MCB3020 Week 6: Phylogeny & Diversity

Cyanobacteria

Earliest oxygen-producing organisms as oxygenic phototrophs, created O2 as a byproduct which caused a major shift in the biosphere from anoxic -> oxic

Ozone

Conversion of O2 -> O3 generates an _ shield by absorbing radiation from the sun, allowed more organism to inhabit Earth's terrestrial habitats rather than just the ocean

Endosymbiosis

Mitochondria and chloroplasts came from a symbiotic relationship with prokaryotes within another kind of cell

Evolution

Change in allele frequencies in a population of organisms over time, with alleles being alternative versions of a gene that came from mutation and recombination

Mutation

Random changes in DNA sequence that can be neutral, deleterious, or beneficial which are a result of substitutions, deletions, insertions, or duplications

Recombination

Segments of DNA are broken and rejoined together to make new genetic material

Selection

Defined by fitness (ability to produce offspring) which can act on mutations

Genetic drift

Random process that causes gene frequencies to change over time, resulting in evolution without natural selection

Phylogeny

Evolutionary history of a group of organisms

Molecular clocks (chronometers)

Certain genes and proteins are measures of evolutionary change assuming that nucleotide changes occur at a constant rate, are generally neutral, and random; examples include 16S rRNA and 18S rRNA

16S rRNA

Found in prokaryotes, mitochondria, and chloroplast organelles; functionally constant, changes slowly, and a sufficient length; not good for closely related species

Gold standard

16S rRNA gene sequences are useful in taxonomy as they serve as the _ for identifying and describing new species, where a bacteria is a new species if 16S rRNA differs more than 3%, and a new genus if 16S rRNA differs more than 5%

Phylogenetic tree

An illustration that shows the relationships between sequences made of nodes and branches; branch length represents the number of changes that occurred along the branch

Phylogenetic diversity

Evolutionary relationships between organisms

Functional diversity

Form and function as related to microbial physiology and ecology

Convergent evolution

Reason for functional traits being seen in different species; a trait has evolved independently in two or more lineages and not encoded by homologous genes

Horizontal gene transfer

Reason for functional traits being seen in different species; genes coding for a trait are homologous and have been exchanged between distantly related lineages

Phototrophic bacteria

Functional group

- Able to conserve energy from light due to living in anoxic early Earth

- The first of these were anoxygenic ________

- Only photosystems 1 or 2 are present in anoxygenic ___________

- Many ________________ fix carbon

Cyanobacteria

Phylum, acts as a functional and taxonomic group under phototrophic bacteria

- Both photosystems 1 and 2 are present

- Key genera: Prochlorococcus, Trichodesmium, Oscillatoria, Anabaena

- All fix CO2 by the Calvin cycle, many fix N2

- Many display gliding motility

- Some form hormogonia and akinetes, many form cyanophycin

- Nitrogenase fixes nitrogen, but is sensitive to oxygen and it's fixation cannot happen with oxygenic photosynthesis; housed in heterocysts that has an anoxic cell wall

- Synechococcus and Prochlorococcus are the most abundant ocean phototrophs

Hormogonia

In some cyanobacteria, these are short motile filaments that break off and disperse

Akinetes

In some cyanobacteria, these are thickened outer walls that protect the organism from harsh conditions such as darkness, desiccation, or cold

Cyanophycin

In many cyanobacteria, this is the nitrogen storage product

Heterocysts

In cyanobacteria, nitrogenase fixes nitrogen, but is sensitive to oxygen and it's fixation cannot happen with oxygenic photosynthesis; housed in __ that has an anoxic cell wall. Most visible in Anabaena

Proteobacteria

Phylum of only gram-negative bacteria and includes the most common bacteria, six classes of alpha, beta, delta, gamma, epsilon, zeta.

Purple phototrophic bacteria

Functional group under functional group phototropic bacteria; anoxygenic photosynthesis; no O2 produced, contains bacteriochlorophylls and carotenoid pigments, found in H2S rich anoxic zones in water and microbial mats

Purple sulfur bacteria

Functional group under purple phototrophic bacteria; Gamma-proteo, H2S e- donor, found in anoxic zones of sulfur springs

Purple non-sulfur bacteria

Functional group under purple phototrophic bacteria; alpha or beta proteo, most grow photoheterotrophically where light is an energy source and organic compound are carbon sources

Nitrifying bacteria

Functional group that grows chemolithotrophically, are obligate aerobes, performs nitrification as either an ammonia oxidizer (gamma-proteo) or as a nitrite oxidizer (Nitrobacter; alpha-proteo), plays vital role in wastewater treatment

Nitrification

Oxidation of ammonia to nitrate, can be done by nitrifying bacteria

Nitrobacter

Alpha-proteo bacteria capable of oxidizing nitrite, falls under the nitrifying bacteria functional group

Sulfur oxidizing bacteria

Functional group; Grows chemolithotrophically on reduced sulfur compounds, neutrophilic or acidophilic, ex. beggiatoa (gamma-proteo)

Hydrogen oxidizing bacteria

Functional group; grows autotrophically, H2 donates e- and O2 accepts e-, hydrogenase binds H2, ex. ralstonia, pseudomonas, paracoccus (beta, gamma, alpha proteo)

Myxobacteria

Functional group; key genus myxococcus, creates fruiting bodies that turn into myxospores, typically seen on decaying wood

Microbial bioluminescence

Functional group; key genera include vibrio and aliivibrio, this process requires O2 to happen by luxCDABE genes being catalyzed by luciferase that uses O2 to create light

Pseudomonas and pseudomonads

Taxonomic group; chemoorganotrophs that cannot ferment, good detritivores, some species are pathogenic- ex. P. aeruginosa

Nosocomial

More likely to go into the hospital without the pathogen, and then proceed to leave the hospital with the pathogen, ex. P. aeruginosa

Acetic acid bacteria

Taxonomic group, alpha-proteo; Partially oxidizes alcohols and sugars to make wine and vinegar, aerobic and very acidic

Neisseria

Under the taxonomic group of gram negative cocci; ex. N. gonorrhoeae (beta-proteo) causes gonorrhea

Acinetobacter

Under the taxonomic group of gram negative cocci; gamma-proteo, common soil and water org that can cause nosocomial infections

Family Enterobacteriaceae

Taxonomic group; ALL gamma-proteo, ferments sugars into either mixed-acid fermenters or 2,3-butanediol fermenters

Eschericha

Under taxonomic group of family Enterobacteriaceae; includes e. coli which synthesizes vitamins for host in the intestinal tract, some e. coli are pathogenic though

Salmonella and shigella

Under taxonomic group of family Enterobacteriaceae; usually pathogenic and is closely related to Escherichia

Proteus

Under taxonomic group of family Enterobacteriaceae; rapidly motile bacteria that produces urease, ex. P. vulgaris

Butanediol fermenters

Under taxonomic group of family Enterobacteriaceae; key genera include Enterobacter, klebsiella, serratia with some being capable of pigment production such as Serratia marcescens

Family Vibrionaceae

Taxonomic group; all are gamma-proteo, commonly in aquatic environments, includes V. cholerae (cholera), V. parahaemolyticus (diarrhea, shellfish poisoning), and Vibrio vulnificus (sepsis and infection)

Pseudomonas

This bacteria is aerobic and motile, tests oxidase positive, and cannot ferment

Enterobacteriaceae

This bacteria is facultative and fermentative, may be motile, and tests oxidase negative

Vibrio

This bacteria is facultative and fermentative, tests oxidase positive, and most are motile

Epsilonproteobacteria

Taxonomic group; includes campylobacter and helicobacter with most being autotrophs and microaerophilic

Campylobacter

Under taxonomic group epsilonproteobacteria; several species are pathogenic and produce enterotoxins with C. jejuni being a common cause of gastroenteritis

Helicobacter

Under taxonomic group epsilonproteobacteria; includes H. pylori that causes stomach ulcers

Nonsporulating gram-positive bacteria (firmicutes)

Taxonomic group; key genera include staphylococcus, streptococcus, lactobacillus, listeria

Staphylococcus

Under taxonomic group nonsporulating gram-positive bacteria; tests catalase positive, excellent at maintaining osmotic balance (halophilic), ex. S. aureus which acts as a pathogen, but is also able to ferment mannitol

Lactic acid bacteria

Under taxonomic group nonsporulating gram-positive bacteria; only capable of performing substrate level phosphorylation (fermentation), aerotolerant anaerobes, fastidious

Streptcocci

Under taxonomic group nonsporulating gram-positive bacteria; ex. streptococcus and enterococcus with streptococcus group A causing strep throat, streptococcus pneumoniae causing pneumonia, and enterococcus having fecal origins and is a good water quality indicator

Lactobacillus

Under taxonomic group nonsporulating gram-positive bacteria; ex. L. acidophilius is a good bacteria in yogurt

Listeria

Under taxonomic group nonsporulating gram-positive bacteria; ex. L. monocytogenes which causes listeriosis, commonly found in prepared deli products

Endospore forming gram positive bacteria

Taxonomic group; key genera are bacillus and clostridium, generally found in soils

Bacillus

Under taxonomic group endospore forming gram positive bacteria; ex. B. anthracis

Anthrax

Caused by B. antracis, from contaminated animal products in temperate zones, spores are viable in the soil for years and can either be cutaneous, gastrointestinal, or respiratory. 22 people died from the anthrax mail incident in 2001, 20% die to cutaneous, 25%-50% to gastrointestinal, 50% or more to respiratory. In respiratory anthrax, spores attach to aveolic sacks in the lungs which then germinate and release bacilli in the lymph nodes that then causes cell death, blood poisoning and pulmonary edema. Symptoms show within 1-7 days of exposure

Clostridium

Under taxonomic group endospore forming gram positive bacteria; obligately anaerobic, some perform stickland reactions, includes pathogenic diseases such as botulism (C. botulinum), tetanus (C. tetani), gangrene (C. perfringens)

Cell wall less gram positive bacteria

Taxonomic group; key genus is mycoplasma, lacks cell walls and is missing the key components of peptidoglycan which is the important role of sterols, ex. M. pneumoniae (atypical cause of pneumonia)

Actinobacteria

Taxonomic group; key genera are mycobacterium and propionibacterium, mostly harmless bacterias

Propionic acid bacteria

Under taxonomic group actinobacteria; uses the metabolic strategy of secondary fermentation and is the causative agent of acne

Secondary fermentation

Used by propionic acid bacteria, this method of fermentation obtains energy from the fermenetation products produced by other bacteria

Mycobacterium

Under taxonomic group actinobacteria; acid-fast bacteria, ex. M. tuberculosis which exhibits cord-like growth

Filamentous actinobacteria

Taxonomic group; key genus is streptomyces, streptomyces spores are called conidia, responsible for the earthy odor of soil (geosmins), most streptomyces produce antibiotics

Chlamydia

Taxonomic group; key genus is chlamydia, obligately parasitic with poor metabolic capacities, intracellular parasites, gram negative, ex. C. trachomatis which causes trachoma, eye disease, blindness, and chlamydia

Spirochetes

Taxonomic group; key genera include treponema, leptospira, borrelia, gram-negative and tightly coiled, has endoflagella located in the periplasm of the cell

Treponema

Under taxonomic group spirochetes; ex. T. pallidium causes syphilis

Borrelia

Under taxonomic group spirochetes; ex. B. burgdoferi causes lyme disease

Leptospira

Under taxonomic group spirochetes; rodents are this bacteria's natural host and is the cause of leptospirosis in humans