Dominio Bacteria PDF

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Apuntes 2.º Biología...

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Tema 6. Dominio Bacteria 1. Diversidad y filogenia del dominio Bacteria >80 phyla. Phyla: defined as groups of organisms that share 85% ➔ same phylum; 97% ➔ same species.

2. Phylum Cyanobacteria green but not wall of them ➔ photosynthetic ➔ they use light to obtain ATP and reducing power. *chloroplast is a cyanobacteria inside an eukaryotic cell. cyanobacteria with very high morphological diversity. The C source could be: CO 2  yanobacteria) ➔ ONLY IN organic matter: photoheterotroph (lots of C PROKARYOTES. BChl *retinal photosynthesis (protobacteria) is the most extended kind of photosynthesis -

❖ Fotosíntesis en el dominio B  acteria ● ● ● ● ● ●

Fotosíntesis oxigénica: Cyanobacteria. Fotosíntesis anoxigénica (Heliobacterias): Firmicutes. Fotosíntesis anoxigénica (bacterias verdes del azufre): Chloroflexi. Fotosíntesis anoxigénica (bacterias rojas del azufre y no del azufre): Proteobacteria. Fotosíntesis basada en retinal: Proteobacteria. Fotosíntesis anoxigénica (bacterias verdes del azufre): Chlorobi.

❖ Cianobacterias: bacterias fotosintéticas oxigénicas ● ● ● ● ● ●

Gram - (unicelulares o filamentosas). Tamaño: 0,5 - 60 µm. Ácidos grasos poliinsaturados en mbr. Pueden presentar capas mucosas.  oseen clorofila a (o derivados). Todas p Movilidad por deslizamiento y/o vacuolas de gas (si son móviles).

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Todas son potencialmente fotoautrótofas. Pueden respirar (cadena respiratoria en membrana celular). Algunas pueden fijar N2 atmosférico. Ecología: muy ubicuas. Neurotoxinas, geosminas.

฀ Importancia evolutiva: ‘antiguas’, O2, endosimbiosis.

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 if) ❖ Algunas fijan N2  (genes n ● ●

Cianobacterias: unicelulares y filamentosas ➔ separación temporal. Algunas cianobacterias filamentosas ➔ separación espacial: heterocistos.

❖ Estructuras y orgánulos ●

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Hormogonio: filamento móvil de células formadas por cianobacterias. Se forman durante la reproducción asexual en cianobacterias filamentosas unicelulares, algunos contienen heterocistos y acinetos. Acineto: tipo especializado de células parecidas a las endosporas que producen algunas cianobacterias como respuesta a condiciones de vida desfavorables. Heterocisto.

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❖ Grupos de cianobacterias ●

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Grupo I: Chroococcales. ○ géneros: Synechococcus, Prochlorococcus. Grupo II: Pleurocapsales. Grupo III: Oscillatoriales. ○ género: Trichodesmium. Grupo IV: Nostocales. Grupo V: Stigonematales.

❖ Cianobacterias marinas ●

Prochlorococcus: ○ microorganismo fotoautótrofo más abundante del planeta. ○ 20 - 50% biomasa fotosintética oceánica. ○ coco alargado; microorganismo fotoautótrofo más pequeño; picofitoplancton. ○ posee clorofila a y b modificadas (divinilclorofila) y no posee ficobilisomas. Pueden alcanzar hasta 200 metros de profundidad. ○ existencia de ecotipos: ■ adaptado a la luz abundante: black spots.  septicemic plague: after the 1st bite, the replication replicates directly in the blood and it causes directly septicemia. you would die before a diagnosis. pneumonic plague: from the lymph nodes, the bacteria can go directly to our lungs. you can spread the bacteria while talking.

gangrene and black spots (“black death”); buboes.

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 ibrio 3.3. γ-Proteobacteria: V ● ● ● ●

Carbon cycle. Curved and straight rods. Aquatic media. Many species; some pathogenic: ○ V. cholerae cholera: most important waterborne disease. original from Ganges delta (India). because of the monzón, the bacterium can be spread. most severe diarrhea, you can lose up to 20 L of water per day. it is produced when you drink water and the bacteria cells arrive to your small intestine. the cholera toxin is released outside the cell. the region in the V. cholerae which codes for the toxin is a prophage (infected by a phage and its DNA is in their chromosomes). these virus can only affect bacteria, and the toxin can only affect humans. the toxin presents two subunits. subunit B allows subunit A to enter inside our cells. A activates the synthesis of cAMP; as a consequence of cAMP inside the epithelium, there is a transport of chloride and bicarbonate from our internal tissues to the intestine. because of the osmotic pressure, passive but massive transport of water through our intestine. it is more important to try to stay hydrated instead of the use of antibiotics. how many V  . cholerae cells do you need to drink in  order to get the disease? 108 V. cholerae cells. for resisting waterborne and foodborne diseases, our stomach must have an acidic pH. if you take a lot of bicarbonate, you cannot be more resistant because the pH increases.

 hotobacterium 3.3. γ-Proteobacteria: P ●

C cycle.

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when P  hotobacterium is a free-living microbe, they cannot produce light. density-dependant mechanisms --> bioluminescence. lux operon codes for luciferase. this enzyme can produce light. it is an example of "quorum sensing".

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 cidithiobacillus 3.3. γ-Proteobacteria: A ● ● ● ●

C, S and Fe cycles. Aerobic, iron-oxidizing chemolithoautotrophs. Acidophilic. Acid mine drainage (formation of H2 SO4 and Fe3+  ). pyrite (FeS 2 );  S)  chalcosite (Cu2  you can inoculate the rock. the microbe can oxidize:  Fe 2+  ➔ Fe3+  ; Cu+ ➔ Cu2+  ; or S0  ➔ SO 4 2 .

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Remember than in acidic environments, Fe3+  could be good e- acceptor.

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A. ferrooxidans: most important species most abundant inhabitants in Tinto river. its importance is related with astrobiology, a lot of iron dissolved in there. we can find lots of microbes which use Fe as an energy source. pH = 2; acidic environment. that environment can be found in Mars. application: biolixiviation: extraction of metals in mines.

3.4. δ-Proteobacteria: B  dellovibrio ●

“Predator” of other bacteria.

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few bacteria that can kill other bacteria by predating Gram - bacteria , Gram + are resistant.

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3.4. δ-Proteobacteria: sulfate (and sulfur) reducing bacteria (SRB) the kind of respiration is not related with any metabolic category!!

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They also perform C cycle. Acceptors: SO4 2-, S0 and others (anoxic environments; strict anaerobes). why  do they exist in nature if O2  is the best e-  acceptor? they cannot defend from O2  toxic forms.

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NAD(P)H from reverse electron flow.

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Desulfo- generally. Anoxic environments: ○ gut ○ marine sediments: ■ stratification of electronic acceptors ■ limited organic matter ■ most important metabolism: sulfate reduction ■ competence with methanogenic Archaea (H2) but also consortia... ○

NO 3 -  organisms: they are going to use O 2  if they can. SO 4 2are really distant from O2 , so they are strict  anaerobes.

 ixobacteria 3.4. δ-Proteobacteria: M ●

Carbon cycle.

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they live in soils associated to organic matter from animals or plants. chemoorganotrophic aerobic source.

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Vegetative cells: long rods (gliding); aerobic chemoorganotrophs; exoenzymes. Produce fruiting bodies: cell-to-cell communication and differentiation. 15

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when the concentration of nutrients decreases, these cells aggregate by using a gliding mechanism and they form the fruiting bodies ("prokaryotic mushrooms"). they're resting structures. spores as a dispersion mechanism. they produce carotenoids but they are not phototrophic. which is the function? ---> prevent the is produced as a consequence of action of the singlet oxygen: very reactive form of O 2 which  sunlight.

 ampylobacter and H  elicobacter 3.5. ε-Proteobacteria: C ● ●

Campylobacter: acute gastroenteritis (foodborne disease: chicken, meat...) Helocobacter: gastritis and ulcers, and even stomach cancer. ○ Helicobacter pylori : the most important.

3.6. Other Proteobacteria: ‘Rickettsiae’ and other intracellular parasites α/γ Proteobacteria ● ● ● ●

Obligate intracellular parasites (do not survive outside hosts; some exceptions). Induce phagocytosis. Synthesize few compounds. Many transmitted by arthropod vectors.

Rickettsia (α ) : ● epidemic typhus - vector: human louse 1. fever, headache, weakness, rash 2. organ infections 3. high mortality if untreated ● other diseases (fevers...) - vector: tick 1. fever, headache, weakness, rash 2. grastroenteritis, etc.

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Coxiella (γ ) : ● Q fever - vectors: tick, aerosols, dairy products ○ flu (mild), pneumonia, endocarditis (serious): infection in the heart, you would die immediately if not treated. you only need 1 cell to get the disease. vaccines are not available for everyone, what could you do if you were a terrorist? BIOLOGICAL WEAPON.

3.6. Other Proteobacteria: aerobic nitrifying bacteria ● ● ● ● ● ● ●

Carbon and N cycles. Donors: NH4 +, NO2Acceptor: O2 (aerobic respiration) NAD(P)H: reverse electron flow C source: CO2/organic C Nitrosomonas. Nitrobacter.

3.6. Other Proteobacteria: non photosynthetic sulfur oxidizing bacteria ● ● ● ● ● ● ● ●

Carbon and S cycles. Donors: H2S, S0, S2O3 2-, metal sulfides Acceptor: O2 /NO3 - (aerobic/anaerobic respiration) ATP: oxidative phosphorylation NAD(P)H: reverse e- flow C source: CO2/organic C The cells are attached to S0 particles. S0 is accumulated inside the cells. Thiomargarita namibiensis: c hemolithoautotrophic and anaerobic bacteria. H 2 S is their energy source, and it is oxidized to elemental S. Sulfur is accumulated inside the   cell, they can use that which then is oxidized to SO 4 2 in order to get energy.

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They can form filaments or not.

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important in benthic communities in oceans because they are thought to be the primary producers. scientists took a worm and they observe it didn't present any kind of digestive system. inside it, there was a bacterial community, composed by bacteria which used H 2 S as e- donor, O2 as e  acceptor, and they had also the capability of fixing CO2 , coming from bicarbonate dissolved in water. the bacteria are actually the food of the worm. in their "blood", they present a modified and O2 , so they offer the e- donors and acceptors. this hemoglobin which can transport H2 S  was the first example of an ecosystem where the primary producers don't depend on light. really important in ecology. first step in the trophic way is always associated with CO2  fixation (autotrophy). *black smokers.

3.6. Other Proteobacteria: ‘purple bacteria’ ● ● ●

C, N, S and Fe cycles. Anoxygenic phototrophs (aerobic/anaerobic, autotrophs/heterotrophs, other metabolisms) For ATP: ○ donor: BChl* ○ acceptor: oxidized BChl ○ ATP: oxidative photophosphorylation (cyclic)

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For reducing power: reverse e- flow from different compounds. Elements in photosynthesis: ○ reaction center: BChl ○ antenna pigments: BChl/carotenoids ○ electron transport chains: invaginations of the cell mbr

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they can carry an anoxygenic photosynthesis by using a bacteriochlorophyll for reducing power, they use external compounds different groups: inside this group we 1. non-marine bacteria: anoxic but photic environment (BChl without O 2 ).  0 have purple sulfur bacteria (to obtain reducing power, they can use H 2 S or S  , and they tolerate  so they can stand acidic environments) and purple non-sulfur high concentrations of H2 S,  bacteria. 2. marine bacteria: BChl O2 . they obtain reducing power by reverse electron flow and by means   or organic matter. of Fe 2+

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γ-Proteobacteria (purple sulfur bacteria): anaerobes; tolerant to H2S. Photoautotrophs. S compounds to obtain reducing power. They can fix N2. Non marine. BChl is not produced if O 2  is present. α/β-Proteobacteria (purple non sulfur bacteria): more tolerance to O2. High metabolic versatility. They can fix N2. Sensitive to high H2S, S compounds, H2, Fe2+ or organic matter to obtain reducing power. Non marine. BChl is not produced if O 2 is present.  nd  a α/β/γ -Proteobacteria (marine): aerobic anoxygenic phototrophs. Roseobacter Erythrobacter are really important. Photoheterotrophs. Light as an extra supply of  Chl is only ATP. aerobic (oxic environment and O 2 is needed for producing BChl; B produced if O2 is present); anoxygenic.

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en el termoclina, debajo de ella es donde podemos encontrar purple sulfur bacteria. they take directly C from environment and light is used to obtain extra ATP, they are not primary phototrophs.

❖ Metabolic diversity of nonsulfur purple bacteria

3.6. Other Proteobacteria: methanotrophic bacteria aerobic microorganisms and they use CH4  as carbon source but also as donor and reducing power.

Methylotrophs are organisms that grow using organic compounds lacking C-C bonds as e- donors in E metabolism and as C sources. Methylotrophy occurs in several bacteria phyla, as  ethanotrophs are subset of methylotrophs defined by their ability to use Proteobacteria. M methane as a substrate for growth. 18

Aerobic methylotrophs are common in soil and aquatic environments where O2 is present. Anaerobic methylotrophs are common in anoxic environments, particularly in marine sediments. Where does the methane come from? F  ossil fuels, animal digestion, wastewater treatment, agriculture, plant emissions… There exist two kinds of bacteria:

Type I: if we can see the structures in the center. Type II: structures surrounding the cell mbr. Methanotrophy in Bacteria methane as C source: methane ➔ methanol ➔ formaldehyde ➔ type I / type II Type I: ribulose monophosphate pathway. Type II: serine pathway.

origin of methane? ➔ methanogenic archaea, using CO2  as e -  acceptor.

*Methanotrophic symbionts of marine mussels as “primary producers”. 4. Phylum Spirochaetes ● ● ●

Gram-negative. Aquatic and animal-associated environments; some pathogens. Unique morphology; endoflagella. 19

❖ Genus T  reponema ● ●

Animal and humans hosts. Microaerophilic and very sensitive to environmental stress. T. pallidum: syphilis. Here we can talk about ‘chancros sifilíticos’. If untreated, it can end with insuficiencia aórtica, granuloma en los huesos e inflamación meningovascular.

5. Phylum Bacteroidetes ● ● ●

Gram-negative. Chemoorganoheterotrophs (most), aerobes/anaerobes. Habitats: gastrointestinal tracts, hypersaline environments, water and soil.

 acteroides ❖ Genus B ● ●

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Rods, strict anaerobes (fermentation). Intestinal comensals (pathogens). They form part of the human microbiota, concretely of the small and large intestines (the most abundant). They also are part of the rumen microbiota in ruminant animals, like cows, sheeps, goats and deers. They perform microbial metabolism and they have to do with obesity. they don’t have e.t.c., so the only way to obtain ATP is by substrate-phosphorylation.

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intraabdominal infections. appendicitis.

 ytophaga ❖ Genera C ● ● ●

Abundant in soils and waters. Many species degrade complex exoenzymes. Some fish pathogens.

polymers

(cellulose,

agar,

chitin...)

with

❖ Genera S  alinibacter ● ● ● ●

Extremely halophilic (hypersaline environments: solar salterns, hypersaline lakes, saline soils…). Aerobic chemoorganotrophic rod. Xanthorhodopsin. Accumulates K+ intracellularly (halorhodopsin). Most important species: S. ruber

6. Phylum Actinobacteria ●

Gram-positive.

❖ Genera C  orynebacterium ● ● ●

Facultative anaerobic rods. Harmless and pathogens. C. diphtheriae: diphtheria toxin. It affects the upper respiratory tract.

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“Se mantiene por los portadores asintomáticos y por los huéspedes no vacunados. Portadores: faringe y piel. Se transmite de persona a persona mediante la exposición a las gotas respiratorias o el contacto cutáneo”. It can be fatal if untreated.

❖ Genera Mycobacterium ● ● ●

Mycolic acids in the cell mbr. Ziehl-Neelsen (or acid fast) staining. Mycobacterium tuberculosis .

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Mycobacterium leprae. “Folded, bulblike lesions on the body, especially on cooler parts such as the face and extremities. The lesions are due to the growth of M. leprae cells in the skin and contain large numbers of bacterial cells. In severe cases, the disfiguration leads to destruction of peripheral nerves; muscles then atrophy and motor function is impaired.” only transmitted by air. not very easy to transmit, you have to have a really close contact to get the disease.

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 treptomyces ❖ Genera S ● ● ● ● ● ● ●

Filaments without cross walls.  ndospores). Mycelium and spores (not  e > 500 species, soil bacteria. Pigments / geosmines. Aerobic chemoorganotrophs. Many produce antibiotics. Antibiotic production.

8. Phylum Firmicutes ●

Gram-positive.

8.1. Endospore-forming bacteria ●

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Rods: ○ aerobic or facultatively aerobic: Bacillus. ○ anaerobic: Clostridium. ○ phototrophic: Heliobacter. Cocci.

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❖ Bacillus ● ●

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 nd B. Some of them are mesophiles, for example: B. cereus, B. anthracis a thuringiensis. B. thuringiensis: insect pathogen (parasporal crystal).

B. anthracis: transmission: contact (cutaneous), ingestion (gastrointestinal) or inhalation (respiratory, fatal septicemia) of endospores. B. cereus: foodborne toxiinfection.

❖ Clostridium ● ● ● ● ●

C, N and S cycles. Some of them are able to fix N2. They perform two kinds of fermentations: butyric fermentation and Stickland reaction (with acetate as product). C. perfringens: gas gangrene. Infection causing necrosis of multiple tissues. Ischemic injures. Septicemia, surgery. Some strains also produce food poisoning. C. tetani: tetanus toxin.

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C. botulinum: botulinum toxin. It is the most potent. Botox. You can find it in canned foods (pH > 4.6). Infant botulism: honey.

❖ Heliobacteria: anoxygenic phototrophs ● ● ● ● ● ●

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C and S cycles. Strict anaerobes and heterotrophs. Reducing power from sulfur compounds. They can fix N2 . Helio-. ATP: ○ donor: BChl* ○ acceptor: Bchl oxidized ○ ATP: cyclic photophosphorylation Reducing power: non-cyclic photosynthetic flow Elements: ○ reaction center: BChl ○ antenna: BChl/carotenoids ○ electron transport chain: cell mbr

8.2. Lactic acid bacteria (LAB) ● ● ● ●

Cocci (in chains or tetrads) and rods (typically in chains). They produce lactic acid by fermentation. Homofermentatives: glucose ➔ 2 lactates Heterofermentatives: glucose ➔ 1 lactate + 1 ethanol + 1 CO2

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❖ Streptococci ● ● ● ●

Chains of cocci. Homofermentatives. We can distinguish between hemolytic and non-hemolytic. Genera: Streptococcus, Lactococcus and Enterococcus.

❖ Streptococcus ● ●

β - hemolytic: S. pyogenes ➔  faringitis, celulitis, bacteriemia… U  pper respiratory tract infections. Non β - hemolytic: S. pneumoniae ( neumococcus) and S. mutans ( dental decay). Lower respiratory tract infections.

❖ Lactobacillus ● ●
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