Bacteria and Archaea PDF

Bacteria and Archaea Fig. 27-UN1 The Problem with Prokaryotes Biologically, Prokaryotes are a non- monophylitic group Thus, the term Prokaryote is not a biologically sensible term Bacteria and Archaea Life is really mostly single celled Highly adaptable...

Bacteria and Archaea Fig. 27-UN1 The Problem with Prokaryotes Biologically, Prokaryotes are a non- monophylitic group Thus, the term Prokaryote is not a biologically sensible term Bacteria and Archaea Life is really mostly single celled Highly adaptable – Live just about everywhere – Hot, Cold, Acid, Sulphurous, Salty conditions Vast numbers – More bacteria in a cup of soil than the number of humans that have ever existed Very high genetic diversity  You and your Microbiome There are more cells in you that are not you than are you By volume, you are much bigger than your microbiome Gut bacteria – Affect obesity (shown in mice) – Sexual Behavior (shown in flies) – Affect stress, depression (shown in mice) – May affect OCD (in humans)  You and your little critters Bacteria provide mutualisms with humans – Direct inhibition of pathogens – Digestive processes Short Chain Fatty Acids from bacterial fermentation Metabolize drugs – Development of the immune system Fine control of cytokines (inflammatory response) – Antibiotics can harm your mutualists – Facilitate absorption of minerals – Synthesize certain vitamins  But Beware the News All too often you will see articles showing that the microbiome is responsible for Inflammatory Bowel Disease, Diabetes, Cancer, or some other condition CORRELATION ≠CAUSATION  Bacteria are unicellular, although some species form colonies Most bacterial cells are 0.5–5 µm, much smaller than the 10–100 µm of many eukaryotic cells Bacterial cells have a variety of shapes The three most common shapes are spheres (cocci), rods (bacilli), and spirals  1 µm 2 µm 5 µm (a) Spherical (b) Rod-shaped (c) Spirillum (cocci) (bacilli)  Bacteria cell walls Gram positive bacteria – Thick, complex network of peptidoglycan – Also contains lipoteichoic and teichoic acid Gram negative bacteria – Thin layer of peptidoglycan – Second outer membrane with lipopolysaccharide – Resistant to many antibiotics  Both Eukaryotes and Archaea contain polysaccharides and proteins but lack peptidoglycan Gram stain Used to make bacteria visible Classifies many bacterial species Gram-positive Gram-negative Gram-negative bacteria Have less peptidoglycan Have outer membrane that can be toxic More likely to be antibiotic resistant Some bacteria have fimbriae (also called attachment pili), which allow them to stick to their substrate or other individuals in a colony (biofilms) Fimbriae 1 µm  Bacterial movement Flagella – Slender, rigid, helical structures – Composed of the protein flagellin – Involved in locomotion – spin like propeller – Structurally and functionally different from eukaryotic flagella Allows for taxis – the ability to move in response to stimuli  Figure 28.9 The flagellar motor of a gram-negative bacterium  Both bacteria and archaea cells usually lack complex compartmentalization No membrane-bound organelles (generally) Some bacteria and archaea have specialized membranes that perform metabolic functions Respiratory membranes in aerobic bacteria Thylakoid membranes in photosynthetic bacteria 0.2 µm 1 µm Respiratory membrane Thylakoid membranes  Bacteria DNA The genome of bacteria is smaller than eukaryotic genomes Most of the genome consists of a circular chromosome Some species of bacteria also have smaller rings of DNA called plasmids The typical bacterial genome is a ring of DNA that is not surrounded by a membrane and that is located in a nucleoid region Fig. 27-8 Chromosome Plasmids 1 µm  Bacteria can form exospores or endospores Endospores – Internal to the bacterium – Resistant to heat, UV radiation, desiccation, alcohol, and chemicals – Can survive for extended periods of time – Bacteria causing tetanus, botulism, and anthrax Exospores Endospore – Formed differently – Less robust 0.3 µm Reproduction (even bacteria do it) Bacteria reproduce quickly by binary fission and can divide every 1–3 hours Generally, each offspring is identical genetically Mutations can cause variation in offspring – Mutations are rare, but reproduction is very fast  Genetic Variation Bacteria and archaea have considerable genetic variation Three factors contribute to this genetic diversity: – Rapid reproduction – Mutation – Genetic recombination  Genetic Recombination Bacterial DNA from different individuals can be brought together by transformation, transduction, and conjugation A bacterial cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria)  Transformation First shown in 1928 Bacteria that can transform are competent – About 1% of bacteria species are naturally competent under laboratory conditions Techniques can make bacteria artificially competent  Transduction Generalized transduction Virtually any gene can be transferred Occurs via accidents in the lytic cycle Viruses package bacterial DNA and transfer it in a subsequent infection Specialized transduction Occurs via accidents in the lysogenic cycle Imprecise excision of prophage DNA These phage carry both phage genes and chromosomal genes  Sharing is a good thing Conjugation is the process where genetic material is transferred between bacterial cells Sex pili allow cells to connect and pull together for DNA transfer A piece of DNA called the F factor is required for the production of sex pili The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome  F plasmid transfer F + cell produces F pilus that connects it to F − cell Transfer of F plasmid occurs through conjugation bridge F plasmid copied through rolling circle replication The end result is two F + cells  The F plasmid can integrate into the bacterial chromosome Events similar to crossing over in eukaryotes Hfr cell (high frequency of recombination) The F plasmid can also excise itself by reversing the integration process Integration and excision of F plasmid  R plasmids carry genes for antibiotic resistance Antibiotics select for bacteria with genes that are resistant to the antibiotics Antibiotic resistant strains of bacteria are becoming more common  Antibiotic Resistance Misuse and overuse of antibiotics – Agricultural uses – Patients demanding antibiotics for nonbacterial infections Majority of ear and sinus infections are viral Patients not using antibiotics properly – Antibiotic products Soaps, toys treated with antibiotics, etc. – Lateral gene transfer allows multiple resistance  Antibiotic Resistance – One case MRSA – Methicillin Resistant Staphylococcus aureus – First appeared in 1961, 2 years after Methicillin was first used – Now resistant to penicillin, oxacillin, and amoxicillin, tetracycline, erythromycin, and clindamycin – 85% of infections occur in hospitals – Over 11,000 deaths in 2011 – Most are skin infections Can spread to other organs  Bacterial nutritional adaptations Phototrophs obtain energy from light Chemotrophs obtain energy from chemicals Autotrophs require CO2 as a carbon source Heterotrophs require an organic nutrient to make organic compounds  Chemoautotrophs – Black smoker deep sea vents – Major primary producers  The Role of Oxygen in Metabolism Bacteria metabolism varies with respect to O2: – Obligate aerobes require O2 for cellular respiration – Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration – Facultative anaerobes can survive with or without O2  Nitrogen Metabolism Bacteria can metabolize nitrogen in a variety of ways In nitrogen fixation, some bacteria convert atmospheric nitrogen (N2) to ammonia (NH3)  Metabolic Cooperation Cooperation between bacteria allows them to use environmental resources they could not use as individual cells In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells called heterocytes exchange metabolic products  Proteobacteria These gram-negative bacteria include photoautotrophs, chemoautotrophs, and heterotrophs Some are anaerobic, and others aerobic  Subgroup: Alpha Proteobacteria Many species are closely associated with eukaryotic hosts Scientists hypothesize that mitochondria evolved from aerobic alpha proteobacteria through endosymbiosis Example: Rhizobium, which forms root nodules in legumes and fixes atmospheric N2 Subgroup: Gamma Proteobacteria Examples include sulfur bacteria such as Chromatium and pathogens such as Legionella, Salmonella, and Vibrio cholerae Escherichia coli resides in the intestines of many mammals and is not normally pathogenic  Subgroup: Epsilon Proteobacteria This group contains many pathogens including Campylobacter, which causes blood poisoning, and Helicobacter pylori, which causes stomach ulcers  Ulcers and their history Drs. Marshall and Warren Nobel Prize in 2005 Helped define the concept of “don’t try this at home”  Gram-Positive Bacteria Gram-positive bacteria include – Actinobacteria, which decompose soil – Bacillus anthracis, the cause of anthrax – Clostridium botulinum, the cause of botulism – Some Staphylococcus and Streptococcus, which can be pathogenic – Mycoplasms, the smallest known cells – Streptomyces, the source of many antibiotics, anti- cancer, and antiviral drugs  Ecological Relationships and Bacteria Symbiosis is an ecological relationship in which two species live in close contact: a larger host and smaller symbiont Bacteria often form symbiotic relationships with larger organisms Parasites that cause disease are called pathogens  Bacteria are our friends Fermentation Waste Management Toxic spill cleanup Genetic Engineering Antibiotics  Archaea share traits with both groups and traits unique to themselves Bacteria Archaea Eukarya Nuclear Envelope Absent Absent Present Peptidoglycan Present Absent Absent Introns Very Rare Present in some Present in many genes genes Histones w/ DNA Absent Present in some Present species Circular Present Present Absent Chromosome Growth at temps > No Some species No 100° C  Some archaea live in extreme environments and are called extremophiles Extreme halophiles live in highly saline environments Extreme thermophiles thrive in very hot environments Methanogens live in swamps and marshes and produce methane as a waste product Methanogens are strict anaerobes and are poisoned by O2  Archaea and humans Archaea produce methane in the human digestive track – Found in the mouth and can influence tooth heath – Many species found in the intestine