1. Naming and classifying microorganisms lecture 3 Dr. Samah NoorGeneral microbiology 2311

2. Naming Microorganisms (Binomial nomenclature) was established by Carolus LInnaeus- in 1735Naming Microorganisms (Binomial nomenclature) was established by Carolus LInnaeus- in 1735 Purpose : provide a means of international reference Purpose : provide a means of international reference Each organism was assigned a Latin or Latinized genus name (capitalized) and specific epithet (species) (follows and not capitalized)Each organism was assigned a Latin or Latinized genus name (capitalized) and specific epithet (species) (follows and not capitalized) Even when derived from a proper noun such as the name of a person or place, both parts are italicized.Even when derived from a proper noun such as the name of a person or place, both parts are italicized. Thus the binomial name of the e. coli is now written as E. coliThus the binomial name of the e. coli is now written as E. coli Latin was used because it was the language used by scholarsLatin was used because it was the language used by scholars Dr. Samah NoorGeneral microbiology 2312

3. naming microbes Taxonomy : is the science of classification and systematic arrangement of organisms into groups-taxa Taxonomy : is the science of classification and systematic arrangement of organisms into groups-taxa Microbial systematics : is classifying, naming, and identifying Microbial systematics : is classifying, naming, and identifying Taxonomy orderly arrangement of units into groups of larger groups of increasing inclusiveness Taxonomy orderly arrangement of units into groups of larger groups of increasing inclusiveness Nomenclature : naming of units characterized and delineated by classification Nomenclature : naming of units characterized and delineated by classification Objective: group organisms so as to reflect similarities and differences Objective: group organisms so as to reflect similarities and differences Dr. Samah NoorGeneral microbiology 2313

4. naming microbes Binomial nomenclature is now governed by various internationally agreed codes of rules,Binomial nomenclature is now governed by various internationally agreed codes of rules, Rules for naming protozoa and parasitic worms are in the International Code of Zoological Nomenclature.Rules for naming protozoa and parasitic worms are in the International Code of Zoological Nomenclature. Rules for naming fungi and algae are in the International Code of Botanica Nomenclature.Rules for naming fungi and algae are in the International Code of Botanica Nomenclature. Rules for naming newly classified bacteria are established by the International Committee ON Systematics Of Prokaryocytes and published in the International Bacteriological Code.Rules for naming newly classified bacteria are established by the International Committee ON Systematics Of Prokaryocytes and published in the International Bacteriological Code. They are then included in the standard of reference for bacteria, Bergey’s Manual of Systematic Bacteriology.They are then included in the standard of reference for bacteria, Bergey’s Manual of Systematic Bacteriology. Dr. Samah NoorGeneral microbiology 2314

5. naming microbes New laboratory techniques, involving analysis of DNA and RNA, have caused some bacteria to be reclassified.New laboratory techniques, involving analysis of DNA and RNA, have caused some bacteria to be reclassified. Sometimes organisms which have been in separate genera are combined into one genus; other times organisms previously in the same genus are split out into separate genera.Sometimes organisms which have been in separate genera are combined into one genus; other times organisms previously in the same genus are split out into separate genera. Even if the genus name is changed, the species name usually remains the same.Even if the genus name is changed, the species name usually remains the same. Dr. Samah NoorGeneral microbiology 2315

6. TAXONOMIC HIERARCHY This is the complete list of taxa (classification groups) which are used to classify living organisms:This is the complete list of taxa (classification groups) which are used to classify living organisms: Domain (this is the relatively new one) KingdomPhylum Division (this one may be used in place of phylum in botany) ClassOrderFamilyGenusSpecies Dr. Samah NoorGeneral microbiology 2316

7. CLASSIFICATION OF PROKARYOCYTES Bergey’s Manual, the standard for classification of prokarocytes. Bergey’s Manual, the standard for classification of prokarocytes. Two domains, Bacteria and Archaea, are included. Two domains, Bacteria and Archaea, are included. The taxon Kingdom is not used, so then each domain is divided into phyla, based on similarities in rRNA.The taxon Kingdom is not used, so then each domain is divided into phyla, based on similarities in rRNA. Organisms continue to be divided into taxa that are more and more specific until, eventually reaching the species level.Organisms continue to be divided into taxa that are more and more specific until, eventually reaching the species level. In eukaryocytes, a species is defined as a group of closely related organisms that breed among themselves. A bacterial species is defined as a population of cells with similar characteristics.In eukaryocytes, a species is defined as a group of closely related organisms that breed among themselves. A bacterial species is defined as a population of cells with similar characteristics. Members of the species are VERY similar to each other, but all may not be totally identical.Members of the species are VERY similar to each other, but all may not be totally identical. Strains are identified by numbers, letters, or names that follow the species name.Strains are identified by numbers, letters, or names that follow the species name. Dr. Samah NoorGeneral microbiology 2317

8. CLASSIFICATION OF EUKARYOCYTES DOMAIN: EUKARYA---contains 4 kingdoms KINGDOM: PROTISTA---unicellular eukaryocytes except yeasts & molds KINGDOM: PROTISTA---unicellular eukaryocytes except yeasts & molds KINGDOM: FUNGI---unicellular yeasts, multicellular molds, macroscopic fungi--these all absorb organic matter through their plasma membranes KINGDOM: FUNGI---unicellular yeasts, multicellular molds, macroscopic fungi--these all absorb organic matter through their plasma membranes KINGDOM: PLANTAE---plants--macroscopic algae, flowering plants--all are multicellular, all carry on photosynthesis KINGDOM: PLANTAE---plants--macroscopic algae, flowering plants--all are multicellular, all carry on photosynthesis KINGDOM: ANIMALIA---animals--sponges, worms, insects, vertebrates--all ingest nutrients KINGDOM: ANIMALIA---animals--sponges, worms, insects, vertebrates--all ingest nutrients Dr. Samah NoorGeneral microbiology 2318

9. CLASSIFICATION OF VIRUSES Virus classification is a mess.Virus classification is a mess. Viruses are not composed of cells, so there are arguments about whether they are even really alive.Viruses are not composed of cells, so there are arguments about whether they are even really alive. Alive: They have either DNA or RNA, which must mean they are living Alive: They have either DNA or RNA, which must mean they are living Not alive: No cellular structure Not alive: No cellular structure No metabolism and no reproduction until they invade a living cell No metabolism and no reproduction until they invade a living cell Do not have DNA and RNA both—living things have both Do not have DNA and RNA both—living things have both Viruses are described as obligate intracellular parasites.Viruses are described as obligate intracellular parasites. A viral species is a population of viruses with similar characteristics that occupies a particular ecological niche. (The ecological niche of a virus is its host cell). There are two hypotheses on the origin of viruses:A viral species is a population of viruses with similar characteristics that occupies a particular ecological niche. (The ecological niche of a virus is its host cell). There are two hypotheses on the origin of viruses: 1. They arose from strands of DNA similar to plasmids 1. They arose from strands of DNA similar to plasmids 2. They developed from degenerative cells that lost their ability to function independently 2. They developed from degenerative cells that lost their ability to function independently Dr. Samah NoorGeneral microbiology 2319