Module 5 Taxonomy

Murray

Proposed protist as 4th kingdom

Classification

is the orderly arrangement of organisms into groups,

Nomenclature

process of assigning names to the various taxonomic rankings of each microbial species.

Identification

is the process of discovering and recording the traits of organisms so that they may be placed in an overall taxonomic scheme.

Systematics

infers a more general scientific study of organisms with the ultimate objective of arranging them in an orderly manner

Ernst Haeckel

Proposed the 3 kingdoms, Animal plants and protist

Taxonomy

Science of classification and naming of organisms

order

Taxis is greek word for what

Law

Nomos is greek word for what

Taxon

A group or “level” within the classification system

Phylogenetic/Phyletic Classification System

Groups reflect genetic similarity and evolutionary relatedness

phylogeny

refers to the evolutionary development of a species.

Phenetic Classification System:

Groups are based on convenient, observable

characteristics.

Polyphasic taxonomy

This approach includes phenotypic,

phylogenetic, and genotypic features.

Genotypic Classification

seeks to compare the genetic similarity

between organisms.

International Journal of Systematic and Evolutionary

Microbiology

To be recognized as a new species, genomic,

metabolic, morphological, reproductive, and

ecological data must be accepted and

published in the

Bergey’s Manual of Systematic Bacteriology

a manual that grouped bacteria into phenetic

groups, used in identification of unknowns.

Volume 1

volume of bergey that Covers Archaea and deeply branching bacteria.

Volume 2

volume of bergey that Focuses on Proteobacteria.

Volume 3

volume of bergey that Discusses Firmicutes.

Volume 4

volume of bergey that Includes Spirochaetes, Bacteroidetes, and other groups.

Volume 5

volume of bergey that Addresses Actinobacteria.

Archaea, Eukarya, Bacteria

3 domains

Carl woese

Proposed 3 domains

kingdom

Many microbiologists reject a specific classification designation

Genus

a taxonomic category that groups together

species that share common

characteristics and are closely related.

species

most basic unit of biological

classification; single unique organism group

Strain

A population of microbes descended from a single

individual or pure culture

Biovar

Strains that differ in biochemical or

physiological differences

Morphovar

Strains that vary in morphology

Serovar

Strains that vary in their antigenic properties

Phylum Thermoproteota

Originally containing thermophilic and hyperthermophilic

sulfur-metabolizing archaea Recently discovered

Crenarchaeota are inhibited by sulfur & grow at lower

temperatures

Phylum Euryarchaeota

Contains primarily methanogenic archaea, halophilic

archaea, and thermophilic, sulfur-reducing archaea

Phylum Korarchaeota

A relatively small phylum that are often found in hot

springs and geothermal areas

Phylum Nanoarchaeota

This phylum is characterized by its extremely small size

and parasitic lifestyle.

Phylum Thaumarchaeota

This phylum includes organisms that are important for

nitrogen cycling in the environment. They are often found

in soil and aquatic environments

Phylum Aquiflexa/Aquifex

The earliest “deepest” branch of the Bacteria

Phylum Aquiflexa/Aquifex

Contains genera Aquifex 9e.g., A. aeolicus)

and Hydrogenobacter that can obtain energy

from hydrogen via chemolithotrophic

pathways

Phylum Cyanobacteria

Oxygenic photosynthetic bacteria

Also known as blue-green algae

Phylum Chlorobi

The “green sulfur bacteria”

Anoxygenic photosynthesis

Includes genus Chlorobium

Phylum Proteobacteria

The largest group of gram-negative bacteria

Phylum Proteobacteria

Sometimes called the “purple bacteria,”

Alphaproteobacteria

Rickettsia,is under what class

Alphaproteobacteria

Brucella,is under what class

Alphaproteobacteria

Rhizobium is under what class

Betaproteobacteria

Nitrosomonas, is under what class

Betaproteobacteria

Neisseria, is under what class

Betaproteobacteria

Burkholderia is under what class

Gammaproteobacteria

Escherichia is under what class

Gammaproteobacteria

Salmonella, is under what class

Gammaproteobacteria

Pseudomonas. is under what class

Deltaproteobacteria

Campylobacter. is under what class

Epsilonproteobacteria

Helicobacter pylori

Rhodospirillum

(a purple non-sulfur bacterium)

Chromatium

(a purple sulfur bacterium)

Thiobacillus and Beggiatoa

Sulfur chemolithotrophs, genera

Nitrobacter and Nitrosomonas

Nitrogen chemolithotrophs (nitrifying bacteria)

Phylum Firmicutes

“Low G + C gram-positive” bacteria

»Class I – Clostridia;

includes genera Desulfotomaculatum and Clostridium

»Class II – Mollicutes;

bacteria in this class cannot make peptidoglycan and lack cell walls;

»Class II – Mollicutes;

includes genera Mycoplasma, Ureaplasma, and others

»Class III – Bacilli;

includes genera ,Streptococcus, Lactococcus, Enterococcus, Listeria, Staphylococcus,Bacillus

Phylum Actinobacteria

“High G + C gram-positive” bacteria

Phylum Actinobacteria

Includes genera Actinomyces, Streptomyces,

Corynebacterium, Micrococcus, Mycobacterium,

Propionibacterium

Phylum Chlamydiae

Small phylum containing the genus Chlamydia

Phylum Spirochaetes

Characterized by flexible, helical cells with a modified

outer membrane (the outer sheath) and modified

flagella (axial filaments) located within the outer

sheath

Phylum Spirochaetes

Important pathogenic genera include Treponema,

Borrelia, and Leptospira

Phylum Bacteroidetes

Includes genera Bacteroides, Flavobacterium, Flexibacter, and Cytophaga;

Flexibacter and Cytophaga

are motile by means of “gliding motility”

Carl Linnaeus

He developed his naming system in the

middle 1700’s, which essentially the same

one we use today

Yersinia pestis

causative agent of plague

Biochemical tests

-probe for specific enzyme activities:

Serological Tests

Use group specific antiserum isolated from the

plasma of animals that have been sensitized to the

organism

G + C content

Estimated by determining the melting

temperature of the DNA

Nucleic acid hybridization

mixing ssDNA from two different species and

determining the percentage of the DNA that can

form dsDNA hybrids

Phage Typing

Determining a strains susceptability to certain phage or bacterial

viruses

Flow Cytometry

Uses differences in electrical conductivity between species