Nucleoid is just an area ➔ Most prokaryotic cells have only a single chromosome, but many also contain one or more small circles of DNA distinct from that of the chromosome, called plasmids. Contains plasmid = extra chromosomal DNA ◆ Plasmid may have antibiotic resistance are not included in the genome gene Nucleoid area where genome bacteria ◆ Plasmid can be transferred horizontally ACTIVITIES OF MICROBIAL CELLS Eukaryotic Cell ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 4  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 - Endospores are eliminated SURFACE-TO-VOLUME RATIOS, GROWTH - When endospores survived, it will germinate RATES AND EVOLUTION to new microorganism, bacteria is alive, ➔ The S/V of a rod-shaped organism can be hibernation estimated as if it were a cylinder; hence, the S/V - Flagella for propulsion (motility) of the cell will decrease as its radius increases. - Not all mutation are bad and negative effect ◆ Higher nutrients NEED more surface - Some mutation serve as beneficial volume ratio - 16S for prokaryotes 18RS for eukaryotes ◆ 3/r in which the surface radius is 1um ◆ If more cell membrane more sufficient 1.3 CELL SIZE AND MORPHOLOGY to get more nutrients ◆ The bigger the cell is the less nutrients ➔ Microscopic examination of microorganisms as compared to the smaller cells immediately reveals their morphology which is ➔ As cell size decreases, the S/V ratio of the cell defined by cell cell size and shape. increases, and this means that small cells can THE SMALL WORLD exchange nutrients and wastes more rapidly (per unit cell volume) than can large cells. ◆ Small cells are faster than the big cells ➔ As a result, free-living cells tend to be more efficient than those that are larger and any given mass of nutrients will support the synthesis of more small cells than large cells. ◆ The higher number genome more cell will produce Epulpiscium MAJOR MORPHOLOGIES OF PROKARYOTIC ○ It's important to have more genome CELLS to distribute the nutrients that's why it has multiple copies ➔ A spirochete is a special kind of organism that Thiomargarita has a spiral shape, but which differs from 750 micrometers or 0.6ML long compared to spirilla because the cells of spirochetes are E.coli micrometers and can be seen in the flexible, whereas cells of spirilla are rigid. naked eye ◆ Spirochete are highly pathogenic, if infected it will insert deeply into the tissue of the host ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 5  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ◆ Stalk and Hypha help microorganisms IDENTIFICATION to adhere to the surface so that they will not be wiped away ➔ Characterization of an isolate to determine ◆ Filamentous allows microorganisms to what species it is get more nutrients in the surface area NOMENCLATURE ➔ Assignments of names to taxonomic groups in agreement with published rules SYSTEMATICS ➔ Study of the diversity of life (both past and present) and the relationship among living things through time ➔ Uses taxonomy to understand organism (1) MAJOR MORPHOLOGIES OF SPECIES (IN PROKARYOTES) PROKARYOTIC CELLS ➔ Collection of strains that shares stable ➔ Cells division has a major impact on properties in common and differ significantly morphology because cells that remain from other groups of strains attached to each other can form distinctive ◆ Strains that never change shapes ◆ Strain are subspecies ◆ Cocci occur in pairs (diplococci) ◆ Long chains (streptococci) SPECIES (IN EUKARYOTES) ◆ Three-dimensional cubes (tetrads or ➔ A group of closely related organisms that sarcinae) breed among themselves ◆ Grapelike clusters (staphylococci) ◆ Multiply by coupling ➔ Filamentous bacteria are long, thin, rod-shaped bacteria that divide terminally and then form STRAIN long filaments composed of many cells ➔ Population of organism that descends from a attached end to end. pure culture isolate or from a species ➔ The cell morphologies described here are ◆ Quadrant streaking or clock streaking representative but certainly not exclusive; many ◆ Pure culture = create strain variations of these morphologies are known. microorganisms ➔ While different strains may be nearly identical CLASSIFICATION OF MICROORGANISMS genetically, they can have very different attributes TAXONOMY ◆ Strain can be subspecies, same species ➔ The science of biological classification but different purposes, one infected ➔ Describing, identifying, classifying, and amig of and one can be beneficial organisms ➔ E.coli O157:H7 vs E.coli HS ◆ Pathogen VS beneficial CLASSIFICATION ◆ 157:H7 original discover of the antigen ➔ Grouping organisms into taxa based on mutual ◆ H for flagella similarity or evolutionary relatedness ◆ Morphology and molecular biology should still be utilized both. ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 6  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 ◆ Magnetospirillum magnetotacticum CAROLUS LINNAEUS ➔ *Candidatus - provisional taxonomic name ➔ The most famous early taxonomist was a appended to candidate taxonomic ranks (i,e, Swedish botanist, zoologist, and physician Candidatus Pelagibacter ubique) named Carolus Linnaeus (1700-1776). ◆ Adding an additional name and there is ➔ Published Systema Naturae in which he no pure culture yet. proposed the Linnaean taxonomy ◆ Candidate scientific name but because ➔ Kingdom, class, order, family, genus, (plural: it is not pure culture yet, the term genera), and species candidatus is added Its not applicable that are not unculturable Some microorganism are unculturable due to unable to mimic their environment. ◆ Once pure culture, will be able to study in terms of morphology and microscopically Names are Descriptive PRINCIPLES OF NOMENCLATURE BINOMIAL NOMENCLATURE ➔ A two-word naming system for identifying organisms by genus and species. ◆ Escherichia coli ◆ Escherichia coli Term describe the morphology for example ➔ Each organisms is placed in a genus and given pearl a specific epithet (specific name/species Thiomargarita namibiensis- “biggest name) bacteria” and shines like a pearl. (1) PRINCIPLES OF NOMENCLATURE (2) PRINCIPLES OF NOMENCLATURE ➔ Generic Name: can change if the organism is assigned to another genus because of new ➔ Designation of categories is required for information classification of organisms ➔ Specific Name: stable, the modest epithet for a ➔ Taxon = group particular organisms takes precedence and ➔ Taxa = groups must be used ◆ Pseudomonas solanacearum Formal Rank Example ◆ Pseudomonas cepacia ◆ Aquaspirillum magnetotacticum Domain Bacteria ◆ Ralstonia solanacearum ◆ Burkholderia cepacia Phylum Proteobacteria ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 7  MICROBIOLOGY LECTURE N01-N02 | Ms. Querubin, Florabelle | LE1: Oct. 3, 2024 Class Gammaproteobacteria IJSEM (International Journal of Systematic & Evolutionary Microbiology) Order Enterobacteriales ➔ Official publication of record for taxonomy and Family Enterobacteriaceae classification of Bacteria, Archaea, and microbial eukaryotes Genus Escherichia ◆ Before naming the microorganism it should be published first Species Coli Table 1: Taxonomic Ranks of the Bacterium Escherichia CHARACTERIZATION AND IDENTIFICATION Coli Why do microorganism change genus due to ➔ Involves the study, not of a single cell, but of a new discovery population of identical cells ○ That this microorganism is more ➔ Prerequisites: pure culture related to another organism REASONS FOR DOING CHARACTERIZATION First largest group domain ○ In organisms there can be three ➔ Identification purposes domain ➔ Comparison with other organisms PCOFGS (smallest doman) ➔ Exploit characteristics which may be beneficial (3) PRINCIPLES OF NOMENCLATURE 1.4 AN INTRODUCTION TO MICROBIAL ➔ Each distinct kind of organism is designated as LIFE a __ ➔ All cells fall into one of three major groups: ➔ List of species of prokaryotes Bacteria, Archaea, or Eukarya ◆ Bergey’s Manual of Systematic ➔ These three major cell lineages are called Bacteriology domains and all known cellular organism ◆ Bergey’s Manual of Determinative belong to one of these three domain Bacteriology ◆ Both are standard book for prokaryotes (always updated) ➔ These books act as standard references for identifying and classifying different prokaryotes ◆ Do not just rely on morphological (phenotype) but also molecular RULES FOR NAMING BACTERIA BACTERIA ➔ International code for the Nomenclature of ➔ Among the Bacteria, 30 major phylogenetic Bacteria (1991) lineages (called phylum) have at least one QUESTIONS ON NOMENCLATURE species that has been grown in culture, though many more pyla exist which remain largely ➔ International Journal of Systematic Bacteriology uncharacterized (IJSB) ◆ Largely remain uncharacterized. ◆ Question will be addressed to IJSB ABELLA, CLEMENTE, RAMIREZ, SALAS 2024-2025 8