Biology: Phylogeny, Bacteria & Archaea

• The Week 5 reading assignment is Phylogeny and the tree of life, Chapter 26, and Bacteria and Archaea, Chapter 27.
• The Week 5 homework assignment is due on Sunday, February 16th, at 11:59 PM.
• The in-class science case study discussion will be on Monday, February 17th, with reflection due on Canvas on Wednesday.
• Lab next week requires reading pages 51-55 and 57-65

Tree of Life

• The tree of life has 3 domains
• Currently, there are three Domains grouped from the original two and then five kingdoms
• Prokaryotes were divided into Bacteria and Archaea based on genetic evidence.

Bacteria and Archaea

• Prokaryotes, including domains Archaea and Bacteria, consist of single-celled organisms
• Prokaryotes lack a nucleus and possess a single piece of circular DNA within the cell's nucleoid area.

Bacteria

• Bacteria encompasses numerous familiar prokaryotic species.

Archaea

• Archaea share specific traits with both bacteria and eukaryotes

Key Chapters on Bacteria and Archaea

• Focus on the Bacteria and Archaea Chapter 27, sections: 27.1, 27.2, 27.3, 27.4, 27.5, and 27.6
• Table 27.2 is important

History of Single-Celled Organisms

• Earth's first organisms were likely prokaryotes
• Stromatolites represent the oldest known fossils, formed by sedimentary layers on bacterial mats
• Stromatolites date back 3.5 billion years
• Prokaryotes were the only inhabitants of Earth for more than 1.5 billion years.

Bacteria and Archaea Environments

• Prokaryotes, simpler than eukaryotic cells, are highly evolved
• Prokaryotes inhabit a wide range of environments, including acidic, salty, cold, and hot conditions

Extremophile Archaea

• Some archaea thrive in extreme environments and are classified as extremophiles
• Extreme halophiles are archaea that live in highly saline environments
• Some halophiles thrive in the Dead Sea, where salt concentrations exceed 30%
• Extreme thermophiles are archaea that thrive in very hot environments
• Some hydrothermal vents house archaea that grow at temperatures of 121°C/250°F.

Ecological Roles

• Bacteria and Archaea play roles in ecosystems:
• Chemical recycling: decomposition to alter carbon availability and nitrogen-fixation makes atmospheric nitrogen available.
• increasing soil nutrients for plant growth

Ecological Interactions

• Bacteria and Archaea's ecological interactions with plants and animals
• Some are pathogenic, but many have positive interactions
• Gut microbes aid in food digestion

Bacteria's Roles for Humans

• Bacteria act as pathogens
• Bacteria contribute to deaths attributable to antimicrobial resistance each year

Bacterial Benefits

• Bacteria have roles for humans:
• Some bacteria act as pathogens
• Some bacteria act as both beneficial to people
• Microbes play a role in agriculture, industry, and scientific research.

Key Prokaryotic Aspects

• Most prokaryotic cells (microscopic) are 0.5-5 μm
• Eukaryotic cells of 10-100 μm are much larger cells
• Most prokaryotes are single-celled, but some species form colonies.

Prokaryotic Cell Shapes

• Prokaryotes exhibit a range of shapes, including spheres (cocci), rods (bacilli), and spirals.

Archaea vs Bacteria

• Nuclear Envelope: Absent in Bacteria and Archaea, present in Eukarya
• Membrane-enclosed organelles: Absent in Bacteria and Archaea, present in Eukarya
• Peptidoglycan in the cell wall: Present in Bacteria, absent in Archaea and Eukarya
• Membrane lipids: Unbranched hydrocarbons in Bacteria, some branched hydrocarbons Archaea and unbranched hydrocarbons Eukarya
• RNA polymerase: Bacteria has one kind, while Archaea and Eukarya have several kinds
• Initiator amino acid for protein synthesis: Formyl-methionine in Bacteria, Methionine in Archaea and Eukarya.
• Introns in genes are very rare for Bacteria, present in some genes Archaea and present many genes Eukarya. Response to antibiotics Growth is usually inhibited in Bacteria, and no growth is inhibited in Archaea or Eukarya.
• Histones associated with DNA Absent in Bacteria, present in species Archaea/Eukarya
• Circular chromosome Present in Bacteria/Archaea, Absent Eukarya
• Growth at temperatures >100 degrees is a no for Bacteria. Some species of Archaea can and No for Eukarya

Cell Features

• Cell features include: Fimbriae, capsule, cell wall, circular chromosome, pilus, internal organization, and flagella

Cell Surface Features

• Prokaryotic cell wall maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment
• A hypotonic cell has a surrounding solution lower in solutes
• Cell walls of bacteria contain peptidoglycan, a polymer of sugar cross-linked by peptides
• Most archaea lack peptidoglycan but have glycoproteins which are peptides with sugars attached
• Eukaryote cell walls are comprised of cellulose, like plants, or

Capsule Benefits

• Many prokaryotes have a polysaccharide or protein layer called a capsule
• A capsule can stabilize or join bacteria together
• Capsules limit dehydration and protect against hosts.

Cell Structures

• Some prokaryotes form metabolically inactive endospores, that can remain viable in harsh conditions for centuries

Historical Use

• Anthrax endospores were utilized on Gruinard Island as bioweapons
• It was originally tested in 1942, but only fully decontaminated in 1990

Cell Structures

• Fimbriae are hair-structures that allow it to stick to the substrate.
• Fimbriae, capsules and other structures aid in biofilm formation

Taxis

• Taxis is the ability to move towards or away from a stimulus
• Chemotaxis: movement toward or away from a chemical stimulus

Flagella

• Flagella is scattered on the cell or concentrated at one or both ends
• Bacteria, archaea, and eukaryote all utilize flagella but they made of different proteins It suggests they evolved independently for a similar function

Internal Organization

• Prokaryotes usually lack complex internal compartmentalization
• Some might have specialized membranes for metabolic functions such as infoldings just inside the cell walls
• Prokaryotes and Eukaryotes both contain interal organization of DNA although is it simple in prokaryotes

DNA Specifics

• The prokaryotic genome has less DNA than the eukaryotic genome, encoding fewer proteins
• Most consist of a circular chromosome not surrounded by a membrane
• Some species of bacteria also have smaller rings of DNA called plasmids

Prokaryotic Genetic Diversity

• There are 3 factors that are promoting genetic diversity in prokaryotes are:

Rapid reproduction

• In prokaryotes, short generations (20mins-3 hours) enable quick organism evolution
• Prokaryotes reproduce by binary fission this then leads to identical cells mutation then result in variances

Mutation

• Mutation rates are low in cells, but with rapid reproduction this can leads to accumulation mutations in a given short space of time

Genetic Recombination

• Genetic recombination is combining DNA from two sources

Prokaryote Genetic Recombination

• Prokaryotic DNA from different individuals can be brought together by
• Transduction: the process in which foreign DNA is introduced into a cell by a virus or viral vector.
• Transformation: the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material (exogenous DNA) from its surroundings through the cell membrane(s).
• Conjugation: the process by which one bacterium transfers genetic material to another through direct contact. Movement of genes among individuals from different species is called horizontal gene transfer

Transformation Specifics

• A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment
• Genotype, which is the genetic makeup of a cell, and possibly the phenotype can then be altered

Transduction

• Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria)

Conjugation Specifics

• Conjugation is the process where genetic material is transferred between prokaryotic cells
• The bacteria DNA transfer is one unidirectional
• Donor cells then attaches to recipient with the pilus which then pulls it closer.
• The newly incorporates that information and synthesizes with it for future reproduction

Nutritional and Metabolic Adaptations

• Prokaryotes obtain different means on how they optain energy and carbon
• The ways can be classified as:
• Phototrophs obtain energy from light
• Chemotrophs obtain energy from chemicals
• Autotrophs require CO2 as a carbon source
• Heterotrophs require organic nutrients to make organic compounds

Nutrition Modes

• There combined Energy and carbon sources leads to different paths of nutrition in the cell
• Photoautotrophs which use photosynthesis, utilize light, CO2 and other related compounds for nutrients
• Chemoautotrophs which are unique to certain prokaryotypes also use CO2 and related compounds but derive their energy from inorganic chemicals.
• Photoheterotrophs unique certain aquatic cells get nutients from the ligh but use organic comppounds
• Chemoheterotrophs gets enerygy from organic compounds like protists and fungi do

Oxygen for Survival

• Obligate aerobes are required for cellular respiration
• Obligate anaerobes use fermentation or anaerobic respiration and are then often poisoned O2 due to the process
• Facultative anaerobes use can survive with or without O2

Essential Nutrients

• Nitrogen is essential to generate amino acids and nucleic acids
• Prokaryotes can produce nitrogen in multiple ways.

Microbiology Courses

• BSC 160 Microbiology and Society (non-majors)
• BSC 260 Microbiology (majors)
• BSC 361 Microbial Pathogens (majors)