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Gifted Microbes Elevate the Case for Intelligent Design to the Entire Biosphere

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Far from being humble, primitive steppingstones to higher life, microbes display superpowers that so-called “higher” forms of life depend on. Here are some recent examples.

Never Say Forever

So-called “forever chemicals” known as PFAS (poly-fluoroalkyl substances) have been in the news as a pollution concern because they resist breakdown for decades in the soil and water. UC Riverside says that our lust for industrial applications comes at a price:

Chlorinated PFAS are a large group in the forever chemical family of thousands of compounds. They include a variety of non-flammable hydraulic fluids used in industry and compounds used to make chemically stable films that serve as moisture barriers in various industrial, packaging, and electronic applications. [Emphasis added.]

The “unusually strong carbon-to-fluorine bonds” in these compounds make them resistant to natural decomposition. Yujie Men’s team at UCR recently found two species of bacteria, Desulfovibrio aminophilus and Sporomusa sphaeroides, that know how to break those bonds. 

“What we discovered is that bacteria can do carbon-chlorine bond cleavage first, generating unstable intermediates,” Men said.

“And then those unstable intermediates undergo spontaneous defluorination, which is the cleavage of the carbon-fluorine bond.”

The team believes that providing these naturally occurring bacteria with nutrients like methanol in groundwater could increase their numbers. If they are not present, contaminated water could be inoculated with the bacteria. Why try to imitate their chemistry prowess when they are already at work doing what is needed? Just pamper them and PFAS can disappear. 

The UCR team published their award-winning findings in Nature Water, but the bacteria are the deserving ones for a prize. This discovery adds to other abilities of bacteria to degrade pollution:

Microbes have long been used for biological cleanup of oil spills and other industrial pollutants, including the industrial solvent trichloroethylene or TCE, which Men has studied.

But what’s known about using microorganisms to clean up PFAS is still in its infancy, Men said. Her discovery shows great promise because biological treatments, if effective pollutant-eating microbes are available, are generally less costly and more environmentally friendly than chemical treatments. Pollutant-eating microbes can also be injected into difficult-to-reach locations underground.

While not an excuse to pollute, the findings give hope for cleaning our messes with gifted microbes.

Proficient Sorters

Some of the rare earth elements (REE) that are high in demand these days are difficult to separate. Again, a gifted bacterium is able to sort them better than humans can, announced researchers at Penn State. A protein in a bacterium may help pave the way for “green tech” with less cost.

Rare earth elements, like neodymium and dysprosium, are a critical component to almost all modern technologies, from smartphones to hard drives, but they are notoriously hard to separate from the Earth’s crust and from one another.

Penn State scientists have discovered a new mechanism by which bacteria can select between different rare earth elements, using the ability of a bacterial protein to bind to another unit of itself, or “dimerize,” when it is bound to certain rare earths, but prefer to remain a single unit, or “monomer,” when bound to others.

Instead of requiring toxic chemicals to do the separation, bacteria equipped with the LanM protein may be able to do it cleanly and quickly. The news item says that this bacterium lives on buds of English oak trees. Its ability to discriminate similar elements is very precise:

“This was surprising because these metals are very similar in size,” Cotruvo said. “This protein has the ability to differentiate at a scale that is unimaginable to most of us — a few trillionths of a meter, a difference that is less than a tenth of the diameter of an atom.”

Nature has reported on Penn State’s welcome discovery.

Mercury Impacts Earth

Concerned about mercury in your tuna and other seafood? Bacteria are coming to the rescue here, too. Scientists at Oak Ridge National Laboratory warn of the dangers of methylated mercury:

Methylmercury is a neurotoxin that forms in nature when mercury interacts with certain microbes living in soil and waterways. It accumulates at varying levels in all fish — particularly large predatory fish such as tuna and swordfish — and, when consumed in large quantities, can potentially cause neurological damage and developmental disorders, especially in children

While microbes are involved in the formation of the toxin, scientists at Oak Ridge have discovered two species of methanotrophic bacteria that can degrade it.

Bacteria called methanotrophs feed off methane gas and can either take up or break down methylmercury, or both. Methanotrophs are widespread in nature and exist near methane and air interfaces, and both methane and methylmercury are usually formed in similar anoxic, or oxygen-deficient, environments. 

To single out how and which methanotrophs perform demethylation, the ORNL-led team — along with methanotroph experts from the University of Michigan and Iowa State University — investigated the behavior of many different methanotrophs and used sophisticated mass spectrometry to analyze methylmercury uptake and decomposition by these bacteria. They discovered that methanotrophs such as Methlyosinus trichosporium OB3b can take up and break down methylmercury, while others such as Methylococcus capsulatus Bath only take up methylmercury. 

In either case, the bacteria’s interactions can lower mercury toxicity levels in water.

The work is published in the open-access journal Science Advances by the AAAS. Perhaps safe tuna sandwiches are in our future, thanks to microbes.

Gut Helpers

A health partner inside our GI tract that many of us never heard of is named Akkermansia muciniphila. After enjoying a tuna sandwich, we depend on this little bacterium that lives inside us to avoid metabolid disorders. Here’s what it does for us, according to’s report on findings at Duke University:

A. muciniphila can make up as much as 3 to 5% of the biota found in stool. It is present in wild animals, and its abundance in humans seems critical for healthy physiological functions, as abnormal levels are associated with immune disorders, pregnancy complications, cancer, neurological disorders and every kind of metabolic disease.

This gut germ helps regulate lipid biosynthesis and cholesterol levels. Would evolution generate as many redundant machines as this bacterium possesses?

A. muciniphila is known to use mucins as its preferred nutrient source. Mucins are large, highly glycosylated proteins that comprise the bulk of the intestinal mucus lining. The study found that, despite having the capability to produce a wide range of glycoside hydrolase enzymes, estimated to be around 60, only a few are needed to degrade intestinal mucins. This redundancy means that even if there were a mutation in one or most of these genes, the organism would still have the ability to survive.

Learn more about this essential microbe in Nature Microbiology.

Ocean Fertilizer

Another microbe — this one a cyanobacterium — performs a vital function for life in the seas. New Scientist describes how it changes its behavior depending on light levels.

These bacteria don’t just provide food for other organisms, they also turn nitrogen from the atmosphere into chemicals that other photosynthetic organisms can use. They fertilise vast areas of the ocean that would otherwise be too poor in nutrients for anything to grow, says [Ulrike] Pfreundt.

“It’s the living fertiliser for the oceans, essentially,” she says. “They provide a very large part of the nitrogen that is fixed in the ocean, and a whole lot of other organisms that sequester CO2 depend on this nitrogen.”

Our world could not function without microbes such as these, and uncountable numbers of additional species remain to be discovered. They are far from being mere primitive steppingstones to complex life. Without their engineering prowess to degrade harmful substances and provide nutrients for others, large organisms — animals and plants — could not exist. This elevates the evidence for intelligent design beyond cells and individuals to the entire biosphere.