Microbial planet

Question 1

Microbes

Answer 1

Microbe – an organism that is too small to be seen by eye (microscopic)
May exist in single celled form, or in a collection of cells (a microbiome)
Come in many different shapes and sometimes form chains, filaments or aggregates (e.g biofilms)
Some bacteria can be seen with the naked eye
Microbes are more phylogenetically diverse than plants and animals
Can be classified into one of the three domains of life

Question 2

Eukaryotic microbes

Answer 2

Includes fungi, algae and protists
Yeats are microbes, mushroom are not
Some algae are unicellular but some are pluricellular
How long have microbes been on earth?
First evidence of life is from around 4 billion years ago
Last universal common ancestor (LUCA) gave rise to prokaryotic cells
Bacteria and archaea branched soon after life began
Microbial life was anaerobic until the emergence of cyanobacteria
Cyanobacteria photosynthetic bacteria – produces O2 as a by-product
Oxygenation of the atmosphere – caused the mass extinction of anaerobic life and ice age (Huranian glaciation)
Atmospheric oxygen gave rise to aerobic bacteria and eukaryotic microbes
Microbial life dominated the planet for the first 3 billion years, until the first multicellular eukaryotes emerged

Question 3

Microbial evolution

Answer 3

Mutations – changes in the nucleotide sequence of an organisms genome (insertion, deletion, substitution), occurs because of errors in replication, UV radiation and other factors, organisms adapt to new conditions using mutations, mutation rates are generally constant over time
Other genetic changes include/are caused by – gene loss, gene duplication, horizontal gene transfer (HGTO or transposable elements
New traits can evolve quickly
Nucleotides can mutate via substitution, deletion and insertion

Question 4

Mutation substitutions

Answer 4

Silent mutation – does not affect amino acid sequence
Missense mutation – amino acid changed; polypeptide altered
Nonsense mutation – codon becomes stop codon; polypeptide is incomplete
Deletions and insertions cause more dramatic changes in DNA
Frameshift mutations – deletions or insertions that result in a shift in the reading frame, often result in complete loss of gene function

Question 5

Mutation and reversion

Answer 5

Point mutations are typically reversible
Reversion – alteration in DNA that reverses the effects of a prior mutation

Question 6

Recombination

Answer 6

Recombination – physical exchange of DNA between genetic elements
Prokaryotes – transformation, transduction, conjugation
Eukaryotes – meiosis

Question 7

Evolution of cell power

Answer 7

All organisms living on earth are descended from LUCA
LUCA is not the first living organism on earth it is the one that didn’t hit an evolutionary dead end and die out
Bacteria and archaea (pro) branched first and eukarya branched out from archaea
At some point one ancestral eukaryotic cell acquired a bacteria endosymbiont, which evolved to be the mitochondria

Question 8

From endosymbiont to organelles

Answer 8

From endosymbiont to organelles
1. Endosymbiont lysis or DNA escape during endosymbiont division – genetic transfer to nucleus
2. Both the endosymbiont and the nucleus made the same proteins – genetic redundancy
3. Evolution of protein translocation - can be transported to the proto-organelle
4. Gene loss in the organelle

Question 9

From bacteria to mitochondria

Answer 9

Gene loss in mitochondria resulted in:
- Specialised for energy production – each mitochondrion produces as much ATP as bacteria, but at the fraction of the normal bacteria costs
- Eukaryotic cells having 100,000 times more energy per gene than available in bacteria
- Eukaryotic cells supporting larger genomes, make more proteins from each gene and retain large families of duplicated gene to craft new functions
Organelles genomes are usually (but not always) circular DNA molecules
Organelles genomes encode some but not all the proteins used in the organelle
In sexual reproduction mitochondrial genome (mtDNA) is inherited from the mother as mitochondria in the sperm is usually destroyed by the egg cell after fertilisation
Energy no longer a constraint to evolution

Question 10

Why are microbes so abundant

Answer 10

Small size/high SA:V
Simple design
Reproduce fast and adapt quickly
Have been around 4000 MYA

Question 11

How microbes impact planet

Answer 11

They can live in environments such as soil or thrive under harsh conditons such as – extreme temp about 100 degrees Celsius and under -15 degrees Celsius (hydrothermal vents and glaciers), high hydrostatic pressures (deep sea), high salt concentrations (Salt lake Utah), extreme pH (Yellowstone acid pools pH low as 2)

Question 12

Microbes as earths greatest allies

Answer 12

Microbes sustain life by carrying out transformation of matter essential for life
Bacteria originally oxygenated the earths atmosphere
Cyanobacteria and algae replenish the atmosphere with oxygen (with plants and photosynthesis)
Participate in the decomposition of organic matter without microbes carbon accumulates in dead matter and there would not be enough CO2 for plants
Helps plants fix atmospheric nitrogen making it available for other organisms

Question 13

Microbes help sequester atmospheric CO2

Answer 13

Atmospheric CO2 enters the ocean where it can either:
1. Be converted into organic carbon via photosynthesis (phytoplankton)
2. React with seawater to from carbonic acid (H2CO3). H2CO3 dissociates to form carbonate (CO3^2-) and bicarbonate (HCO3^-)
Leads to release and therefore increase in H+, lowering the pH of the seawater
The additional carbonate required to create bicarbonate decreases the available carbonate
Without microbes CO2 enters the ocean via route 2
- Oceans are slightly alkaline (pH 8.06) but ocean acidification can result when the pH towards the acid end of the scale due to an increase in H+
- Reduced carbonate means marine organisms have a harder time making new shells and maintaining the ones they’ve already got

Question 14

Microbes carry out geological processes

Answer 14

Coccolithophores (phytoplankton) produce oxygen, sequester carbon (via photosynthesis) and are food source - coccolithophores use calcium carbonate (in the form of calcite) to from tiny plates or scales (coccoliths), calcite is the main constituent of limestone
Caverns structures can be formed because of microbial activity – microbes oxidise hydrogen sulphide (H2S) to sulphuric acid (H2SO4), sulphuric acid dissolves calcium carbonate (CaCO3) which is washed away by water

Question 15

Microbes can affect cloud formation

Answer 15

Marine algae and bacteria produce dimethylsulfide (DMS) and dimethyl sulfoniopropionate (DMSP) – DMS turns into sulphate in the atmosphere, sulphate acts as a nucleating agent for water vapour to become water droplets = clouds are formed

Question 16

Microbes are symbiotic

Answer 16

Microbes have symbiotic relationships. e.g:
Mammals – mammals do not produce the enzymes that break down cellulose in plant material, cattle (and other ruminants) harbor cellulose-digesting microbes in their rumen which break it down int volatile fatty acids the animal uses as a major source of energy, animals provide microbes with a suitable habitat for growth
Termites – have bacteria in their guts that break down cellulose but also the termites produce cellulases

Question 17

Microbes in daily life

Answer 17

Carrying out industrial activities (food and drink) – bread, wine, beer, liquor, cheese, yoghurt
Producing medically important proteins – insulin, vaccines (hepatitis B)
Providing public health measures – sewage treatment (microorganisms consume biodegradable soluble containments)
Bioremediation of polluted sites – oil spill cleanup with oil-degrading microbes

Question 18

Microbes as troublemakers

Answer 18

The biosphere 2 project
- Closed system experiment ran from 1991 to 1993
- Closed system = where plants and animals could live in a self-sustained manner
- Investigate the viability of a closed ecological system to support and maintain life in the outer space
- After 16 months the oxygen concentration in Biosphere 2 dropped by half and flora and fauna began to die
- The atmospheric oxygen was disappearing at a rate much faster than predicted
- The topsoil contained two to five times more peat and compost than typical soil
Bacteria are most numerous in compost, metabolising organic matter and in the process consuming oxygen and producing carbon dioxide
As a closed ecosystem the plants should have been able to use the excess CO2 to produce O2 but there were problems
1. Photosynthetic rates were low as the glass cover blocked more than half the sunlight
2. Not enough CO2 was available
CO2 was being sequestered by the calcium hydroxide (Ca(OH)2) in the concrete used to make the domes to produce calcium carbonate instead of being consumed by the plants to make more oxygen
Ca(OH)2 + CO2 = CaCO3 + H2O
Other examples where microbes use up all the oxygen:
- Fertiliser run-off ends up being transported by rivers eventually reaching the ocean (eutrophication), algae and cyanobacteria thrive in the nutrient rich water causing oxygen depletion and loss of macrofaunal
- E.g dead zones in the delta of the Mississippi river (gulf of Mexico), cyanobacterial bloom (Microcystis aeruginosa) in lake Okeechobee (Florida July 2018)