Bacteria : The Proteobacteria

1. Bacteria: The Proteobacteria Chapter 17

2. The Phylogeny of Bacteria I. Phylum Proteobacteria

3. The Phylogeny of Bacteria – Major phyla of domain Bacteria Phylogenetic Overview of Bacteria

4. Phylum Proteobacteria • A major lineage (phyla) of Bacteria • Includes many of the most commonly encountered bacteria • Most metabolically diverse of all domain Bacteria • E.g., chemolithotrophy, chemoorganotrophy, phototrophy • Morphologically diverse • Divided into five classes • Alpha-, Beta-, Delta-, Gamma-, Epsilon-

5. Major Genera of Proteobacteria

6. 1. Purple Phototrophic Bacteria 2. The Nitrifying Bacteria 3. Sulfur- and Iron-Oxidizing Bacteria 4. Hydrogen-Oxidizing Bacteria 5. Methanotrophs and Methylotrophs II Phototrophic, Chemolithotrophic & Methanotrophic Proteobacteria

7. 1. Purple Phototrophic Bacteria • Purple Phototrophic Bacteria • Carry out anoxygenic photosynthesis; no O2 evolved • Morphologically diverse group • Genera fall within the Alpha-, Beta-, or Gammaproteobacteria • Contain bacteriochlorophylls and carotenoid pigments • Produce intracytoplasmic photosynthetic membranes with varying morphologies

8. Liquid Cultures of Phototrophic Purple Bacteria Figure 15.2

9. Membrane Systems of Phototrophic Purple Bacteria Figure 15.3

10. Purple Phototrophic Bacteria • Purple Sulfur Bacteria • Use hydrogen sulfide (H2S) as an electron donor for CO2 reduction in photosynthesis • Sulfide oxidized to elemental sulfur (So) that is stored as globules either inside or outside cells • Sulfur later disappears as it is oxidized to sulfate (SO42-)

11. Photomicrographs of Purple Sulfur Bacteria Figure 15.4

12. Purple Phototrophic Bacteria • Purple Sulfur Bacteria (cont’d) • Many can also use other reduced sulfur compounds, such as thiosulfate (S2O32-) • All are Gammaproteobacteria • Found in illuminated anoxic zones of lakes and other aquatic habitats where H2S accumulates, as well as sulfur springs

13. Genera and Characteristics of Purple Sulfur Bacteria

14. Genera and Characteristics of Purple Sulfur Bacteria

15. Genera and Characteristics of Purple Sulfur Bacteria

16. Blooms of Purple Sulfur Bacteria Figure 15.5

17. Purple Non-sulfur Bacteria • Purple Nonsulfur Bacteria • Originally thought organisms were unable to use sulfide as an electron donor for CO2 reduction, now know most can • Most can grow aerobically in the dark as chemoorganotrophs • Some can also grow anaerobically in the dark using fermentative or anaerobic respiration • Most can grow photoheterotrophically using light as an energy source and organic compounds as a carbon source • All in Alpha- and Betaproteobacteria

18. Representatives of Purple Nonsulfur Bacteria Figure 15.6

19. Genera and Characteristics of Purple Nonsulfur Bacteria

20. Genera and Characteristics of Purple Nonsulfur Bacteria

21. 2. The Nitrifying Bacteria • Nitrifying Bacteria • Able to grow chemolithotrophically at the expense of reduced inorganic nitrogen compounds • Found in Alpha-, Beta-, Gamma-, and Deltaproteobacteria • Nitrification (oxidation of ammonia to nitrate) occurs as two separate reactions by different groups of bacteria • Ammonia oxidizers (nitrosifyers) (e.g., Nitrosococcus) • Nitrite oxidizer (nitrifyer) (e.g., Nitrobacter) • Many species have internal membrane systems that house key enzymes in nitrification • Ammonia monooxygenase: oxidizes NH3 to NH2OH • Nitrite oxidase: oxidizes NO2- to NO3-

22. Nitrifying Bacteria (cont’d) • Widespread in soil and water • Highest numbers in habitats with large amounts of ammonia • i.e., sites with extensive protein decomposition and sewage treatment facilities • Most are obligate chemolithotrophs and aerobes • One exception is annamox organisms, which oxidize ammonia anaerobically

23. Figure 15.7

24. As carbon dioxide rises, food quality will decline without careful nitrogen management http://californiaagriculture.ucanr.edu/landingpage.cfm?article=ca.v063n02p67&fulltext=yes

25. http://hoorayfordecaycomposting.com/2013/01/28/the-nitrogen-cycle/http://hoorayfordecaycomposting.com/2013/01/28/the-nitrogen-cycle/

26. 3. Sulfur- and Iron-Oxidizing Bacteria • Sulfur-Oxidizing Bacteria • Grow chemolithotrophically on reduced sulfur cmpds • Two broad classes • Neutrophiles • Acidophiles (some also use ferrous iron (Fe2+) • Thiobacillus (rods) • Sulfur compounds most commonly used as electron donors are H2S, So, S2O32-; generates sulfuric acid • Achromatium (spherical cells) Common in freshwater sediments • Some obligate chemolithotrophs possess special structures that house Calvin cycle enyzmes (carboxysomes)

27. Beggiatoa • Filamentous, gliding bacteria • Found in habitats rich in H2S • e.g., sulfur springs, decaying seaweed beds, mud layers of lakes, sewage polluted waters, and hydrothermal vents • Most grow mixotrophically • with reduced sulfur compounds as electron donors • and organic compounds as carbon sources • Thioploca • Large, filamentous sulfur-oxidizing bacteria that form cell bundles surrounded by a common sheath • Thick mats found on ocean floor off Chile and Peru • Couple anoxic oxidation of H2S with reduction of NO3- to NH4+

28. Non-filamentous Sulfur Chemolithotrophs Filamentous Sulfur-Oxidizing Bacteria Figure 15.9

29. Sulfur- and Iron-Oxidizing Bacteria • Sulfur-Oxidizing Bacteria (cont’d) • Thiothrix • Filamentous sulfur-oxidizing bacteria in which filaments group together at their ends by a holdfast to form cellular arrangements called rosettes • Obligate aerobic mixotrophs

30. Thiothrix Figure 15.12

31. 4. Hydrogen-Oxidizing Bacteria • Hydrogen-Oxidizing Bacteria: • Most can grow autotrophically with H2 as sole electron donor and O2 as electron acceptor (“knallgas” reaction) • Both gram-negative and gram-positive representatives known • Contain one or more hydrogenase enzymes that function to bind H2 and use it to either produce ATP or for reducing power for autotrophic growth • Most are facultative chemolithotrophs and can grow chemoorganotrophically • Some can grow on carbon monoxide (CO) as electron donor (carboxydotrophs)

32. Hydrogen Bacteria Figure 15.13

33. Characteristics of Common Hydrogen-Oxidizing Bacteria

34. 5. Methanotrophs and Methylotrophs • Methylotrophs • Organisms that can grow using carbon compounds that lack C-C bonds [(CH3)2N (trimethylamine)HCOO-(formate), CH3OCOO CH3 (Dimethyl carbonate), (CH3)2SO (dimethyl sulfoxide), CH3OH (methanol), CH3NH2 (methylamine), CH3)2NH (dimethylamine)] • Most are also methanotrophs – use CH4 • Methanotrophs • Use CH4and a few other one-carbon (C1) compounds as electron donors and source of carbon • Widespread in soil and water • Obligate aerobes • Morphologically diverse

35. 5. Methanotrophs and Methylotrophs Methanotrophs (cont'd) • Methanotrophs methane monooxygenase • Which incorporates an atom of oxygen from O2 into methane to produce methanol • Methanotrophs contain large amounts of sterols Classification of Methanotrophs • Two major groups: • Type I • Type II • Contain extensive internal membrane systems for methane oxidation

36. 5. Methanotrophs and Methylotrophs Type I Methanotrophs • Assimilate C1 compounds via the ribulose monophosphate cycle • Gammaproteobacteria • Membranes arranged as bundles of disc-shaped vesicles • Lack complete citric acid cycle • Obligate methylotrophs Type II Methanotrophs • Assimilate C1 compounds via the serine pathway • Alphaproteobacteria • Paired membranes that run along periphery of cell

37. Electron Micrographs of Methanotrophs Type I membrane system Methylococcus capsulatans (β-Proteobacteria) Carbon asimilation pathwy: ribulose monophosphate pathway Type II membrane system Methylosinus (α Proteobacteria) Carbon assimilation pathway: serine Lookup the metabolic pathways for Methylomonas methanica (type II) and Methylococcuscapsulatans (type 1) in KEGG (http://www.genome.jp/kegg-bin/show_pathway?scale=0.35&query=methylocystis&map=map01100&scale=0.35&auto_image=&show_description=hide&multi_query=&show_module_list) Figure 15.14

38. Some Characteristics of Methanotrophic Bacteria

39. 5. Methanotrophs and Methylotrophs • Widespread in aquatic and terrestrial environments • Methane monooxygenase also oxidizes ammonia; competitive interaction between substrates • Certain marine mussels have symbiotic relationships with methanotrophs Ecology and Isolation of Methanotrophs

40. III Aerobic & Facultatively Aerobic Chemoorganotrophic Proteobacteria 1. Pseudomonads including Pseudomonas 2. Acetic Acid Bacteria 3. Free-Living Aerobic Nitrogen-Fixing Bacteria 4. Neisseria, Chromobacterium, & Relatives 5. Enteric Bacteria 6. Vibrio, Alivibrio, and Photobacterium 7. Rickettsias

41. 1. Pseudomonads including Pseudomonas • Key Genera: • Pseudomonas • Burkholderia • Zymomonas • Xanthomonas • All genera are: • Straight or curved rods with polar flagella • Stain gram negative Chemoorganotrophs • Obligate aerobes • Posses polar flagella • Phylogenetically, the group is scattered within the Proteobacteria

42. Typical Pseudomonad Colonies – eg Burkholderia cepacia Lophotrichous polar flagella Figure 15.16a Figure 15.16b

43. 1. Pseudomonads including Pseudomonas • Members of the genus Pseudomonas and related genera can be defined on the basis of phylogeny and physiological characteristics • Nutritionally versatile • Ecologically important organisms in water and soil • Some species are pathogenic • Includes human opportunistic pathogens and plant pathogens • Refer to the next two slides for an over view

44. Subgroups and Characteristics of Pseudomonads

45. Pathogenic Pseudomonads

46. Genus Zymomonas • Genus of large, gram-negative rods that carry out vigorous fermentation of sugars to ethanol • Used in production of fermented beverages

47. 2. Acetic Acid Bacteria • Organisms that carry out complete oxidation of alcohols & sugars • Leads to the accumulation of organic acids as end products • Motile rods • Aerobic • High tolerance to acidic conditions • Commonly found in alcoholic juices • Used in production of vinegar • Some can synthesize cellulose • Colonies can be identified on CaCO3 agar plates containing ethanol

48. A variety of soil microbes are capable of fixing N2 aerobically • Distributed in alpha, beta and gamma Proteobacteria 3. Free-Living Aerobic Nitrogen-Fixing Bacteria • The major genera of bacteria capable of fixing N2 nonsymbiotically are Azotobacter, Azospirillium, and Beijerinckia • Azotobacter are large, obligately aerobic rods; can form resting structures (cysts) • All genera produce extensive capsules or slime layers; believed to be important in protecting nitrogenase from O2 (nitrogenase is oxygen-sensitive)

49. Cells (2 um) Cysts (3 um) Azotobacter vinelandii Figure 15.18

50. Beijerinckia species produce colonies with abundant slime Cells of Derixia gummosa encased in slime Slime producing Nitrogen2-fixing Bacteria Figure 15.19a