Chapter 18 Deep branching: * Characteristics - Diverge earliest from archaea and eukarya - Share many features and habitat

with Archaea (horizontal gene transfer) - ie. Ether linked membrane lipids - Contain moderate to extreme hyperthermophiles - fastest doubling rates - high mutation rate * examples - Thermus aquaticus: derive Taq polymerase for PCR because its heat resistant. - Deinococcus radiodurans: they are non-thermophiles that are resistant to ionizing radiation and desiccation because it has the ability to repair damage DNA as well as high mutation rate. - Chloroflexi: filamentous green non-sulfur phototrohp (an-oxygenic phototroph) that are associated with cyan bacteria and possess chlorosomes and forms filamentous photosynthetic microbial mats in hot springs. Cyanobacteria - difference between cyan bacteria and chloroplasts + mitochondria is the loss of eukaryotic nucleus *Characteristics - Only oxygenic photosynthetic bacteria - same Chlorophylls as found in plants - Thylakoids - Carboxysomes - Gas vesicles - fix nitrogen as well as CO2 - house in heterocysts to exclude O2 - share ancestry with chloroplasts - fungi + lichens * examples - Anabaena: phototrophic filamentous, form spore cells heterocycsts and akinetes where it stores nitrogen. - Prochlorococcus: most abundant oxygen producers in the biosphere. Gram + Firmicutes: - low GC - rods and cocci - Firmicutes as gut flora has been shown to be involved in energy resorption and obesity. spore formers - Bacillus anthracis: causes anthrax acute disease by producing anthrax toxin - B. Thuringiensis: generates toxic crystals that contains an insecticidal protein known as delta-endotoxin. The toxin is only activated in high pH in the digestive tract of insect. Plant engineering introduced Bt genes into plants to fight off insects, but then it might harm other species. - Clostridium Botulinum: causes botulism which is a toxin that is famous for its therapeautic use to relax muscle spasams and to smooth wrinkles in skin. - they have a drumstick appearance. - Clostridium Tetanus: causes tetanus - Metabacterium polyspora (large): multiple endospore producing and isolated from the cecum of guinea pigs. Very similar to Epulopiscium fishelsoni. - a forespore forms at each pole forespores fission and multiply within the motherspore, then are released. Germinated cells undergo limited or no binary fission. - Epulopiscium fishelsoni (large): unusual reproductive cycle of multiple endospore formation; limited binary fission. - an offspring cell forms by fission at each pole. The cells grow internally until released = live birth of offsping; NO binary fission.

Non-spore formers - Listeria: causes listeriosis, infected by food that has been contaminated by this bacteria. It uses actin bioskeleton to invade human hosts: the bacteria gets taken up by phagocytes forms long actin to move around in the cell penetrate out into another host. - Lactobacilliales: lactic acid bacteria for fermenting milk product - Strephylococcus aureus: skin flora but can be serious pathogens that causes impetigo and toxic shock syndrome, as well as pneumonia, mastitis, osteomyelitis. - Streptococcus pneumonia: causes pneumonia - Mollicutes: lack cell wall and S layer Ex. Mycoplasma: causes pneumonia and meningitis. Gram + Actinobacteria: - High GC - popular in soil life, firewater and marine life, play an important role in decomposition of organic materia. Actinomyces: form multicultural filamentous that also form spores - Streptomycetes: - obligated anaerobe -soil microbe that produces geosmin that gives soil an odor. Many antibiotics are made from these. - chromosomes are linear with special telomeres at the end. - causes actinomycosis that infects skin of humans and cattle. - many mutually beneficial associations with plants. - form arthrospores Nonmycelial actinomycetes: - Mycobacteria: - contain thick mycolic acids of long chain fatty acids. - includes M. Tuberculosis and M. leprae. - Corynebacterium - unusual shaped rods; divides by elongates and then snape - causes lung disease diphtheria - Arthrobacter - shows morphology variation: cocci to rod to cocci again - reduce toxic metal pollutant to a less toxic oxidation state Gram - Proteobacteria - they all share triple layered, gram-negative cell envelope - wide variety of metabolism: electron acceptor may be oxygen or nitrate or sulfate - many are photoheterolithotrophs - Alphaproteobacteria: include many heterotrophy; many highly evolved intracellular symbionts - Rhizobium: nitrogen fixing endosymbionts by colonizing plants, usually legumes such as alfaalfa - Rickettsias: intracellular pathogens and associated with mitochondria - causes rocky mountains spotted fever spread by ticks - lack flagella so propel the same as Listeria. - associated with mitochondria. - Agrobacterium tumafaciens: causes tumors in plants called galls and using its DNA to insert into plant genomes has made it a major tool for plant biotechnology. - Betaproteobacteria: lithographic nitrifier - Nitrosomonas: nitrifying lithotrophs; oxidizes ammonia to nitrite which can be used for wastewater treatment to remove ammonia. - Neisseria: pathogen - N. Gonorrhea: causes sexually transmitted disease gonorrhea - N. meningitides: causes meningitis - Burkholderia: plant root pathogen that invade the lungs of cystic fibrosis patients.

- Gammaproteobacteria: well known for the Enterobacteraceae family found in the human colon. - purple Sulfur and iron bacteria: uses sulfide as energy source to produce sulfur. - Enteric bacteria: - E. coli: grow in human guts and can cause illness - Salmonella: typhoid fever and food poisoning - Proteus: causes bladder and kidney infections with swarming behavior to form rafts that becomes biofilm. - Pseudomona aeruginosa causes lethal infections of cystic fibrosis patients. - Legionella: causes legionares disease and have an unusual dual lifestyle, grows in macrophages in human and intracellular within freshwater amebas. - Deltaproteobacteria: include important sulfur and iron reducers - Myxobacteria: forms multicultural fruiting body: starving mycobacterium glude toward each other to aggregate. The aggregation generates a fruiting body with bulges packed with small, spherical myxospores. - Bdellovibrios: parasitize bacteria - finds host by chemo taxis invade host periplasm growth of spiral chain chain fragments into flagellated cells host lysis releases Bdellovibrio cells. - Epsilonproteobacteria: - Helicobacter pylori: causes ulcer and requires flavodoxin to survive in the human stomach and produces ammonia that damages the epithelial cells in the stomach lining. - Bacteroidetes: they break down complex plant materials that are toxic to humans in the colon and enter body tissues through wounds and cause abscesses. - Green sulfur bacteria - Chlorobi: green sulfur phototroph - Spirochetes: - causes lyme disease and syphilis disease - need vectors such as insects or humans - strange motility: internal flagella for motility - form clusters and can go backwards or forwards by changing its rotating direction. - Chlamydiae: - intracellular pathogens - 2 phases in life cycle: elementary body phase (extra cellular) and reticulum body phase (intracellular) Life cycle: elementary body attaches to host cell elementary body is taken up by endocytosis elementary body differentiates into reticulate body reticulate body replicates and persists in cell for long periods reticulate bodies develop into elementary bodies cell lyses, releasing elementary bodies. - Planctomycetes: nuclear membrane bound around chromosomes = double membrane - Verrucomicrobia: - irregular cell shape - have cytoskeleton (actin and tubulin) form horizontal transfer from eukaryotes. * Plantomycetes and Verrucomicrobia are closest microbes to eukaryotes ------------------------------------------------------------------------------------------Chapter 19 Archaeal Diversity - similarities to bacteria: cell size; genome size; genes in operons; pseudopeptidoglycan and S-layer - similarities to eukaryote: introgenic sequences; DNA and RNA pol; transcription factors: TATA-binding proteins and TFIIB; histones - cell membrane: has peptide linkage but different variety of S-layer - lipid structure: ether linkage attach to head group and isopernoidal = prevent leaky. * these are to adapt to low energy stress prevent loss of protons so they have all these structures. Isopernoid prevent H+ permeability. - Hyperthermophilic Crenarchaeota

- hot springs and hydrothermal vents - 70-110 C - rich in reduced minerals - low oxygen permeability - biomarker that characterizes crenarchaeota - Desulfurococcales Desulfurococcus mobilis: S layer but no pseudomurein and sulfur reducer - Pyrodictium abyssi: - black smokers: precipitaate FeS upon cooling - sulfur reducer - 80% soluble proteins are thermostable chaperones - baRophilic - produces biofilm to stick to the vents - Sulfolobales (we study a lot of these) - pH 2-3 - generate no ATP - oxidize sulfur - multiple ORI - gets infected by Fuselloviruses - Ignicoccus hospitalis: hyperthermophile with archael symbionts - Mesophilic Thaumarchaeota: - Cenarchaeum symbioosum - marine sponge symbiotic - oxidize NH4 to NO3 - Nitrosopumilus maritimus: - nitrifier oxidize NH4 to NO3 - adapted to low concentration of NH4 - Methanogenic Euryarchaeota - diverse group of Archaea form mesophilic to thermophilic, produce methane in energy - reversible metabolism - symbiosis between a Methanosarcina-like ANME Archaea and Desulfococcus - So4 reducing bacteria - only energetic when SRB remove reducing equivalents - Methanocaldococcus anarchic - Methanothermobacter thermautotrophicus - Methanocelleus submarinus - Methanopyrus Kandleri - Haloarchaea are extreme halophiles - Adaptations: - high GC content of DNA to protect DNA from denaturing in high salt because GC holds stronger - Acidic proteins: this hydration layer keeps the acidic proteins soluble in the high salt in the cytoplasm - Gas vesicles: maintaining their buoyancy in the upper layer of water column. - Halobacterium salinru - Haloquadratum walsbyi - Retinal-based photoheterotrophy: - Has Bacterodopsin absorbs light and pumps H+ out of the cell - light activated halorhodopsin pumps chloride into the cell - sensory Rhodesians absorb light, they signal the cell to swim using its flagella toward the red light and away from blue to UV light which causes photo oxidative damage to DNA. - Thermophilic Euryarchaeota: - Thermococcales: - basophilic hyperthermophiles - foud in submarine solfataras that produces gas only

- anaerobic fermentation and sulfur oxidation - Archaeoglobus fulgidis: - acetyl CoA metabolism via reverse similar to methanogens - methanogenesis coupled to sulfate respiration - very unique bc of acetyl CoA - Thermus aquaticus: source of Taq pol - Nanoarchaeota - Nanoarchaeum equitans: - obligate symbiotic of Ignicoccus hospitalis(cren) -------------------------------------------------------------Chapter 20: Eukaryotes - Picoeukarya: very small 0.2-2 microns in length - Choanoflagellates: - unpaired flagella - tubulin compossition - weird collar cells that may be the missing link to evolutionary to every protists. - Viridoplantae - Green algae: chlorophil a and b for photosynthesis; flagella are different than bacterias because they are made of microtubules - Sexual life cycle (can produce asexually as well haploid)/(he talked about it): sexual reproduction occurs by fusion of opposite mating types to form a zygote, which loses flagella and forms a spiny protective coat. The zygote undergoes meiosis to regenerate haploid cell. - Clamydomas: unicellular with mating types, eyespot for phototrphy - Volvox: unicellular, colonial, hallow ball of cells, very pretty - Spyrogya: multicEllular long chain of cells that are spiral - Ulva: multicEllular, large sheet of cells, seaweed - Red algae: commercially polysaccharides - rhodophytes - has red pigment phycoerythrin * both green and red are primary symbionts - Heterokonts: similar to viridoplantae - Diatom: - Silicone: glass cell wall - aquatic and marine - their shells sediment can be used to track a lakes environment. - secondary endo-symbiotic - Brown algae - Chrytophyte algae is a secondary symbiotic: engulf primary symbiotic Ex. Kelp - Coccolithophorids (CaCO3 shells): marine, enclosed by calcareous plates as shells. - Amoeba: hunt prey to eat - lifecycle (slug): starvation emit cAMP to attract nearby amebas aggregation pile on top of each other to form a slug forms a fruiting body at an appropriate place disperse cysts/spores - Dictyostellium: multicultural fruiting body, swarms into slugs for hunting - Radiolarans: silica shells reinforced by microtubule; recognized as fossil rocks - Foraminifera: calcium carbonate shells that are very ordered and thick; best preserved for fossil record for the level of past CO2 - Alveolates: include voracious predators and include ciliates, din flagellates, and apicomplexans. - Ciliates: - Paramecium: sweep food oral and has a contractile vacuole to get rid of waste. - functions of cilia: sweep food through oral and cell propulsion - contain 9+2 microtubules

- Tetrahymena: dinucleate: micro and macronuclei - complex genetic system: - micronuclei: contains diploid set of chromosomes that undergoes meiosis for sexual exchange. - macronuclei (edited): formed by genetic rearrangement and excision of some micronuclear DNA and only macronuclear genes are transcribed to RNA and translated to protein. - Dinoflagellate: marine phytoplankton that has two long flagella and forms red tide. Endosymbionts with coral reefs. - Apicomplexans: specialized parasites - plasmodium falciparum: - causes malaria - life cycle: mosquito salivary gland transmits porosities to human bloodstream porosities travel to liver Schizogony: merozoites repeatedly invade red blood cells meiosis forms gamonts which are transmitted to mosquitoes fertilization differentiation (progeny: mitosis to form porosities within mosquito cells) - life cycle: can change proteins, differentiation of cell coat at each stage of infection. - Trypanosomes: - causes African sleepy sickness carried by Tsetse flies - They an change their proteins when white blood cells recognize - Leishmania major: - causes leishmaniaisis, causes swelling and decay of extremities and eventually death - related to Trypanosomes - Fungi - absorptive nutrition - forms hyphae - cell wall made of chitin - many fungi has haploid form predomintates - unicellular fungi: yeast -some reproduce by budding - some can undergo sexual alternation of generations: gametes of two different mating types fuse, their nuclei combine to form a zygote. - Chytridiomycota: - motile zoospores - pathogens in sheep rumen and frogs - Zygomycota: - bread molds - nonmotile sporangia - vesicular arbuscular mycohrizae: mutuality associations with plant roots - Penicillium (bread mold, diploid Zygospores): form small asexual fruiting bodies called conidiophores for airbone spore dispersal. Known for antibiotic production - Ascomycota (haploid ascospores) Ex. Truffles - Neurospora: filamentous, important in genetics history - Aspergillus (opportunistic pathogen of immunocompromised patients): forms conifiophores for airborne spore dispersal. * conidiospore-forming ascomycetes are the major form of mold associated with dampness in human dwellings - Candida albicans: alternate between plank tonic cells and hyphae/filamentous forms - causes thrush, vaginal yeast infection - spores are single cell

- coccidiomycodes: causes valley fever - they are dimorphic ascomycetes - differentiates between mats in soils and single cells in lungs - Basidiomycota: typical mushroom forms - has ectomycorrhizal --------------------------------------------------------------------------------------------------------- Metagenomics: is a combo of the fields of molecular biology in genetics, whereby researchers attempt to analyze genetic information, by direct cloning of DNA from environment samples. It sequences all DNA in sample and select DNA based on universal sequences. It is referred to the idea that a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome. Remove bacteria from the environment isolate DNA samples from the bacteria and called it the genomic DNA cleave demonic DNA into fragments using restriction endo-nuclease fuse fragments with a vector complete the genetic copy of Metagenomic DNA fragment cultured sequenced: either randomly or targeted compared with identified sequence determine the function of the fragment. - Gut micro biome: - Vertebrate gut fermentations - foregut and hindgut - foregut fermenters are more efficient at breaking down cellulose and bacteria lost from the chamber can be digested and serve as a source of protein. Allows for microbial detoxification. Its a slow process so it needs the rumen to regurgitate the food and re-chewing it