Archaea Flashcards
(17 cards)
1
Q
Three domains of life based on ribosomal DNA sequencing
A
- bacteria
- archaea
- eukarya
- microorganisms
2
Q
A new view of the tree of life
A
- lots of metagenomic sequencing - sequencing of sediments from many places
- They also included ribosomal proteins - more cross genomic comparison
- It appears that bacteria are the most diverse group, while eukaryotes (incl. humans) are merely a branch of the archaea
3
Q
Facts about archaea
A
- identified as distinct group by Woese and Fox in 1977 - they were just thought to be a weird type of bacteria before this
- isolated from volcanic hot springs in Yellowstone
- domain consist of several orders
- inhabit all types of extreme environments (extremophiles - e.g hyperthermophiles, halophiles, acidophilus and psychrophiles)
- major producers of methane - important in the nutrient cycle - the reason why cows can digest cellulose grass
- several other unique features
4
Q
Archaea are major players but no pathogens have been identified
A
- inhabit all types of extreme environments
- Salt, temperature, pH, pressure
- Archaea inhabit some of the mist extreme environments on our planet, e.g. halophilic archaea in high salt environments (up to 32% NaCl compared to 3.5% on average in the sea)
- most extreme halophiles are obligate aerobes, have a high GC-content in their DNA (to provide more stability as they are stronger than AT binds) . Proteins have a high proportion of acidic amino acids and low proportion of hydrophobic amino acids - Major producers of methane from a range of substrates
- H2, CO2, formate, alcohol, pyruvate, methanol, methylamine, acetate, methyl suffice, dimethyl sulfide - unique features
- Cell envelope: pseudo-PG, s-layer adjoining cytoplasmic membrane, unusual lipids in membrane
- eukaryote like transcriptional and translational machinery
5
Q
Methanogens
A
occur in seven orders:
- Methanobacteriales
- Methanococcales
- Methanopyrales
- Methanomassiliicoccales (lost ability to produce methane by CO2 reduction)
- Methanomicrobiales
- Methanocellales
- Methanosarcinales (lost ability to produce methane by CO2 reduction)
- they are united by their ability to produce methane and their intolerance to oxygen
- Several co factors required by methanogenic pathways are inhibited by oxygen so all methanogens are obligate anaerobes
- Strict anoxic techniques are therefore required for their cultivation in isolation
- Most methanogens are are mesophilic some grow in extreme environments
6
Q
methanocaldococcus jannaschii
A
Check slides
-from undersea hypothermic vents, the characteristic make them very difficult to grow them in the lab but there are special labs for these with large tanks to imitate the pressure temp etc.
- big contribution to start of post genomic era as it was the first ever whole genome sequence
- All of a sudden here was so many characterisations that could be done based on genome analysis and gene comparisons
- Done with normal automated sequencing - today we use ……. So we have metagenomic sequencing
- Contains about 1700 genes
- Majority of genes encoding functions such as central metabolic pathways and cell division are similar to those in bacteria
- However, most genes in this encoding core molecular processes such as transcription and translation more closely resemble those of eukaryotes
- Some of these are genes that encode enzymes needed for methanogenesis
7
Q
Methanospirillium hungatei
A
Degrades waste before it is further treated and let back into nature
8
Q
Methanobrevibacter ruminatium
A
Cows cannot digest cellulose but this archaea can- symbiotic relationshi between this archaea and ruminating cattle
9
Q
Methanogenesis in various archaea
A
- methanogenesis can be performed through three different pathways (look at figures pg 572)
- Methanogenesis by CO2 reduction
- Methylotrophic methanogenesis
- Acetoclastic methanogenesis - all these pathways rely on coenzyme M with methane produced by the reduction of methyl-CoM to methane
- methanogens often form syntrophic associations with fermentative anaerobes
- in this way the fermentative organisms degrade a wide range of organic carbon molecules into H2, CO2 and acetate which are ultimately used as substrates for methanogenesis
- The CO2 reduction pathway can also be used by some species to produce methane from formate, or carbon monoxide
- While most species use H2 to reduce CO2, some can also reduce CO2 by using electrons from Pyruvate or certain alcohols
- The acetoclastic and methylotrophic pathways of methanogenesis are found mainly within the Methanosarcinales
- Methylated substrates include methanol and many others.
- Many species in Methanosarcinales will oxidise one molecule of methane to CO2 to generate the electrons needed to reduce three molecules of methane to CH4 and H2O
- Others need an external electron donor such as H2 to reduce methylated compounds to CH4only few methanogens are known to use acetate as a substrate and they are all members of the Methanosarcinales
10
Q
Crenarchaeota
A
- consists of many hyperthermophiles and sulfur lovers
- Habitats of hyperthermophilic archaea in Yellowstone:
- Sulfur-rich, hot-springs
- pH 1-8
- temperatures up to 100 degrees Celsius
11
Q
Sulfolobales:
A
- sulphur rich acidic thermal areas
- Aerobic chemolithotroph that oxidises H2S or S0 to H2SO4 and fixes CO2 as a carbon source
- Cells adhere tightly to sulfur crystals where they can be seen with a microscope after staining with fluorescent dyes
- Can also oxidise Fe2+ to Fe3+ and this ability has been harnessed for the high temperature leaching of iron and copper ores
12
Q
Thermoproteales
A
- neutral or slightly acidic hot springs
- It’s filaments oof thermofilum are thinner
- Carry out S0 anaerobic respiration
- Most isolates can grow chemolithotrophically on H2 or chemoorganotrophically on complex carbon substrates such as yeast extract, small peptides, starch, glucose, ethanol, malate, fumarate, or formate.
- Pyrobaculum - rod shaped hyperthermophile - they have some species of can respire aerobically
- However it can also grow by anaerobic respiration with NO3-, Fe3+, of S0 as electron acceptors and H2 as an electron donor.
- Other species, can grow anaerobically on organic electron donors, reducing S0 to H2S. The growth temp optimum of Pyrobaculum is 100 degrees Celsius, and species of this organism have been isolated from terrestrial hot springs and from hydrothermal vents
13
Q
Pyrodictium and pyrolobus (from submarine volcanic habitats)
A
- Cells of Pyrodictium are irregularly disk-shaped and grow in culture in a mycelium-like layer attached to crystals of S0
- The cell mass consists of a network of fibers to which individual cells are attached
- The fibers are hollow and consist of protein arranged in a fashion similar to that of bacterial flagella
- However, the filaments do not function in motility but instead as organs of attachment.
- The cell walls of Pyrodictium are composed of glycoprotein.
- Physiologically, Pyrodictium is a strict anaerobe that grows chemolithotrophically on H2 as an electron donor and S0 as an electron acceptor or chemoorganotrophically on complex mixtures of organic compounds.
14
Q
Desulfurococcus and Ignicoccus
A
- Other notable members of the Desulfurococcales include Desulfurococcus, the genus for which the order is named, and Ignicoccus.
- Desulfurococcus is a strictly anaerobic S0-reducing organism like Pyrodictium, but differs from this organism in its phylogeny and the fact that it is much less thermophilic, growing optimally at about 85°C.
- Some Ignicoccus species are hosts to the small parasitic Acheson Nanoarchaeum equitans
- Ignicoccus has a novel cell structure that lacks an S layer and possesses a unique outer cellular membrane.
- This outer cellular membrane is distinct in several ways from the outer membrane of gram negative Bacteria
- Ignicoccus also contains an inner cellular membrane that contains the cytoplasm and the enzymes responsible for biosynthesis and information processing.
- The periplasm of Ignicoccus also contains membrane-bound vesicles that may function in exporting substances outside the cell. In this way, the cell structure of Ignicoccus resembles that of Eukarya. Because of this, Ignicoccus has been proposed to be a modern descendant of the ancestral cell type that gave rise to the origin of eukaryotic cells, a topic we covered earlier
15
Q
Asgard archaea
A
- very recent addition
- all have name that are related to “gods”
- provide info about how eukaryotes came about
- it is widely seen as the “missing link”
- encode multiple genes previously thought to be unique to eukaryotes
- They were identified via metagenomic analysis of microbial communities from Loki’s castle
- Loki’s castle is a hyperthermal vent
- so far only grown in enriched (not pure) culture (syntrophic organisms- they do require some mate which is not the same species)
- They have protrusions (they look kind of like macrophages)
16
Q
Staphylothermus
A
- Cells of Staphylothermus are spherical, about 1 mm in diameter, and form aggregates of up to 100 cells, much like its morphological but mesophilic counterpart among the Bacteria, Staphylococcus
- Unlike many hyperthermophiles, Staphylothermus is not a chemolithotroph but instead a chemoorganotroph, with species that grow optimally at 92°C. Organic carbon sources are used as electron donors in sulfur reduction, producing H2S, acetate, and isovalerate as products
- Isolates of Staphylothermus have been obtained from both shallow marine hydrothermal vents and very hot black smokers
- This organism is apparently widely distributed in submarine thermal areas, where it is likely to play a significant role in consuming proteins released from dead organisms.
17
Q
Enriched culturing of Loki-archae on from sediment core fraction
A
- they cannot be grown in isolation so this was devised to get as much as possible of the archaea of interest
- they will however not be pure as there are other organisms there to support its growth
- take a bit of sediment and inoculate and dilute and follow the growth (they are grown over a very long period of time)
- they then identify how big a proportion of the final culture is the one that we are interested in which in this case is the Loki B35
- they did staining to show the enrichment
- the enrichment shows that the results are largely due to the archaea though there may be contribution from the other organisms present as well
- Limits the experiments you can do if you know that there is always a bit of noise in the experiment but this applies to a lot of experiments
- using electron microscopy indications of actin like filaments were found - which are a very eukaryotic trait so it could be an indication of a common ancestral actin
