Chapter 1

Microbial Life: Origin and Discovery

What Is a Microbe? Microbes are microscopic organisms

Through most of its lifespanCan only be seen through a microscope

mm (10-3 m) to 0.2 μm (2x10-7 m)

Usually single-celledSelf-contained genome

Capacity to reproduce

What Is a Microbe? Exceptions exist1. Super-sized microbial cells

Thiomargarita namibiensis

“sulfur pearl of Namibia” Caulerpa taxifolia

“killer algae” with acres of single cell

2. Microbial communitiesmulticellular assemblages: biofilm, mushrooms

microscopic worms and arthropods NOT microbes

3. Living? viruses viroids prions

What Is a Microbe? 6 major groups studied by microbiologists

Prokaryotes Bacteria

Eukaryotes Algae

Viruses

Archaea

Protists Fungi

What Is a Microbe? Microbial genomes are easily sequenced

Genome = organism’s total genetic content Complete gene sequence known for many species

Over 1000 bacteria, archaea Tens of thousands of viruses First sequenced genomes

Bacteriophage ΦX174 (1977) Haemophilus influenzae (1995) Saccharomyces cerevisiae (1996)

Microbes have greatest diversity of genomes Important for understanding evolution Comparative genomics shows core genes

© 2008 W.W. Norton & Company, Inc. MICROBIOLOGY 1/e

Why study microorganisms?

Microbes Shape Human History Microbes affect food availability

Destroy crops, preserve food bread, wine, cheese Chocolate!

Microbial diseases change historyBlack plague in EuropeSmallpox in AmericasHIV/AIDS worldwide

Discovery of Microbes Light microscope invented in 1600s

Quality improved continuously

mid-1600s: Robert Hooke observes small eukaryotes (mold) Saw “cells” in cork

1676: Antoni van Leeuwenhoek discovers bacteria First to see single-celled microbes

Microbes Are Living Organisms Microbes arise only from other microbes

No spontaneous generation1688: Francesco Redi shows that maggots do

not spontaneously generate1861: Louis Pasteur shows that microbes do

not grow in liquid until introduced from outside

Contradiction by John Tyndall: Boiled broth still spoil Contaminated with endospores

Germ Theory of Disease Observations:

Germs can infect and grow on food. Hypothesis:

Can germs infect and grow on people? i.e. Do germs cause disease?

Hypothesis is testable:Are germs can be found in infected tissue?Can transmission of germs cause disease?

Germ Theory of Disease Pasteur’s Theory:

Transmission of germs causes disease All Scientific Theories:

Explain many known observations e.g. Transmission of rabies

Provide framework for understanding Where do diseases come from?

Can be tested further Do germs cause anthrax?

A scientific theory is NOT a “guess”

Koch’s Postulates Provides means of testing hypothesis:

“Does this germ cause that disease?” Organism must meet 4 criteria:

1. Microbe always present in diseased Absent in healthy

2. Microbe is grown in pure culture No other microbes present.

3. Introduce pure microbe into healthy individual Individual becomes sick

4. Same microbe re-isolated from now-sick individual

Corollary to Germ Theory Stop germ transmission, stop disease spread

Kill germ, prevent disease Antiseptics

1865: Antiseptic surgery Joseph Lister

Antibiotics 1929-1941: Penicillin

Alexander Fleming Many newer antibiotics Bacteria become resistant

Corollary to Germ Theory Stop germ transmission, stop disease spread

Stop spread of germs Epidemiology, public health measures

Resistant individuals prevent spread of germs 1798: Vaccination with cowpox prevents smallpox

Turkish physicians, Lady Montagu, Edward Jenner

Microbial Ecology Most microbes don’t grow on typical medium

Many live in varied conditions Anaerobic

bottom of swamp, in our gut

High pressure Bottom of ocean

Hot or cold temperatures Below 0°C to 113°C

No organic carbon Use light for energy, CO2 for carbon

Microbes existed before animals, plants Early earth contained mainly reduced compounds,

such as ferrous iron, methane, ammonia

Microbial Ecology Culture some microbes in

natural mud environmentWinogradsky column

Layers grow different species Reflects different conditions

Can see variations in nature Yellowstone geyser runoff

Colors reflect different species Different growth temperatures

<50°C

>56°C

Microbial Ecology Microbes cycle most elements on earth

Nitrogen cycle Bacteria fix N2 to NH4

+

Nitrify NH4+ to NO3

-

Carbon cycle Photosynthetic microbes

fix most carbon Many other conversions

Sulfur cyclePhosphorus cycle

The Microbial Family Tree Microbial species are difficult to classify

Difficult to distinguish by shapeOften reproduce asexuallyPass DNA to each other without reproduction

Use biochemical properties to classifyGram stainAbility to metabolize different substrates

Use DNA sequence to classifyBacterial genomes relatively small

The Microbial Family Tree Archaea are not bacteria

Similar size, shapeVery different biochemistry

Different membranes Archaeal ribosomes similar to eukaryotic

ribosomes Many archaea live in harsh environments

16s rRNA gene sequence Found in all creatures Archaea is a separate domain

Endosymbiont Theory How did eukaryotes arise?

DNA similar to archaea’s Mitochondrial, chloroplast DNA

Similar to bacterial DNA Endosymbiont theory:

Mitochondria WERE bacteriaChloroplasts WERE cyanobacteria Infected or eaten by other speciesEnded up living together inside

Endo-sym-biosis

Cell Biology Techniques Electron microscopy

Observation of cell components Eukaryotic organelles Membranes

UltracentrifugeSeparation of cell components

Study of biochemistry of organelles

Fluorescence microscopy Identification of cell components

Subcellular location of individual proteins

Genetics and DNA Revolution Molecular genetics depends on bacteria

Concept of “gene” proposed for bacteriaDNA structureGenetic codeTranscription, translationRestriction enzymesRecombinant DNACloningPCR reactionE. coli has best understood genome