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Selfsim
2013-Jun-27, 12:02 AM
A stepping-stone for oxygen on Earth: Researchers find evidence of an early manganese-oxidizing photosystem (http://phys.org/news/2013-06-stepping-stone-oxygen-earth-evidence-early.html)

Now, a team led by geobiologists at the California Institute of Technology (Caltech) has found evidence of a precursor photosystem involving manganese that predates cyanobacteria, the first group of organisms to release oxygen into the environment via photosynthesis.
...
"Manganese plays an essential role in modern biological water splitting as a necessary catalyst in the process, so manganese-oxidizing photosynthesis makes sense as a potential transitional photosystem,"
...
The manganese in the deposits had indeed been oxidized and deposited before the appearance of water-splitting cyanobacteria. This implies, the researchers say, that manganese-oxidizing photosynthesis was a stepping-stone for oxygen-producing, water-splitting photosynthesis
...
'Can we make a photosystem that's able to oxidize manganese but doesn't then go on to split water? How does it behave, and what is its chemistry?' Even though we know what modern water splitting is and what it looks like, we still don't know exactly how it works. There is a still a major discovery to be made to find out exactly how the catalysis works,
..
Next up in Fischer's lab, Johnson plans to work with others to try and mutate a cyanobacteria to "go backwards" and perform manganese-oxidizing photosynthesis.Manganese based photosynthesis, eh?

Yet another 'pre-cursor' bio-sign to look for?

Interesting ...

Swift
2013-Jun-27, 01:45 AM
Nice piece of work and a very interesting hypothesis.

Colin Robinson
2013-Jun-28, 06:37 AM
A stepping-stone for oxygen on Earth: Researchers find evidence of an early manganese-oxidizing photosystem (http://phys.org/news/2013-06-stepping-stone-oxygen-earth-evidence-early.html)
Manganese based photosynthesis, eh?

Yet another 'pre-cursor' bio-sign to look for?

Interesting ...



Thanks for the link, and I agree it is very interesting research, but I'm not sure it matches the title that you've given this thread.

The article is about emergence of the family of oxygen-producing micro-organisms known as cyanobacteria (the "blue-green algae" as they used to be known), not about emergence of life as such. It mentions that "Johnson plans to work with others to try and mutate a cyanobacteria to "go backwards" and perform manganese-oxidizing photosynthesis." This suggests to me that the researchers think the manganese-oxidizing was done by living organisms related to the cyanobacteria, though chemically less sophisticated.

Isn't this more a matter of "manganese in early evolution" rather than "manganese in abiogenesis"?

Selfsim
2013-Jun-28, 10:03 AM
Hehe ... point taken ...

The researchers seem to be cautious about making any references to whether or not the systems involved in this are 'living' or 'not living' ... (which I think is quite a wise move for them). Going back in time, at some stage, there has to be a point where 'living' no longer has the same meaning as we presently assign to it. They seem to refer to it as a 'system' and 'molecular machinery'.

Anyway, the main point is that it predates cyanobacteria's estimated widespread production of oxygen. That makes it more primitive.
Wiki says:
Stromatolites of fossilized oxygen-producing cyanobacteria have been found from 2.8 billion years ago, possibly from 3.5 billion years ago. The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria. The geologic record indicates that this transforming event took place early in our planet's history, at least 2450-2320 million years ago (mya), and probably much earlier.So, it looks like this mechanism fits in around the ~2.4 (~2.8?) to 3.5bya timeframe ... that's getting pretty close to abiogenesis if ya ask me(!?!)

iquestor
2013-Jun-28, 11:55 AM
What a great article! thanks selfsim. very interesting.

BioSci
2013-Jun-28, 04:41 PM
Hehe ... point taken ...

The researchers seem to be cautious about making any references to whether or not the systems involved in this are 'living' or 'not living' ... (which I think is quite a wise move for them). Going back in time, at some stage, there has to be a point where 'living' no longer has the same meaning as we presently assign to it. They seem to refer to it as a 'system' and 'molecular machinery'.

Anyway, the main point is that it predates cyanobacteria's estimated widespread production of oxygen. That makes it more primitive.
Wiki says:So, it looks like this mechanism fits in around the ~2.4 (~2.8?) to 3.5bya timeframe ... that's getting pretty close to abiogenesis if ya ask me(!?!)


First evidence of earth life is thought to have occurred ~ 3.8 to 4 bya...
Once a reproducing life-form got established on earth, there would be many potential metabolic and chemo-biotic reactions that evolving organisms could use. A few hundred million years is a long time in evolutionary terms and life history (first primitive land plants were "only" 360-400 mya).

But we really know little about the detailed biochemistry of the first life on earth. One can certainly speculate that pre-photosynthetic activity may have occurred earlier than currently assumed but the current best evidence does not go back to abiogenesis. But it certainly might if evidence could be found to support an alternative early biochemistry. Some of the ideas around the emergence of life from underwater volcanic vents would place a greater emphasis on inorganic chemical processes.

Selfsim
2013-Jun-28, 10:07 PM
First evidence of earth life is thought to have occurred ~ 3.8 to 4 bya...
Once a reproducing life-form got established on earth, there would be many potential metabolic and chemo-biotic reactions that evolving organisms could use.Whilst the view that a self-reproducing life-form might be considered a pre-requisite, the reversal of this is also considered equally possible …ie: such organisms might have developed from chemistries just like the Manganese based photosystem. For instance, once a localised energy release and storage mechanism exists, all sorts of other 'systems' might well become attracted to it(?) AIUI, the manganese also acts as a catalyst in these reactions .. so to a limited extent, this could also be viewed as an autocatalytic system(?)


But we really know little about the detailed biochemistry of the first life on earth. One can certainly speculate that pre-photosynthetic activity may have occurred earlier than currently assumed I think you'll find that these guys have found the evidence that it did occur earlier than currently assumed.
.. but the current best evidence does not go back to abiogenesis. But it certainly might if evidence could be found to support an alternative early biochemistry. Some of the ideas around the emergence of life from underwater volcanic vents would place a greater emphasis on inorganic chemical processes.It seems these guys might be now going after other manganese-bearing rocks, elsewhere. I'd say they'd be looking pretty closely at stromatolite formations as well. Meteoric minerals may also be of interest when viewed from this perspective although, I don't recall any manganese being reported as being found extant to any meteorites(?)

Colin Robinson
2013-Jun-28, 10:46 PM
Hehe ... point taken ...

The researchers seem to be cautious about making any references to whether or not the systems involved in this are 'living' or 'not living' ... (which I think is quite a wise move for them). Going back in time, at some stage, there has to be a point where 'living' no longer has the same meaning as we presently assign to it. They seem to refer to it as a 'system' and 'molecular machinery'.

Anyway, the main point is that it predates cyanobacteria's estimated widespread production of oxygen. That makes it more primitive.
Wiki says:So, it looks like this mechanism fits in around the ~2.4 (~2.8?) to 3.5bya timeframe ... that's getting pretty close to abiogenesis if ya ask me(!?!)

Cyanobacteria are one of 30 known phyla of the domain bacteria. They seem to be the only bacterial phylum that performs photosynthesis in a way that produces oxygen molecules (O2). Although there are other bacterial phyla with members that perform photosynthesis without producing oxygen: the chlorobi (green sulfur bacteria) and the proteobacteria (the phylum that includes purple sulfur bacteria).

If it is suggested that cyanobacteria emerged via abiogenesis from non-living systems, then what about the other 29 bacterial phyla — where did they come from? And what about the archaea?

Selfsim
2013-Jun-29, 12:39 AM
Cyanobacteria are one of 30 known phyla of the domain bacteria. They seem to be the only bacterial phylum that performs photosynthesis in a way that produces oxygen molecules (O2). Although there are other bacterial phyla with members that perform photosynthesis without producing oxygen: the chlorobi (green sulfur bacteria) and the proteobacteria (the phylum that includes purple sulfur bacteria).

If it is suggested that cyanobacteria emerged via abiogenesis from non-living systems, then what about the other 29 bacterial phyla — where did they come from? And what about the archaea?Hmm .. well it is possible that the last common ancestor of bacteria and archaea occurred before the evolution of actual 'cells', and 'gene' transfer arose thru fixation of certain 'gene' subsets.

This phase is pretty sketchy, but the generalised fixation process itself seems to be common, (although varied).

It seems to me that the definitions of 'inorganic' and 'organic' during this phase, may not be entirely adequate for describing what may have been going on, either.

Colin Robinson
2013-Jun-29, 01:49 AM
Hmm .. well it is possible that the last common ancestor of bacteria and archaea occurred before the evolution of actual 'cells', and 'gene' transfer arose thru fixation of certain 'gene' subsets.

This phase is pretty sketchy, but the generalised fixation process itself seems to be common, (although varied).

I think the overall chemistry of carbon fixation was summed up by Sean Carroll, when he said "The purpose of life is to hydrogenate carbon dioxide." It is already known that organisms have done this in varied ways, some powered by light energy, some by chemical energy.

The simplest way of hydrogenating carbon dioxide (chemically speaking) is probably the direct use of hydrogen molecules in habitats where they are available.

I think the method involving manganese is important, not because it is more primitive than any other method used by living organisms, but because it is an evolutionary missing link to oxygen-generating photosynthesis (which involves manganese as an intermediary).

Another article about the research on ancient manganese:

Captured: the moment photosynthesis changed the world (http://www.newscientist.com/article/mg21628944.500-captured-the-moment-photosynthesis-changed-the-world.html#.Uc4wiEYhpMs)

An abstract of the paper itself

Manganese-oxidizing photosynthesis before the rise of cyanobacteria (http://www.pnas.org/content/early/2013/06/20/1305530110.abstract)

Selfsim
2013-Jun-29, 04:08 AM
Hmm ... whilst I agree that the electron depletion of Mn, by some process, can explain the production of oxygen, (and that is the primary inference from the study), the origins of the idea that it was done by already photosynthesising cyanobacteria, is not necessarily altogether a 'slam-dunk'.

Using the link posted by Colin (as a summary of the line of argument):
They believe that modern photosynthesis was born when early cyanobacteria by chance floated into a watery environment rich in manganese, and quickly adapted to take advantage of the new source of electrons.Quite plausible ... and if one looks carefully at this, it is dependent on there actually being solid evidence of cyanobacteria predecessors existing prior, (ie: from the 2.4Gya to 3.6Gya era). Looking at the evidence of that, in turn, leads one to interpretations of the Strelley Pool stromatolite formations on the Western Australia coastline.

The ties between sulfur metabolising cyanobacteria/microbes, and the stromatolytic laminations in the Strelley Pool formations, is by no means firmly established as yet. (Admittedly, this may also not be do-able .. given the age of the surrounding geology, and the probably long-gone direct evidence of whatever 'agent' might have been at cause. The possible similarities between the 3.5Gya 'agent' remnants, and modern cyanobacteria formations however, is quite close. Whether the 3.5Gya 'agent' was 'living' or not, I think, is still up for discussion(?) ).

Colin Robinson
2013-Jun-29, 06:12 AM
Hmm ... whilst I agree that the electron depletion of Mn, by some process, can explain the production of oxygen, (and that is the primary inference from the study), the origins of the idea that it was done by already photosynthesising cyanobacteria, is not necessarily altogether a 'slam-dunk'.

Using the link posted by Colin (as a summary of the line of argument):Quite plausible ... and if one looks carefully at this, it is dependent on there actually being solid evidence of cyanobacteria predecessors existing prior, (ie: from the 2.4Gya to 3.6Gya era). Looking at the evidence of that, in turn, leads one to interpretations of the Strelley Pool stromatolite formations on the Western Australia coastline.

The ties between sulfur metabolising cyanobacteria/microbes, and the stromatolytic laminations in the Strelley Pool formations, is by no means firmly established as yet. (Admittedly, this may also not be do-able .. given the age of the surrounding geology, and the probably long-gone direct evidence of whatever 'agent' might have been at cause. The possible similarities between the 3.5Gya 'agent' remnants, and modern cyanobacteria formations however, is quite close. Whether the 3.5Gya 'agent' was 'living' or not, I think, is still up for discussion(?) ).

Apparently manganese-oxidizing bacteria do exist today. I found this reference to them on the Wikipedia page Chemotroph (https://en.wikipedia.org/wiki/Chemotroph).



Manganese-oxidizing bacteria also make use of igneous lava rocks in much the same way—by oxidizing Mn2+ into Mn4+. Manganese is much rarer than iron in oceanic crust, but is much easier for bacteria to extract from the igneous glass. In addition, each manganese oxidation yields around twice the energy as an iron oxidation due to the gain of twice the number of electrons. Much still remains unknown about manganese-oxidizing bacteria because they have not been cultured and documented to any great extent.

I also found a short scientific paper about the genome of one strain:
Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272940/)

Selfsim
2013-Jun-29, 07:54 AM
Apparently manganese-oxidizing bacteria do exist today. I found this reference to them on the Wikipedia page Chemotroph (https://en.wikipedia.org/wiki/Chemotroph).

I also found a short scientific paper about the genome of one strain:
Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272940/)Well, the one theme in common is that life, no matter which version of it .. (ie: ancient or recent) ... always makes a grab for the easiest to metabolise energy source, eh?
This even works when it comes to the isotopic preferences (ie: life's chemical affinity for the lighter isotopes).

This is classic organic chemistry at work, too .. not limited to just life.

Selfsim
2013-Jun-29, 11:43 PM
I notice that 'Astrobiology Australia' is having a pow-wow this week at the UNSW .. with 'Ms. SETI' herself, Jill Tarter kicking it off!

Many of the more meaty science topics however, are relevant to the matters discussed in this thread including:

- Life in the Dresser Formation: Microbial-Hydrothermal Ecosystems at c. 3.5Ga in the North Pole Dome, Pilbara Craton, Western Australia;
- Assessing the microbial composition of extant Australian stromatolites
- Living stromatolites of Shark Bay: a walk through technological time from differing geochemical settings;
- The possible influence of the evolution of photosynthesis on genome size and function in organisms of the Early Earth
- Formation of macroscopic patterns in microbial mats in the presence of sediments and water flow;
- Cyanobacteria of arid land soil crusts: A hard life
- How Chemistry becomes Biology? Identifying the Driving Force for Evolution
- Did life originate from a global chemical reactor?
- Investigating the syngeneity and paleobiology of hydrocarbons in stromatolites from the Fortescue Group, (2.7–2.8 Ga), NW Australia.
- The oxygenation time of Earth: Insights from the Neoarchean microbialite record
- Biogenic Minerals in Banded Iron Formations
- Whither the Whiff? A Status Report on Evidence of Environmental Oxygenation before the Great Oxidation Event.

Might be of interest to our Aussie folk .. (??)

I guess we should expect reports on the materials presented, here at CQ LiS?

The program is here. (http://www.astrobiologyaustralia.com.au/uploads/1/7/4/5/17458617/program_29-06-13.pdf)

lpetrich
2013-Jul-25, 09:03 AM
The original article:
Manganese-oxidizing photosynthesis before the rise of cyanobacteria (http://www.pnas.org/content/110/28/11238.abstract)

The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown. To illuminate this history, we examined the behavior of the ancient Mn cycle using newly obtained scientific drill cores through an early Paleoproterozoic succession (2.415 Ga) preserved in South Africa. These strata contain substantial Mn enrichments (up to ∼17 wt %) well before those associated with the rise of oxygen such as the ∼2.2 Ga Kalahari Mn deposit. Using microscale X-ray spectroscopic techniques coupled to optical and electron microscopy and carbon isotope ratios, we demonstrate that the Mn is hosted exclusively in carbonate mineral phases derived from reduction of Mn oxides during diagenesis of primary sediments. Additional observations of independent proxies for O2—multiple S isotopes (measured by isotope-ratio mass spectrometry and secondary ion mass spectrometry) and redox-sensitive detrital grains—reveal that the original Mn-oxide phases were not produced by reactions with O2, which points to a different high-potential oxidant. These results show that the oxidative branch of the Mn cycle predates the rise of oxygen, and provide strong support for the hypothesis that the water-oxidizing complex of photosystem II evolved from a former transitional photosystem capable of single-electron oxidation reactions of Mn.
Like iron (oxidation states +2 and +3), manganese has several oxidation states, notably +2 and +4. What happened is that something stripped some electrons from manganese ions, and that that something was almost certainly not oxygen. So it was likely photosynthesis.

There are lots of organisms that practice non-oxygenic photosynthesis: the purple bacteria, the green bacteria, the heliobacteria, and the halobacteria. Photosynthetic eukaryotes like plants also practice oxygenic photosynthesis, but it's the chloroplasts / plastids in them that do so, and those organelles are captured cyanobacteria.

There are two types of photosynthesis that organisms practice, types which I call the rhodopsin and the chlorophyll types.

Only the halobacteria do rhodopsin photosynthesis. Their bacteriorhodopsin molecules pump hydrogen ions out of the cell, and they return through ATP synthase complexes. Those complexes, which are ubiquitous in cellular organisms, assemble ATP molecules from AMP and inorganic phosphate. The ATP molecules then supply energy to various cellular processes, breaking back up into AMP and inorganic phosphate as they do so. AM,D,TP = adenosine mono,di,triphosphate, a RNA nucleotide.

That makes rhodopsin photosynthesis *very* limited.

However, chlorophyll photosynthesis is *much* less limited. Chlorophyll molecules, along with carotenoids and phycobilins, capture photons, which then excite electrons. These excited electrons are then fed into an electron-transfer chain that then extracts energy from them by pumping hydrogen ions and/or adds them to various molecules to chemically reduce them, molecules like carbon dioxide.

Chlorophyll photosynthesis needs a source of electrons, and the best-known source is water. It gets turned into oxygen and hydrogen ions. There are several non-oxygenic sources that various organisms use, like sulfur, iron, and manganese.


So that manganese oxidation is evidence of organisms practicing a form of photosynthesis similar to present-day forms of chlorophyll photosynthesis.

Selfsim
2013-Jul-25, 11:35 PM
The original article:
Manganese-oxidizing photosynthesis before the rise of cyanobacteria (http://www.pnas.org/content/110/28/11238.abstract)

Like iron (oxidation states +2 and +3), manganese has several oxidation states, notably +2 and +4. What happened is that something stripped some electrons from manganese ions, and that that something was almost certainly not oxygen. So it was likely photosynthesis.

There are lots of organisms that practice non-oxygenic photosynthesis: the purple bacteria, the green bacteria, the heliobacteria, and the halobacteria. Photosynthetic eukaryotes like plants also practice oxygenic photosynthesis, but it's the chloroplasts / plastids in them that do so, and those organelles are captured cyanobacteria.

There are two types of photosynthesis that organisms practice, types which I call the rhodopsin and the chlorophyll types.

Only the halobacteria do rhodopsin photosynthesis. Their bacteriorhodopsin molecules pump hydrogen ions out of the cell, and they return through ATP synthase complexes. Those complexes, which are ubiquitous in cellular organisms, assemble ATP molecules from AMP and inorganic phosphate. The ATP molecules then supply energy to various cellular processes, breaking back up into AMP and inorganic phosphate as they do so. AM,D,TP = adenosine mono,di,triphosphate, a RNA nucleotide.

That makes rhodopsin photosynthesis *very* limited.

However, chlorophyll photosynthesis is *much* less limited. Chlorophyll molecules, along with carotenoids and phycobilins, capture photons, which then excite electrons. These excited electrons are then fed into an electron-transfer chain that then extracts energy from them by pumping hydrogen ions and/or adds them to various molecules to chemically reduce them, molecules like carbon dioxide.

Chlorophyll photosynthesis needs a source of electrons, and the best-known source is water. It gets turned into oxygen and hydrogen ions. There are several non-oxygenic sources that various organisms use, like sulfur, iron, and manganese.


So that manganese oxidation is evidence of organisms practicing a form of photosynthesis similar to present-day forms of chlorophyll photosynthesis.Hmm .. interesting! Thanks for this! :)
So, one can only wonder about just how much organelle machinery might have been needed, in order for 'similar-to-chlorophyll based photosynthesis' to have left its mark on the Manganese(?)

Lipids are usually required for the formation of present-day membranes, and I think photosynthetic organelles have their own particular present-day preferences in this regard, (in their photosynthetic structures).

Would one call the 'similar-to-chlorophyll photosynthetic process', 'life'?

Its an interesting question, but it also comes close to the old 'Irreducible Complexity' (IR) mode of thinking also .. and whilst this may be a convenient way of thinking, things rarely turn out to be as simple as IR assumes, eh?