Chapter 2 Biodiversity of Microorganism PDF

CHAPTER 2 (CHAPTER 2.1) MICROORGANISM BIODIVERSITY Classification of Microorganisms Intro to bacteria, archaea and fungi Intro to protozoa, algae and virus Classification of Microorganisms The science of classifica...

CHAPTER 2 (CHAPTER 2.1) MICROORGANISM BIODIVERSITY Classification of Microorganisms Intro to bacteria, archaea and fungi Intro to protozoa, algae and virus Classification of Microorganisms The science of classification of living forms is called Taxonomy Objective of taxonomy :  to establish relationships between one group of organisms and another and differentiate them  to provide universal names for organisms  to provide a common reference for identifying organisms The Three-Domain System Scientific Nomenclature Common names – Vary with languages – Vary with geography Binomial Nomenclature  [genus + specific epithet (species)]  genus (noun) + species (adjective) – Homo (man) sapiens (wise) – Rhizopus (root) stolonifer (shoot or long hyphae) Scientific Binomial Source of Genus Source of Name Specific Epithet Klebsiella Honors Edwin Klebs The disease pneumoniae Escherichia coli Honors Theodor Found in the colon Escherich Salmonella Honors Daniel Stupor (typh-) in typhimurium Salmon mice (muri-) Streptococcus Chains of cells Forms pus (pyo-) pyogenes (strepto-) Penicillium Tuftlike (penicill-) Produces a yellow chrysogenum (chryso-) pigment Trypanosoma cruzi Corkscrew-like Honors Oswaldo (trypano-, borer; Cruz soma-, body) Neisseria Honors Albert L. Causes gonorrhea gonorrhoeae Neisser Taxonomic Hierarchy  Methods of Classifying and Identifying Microorganisms Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms. Identification: Matching characteristics of an “unknown” organism to lists of known organisms. – Clinical lab identification  Methods of Classifying and Identifying Microorganisms Morphological characteristics: Useful for identifying eukaryotes Differential staining: Gram staining, acid-fast staining Biochemical tests: Determines presence of bacterial enzymes (enzymatic activity) Taxonomic Key Dichotomous key-paired statements describing characteristics of organisms Example: Morphological characteristics Euglenoids Example: Differential staining  Example: Biochemical test API KIT ENTEROTUBE VITEX Methods of Identifying Microorganisms Serology ELISA Genetic FISH Serology Combine known antiserum plus unknown bacterium Slide agglutination test  ELISA Enzyme-linked immunosorbent assay Known antibodies Unknown type of bacterium Antibodies linked to enzyme Enzyme substrate a  positive control serum in the first row  negative control serum in the second row  The unknown samples are in the rest of the wells.  Positive samples are blue and the negative ones are colorless. Example of ELISA KIT  Genetic DNA base composition – Guanine + cytosine moles% (GC) – base composition of deoxyribonucleic acid (DNA) is quite variable from organism to organism. – The percentage of G-C base pairs in the nucleic acid of cells can be used in the classification of organisms. – closely related organisms should have similar %G-C numbers, those that vary considerably are not closely related.  Polymerase chain reaction (PCR) The polymerase chain reaction (PCR) can be used to detect small amounts of microbial DNA in a sample. Amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. Amplification by PCR may be used for DNA fingerprinting, sequencing, and detection of specific nucleotide sequences characteristic of specific organisms.  DNA fingerprinting “DNA typing”- method of isolating and making images of sequences of DNA. Electrophoresis of restriction enzyme digests The procedure for creating a DNA fingerprint consists of first obtaining a sample of cells containing DNA (e.g., from skin, blood, or hair), extracting the DNA, and purifying it. The DNA is then cut at specific points along the strand with substances called restriction enzymes. This produces fragments of varying lengths that are sorted by placing them on a gel and then subjecting the gel to an electric current (electrophoresis)  FISH Fluorescent in situ hybridization Many bacteria, however, even well-known species, do not grow well under laboratory conditions. FISH can be used to detect directly the presence of the suspect on small samples of patient's tissue. **is a powerful technique used in the detection of chromosomal abnormalities FISH is based on DNA probes annealing to specific target sequence of sample DNA. Attached to the probes are fluorescent reporter molecules which under fluorescence microscopy confirm the presence or absence of a particular genetic aberration when viewed under fluorescence microscopy. Metagenomic What is it?? Metagenomic Metagenomics is the study of metagenomes, the genetic material recovered directly from environmental samples. Application of techniques to the study of communities of microbial organisms directly in their natural environments, by passing the need for isolation and lab cultivation of individual species It is based on the recent development of high troughput sequencing technology. Why is it revolutionnary? Metagenomics  If you want to identify one colony, you need to isolate and send this colony for Bacterial diversity profile sequencing  If you want to identify more colonies, you have to repeat 1 analysis Over 5.000 operations for identifications amongst the most each single Metagenomic Metagenomic analysis offers a new tool to identify microorganisms present in foods and their evolution depending of environmental conditions Information given by metagenomics analysis provides a clear picture of the microbial community  --- To be continued-- Intro to bacteria, archaea and fungi  CHAPTER 2 (CHAPTER 2.2) MICROORGANISM BIODIVERSITY Classification of Microorganisms Intro to bacteria, archaea and fungi Intro to protozoa, algae and virus Introduction to bacteria  ! ! A P E C R Began with van Leeuwenhoek’s first examination of tooth scrapings. The most thoroughly studied microorganism. Majority with the same characteristics:  single-celled  spherical, rod, spiral or filamentous  lack cell nucleus  lack membrane-enclosed intracellular structure  absorb nutrient from environment Phylum: Proteobacteria, Gram negative Alphaproteobacteria Betaproteobacteria Gammaproteobacteria Deltaproteobacteria Epsilonproteobacteria Phylum: Nonproteobacteria, Gram negative Cyanobacteria Chlamydiae Phylum: Purple and green photosynthetic bacteria, Gram negative Chlorobi Chloroflexi Phylum: Firmicutes (Gram positive)- Low G+C Clostridia, Mollicutes, Bacilli Phylum: Actinobacteria (Gram positive)- High G+C Streptomyces  Role of bacteria Nitrogen fixation Decomposer: sewage treatment Food industry: lactic acid as preservatives, acetic acid as vinegar Probiotic: digestion systems Medicine and cloning : insulin, hormone and antibiotics Nitrogen-fixing bacteria – Azospirillum Grow in soil, using nutrients excreted by plants Fix nitrogen – Rhizobium Fix nitrogen in the roots of plants  Microbial Diversity In 1tbs of garden soil ~ 100,000 microbes. In 1L of seawater, ~1billion microbes. There are so many microbes, that scientists have only named 0.5% of them. Many bacteria have not been identified because they: – Haven't been cultured – Need special nutrients – Are a part of complex food chains requiring the products of other bacteria – Need to be cultured to understand their metabolism and ecological role  Bacteria identification by Differential agar: MacConkey Agar Uninoculated MacConkey MacConkey agar plate inoculated agar plate. with the Gram-negative lactose fermenter Escherichia coli and the Gram-negative non-lactose fermenter Serratia marcescens. (David Miller and Patrick Hanley, Hartwick College) (a) (b ) Example of mixed fecal flora on MacConkey agar. One colony type of lactose fermenter and two of non-lactose fermenters (a) at 24 hours, (b) at 48 hours. (Rebecca Buxton, University of Utah) Bacteria News Listeria costaricensi is the name for a new bacteria identified by scientists from the Biotechnology Research Center at the Costa Rican Institute of Technology Listeria (TEC) is not costaricensis harmful, lead to the discovery of antibiotics that could help treat people facing bacterial infections. Introduction to archaea  Three major groups of archaea (extremophiles) Hyperthermophiles- grow in extremely hot environment – Pyrodictium – Sulfolobus Methanogens- strict anaerobes that produce methane (CH4) from CO2 and H2 – Methanobacterium Extreme halophiles- require high concentrations of salt for survival – Halobacterium  Archaea classification based on physiological characteristics: Methanogens Strictly anaerobe Waterlogged soils, lake sediments, G.I. tracts of animals and human Extreme Obligate aerobe Great Salt Lake, salt- halophiles preserved food Extreme Obligate aerobe, Hot springs, thermoacidophile facultative aerobe, geothermally heated s or obligate marine sediments, anaerobe submarine hydrothermal vents Archaea were first found in extreme environments, such as volcanic hot springs Pictured here is Grand Prismatic Spring of Yellowstone National Park. The Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) are a new group of archaea recently discovered in acid mine drainage. Pyrodictium abyssi an unusual member of archaea found growing in deep-ocean sediment at a temperature of 110° C  Archaea News In a Lake Erie wetland, scientists showed that microbes produce methane in an oxygen-rich environment. This finding disproves the long- accepted idea that oxygen limits microbe’s ability to produce Methane-producing methane. (methanogen) organism that belongs to the Archaea group of microbes and they named it Candidatus Methanothrix paradoxum. Introduction to fungi  Mycology is the study of fungi Kingdom Fungi Nutritional Type Chemoheterotroph Multicellularity All, except yeasts Unicellular, filamentous, Cellular Arrangement fleshy Food Acquisition Method Absorptive Characteristic Features Sexual and asexual spores Embryo Formation None  Molds The fungal body (thallus) consists of long filaments (hyphae); a mass of hyphae is a mycelium. Aerial hyphae: reproduction Vegetative hyphae: obtaining nutrients Yeasts Non filamentous, unicellular fungi Fission yeasts divide symmetrically Budding yeasts divide asymmetrically (example?) Electron microscope image of budding yeast, Saccharomyces cerevisiae Fungal Dimorphism Morphological and physiological conversion of certain fungi from one phenotype to another when such fungi change from one environment to another. Pathogenic dimorphic fungi are yeast-like at 37°C and mold-like at 25°C Economic Effects of Fungi Saccharomyces cerevisiae: Bread, wine, HBV vaccine Trichoderma: Cellulase enzyme Taxomyces: Taxol drug Entomophaga: Biocontrol Paecilomyces: Kills termites The Pacific yew tree is an important source Termites feed on trees and wood structures. Scientists of both the Taxol have developed a foaming compound and fungal biocontrol endophytes like treatment that kills the Taxomyces insects Gypsy moth andreanae that caterpillar killed by also produce Taxol. the fungus Entomophaga maimaiga  Fungal Diseases (Mycoses) 1. Systemic mycoses: Deep within body 2. Subcutaneous mycoses: Beneath the skin 3. Superficial mycoses: Localized, e.g., hair shafts 4. Cutaneous mycoses: Affect hair, skin, and nails Opportunistic mycoses: Caused by normal microbiota or environmental fungi Fungi News The fungal spores, together with nutrients, will be placed into the concrete matrix during the mixing process. When cracking occurs, water and oxygen will find their way in. With enough water and oxygen, the dormant fungal spores will germinate, grow and precipitate calcium carbonate to heal the  --- To be continued-- Intro to protozoa, algae and virus  CHAPTER 2 MICROORGANISM BIODIVERSITY Classification of Microorganisms Intro to bacteria, archaea and fungi Intro to protozoa, algae and virus Introduction to protozoa Kingdom Protist Nutritional Type Chemoheterotroph Multicellularity None Cellular Arrangement Unicellular Food Acquisition Absorptive; ingestive Method Characteristic Motility; some form cysts Features Embryo Formation None  Characteristics of Protozoa Moist habitats (freshwater, marine environment,soil) Asexual reproduction is by fission, budding, or schizogony (multiple fission) Sexual reproduction by conjugation Some produce cysts (under adverse conditions to allow survival when food, moisture or oxygen are lacking) Some species parasites of plants and animal Vegetative form is a trophozoite (growing stage) Medically Important Phyla of Protozoa Archaezoa Amoebozoa Apicomplexa Ciliophora Euglenozoa  Archaezoa No mitochondria Multiple flagella ◦Giardia lamblia ◦Trichomonas vaginalis (no cyst stage) Archaezoa Amoebozoa Move by pseudopods ◦Entamoeba- Amebiasis ◦Acanthamoeba- chronic granulomatous amoebic encephalitis (GAE) Apicomplexa Nonmotile Plasmodiu Intracellular parasites m Complex life cycles ◦Plasmodium- Malaria ◦Babesia- Babesiosis ◦Cryptosporidium- Babesia Cryptosporidiosis ◦Cyclospora- Cyclosporiasis Ciliates Move by cilia Complex cells ◦Balantidium coli is the only human parasite ◦Balantidiasis Euglenozoa Move by flagella ◦Euglenoids (Photoautotrophs)- harmless ◦Trypanosoma – African trypanosomiasis or sleeping sickness Trypanosoma spp. Euglenoids  Protozoa News The closing is due to the threat of Cryptosporidium parasite potentially endangering the health of the general public.  Introduction to algae “plant without roots, stem and leaves” Kingdom Protist Nutritional Type Photoautotroph Multicellularity Some Unicellular, colonial, Cellular Arrangement filamentous, tissues Food Acquisition Diffusion Method Characteristic Pigments Features Embryo Formation None Algal Habitats Availability of wavelength of light Appropriate nutrient Surfaces on which to grow  Characterized by color Brown algae (kelp) Red algae grow at deeper levels. Green algae similar to plants. Diatoms unicellular produce neurotoxins. Dinoflagellates also cause neurotoxins.  Diatoms Pectin and silica cell walls Unicellular Store their energy mostly as fat and oil in large globules Fossilized diatoms formed oil Produce domoic acid- toxin in mussels that can cause diarrhea and memory loss  Dinoflagellates (plankton) Cellulose in plasma membrane Unicellular Store starch Some are symbionts in marine animals Neurotoxins cause paralytic shellfish poisoning  Role in nature Primary producers in aquatic food chains. Produce most of molecular oxygen Much of our petroleum is fossil remains of plankton. Many unicellular algae are symbionts in animals. Algae News Diatoms—microalgae that produce the oxygen for every fifth breath we take !!! —survive their harsh environment EPS protect diatom cells from the environment, helping them move and float and influence the formation of sea ice. They can trap bubbles and get carried into the atmosphere, get eaten by bacteria and enter the food chain or get buried in Introduction to viruses  General characteristics of viruses Obligatory intracellular parasites Contain DNA or RNA Contain a protein coat (capsid) Some are enclosed by an envelope Some viruses have spikes Most viruses infect only specific types of cells in one host Host range is determined by specific host attachment sites and cellular factors Virus Sizes Figure 13.1  Virion structure Nucleic acid ◦DNA or RNA Capsid ◦Capsomeres Envelope Spikes Enveloped Virus Figure 13.3 Enveloped Viruses Figure Helical Virus Figure 13.4  The classical classification and nomenclature Characteristics were to be used in the classification of all viruses: 1. Nature of the nucleic acid in the virion (DNA or RNA) (e.g Hepadnaviridae). 2. Whether or not the genome is segmented. 3. The size of the virion [e.g Parvoviridae- Parvus (small)]. 4. Symmetry of the protein shell (capsid) [eng. Baculoviridae – Baculum (stick). 5. Presence or absence of a lipid membrane (envelope) [e.g Cyctoviridae- Kystic (bladder, sack)] 6. Type of nucleic acid whether single stranded or double stranded.  Modern virus classification and nomenclature Taxonomy based on virus Order, Family, Genus & Species Each virus is defined by its characteristics that are necessary for membership of the group (nucleic acid type, replication strategy, morphology) Suffix - virales - viridae - virinae - virus - virus  The Baltimore classification The Baltimore classification, developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc.) and their method of replication.  Growing Viruses Animal viruses may be grown in embryonated eggs, cell culture or lab animal. Viruses News Three people in Uganda and Kenya have died from an extremely rare and deadly disease caused by the Marburg virus !! --- End of Chapter 2 ---