Microbial Diversity .docx

Microbial Diversity Ubiquity of Microorganisms Types Bacteria Archaea Algae Protozoa Viruses Fungi Dominated by study of microorganisms associated with diseases. Discovery of microbial life at deep-sea vents and other habitats changed the view of where microorganisms live. Extremophiles inhabit ex...

Microbial Diversity Ubiquity of Microorganisms Types Bacteria Archaea Algae Protozoa Viruses Fungi Dominated by study of microorganisms associated with diseases. Discovery of microbial life at deep-sea vents and other habitats changed the view of where microorganisms live. Extremophiles inhabit extreme environments. thrive in habitats which for other terrestrial life forms are intolerably hostile or even lethal. May be divided into two broad categories. Categories Extremophilic: Require one of more extreme conditions in order to grow. Extremotolerant: tolerate extreme values of one or more physiochemical parameters through growing optimally at “normal” conditions. Conditions Classified according to the conditions in which they grow. Thermophiles, Hyperthermophiles: grow at high, or very high temperatures, respectively. Psychrophiles: grow at low temperatures. Acidophiles and Alkaliphiles: optimally adapted to acidic or basic pH values respectively. Barophiles: grow best under pressure. Halophiles: require NaCl for growth. Polyextremophiles: being adapted to live in habitats where various physicochemical parameters reach extreme values. Extremophiles include members of all three domains. Archaea main group to thrive in extreme environments. Methanopyrus kandleri strain 116 grows at 112 hUk C (252 F, the highest recorded temperature). genus Picrophilus include the most acidophilic organisms currently known, with the ability to grow at a pH of 0.6. Cyanobacteria best adapted group of Bacteria to various extreme conditions. often form microbial mats with other bacteria, from Antarctic ice to continental hot springs. can also develop in hypersaline and alkaline lakes, support high metal concentrations, and tolerate xerophilic conditions (i.e., low availability of water), forming endolithic communities in desertic regions. rarely found in acidic environments at pH values lower than 5-6. Among eukaryotes, fungi (alone or in symbiosis with cyanobacteria or algae forming lichens) are the most versatile and ecologically successful With the exception of hyperthermophiles, they adapt well to extreme environments. Fungi live in acidic and metal-enriched waters from mining regions, alkaline conditions, hot and cold deserts, the deep ocean and in hypersaline regions such as the Dead Sea. Diversity of Morphologies Commonly observed morphologies between bacteria and archaea include round (coccoid), rod, filamentous, and comma (vibrio). Different shapes help organisms find food, attach to surfaces, escape predators, move, and divide. Other shapes: Pear shaped. Triangular disk shape Bacillus arranged in rosette attached by stalks. Lobed spear Star Shaped -> Stella. Winogradsky’s Experiments with Chemolithotrophs Sergei Winogradsky: pioneered work with chemolithotrophs. Winogradsky column: gradients of anoxic and oxic environments using tightly packed mud containing organic carbon sources and sulfide, covered with water. Aerobic organisms developed at the top, and anaerobic community developed in the bottom. Diversity of Domain Bacteria Phototrophs Phyla Firmicutes, Proteobacteria, Chloroflexi, Cyanobacteria, ad recently, Acidobacteria. utilize photochemical reaction centers (a complex of proteins in which energy from the sun is converted in a series of electron transfer reactions) uses light energy. Oxygenic Cyanobacteria have type 1 and type 2 reaction centers (RC) Type 1 RC: FeS as terminal electron acceptor Green sulfur bacteria (Chlorobi). Heliobacteria. Phototrophic Acidobacteria Type 2 RC: Quinones as terminal e-accepter. Green non-sulfur bacteria (chloroflex). Purple bacteria (proteobacteria). Inorganic donor (H2S) Purple sulfur bacteria (proteobacteria), green sulfur bacteria (chloroflexi). Organic electron donor purple non-sulfur bacteria, green non-sulfur bacteria Phylum Cyanobacteria Formerly known as blue-green algae. Gram negative thin peptidoglycan, pink/red under gram staining. All members are primarily phototrophs. Contains oxygen-evolving photosynthetic bacteria. Have Type 1 and Type 2 RC and use calvin-benson-bassham cycle to reduce CO2. Light is gathered by the light harvesting antennae. Phylum Chlorobi Green sulfur bacteria All members are known to be primarily phototrophs. Obligate anaerobic photoautotrophs. Oxidize sulfur compounds, iron, or hydrogen. Have Type 1 RC and chlorosomes (light-harvesting organelle) coupled to Gemma Matthews Olson (FMO) proteins, for photosynthesis. Contains bacteriochlorophyll (Bchl) c (745-755 nm), d(705 – 740nm), and e (719 – 726 nm) Photosynthesis can be powered by light other tan sunlight. Lives in deep sea vent Phylum Proteobacteria purple bacteria Gram negative Contains pathogenic members such as Salmonella, E.coli, and Vibrio. Contains only a single photosystem which is bacteriochlorophyll present within the intracellular membrane. Unable to split water molecule release oxygen molecules. a, y, B, classes harbor photosynthetic bacteria. Purple silver bacteria: utilize sulfur and hydrogen as electron donors. Purple non-sulfur bacteria utilize organic carbon compounds. Phylum Chloroflexi Filamentous anoxygenic phototrophs. most exhibit gliding motility and flexing. Formerly called green non-sulfur bacteria. Members of Chloroflexales grow facultatively as aerobic chemoheterotrophs in the dark and grow as anaerobic photoheterotrophs in the light. Type 2 RC and lack FMO. Phylum Firmicutes Heliobacteriacea contain reaction centers. Obligate anaerobes. Capable of both photoheterotrophic growth in the light and chemoheterotroph in the dark. Autotrophic growth is not possible, with cell generally relying on a limited set of small organic acids, fatty acids, and sugars as carbon sources. only known members of the phylum firmicutes capable pf phototrophy using chlorine containing photochemical RC. Produce Heat resistance endospores. Phylum Acidobacteria 6th known phylum to carry out photosynthesis with recent discovery of Chloracidoacterium thermophilum. Live under oxic conditions. Detailed physiological characterization remains to be carried out. Thermophiles Phylum Aquificae Contains several families of extreme thermophiles found i either marine or terrestrial hydrothermal features. Aquifex aeolicus (Topi ~85°C-90°C) and Aquifex pyrophilus (Toot ~85°C) Some theories of the origin of life suggest that early life was thermophilic and used reduced substrates such as hydrogen. Organisms such as the Aquificae that are thermophilic and utilize hydrogen may shed light on lifestyles on early Earth. Nitrogen-fixing bacteria can participate in obligate or facultative symbioses with a wide variety of eukaryotic hosts across animals, fungi, and plants. illustrate several important ecological concepts. a range of obligate to facultative symbiotic mutualisms across many eukaryotic groups. Nutrient cycling. Widespread diversity. The importance of microorganisms in the ecosystem. Rhizobia – microorganisms in root modules and stomach of termites ; with symbiotic relationships with animals and plants. Benefit to plants: provides nitrogen in usable form of plants. Benefit to bacteria: nutrient and housing. In termites, they have spirochetes, which digest wood particles. Epulopiscium spp.: A Case of Extreme Polyploidy. One of the largest bacteria known (600 um) Symbiotes of surgeonfish; aquatic. Maintains extreme polyploidy throughout its life and has tens of thousand of genome copies in each individual which lie the cell periphery. They need polyploidy because their size is big and thus need a repeat of their genes. Only 1% if the genetic material in the mother cell is directly inherited by its offspring cells. Cell division within mother cell results in several intracellular daughter cells mother cell disintegrates, daughter cells emerge. coordinated release of DNA from dying mother cells and recombinated of these fragments in genome copies within newly emerged offspring. Diversity of Domain Archaea They are also able to live in normal conditions like normal bacteria. Hyperthermophiles Quite numerous within the Phylum Crenarchaeota. Most often found in solfataric fields in association with volcanoes. Abundance of pyrite or iron hydroxides, CO2, H2S, H2, CH4. Pyrudictum occultum: 110C Pyrolobus fumarii: 113 C Nanoarchaeum equitans: smallest thermophile ever found at 40nm in diameter. Nanoarchaeum equitans; A dwarf, thermophilic archaeon. Phylum Nanoarchaeota (the dwarf archaea) N. equitans: sole representative of the group. Grows at 70-98C. grows in coculture with another archaeon Ignicoccus hospitalis. Ferroplasma Member of order Theroplasmatales under Phylum Eiryachaeto. Ferroplasma acidiphilum often found associated with acidic sulfide ores and cultured and described from a pyrite-leaching bioreactor. Intriguing cell wall-less nature in acidic environments cell membranes contain novel caldarchaetidylglycerol tetraether lipids, which have extremely low proton permeabilities. Useful in biogeochemical cycling of sulfur and sulfide metals in highly acidic environments potential for biotechnological applications such as biomining/ bioleaching Biomining, the use of microbes to solubilize and extract metals from ores, is becoming increasingly important in mining as an alternative to thermal processes (smelting) because of its lower and containable pollutant outputs. 500 mm. Methanogens Member of Phylum Euryarchaeota live at moderate pH, temperature, and salinity, in contrast to many other archaea. often live syntrophically ("feed together") with other bacteria such as fatty-acid-oxidizing bacteria production of large amounts of methane (greenhouse gas), which they produce under anaerobic conditions. theory that methanogens may have contributed to the largest extinction in Earth's history (Permian period, 250mya) sharp rise in greenhouse methane seems to have caused global warming and climate changes that drove 99% of all vertebrate life on Earth to extinction. unchecked methanogenesis can alter global climate. Methane produced by methanogens is primarily oxidized to CO, by anaerobic methanotrophic archaea or bacteria, or by aerobic methanotrophic bacteria. It is estimated that <1% of biological methane from the subsurface is released to the atmosphere (Buan, 2018) Halophilic Archaea Order halobacteriales within Euryarchaeota encompass halophilic organisms found in hypersaline environments. Color comes from carotenoid in the cell membranes. Presence of retinal pigment Similar to pigment found in humans. Bacteriorhodopsin: Absorbs light and pumps proton out of the cell. Halorhodopsin: pumps chloride ions into the cell. Haloquadratum walsbyi (Walsby square “bacterium”) maintain buoyancy in water through gas filled vacuoles. Diversity of Domain Eukarya Protist Diversity Diplomonads – flagellated, unicellular organisms that contain two nuclei and mitosomes (simplest forms of mitochondria); e.g., Giardia. Parabasalids – organisms that contain: parabasal body gives structural support to the Golgi complex and hydrogenosomes anaerobic organelles that resemble evolved from mitochondria and produce ATP through fermentation reactions resulting in the production of H2 and acetate. Euglenozoans – flagellated protists including free-living symbiotic and parasitic species. Trypanosoma sp. lives in lymph nodes or blood. Causative of trypanosomiasis. Alveolates – organisms that contain sacs in the cytoplasmic membrane called alveoli, which include: Dinoflagellates named after their flagella that cause a spinning movement. highly beneficial in their role as the zooxanthellae symbionts of corals. very harmful as members of the algal looms that cause red tide producing xanthophyll pigments that give red coloration. One hypothesis concerning coral bleaching suggest that loss of these zooxanthellae may contribute to coral bleaching. Stramenophiles – presence of tubular cristae in their mitochondria. Heterokont flagella at some point in their life cycle. Characterized by 2 Flagella – one extending anteriorly and the other posteriorly. Stramenopila – straw hair. Diatoms External silica structure (frustule) resistant to decay and from and important part of geologic record as fossils. Cercozoans - previously called amoeba; includes organisms that are amoeboid, flagellate, or both. Majority are heterotrophic amoebae. Radiolarians - Possess thread-like pseudopodia. Amoebozoa Use pseudopodia that are lobe-shaped. Group of morphologically diverse amoebae which includes slime molds, loose amoeba, an Fungal Diversity major pathogens in plants in animals Have symbiotic relationships such as mycorrhizae and lichens. Decomposers and recyclers ­ Zooosporic Fungi – display a single, posterior flagellum at some point in their life cycle. Microsprodia – members have unique morphology and are obligated intracellular pathogens. Chytridiomycota – produce motile spores; most are saprophytic; chytridiomycosis is causing massive, global amphibian die-offs. Zygomycetous fungi – form hyphae that lack septa and are therefore coenocytic. In most cases sexual reproduction produces tough. Dikaryotic fungi – so named during sexual reproduction, cytoplasmic fusion, precedes nuclear fusion, so there is a period of time during which the two haploid nuclei coexist in the same cell prior to nuclear fusion. Members of Basidiomycota – club fungi named after their basidium that produces basidiospores; include important plant pathogens called smuts and ruts. Ascomycota – sac fungi because of sac-shaped reproductive structure called ascus; can have yeast or mold morphology.