Lecture 2 Overview of Microbial Diversity Prokaryotic and Eukaryotic Cells Taxonomy and Nomenclature

1. Lecture 2Overview of Microbial DiversityProkaryotic and Eukaryotic CellsTaxonomy 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