B acteria and Archaea : T he Prokaryotes

1. Bacteria and Archaea: The Prokaryotes http://www.mhhe.com/biosci/genbio/raven6b/graphics/raven06b/other/ch04.pdf

2. Kingdom Eubacteria • Diverse kingdom of unicellular prokaryotes • no membrane bound organelles • Contains mostly mesophiles and neutrophiles • Encompasses 21+ phyla, and includes gram positive, gram negative, and proteobacteria. • “Eu” bacteria = “true” bacteria • http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter21/study_outline.html • http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter22/study_outline.html • http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter23/study_outline.html • http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter24/study_outline.html • http://kdhellner.tripod.com/id2.html

3. Eubacteria Phyla • Gram positive: Includes three phyla with notable genera such as the Mycoplasma(stains negative but is structurally positive), UreaplasmaandStreptomyces, Phytoplasma. • Gram negative: Includes many phyla such as Spirochaeteswhich are a phylum of double-membranebacteria, most of which have long, helically coiled cells. • Leptospiraspecies, which causes leptospirosis (field fever) • Borreliaburgdorferi, B. garinii, and B. afzelii, which cause Lyme disease • Borreliarecurrentis, which causes relapsing fever • Treponemapallidumsubspecies which cause treponematoses such as syphilis and yaws. • Proteobacteria: Includes many phyla which are all gram negative. They include a wide variety of pathogensgenre such as Escherichia (E. coli), Salmonella, Vibrio (V. cholerae), and Helicobacter (H. pylori).  Others are free-living (non-parasitic) bacteria that are called purple bacteria, referring to their mostly reddish pigmentation, they use photosynthesis to obtain energy. • Cyanobacteria: is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria. They are often called blue-green algae.

4. Kingdom Archaea • “archae” bacteria= “ancient” bacteria • Contains most of the “extremophiles” • Prokaryotes- no membrane bound organelles • Encompasses 5 phyla, and includes the methanogens and extreme halophiles and thermophiles. • Until 1977 archaea were classified as bacteria. Comparative molecular biology studies gave new evidence for reclassification as a separate domain and kingdom. • http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter20/study_outline.html • http://plantphys.info/organismal/lechtml/archaea.shtml • http://kdhellner.tripod.com/id15.html

5. Archaea Phyla • Methanogens: are microorganisms that produce methane as a metabolic byproduct. Methanogens are usually coccoidor bacilli. https://www.sciencenews.org/blog/science-ticker/microbes-indicted-ancient-mass-extinction • Halophiles: Halophiles are organisms that live in high salt concentrations. The fermentation of salty foods often involves halobacteria, as either essential ingredients or accidental contaminants. One example is Chromohalobacterbeijerinckii, found in salted beans preserved in brine and in salted herring. Tetragenococcushalophilusis found in salted anchovies and soy sauce. • Thermophiles Live in extreme temperatures such as those found in geothermal vents. http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/archaea

6. Evolution • Some scientific evidence shows that archaea are genetically more closely related to eukaryotes than eubacteria. • Eubacteria could not have survived in early Earth conditions. • The fossil record doesn’t give a clear picture as to when the distinction between archaea and eubacteria evolved but we do know that fossils of “bacteria” like organisms are found in rock formations that are about 3.5 billion years old and fossils of the earliest “eukaryote” like organisms are seen in rock formations that are around 1.5-2.1 billion years old (Smithsonian). • Therefore we can only hypothesize that archaea and eubacteria share a common ancestor and that ancestor evolved into two distinct lineages. One lineage continued to evolve and became eubacteria, the other lineage became archaea which over time evolved further to split in the eukaryote lineage.

7. Environment • Bacteria live in standard terrestrial or marine environments. • The majority of eubacteria are mesophiles live in standard temperature ranges 20-45C. Some thermophilic eubacteria exist and are believed to be the oldest eubacteria or the missing kink between the evolutionary branches. • The majority of eubacteria are neutrophiles and live in the standard pH range of 4-8. • The majority of eubacteria either require oxygen and are aerobic. • Archaea live in extreme terrestrial or marine environments. • The majority of archaea are extremophiles. • Acidophile An organism with optimal growth at pH levels of 3 or below • Alkaliphile An organism with optimal growth at pH levels of 9 or above • Anaerobe An organism that does not require oxygen for growth. • Cryptoendolith An organism that lives in microscopic spaces within rocks, such as pores between aggregate grains • .Halophile An organism requiring at least 0.2M concentrations of salt (NaCl) for growth • Hypolith An organism that lives underneath rocks in cold deserts • Metallotolerant capable of tolerating high levels of dissolved heavy metals in solution • Cryophile An organism capable of survival, growth or reproduction at temperatures of -15 °C or lower for extended periods • Radioresistant Organisms resistant to high levels of ionizing radiation, most commonly ultraviolet radiation, but also including organisms capable of resisting nuclear radiation • Thermophile An organism that can thrive at temperatures between 45–122 °C • XerophileA n organism that can grow in extremely dry, desiccating conditions

8. Morphology • Bacteria are classified into 5 groups according to their basic shapes: spherical (cocci), rod (bacilli), spiral (spirilla), comma (vibrios) or corkscrew (spirochaetes). They can exist as single cells, in pairs (diplo), chains (strepto) or clusters (Staphyo). • Eubacteria are usually between 1-5 microns in size. • Archaea are much smaller at usually less than 1 micron. • Some archaea have unusual shapes such as cubes and pyrimids but most archaea are either bacilli, cocci, or spirilla.

9. Cell Wall Composition • Cell wall composition is determined by Gram staining, which uses a violet and a red stain to distinguish between wall types. • Violet/Iodine primary stain • Alcohol wash • Red counterstain • Gram positive (+) bacteria have a thick peptidoglycan cell wall that soaks up the violet stain giving them a violet appearance under the microscope. • Gram negative (-) bacteria have a thinner peptidoglycan wall that is surrounded by lipids. The alcohol wash removes the lipid layer as well as the violet dye, then the red counterstain stains the thin wall a red/pink. • Archaea do have have cell walls made of peptidoglycan. Their cell wall composition varies in types of glycans. Archaeathat stain as positive have a think cell wall made of glycan that is not peptidoglycan. Archaea that stain as gram negative have a thin cell wall, or no cell wall.

10. Metabolism • Most Eubacteria are heterotrophs- consume organic compounds for growth. • Chemoheterotrophs use inorganic compounds for energy. • Photoheterotrophs use light for energy. • Some Eubacteria are autotrophs that produce their own compounds for growth. • Photosynthetic bacteria such as Cyanobacteria are photoautotrophs, they use light as their energy source. • Chemoautotrophs use inorganic compounds for energy. • Most Archaea are autotrophs- the produce compounds for growth. • Chemoautotrophs- they use inorganic compounds like hydrogen sulfide and ammonia to create energy as well as producing their own compounds for growth. • Some evolutionary scientists believe that the first organisms to inhabit Earth were heterotroph which ate organic compounds from the environment and produced CO2. This allowed for the evolution of photoautotrophs which eat CO2 and produce oxygen. “The Heterotroph Hypothesis”

11. Growth and Reproduction • Both bacteria and archaea reproduce asexually through binary fission. • Both bacteria and archaea perform conjugation- a genetic exchange through a pilus link. • Some eubacteria and NOT archaea have the ability to form spores, called endospores, when environmental conditions are unfavorable. This allows them to survive until conditions are more hospitable and the endospores can germinate.