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

    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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    Taylor Perron receives 2021 MacArthur Fellowship

    Taylor Perron, professor of geology and associate department head for education in MIT’s Department of Earth, Atmospheric, and Planetary Sciences, has been named a recipient of a 2021 MacArthur Fellowship.

    Often referred to as “genius grants,” the fellowships are awarded by the John D. and Catherine T. MacArthur Foundation to talented individuals in a variety of fields. Each MacArthur fellow receives a $625,000 stipend, which they are free to use as they see fit. Recipients are notified by the foundation of their selection shortly before the fellowships are publicly announced.

    “After I had absorbed what they were saying, the first thing I thought was, I couldn’t wait to tell my wife, Lisa,” Perron says of receiving the call. “We’ve been a team through all of this and have had a pretty incredible journey, and I was just eager to share that with her.”

    Perron is a geomorphologist who seeks to understand the mechanisms that shape landscapes on Earth and other planets. His work combines mathematical modeling and computer simulations of landscape evolution; analysis of remote-sensing and spacecraft data; and field studies in regions such as the Appalachian Mountains, Hawaii, and the Amazon rainforest to trace how landscapes evolved over time and how they may change in the future.

    “If we can understand how climate and life and geological processes have interacted over a long time to create the landscapes we see now, we can use that information to anticipate where the landscape is headed in the future,” Perron says.

    His group has developed models that describe how river systems generate intricate branching patterns as a result of competing erosional processes, and how climate influences erosion on continents, islands, and reefs.

    Perron has also applied his methods beyond Earth, to retrace the evolution of the surfaces of Mars and Saturn’s moon Titan. His group has used spacecraft images and data to show how features on Titan, which appear to be active river networks, were likely carved out by raining liquid methane. On Mars, his analyses have supported the idea that the Red Planet once harbored an ocean and that the former shoreline of this Martian ocean is now warped as a result of a shift in the planet’s spin axis.

    He is continuing to map out the details of Mars and Titan’s landscape histories, which he hopes will provide clues to their ancient climates and habitability.

    “I think answers to some of the big questions about the solar system are written in planetary landscapes,” Perron says. “For example, why did Mars start off with lakes and rivers, but end up as a frozen desert? And if a world like Titan has weather like ours, but with a methane cycle instead of a water cycle, could an environment like that have supported life? One thing we try to do is figure out how to read the landscape to find the answers to those questions.”

    Perron has expanded his group’s focus to examine how changing landscapes affect biodiversity, for instance in Appalachia and in the Amazon — both freshwater systems that host some of the most diverse populations of life on the planet.

    “If we can figure out how changes in the physical landscape may have generated regions of really high biodiversity, that should help us learn how to conserve it,” Perron says.

    Recently, his group has also begun to investigate the influence of landscape evolution on human history. Perron is collaborating with archaeologists on projects to study the effect of physical landscapes on human migration in the Americas, and how the response of rivers to ice ages may have helped humans develop complex farming societies in the Amazon.

    Looking ahead, he plans to apply the MacArthur grant toward these projects and other “intellectual risks” — ideas that have potential for failure but could be highly rewarding if they succeed. The fellowship will also provide resources for his group to continue collaborating across disciplines and continents.

    “I’ve learned a lot from reaching out to people in other fields — everything from granular mechanics to fish biology,” Perron says. “That has broadened my scientific horizons and helped us do innovative work. Having the fellowship will provide more flexibility to allow us to continue connecting with people from other fields and other parts of the world.”

    Perron holds a BA in earth and planetary sciences and archaeology from Harvard University and a PhD in earth and planetary science from the University of California at Berkeley. He joined MIT as a faculty member in 2009. More

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    A new approach to preventing human-induced earthquakes

    When humans pump large volumes of fluid into the ground, they can set off potentially damaging earthquakes, depending on the underlying geology. This has been the case in certain oil- and gas-producing regions, where wastewater, often mixed with oil, is disposed of by injecting it back into the ground — a process that has triggered sizable seismic events in recent years.

    Now MIT researchers, working with an interdisciplinary team of scientists from industry and academia, have developed a method to manage such human-induced seismicity, and have demonstrated that the technique successfully reduced the number of earthquakes occurring in an active oil field.

    Their results, appearing today in Nature, could help mitigate earthquakes caused by the oil and gas industry, not just from the injection of wastewater produced with oil, but also that produced from hydraulic fracturing, or “fracking.” The team’s approach could also help prevent quakes from other human activities, such as the filling of water reservoirs and aquifers, and the sequestration of carbon dioxide in deep geologic formations.

    “Triggered seismicity is a problem that goes way beyond producing oil,” says study lead author Bradford Hager, the Cecil and Ida Green Professor of Earth Sciences in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “This is a huge problem for society that will have to be confronted if we are to safely inject carbon dioxide into the subsurface. We demonstrated the kind of study that will be necessary for doing this.”

    The study’s co-authors include Ruben Juanes, professor of civil and environmental engineering at MIT, and collaborators from the University of California at Riverside, the University of Texas at Austin, Harvard University, and Eni, a multinational oil and gas company based in Italy.

    Safe injections

    Both natural and human-induced earthquakes occur along geologic faults, or fractures between two blocks of rock in the Earth’s crust. In stable periods, the rocks on either side of a fault are held in place by the pressures generated by surrounding rocks. But when a large volume of fluid is suddenly injected at high rates, it can upset a fault’s fluid stress balance. In some cases, this sudden injection can lubricate a fault and cause rocks on either side to slip and trigger an earthquake.

    The most common source of such fluid injections is from the oil and gas industry’s disposal of wastewater that is brought up along with oil. Field operators dispose of this water through injection wells that continuously pump the water back into the ground at high pressures.

    “There’s a lot of water produced with the oil, and that water is injected into the ground, which has caused a large number of quakes,” Hager notes. “So, for a while, oil-producing regions in Oklahoma had more magnitude 3 quakes than California, because of all this wastewater that was being injected.”

    In recent years, a similar problem arose in southern Italy, where injection wells on oil fields operated by Eni triggered microseisms in an area where large naturally occurring earthquakes had previously occurred. The company, looking for ways to address the problem, sought consulation from Hager and Juanes, both leading experts in seismicity and subsurface flows.

    “This was an opportunity for us to get access to high-quality seismic data about the subsurface, and learn how to do these injections safely,” Juanes says.

    Seismic blueprint

    The team made use of detailed information, accumulated by the oil company over years of operation in the Val D’Agri oil field, a region of southern Italy that lies in a tectonically active basin. The data included information about the region’s earthquake record, dating back to the 1600s, as well as the structure of rocks and faults, and the state of the subsurface corresponding to the various injection rates of each well.

    This video shows the change in stress on the geologic faults of the Val d’Agri field from 2001 to 2019, as predicted by a new MIT-derived model. Video credit: A. Plesch (Harvard University)

    This video shows small earthquakes occurring on the Costa Molina fault within the Val d’Agri field from 2004 to 2016. Each event is shown for two years fading from an initial bright color to the final dark color. Video credit: A. Plesch (Harvard University)

    The researchers integrated these data into a coupled subsurface flow and geomechanical model, which predicts how the stresses and strains of underground structures evolve as the volume of pore fluid, such as from the injection of water, changes. They connected this model to an earthquake mechanics model in order to translate the changes in underground stress and fluid pressure into a likelihood of triggering earthquakes. They then quantified the rate of earthquakes associated with various rates of water injection, and identified scenarios that were unlikely to trigger large quakes.

    When they ran the models using data from 1993 through 2016, the predictions of seismic activity matched with the earthquake record during this period, validating their approach. They then ran the models forward in time, through the year 2025, to predict the region’s seismic response to three different injection rates: 2,000, 2,500, and 3,000 cubic meters per day. The simulations showed that large earthquakes could be avoided if operators kept injection rates at 2,000 cubic meters per day — a flow rate comparable to a small public fire hydrant.

    Eni field operators implemented the team’s recommended rate at the oil field’s single water injection well over a 30-month period between January 2017 and June 2019. In this time, the team observed only a few tiny seismic events, which coincided with brief periods when operators went above the recommended injection rate.

    “The seismicity in the region has been very low in these two-and-a-half years, with around four quakes of 0.5 magnitude, as opposed to hundreds of quakes, of up to 3 magnitude, that were happening between 2006 and 2016,” Hager says. 

    The results demonstrate that operators can successfully manage earthquakes by adjusting injection rates, based on the underlying geology. Juanes says the team’s modeling approach may help to prevent earthquakes related to other processes, such as the building of water reservoirs and the sequestration of carbon dioxide — as long as there is detailed information about a region’s subsurface.

    “A lot of effort needs to go into understanding the geologic setting,” says Juanes, who notes that, if carbon sequestration were carried out on depleted oil fields, “such reservoirs could have this type of history, seismic information, and geologic interpretation that you could use to build similar models for carbon sequestration. We show it’s at least possible to manage seismicity in an operational setting. And we offer a blueprint for how to do it.”

    This research was supported, in part, by Eni. More