How do Plants Make Oxygen? Ask Cyanobacteria

Researchers reveal the family tree of the group of microorganisms responsible for “inventing” the oxygen-producing photosynthesis that lets you breathe
News Writer: 
Robert Perkins

Bacterial mats

Oxyphotobacteria in microbial mats in Yellowstone.
Credit: Fischer Laboratory/Caltech

The ability to generate oxygen through photosynthesis—that helpful service performed by plants and algae, making life possible for humans and animals on Earth—evolved just once, roughly 2.3 billion years ago, in certain types of cyanobacteria. This planet-changing biological invention has never been duplicated, as far as anyone can tell. Instead, according to endosymbiotic theory, all the “green” oxygen-producing organisms (plants and algae) simply subsumed cyanobacteria as organelles in their cells at some point during their evolution.

“Oxygenic photosynthesis was an evolutionary singularity,” says Woodward Fischer, professor of geobiology at Caltech, referring to the process by which certain organisms use the energy of sunlight to convert carbon dioxide and water into sugar for food, with oxygen as a by-product. “Cyanobacteria invented it, and then ultimately become the chloroplasts of algae. Plants are just a group of algae that moved on land.”

Yet as world-shaping as cyanobacteria are, relatively little is known about them. Until a couple of decades ago, they were called “blue-green algae” by taxonomists, though it was later revealed that they are not algae at all, but rather a completely different type of organism. That lack of taxonomic understanding made deciphering the riddle of their evolution all but impossible, Fischer says.

“For the longest time, they were just their own group. We had no answer about where they came from, or what other organisms they were related to,” Fischer says. “Imagine trying to understand something about human evolution without knowledge of the great apes.”

Publishing in the journal Science on March 30, Fischer and colleagues from Caltech and the University of Queensland in Australia finally have fleshed out cyanobacteria’s family tree. They added the genomes of 41 uncultured microorganisms, which helped to pin down the precise point in the evolution of cyanobacteria at which oxygenic photosynthesis arose. The 41 species are all types of cyanobacteria but none carry genes for photosynthesis, and therefore they don’t produce organic matter, like algae and plants do. Rather, they consume it.

Fischer and his colleagues found that a single branch of cyanobacteria—dubbed Oxyphobacteria—were likely the first and only group to evolve oxygenic photosynthesis. Their closest relatives, Melainabacteria, live in the guts of animals (including humans) among other environments, and do not produce oxygen. And while one might suggest that Melainabacteria simply lost the ability to produce oxygen over time, the next most closely related cyanobacteria after those, described in the paper as Sericytochromatia, also do not engage in oxygenic photosynthesis.

“This nails down that Oxyphobacteria were really the only ones to ever invent this globe-shaping chemical process,” Fischer says.

The 41 new species fall into both Melainabacteria and Sericytochromatia, the latter of which had not been described before this paper. All names of these organisms are subject to change, as taxonomists catch up with the team’s discoveries. “We know they’re there, and we know their gene repertoire. Now we can start putting them into evolutionary trees, and begin efforts to isolate them and study their physiology and ecology,” says James Hemp, an Agouron Postdoctoral Scholar at Caltech when the research was conducted, and coauthor of the Science article.

These discoveries were made thanks to new technology that allows researchers to sequence the genome of an organism without first having to isolate that organism in the lab and culture a large quantity of it, as has been required in the past. 

“Now we have culture-independent ways of assessing microbial diversity,” says Rochelle M. Soo, postdoctoral researcher at the University of Queensland in Australia and coauthor of the Science article. “We can go into any environment, remove a sample of DNA, sequence it, and recover genomes of microbes living in that environment. We don’t have to grow anything ourselves—instead we let the environment do the work and just sequence what’s already there.” Some of the 41 new species were found in situ, such as in the intestines of animals, while others came from the databases of other biology studies—which had been sampled, but never characterized and analyzed. 

Unraveling the evolutionary mystery of photosynthesis and its genesis could shed light on everything from sustainable energy sources to the potential for life to exist on other planets.

“Cyanobacteria are planetary-scale engineers, capable of splitting water. They invented the most challenging chemistry on the face of the planet. We would love to be able to do their water-splitting chemistry as effortlessly as they do to make fuels, and these guys figured out how to do it two and a half billion years ago,” Fischer says.

Next, the team plans to learn more about the ecology and physiology of the new bacteria by probing them in a lab. “We’ve really just scratched the surface,” Fischer says.

The study is titled “On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria.” Coauthors include Donovan H. Parks and Philip Hugenholtz of the University of Queensland in Australia. This research was funded by a Discovery Outstanding Researcher Award, the Australian Research Council, the Agouron Institute, NASA, and the David and Lucile Packard Foundation. Sequencing data have been deposited at the National Center for Biotechnology Information. 

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Caltech Grad Student Wins Hertz Fellowship

Preston Cosslett Kemeny will receive full funding for his research for up to five years
News Writer: 
Robert Perkins

Preston

Preston Cosslett Kemeny
Credit: Michael Wong

Caltech graduate student Preston Cosslett Kemeny has been selected by the Fannie and John Hertz Foundation to receive a 2017 Hertz Fellowship. Twelve students were selected to receive the award from a pool of more than 700 applicants, and will receive up to five years of support for their graduate studies.

Kemeny is a first-year graduate student in geochemistry in the Division of Geological and Planetary Sciences. A native of Garrison, New York, he received his bachelor’s degree in geosciences from Princeton University, summa cum laude, in June of 2015. At Caltech, Kemeny’s initial PhD work will combine isotope geochemistry with paleoclimate research to better understand global elemental cycles throughout Earth’s history.

By studying the interactions between Earth’s changing chemistry and biology, as recorded in the isotope ratios preserved in the geologic record, Kemeny hopes to shed light on the coevolution of life and climate. In particular, he is interested in the rise of atmospheric oxygen, oscillations between glacial and interglacial climates, and the physical chemistry underlying isotopic variation. Ultimately, he hopes his work will improve models of climate change and help combat the impacts of modern carbon emissions.

“I was originally attracted to Earth science because it combines my passions for experimentation and the outdoors,” Kemeny says. “To me, nature is theory in experiential form, a way to walk through equations and physically interact with concepts. I love what I study and I love to be outside because they are two complementary sides, the theoretical and the real. When outdoors, I am reminded how complex and powerful reality actually is. Ultimately, modern ecosystems are the solutions to my research questions.”

At graduation from Princeton, Kemeny received the Edward Sampson, Class of 1914, Prize in Environmental Geosciences and the Sigma Xi Book Award. Last year he was awarded a 2016 National Defense Science and Engineering Graduate Fellowship.

“The 2017 Fellow class is among the best and brightest we’ve ever seen, and we are proud to welcome them to the Hertz Community,” Robbee Baker Kosak, president of the Fannie and John Hertz Foundation, said in a statement. “Hertz Fellows are developing solutions to issues of worldwide importance, from helping solve global health crises to addressing climate change and energy consumption. We look forward to seeing our new Fellows make similarly outstanding contributions as they pursue their research in the coming years.”

The Hertz Foundation is the legacy of John Hertz, a Hungarian immigrant who became an entrepreneur in the automotive industry. The foundation has been supporting budding scientists and engineers for 60 years.

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Study: Cold Climates and Ocean Carbon Sequestration

Deep-sea corals reveal why atmospheric carbon was reduced during colder time periods
News Writer: 
Robert Perkins

Fossils

Tony Wang (left) and Jess Adkins (right) with samples of Desmophyllum dianthus fossils.
Credit: Caltech

We know a lot about how carbon dioxide (CO2) levels can drive climate change, but how about the way that climate change can cause fluctuations in CO2 levels? New research from an international team of scientists reveals one of the mechanisms by which a colder climate was accompanied by depleted atmospheric CO2 during past ice ages.

The overall goal of the work is to better understand how and why the earth goes through periodic climate change, which could shed light on how man-made factors could affect the global climate.

Earth’s average temperature has naturally fluctuated by about 4 to 5 degrees Celsius over the course of the past million years as the planet has cycled in and out of glacial periods. During that time, the earth’s atmospheric CO2 levels have fluctuated between roughly 180 and 280 parts per million (ppm) every 100,000 years or so. (In recent years, man-made carbon emissions have boosted that concentration up to over 400 ppm.)

About 10 years ago, researchers noticed a close correspondence between the fluctuations in CO2 levels and in temperature over the last million years. When the earth is at its coldest, the amount of CO2 in the atmosphere is also at its lowest. During the most recent ice age, which ended about 11,000 years ago, global temperatures were 5 degrees Celsius lower than they are today, and atmospheric CO2 concentrations were at 180 ppm.

Using a library of more than 10,000 deep-sea corals collected by Caltech’s Jess Adkins, an international team of scientists has shown that periods of colder climates are associated with higher phytoplankton efficiency and a reduction in nutrients in the surface of the Southern Ocean (the ocean surrounding the Antarctic), which is related to an increase in carbon sequestration in the deep ocean. A paper about their research appears the week of March 13 in the online edition of the Proceedings of the National Academy of Sciences.

“It is critical to understand why atmospheric CO2 concentration was lower during the ice ages. This will help us understand how the ocean will respond to ongoing anthropogenic CO2 emissions,” says Xingchen (Tony) Wang, lead author of the study. Wang was a graduate student at Princeton while conducting the research in the lab of Daniel Sigman, Dusenbury Professor of Geological and Geophysical Sciences. He is now a Simons Foundation Postdoctoral Fellow on the Origins of Life at Caltech.

There is 60 times more carbon in the ocean than in the atmosphere—partly because the ocean is so big. The mass of the world’s oceans is roughly 270 times greater than that of the atmosphere. As such, the ocean is the greatest regulator of carbon in the atmosphere, acting as both a sink and a source for atmospheric CO2.

Biological processes are the main driver of CO2 absorption from the atmosphere to the ocean. Just like photosynthesizing trees and plants on land, plankton at the surface of the sea turn CO2 into sugars that are eventually consumed by other creatures. As the sea creatures who consume those sugars—and the carbon they contain—die, they sink to the deep ocean, where the carbon is locked away from the atmosphere for a long time. This process is called the “biological pump.”

A healthy population of phytoplankton helps lock away carbon from the atmosphere. In order to thrive, phytoplankton need nutrients—notably, nitrogen, phosphorus, and iron. In most parts of the modern ocean, phytoplankton deplete all of the available nutrients in the surface ocean, and the biological pump operates at maximum efficiency.

However, in the modern Southern Ocean, there is a limited amount of iron—which means that there are not enough phytoplankton to fully consume the nitrogen and phosphorus in the surface waters. When there is less living biomass, there is also less that can die and sink to the bottom—which results in a decrease in carbon sequestration. The biological pump is not currently operating as efficiently as it theoretically could. 

To track the efficiency of the biological pump over the span of the past 40,000 years, Adkins and his colleagues collected more than 10,000 fossils of the coral Desmophyllum dianthus.

Why coral? Two reasons: first, as it grows, coral accretes a skeleton around itself, precipitating calcium carbonate (CaCO3) and other trace elements (including nitrogen) out of the water around it. That process creates a rocky record of the chemistry of the ocean. Second, coral can be precisely dated using a combination of radiocarbon and uranium dating.

“Finding a few centimeter-tall fossil corals 2,000 meters deep in the ocean is no trivial task,” says Adkins, Smits Family Professor of Geochemistry and Global Environmental Science at Caltech.

Adkins and his colleagues collected coral from the relatively narrow (500-mile) gap known as the Drake Passage between South America and Antarctica (among other places). Because the Southern Ocean flows around Antarctica, all of its waters funnel through that gap—making the samples Adkins collected a robust record of the water throughout the Southern Ocean.

Wang analyzed the ratios of two isotopes of nitrogen atoms in these corals – nitrogen-14 (14N, the most common variety of the atom, with seven protons and seven neutrons in its nucleus) and nitrogen-15 (15N, which has an extra neutron). When phytoplankton consume nitrogen, they prefer 14N to 15N. As a result, there is a correlation between the ratio of nitrogen isotopes in sinking organic matter (which the corals then eat as it falls to the seafloor) and how much nitrogen is being consumed in the surface ocean—and, by extension, the efficiency of the biological pump.

A higher amount of 15N in the fossils indicates that the biological pump was operating more efficiently at that time. An analogy would be monitoring what a person eats in their home. If they are eating more of their less-liked foods, then one could assume that the amount of food in their pantry is running low.

Indeed, Wang found that higher amounts of 15N were present in fossils corresponding to the last ice age, indicating that the biological pump was operating more efficiently during that time. As such, the evidence suggests that colder climates allow more biomass to grow in the surface Southern Ocean—likely because colder climates experience stronger winds, which can blow more iron into the Southern Ocean from the continents. That biomass consumes carbon, then dies and sinks, locking it away from the atmosphere.

Adkins and his colleagues plan to continue probing the coral library for further details about the cycles of ocean chemistry changes over the past several hundred thousand years.

The study is titled “Deep-sea coral evidence for lower Southern Ocean surface nitrate concentrations during the last ice age.” Coauthors include scientists from Caltech, Princeton University, Pomona College, the Max Planck Institute for Chemistry in Germany, University of Bristol, and ETH Zurich in Switzerland. This research was funded by the National Science Foundation, Princeton University, the European Research Council, and the Natural Environment Research Council.

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Three New Minerals Discovered in a Unique Meteorite

Same meteorite contains the only known naturally occurring quasicrystals—solid matter with symmetries once thought impossible
News Writer: 
Robert Perkins

Minerals

The new minerals were found in a tiny fragment of the Khatyrka meteorite, seen here in a backscattered electron image.
Credit: Chi Ma/Caltech

Researchers led by mineralogist Chi Ma have identified three new minerals in a tiny sample of the Khatyrka meteorite. The meteorite, recovered in pieces from the Koryak Mountains in eastern Russia in 1979 and 2011, made news in recent years for containing the first three natural quasicrystals ever found. (A quasicrystal is a phase of solid matter with symmetries previously thought to be impossible).

Ma, the director of the Geological and Planetary Sciences division’s Analytical Facility at Caltech, and his colleagues have discovered 35 new minerals to date, including 32 in meteorite samples. Out of more than 5,000 known minerals approved and cataloged by the International Mineralogical Association, which confirms new minerals, about 430 are from meteorites—meaning that Ma can be credited with discovering roughly 7 percent of the minerals sourced from meteorites.

The new minerals—dubbed “stolperite” (after Edward Stolper, the William E. Leonhard Professor of Geology and Caltech’s provost); “hollisterite,” in honor of Princeton geologist Lincoln Hollister (PhD ’66); and kryachkoite, for Valery Kryachko, who discovered the original samples of the Khatyrka meteorite in 1979—contribute to the nascent field of nanominerology, the study of rock samples at nanoscales.

Nanomineralogy usually uses a technique called high-resolution analytical scanning electron microscopy (SEM), in which a beam of high-energy electrons is focused onto a polished sample’s surface. Various emitted signals, produced from the interaction of the electrons and atoms in a sample, allow scientists to observe the mineral down to a 1-nanometer resolution and to analyze its chemical composition and crystal structure at a submicrometer scale.

The newly dubbed stolperite—so named in recognition of Stolper’s “many fundamental contributions to petrology and meteorite research, and support for natural quasicrystal research,” Ma says—is an alloy of metallic aluminum and copper (chemical formula: AlCu). Structurally, stolperite is arranged in a cubic form, with each copper atom at the center of a cube with aluminum atoms at all eight corners (and, likewise, each aluminum atom sits at the center of a cube of eight copper atoms).

“Normally we don’t observe such aluminum-rich metal in space rocks because the aluminum would have reacted to form aluminum oxide,” Ma says. This means that the likelihood of finding other stolperite samples is low. In fact, the Khatyrka meteorite is the only meteorite ever found that contains metallic aluminum; the meteorite fragment hosting the trio of new minerals is now in the holdings of the Smithsonian Institution National Museum of Natural History, which maintains a catalog of more than 600,000 specimens.

The three new minerals and names have been confirmed by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, which was established in 1959. To name a new mineral, a researcher must demonstrate that its chemical composition and crystal structure make it unique. A few months ago, Ma also had a mineral named in his honor, an aluminum-titanium-oxide mineral (Al2Ti3O9) called machiite by Sasha Krot at the University of Hawaii, was also found in a meteorite. This one formed by condensation in the solar nebula, making it one of the oldest solids to have formed in the solar system.

Ma’s paper announcing the minerals is titled “Hollisterite (Al3Fe), kryachkoite (Al,Cu)6(Fe,Cu), and stolperite (AlCu): Three new minerals from the Khatyrka CV3 carbonaceous chondrite.” Other co-authors on the paper are Chaney Lin and Paul Steinhardt (BS ’74) from Princeton University, and Luca Bindi from University of Florence in Italy. This research was carried out at the Caltech GPS Division Analytical Facility, which is supported, in part, by National Science Foundation grants.

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Computer Model Shows Breakup of Iceberg Logjams

Model focuses on triggers for seasonal ice breakup that could improve accuracy of sea-level rise predictions
News Writer: 
Robert Perkins

photo of icebergs

Credit: B. Minchew/Caltech

Projections of how much the melting of ice sheets will contribute to sea-level rise can vary by several meters based on the rate of iceberg calving at the edges of those ice sheets. To provide climate scientists with models that make more accurate forecasts, a postdoctoral researcher at Caltech has created a computer simulation of one of the key processes controlling glacial calving.

Glaciers are moving slabs of ice that slowly grind downhill. Where they end in the sea, chunks break off, forming icebergs in a process known as calving. When temperatures plummet in the winter, those icebergs can freeze together and create a traffic jam that prevents further icebergs from breaking off from the glacier.

During the winter, the glacier loses much less ice to the sea. The eventual spring breakup of what is known as the mélange—that frozen iceberg logjam—occurs suddenly, and is the focus of research by Caltech’s Alexander Robel.


This animation shows how a single calving event sends out a shockwave that triggers a breakup of the frozen mélange.
Credit: Alexander Robel

“I developed a computer model that simulates how the first iceberg calving of the warm season creates a shock wave that travels through the jammed mélange, breaking it up,” says Robel, a National Oceanic and Atmospheric Administration (NOAA) Postdoctoral Scholar and a Stanback Postdoctoral Scholar at Caltech. His new model was featured in Nature Communications on February 28.

The mélange is a frozen granular material, so Robel adapted an open-source computer simulation called the Discrete-Element Bonded-Particle Sea Ice Model to show how icebergs freeze together in the winter and then transmit the shock of the first iceberg calving in the summer.

That first calving is made possible by the thinning of sea ice in warmer water, which reduces the ability of the mélange to act a bulwark against the glacier.


This animation shows how mélange responds to pressure applied by the movement of a glacier.
Credit: Alexander Robel

Robel tailored his modeled glaciers to resemble fjords in Greenland. Those fjords are narrow channels of water that are prone to trapping mélange. Robel was able show that the threshold at which spring sea-ice breakup is likely to occur is based in part on the thickness of sea ice within the mélange, but also on the shape of the channel within which the mélange is trapped.

Robel, who is a researcher in Caltech’s Division of Geological and Planetary Sciences, home to the Seismological Laboratory, says his work was inspired in part by seismological studies of the way fractures propagate through elastic materials—drawing a connection between earthquakes and iceberg calving.

Robel’s paper is titled “Thinning Sea Ice Weakens Buttressing Force of Iceberg Mélange and Promotes Calving.” His research was supported by NOAA and the Foster and Coco Stanback Postdoctoral Fellowship in Global and Environmental Science.

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