Monday, September 21, 2020

Plastic eating microbes - evolution too rapid for Darwin


Plastic-Eating Microbes — “Rapid Evolution” May Not Be Darwinian at All

Evolution News @DiscoveryCSC

September 17, 2020, 2:01 PM


plastic in the ocean

Photo credit: tkremmel via Pixabay.

Environmental scientists warn frequently that the world is drowning in plastic. In addition to the plastic bottles that circle in gyres out at sea, synthetic microfibers from the laundry loads of millions of people each week are being found at coral reefs and in almost every bucket of sea water dredged up by marine biologists. According to Wired, “A single pair of jeans may release 56,000 microfibers per wash.” Run the numbers and multiply that by billions of people wearing blue jeans, and you glimpse the scope of the problem. Blue jean fibers have been found in the Arctic. Marine biologists are rightly concerned about the rapidly rising accumulation of plastics and synthetic fibers at sea, and the impacts these could have on sea turtles, fish, coral reefs, and the entire marine ecosystem.

Unexpected Good News

In this worrying context, the following should not at all appear to minimize the environmental crisis of plastic in the oceans. It is, however, interesting and unexpected. A team of scientists from Saudi Arabia wrote a paper for the biology preprint server bioRxiv recently with the intriguing title, “Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean.” They were surprised that plastic input (production by humans, some 150 teragrams of plastic waste) is not matching plastic output (measurements at sea). What could account for the mismatch? The team discovered that microbes are learning to eat plastic!

Estimates of marine plastic stocks, a major threat to marine life, are far lower than expected from exponentially-increasing litter inputs, suggesting important loss factors. These may involve microbial degradation, as the plastic-degrading polyethylene terephthalate enzyme (PETase) has been reported in marine microbial communities. An assessment of 416 metagenomes of planktonic communities across the global ocean identifies 68 oceanic PETase variants (oPETase) that evolved from ancestral enzymes degrading polycyclic aromatic hydrocarbons. Twenty oPETases show predicted efficiencies comparable to those of laboratory-optimized PETases, suggesting strong selective pressures directing the evolution of these enzymes. We found oPETases in 90.1% of samples across all oceans and depths, particularly abundant at 1,000 m depth, with a strong dominance of Pseudomonadales containing putative highly-efficient oPETase variants in the dark ocean. Enzymatic degradation may be removing plastic from the marine environment while providing a carbon source for bathypelagic microbial communities. [Emphasis added.]

They say that “99 percent of the plastic that entered the oceans cannot be accounted for.” Now while this “rapid evolution” sounds like good news, it raises a number of questions. How did multiple species of microbes independently “evolve” the ability to digest plastic? How did they do it so fast? Is it a case of Darwinian evolution? The authors have no reason to doubt it, since they refer to “selection pressures” pushing the microbes to evolve the oPETase enzymes, presumably for their selfish fitness. It just adventitiously provides ecological benefits (a carbon source) for deep microbial communities. 

The first case of a natural oPETase enzyme able to digest polyethylene, they note, was observed very recently.

Exponential growth in plastic production along with poor waste management practices have led to over 150 Tg plastic waste delivered to the ocean since 1950, where it harms marine life, from zooplankton to whales. Synthetic plastic polymers are derived from oil hydrocarbons and designed to be durable in the environment, being largely resistant to microbial degradation. However, a newly-evolved plastic-degrading enzyme, polyethylene terephthalate hydrolase (PETase), was recently discovered in a Japanese waste processing plant. This PETase was inferred to have evolved since 1970, when the polyethylene terephthalate polymer was introduced at industrial scale.

Evolution’s Edge

Whatever happened “evolved” very rapidly, not in the slow-and-gradual Darwinian way. Readers might recall the case of the “nylonase” enzyme that evolutionists used to tout Darwinian evolution, leading to a flurry of debates about it in these pages (e.g., see Ann Gauger, “Adaptation in Action Yields a Repurposed Enzyme”). Gauger agrees with Michael Behe that adaptation by mutation and selection can occur in limited cases where the number of required mutational steps is small (one or two), the number of trials is large, and each step yields a benefit. These kinds of changes fall within the “Edge of Evolution,” and are within the reach of chance, provide an existing enzyme exists and the modifications are minor. Examples of this can be found in Behe’s book, The Edge of Evolution. Clearly ocean microbes are abundant enough for many trials to take place.

In that same article, Gauger called attention to a discovery by Austin et al., published in 2018 in PNAS, of a PET enzyme that not only dissolved a type of polyesterase, but appeared to get more efficient at it over time. The functional change was minor; it involved a change to the size of a cleft in an existing enzyme to accommodate the new substrate. Further slight modifications to the cleft improved the efficiency since there was an immediate benefit to the microbe to digest the molecule at each step. The evolution of an enzyme de novo by a major chance event such as a frameshift mutation, she argued, is beyond the reach of chance, because enzymes must fold to work, and the space of possible folds is vanishingly small compared to the sequence space of random amino acid chains. The discovery, therefore, was within the edge of evolution and not a threat to intelligent design.

A Boon to the Biosphere

What’s new in the current study? The authors refer to the same paper by Austin et al. from 2018, adding that rapid adaptation of enzymes to digest plastics appears to be much more widespread than thought. Like Gauger, the authors see this is as a boon to the biosphere, providing hope that at least some of human plastic pollution can be ameliorated by microbes. Plastics are derived from hydrocarbons, after all, which microbes have been digesting from the beginning. Indeed, environmental scientists rushing to clean up catastrophic oil spills have been surprised to see how quickly microbes aided the effort.

In summary, the results obtained confirm that PETases are prevalent and abundant in the global ocean microbiome, where they must have evolved recently, following the mass production of polyethylene terephthalate [reference to Austin et al.]. PETases are widespread from the surface to the deep ocean, reaching a maximum abundance and prevalence at about 1,000 m, where Pseudomonas has evolved an efficient PETase. PETases were found in high abundance in some areas known to receive high loads of plastic waste, such as waters off the Indian subcontinent, Brazil, and Southern Africa. The phylogeny constructed also shows a putative pathway for the evolution of oPETases from ancestral genes involved in hydrocarbon degradation. The increased efficiency of the PETase along the phylogenetic sequences, along with the high abundance of bacteria containing efficient PETases, points at an ongoing evolutionary process driven by selection pressures providing advantages to bacteria able to use an increasingly available resource, plastic polymers, in the deep ocean, mainly where all other naturally-occurring organic substrates are extremely diluted. The widespread prevalence, 90.1%, of PETases across the ocean together with the acute carbon limitation in bathypelagic waters suggests that the ocean microbiome is rapidly evolving to degrade plastic waste, providing a hopeful, nature-based solutions for plastic already in the marine environment.

It’s great news. None of this should rationalize pollution, of course; humans need to be responsible stewards of the environment. It is encouraging, though, to see microbial helpers with complex molecular machines that can be repurposed or retooled to clean up some of our waste products without our help.

Another Possible Design Hypothesis

Evolutionists tend to look at life as a collection of selfish individuals competing for their own fitness. Individuals with the good fortune to hit on the right mutations outcompete others and become predominant. Lately, Darwinians have been noticing more cases of cooperation in nature. Advocates of intelligent design might look wider and see a global case of design here. Is it not remarkable how quickly these microbes adapted to help other organisms unrelated to them? Is more than chance involved?

Physiologists know of another case where apparent “random” mutations serve a greater good: the human adaptive immune system. In the B-cell genes, a programmed pathway randomly assembles gene segments, providing millions of combinations of antibodies, one or more of which matches an antigen. When successful, the resulting antibody fits the intruder and is rapidly cloned, stopping the infection. Is the winning antibody selfish? In a way, yes; it does benefit if the host lives, so that it doesn’t “go down with the ship” so to speak. But the complexity of the immune system looks more like a case of foresight, using a stochastic process to provide robustness for unpredictable threats. Perhaps in a wider context, the ocean ecosystem is like that. If it was designed for the good of biosphere, it would make sense that robustness is built in to resist catastrophic perturbations, providing ecological homeostasis. Given that de novo enzymes are beyond the reach of chance anyway, a designer would make them “evolvable” to a point — as in the antibody system — able to “find” a match for an unexpected intruder (like plastic) and reduce its harm. Biochemists already know that mutational hotspots exist in genomes, indicating that not all mutations are purely random. 

One clear difference is that the random antibody search occurs within a body, while microbes are solitary organisms. Still, microbes are good at signaling one another and sharing genetic information by horizontal gene transfer. How could the hypothesis of a guided search for plastic-digesting enzymes be tested? We’ll leave that up to a creative scientist intrigued with the thought. The rapid adaptation of existing complex molecular machines to handle unpredicted environmental threats, though, resulting in benefit to other organisms and homeostasis for the biosphere, looks too good for a blind, unguided, natural process.