Lab 2 - Introduction to Bacteria and Archaea

textbook Ch 24

3 domains of life

• Bacteria, archaea, eukarya

• bacteria and archaea are prokaryotes, but they are not each others closest relatives (archaea and eukarya are sister taxa)

microbe

a microscopic organism (of any domain)

prokaryotic vs eukaryotic genome size

eukaryotic genome >> prokaryotic genome

two domain hypothesis

• the two domains are bacteria and archaea

• eukaryotes are a subgroup of archaea, are sister to some (but not all) archaea

3 common morphologies of bacteria and archaea

• coccus (spherical)

• bacillus (rod shaped)

• helical/spiral (elongated spiral)

how do most bacteria reproductive?

• asexually, by binary fission

• chromosome is replicated so that the daughter cell is genetically identical to the parent

what three components drive metabolism?

1. energy source: light (phototrophy) or chemical rxns (chemotrophy)

2. electron source: inorganic or organic compounds that act as oxidizers

3. carbon source: inorganic compounds (like CO2) or organic compounds (like sugars)

lithiotrophs vs organotrophs

• lithiotrophs: use inorganic electron donors like H₂S

• organotrophs: use organic electron donors like CH₄

autotrophs vs heterotrophs vs carbon fixers

• autotrophs: use inorganic carbon

• heterotrophs: use organic carbon

• carbon fixers: use CO₂ from the atmosphere (like plants)

syntrophic networks

• the biochemical reactions driving metabolism are connected/coupled

• ex. In hot springs, one layer of the biofilm is bacteria that produce CO₂ and H₂ and the other layer is archaea that uses those products to produce methane

extremophiles vs mesophiles

• extremeophiles: thrive at extreme environmental conditions (very hot/cold, very acidic/basic, etc)

• mesophiles: live at more normal conditions

vertical transmission

the passing of genes from parents to descendants

lateral gene transfer (LGT)

• the mixing of DNA from different lineages

• occurs through:

  1. Transformation

  2. Conjugation

  3. Transduction

mechanisms of LGT: transformation

DNA foud in the environment is moved into an intact cell via crossing over (replacing a portion of DNA), direct insertion (adding new DNA), or stays as a separate replicating entity (like a plasmsid)

mechanisms of LGT: conjugation

• the replication and transfer of a plasmid (a small piece of DNA) between cells via the formation of a sex pilus

• does not result in offspring

mechanisms of LGT: transduction

the incorporation of DNA into a host through viral particles via incorporation into host’s chromosome or replication as a separate entity

pure culture

• a culture that only contains a single species

• difficult to grow: must replicate the exact environmental conditions, nutrients, and ecological interdependencies

culture independent DNA studies

extracting genetic material directly from the environment and identifying microbes using their nucleotide sequences

metagenomics

sequencing the whole genome to make predictions about the metabolic functions occuring in uncultured organisms

metabolism

the process of acquiring energy, transferring electrons, and transforming carbon compounds into other biomolecules

how do the metabolisms of prokaryotic vs eukaryotic organisms differ?

prokaryotes have a wider range of metabolic processes than eukaryotes

LUCA

• Last Universal Common Ancestor

• the most recent common ancestor of all life

vertical inheritance

inheritance from a common ancestor