Bacteria and Archaea: Prokaryotes Up Close

Small but mighty

Prokaryotes such as bacteria are the earliest known life on Earth, and bacteria are still the most numerous organisms. They turn dead leaves into soil, fix nitrogen for crops, make yogurt and cheese, and live by the trillions in your gut. A small number cause disease. Archaea, their look-alike prokaryotic cousins, live everywhere from hot springs to Ontario wetlands to your intestines.

In this lesson you will learn how microbiologists identify and classify these prokaryotes, and why they matter.

Identifying bacteria: shape and arrangement

Under a microscope, bacteria have three basic shapes:

• cocci (singular coccus): spheres;
• bacilli (singular bacillus): rods;
• spirilla (singular spirillum): spirals. Thin, flexible spirals are called spirochetes.

After dividing, some stay stuck together, giving arrangements. The prefix tells you the arrangement:

• diplo- = pairs; strepto- = chains; staphylo- = grape-like clusters.

That is how Streptococcus (chains of spheres) and Staphylococcus (clusters of spheres) got their names.

Identifying bacteria: the Gram stain

In 1884 the Danish scientist Hans Christian Gram developed a stain that is still the first test used on unknown bacteria. Cells are stained with purple crystal violet, treated with iodine, rinsed with alcohol, then stained with pink safranin.

• Gram-positive bacteria have a thick peptidoglycan wall that traps the violet dye. They look purple.
• Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane. The alcohol washes the violet out, and they pick up the safranin. They look pink.

This matters in medicine: the outer membrane of Gram-negative bacteria blocks some antibiotics, so the Gram result helps doctors choose treatment.

How bacteria live

Getting energy and carbon:

• Photoautotrophs use light. Cyanobacteria carry out photosynthesis that releases oxygen.
• Chemoautotrophs get energy from inorganic chemicals. Nitrifying bacteria in soil turn ammonium into nitrate that plants can use.
• Heterotrophs use organic food. Most are decomposers; some are parasites that feed on living hosts.

Oxygen:

• Obligate aerobes need oxygen.
• Obligate anaerobes are killed by it. Clostridium botulinum, which can grow in badly home-canned food, is one.
• Facultative anaerobes use oxygen when they can but survive without it, like E. coli.

Reproduction: bacteria reproduce asexually by binary fission. In ideal conditions E. coli can divide about every 20 minutes. Some, such as Bacillus and Clostridium, form endospores that survive boiling and drying for years.

Sharing genes without sex

Binary fission makes clones, but bacteria still gain new genes in three ways:

1. Conjugation: one bacterium passes a copy of a plasmid to another through a connecting pilus.
2. Transformation: a bacterium picks up loose DNA released by dead cells.
3. Transduction: a bacteriophage accidentally carries bacterial DNA from one cell to the next.

Plasmids often carry antibiotic resistance genes, so these processes help resistance spread quickly. You will study antibiotic resistance as natural selection in the Evolution unit.

Bacteria in our world

• Ecosystems: decomposers recycle nutrients. Rhizobium bacteria live in root nodules of legumes (peas, beans, clover) and fix nitrogen gas into forms plants can use.
• Food: yogurt, cheese, sauerkraut and kimchi are made with bacteria.
• Medicine and industry: since the 1980s, genetically modified bacteria have produced human insulin for people with diabetes. Many antibiotics come from soil bacteria called Streptomyces.
• Disease: a minority are pathogens: Streptococcus pyogenes (strep throat), Mycobacterium tuberculosis (tuberculosis) and Borrelia burgdorferi, the spirochete that causes Lyme disease and is spread by blacklegged ticks in parts of Ontario.

Archaea

Archaea look like bacteria, but their chemistry is different: no peptidoglycan in their cell walls, unusual membrane lipids, and some genes and enzymes that are more like ours. Main groups include:

• Methanogens produce methane. They live in wetlands, lake mud, the stomachs of cows and moose, and the human gut. Their methane is an important greenhouse gas.
• Extreme halophiles ("salt lovers") live in very salty water such as salt lakes and salt evaporation ponds, where they can turn the water pink.
• Thermoacidophiles thrive in hot, acidic springs.

Archaea were first noticed in extreme places, but DNA sampling shows they are common in oceans and soils too. No archaea are known to cause disease in humans.