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      in Environment

      Zeroing in on the origins of Earth’s “single most important evolutionary innovation”

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      Some time in Earth’s early history, the planet took a turn toward habitability when a group of enterprising microbes known as cyanobacteria evolved oxygenic photosynthesis — the ability to turn light and water into energy, releasing oxygen in the process.

      This evolutionary moment made it possible for oxygen to eventually accumulate in the atmosphere and oceans, setting off a domino effect of diversification and shaping the uniquely habitable planet we know today.  

      Now, MIT scientists have a precise estimate for when cyanobacteria, and oxygenic photosynthesis, first originated. Their results appear today in the Proceedings of the Royal Society B.

      They developed a new gene-analyzing technique that shows that all the species of cyanobacteria living today can be traced back to a common ancestor that evolved around 2.9 billion years ago. They also found that the ancestors of cyanobacteria branched off from other bacteria around 3.4 billion years ago, with oxygenic photosynthesis likely evolving during the intervening half-billion years, during the Archean Eon.

      Interestingly, this estimate places the appearance of oxygenic photosynthesis at least 400 million years before the Great Oxidation Event, a period in which the Earth’s atmosphere and oceans first experienced a rise in oxygen. This suggests that cyanobacteria may have evolved the ability to produce oxygen early on, but that it took a while for this oxygen to really take hold in the environment.

      “In evolution, things always start small,” says lead author Greg Fournier, associate professor of geobiology in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “Even though there’s evidence for early oxygenic photosynthesis — which is the single most important and really amazing evolutionary innovation on Earth — it still took hundreds of millions of years for it to take off.”

      Fournier’s MIT co-authors include Kelsey Moore, Luiz Thiberio Rangel, Jack Payette, Lily Momper, and Tanja Bosak.

      Slow fuse, or wildfire?

      Estimates for the origin of oxygenic photosynthesis vary widely, along with the methods to trace its evolution.

      For instance, scientists can use geochemical tools to look for traces of oxidized elements in ancient rocks. These methods have found hints that oxygen was present as early as 3.5 billion years ago — a sign that oxygenic photosynthesis may have been the source, although other sources are also possible.

      Researchers have also used molecular clock dating, which uses the genetic sequences of microbes today to trace back changes in genes through evolutionary history. Based on these sequences, researchers then use models to estimate the rate at which genetic changes occur, to trace when groups of organisms first evolved. But molecular clock dating is limited by the quality of ancient fossils, and the chosen rate model, which can produce different age estimates, depending on the rate that is assumed.

      Fournier says different age estimates can imply conflicting evolutionary narratives. For instance, some analyses suggest oxygenic photosynthesis evolved very early on and progressed “like a slow fuse,” while others indicate it appeared much later and then “took off like wildfire” to trigger the Great Oxidation Event and the accumulation of oxygen in the biosphere.

      “In order for us to understand the history of habitability on Earth, it’s important for us to distinguish between these hypotheses,” he says.

      Horizontal genes

      To precisely date the origin of cyanobacteria and oxygenic photosynthesis, Fournier and his colleagues paired molecular clock dating with horizontal gene transfer — an independent method that doesn’t rely entirely on fossils or rate assumptions.

      Normally, an organism inherits a gene “vertically,” when it is passed down from the organism’s parent. In rare instances, a gene can also jump from one species to another, distantly related species. For instance, one cell may eat another, and in the process incorporate some new genes into its genome.

      When such a horizontal gene transfer history is found, it’s clear that the group of organisms that acquired the gene is evolutionarily younger than the group from which the gene originated. Fournier reasoned that such instances could be used to determine the relative ages between certain bacterial groups. The ages for these groups could then be compared with the ages that various molecular clock models predict. The model that comes closest would likely be the most accurate, and could then be used to precisely estimate the age of other bacterial species — specifically, cyanobacteria.

      Following this reasoning, the team looked for instances of horizontal gene transfer across the genomes of thousands of bacterial species, including cyanobacteria. They also used new cultures of modern cyanobacteria taken by Bosak and Moore, to more precisely use fossil cyanobacteria as calibrations. In the end, they identified 34 clear instances of horizontal gene transfer. They then found that one out of six molecular clock models consistently matched the relative ages identified in the team’s horizontal gene transfer analysis.

      Fournier ran this model to estimate the age of the “crown” group of cyanobacteria, which encompasses all the species living today and known to exhibit oxygenic photosynthesis. They found that, during the Archean eon, the crown group originated around 2.9 billion years ago, while cyanobacteria as a whole branched off from other bacteria around 3.4 billion years ago. This strongly suggests that oxygenic photosynthesis was already happening 500 million years before the Great Oxidation Event (GOE), and that cyanobacteria were producing oxygen for quite a long time before it accumulated in the atmosphere.

      The analysis also revealed that, shortly before the GOE, around 2.4 billion years ago, cyanobacteria experienced a burst of diversification. This implies that a rapid expansion of cyanobacteria may have tipped the Earth into the GOE and launched oxygen into the atmosphere.

      Fournier plans to apply horizontal gene transfer beyond cyanobacteria to pin down the origins of other elusive species.

      “This work shows that molecular clocks incorporating horizontal gene transfers (HGTs) promise to reliably provide the ages of groups across the entire tree of life, even for ancient microbes that have left no fossil record … something that was previously impossible,” Fournier says. 

      This research was supported, in part, by the Simons Foundation and the National Science Foundation. More

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      in Environment

      Making catalytic surfaces more active to help decarbonize fuels and chemicals

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      Electrochemical reactions that are accelerated using catalysts lie at the heart of many processes for making and using fuels, chemicals, and materials — including storing electricity from renewable energy sources in chemical bonds, an important capability for decarbonizing transportation fuels. Now, research at MIT could open the door to ways of making certain catalysts more active, and thus enhancing the efficiency of such processes.

      A new production process yielded catalysts that increased the efficiency of the chemical reactions by fivefold, potentially enabling useful new processes in biochemistry, organic chemistry, environmental chemistry, and electrochemistry. The findings are described today in the journal Nature Catalysis, in a paper by Yang Shao-Horn, an MIT professor of mechanical engineering and of materials science and engineering, and a member of the Research Lab of Electronics (RLE); Tao Wang, a postdoc in RLE; Yirui Zhang, a graduate student in the Department of Mechanical Engineering; and five others.

      The process involves adding a layer of what’s called an ionic liquid in between a gold or platinum catalyst and a chemical feedstock. Catalysts produced with this method could potentially enable much more efficient conversion of hydrogen fuel to power devices such as fuel cells, or more efficient conversion of carbon dioxide into fuels.

      “There is an urgent need to decarbonize how we power transportation beyond light-duty vehicles, how we make fuels, and how we make materials and chemicals,” says Shao-Horn, emphasizing the pressing call to reduce carbon emissions highlighted in the latest IPCC report on climate change. This new approach to enhancing catalytic activity could provide an important step in that direction, she says.

      Using hydrogen in electrochemical devices such as fuel cells is one promising approach to decarbonizing fields such as aviation and heavy-duty vehicles, and the new process may help to make such uses practical. At present, the oxygen reduction reaction that powers such fuel cells is limited by its inefficiency. Previous attempts to improve that efficiency have focused on choosing different catalyst materials or modifying their surface compositions and structure.

      In this research, however, instead of modifying the solid surfaces, the team added a thin layer in between the catalyst and the electrolyte, the active material that participates in the chemical reaction. The ionic liquid layer, they found, regulates the activity of protons that help to increase the rate of the chemical reactions taking place on the interface.

      Because there is a great variety of such ionic liquids to choose from, it’s possible to “tune” proton activity and the reaction rates to match the energetics needed for processes involving proton transfer, which can be used to make fuels and chemicals through reactions with oxygen.

      “The proton activity and the barrier for proton transfer is governed by the ionic liquid layer, and so there’s a great tuneability in terms of catalytic activity for reactions involving proton and electron transfer,” Shao-Horn says. And the effect is produced by a vanishingly thin layer of the liquid, just a few nanometers thick, above which is a much thicker layer of the liquid that is to undergo the reaction.

      “I think this concept is novel and important,” says Wang, the paper’s first author, “because people know the proton activity is important in many electrochemistry reactions, but it’s very challenging to study.” That’s because in a water environment, there are so many interactions between neighboring water molecules involved that it’s very difficult to separate out which reactions are taking place. By using an ionic liquid, whose ions can each only form a single bond with the intermediate material, it became possible to study the reactions in detail, using infrared spectroscopy.

      As a result, Wang says, “Our finding highlights the critical role that interfacial electrolytes, in particular the intermolecular hydrogen bonding, can play in enhancing the activity of the electro-catalytic process. It also provides fundamental insights into proton transfer mechanisms at a quantum mechanical level, which can push the frontiers of knowing how protons and electrons interact at catalytic interfaces.”

      “The work is also exciting because it gives people a design principle for how they can tune the catalysts,” says Zhang. “We need some species right at a ‘sweet spot’ — not too active or too inert — to enhance the reaction rate.”

      With some of these techniques, says Reshma Rao, a recent doctoral graduate from MIT and now a postdoc at Imperial College, London, who is also a co-author of the paper, “we see up to a five-times increase in activity. I think the most exciting part of this research is the way it opens up a whole new dimension in the way we think about catalysis.” The field had hit “a kind of roadblock,” she says, in finding ways to design better materials. By focusing on the liquid layer rather than the surface of the material, “that’s kind of a whole different way of looking at this problem, and opens up a whole new dimension, a whole new axis along which we can change things and optimize some of these reaction rates.”

      The team also included Botao Huang, Bin Cai, and Livia Giordano in the MIT’s Research Laboratory of Electronics, and Shi-Gang Sun at Xiamen University in China. The work was supported by the Toyota Research Institute, and used the National Science Foundation’s Extreme Science and Engineering Environment. More