From Newsgroup: talk.origins


https://www.quantamagazine.org/the-cells-that-breathe-two-ways-20250723/

...
Instead of using oxygen to harvest energy, many
single-celled life-forms that live in environments
far from oxygenrCOs reach, such as deep-sea
hydrothermal vents or stygian crevices in the
soil, wield other elements to respire and unlock
energy.

This physical separation of the oxygen-rich and
oxygen-free worlds is not merely a matter of life
utilizing available resources; itrCOs a biochemical
necessity. Oxygen doesnrCOt play nice with the
metabolic pathways that make it possible to
respire with the use of other elements, such as
sulfur or manganese. It gives aerobes like us
life, but for many anaerobes, or creatures that
respire without oxygen, oxygen is a toxin that
reacts with and damages their specialized
molecular machinery.
...
An ongoing mystery for researchers is how life
navigated the shift from anaerobic to aerobic
respiration; so much microbial biodiversity had
to adapt to a world filled with what was once a
biochemical bane. Now researchers have fresh
insight into what that transition could have
looked like billions of years ago, gleaned from
an organism living today. A bacterium that
researchers collected from the cauldron of a
Yellowstone National Park hot spring does
something that life really shouldnrCOt be able to
do: It runs aerobic and anaerobic metabolisms
simultaneously. It breathes oxygen and sulfur
at the same time.
...

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From Newsgroup: talk.origins

On 7/24/2025 11:06 PM, Pro Plyd wrote:

https://www.quantamagazine.org/the-cells-that-breathe-two-ways-20250723/

...
Instead of using oxygen to harvest energy, many
single-celled life-forms that live in environments
far from oxygenrCOs reach, such as deep-sea
hydrothermal vents or stygian crevices in the
soil, wield other elements to respire and unlock
energy.

This physical separation of the oxygen-rich and
oxygen-free worlds is not merely a matter of life
utilizing available resources; itrCOs a biochemical
necessity. Oxygen doesnrCOt play nice with the
metabolic pathways that make it possible to
respire with the use of other elements, such as
sulfur or manganese. It gives aerobes like us
life, but for many anaerobes, or creatures that
respire without oxygen, oxygen is a toxin that
reacts with and damages their specialized
molecular machinery.
...
An ongoing mystery for researchers is how life
navigated the shift from anaerobic to aerobic
respiration; so much microbial biodiversity had
to adapt to a world filled with what was once a
biochemical bane. Now researchers have fresh
insight into what that transition could have
looked like billions of years ago, gleaned from
an organism living today. A bacterium that
researchers collected from the cauldron of a
Yellowstone National Park hot spring does
something that life really shouldnrCOt be able to
do: It runs aerobic and anaerobic metabolisms
simultaneously. It breathes oxygen and sulfur
at the same time.
...

It dosn't look like this is not any type of transitional. It looks like horizontal gene transfer from eubacteria.

https://www.nature.com/articles/s41467-025-56418-4

Their figure 2 indicates that this Archaea bacteria acquired the
eubacteria oxidative phosphorylation pathway. Apparently oxygen usually interferes with sulfur metabolism, but this Archaea has acquired the
ability to use oxygen. It looks like they have just added the oxidative phosphorylation pathway to their double membrane and it uses the proton gradient to produce ATP that they were already generating by their
sulfur metabolism. Normally oxygen is toxic to anaerobic bacteria. It
is even bad news for aerobic bacteria, but they have evolved mechanisms
to deal with reactive oxygen species (ROS). My guess is that when this Archaea bacteria acquired the oxidative phosphorylation pathway that it
also acquired the genes to take care of the ROS issue. Anaerobic
chemotrophes generate a proton gradient and were using F0 ATPase to use
this proton gradient to produce ATP before F0 ATPase was used to produce
ATP in the eubacterial oxidative phosphorylation. I call them both F0
ATPase, but they are just members of that ATPase gene family. It is
ancient and is used by chemotrophes, aerobic bacteria, and
photosynthetic bacteria to generate ATP. It is also the flagellar
motor, and was spinning in order to burn or make ATP long before the
flagellum evolved. It has evolved to transport more than just protons
across the bacterial membrane. It can transport solutes and even
peptides. The flagellar ATPase transports proteins out of the cell. It transports it's flagellar tail proteins, but other versions transport
peptide toxins.

Google claims that there are aerobic Archaea bacteria that are known to
use oxygen, but I couldn't find out how they were doing it.

Ron Okimoto

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From Newsgroup: talk.origins

On 7/25/2025 7:42 AM, RonO wrote:

On 7/24/2025 11:06 PM, Pro Plyd wrote:

https://www.quantamagazine.org/the-cells-that-breathe-two-ways-20250723/

...
Instead of using oxygen to harvest energy, many
single-celled life-forms that live in environments
far from oxygenrCOs reach, such as deep-sea
hydrothermal vents or stygian crevices in the
soil, wield other elements to respire and unlock
energy.

This physical separation of the oxygen-rich and
oxygen-free worlds is not merely a matter of life
utilizing available resources; itrCOs a biochemical
necessity. Oxygen doesnrCOt play nice with the
metabolic pathways that make it possible to
respire with the use of other elements, such as
sulfur or manganese. It gives aerobes like us
life, but for many anaerobes, or creatures that
respire without oxygen, oxygen is a toxin that
reacts with and damages their specialized
molecular machinery.
...
An ongoing mystery for researchers is how life
navigated the shift from anaerobic to aerobic
respiration; so much microbial biodiversity had
to adapt to a world filled with what was once a
biochemical bane. Now researchers have fresh
insight into what that transition could have
looked like billions of years ago, gleaned from
an organism living today. A bacterium that
researchers collected from the cauldron of a
Yellowstone National Park hot spring does
something that life really shouldnrCOt be able to
do: It runs aerobic and anaerobic metabolisms
simultaneously. It breathes oxygen and sulfur
at the same time.
...

It dosn't look like this is not any type of transitional.-a It looks like horizontal gene transfer from eubacteria.

https://www.nature.com/articles/s41467-025-56418-4

Their figure 2 indicates that this Archaea bacteria acquired the
eubacteria oxidative phosphorylation pathway.-a Apparently oxygen usually interferes with sulfur metabolism, but this Archaea has acquired the
ability to use oxygen.-a It looks like they have just added the oxidative phosphorylation pathway to their double membrane and it uses the proton gradient to produce ATP that they were already generating by their
sulfur metabolism.-a Normally oxygen is toxic to anaerobic bacteria.-a It
is even bad news for aerobic bacteria, but they have evolved mechanisms
to deal with reactive oxygen species (ROS).-a My guess is that when this Archaea bacteria acquired the oxidative phosphorylation pathway that it
also acquired the genes to take care of the ROS issue.-a Anaerobic chemotrophes generate a proton gradient and were using F0 ATPase to use
this proton gradient to produce ATP before F0 ATPase was used to produce
ATP in the eubacterial oxidative phosphorylation.-a I call them both F0 ATPase, but they are just members of that ATPase gene family.-a It is ancient and is used by chemotrophes, aerobic bacteria, and
photosynthetic bacteria to generate ATP.-a It is also the flagellar
motor, and was spinning in order to burn or make ATP long before the flagellum evolved.-a It has evolved to transport more than just protons across the bacterial membrane.-a It can transport solutes and even peptides.-a The flagellar ATPase transports proteins out of the cell.-a It transports it's flagellar tail proteins, but other versions transport peptide toxins.

Google claims that there are aerobic Archaea bacteria that are known to
use oxygen, but I couldn't find out how they were doing it.

Ron Okimoto

They note that the pathway may be wide spread among Archaea, but not
noticed. It looks like this bacteria has the whole oxidative
phosphorylation pathway of eubacteria. They seem to miss the
possiblility that this may be due to the endosymbiosis with a eubacteria
that may have been the first eukaryote that evolved from Archaea, or a
similar endosymbiotic event. It would not have been just one gene transferred, but a couple hundred. The endosymbiosis that resulted in
this Archaea bacteria may have ultimately resulted in a cell fusion to transfer all the genes needed to keep the oxidative phosphorylation
intact and functioning in the Archaea's double membrane.

Eukaryotes are derived from bacteria, or some lifeform with a single
lipid bilayer membrane existed to incorporate an arachaea bacteria and eventually use it to organized all it's genetic material, but eukaryotes
also formed endosymbiotic associations with eubacteria. Early in the
adoption of archaea and eubacteria the two would have lost their cell
walls and would have been able to fuse together. It would be one way to transfer so many genes to Archaea and maintain a functioning oxidative phosphorylation pathway in the fusion product.

Ron Okimoto

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