Transcript Lecture 1 Introduction, History and Microscopy

Lecture 2
Overview of Microbial Diversity
Prokaryotic and Eukaryotic Cells
Taxonomy and Nomenclature
(Text Chapters: 2; 11)
Cell Structure
• All microbial cells have certain basic
structures in common
– Cytoplasmic cell membrane
– Cytoplasm
– Ribosomes (protein synthesis)
• Most microbial cells have also a cell wall
• Two structural types of cells
– Differ in arrangement of genetic material
– Prokaryotes
– Eukaryotes
Viruses
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Acellular
Size in nm range
No metabolic activity on their own
Require a host cell for replication
– Eukaryotes
– Prokaryotes
Eukaryotic Cell
Prokaryotic Cell
• Simpler internal structure than eukaryotic cells
• No nucleus, instead freely accessible DNA (nucleoid)
• No membrane-enclosed organelles
The size comparison
Genetic Materials
• Genes : govern the properties of cells
• genome : cell's complement of genes
• Chromosomes : A structure that DNA is arranged
in the cells
• Prokaryotes: usually contains a single circular
chromosome (nucleoid)
• Eukaryotes: several linear chromosomes enclosed
in nucleus
• Plasmids
– circular extrachromosomal genetic elements (DNA)
– found in prokaryotes
– nonessential for growth
Ribosomes (From Gene to Protein)
• Molecule complex consisting of RNA (rRNA)
and proteins
• Site of translation and protein synthesis
• Small and large subunits
• Highly specific-species sequences found in
rRNA of the small subunit
The Tree of Life
• Evolution is the change in a line of descent over
time leading to new species or varieties.
• The evolutionary relationships between life forms
are the subject of the science of phylogeny.
The Tree of Life
• Comparative ribosomal RNA sequencing has
defined the three domains of life: Bacteria,
Archaea, and Eukarya.
• Molecular sequencing has also shown that the
major organelles of Eukarya have evolutionary
roots in the Bacteria and has yielded new tools for
microbial ecology and clinical microbiology.
• Although species of Bacteria and Archaea share a
prokaryotic cell structure, they differ dramatically
in their evolutionary history.
Microbial Diversity: Diverse Energy Sources
• All cells need energy and carbon sources.
• Chemoorganotrophs obtain their energy from the
oxidation of organic compounds.
• Chemolithotrophs obtain their energy from the
oxidation of inorganic compounds.
• Phototrophs contain pigments that allow them to
use light as an energy source.
Metabolic options for
obtaining energy
Microbial Diversity
: Diverse Carbon Sources
• Autotrophs use carbon dioxide
• Heterotrophs use organic carbon
Microbial Diversity
: Habitats and Extrem Environments
• Thrive under environmental conditions in
which higher organisms cannot survive
– Temperature
– pH
– Pressure
– Salt(NaCl)
“Extremophiles”
Prokaryotic Diversity
• Several lineages are present in the domains
Bacteria and Archaea, and an enormous diversity
of cell morphologies and physiologies are
represented there.
• Retrieval and analysis of ribosomal RNA genes
from cells in natural samples have shown that
many phylogenetically distinct but as yet
uncultured prokaryotes exist in nature.
Detailed Phylogenetic Tree of Bacteria
Prokaryotic Bacterial Diversity
• The Proteobacteria is the largest division
(called a phylum) of Bacteria
• The Cyanobacteria are phylogenetic relatives
of gram-positive bacteria and are oxygenic
phototrophs
Filamentous Cyanobacteria
Prokaryotic Archaea Diversity
• Two main lineages
of Archaea
– Euryarchaeota
– Crenarchaeota
hyperthermophils
Eukaryotic Microorganisms
• Microbial eukaryotes are a diverse group that
includes algae, protozoa, fungi, and slime molds.
Eukaryotic Microorganisms
• Collectively, microbial eukaryotes are known as
the Protista. Some protists, such as the algae,
are phototrophic.
• Cells of algae and fungi have cell walls,
whereas the protozoa do not.
• Some algae (or cyanobacteria) and fungi have
developed mutualistic associations called
lichens.
Origin of Life: First Microbes
• Planet Earth is approximately 4.6 billion years old
• First evidence for microbial life on rocks
(stromatolites) dates back about 3.86 billion years
• Stromatolites are fossilized microbial mats
consisting of layers of filamentous prokaryotes and
trapped sediment.
• By comparing ancient stromatolites with modern
stromatolites, it has been concluded that filamentous
phototrophic bacteria, perhaps relatives of the green
nonsulfur bacterium Chloroflexus, formed ancient
stromatolites.
Origin of Life: First Cells
• The first life forms may have been self-replicating
RNAs (RNA life).
– Catalytic and informational
• Eventually, DNA became the genetic repository of
cells.
• Then the three-part system—DNA, RNA, and
protein—became universal among cells.
Evolutionary Chronometers
• Certain genes and proteins are evolutionary
chronometers—measures of evolutionary change.
Comparisons of sequences of ribosomal RNA can be
used to determine the evolutionary relationships
among organisms.
• SSU (small subunit) RNA sequencing is
synonymous with 16S or 18S sequencing.
• Differences in nucleotide or amino acid sequence of
functionally similar (homologous) macromolecules
are a function of their evolutionary distance.
rRNA Sequencing
• Phylogenetic trees based on ribosomal RNA
have now been prepared for all the major
prokaryotic and eukaryotic groups.
• A huge database of rRNA sequences exists. For
example, the Ribosomal Database Project
(RDP) contains a large collection of such
sequences, now numbering over 100,000.
• The universal phylogenetic tree is the road
map of life.
The Universal Phylogenetic Tree
Three Domains
• Although the three domains of living organisms
were originally defined by ribosomal RNA
sequencing, subsequent studies have shown
that they differ in many other ways.
• Table 11.3 summarizes a number of other
phenotypic features, physiological and
otherwise, that can be used to differentiate
organisms at the domain level.
Classical Taxonomy
• Conventional bacterial taxonomy places heavy
emphasis on analyses of phenotypic properties
of the organism (Table 11.4).
Identification of newly isolated enterics
Species Concept in Microbiology
• The species concept applies to prokaryotes as
well as eukaryotes, and a similar taxonomic
hierarchy exists.
• Groups of genera (singular: genus) are collected
into families, families into orders, orders into
classes, classes into phyla (singular: phylum),
and phyla into the highest-level taxon, the
domain.
Species Concept in Microbiology
: Taxonomic Hierarchy
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Domain
Phylum
Class
Order
Family
Genus
Species
HIGH Hierarchy
LOW Hierarchy
Species Concept in Microbiology
: New Species
A prokaryote whose 16S ribosomal RNA
sequence differs by more than 3% from that of
all other organisms (that is, the sequence is
less than 97% identical to any other sequence
in the databases
Nomenclature
• Following the binomial system of nomenclature
used throughout biology, prokaryotes are given
descriptive genus names and species epithets.
– Escherichia coli
– Staphylococcus aureus