Lecture 2 Overview of Microbial Diversity Prokaryotic and Eukaryotic Cells Taxonomy and Nomenclature...
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Transcript of Lecture 2 Overview of Microbial Diversity Prokaryotic and Eukaryotic Cells Taxonomy and Nomenclature...
Lecture 2
Overview of Microbial DiversityProkaryotic 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
• Acellular• Size in nm range• No metabolic activity on their own• Require a host cell for replication
– Eukaryotes– Prokaryotes
Prokaryotic Cell
• Simpler internal structure than eukaryotic cells
• No nucleus, instead freely accessible DNA (nucleoid)
• No membrane-enclosed organelles
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.
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)
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.
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
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.
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).
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
• Domain HIGH Hierarchy• Phylum• Class• Order• Family• Genus• Species 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