Chapters 15 and 17

Proteobacteria
Largest group: The Proteobacteria

The Proteobacteria consist of five clusters (a,b,c,d,e) containing several genera. Greek letters: alpha, beta, gamma, delta, or epsilon

You do not have to know individual species
Proteobacter
Purple phototrophic bacteria
Nitrifying Bacteria
Sulfur and Iron-oxidizing
Hydrogen-Oxidizing
Methanotrophs and methylotrophs
Pseudomonas
Nitrogen-fixing

Phylum 1
Purple bacteria
Nitrifying (soil and water)
Sulfur and Iron-oxidizing
Hydrogen-Oxidizing Bacteria
Methanotrophs and methylotrophs
Pseudomonads
Nitrogen-fixing
Neisseria et al
Enterics
Vibrios and photobacterium
Rickettsias
Spirilla
Sheathed Proteobacteria
Budding and Prosthecate/Stalked Bacteria
Gliding Myxobacteria
Sulfate and sulfur- reducing Proteobacteria

Phyla 2 and 3
Non-sporulating, Gram-positive bacteria;Lactic Acid Bacteria and relatives
Staphylococcus;Micrococcus
Lactic Acid Bacteria; Lactobacillus
Streptococcus and other coccus
Listeria

Endospore-Forming, Gram-Positive Bacteria: Bacillus, Clostridium and relatives

Cell-Wall Less, Gram-Positive Bacteria: the Mycoplasma

Gram-Positive Bacteria: Corynebacteriua and Proprionic Acid Bacteria (Propionibacterium)

Mycobacterium

Streptomyces and other Actinomycetes

Human Inhabitants
Enteric rods: E. coli, Salmonella and Shigella, Proteus, Enterobacter, Klebsiella and Serratia
Vibrios
Rickettsias
Campylobacter and Helicobacter
Staphylococcus and Micrococcus
Lactobacillus
Streptococcus
Listeria
Bacillus
Clostridium
Mycoplasma
Corynebacteria
Mycobacteria
Actinomycetes
Chlamydia
Bacteriodes
Non-fermentative gram-negative rods

Taxonomy
Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions

Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.
G:C Ratios
Multilocus Sequence Typing
DNA:DNA Hybridization

Types of Metabolism
Phototrophic: obtains energy from light

Chemolithotrophic: oxidize inorganic compounds for energy

Chemoorganotrophic: obtains energy from the oxidation of organic compounds.

Autotrophic: use CO2 as nutrient source

Methanotrophs: use methane for energy

Nitrogen-fixing: reduction of nitrogen gas to ammonia

Homofermentative: fermentation of glucose or other sugar to lactic acid

Heterofermentative: fermentation of glucose or another sugar to a mix of reduced products.

Facultative: grows in either the presence or absence of an environmental factor

Oxygen and Temperature Response
Oxygen Response
Aerobic
Anaerobic
Facultative Anaerobic

Temperature Response
Mesophile
Thermophile

Role in Ecosystem
Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.

Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.

Nitrogen Fixation: These bacteria convert gaseous nitrogen into nitrates or nitrites as part of their metabolism. The resulting products are released into the environment and used by plants. Some plants, house the bacteria in their own tissues.

Denitrifying bacteria turn nitrates into nitrogen gas or nitrous oxide.

Methane decomposed to ammonia

Utilization of sulfur and Iron as electron donors. Changes in soil or water content.

Cell Division in Bacteria
Binary Fission: The cell grows to twice its size, Duplicates its DNA and other cellular constituents, and lays down a cross-wall called a septum that separates the cells.

Polar Growth: the cell grows from one end and the two cells that result from cell division are similar in size.

Simple Budding:,the cell wall grows from one end of the bacterium, producing a smaller cell that separates off and. grows.

Buds-Hyphae-swarmer: The cell buds at the end of extensions called hyphae. As the bud increases in size, it forms a flagellum. A septum forms between the bud and the hypha,and the cells separate.

The daughter cell, called a swarmer, matures, lengthens, and eventually loses its flagellum,forms a hypha, and begins the cell division process again.

Stalk: The cell creates two distinct cells during division. One has a Stalk from which the cell grows. The cell divides by unequal binary fission,producing a second, slightly smaller swarmer cell with a flagellum. The swarmer cell swims off, and when it comes to rest, it lose its flagellum and forms a stalk,again.

Phyla of Bacteria

Purple Phototrophic Bacteria
Purple Phototrophic Bacteria
Anoxygenic photosynthesis. They contain pigments - purple, red and brown.

They are divided into two groups: use of hydrogen sulfide, H2S, as an electron donor for carbon dioxide reduction. (Redox Reactions)

Purple sulfur bacteria: normally respire anaerobically in aquatic environments.

Purple Non-sulfur bacteria: Most species are aerobic and utilize a variety of carbon sources.

Sulfate and Sulfur Reducing Proteobacteria
About 90 species of bacteria from over 20 genera are known which are anaerobic obligate sulphur or sulphate reducers .
Most species live in aquatic environments.
Nitrifying Bacteria
Most species are obligatory chemolithotrophs.

These bacteria can be divided into two groups, those that:

oxidize ammonia to nitrite
oxidize the nitrite to nitrate.

Nitrifying bacteria are widespread in soil and aquatic environments where they are an important part of the nitrogen cycle.
Sulfur and Iron Oxidizing Bacteria
Beggiatoa is a filamentous gliding bacterium which oxidizes sulfur commonly found in sulfur springs, sewage works and hydrothermal vents, and other environmental areas.

Thioploca, Thiotrix and Leucathrix are also filamentous sulphur-oxidizing bacteria that aggregate within a star or rosette with their filaments in a central core. Primarily found in marine habitats where they can form thick mats.

Hydrogen-Oxidizing Bacteria-A wide variety of bacteria can grow with:
H2 as the sole electron donor and O2 as the electron acceptor

Methanotrophs
These are aerobic methane oxidizing bacteria (methane to methanol). An important aspect of the carbon cycle. CH4-CH3OH

Some Methanotrophs are also Methylotrophs meaning that they are limited to using single carbon sources, thus they cannot utilize even simple sugars to grow.

Pseudomonas and the Pseudomonads
Chemoorganotrophic
Aerobic rods
Nitrogen-fixing
Phylogenetically closely related.
Metabolize glucose via the Entner- doudoroff pathway
Opportunists

Acetic Acid Bacteria
they partially oxidize various organic compounds, particularly ethanol, into acetic acid. Used commercially to make vinegar.

Free-living Aerobic Nitrogen Fixers
These are an ecologically important group of bacteria that live in the soil or in water.
Use gaseous nitrogen (N2) from the atmosphere and combine it with carbon and hydrogen, to make organic molecules.
Nearly all the organic molecules in the world are derived from bacterially fixed nitrogen.

Other Gram Negative Bacteria
This is a group of related bacteria that don't fit into any other group.
They contain both free-living species and species found living inside animals.
Among this latter division is the genus Neisseria including the species Neisseria gonorrhoeae which is responsible for the human sexually transmitted disease gonorrhoea.
Other species of Neisseria plus species of Kingella, Moraxella and Acinetobacter may be pathogenic (disease-causing) at times.

Enteric Bacteria
A large group of facultative aerobic rods. Human faeces generally comprise 30% (dry weight) of dead bacteria
Enteric bacteria are separated by the type of fermentation products produced by anaerobic fermentation of glucose.
Some cause gastroenteritis; others are opportunists

Bioluminescent and Related Bacteria
Gram-negative, facultatively aerobic curved rods with a fermentative metabolism. Both aquatic.
Two species of Vibrio cause disease in humans. V. cholorae causes cholera. V. parahemolyticus, causes gastroenteritis due to ingestion of contaminated seafood.
Photobacterium emit light mediated by the enzyme luciferase, an oxidation reaction. Bioluminescent bacteria are mostly associated with fish.

Rickettsia
Rickettsias are obligate intracellular parasites of eucaryotic cells. They have leaky membranes and are unable to obtain nutrients in an extracellular habitat.
Rickettsias occur in nature in the gut of arthropods (ticks, fleas, lice, etc.). They are transmitted to vertebrates by an arthropod bite and produce typhus fever, Rocky Mountain Spotted Fever, Q fever and canine ehrlichiosis.

Spirilla
Spirilla are chemoorganotrophic prokaryotes widespread in the environment.
Campylobacter and Helicobacter which are pathogenic to humans cause acute enteritis, chronic gastritis and peptic ulcers.

Spirilla
Bdellovibrio are predators on other bacteria. They attack by dissolving a hole in their prey's cell wall feeding on the cytoplasm.

Ancylobacter, a ring-shaped bacterium and Magnetospirillum magnetobacterium, a curved rod shaped bacterium, contain 5 to 40 magnetic particles magnetosomes and they allow the organism to align itself in relationship to magnetic fields.

Sheathed Bacteria
Sheathed filamentous bacteria in which individual cells form chains within an outer layer called the sheath. When nutrients are low, the individual cells develop a flagella tuft and are called swarmers

Gliding Myxobacteria
The fruiting myxobacteria are gliding bacteria that aggregate to form complex masses of cells called fruiting bodies.

Myxobacteria are chemoorganotrophic soil bacteria that live by consuming dead organic matter or other bacterial cells.
Gram-positive Bacteria
Gram-positive Bacteria are a large phylogenetic group that contains rods and cocci, sporulating and nonsporulating species.
The lactic acid bacteria are used in dairy production and are human commensals

Endospore Producers
Production of endospores is a hallmark of the key genera Bacillus and Clostridium.
These bacteria are major agents for the degradation of organic matter in soil, and a few species are pathogenic.(C. tetani and botulinum)

Mycoplasma
Lack cell walls and contain a very small genome.
Several are pathogenic for humans, other animals, and plants.
Walking pneumonia and neonatal infections

Small Gram-Positive Rods
Nonsporulating gram positive bacteria; lactic acid bacterial et al, coryneform and propionic Acid Bacteria
Swiss Cheese
The propionic acid bacteria were first discovered in Swiss cheese, where their fermentative production of CO2 results in the characteristic holes. shows the enzymatic reactions leading from glucose to propionic acid.

Actinobacteria: Mycobacterium
The genus Mycobacterium consists of rod-shaped organisms that are acid-fast.
The surface of the cell has unique lipids called mycolic acids, found only in the genus Mycobacterium
Main Pathogen: M. tuberculosis
Actinomycetes: Streptomyces
The streptomycetes are a large group of filamentous, gram-positive bacteria that form spores at the end of aerial filaments.
Other species: Nocardia causes brain infections and pneumoniae.

Cyanobacteria
Cyanobacteria comprise a large and mixed group of phototrophic Bacteria.
Cyanobacteria are oxygenic phototrophs.
Oxygen in Earth's atmosphere is thought to have originated from cyanobacterial photosynthesis

Chlamydia
Obligate intracellular parasites
The life cycle contains two cell types:
The elementary body: non-multiplying,transmit infection
The reticulate body: noninfectious replication form
Sexually-Transmitted Disease
Trachoma

Planctomyces
The Planctomyces group contains stalked, budding bacteria.
The Verrucomicrobia are distinguished by their multiple prosthecate cells

VerrocomicrobiaPhylum 7
Verrocomicrobia

Bacteroides: Phylum 8
The genus Bacteroides contains obligate anaerobic species.
Bacteroides are normally found in the intestinal tract of humans and animals, and can cause infection.
They are the largest group of bacterial in the human colon.

Phylum 9 and 10
Cytophaga
Green Sulfur Bacteria

Spirochete-Phylum 11
Tightly coiled, motile, helical prokaryotes that contain both free-living and pathogenic species.
Treponema pallidum: syphillis
Borrelia: Lyme Disease

Stalked Bacteria
The new cell wall that separates the cytoplasm into two sections starts from a single point. This is called 'Polar Growth'.
A simple hyphae forms a bud at the distant end of the cell. This bud grows to be a new daughter cell. The daughter cell may develop a flagellum and swims away.

Deinococcus: Phylum 12
Deinococcus radiodurans is the most radiation resistant of all known organisms.

Green non-sulfur bacteria: Phylum 13
Chloroflexus

Branching Hyperthermophilic Bacteria: Phylum 14-16

Grow at temperatures > 80C
Netrospira: Phylum 17

Chemolithotrophs to Chemoorganotrophs
Mesophiles to Thermophiles

Characteristics of Different Organisms
Nitrogen oxidizing
Iron oxidizing
Use of metals for electron acceptors
Budding Bacteria
Budding and prosthecate bacteria are appendaged cells that form stalks or prosthecae used for attachment or nutrient absorption and are primarily aquatic.


Archaea
Archaea were once known as archaebacteria and live in extreme environments.
The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma
Types of Archaea
Extremely Halophilic
Methane-Producing
Thermophilic/Acidophilic
Hyperthermophilic
Cold Dwelling
Hyperthermophiles from volcanic habitats
Hyperthermophiles for submarine volcanic habitats
Environments
Soil
Mineral deposits
Aquatic areas
Volcanic areas
Animals

Archaeal Cell Walls
Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.
Particular species may contain pseudopeptidoglycan, polysaccharide, glycoprotein, or protein in their cell walls.
Archaeal Membranes
The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol.
Glycerol diethers and diglycerol tetraethers are the major types of lipids present in the cell membrane.
The Archaea also contain large amounts of non-polar lipids.

Metabolism in Archae
Chemoorganotrophic: use organic compounds as energy sources for growth.

Chemolithotrophy: anaerobic growth with H2 being a common electron donor and Sulfur, Nitrite, Iron or Oxygen as electron acceptor.

Autotrophy: Use of CO2 for energy source;widespread in the Archaea

Methanogens
Methanogens are obligate anaerobes

Anaerobic environments include marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals and humans, and sewage treatment facilities
Methanogens
Methanogens have a type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth.
In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process.
The end product (methane gas) accumulates in their environment.
Halophilic Archaea
Extremely halophilic Archaea require large amounts of NaCl for growth.

These organisms accumulate high levels of KCl in their cytoplasm as a compatible solute.

These salts affect cell wall stability and enzyme activity. The light-mediated proton pump bacteriorhodopsin helps extreme halophiles make ATP
Use of Bacteriorhodopsin
Certain species of Halobacterium can synthesize ATP using light energy.
The process uses a membrane protein called bacteriorhodopsin.
The absorption of light by retinal associated with this protein is used to pump protons across the cell membrane.
The resulting proton motive force can drive ATP synthesis via a membrane-bound ATPase.

Hyperthermophiles
“Hyperthermophiles" require temperatures of 80 degrees to 150 degrees for growth.
Most of these Archaea require elemental sulfur for growth. Some are anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen.
Sulfur-oxidizers grow at low pH (less than pH 2), partly because they acidify their own environment by oxidizing SO (sulfur) to SO4 (sulfuric acid). 
Temperature Limits

Although hyperthermophiles live at very high temperatures, in some cases above the boiling point of water, there are temperature limits beyond which no living organism can survive. This limit is likely 140ºC to 150°C
Molecular chaperones
Assist in the folding process.
Fold newly synthesized proteins
Refolding of partially denatured proteins.
Chaperones =heat shock proteins
Refold before proteases destroy them

Reverse DNA Gyrase. 
All hyperthermophiles produce a DNA topoisomerase called reverse DNA gyrase.

Reverse gyrase introduces positive supercoils into DNA (in contrast to the negative supercoils introduced by DNA gyrase, found in all nonhyperthermophilic prokaryotes).
Supercoils
The structure of supercoils.  (a) Positive supercoils - the front segment of a DNA molecule cross over the back segment from left to right.  (b) Negative supercoils.  (c) The positive supercoil in bacteria during DNA replication.

DNA-Binding Proteins
Proteins may also function to maintain double stranded DNA.
Histones: wind and compact DNA into nucleosome-like structure.

Early Life Forms
Hyperthermophilic Archaea and Bacteria are likely the closest living relatives to early life forms that remain today.

Hydrogen catabolism may have been the first energy-yielding metabolism of cells.

Pyrodictium and Pyrolobus
Pyrodictium and Pyrolobus are examples of prokaryotes whose growth temperature optimum lies above 100ºC. The optimum for Pyrodictium is 105ºC and for Pyrolobus is 106ºC.

Cells of Pyrodictium are irregularly disc-shaped and grow in culture in a mycelium-like layer attached to crystals of elemental sulfur.

Nanoarchaeum
Nanoarchaeum is a small, parasitic, early-branching member of the Archaea. Its genome is the smallest of all known organisms.
Nanoarchaeum lacks genes for all but core molecular processes and thus depends on its host, Ignicoccus, for most of its cellular needs.