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)

• polyphyletic

• compose the majority of the biodiversity on Earth

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 (CO2)

• heterotrophs: use organic carbon (sugars)

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

syntrophic networks

• the biochemical reactions driving metabolism are connected/coupled: the products of one group is used by the other

• 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/metagenomics

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

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

• DNA

• central dogma

• lipid bilayer membrane

• ribosomes

Ether vs ester linkages

• ether: branched —> stronger, archaea

• ester: unbranched, bacteria and eukarya

  

peptidoglycan

• polymer of amino sugars located either outside the cell wall or between cell membranes

• only found in bacteria

gram positive vs gram negative

+: thick outer layer of peptidoglycan

-: thin layer of peptidoglycan between membranes

Characteristics of ALL prokaryotes

• cell membrane

• nucleoid

• cytoplasm

• ribosome

characteristics of SOME prokaryotes

• cell wall

• internal membranes

• flagella and pili

LGT vs sexual reproduction

• LGT: unidirectional, involves small portions of genome, can occur over large phylogenetic distances

• sexual reproduction: bidirectional, whole genome, between closely related individuals

Plasmids

small circular chromosome separate from main chromosome

characteristics of prokaryotic DNA

• circular

• haploid

biofilms

• groups of bacteria/archaea that secrete an extracellular polymer that binds them together

Quorum sensing

• once organisms reach a high enough density, they communicate via chemical signals which activate group behavior genes

types of bacteria: spirochetes

• gram -

• motile

• axial filaments (modified flagella)

• many are pathogenic (ex. Syphilis and Lyme)

types of bacteria: chlamydias

• gram -

• cocci/rod

• very small

• intracellular parasites

• STDs, pneumonia

types of bacteria: actinobacteria

• more C/G than A/T

• branching (often mistaken for fungi)

• decomposers, often symbiotic w/ plant roots

• used in antibiotics

• TB and leprosy

types of bacteria: firmicutes

• low C/G to A/T

• some produce endospores: resistant seeds that only germinate in ideal conditions

• anthrax, MRSA, etc

types of bacteria: cyanobacteria

• photolithoautotrophs

• fix N

• internal membrane for photosynthesis

• ancestors of chloroplasts

types of bacteria: proteobacteria

• gram -

• largest

• ancestors of mitochondria

• E.coli, plague, etc

what characteristics allow archaea to survive in extreme conditions?

• have ether linkage membranes, which are stronger

• lipid monolayer is resistant to extreme temps

types of archaea: crenarchaeota

• thermophilic and acidophilic

types of archaea: euryarchaeota

• methanogens (produce methane by reducing CO2) and/or halophiles (prefer high salt)

types of archaea: asgard archaea

• genes are similar to eukaryotic genes

• eukaryotes are within asgard

The Great Plate Count Anomaly

• there are a lot more cells present in the environment than can be grown in a lab

• very hard to grow a pure culture

pathogens

• a parasite that causes disease

• all are eukarya and bacteria (there are no known pathogenic archaea)

legume/Rhizobium symbiosis

• mutualistic relationship where Rhizobium fixes N for the legume and the legume provides Rhizobium with sugar from photosynthesis

water fern symbiosis

• mutualistic relationship where Anabaena cyanobacterium fixes N for the water fern (azolla), which provides a protected environment for Anabaena