BIOS 312 Bacteria

Culture dependent isolation

Relies on the culture of organisms in different types of media to characterize them

Can also involve enrichment to find rare microorganisms

Culture independent isolation

• Uses molecular tools to look for specific genes which can be used to measure diversity

• Methods: PCR, DGGE, molecualar cloning, DNA sequence analysis

• These tools have revealed the undescribed majority of life

Metagenome Analyses

Metagenome assembled genomes have expanded our understanding of microbial diversity

More than 90% of characterized genera and species come from 4 phyla, which are

1. Protobacteria

2. Bacteriodetes

3. Actinobacteria

4. Firmicutes

Proteobacteria

• Gram-negative

• Divided into 6 families

• 1/3 of all bacteria is from this group

• Most metabolically diverse (chemolithotrophy, chemoorganotrophy, phototrophy)

• Morphologically diverse

• Divided into 5 classes (alpha, beta, delta, gamma, epsilon)

Alpha Proteobacteria

• The second largest class of Proteobacteria

• Many prefer to grow in environments with low nutrient concentrations

• Key genera: Rickettsia, Wolbachia

  • Rickettsia: small, coccoid or rod-shaped cells that are mostly obligate intracellular parasites that cause disease like Typhus and Rocky Mountain spotted fever

Rhodospirillales

Include things like Magnetospirillum magneticum

Caulobacterales

Include stalked bacteria like Caulobacter crescentus

Rhizobales

• Include Bartonella, Methylobacterium, Pelagibacter, Rhizobium, Agrobacterium

• Largest and most metabolically diverse order

• Contains phototrophs, chemolithotrophs, symbionts, nitrogen-fixing bacteria, pathogens, and chemoorganotrophs

• Nine genera contain rhizobia

What is the third largest class of Proteobacteria?

Betaproteobacteria

• Has lots of functional diversity

Rhodocyclales

• Key genera: Rhodocyclus, Zooglea

• Wide range of metabolic and ecological characteristics

Rhodocyclus

• Purple nonsulfur bacterium

• Grows best as photoheterotroph

• Can grow as photoautotroph

• Can also grow by respiration

Zooglea

• Chemoorganotroph that produces thick capsule

• Important in wastewater treatment

Hydrogenophilales

Includes lithotrophs that oxidize sulfur and iron such as Thiobacillus denitrificans

Neisseriales

• Key genera: Neisseria, Chromobacterium

Neisseria

• Can be isolated from animals

• Some species of this group are pathogenic

Chromobacterium

• Rod-shaped, facultative aerobe

• Some species produce pigment violacein

Nitrosomonadales

Nitrifying bacteria like Nirosomonas europea

Gammaproteobacteria

• Largest, most diverse group

• Contains half of the Proteobacteria

• Many pathogens are found in this class

Enterobacteriales

• Most well known for the members of the Enterobacteraceae family (found in the human colon)

• Enteric bacteria

  • comprise a relatively homogenous phylogenetic group and consists of facultatively aerobic, gram-negative, nonsporulating rods

  • fermentation patterns

    • mixed-acid: produces acetic, lactic, and succinic acid

    • butanediol: produces butanediol, ethanol, CO2, H2 and smaller amounts of acid

    • identified by diagnostic tests and differential media to separate various genera, but positive identification limited because they are genetically very closely related

Enteroacteriales Genus: Escherichia

• Universally inhabitants of the intestinal tract of humans and other warm-blooded animals; some strains are pathogenic

Enterobacteriales Genus: Salmonella and Shigella

• Salmonella closely related to Escherichia, show about 50% genomic hybridization

  • Usually pathogenic (humans/warm-blooded animals)

  • Causes typhoid fever and gastroenteritis

• Shigellas also closely related to Escherichia and commonly pathogenic to humans, causing severe gastroenteritis (bacillary dysentery)

Enterobacteriales Genus: Proteus

Characterized by rapid motility and by the production of the enzyme urease

What are the butanediol fermenters?

Enterobacter, Klebsiella, and Serratia

• Genetically more closely related to each other than to the mixed-acid fermenters

• E. aerogenes common species in water and sewage as well as the intestinal tracts of warm-blooded animals

• K. pneumoniae occasionally causes pneumonia in humans, but is most commonly found in soil and water

• Serratia forms a series of red pyrrole-containing pigments called prodigiosins

Pseudomonads

Pseudomonas: polar flagella and oxidase positive

• Very large genus that is now being broken up into many different ones

• P. putida and P. aeruginosa

• Fluorescent pigments are iron chelating compounds (siderophores)

Beggiatoa

• Filamentous, gliding bacteria

• Found in habitats rich in H2S

• Most grow mixotrophically

  • with reduced sulfur compounds as electron donors

  • and organic compounds as carbon sources

Purple Sulfur Bacteria

• All purple sulfur bacteria discovered thus far are Gammaproteobacteria

• Use H2S as an electron donor for CO2 reduction in photosynthesis

• Sulfide oxidized to elemental sulfur (S⁰) that is stored as globules either inside or outside cells

  • Sulfur later disappears as it is oxidized to sulfate

Deltaproteobacteria

• Key genera: Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter, Syntrophobacter

• Sulfate and sulfur reducers

• Dissimilative iron reducers

• Bacterial predators

• Anaerobic chemoorganotrophic bacteria capable of iron and sulfur reduction

• Common in saturated soils and sediments

• Geobacter sp. and Desulfovibrio sp. are common

Myxococcales

• Myxobbacteria

  • Group of gliding bacteria that form multicellular structures (fruiting bodies) and show complex developmental life cycles

  • Chemoorganotrophic soil bacteria

  • Lifestyle includes consumption of dead oragnic matter or other bacterial cells

• Fruiting myxobacteria exhibit complex behavioral patterns and life cycles

  • Vegetative cells are simple, nonflagellated rods that glide across surfaces

  • Under appropriate conditions, vegetative cells aggregate, construct fruiting bodies, and undergo differentiation into myxospores

Bdellovibrionales

• Prey on other bacteria

• Obligate aerobes

• Members of deltaproteobacteria

• Widespread in soil and water, including marine environments

Bdellovibrio

• Prey on other bacteria including human pathogens (iE. coli, Salmonella, Legionella sp)

• This has potential as a therapeutic agent

• Two stages of penetration

• Obligate aerobes

• Widespread in soil and water, including marine environments

Desulfonsmonadales

• Anaerobes and chemoorganotrophs

• Ex: Geobacter sulfurreducens (reduces iron and is an electrogen)

Epsilonproteobacteria

• This group contains fewer species and less diversity than other classes

• Key genera: Campylobacter, Helicobacter

  • Gram-negative, motile spirilla

  • Oxidase and catalase positive

  • Pathogenic to humans and animals

  • Abundant in oxic-anoxic interfaces in sulfur-rich environments (hydrothermal vents)

  • Many are autotrophs using H2, formate, sulfide, or thiosulfate as electron donor

  • Pathogenic and non-pathogenic

Helicobacter Pylori

• Must well studied member of the Epsilonproteobacteria

• Gram-negative, slow growing

• Common human pathogen causing gastritis and stomach ulcers

• Lives on the mucous lining of the stomach

• Multisubunit urease enzyme that enables it to survive in acidic pH environments and colonize the gastric environment

Sulfurspirillum

• Free-living bacteria capable of a variety of metabolisms

• Oxidation of sulfides couples to nitrate reduction (a proposed bioremeditative technique to prevent oil reservoir biosouring)

• Members of this genera have also been identified as symbionts of Alvinella pompejana

Nautilli lithotrophica

Members of the family Nautilaiales which have been identified as the predominant microorganisms living as episymbionts on Alvinella pompejana

Firmicutes

• Key genera: Lactrobacillus, Streptococcus

• Fermentative bacteria that produce lactic acid

• Lactobacillus

  • Rod-shaped in dairy products

  • Resistant to acidic conditions

  • L. reuteri: Heterofermentatic lactic acid bacterium that colonizes stomach and intestine of animals; also produces folate and vitamin B12 as probiotic

• Large and diverse group of organisms (4 classes, 11 orders, 35 families, and more than 240 species)

• Key genera: Bacillus, Clostridium, Sporosarcina

  • Distinguished on the basis of cell morphology and on the shape and cellular position of endospore

  • Generally found in soils

  • Endospores are advantageous for soil microorganisms

  • B. anthracis: Gram-positive, rod-shaped, facultative anaerobe that lives in soil and first to be shown to cause disease by Koch and Pasteur

Planctomycetes

• Key genera: Planctomyces, Blastopirellula, Gemmata, Brocadia

• Gram-negative

• Divide by budding

• Stalked or appendaged

• Extensive cell compartmentalization, including a membrane-enclosed nuclear structure

• Plantomyces: stalked bacterium primarily aquatic

• Gemmata has equivalent of nucleus; nucleoid is surrounded by a nuclear envelope and contains ribosomes

• Brocadia anammoxidans is different phenotypically from the other Plantcomycetes because it is an anaerobic autotroph

Thermatoga

• Key genera: Thermatoga, Thermodesulfobacterium

• Thermatoga

  • Rod-shaped, hyperthermophile (can grow at 90C)

  • Anaerobic, fermentative, chemoorganotroph

  • 20% of genes likely originated from Archaea