Chapter 16 Lecture 1 Phylogenetic Diversity of Bacteria PDF

Phylogenetic Diversity of Bacteria Lecture 1 Gram-negative Bacteria T: +27(0)51 401 9111 | [email protected] | www.ufs.ac.za  Contents Background – Lecture 1 Gr...

Phylogenetic Diversity of Bacteria Lecture 1 Gram-negative Bacteria T: +27(0)51 401 9111 | [email protected] | www.ufs.ac.za  Contents Background – Lecture 1 Gram-negative Bacteria – Lecture 1 Gram-positive Bacteria – Lecture 2 Chlamydiae, Planctomycetes, and Verrucomicrobia – Lecture 3 Hyperthermophilic Bacteria – Lecture 3 Other Bacteria – Lecture 3  Background to Diversity of Bacteria Hierarchical System of Classification © 2019 Pearson Education Ltd.  Background to Diversity of Bacteria Phylogenetic overview of Bacteria 80+ phyla can be distinguished based on 16S rRNA sequences Only 30 phyla have species successfully cultured More than 90% of characterized genera and species come from four phyla (out of 100 phyla) Proteobacteria (Gram -) Actinobacteria (Gram +) Firmicutes (Gram +) Bacteroidetes should be Bacteroidota (Gram -) © 2019 Pearson Education Ltd. PHYLUM: PROTEOBACTERIA  Proteobacteria Largest group – best studied – easy to culture Exceptionally metabolically diverse 6 Classes – Alpha () – Beta () – Gamma () – Delta () – Epsilon () – Zeta (z)  Proteobacteria Only generalization is Gram-negative Majority of known medically, industrially, and agriculturally significant bacteria Diverse energy generation mechanisms Diverse relationships with oxygen Variety of morphologies  Proteobacteria Class: Alphaproteobacteria Nearly 1000 described species Most are obligate aerobes or facultative aerobes Many are oligotrophic (grow at low nutrient concentrations) Ten orders described Majority of species in six major orders  Alphaproteobacteria Order: Rhizobiales Many host-associated intracellular species Nine genera contain rhizobia – collection of genera that form root nodules and fix nitrogen in symbiotic association with legumes – HGT Agrobacterium tumefaciens – crown gall disease (forms tumors) – cannot form nodules – gall formation genes unrelated to nodule formation genes but found on plasmid  Alphaproteobacteria Order: Rhizobiales Methylobacterium: “pink-pigmented facultative methylotrophs” Found on plants, in soils and freshwater systems, in toilets and baths Bartonella: Intracellular pathogens mediated by arthropod vectors Pelagibacter P. ubique: oligotrophic, obligately aerobic chemoorganotroph that grows in ocean photic zones; likely most abundant bacterial species on Earth © 2019 Pearson Education Ltd.  Alphaproteobacteria Order: Rickettsiales Obligate intracellular parasites or mutualists of animals Not yet cultured in absence of host cells; require growth in chicken eggs or host cell tissue culture Typically associated with arthropods © 2019 Pearson Education Ltd.  Alphaproteobacteria Order: Rickettsiales Rickettsia Causative agent of several human diseases Typhus (Rickettsia prowazekii) Rocky Mountain spotted fever (Rickettsia rickettsii) Transmitted by ticks, fleas, lice, and mites Unable to synthesize some metabolites and obtain them from host Have cell walls Replication occurs in cytoplasm, host cell bursts and frees cells © 2019 Pearson Education Ltd.  Alphaproteobacteria Order: Ricketssiales Wolbachia Intracellular parasites of many insects Can induce parthenogenesis (development of unfertilized eggs) killing of males Figure 16.6 Wolbachia. Photomicrograph feminization (conversion of male into female) of a DAPI-stained egg of the parasitoid wasp Trichogramma kaykai infected with W. pipientis best studied Wolbachia pipientis, which induces parthenogenesis. The W. pipientis cells are primarily located in the narrow end of the egg (arrows).  More Alphaproteobacteria Rhodobacterales and Rhodospirillales Purple nonsulfur bacteria, aerobic anoxygenic phototrophs, nitrogen-fixing bacteria, denitrifiers, methylotrophs, magnetotactic bacteria Caulobacterales Typically oligotrophic and strictly aerobic chemoorganotrophs Form prosthecae or stalks Many divide asymmetrically Sphingomonadales Diverse aerobic and facultatively aerobic chemoorganotrophs, aerobic anoxygenic phototrophs, few obligate anaerobes Notable for ability to metabolize organic compounds including aromatic environmental  Class: Betaproteobacteria > 500 described species – Third largest class of Proteobacteria Most are aerobic 6 major orders – Burkholderiales (will discuss) – Rhodocyclales (will discuss) – Neisseriales (will discuss) – Nitrosomonadales - Nitrosifying bacteria - ammonia-oxidizing – Hydrogenophilales – use H2 as e- donor – Methylophilales - obligate and facultative methylotrophs that grow on methanol and other C1 compounds, but not on CH4  Class: Betaproteobacteria Order: Burkholderiales Wide range of metabolic and ecological characteristics Organic decomposers Burkholderia Strict respiratory chemoorganotrophs All species grow aerobically Some can grow anaerobically Some can fix nitrogen B. cepacia (Figure 16.8) Pathogenic Can produce antifungal and antinematodal compounds Opportunistic hospital-acquired infection in humans  Class: Betaproteobacteria Order: Rhodocyclales Rhodocyclales: Rhodocyclus, Zoogloea Diverse metabolic and ecological characteristics Rhodocyclus Purple nonsulfur Zoogloea Produces thick capsule – causes flocculation – important in wastewater treatment  Class: Betaproteobacteria Order: Neisseriales Genera: Chromobacterium, Neisseria Diverse chemoorganotrophs Neisseria Commonly isolated from animals Some pathogenic (N. gonorrhoeae and N. meningitides) Always cocci Chromobacterium Rod-shaped, facultative aerobe Some species produce antimicrobial and antioxidant pigment violacein Class: Gammaproteobacteria  Class: Gammaproteobacteria Order: Enterobacteriales Key genera: Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, Serratia, Shigella Largest, most diverse class of Proteobacteria Diverse metabolic and ecological characteristics Enteric bacteria  Class: Gammaproteobacteria Order: Enterobacteriales Phylogenetic group within the Gammaproteobacteria Facultative aerobic, nonsporulating rods, sometimes motile by peritrichous flagella Oxidase (negative) and catalase (positive) tests can be used to discriminate enteric from many other bacteria Relatively simple nutritional requirements Ferment sugars to a variety of end products Many pathogens and many industrially important bacteria  Class: Gammaproteobacteria Order: Enterobacteriales Fermentation patterns: two broad groups - type and proportion of fermentation products generated by anaerobic fermentation of glucose Mixed-acid fermentation: acetic, lactic, and succinic acid formed in significant amounts; ethanol, CO2, and H2 also formed with CO2 and H2 in equal amounts via formate hydrogenlyase Escherichia, Salmonella, Shigella, Citrobacter, Proteus, Yersinia 2,3-butanediol fermentation: Butanediol, ethanol, CO2, H2 are main products; smaller amounts of acids formed Enterobacter, Klebsiella, Erwinia, Serratia Figure 16.12 Enteric fermentations. Distinction between (a) mixed-acid and (b) butanediol fermentation in enteric bacteria ( Figure 14.57). The solid arrows indicate reactions leading to major products. Dashed arrows indicate minor products. (a) The photo shows the production of acid (yellow) and gas (in the inverted Durham tube) in a culture of Escherichia coli carrying out a mixed-acid fermentation (purple tube was uninoculated). (b)(b) The photo shows the pink- red color in the Voges– Proskauer (VP) test, which indicates butanediol production, following growth of Enterobacter aerogenes. The left (yellow) tube was not  Gammaproteobacteria Order: Enterobacteriales Mixed-acid fermenters: Escherichia, Salmonella, Shigella, and Proteus Escherichia Universal inhabitants of intestinal tract of humans and warm-blooded animals Synthesize vitamins (particularly vitamin K) for host Facultative aerobe that helps make large intestine anoxic Some strains are pathogenic (diarrhea, urinary tract infections in women, gastrointestinal infections and foodborne disease) Salmonella and Shigella Closely related to Escherichia Almost always pathogenic Typhoid fever and gastroenteritis (Salmonella) and bacillary dysentery (Shigella) Proteus – Urinary tract infections (swarming motility)  Gammaproteobacteria Order: Enterobacteriales Butanediol fermenters: Enterobacter, Klebsiella, and Serratia Closely related group of organisms Enterobacter aerogenes Found in water, sewage, and intestinal tract of warm-blooded animals May cause urinary tract infection Klebsiella K. pneumoniae occasionally causes pneumonia Found in soil and water Most strains fix nitrogen Serratia – Forms red pyrrole-contaning pigments called prodigiosins (Figure 16.14) – Found in water, soil, and intestinal tracts of insects and vertebrates – May cause infection (S. marcescens)  Gammaproteobacteria Order: Pseudomonadales Key genera: Pseudomonas Aerobic respiratory chemoorganotrophs Oxidase- and catalase-positive Some can respire anaerobically with nitrate as electron acceptor Most use a variety of organic compounds Can cause plant and animal diseases Pseudomonad: polarly flagellated, aerobic rod that uses diverse carbon sources P. aeruginosa (Figure 16.15) associated with opportunistic urinary and respiratory disease P. syringae and P. marginalis are plant pathogens  Gammaproteobacteria Order: Vibrionales Key genera: Vibrio Facultatively aerobic rods and curved rods that ferment Oxidase-positive Mostly aquatic Several bioluminescenct V. cholera causes cholera in humans, not other hosts V. parahaemolyticus causes gastroenteritis  Class: Deltaproteobacteria Key genera: Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter, Syntrophobacter Eight orders characterized Bacterial predators (Myxococcales and Bdellovibrionales) Metal and sulfur reducers (Desulfuromonadales, Desulfovibrionales, Desulfobacterales, Desulfarculales, Syntrophobacterales)  Class: Epsilonproteobacteria Many oxidize H2S Key genera: Campylobacter, Helicobacter Important ecological roles (Table 16.2) Campylobacter and Helicobacter Oxidase- and catalase-positive, motile spirilla Most pathogenic to humans and animals Microaerophilic Campylobacter cause acute gastroenteritis resulting in bloody diarrhea Helicobacter pylori causes chronic and acute gastritis and peptic ulcers Table 16.2  Class: Epsilonproteobacteria Ubiquitous in marine and terrestrial environments Particularly abundant where sulfur-cycling occurs (deep-sea hydrothermal vents and marine sediments) Thermophiles common Chemolithotrophy and autotrophy (reverse TCA) Many grow aerobically or anaerobically with oxidized nitrogen/sulfur as electron acceptor and using inorganic electron donors CO2 fixation important for animals living in sulfur-rich environments Ecto- and endosymbionts with many animals PHYLUM: BACTEROIDOTA  Phylum: Bacteroidota 1000+ characterized species Four primary orders: Bacteroidales, Cytophagales, Flavobacteriales, Sphingobacteriales Gram-negative, nonsporulating rods Typically saccharolytic Aerobic or fermentative Gliding motility common; many nonmotile; few flagellated  Phylum: Bacteroidota Order: Bacteroidales Key genera: Bacteroides – Primarily obligately anaerobic fermenters – Normally commensals found in human and animal intestinal tracts – Numerically dominant bacterium in human large intestine – Occasionally pathogenic; can be associated with bacteremia (bacteria in blood) – Bacteroides thetaiotaomicron Degrades polysaccharides in human digestive tract Synthesize sphingolipids, which are normally found in mammalian tissues but rare in bacteria  Phylum: Bacteroidota Orders: Cytophagales, Flavobacteriales, and Sphingobacteriales Key genera: Cytophaga, Flavobacterium, Flexibacter Cytophagales – Almost exclusively obligate aerobes, though some ferment – Long, slender, Gram-negative rods – Move by gliding (Figure 16.42) – Degrade complex polysaccharides such as cellulose or chitin – Widespread in soils and freshwaters – Some fish pathogens (columnaris and cold-water diseases)  Phylum: Bacteroidota Orders: Cytophagales, Flavobacteriales, and Sphingobacteriales Flavobacteriales and Sphingobacteriales – Typically aerobic and facultatively aerobic chemoorganotrophs – Saccharolytic rods that often move by gliding – Found widely in soils and aquatic habitats – Flavobacterium Found primarily in aquatic environments and foods/food-processing plants Mostly obligate aerobes Frequently yellow pigmented Rarely pathogenic, though F. meningosepticum affects infants, and several fish pathogens known  Phylum: Bacteroidota Orders: Cytophagales, Flavobacteriales, and Sphingobacteriales Flavobacteriales and Sphingobacteriales – Some Flavobacteriales are psychrophilic or psychrotolerant (e.g., Polaribacter and Psychroflexus) – Sphingobacteriales phenotypically similar to many Flavobacteriales Able to degrade a wide range of complex polysaccharides e.g., Flexibacter – differs from Cytophaga because it requires complex media for growth and not cellulolytic – common in soil and freshwater – none pathogenic