SYSTEMATICS

Taxonomy Classification Identification Nomenclature

Definition of Systematics
Scientific study of the kinds and diversity of organisms and of any and all relationships among them Includes
Classification or Taxonomy Identification Nomenclature

Definitions
Taxonomy
Science of classification, description and naming of microorganisms

Classification
Assignment into groups There is no absolute rule for designing a classification; can classify things by any criterion of choice

Taxonomy
Concerned with
What belongs where? Arrangement into groups Evolution

Two types
Phenetic taxonomy Phylogenetic taxonomy

Taxonomy contd
Phenetic Taxonomy
Based on mutual similarity of phenotypic characteristics Approach is Numerical taxonomy (taxometrics)

Phylogenetic Taxonomy
Based on shared evolutionary heritage Classification based on evolutionary history is considered as a natural system

Terminologies
Strain
Descended from a single organism Non-taxonomic category

Type strain
First strain isolated or best characterised Kept in collections freeze-dried

Species
Organisms that can reproduce Defined by similarities e.g. biochemical reaction, chemical composition etc

Terminologies contd
Taxon/Taxa
Group or category of related organisms Examples: species, genus, kingdom Membership become increasingly inclusive as taxa become larger Members are more similar to each other in lower taxa Membership is dynamic due to changes in knowledge and evolutionary relationships

Terminologies contd
Binomial nomenclature
Applied to organisms except viruses Employs names of 2 lower level taxa, i.e. genus and species

Taxonomic Ranks
The hierachial organisation of the classification system is as follows
Domain (not widely used) Kingdom Phylum Class Order Family (ends with aceae) Genus Species

Non-taxonomic ranks
Subspecies
Variants within species

Biovar/Biovariety
Have special and consistent biochemical or physiologic properties

Serovars/serovariety
Have different antigenic properties

Classification
Originally 2 kingdoms: Animalia & Plantae (Linnaeus work) Anton van Leewenhoeks discovery, a 3rd kingdom Protista was proposed for all singlecelled organisms In 1969, a five-kingdom system based on three modes of nutrition
Ingestion of food, food production via photosynthesis, absorb food in a liquid form The other 2 kingdoms include organisms without complex structures, separated based on their cell types

Five Kingdom system (1969)

Plantae Fungi Animalia Protista (Unicellular eukaryotes) Monera (Procaryotes)

Kingdom Monera
These are categorised phenotypically rather than by evolutionary distinctions
Eubacteria Cyanobacteria Archaeobacteria

Kingdom Protista
Unicellular, some multicellular More or less aquatic Eukaryotic

Kingdom Fungi
Non-aquatic but the Chytrids are aquatic Eukaryotic

The Three-Domain System

Established by Carl Woese Accepted in late 1980s or early 1990s Domain is a category above the Kingdom or supercedes the kingdom Domain? Super Kingdom?
Archaea Eubacteria/Procaryota Eucaryota

Classification systems
Phenetic
Assess phenotypic similarity

Phylogenetic
Assess evolutionary relationships Involves use of Chronometers

Linnaean taxonomy
Method of classifying living things, originally devised by (and named for) Carolus Linnaeus His groupings were based upon shared physical characteristics The greatest innovation and still the most important aspect, is the general use of binomial nomenclature Use of a genus name and a single specific epithet to uniquely identify each species of organism

Phenetic taxonomy
Phenetics/ numerical taxonomy or taximetrics Classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation Phenetic analyses do not distinguish between plesiomorphies and apomorphies - traits that evolved anew in one or several lineages Liable to be misled by convergent evolution and adaptive variation

Phenetic taxonomy contd

Can be superior to cladistics when only the distinctness of related taxa is important But, when evolutionary history of taxa is needed for a study, cladistic methods are better It is exclusively based on cluster analysis and neighbor joining to best-fit numerical equations that characterize all measurable quantities of a number of organisms

Phylogenetic taxonomy
Study of evolutionary relatedness among various groups of organisms discovered through molecular sequencing data Refers to how characters arose but not to their present properties In phylogenetic taxonomy, cladistic taxonomy or cladism, organisms are classified into "clades", which are discovered by grouping taxa using derived traits The evolutionary connections between organisms are represented graphically through phylogenetic trees Molecular data, which includes protein and DNA sequences, are used to construct phylogenetic trees

Molecular Phylogeny
Simpler morphologies and physiologies in prokaryotes than those of eukaryotes But a large amount of information in the molecular sequences of bacterial DNA, RNAs and proteins exist Hence molecular similarities are used to infer the relationships of genes, and, by extension, the relationships of the organisms themselves is established

DNA-DNA Hybridization
Important technique for comparing prokaryotes at the molecular level The genomic DNA from one species is mixed with the DNA from a second species Extent to which strands of DNA from one organism anneal with strands of DNA from the other organism reflect levels of similarity

DNA-DNA Hybridization
The sensitivity of DNA-DNA hybridization declines rapidly as the organisms become more divergent Method limited to characterization of closely related strains, species and genera Testing the relationships of a new organism can require many hybridizations If no close relative is found by this test, then its identity cannot be established Gives a measure of relatedness across the whole genome

Phylogenies Based on Specific Genes

By DNA-DNA hybridization the average similarity falls off rapidly when looking at more diverged species In principle, the range accessible to molecular analysis could be increased by looking at specific genes with above average conservation Such are used as molecular clocks for reconstructing phylogenies There are several important requirements if we wish to use a gene phylogeny to infer organismal relationships

Criteria for Gene phylogeny -1

The gene must be present in all organisms of interest
Thus, to infer relationships that span the diversity of prokaryotes (or life), we must look at the central (universal) cellular functions Examples include genes whose products function in replication, transcription, or translation-the processes constituting the "Central Dogma" of molecular biology.

Criteria for Gene phylogeny -2

The gene cannot be subject to transfer between species (no lateral transfer)
If a gene is transferred, then the gene history is not the same as the organismal history If a gene performs a central function, an organism is unlikely to acquire a copy by lateral transfer, since the organism must already have a functional copy to be alive Plasmids are not suitable

Criteria for Gene phylogeny -3

The gene must display an appropriate level of sequence conservation for the divergences of interest
If there is too much change, then the sequences become randomized, and there is a limit to the depth of the divergences that can be accurately inferred If there is too little change (if the gene is too conserved), then there may be little or no change between the evolutionary branchings of interest, and it will not be possible to infer close (genus or species level) relationships

Criteria for Gene phylogeny -4

The gene must be sufficiently large to contain a record of the historical information
Although transfer RNA (tRNA) genes are present in all species, they are too small (about 75 nucleotides) to provide an accurate sample of evolutionary history

Ribosomal RNA Genes

Genes conserved through the billions of years of evolutionary divergence are used to establish diversity of known life, such as
Genes that define the ribosomal RNAs (rRNAs)

Most prokaryotes have three rRNAs, called the 5S, 16S and 23S rRNA The 5S has been extensively studied, but it is usually too small for reliable phylogenetic inference The 16S and 23S rRNAs are sufficiently large to be quite useful By comparing the inferred rRNA sequences (or those of any other appropriate molecule) it is possible to estimate the historical branching order of the species, and also the total amount of sequence change

A 16S rRNA-based phylogenetic tree showing the three (identified) Domains of life-Bacteria, Archaea & Eucarya

Identification
Classification requires knowledge on the characteristics of the organism Identification helps to know the characteristics of unknown and allocating it to a defined taxon A diverse range of phenetic characters are determined and compared to appropriate database containing information of known taxa

Numerical taxonomy
Computer assisted classification Groups are based on shared characteristics Assessment of likelihood of MOs matching a specific taxon Require large databanks, information storage & retrieval systems

Molecular Systematics
More modern Taxonomic information is derived from analysis of DNA, the structure and analysis of RNA

Basing on DNA
Hybridisation

G+C%

DNA

Sequences

Restriction analysis

Basing on RNA
Structures

DNA

RNA

Probes

Sequences

Chemosystematics
Information from whole organism is used to classify & identify Relevant techniques include
Protein electrophoresis Cell wall composition Cell membrane composition
Phospholipids, glycolipids, LPS, quinones, cytochromes

Fatty acid profiles Whole organism fingerprinting

Pyrolysis, mass chromatography or spectroscopy, IR spectroscopy

Serology

Numerical analysis of taxonomic data

Hierachical and non-hierachical grouping techniques Hierachical
End product is a hierachical presentation of grouping results in form of a dendrogram

Non-hierachical
Partitioning into groups
Principal component analysis Based on binary or numerical data

Dendrogram
Is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm (see cluster analysis). Dendrograms are often used in computational biology to illustrate the clustering of genes

 A tree diagram frequently used to illustrate the arrangement of the clusters produced by hierarchical clustering Often used in computational biology to illustrate the clustering of genes or any molecule analysed

A dendrogram

POLYPHASIC TAXONOMY
Refers to a taxonomy that assembles and assimilates many levels of information, from molecular to ecological Aims at utilizing all the available data in delineating consensus groups to get a decisive final conclusion Both genotypic and phenotypic information is incorporated

 Total DNA (include Plasmid DNA)

Mol % G+C Restriction patterns (RFLP, PFGE) Genome size DNA-DNA hybridisation

Genotypic Information: DNA

DNA Segments
PCR based DNA fingerprinting (Ribotyping, ARDRA, RAPD, AFLP, AP-PCR, rep-PCR) DNA probes DNA sequencing

Some commonly used terms

ARDRA- amplified rDNA restriction analysis RAPD Random amplification of polymorphic DNA AFLP Amplified length Polymorphism AP-PCR arbitrarily primed PCR rep-PCR PCR using naturally occurring repetitive sequences RFLP Restriction fragment length polymorphism PFGE Pulsed Field Gel electrophoresis

Genotypic Information: RNA

RNA sequencing
23S, 16S, 5S, tRNA

LMW RNA profiles

Proteins
Electrophoretic patterns of total cellular or cell envelope proteins (One or two dimentional) Enzyme patterns (mulitlocus enzyme electrophoresis)

Phenotypic: Chemotaxonomic Markers

Cellular fatty acids (FAMEs) Mycolic acids Polar lipis Quinones Polyamines Cellwall compounds Exopolysaccharides

Phenotypic: Expressed Features

Morphology Physiology (Biological, API) Enzymology (APIZYM) Serology (monoclonal, polyclonal)

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2. 3. 4. 5. 6. 7. 8.

Assignments/Seminar topics? Physical and chemical manipulation of the

structural components of viruses Microbial macromolecule identification techniques Methods of cell fractionation Physical, chemical and enzymatic methods used in the study of microbial metabolism* Classification of viruses Classification of fungi Classification of bacteria Taxonomy (interrelating different taxa) of bacteria/fungi*