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Introductory comments

• The syllabus
• The lectures
• The exams
• The labs

What is microbial diversity?

Morphological diversity

• Although most people think of Bacteria as rods, cocci & spirals, they come in all shapes & sizes, including filaments, branched filaments, amorphous (irregular), pleomorphic (different shapes under different conditions, or even in the same culture), star-shaped, stalked, lumpy cocci, etc. Haloarcula is shaped like a bathroom tile!
• Cells can be organized into multicellular arrangements, from simple pairs & tetrads to filaments, sheets, rosettes, and true multicellular organisms. Many species form highly structured multi-species mats that resemble the tissues of animals and plants that carry out complex biochemical transformations.
• Most Bacteria & Archaea are 1-5 microns in size, but they range from 0.1 to 660 microns per cell! At the low end, it is hard to understand how everything that's needed for life could fit into the cell. At the high end, they can be easily seen without a microscope.

Structural diversity

• Most Bacteria have either a Gram-positive (single membrane, thick cell wall) or Gram-negative (double membrane, thin cell wall) cell envelop. There is a variety of cell wall types in the Archaea.
• There are a wide range of external structures: flagella, pili, holdfasts, stalks, buds, capsules, and sheaths, etc.
• There are also a wide variety of internal structures such as spores, daughter cells, thylakoids, mesosomes, & nucleoid. In fact, microbial cells are just as organized, & diverse, as eukaryotic cells.

Metabolic diversity

• Chemoheterotrophs - both carbon & energy are obtained from organic compounds. Saprophytes and pathogenic microbes are examples of this group.
• Chemoautotrophs - Cell carbon is obtained by fixing CO2. Energy is obtained from inorganic sources such as sulfur or nitrogen compounds, iron, hydrogen, etc. These organisms don't need organic compounds for either energy or cell carbon. Sulfur-oxidizing bacteria and methane-producing Archaea are examples of this group.
• Photoheterotrophs - Cell carbon is obtained from organic compounds, but energy is taken from light. Halophilic Archaea and most purple photosynthetic bacteria are examples of this group.
• Photoautotrophs (photosynthetic) - Cell carbon is obtained by fixing CO2. Energy is from light. These organisms don't need organic compounds for either energy or cell carbon. Most cyanobacteria, some purple photosynthetic bacteria, and plants are examples of this group.

Ecological diversity

• Marine or freshwater - As diverse as laboratory distilled water to saturated brines like the Great Salt Lake or the Dead Sea.
• Temperature from -5C to 118C - Pyrodictium is grown in autoclaves!
• pH 0 to 11 - pH0 is 0.5M H2SO4!
• Symbiosis - inter and intra cellular with eukaryotes or other microbes, and complex communities such as microbial mats
• high to low - from the water droplets that make up clouds to deep underground water in various forms:
  • halophilic Archaea in microscopic brine pockets in subterranean salt domes
  • hydrogen utilizing Bacteria in deep crustal groundwater
  • methanogenic Archaea in oil deposits make natural gas!
  • deep sea hydrothermal vent organisms - a major ecosystem
• If there's liquid water, there's almost certainly something growing in it!

Behavioral diversity

• Motility & taxis - microbes get to where they want to be via phototaxis, chemotaxis, magnetotaxis, etc. Many open-water organisms have gas vacuoles used to adjust their depth in the water column.
• Various life & developmental cycles - e.g. sporulation, swarmer phases, etc. We'll talk quite a bit about these as the course progresses.
• Biochemical responses - microbes express the genes needed to compete for the resources that are available at that time.
• Communication between cells of the same & different species - symbiosis, mat formation, quorum sensing, etc.

Evolutionary diversity (genetic diversity)

• Far and away most of evolutionary diversity is microbial, not macroscopic - the macroscopic world is just the tip of the iceburg of life. Even most plants & animals are microscopic! So microbial diversity is really the same as biological diversity, with just a few of the most ponderous organisms overlooked.
• Evolutionary diversity is usually expressed in terms of trees - branched graphs that trace the geneologies of organisms. When these trees are based on genetic diversity, they can be quantitative and objective.

This is the diversity we'll be discussing in this course.

The fundamental similarity of all living things

But before spending the semester describing diversity, i.e. how organisms are different from one another, let's discuss the observation that all cells are fundamentally the same in almost every way. One way to look at this is by walking through the flow of information in the cell - i.e. the "Central Dogma":

• All cells encode information in the form of DNA
  

  The DNA in all cells is composed of the same 4 bases (G, A, T and C), the same sugar (D-ribose), assembled with the same chemical structure and steriochemistry. Information in DNA is stored using a universal 3-letter code (e.g. AAA=Lys in all cells), and DNA synthesis is handled the same in all organisms (the replication fork complexes are all pretty-much alike). The function of DNA is carried out via transcription into RNA, using RNA polymerases that are all essentially alike.
  

• RNA is used primarily to direct protein synthesis based on information in DNA
  

  RNA in all cells has the same structure - same 4 bases, sugar, steriochemistry, etc. Furthermore, all cells have the same types of RNAs, e.g. ribosomal RNA, transfer RNA, messenger RNA, etc. These RNAs are very much alike in sequence and structure in all cells; for example, the ribosomal RNAs in all organisms are greater than 50% identical in sequence, and 80% identical in secondary structure.
  

• Polypeptides (proteins) direct most of the cells catalysis and structure
  

  Proteins in all cells use the same 20 amino acids in the same stereochemical conformations, synthesized in the same way, and use the same post-translation modifications. Most of the reactions catalysed by these proteins are the same (see below) and the enzymes that carry them out are very-much alike in amino-acid sequence, 3-dimensional structure, and mechanism of action.
  

• With few exceptions, all cells use the same metabolic pathways:
  
  • the Krebs/TCA cycle
  • glycolysis (there is some variation in the details)
  • amino acid biosynthesis
  • purine and pyrimidine biosynthesis
  • lipid metabolism
  • electron transport
  • same cofactors, e.g. ATP, NAD
  • ATP synthesis via electron gradient
  • etc, etc, etc...
    
• All cells are bound by a lipoprotein membrane that strictly controls what goes in and what comes out of the cell. This generally defines the cell by separating inside & outside.

So, all cells are pretty-much alike. What does this mean?

1. All organisms share a common ancestry. In other words, all known organisms can trace their past back to a single origin of life. This might not have been; other lineages, if they ever existed, seem to be extinct (or perhaps unrecognized as living?).
   
2. The last common ancestor of all known living things was a complex organism - most of biochemical evolution predates this organism! The last common ancestor had all of the biochemistry that is now universal, which means nearly everything! Biochemical evolution occured very early in the emergence of life. The diversity in extant life (i.e. known modern life) is in peripheral biochemistry - just the details!

Questions for thought...

• What, exactly, do you mean when you mention diversity?
• How are organisms different from one another, and how would you measure objectively (or judge subjectively) how different two or more organisms are? Can you name two animals that are about as different from one another as, say, Escherichia coli and Proteus vulgaris?
• If you had isolated a new microbe, what properties would you examine to determine what kind of organisms it is? Would this tell you what it is related to evolutionarily?
• What metabolic pathways can you think of that are unique to specific groups of organisms?

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