1. Lecture 2 Overview of Microbial Diversity Prokaryotic and Eukaryotic Cells Taxonomy and Nomenclature
(Text Chapters: 2; 11)

2. 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

3. Viruses Acellular Size in nm range No metabolic activity on their own
Require a host cell for replication
Eukaryotes
Prokaryotes

4. Eukaryotic Cell

5. Prokaryotic Cell Simpler internal structure than eukaryotic cells
No nucleus, instead freely accessible DNA (nucleoid)
No membrane-enclosed organelles

6. The size comparison

7. 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

8. 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

9. 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.

10. 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.

12. 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.

13. Metabolic options for obtaining energy

14. Microbial Diversity : Diverse Carbon Sources
Autotrophs use carbon dioxide
Heterotrophs use organic carbon

15. Microbial Diversity : Habitats and Extrem Environments
Thrive under environmental conditions in which higher organisms cannot survive
Temperature pH
Pressure
Salt(NaCl)

16. “Extremophiles”

17. 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.

18. Detailed Phylogenetic Tree of Bacteria

19. 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

20. Filamentous Cyanobacteria

21. Prokaryotic Archaea Diversity
Two main lineages of Archaea
Euryarchaeota
Crenarchaeota
hyperthermophils

22. Eukaryotic Microorganisms
Microbial eukaryotes are a diverse group that includes algae, protozoa, fungi, and slime molds.

23. 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.

24. 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.

25. 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.

28. 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.

29. 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.

30. The Universal Phylogenetic Tree

31. 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.

34. Classical Taxonomy
Conventional bacterial taxonomy places heavy emphasis on analyses of phenotypic properties of the organism (Table 11.4).

35. Identification of newly isolated enterics

36. 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.

37. Species Concept in Microbiology : Taxonomic Hierarchy
Domain HIGH Hierarchy
Phylum
Class
Order
Family
Genus
Species LOW Hierarchy

38. 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

39. Nomenclature
Following the binomial system of nomenclature used throughout biology, prokaryotes are given descriptive genus names and species epithets.
Escherichia coli
Staphylococcus aureus