BM211: Megan's final cram

Ernst Haeckel

Proposed a third kingdom “Protista” in 1866

Robert H. Whittaker

Proposed 5 kingdoms (plant, animal, fungi, protsita, monera)

Carl Woese

Introduced archaea as a domain of life

Phylogenetics

The study of evolutionary history of life

Why are viruses absent on Woese’s phylogenetic tree of life?

Because it is based on ribosomal RNA which they lack

Marker gene (definition)

a gene used to determine if a nucleic acid sequence has been successfully inserted into an organism's DNA

(types of) Marker genes

Selectable, and for screening

Selectable marker (definition)

protects the organism from a selective agent that would normally kill it or prevent its growth

Screenable marker (definition)

Will make cells containing the gene look different

Screenable marker (types)

Green flourescent, blue-white, GUS assay

Green flourescent marker (use)

makes cells glow green under UV light. A specialized microscope is required to see individual cells.

GUS assay (use)

method for detecting a single cell by staining it blue without using any complicated equipment. The drawback is that the cells are killed in the process.

Blue-white marker (use)

used in both bacteria and eukaryotic cells. The bacterial lacZ gene encodes a beta-galactosidase enzyme. When media containing certain galactosides (e.g. X-gal), cells expressing the enzyme convert the X-gal to a blue product and can be seen with the naked eye.

Orthologous

descended from the same ancestral sequence and separated by a speciation event – vertical descent 

How to choose marker genes

Should be- Orthologous, present in species, should be conserved but also have observable differences, evolve slowly

16S ribosomal RNA (overview)

widely used for phylogenetic studies, highly conserved, slows evolution, recognises Shine-Dalgano

16s rRNA (Gene surveys)

have revealed a huge amount of diversity in the environment

Candidate phyla radiation

large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing.

Dominant branch in phylogenetic tree

Bacteria

LUCA

Last Universal Common Ancestor, “top” of the phylogenetic tree. NOT the first cell

How old is earth

4.6 BY

First evidence that cells appeared on earth

3.8-3.9 MYA

Earth’s atmosphere (before life)

Mainly N2 and CO2 - Anaerobic

Methanogenesis

Form of anaerobic respiration utilised before the earth was oxygenated, only present in Archaea

Anoxic phototrophs (evolution)

3.5 BYA

Cyanobacteria (evolution)

2.5 BYA

Hypotheses for emergence of virus

Genome reduction, genome escape - both are controversial

Eukaryotic species (diversity)

estimated to be approx. 8.7 x 10⁶ species in total

Esimated species in 10g soil

8.3 x 10⁶ species, 10¹⁰ bacterial and archaeal cells

Prokarya (structure)

No membrane enclosed organelles no nucleus, negative definition

Eukaryotes (Structure)

DNA enclosed in a membrane-bound nucleus, cells are generally larger and more complex containing organelles.

Morphological diversity in bacteria and archaea

Genome

The full complement of genes for an organism

Haemophilus influenzae

first free-living organism to have its genome sequenced (1995)

Escherichia coli genome

best studied free living organism, 4.4 million base pairs, 4,300 genes

Human genome

6.2 Gigabase pairs, 20,000-25,000 coding base pairs

Axolotol genome

32 Gbp, 23,500 protein coding genes

Catabolism

Breaking down complex molecules

Anabolism

Synthesising complex molecules

What does microbial growth require

Energy, anabolic raw materials, “trace enzymes” as enzyme co-factors

Main anabolic raw materials

C, N, S, P

Trace elements used as enzyme cofactors

Se, metal ions (Mn2+), vitamins

Trace elements important for pathogenic bacteria

Iron (Fe2/3+)

Siderophores

Small compounds secreted by bacteria to help the organism accumulate iron.

Chemolithotroph

Metabolism that generates energy by oxidising inorganic compounds (e.g. Hydrogen sulphide, Fe2+, or ammonia) rather than organic carbon

Phototrophy

Metabolism that uses light (e.g. photosynthesis)

Chemoorganotroph

Metabolism that utilises chemical compounds to supply energy and organic compounds as electron donors (e.g. humans with food)

“Auto”-trophs

Makes it’s own food from inorganic nutrients

“Hetero”-trophs

Relies on others for food uses preformed organic molecules acquired from outside to generate energy

Oligotrophy

“Small feeding” is growth at low nutrient concentrations

Copiotrophs

Associated with richer environments, are generally adapted to using a resource rapidly when available

Synotrophy

“Feeding together”, may/may not involve direct cell-cell contact. An example of mutualism where one organism thrives on the byproducts of another

Horizontal Gene Transfer (HGT)

Evolutionary process that distributes genes between divergent prokaryotic lineages within the same generation

Catabolism of complex sugars in the gut

Xyloglucans can be digested by a (small amount) gut microbes, by breaking down into short oligosaccharides, then monosaccharides which can be transported into the cell

Catabolite repression

Allows microorganisms to adapt quickly to a preferred carbon and energy source first. Prioritises energy efficient sources.

Carbon catabolic pathways - Central metabolism

Glycolysis, TCA cycle - pathways present in most organisms

Glucose Catabolism

Generates pyruvate which can be used in the TCA or as an intermediate for amino/fatty acid synthesis. Usually reversible

Gluconeogenesis

Results in the biosynthesis of glucose from non-carbohydrate carbon substrates

Embden Meyerhof Parnas (EMP) Pathway

The most common form of glycolysis. Breaks glucose to fructose, to produce 2 pyruvate. Produces; 2 ATP, 2 NADH

Entner-Doudoroff (ED)

Alternative glycolysis pathway utilised by bacteria and archaea. Produces less energy (1 ATP, 1 NADH, 1 NADPH) but is efficient in nutrient-limited conditions

Pentose Phosphate Pathway (PPP)

Glycolysis alternative, involved oxidation of glucose however it’s primary role is anabolic. Especially important in RBCs. Produces; 1 ATP, 2 NADPH

Electron Transport system

Set of redox reactions generating an electrochemical gradient across the membrane driving ATP synthesis

Final e- acceptor in Eukaryotes (Electron transport system)

Oxygen (in aerobic process)

Final e- acceptor in microbes (electron transport chain)

Can be O2 (in aerobic systems), or nitrate when O2 levels have depleted. (choice will depend on conditions)

Industrial fermentations

Used to produce; Vitamins, amino acids, fine chemicals

Industrial fermentations

Used to produce; Vitamins, amino acids, fine chemicals

MacConkey Agar (Lac positive)

Diagnostic technique, Lac+ bacteria (like e coli, enterobacter, etc) will reduce the pH of the agar and result in pink colonies

MacConkey agar (Lac negative)

Diagnostic technique, organisms unable to ferment will form normal coloured colonies, e.g. salmonella, proteus

Secondary metabolism

Compounds that are not absolutely required for survival, however are involved in ecological interactions, niche adaptation, and signalling

Secondary metabolite (Examples)

Antibiotics, pigments, toxins

Photoautotrophs (Overview)

Utilise light and inorganic compounds to produce organic materials to sustain metabolism

Photoautotrophs (example)

Cyanobacteria uses H from water, and CO2 to form carbohydrates. Produces oxygen gas

Chemoautotrophs

Obtains energy from (usually inorganic) chemicals, “fixes CO2” as it’s involved in nitrification

Photoheterotrophs (overview)

Use light and organic carbon for energy. Can’t fix CO2

Photoheterotroph (example)

Halobacteria, inhibit high salt environment such as salt lakes and salty soils. Can give water a pink-red colouration

Chemoheterotrophs (overview)

Uses organic carbon for energy and carbon requirement

Chemoheterotrophs (examples)

Most bacterial pathogens; E. coli, pseudomondads, bacillus species

Baas Becking hypothesis

“Everything is everywhere but the environment selects”

Van Niel hypothesis

Every molecule existing in nature can be used as a source of carbon by a microorganism somewhere, microorganisms are found in every environment on earth

Tragedy of the commons

A shared resource will be overused, which will lead to the depletion of the resource

Extremophiles

Microbes living in extreme environments

Psychrophiles

Microbes living in cold temperatures

Thermophiles

Microbes living in hot environments

Hyperthermophiles

Microbes living in very hot environments

Acidophiles

Microbes living in extremely acidic environments

Alkaliphiles

Microbes living in extremely alkaline environments

Halophiles/halotolerant

Microbes living in extremely salty environments (high NaCl conc)

Barophiles/piezophile

Microbes living in extreme pressure environments (e.g. deep submarine)

Xerophiles

Microbes existing in environments without much water

Psychrophile optimal temperature

4*c

Mesophile optimal temperature

39*c

Thermophile optimal temperature

60*c

Hypermophile optimal temperature

88*c

Bacterial qualities

Live in complex communities, altruistic division of labour (e.g. quorom sensing)

Mutualism (overview)

The host benefits, and the microbes benefit from association

Mutualism (examples)

Bioluminescence in aliivibrio fischeri, antibiotic production in actinobacteria, nitrogen fixation in rhizobia

Pathogenesis (overview)

The microbes cause harm to their hosts

Pathogenesis (examples)

Staphylococcus aureus infects hosts, Borrelia (ticks) cause lyme disease, Yersinia pestis (fleas) cause black death

Shannon index (H)

Can be used to measure diversity, =-Σpi * ln(pi)

Calculating colony forming units

cFu/mL= number of colonies counted/ (dilution factor x volume plated)