Proteobacteria PDF

Proteobacteria Largest and most metabolically diverse phylum of bacteria. Account for more than a third of characterized bacteria species. All are gram-negative bacteria. Show a wide variety of energy-generating mechanisms: chemolithotrophic, chemoorganotrophic, and p...

Proteobacteria Largest and most metabolically diverse phylum of bacteria. Account for more than a third of characterized bacteria species. All are gram-negative bacteria. Show a wide variety of energy-generating mechanisms: chemolithotrophic, chemoorganotrophic, and phototrophic. Six classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, and Zetaproteobacteria. Horizontal gene flow has likely played a role in shaping the metabolic diversity of Proteobacteria. Alphaproteobacteria Second largest class of Proteobacteria, with about 1,000 described species. Most species are obligate aerobes or facultative aerobes. Many are oligotrophic, preferring environments with low nutrient concentration. Most species fall within the following orders: Rhizobiales, Rickettsiales, Rhodobacterales, Rhodospirillales, Caulobacterales, and Sphingomonadales. Key Genera of Alphaproteobacteria Rhizobiales: Includes phototrophs (e.g., Rhodopseudomonas), chemolithotrophs (e.g., Nitrobacter), symbionts (e.g., rhizobia), free-living nitrogen-fixing bacteria (e.g., Beijerinckia), some pathogens of plants and animals, and diverse chemoorganotrophs. ○ Rhizobia: a polyphyletic collection of genera that form root nodules and fix nitrogen in symbiotic association with leguminous plants.(Chemoorganotrophs + obligate aerobes) ○ Agrobacterium tumefaciens: closely related to Rhizobium but is a plant pathogen that causes crown gall disease. It cannot form root nodules. ○ Methylobacterium: often called “pink-pigmented facultative methylotrophs” due to their pink colonies and ability to grow on methanol. Commonly found on plants, in soils, and freshwater. Also found in toilets and baths, where they form pink biofilms. ○ Bartonella: intracellular pathogens of humans, transmitted by arthropods like fleas, lice, and sand flies. Cause a variety of diseases in humans and other vertebrates. Fastidious and difficult to cultivate. ○ Pelagibacter ubique: an oligotroph and obligately aerobic chemoorganotroph found in the ocean's photic zone. Can make up to 50% of bacterial cells in temperate waters in summer, making it likely the most abundant bacterial species on Earth. Rickettsiales: All are obligate intracellular parasites or mutualists of animals. ○ Cannot be cultivated without host cells. ○ Closely associated with arthropods and transmitted by their bites.  ○ Rickettsia: causative agents of several human diseases, including typhus and Rocky Mountain spotted fever. ○ Wolbachia: intracellular parasites of many insects, affecting their reproduction by inducing parthenogenesis, killing males, or feminizing them. Other groups: ○ Rhodobacterales and Rhodospirillales: metabolically diverse, including purple nonsulfur bacteria, aerobic anoxygenic phototrophs, nitrogen-fixing bacteria, denitrifiers, methylotrophs, and magnetotactic bacteria. ○ Caulobacterales: typically oligotrophic and strictly aerobic chemoorganotrophs. Form prosthecae or stalks and display asymmetric cell division. Caulobacter is the characteristic genus. ○ Sphingomonadales: diverse aerobic and facultatively aerobic chemoorganotrophs, some aerobic anoxygenic phototrophs, and a few obligate anaerobes. Sphingomonas is the characteristic genus, known for metabolizing various organic compounds, including environmental contaminants. (Bioremediation) Zymomonas - ferments sugars into ethanol Betaproteobacteria Third-largest class of Proteobacteria, with about 500 described species. Contain significant functional diversity. Six orders with many characterized species: Burkholderiales, Hydrogenophilales, Methylophilales, Neisseriales, Nitrosomonadales, and Rhodocyclales. Key Genera of Betaproteobacteria Burkholderiales: Diverse metabolic and ecological characteristics, including aerobic, facultatively aerobic, and anaerobic chemoorganotrophs; anoxygenic phototrophs; chemolithotrophs; nitrogen fixers; and pathogens. ○ Burkholderia: metabolically versatile chemoorganotrophs, some able to fix N2. Their ability to degrade organic compounds makes them potentially useful in bioremediation. Some strains promote plant growth, but many are pathogenic to plants or animals. B. cepacia is an opportunistic pathogen, a major cause of soft rot in onions, and can cause lung infections in humans. ○ Strictly metabolizes through respiratiion Rhodocyclales: diverse metabolic and ecological characteristics. ○ Rhodocyclus: purple nonsulfur bacteria that grow best as photoheterotrophs but can also grow as photoautotrophs or by respiration in darkness. Found in illuminated anoxic environment ○ Zoogloea: aerobic chemoorganotrophs that produce a thick gelatinous capsule, causing flocculation in wastewater treatment. Z. ramigera is important in aerobic wastewater treatment, degrading organic carbon and promoting flocculation and settling.  Neisseriales: at least 29 genera of diverse chemoorganotrophs. ○ Neisseria: cocci commonly isolated from animals, some pathogenic. N. meningitidis causes meningitis, and N. gonorrhoeae causes gonorrhoea. ○ Chromobacterium: rod-shaped, closely related to Neisseria. C. violaceum produces the purple pigment violacein, which has antimicrobial and antioxidant properties. Hydrogenophilales, Methylophilales, and Nitrosomonadales: contain chemolithotrophs and methylotrophs; most are obligate aerobes, and many are autotrophic. ○ Hydrogenophilus thermoluteolus: a facultative chemolithotroph that can use H2 as an electron donor and fix CO2 using the Calvin cycle. Can also grow as a chemoorganotroph. (Obligate aerobes) ○ Thiobacillus: chemoorganotrophs or chemolithotrophs. Chemolithotrophic species are sulfur bacteria that oxidize reduced sulfur compounds and can fix CO2. ○ Methylophilus: obligate and facultative methylotrophs that grow on methanol and other C1 compounds. ○ Nitrosomonadales: obligately chemolithotrophic ammonia-oxidizing bacteria, with Nitrosomonas and Nitrosospira being key genera. Gammaproteobacteria: Enterobacteriales Largest and most diverse class of Proteobacteria, containing almost half of all characterized species. Over 1500 characterized species across 15 orders. Diverse metabolic and ecological characteristics, including phototrophic, chemoorganotrophic, and chemolithotrophic species, with respiratory or fermentative metabolisms. Enterobacteriales (enteric bacteria): a large and well-known order within Gammaproteobacteria. Characteristics of Enterobacteriales Facultatively aerobic, gram-negative, nonsporulating rods. Nonmotile or motile by peritrichous flagella. Oxidase-negative and catalase-positive. Produce acid from glucose and reduce nitrate to nitrite. Simple nutritional requirements and ferment sugars to various end products. Include many species pathogenic to humans, animals, or plants, as well as some with industrial importance. Identification in clinical laboratories is based on a combination of diagnostic tests, immunological analyses, and genomic analyses. Fermentation Patterns in Enteric Bacteria Two broad patterns: mixed-acid fermentation and 2,3-butanediol fermentation.  Mixed-acid fermentation: produces significant amounts of acetic, lactic, and succinic acids, along with ethanol, CO2, and H2. 2,3-butanediol fermentation: produces smaller amounts of acids, with butanediol, ethanol, CO2, and H2 being the main products. Mixed-acid fermenters produce equal amounts of CO2 and H2, while butanediol fermenters produce more CO2 than H2. Key Genera of Enterobacteriales Mixed-acid fermenters: Escherichia, Salmonella, Shigella, and Proteus. ○ Escherichia coli: inhabits the intestinal tract of humans and other warm-blooded animals. Synthesizes vitamins, consumes O2, and renders the large intestine anoxic. Some strains are pathogenic and cause diarrheal diseases, urinary tract infections, and foodborne illnesses. ○ Salmonella: closely related to Escherichia but almost always pathogenic to humans or other warm-blooded animals. Causes typhoid fever and gastroenteritis. ○ Shigella: genetically close to Escherichia, with significant gene exchange through horizontal gene flow. Pathogenic to humans, causing bacillary dysentery. S. dysenteriae invades intestinal epithelial cells and releases a neurotoxin. ○ Proteus: highly motile cells that produce urease. A frequent cause of urinary tract infections. Exhibits a characteristic swarming phenotype on agar plates due to variations in motility between cells at the edge and center of the colony. Butanediol Fermenters: Enterobacter, Klebsiella, and Serratia. ○ Enterobacter aerogenes: commonly found in water, sewage, and the intestines of warm-blooded animals. Occasionally causes urinary tract infections. ○ Klebsiella pneumoniae: can cause pneumonia in humans but is more commonly found in soil and water. Most strains fix nitrogen. ○ Serratia: produces red pigments called prodigiosins, which contain the pyrrole ring found in pigments for energy transfer. Can be isolated from various environments and occasionally causes infections in humans. S. marcescens can cause infections in many body sites and contaminate intravenous fluids. Gammaproteobacteria: Pseudomonadales and Vibrionales Key Genera of Pseudomonadales and Vibrionales Pseudomonadales: chemoorganotrophs with respiratory metabolisms. ○ All species can grow aerobically and are typically oxidase- and catalase-positive. ○ Ubiquitous in soil and aquatic systems, some species are pathogenic to plants and animals.  ○ Pseudomonas aeruginosa: commonly associated with urinary and respiratory tract infections in humans. An opportunistic pathogen that often causes hospital-acquired infections. Naturally resistant to many antibiotics. ○ Pseudomonas syringae: a well-known plant pathogen that releases toxins, enzymes, and growth factors that damage plant tissue. Vibrionales: facultatively aerobic rods and curved rods with a fermentative metabolism. ○ Oxidase-positive, unlike enteric bacteria. ○ Most species are aquatic, found in marine, brackish, or freshwater habitats. ○ Vibrio cholerae: causes cholera in humans, transmitted through water. ○ Vibrio parahaemolyticus: a marine bacterium that causes gastroenteritis, often from consuming raw fish. Deltaproteobacteria and Epsilonproteobacteria Key Genera of Deltaproteobacteria and Epsilonproteobacteria Deltaproteobacteria: primarily sulfate- and sulfur-reducing bacteria, dissimilative iron-reducers, and bacterial predators. ○ Eight orders characterized. ○ Myxococcales (wolf-pack attack) and Bdellovibrionales: contain bacterial predators. ○ Desulfuromonadales: contains metal- and sulfur-reducing genera like Geobacter (consume oil-based). ○ Desulfovibrionales: the largest and most common order containing sulfate reducers. ○ Syntrophobacterales: some species reduce sulfate, but most interact with H2-consuming bacteria in syntrophy. Syntrophobacter wolinii oxidizes propionate and can grow as a sulfate reducer or ferment pyruvate, fumarate, or malate. Epsilonproteobacteria: contain many species that oxidize H2S produced by sulfate and sulfur reducers. Abundant at oxic–anoxic interfaces in sulfur-rich environments. ○ Campylobacter and Helicobacter: gram-negative, oxidase- and catalase-positive, motile spirilla. Most species are pathogenic to humans or animals. Microaerophilic and require low O2 and high CO2 for growth. ○ Campylobacter: causes acute gastroenteritis, often resulting in bloody diarrhea. Pathogenesis is due to an enterotoxin related to cholera toxin. ○ Helicobacter pylori: causes chronic and acute gastritis, leading to peptic ulcers. ○ Sulfurospirillum: nonpathogenic, free-living microaerophiles found in freshwater and marine habitats. Carry out anaerobic respirations using S0, selenate, or arsenate as electron acceptors. ○ Wolinella: an anaerobic bacterium found in the bovine rumen. The only known species, W. succinogenes, grows best anaerobically and can catalyze  anaerobic respirations using fumarate or nitrate as electron acceptors. Its genome suggests it may inhabit diverse environments beyond the rumen. Environmental Epsilonproteobacteria: Play important ecological roles, especially in sulfur-cycling activities. Abundant in deep-sea hydrothermal vent habitats. May detoxify H2S for their animal hosts, allowing them to thrive in these environments. II Firmicutes, Tenericutes, and Actinobacteria Account for almost half of all characterized species of bacteria. Actinobacteria: primarily filamentous soil bacteria with high GC content in their DNA. Tenericutes: cells that lack a cell wall. Firmicutes: include endospore-forming bacteria, lactic acid bacteria, and other groups. Generally have low GC content in their DNA. The document goes on to discuss Firmicutes that do not form endospores.