Lecture 7b: microbial diversity 2, diversity of archaea

How many phyla are Archaea split into phylogenetically? what are the names of these phylums?

Five: Euryarchaeota, Nanoarchaeota, Korarchaeota, Crenarchaeota, and Thaumarchaeota;

How does the phylogenetic diversity of Archaea compare to Bacteria and Eukarya?

It is similar in breadth;

Haloarchaea (also called halobacteria)

Euryarchaeota extreme halophiles with an absolute requirement for high salt. Example: Halobacterium salinarum;

Minimum salt needed by haloarchaea for growth

At least 1.5 M (~9%) NaCl;

Where are haloarchaea found?

Solar salt evaporation ponds and salt lakes near saturation, such as the Great Salt Lake (Utah), the Dead Sea, and soda lakes;

How do halophiles maintain osmotic balance?

By accumulating or synthesizing compatible solutes;

How does Halobacterium salinarum balance osmotic pressure?

It pumps large amounts of K+ into the cell so intracellular K+ exceeds extracellular Na+;

Why must halophiles deal with osmotic balance?

Water flows into the cell in hypersaline environments;

How do some haloarchaea make ATP using light?

They use bacteriorhodopsin instead of chlorophyll;

Bacteriorhodopsin

An integral membrane protein that absorbs light and pumps protons across the membrane to make a PMF, which is used to make ATP;

Do haloarchaea fix CO2 with bacteriorhodopsin?

No, they are photoheterotrophs;

Methanogens

The only microbes capable of significant methane production, in the Euryarchaeota. Example: Methanobacterium;

Methanogenesis reaction (Methanobacterium)

4H2 + CO2 → CH4 + 2 H2O;

Why are methanogens environmentally important?

They produce the bulk of atmospheric CH4, an important greenhouse gas;

Oxygen requirement of methanogens

Strict anaerobes found in anaerobic environments such as a cow's gut and sewage sludge;

Cell wall of Methanobacterium

made of pseudomurein,

this is unique to methanobacteriales as most other methanogens have a S layer made of protein or glycoprotein

Thaumarchaeota

Archaea that accomplish nitrification.
Example: Nitrosopumilus maritimus;

Metabolism of Nitrosopumilus maritimus

Aerobic, ammonia-oxidizing chemolithoautotroph

converts NH3 into NO2- for energy and uses CO2 for carbon;

Where are Thaumarchaeota abundant and why does it matter?

In open ocean water, where they are a major player in nitrogen cycling;

Nanoarchaeum equitans

• Nanoarchaeota member

• one of the smallest cellular organisms with one of the smallest known genomes;

• depends on host for most of its cellular needs

What is Nanoarchaeum equitans's relationship with Ignicoccus?

It is an obligate parasite of the crenarchaeote Ignicoccus and depends on it for most cellular needs;

Korarchaeum cryptofilum

Korarchaeota member.

Obligately anaerobic chemoorganotroph

hyperthermophile

long, thin filament cells;

Why can't Korarchaeum cryptofilum be grown in pure culture?

It lacks many core genes and depends on other members of its hot springs community;

Crenarchaeota

Mostly hyperthermophiles found in boiling hot springs and deep ocean vents. Some are found in extremely cold environments;

Metabolism of Crenarchaeota

Chemoorganotrophs or chemolithotrophs, and most use sulfur in their metabolism;

Sulfolobus acidocaldarius

Crenarchaeote from sulfur-rich acidic hot springs. A hyperthermophile and acidophile;

Metabolism of Sulfolobus acidocaldarius

Aerobic chemolithotroph that oxidizes reduced sulfur or iron;

Sulfur oxidation reaction (Sulfolobus)

2S0 + 3O2 + 2H2O → 2 H2SO4;

Asgard superphylum

A group of Archaea known only from metagenome sequences with metabolism inferred from reconstructed genomes.

Phyla are named after Norse gods;

Examples of Asgard phyla

Lokiarchaeota, Odinarchaeota, Thorarchaeota (also Heimdallarchaeota);

Why are Asgard archaea important?

By sequence similarity they may be the "missing link" between Archaea and Eukarya;

What do Asgard archaea contain that was once thought to be eukaryote-specific?

Versions of genes previously thought to be unique to eukaryotes;

Candidatus Prometheoarchaeum syntrophicum (strain MK-D1)

First cultured Asgard archaeon, isolated from deep marine sediment (Imachi et al. 2020). It is related to Lokiarchaeota;

Growth characteristics of Prometheoarchaeum syntrophicum

Anaerobic, extremely slow-growing small coccus (~550 nm) that took 10 years to isolate and degrades amino acids through syntrophy;

What does Prometheoarchaeum syntrophicum need to grow?

The presence of another bacterium, Halodesulfovibrio (syntrophic growth);

Morphology of Prometheoarchaeum syntrophicum

It grows amorphously with many blebs and long, often branching protrusions, and has no visible organelle-like structures;

E3 model

Entangle-engulf-endogenize, the hypothetical model for eukaryogenesis proposed by Imachi et al. 2020;

Eukaryogenesis model: role of the host archaeon

A syntrophic archaeon degrades amino acids to short-chain fatty acids and H2, interacting with H2-scavenging sulfate-reducing bacteria;

Eukaryogenesis model: role of the aerobic partner

A facultatively aerobic organotrophic partner (future mitochondrion) scavenges toxic O2, then is engulfed by the host (endosymbiosis);

Eukaryogenesis model: final step

The host delegates catabolism and ATP generation to the endosymbiont and a symbiont-to-host ATP channel (ADP/ATP carrier) is established