MCRO 225 lecture w 1-3 – Flashcards
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Origins of Life: Earth: First bacteria: Cyanobacteria:
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Earth: 4.6 billion YA First bacteria: 3.5-3.8 billion YA Cyanobacteria: 2.5-3 BYA from anoxic to oxic once cyanobacteria appeared
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In what kind of environ. did bacteria develop?
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Anaerobic... poor fossil record. Next, aerobic and photosynthetic... cyanobcateria, better fossil record. Once O2 became plentiful, microbial diversity increased
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Fossilized cyanobacteria are called?
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Stromatolites: colonies of fossilized cyanobacteria. Formed by extensive floating mats or reefs in aquatic environments • Mineral deposits connect layers of colonial microbial mats - Eventually harden-->stratified rock
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Modern stromatolites form in two ways:
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• Cyanobacteria trap fine sediment by sticky cell secretions - bind sediment grains to calcium carbonate • Some cyanobacteria deposit calcium carbonate-->framework
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in 1993, the three domains were proposed by and were...?
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Carl Woese. Bacteria, Archaea, Eucarya
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What are domains based on?
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nucleotide sequence of small subunit ribosomal RNAs (SSU rRNA) -16S: proks 18S: euks rRNA sequences suggest prokaryotes split into 2 distinct groups early on: • Bacteria • Archaea • Later, Eucarya developed from earlier groups.
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Review pg 10 and 11 of lecture 1
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How did euk cells originate?
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-from proks about 1.4 BYA -organelles developed via 2 processes
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Genome Fusion hypothesis:
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How did the nucleus & ER develop? • Eukaryotic genome = combination of bacterial and archaeal genes • Ancient gram-negative bacteria lost their cell wall • Archaea (crenarchaeota? eocyte?) were engulfed by these gram negative bacteria • Host cell formed membrane infolds • Archaea lost cell wall & plasma membrane - Host genome transferred to engulfed archaea - formed nucleus & ER
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Endosymbiotic Hypothesis:
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- Endosymbiosis gave rise to mitochondria and chloroplasts - Ancient bacterium engulfed photosynthetic bacteria (cyanobacteria) - formed chloroplasts - Engulfed aerobic endosymbiotic α-proteobacteria (purple bacteria) - formed mitochondria • N2 fixers - ancestors of Agrobacterium, Rhizobium? • Rickettsiae? - Exact sequence of events unclear.
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Look at PG 14 and 15 of lecture 1
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Evidence of Endosymbiotic theory:
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endosymbiotic cyanobacterium - Acts as the chloroplast (cyanelle) of the protozoan Cyanophora paradoxa) • Certain cyanobacteria, such as Prochloron (lives in sea squirts), closely resemble eukaryotic chloroplasts • rRNA trees - chloroplast RNA found in cyanobacteria • DNA & ribosomes in mitochondria & chloroplasts resemble prokaryotes • Protein synthesis in prokaryotes, mitochondria & plastids - similar biological pathways • Mitochondria & chloroplasts - susceptible to certain antibiotics, as are prokaryotes • Mitochondria & chloroplasts multiply by binary fission, like prokaryotes.
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Taxonomical Ranking:
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Domain-phylum-section-class-order-family-genus-species
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Genus:
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well defined group of more than one species clearly separate from other genera
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Species:
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- collection of strains with significant common phenotypic & genotypic characteristics - Reproductive isolation does not hold - Share the same sequences in their core housekeeping genes
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Strain:
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population descends from a single organism or pure isolate - Share stable properties within the species - Slight differences (biochemical, etc.) between strains - Serovars - strains with distinctive antigenic properties (immunological) - biovars: biochemical or physiological differences amongst strains - morphovars: different morphologically
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Type Strain:
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one strain of a species, usually first one studied & most fully characterized
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Binomial system:
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name of organism by genus & species
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taxonomy:
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the science of biological classification
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nomenclature:
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the assignment of names to taxonomical groups
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Phenetic classification:
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grouping based on overall similarity of phenotypic characteristics - May reveal possible evolutionary relationships, but no phylogenetic analysis attempted - Many unweighted traits compared to determine overall similarity • Morphological features depend on gene expression, suggesting phylogenetic relatedness • Physiological/Metabolic features - enzyme activity, transport proteins; as gene products--> indirect genome comparisons • Ecological - habitat preferences, pathogenicity, life cycle patterns, symbiotic relationships, growth requirements... • Genetic Analysis - gene exchange by transformation, conjugation.
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Phylogenetic:
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compares organisms based on evolutionary relationships
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genotypic:
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compares genetic similarities
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Morphological characteristics:
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cell shape, size, colonial morphology, staining behavior, cilia and flagella, mechanism of motility, endospore shape and location, spore morphology and location, cellular inclusions, color
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Physiological/metabolic:
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carbon and nitrogen sources, cell wall constituents, energy sources, fermentation products, general nutrition type, growth temp optimum and range, motility, oxygen relationships, pH optimum and growth range, salt requirements and tolerance
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Numerical taxonomy typically compares:
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- hundreds of characteristics (> 50) within a group of organisms - Binary information • i.e., absent = 0, present = 1 • Each characteristic weighted equally - Traits - morphological, biochemical, physiological, or genetic (RNA or protein sequences) • Generates a simple matching coefficient (Ssm), for each pair of organisms - Represents proportion of characters that match (either present/absent) - Range: 0.0 (no matches) to 1.0 (100% matches).
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Coefficients--> similarity matrix
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- Each value represents coefficient for 2 organisms that intersect at that matrix position • Organisms with largest coefficients (most similarity) grouped into phenons - Separates dissimilar organisms - > ~ 80% similarities in phenons--> considered same species • Also displayed as dendrograms - Tree- like.
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Look at PG 4 on lecture 2
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Phylogenetic:
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grouping based on probable evolutionary relationships rather than phenotypic characteristics - Difficult - poor microbe fossil record • protein comparisons - amino acid sequences reflect mRNA sequences - Relate to structures of genes coding for protein synthesis • Heat shock proteins, flagellin, cytochromes... • nucleic acid sequencing - DNA/RNA - rRNA gene sequences - PCR used to amplify rRNA-->sequenced • nucleic acid base comparisons - direct genome comparisons - G + C content - percent guanine and cytosine bases in DNA • Reflects base sequence & varies with sequence changes • HPLC (high pressure lipto chromatography) or melting temperature of DNA-->G + C content.
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G and C content:
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- when they have similar G and C content, they often have other characteristics in common -DNA base composition: 2 purine (adenine, guanine) and 2 pyrimidine bases (cytosine, thymine) • In double-stranded DNA, AT and GC pair • Mol%G+C = G+C /G+C+A+T x100 • Usually determined from melting temperature (Tm) of the DNA sample - Plot shape of curve to determine midpoint at which 50% of DNA is denatured (Tm), then calculate: • %GC = (Tm- 69.3) x 2.44.
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Look at PG 7 lecture 2
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G and C content varies between organisms: Prokaryotes: Bacterial genus: Bacterial Strain:
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Proks: 25-80% genus: <10% variation Strain: varies little
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Useful only in conjunction with phenotypic similarities....why?
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There could be sequence differences. Highly variable base sequences can be constructed from same proportions of AT and GC pairs.
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Look at PG 10 lecture 2
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Domain Archaea: Phyla: ?
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Woese proposed domain separate from other two domains based on rRNA sequencing in 1990s 2 clear Phyla: Euryarcaeota and Crenarchaeota
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Archaea morphology:
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Diverse: - Gram positive or negative - Polymorphic: cocci, bacilli, spiral, plate-like, lobed, irregular - Cell arrangement: single, filaments or aggregates (colonial) - Cell size: 0.1-15 μm, filamentous forms up to 200 μm - Motility/External Structures • ≥ 1 flagella (usually polar) • Some non-motile • Other appendages - protein networks in some anchor cells in large groups.
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Archaea reproduction and Physiology:
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Division: binary fission, budding, fragmentation, or other mechanisms... fragmentation is more like euks than proks • Physiology: - Oxygen requirements • Aerobic, facultative anaerobes, or obligate anaerobes (almost all oxygen requirements except microaerophiles - Nutrition • Organotrophs (organics) • Chemolithotrophs (inorganics) • Some photosynthetic - None with cholorphyll-based photosynthesis. (have an alternative mode of pigmentation for photosynthesis)
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Archaea habitats: Temp requirements:
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- Psychrophiles (0-15°C) - Mesophiles (20-45°C) - *Hyperthermophiles (80-113°)* *Hyperthermophiles is a term only used for Archaea, not Bacteria. Bacteria will usually denature at 80. Archaea often require this high temp.
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Archaea habitats: harsh environments:
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Volcanic vents (terrestrial and aquatic), thermal geysers, feet under ice • ~34% of prokaryotic biomass in Antarctica • Widespread in nature, not just extreme environments - Also in temperate, tropical habitats - Some symbionts with other microorganisms or invertebrates.
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What are the archaea, bacteria, and eukarya cell membranes made out of?
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Archaea: Ether linkages Bacteria: Ester linkages Eukarya: Ester linkages
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3 types of Archaea lipid membranes:
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1) 20 carbon diethers: more flexible.more fluid. more psychrophiles and mesophiles so they don't freeze 2) 40 carbon tetraethers: rigid. more hyperthermophiles so they dont melt
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Look at PG 23 of lecture 2
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Archaea cells walls composed of:
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Protein, glycoprotein, carbohydrate, or pseudomurein - Absent in some genera, such as Thermoplasma - No peptidoglycan (a.k.a murein) • No muramic acid • Pseudomurein in some (i.e. methanogens) - Chemically similar to peptidoglycan
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Cell walls of Gram positive Archaea:
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- May superficially resemble bacteria - Single, thick, homogenous layer • Pseudomurein or other polymers
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cell walls of Gram negative Archaea:
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- Surface layer of protein or glycoprotein outside plasma membrane - Unusual heterogeneous layer (cobblestone appearance). Thinner than Gram positive
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What feature make G+ archaea stain G+? look at PG 25 of lecture 2
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-the pseudomurein
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Arachaeal genetic characteristics:
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Significantly smaller genome size than bacteria • large range of G+C content (some have lots, some have little... can't use GC content as taxonomic feature) • Some have plasmids • Share genes for translation/transcription with Eukaryotes • Share genes for metabolic pathways with Bacteria (lateral transfer). -have features of Eukaryotes and Bacteria
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Look at PG 27 in lecture 2
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Archaeal metabolism:
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Diverse - Organotrophs • Don't metabolize glucose by glycolysis (lack enzyme) via typical Embden-Meyerhof pathway - Can oxidize pyruvate to acetyl-CoA - Some have functional ETC - Use different pathways and enzymes (i.e. variation of Entner-Doudoroff pathway) - Photosynthesis (Photoautotrophs) • Halobacterium salinarium uses bacteriorhodopsins instead of chlorophyll - Drive flagella to orient cell - Capture light - Avoid lethal UV concentrations • Similar to rhodopsin pigments in vertebrate rods/cones. - bacteriorhodopsins perform multiple functions, not just capturing light. They drive flagella to capture more light. and avoid lethal bubbles that is too intense or weak
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Nanoarcheaota:
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New phylum described in 2002 from Iceland hydrothermal vents (120 meters) - Unusual 16s rRNA - previously undetectable by other PCR-based ecological studies
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Nanoarchaeum equitans habitat:
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-hostile environment: almost boiling water, neutral pH, 70-98°C, pH ~6.0, 2% NaCl , anaerobic. -Attached to a hyperthermophilic crenarchaeote - Ignicoccus hospitalis • Growth requires cell-cell contact with host • Only known parasitic archaea Nanoarchaeum needs ignicoccus, but not other way around
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Nanoarchaeum equitans morphology:
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-spherical & only ~ 400 nm -almost as small as virus - tiny genome size, - only 0.5 megabase • vs. E. coli = 4.6 Mb • Lacks almost all biosynthetic genes - host dependent
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Korarchaeota
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Known almost exclusively from hydrothermal ssu-rRNA sequences • First discovered in Obsidian Pool, Yellowstone - Anaerobic pool: varies from 65°C to boiling (94°C at this altitude) » pH = 6.5, slurry of silica, pyrite, & S » No members of group yet grown in pure culture » Korarchaeum cryptofilum » Very thin, filamentous (0.17μm x 5-100μm) thermophilic heterotroph » Cultivable in 85°C anaerobic community culture from Obsidian Pool » Symbiont? » Missing genes to biosynthesize cofactors/vitamins - get from other organisms? - can't grow by itself, has to grow with others » Genome composition suggests it is a peptidolytic heterotroph that uses only protons as terminal electron acceptor, not O2, S.... (protein based metabolism)
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Archaea Phyla: Crenarchaeota:
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-sulfur metabolizing thermophiles - Hyperthermophiles - psychrophiles or mesophiles in terrestrial, marine, or freshwater habitats have recently been described • Mesophilic - terrestrial in soil or symbionts
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Archaea Phyla: Euryarchaeota:
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- 1.sulfur metabolizing thermophiles - 2.methanogens - most are mesophilic - 3. Extreme halophiles. *require high salinity to live
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PG 6 lecture 3
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Crenarchaeota:
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• Primitive members of Archaea - ~25 known genera • Among the first life on Earth? - Extant species closely related to ancient ancestors (based on fragmentary fossils) - Best characterized members - extremophiles: • Hyperthermophiles/Thermophiles • Acidophiles with sulfur-dependent metabolism • Most isolated from marine/terrestrial volcanic environments (hot springs, steam-heated soils, deep in Earth's crust, hydrothermal vents) • Grow at temperatures up to 140 °C! • Obligate anaerobes, chemolithotrophic or chemoorganotrophic • rRNA sequence-based analyses from environmental samples: -Some psychrophiles/mesophiles - oceans, symbionts of marine invertebrates, & terrestrial sediments/soils • Some at -2 to +4 °C • Psychrophiles not yet lab cultivated • rRNA quantification in Antarctic: novel Crenarchaeota a significant portion of marine bacterioplankton. -cant grow in culture cuz unable to meet nutrient needs
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Crenarchaeota: Sulfolobus spp. EX: S. acidocaldarius Metabolism and habitat:
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Thrive in sulfur hot springs • Aerobic • thermoacidophiles ( produce acid so others can't survive but they can) - pH 2-6.5, optimum 2-3 - Temp. up to 87°C, Optimum 75-85 °C - Heterotrophs or autotrophs - Aerobic chemolithotrophs: sulfur oxidizers • Sulfur + O2-->H2SO4 - First thermophilic archaea isolated.
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Genus Sulfolobus Morphology:
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-Gram negative, Irregular shape, lobed -amoeba like shape, cobblestone appearance (G-), no consistent shape
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Crenarchaeota: • Pyrodictium occultum habitat, morphology, and metabolism:
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Marine - hydrothermal vents - Can grow as heterotrophic anaerobes via sulfur respiration: • Sulfur + organics-->CO2 + H2S - Or, as autotrophic anaerobes via sulfur reduction: • Sulfur + H2 -->H2S - Flat irregular coccus with long cytoplasmic fibrils connecting cells together (almost like biofilms.) - gram negative cell wall - Optimal temp. - 105oC, cultures grow well up to ~110-115oC • One of the most hyperthermophilic species known • One of the most primitive known organisms, though molecular evidence reveals even older archaea.
