Decoding the Genome of Bacteria Capable of Removing Fluorine from Persistent Perfluoro Pollutants.

[NNadir]

The paper to which I'll briefly refer is this one: Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273 Yongchao Xie, Diana Ramirez, Gao Chen, Guang He, Yanchen Sun, Fadime Kara Murdoch, and Frank E. Löffler Environmental Science & Technology 2023 57 (42), 15925-15935.

One of the major environmental problems we face - and future generations will face for a very long time - is persistent halogenated organic molecules in the environment, the most intractable of which are the fluorinated analogues that were used to make everything from fabric protectors ("Scotch Guard&quot to fire fighting foams, to nonstick pans to lubricants and many other products. Collectively these classes of molecules are known as "PFAS" for perfluorinated alkylated substances.

The carbon-fluorine bond is one of the strongest in chemistry, roughly 485 kJ mol^-1, which when translated to light energy puts it in the UV region for cleavage, accounting for its persistence.

I have a critic here, one of those antinuke "solar will save us" fools who fears nuclear energy more than he, she or they fears fossil fuels, even though fossil fuels people continuously without stop and nuclear energy, um, doesn't and who clearly doesn't give a rat's ass about climate change, but who (clock being right twice a day) remarked, offering up the old saw, that I am an example of one of those people when one sees a hammer as the best tool available, every problem is a nail.

As it happens I do believe that exposure to high energy radiation, available from used nuclear fuels, represents a possible way to address fluorocarbon contamination of the air, water and land, and spend a lot of time dreaming up continuous flow systems to do just that as a side product of industrial processes, but such a process would take many many generations to make significant inroads, and will be thus subject to Bateman type equilibria. It is also true that the there are some areas of contamination and contaminated matrices that cannot be exposed to high energy radiation.

Thus a living system that can get into these hard to reach places and mineralize PFAS, and despite the high energy of the bonds, there are apparently microorganisms that can metabolize fluorinated substances. That's what this paper covers.

From the introduction:

Fluorinated chemicals have been utilized in a variety of medical, agricultural, military, industrial, and household applications. (1?3) As a consequence, fluorinated chemicals have been released into the environment, where some of these chemicals, in particular per- and polyfluoroalkyl substances (PFAS), persist and have emerged as ubiquitously distributed, recalcitrant contaminants. (4,5) PFAS, comingled with fluorinated alkanes, are components of aqueous film-forming foams (AFFF) used as fire suppressants. (6,7) Efforts to find microorganisms capable of degrading PFAS have had limited success, although a recent study reported defluorination and degradation in an acidophilic mixed culture dominated by the ammonium-oxidizing bacterium Acidimicrobium sp. strain A6. (8,9) Few studies have explored the degradation of fluorinated alkanes, and the key defluorinating enzyme systems have not been identified.

The strength of the C–F bond has been portrayed as the major hindrance to transform fluorinated organic compounds. Contrary to the belief that enzyme systems cannot cleave C–F bonds, a number of studies have reported the microbial degradation of fluorinated organic compounds. (10,11) Microbial enzyme systems can break the C–F bond through oxygenolytic, (12) hydrolytic, (13) reductive, (14) and hydration (15) mechanisms at neutral pH and at room temperature. Despite this progress, the understanding of the taxonomic diversity of microbes and their enzyme systems involved in defluorination dwarfs in comparison to the existing knowledge base about microbial dechlorination.

Pseudomonas sp. strain 273 was reported to utilize C7 to C10 1-fluoroalkanes and 1,10-difluorodecane (DFD) as the sole sources of carbon and energy for growth under oxic conditions. (16) During growth with fluoroalkanes, this bacterium releases inorganic fluoride, albeit not in stoichiometric amounts, and a fraction of organofluorine is incorporated into cellular phospholipids. (17) Growth experiments determined that the utilization of fluoroalkanes is oxygen-dependent, but the enzyme(s) responsible for defluorination have remained elusive. In this study, we integrated genomic and comparative transcriptomic investigations to identify genes that Pseudomonas sp. strain 273 utilizes during growth with DFD...

It is not clear however that the organism can eat secondary fluorine atoms, surely a major limitation, although one can imagine designing a modified protein that might accomplish this task.

The cute cartoon from the abstract:



One of the more serious graphics in the paper:



The caption:

Figure 3. (A) Phylogenetic affiliation of AlkB-1, AlkB-2, and AlkB-3 identified in Pseudomonas sp. strain 273 and 48 AlkB enzymes from closely related Pseudomonas species and other alkane-degrading bacteria. The tree scale indicates the number of substitutions per amino acid site. The color scheme of the labels C2 to C5 correlates with the gene cluster architecture categories shown in panel B. The C1 category is not labeled in panel A because it is not clear whether all AlkB isolated on the gene cluster work with Rd and Rdr. (B) Features of alkB gene clusters and AlkB enzyme systems. Genes/proteins: alkB/AlkB, alkane monooxygenase; fd/Fd, ferredoxin; fdr/Fdr, ferredoxin reductase; rd/RD, rubredoxin; rdr/RDR, rubredoxin reductase.

I kind of wonder if the authors explored the defluorination of trifluoracetic acid, a penultimate product of decomposition of longer chain perfluorocarboxylic acids, and a molecule that, albeit that it occurs to a small extent naturally, is increasingly accumulating in the environment.

I trust you're enjoying the weekend.

[cachukis]

1. Fascinating. Keep sharing.

[Alliepoo]

2. Very interesting!

Thanks for sharing!

[Easterncedar]

3. I appreciate the information, always

Thank you. I also respect your superior understanding of the issues surrounding nuclear power and climate change, but wish you could be less dismissive of the concerns some, including me, have about the dangers. I can’t quite forget the Reagan era suggestion that we establish a sort of priesthood to guard the nuclear waste depositories through the centuries while civilizations fall and rise.

[NNadir]

4. To be honest, I have almost zero patience for these concerns in light of reality.

Every damned day 19,000 people die from air pollution.

The commercial nuclear industry is now nearly 7 decades old. I will take these "concerns" about so called "nuclear waste" slightly more seriously when someone raising them can show that in the 70 year history of commercial nuclear power, the storage of used nuclear fuel has killed as many people as will die in the next six hours from air pollution, about 4500 people.

The scientific reference for the costs of this terrible and frankly deadly selective attention can be found in this comprehensive publication which I often reference in response to this benighted concern is here:

Global burden of 87 risk factors in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019 (Lancet Volume 396, Issue 10258, 17–23 October 2020, Pages 1223-1249). This study is a huge undertaking and the list of authors from around the world is rather long. These studies are always open sourced; and I invite people who want to carry on about Fukushima to open it and search the word "radiation." It appears once. Radon, a side product brought to the surface by fracking while we all wait for the grand so called "renewable energy" nirvana that did not come, is not here and won't come, appears however: Household radon, from the decay of natural uranium, which has been cycling through the environment ever since oxygen appeared in the Earth's atmosphere.

It is regrettable that so many people have been trained by an illiterate media to say "waste" when discussing nuclear energy, but seem not to give a rat's ass about fossil fuel waste, aka "air pollution" and "climate change," while being unable to demonstrate an example where the storage of used nuclear fuel has killed anyone in this country.

And yet we have this continuous insipid carrying on endlessly.

I personally know the chemistry and physics of used nuclear fuel intimately. I do not regard these valuable materials as "waste," nor can anyone show that they are particularly dangerous. In terms of death toll, they are not as dangerous as automobiles, aircraft, jet skis, and certainly far less dangerous than natural gas, petroleum, and coal.

They are, in fact, extremely valuable materials, not only for the mineralization for PFAS to which I alluded in the OP, but as an essential fuel that can save what is left to save and to restore what is left to restore.

Nuclear energy saves human lives: Prevented Mortality and Greenhouse Gas Emissions from Historical and Projected Nuclear Power (Pushker A. Kharecha* and James E. Hansen Environ. Sci. Technol., 2013, 47 (9), pp 4889–4895)

It follows that the ignorance surrounding and irrational fear of nuclear energy kills people, about 70 million every decade if, as I clearly do, the Lancet publication linked above is accurate.

I hope I make myself clear. I absolutely refuse on ethical and moral grounds to even acknowledge this kind of nonsense.

Nuclear energy need not be perfect; it need not be without risk, to be vastly superior to everything else. It only needs to be vastly superior to everything else, which it clearly and irrefutably is.

We demonize nuclear energy only if we hold all future generations in contempt, which, given that this stuff still floats around despite even a shred of actual evidence to support it, clearly we do.

During the recent Northern Hemisphere summer the planet burst into flames in many places. Glaciers on which billions of people depend for their water supplies are disappearing. People dropped dead in the streets all over the planet from extreme heat and...and...and...and...

...someone wants to tell me about the alleged "danger" of so called "nuclear waste?"

Please spare me. I will only become morally appalled and angry.

Have a nice weekend.

[Easterncedar]

5. I truly do appreciate this.

You make me think. Thank you.

[NNadir]

6. My pleasure. Thank you for thinking. n/t.