An Overview of Microbial Life

1. An Overview of Microbial Life Chapter 2

2. Elements of Cell and Viral Structures: • 3 Domains: Archae, Eubacteria, Eukaryota • Two structural types of cells are recognized: the prokaryote and the eukaryote. • Prokaryotic cells have a simpler internal structure than eukaryotic cells, lacking membrane-enclosed organelles. • Viruses: • Viruses are not cells but depend on cells for their replication.

3. Cells from each domain Eukarya Bacteria Archae

4. The basic components.. • All microbial cells share certain basic structures in common, such as cytoplasm, a cytoplasmic membrane, ribosomes, and (usually) a cell wall. • Note: Animal cells typically do not have a cell wall • The major components dissolved in the cytoplasm include • Macromolecules • Inorganic ions

5. Eukaryotic Cells • Larger and structurally more complex • Euk. microorganisms include algae, fungi and protozoa • Membrane enclosed organelles • Nucleus • Mitochondria • Chloroplasts (photosynthetic cells only)

6. Prokaryotic Cells • Lack membrane enclosed organelles • Include Bacteria and Archae • Smaller than eukaryotic cells (Typically ~1-5 um long and ~1um in width) • However, can vary greatly in size

7. Viruses • Not cells • Static structures which rely on cells for replication and biosynthetic machinery • Many cause disease and can have profound effects on the cells they infect • Cancer, HIV • However, can alter genetic material and improve the cell

9. Arrangement of DNA in Microbial Cells • Genes govern the properties of cells, and a cell's complement of genes is called its genome. • DNA is arranged in cells to form chromosomes. • In prokaryotes, there is usually a single circular chromosome; whereas in eukaryotes, several linear chromosomes exist.

10. Nucleus vs. Nucleoid • Nucleus: a membrane-enclosed structure that contains the chromosomes in eukaryotic cells. • Nucleoid: aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea

12. Prokaryotic DNA • Most DNA is circular • Most have only a single chromosome • Single copy of genes • Haploid • Many also contain plasmids

13. Plasmids • Plasmids are circular extrachromosomal genetic elements (DNA), nonessential for growth, found in prokaryotes. • Typically contain genes that confer special properties (ie unique metabolic properties) • Useful in biotechnology

15. Eukaryotic DNA • Organized into linear molecules • Packaged into chromosomes • Number varies • Typically contain two copies of each gene • Diploid

16. Genes, genomes, and proteins • E.coli genome= a single circular chromosome of 4.68 million base pairs • # of genes: 4,300 • A single cell contains: • 1,900 different proteins • 2.4 million protein molecules • Abundance of proteins varies

17. Genome size, complexity, and the C-value paradox • Genome size does not necessarily correlate with organismal complexity

18. In actuality….

19. The Tree of Life • Evolution: change in allelic frequencies over generations • The evolutionary relationships between life forms are the subject of the science of phylogeny. • Phylogenetic relationships are deduced by comparing ribosomal sequences

21. The three domains of life • Comparative ribosomal RNA sequencing has defined the three domains of life: Bacteria, Archaea, and Eukarya.

22. What has this sequencing revealed?? • Molecular sequencing has shown that the major organelles of Eukarya have evolutionary roots in the Bacteria • Mitochondria and chloroplasts were once free-living cells that established stable residency in cells of Eukarya eons ago. • The process by which this stable arrangement developed is known as endosymbiosis.

23. What has this sequencing revealed?? Cont. • Although species of Bacteria and Archaea share a prokaryotic cell structure, they differ dramatically in their evolutionary history. • Archae are more closely related to eukaryotes than are species of bacteria

24. Molecular sequencing and microbiology • Overall rRNA sequencing technology has helped reveal the overall evolutionary connections between all cells • In particular prokaryotes • Impacted subdispiciplines • Microbial classification and ecology • Clinical diagnostics • Can identify organisms without having to culture them

25. Microbial Diversity • Cell size and morphology • Metabolic strategies (physiology) • Motility • Mechanisms of cell division • Pathogenesis • Developmental biology • Adaptation to environmental extremes • And many more

26. Physiological Diversity of Microorganisms • All cells need carbon and energy sources • Energy can be obtained in 3 ways: • Organic chemicals • Inorganic chemicals • Light • Types of physiological diversity: • Chemoorganotrophs • Chemolithotrophs • Phototrophs • Heterotrophs and Autotrophs • Habitats and Extreme environments

28. Chemoorganotrophs • Chemoorganotrophs obtain their energy from the oxidation of organic compounds. • Energy conserved as ATP • All natural and even synthetic organic compounds can be used as an energy source • Aerobes • Anaerobes • Most microorganisms that have been cultured are chemoorganotrophs

29. Chemolithotrophs • Chemolithotrophs obtain their energy from the oxidation of inorganic compounds. • Found only in prokaryotes • Can use a broad spectrum of inorganic compounds • Advantageous because can utilize waste products of chemoorganotrophs

30. Phototrophs • Phototrophs contain pigments that allow them to use light as an energy source. • ATP generated from light energy • Cells are colored • Oxygenic photosynthesis: • O2 involved • Cyanobacteria and relatives • Anoxygenic photosynthesis: • No O2 • Purple and green bacteria

31. Autotrophs and Heterotrophs • All cells require carbon as a major nutrient • Microbial cells are either: • Autotrophs use carbon dioxide as their carbon source, whereas heterotrophs use organic carbon from one or more organic compounds. • Autotrophs considered primary producers • Synthesize organic matter from CO2 for themselves and that of chemoorganotrophs • All organic matter on earth has been synthesized from primary producers

32. Habitats and Extreme Environments • Microorganisms are everywhere on Earth that can support life • Extremophiles: organisms inhabiting extreme environments • Boiling hot springs, • Within ice, extreme pH, salinity, pressure

33. Examples of Extremophiles:

34. Prokaryotic Diversity • Several lineages are present in the domains Bacteria and Archaea • An enormous diversity of cell morphologies and physiologies are represented • rRNA analysis has shown dramatic differences in phenotypic characteristics within a given phylogenetic group

35. Bacteria

36. Proteobacteria • The Proteobacteria is the largest division (called a phylum) of Bacteria • A major lineage of bacteria that contains a large number of gram(-) rods and cocci • Represent majority of known gram(-) medical, industrial, and agricultural bacteria of significance • Extreme metabolic diversity: • Chemorganotrophs: E.coli • Photoautotrophs: Purple sulfur bacterium • Chemolithotrophs: Pseudomonas, Aztobacter • Pathogens: Salmonella, Rickettsia, Neisseria

37. Proteobacteria examples Chemolithotrophic sulfur-oxidizing bacteria Achromatium Neisseria gonorrhoeae

38. Gram-positive bacteria • United by a common cell wall structure • Examples: • Spore forming: • Clostridium, Bacillus • Antibiotic producing: • Streptomyces • Lactic acid bacteria: • Streptococcus • Lactobacillus • Mycoplasmas: • Lack cell wall • Small genomes • Often pathogenic

39. Cyanobacteria • The Cyanobacteria are phylogenetic relatives of gram-positive bacteria and are oxygenic phototrophs. • First oxygenic phototrophs to have evolved on Earth

40. Planctomyces • Characterized by distinct cells with stalks that allow for attachment to solid surfaces • Aquatic

41. Spirochetes • Helical shaped • Morphologically and phylogenetically distinct • Widespread in nature and some cause disease • Most notable sp cause Syphilis and Lyme Disease Spirochaeta zuelzerae

42. Green sulfur and non-sulfur bacteria • Contain similar photosynthetic pigments • Can grow as autotrophs • Chloroflexus • Inhabits hot springs and shallow marine bays • Dominant organism in stratified microbial mats • Important link in the evolution of photosynthesis

43. Chlamydia • Most species are pathogens • Obligate intracellular parasites • How would this affect an immune response?

44. Deinococcus • Contain sp with unusual cell walls and high level of resistance to radiation • Cells usually exist in pairs or tetrads • Can reassemble its chromosome after high radiation

45. Aquifex, Thermotoga, Env-OP2 • Sp that branch early on the tree • Unified in that they grow at very high temps: hyperthermophily • Inhabitats of hot springs

46. Archaea • There are two lineages of Archaea: the Euryarchaeota and the Crenarchaeota • Many are extremophiles • All are chemotrophic • Many using organic carbon • While others are chemolithotrophs

47. Euryarchaeota & Crenarchaeota • Physiologically diverse groups • Many inhabit extreme environments • From extreme pH, temperature, salinity

48. Limitations of Phylogenetic analyses • Not all Archaea are extremophiles • Difficult to culture • Based on molecular microbial ecology, the extent of diversity is much greater than once thought

49. Eukaryotic Microorganisms • Collectively, microbial eukaryotes are known as the Protista. • Microbial eukaryotes are a diverse group that includes algae, protozoa, fungi, and slime molds • Cells of algae and fungi have cell walls, whereas the protozoa do not. • The “early-branching” Eukarya are structurally simple eukaryotes lacking mitochondria and other organelles • Ex Giardia

50. Eukaryotic microbial diversity