Rock-Dwelling Microbes Remove Methane from Deep Sea

Methane-breathing microbes that inhabit rocky mounds on the seafloor could be preventing large volumes of the potent greenhouse gas from entering the oceans and reaching the atmosphere, according to a new study by Caltech researchers.

The rock-dwelling microbes, which are detailed in the Oct. 14 issue of Nature Communications, represent a previously unrecognized biological sink for methane and as a result could reshape scientists' understanding of where this greenhouse gas is being consumed in subseafloor habitats, says Professor of Geobiology Victoria Orphan, who led the study.

"Methane is a much more powerful greenhouse gas than carbon dioxide, so tracing its flow through the environment is really a priority for climate models and for understanding the carbon cycle," Orphan says.

Orphan's team has been studying methane-breathing marine microorganisms for nearly 20 years. The microbes they focus on survive without oxygen, relying instead on sulfate ions present in seawater for their energy needs. Previous work by Orphan's team helped show that the methane-breathing system is actually made up of two different kinds of microorganisms that work closely with one another. One of the partners, dubbed "ANME" for "ANaerobic MEthanotrophs," belongs to a type of ancient single-celled creatures called the archaea.

Through a mechanism that is still unclear, ANME work closely with bacteria to consume methane using sulfate from seawater. "Without this biological process, much of that methane would enter the water column, and the escape rates into the atmosphere would probably be quite a bit higher," says study first author Jeffrey Marlow, a geobiology graduate student in Orphan's lab.

Until now, however, the activity of ANME and their bacterial partners had been primarily studied in sediments located in cold seeps, areas on the ocean bottom where methane is escaping from subseafloor sources into the water above. The new study marks the first time they have been observed to oxidize methane inside carbonate mounds, huge rocky outcroppings of calcium carbonate that can rise hundreds of feet above the seafloor.

If the microbes are living inside the mounds themselves, then the distribution of methane consumption is significantly different from what was previously thought. "Methane-derived carbonates represent a large volume within many seep systems, and finding active methane-consuming archaea and bacteria in the interior of these carbonate rocks extends the known habitat for methane-consuming microorganisms beyond the relatively thin layer of sediment that may overlay a carbonate mound," Marlow says.

Orphan and her team detected evidence of methane-breathing microbes in carbonate rocks collected from three cold seeps around the world: one at a tectonic plate boundary near Costa Rica; another in the Eel River basin off the coast of northwestern California; and at Hydrate Ridge, off the Oregon coast. The team used manned and robotic submersibles to collect the rock samples from depths ranging from 2,000 feet to nearly half a mile below the surface.

Marlow has vivid memories of being a passenger in the submersible Alvin during one of those rock-retrieval missions. "As you sink down, the water outside your window goes from bright blue surface water to darker turquoise and navy blue and all these shades of blue that you didn't know existed until it gets completely dark," Marlow recalls. "And then you start seeing flashes of light because the vehicle is perturbing the water column and exciting florescent organisms. When you finally get to the seafloor, Alvin's exterior lights turn on, and this crazy alien world is illuminated in front of you."

The carbonate mounds that the subs visited often serve as foundations for coral and sponges, and are home to rockfishes, clams, crabs, and other aquatic life. For their study, the team members gathered rock samples not only from carbonate mounds located within active cold seeps, where methane could be seen escaping from the seafloor into the water, but also from mounds that appeared to be dormant.

Once the carbonate rocks were collected, they were transported back to the surface and rushed into a cold room aboard a research ship. In the cold room, which was maintained at the temperature of the deep sea, the team cracked open the carbonates in order to gather material from their interiors. "We wanted to make sure we weren't just sampling material from the surface of the rocks," Marlow says.

Using a microscope, the team confirmed that ANME and sulfate-reducing bacterial cells were indeed present inside the carbonate rocks, and genetic analysis of their DNA showed that they were related to methanotrophs that had previously been characterized in seafloor sediment. The scientists also used a technique that involved radiolabeled 14C-methane tracer gas to quantify the rates of methane consumption in the carbonate rocks and sediments from both the actively seeping sites and the areas appearing to be inactive. They found that the rock-dwelling methanotrophs consumed methane at a slower rate than their sediment-dwelling cousins.

"The carbonate-based microbes breathed methane at roughly one-third the rate of those gathered from sediments near active seep sites," Marlow says. "However, because there are likely many more microbes living in carbonate mounds than in sediments, their contributions to methane removal from the environment may be more significant."

The rock samples that were harvested near supposedly dormant cold seeps also harbored microbial communities capable of consuming methane. "We were surprised to find that these marine microorganisms are still viable and, if exposed to methane, can continue to oxidize this greenhouse gas long after surface expressions of seepage have vanished." Orphan says.

Along with Orphan and Marlow, additional coauthors on the paper, "Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea," include former Caltech associate research scientist Joshua Steele, now at the Southern California Coastal Water Research Project; Wiebke Ziebis, an associate professor at the University of Southern California; Andrew Thurber, an assistant professor at Oregon State University; and Lisa Levin, a professor at the Scripps Institution of Oceanography. Funding for the study was provided by the National Science Foundation; NASA's Astrobiology Institute; the Gordon and Betty Moore Foundation Marine Microbiology Initiative grant; and the National Research Council of the National Academies. 

Written by Ker Than

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Friday, October 17, 2014
Center for Student Services 360 (Workshop Space)

TA Training: fall make-up session

Tuesday, October 7, 2014
Red Door Cafe

Samba and Salsa Exhibition

Tuesday, October 7, 2014
Center for Student Services 360 (Workshop Space)

Thirty Meter Telescope Groundbreaking and Blessing

Tuesday, October 7, 2014
Center for Student Services 360 (Workshop Space)

Caltech Peer Tutor Training

Wednesday, September 24, 2014
Annenberg Lecture Hall

A chance to meet Pasadena Unified School District Leadership

Textbook Theory Behind Volcanoes May Be Wrong

In the typical textbook picture, volcanoes, such as those that are forming the Hawaiian islands, erupt when magma gushes out as narrow jets from deep inside Earth. But that picture is wrong, according to a new study from researchers at Caltech and the University of Miami in Florida.

New seismology data are now confirming that such narrow jets don't actually exist, says Don Anderson, the Eleanor and John R. McMillian Professor of Geophysics, Emeritus, at Caltech. In fact, he adds, basic physics doesn't support the presence of these jets, called mantle plumes, and the new results corroborate those fundamental ideas.

"Mantle plumes have never had a sound physical or logical basis," Anderson says. "They are akin to Rudyard Kipling's 'Just So Stories' about how giraffes got their long necks."

Anderson and James Natland, a professor emeritus of marine geology and geophysics at the University of Miami, describe their analysis online in the September 8 issue of the Proceedings of the National Academy of Sciences.

According to current mantle-plume theory, Anderson explains, heat from Earth's core somehow generates narrow jets of hot magma that gush through the mantle and to the surface. The jets act as pipes that transfer heat from the core, and how exactly they're created isn't clear, he says. But they have been assumed to exist, originating near where the Earth's core meets the mantle, almost 3,000 kilometers underground—nearly halfway to the planet's center. The jets are theorized to be no more than about 300 kilometers wide, and when they reach the surface, they produce hot spots.  

While the top of the mantle is a sort of fluid sludge, the uppermost layer is rigid rock, broken up into plates that float on the magma-bearing layers. Magma from the mantle beneath the plates bursts through the plate to create volcanoes. As the plates drift across the hot spots, a chain of volcanoes forms—such as the island chains of Hawaii and Samoa.

"Much of solid-Earth science for the past 20 years—and large amounts of money—have been spent looking for elusive narrow mantle plumes that wind their way upward through the mantle," Anderson says.

To look for the hypothetical plumes, researchers analyze global seismic activity. Everything from big quakes to tiny tremors sends seismic waves echoing through Earth's interior. The type of material that the waves pass through influences the properties of those waves, such as their speeds. By measuring those waves using hundreds of seismic stations installed on the surface, near places such as Hawaii, Iceland, and Yellowstone National Park, researchers can deduce whether there are narrow mantle plumes or whether volcanoes are simply created from magma that's absorbed in the sponge-like shallower mantle.

No one has been able to detect the predicted narrow plumes, although the evidence has not been conclusive. The jets could have simply been too thin to be seen, Anderson says. Very broad features beneath the surface have been interpreted as plumes or super-plumes, but, still, they're far too wide to be considered narrow jets.

But now, thanks in part to more seismic stations spaced closer together and improved theory, analysis of the planet's seismology is good enough to confirm that there are no narrow mantle plumes, Anderson and Natland say. Instead, data reveal that there are large, slow, upward-moving chunks of mantle a thousand kilometers wide.

In the mantle-plume theory, Anderson explains, the heat that is transferred upward via jets is balanced by the slower downward motion of cooled, broad, uniform chunks of mantle. The behavior is similar to that of a lava lamp, in which blobs of wax are heated from below and then rise before cooling and falling. But a fundamental problem with this picture is that lava lamps require electricity, he says, and that is an outside energy source that an isolated planet like Earth does not have.  

The new measurements suggest that what is really happening is just the opposite: Instead of narrow jets, there are broad upwellings, which are balanced by narrow channels of sinking material called slabs. What is driving this motion is not heat from the core, but cooling at Earth's surface. In fact, Anderson says, the behavior is the regular mantle convection first proposed more than a century ago by Lord Kelvin. When material in the planet's crust cools, it sinks, displacing material deeper in the mantle and forcing it upward.

"What's new is incredibly simple: upwellings in the mantle are thousands of kilometers across," Anderson says. The formation of volcanoes then follows from plate tectonics—the theory of how Earth's plates move and behave. Magma, which is less dense than the surrounding mantle, rises until it reaches the bottom of the plates or fissures that run through them. Stresses in the plates, cracks, and other tectonic forces can squeeze the magma out, like how water is squeezed out of a sponge. That magma then erupts out of the surface as volcanoes. The magma comes from within the upper 200 kilometers of the mantle and not thousands of kilometers deep, as the mantle-plume theory suggests.

"This is a simple demonstration that volcanoes are the result of normal broad-scale convection and plate tectonics," Anderson says. He calls this theory "top-down tectonics," based on Kelvin's initial principles of mantle convection. In this picture, the engine behind Earth's interior processes is not heat from the core but cooling at the planet's surface. This cooling and plate tectonics drives mantle convection, the cooling of the core, and Earth's magnetic field. Volcanoes and cracks in the plate are simply side effects.

The results also have an important consequence for rock compositions—notably the ratios of certain isotopes, Natland says. According to the mantle-plume idea, the measured compositions derive from the mixing of material from reservoirs separated by thousands of kilometers in the upper and lower mantle. But if there are no mantle plumes, then all of that mixing must have happened within the upwellings and nearby mantle in Earth's top 1,000 kilometers.

The paper is titled "Mantle updrafts and mechanisms of oceanic volcanism."

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Seeing Protein Synthesis in the Field

Caltech researchers have developed a novel way to visualize proteins generated by microorganisms in their natural environment—including the murky waters of Caltech's lily pond, as in this image created by Professor of Geobiology Victoria Orphan and her colleagues. The method could give scientists insights to how uncultured microbes (organisms that may not easily be grown in the lab) react and adapt to environmental stimuli over space and time.

The visualization technique, dubbed BONCAT (for "bioorthogonal non-canonical amino-acid tagging"), was developed by David Tirrell, Caltech's Ross McCollum–William H. Corcoran Professor and professor of chemistry and chemical engineering. BONCAT uses "non-canonical" amino acids—synthetic molecules that do not normally occur in proteins found in nature and that carry particular chemical tags that can attach (or "click") onto a fluorescent dye. When these artificial amino acids are incubated with environmental samples, like lily-pond water, they are taken up by microorganisms and incorporated into newly formed proteins. Adding the fluorescent dye to the mix allows these proteins to be visualized within the cell.

For example, in the image, the entire microbial community in the pond water is stained blue with a DNA dye; freshwater gammaproteobacteria are labeled with a fluorescently tagged short-chain ribosomal RNA probe, in red; and newly created proteins are dyed green by BONCAT. The cells colored green and orange in the composite image, then, show those bacteria—gammaproteobacteria and other rod-shaped cells—that are actively making proteins.

"You could apply BONCAT to almost any type of sample," Orphan says. "When you have an environmental sample, you don't know which microorganisms are active. So, assume you're interested in looking at organisms that respond to methane. You could take a sample, provide methane, add the synthetic amino acid, and ask which cells over time showed activity—made new proteins—in the presence of methane relative to samples without methane. Then you can start to sort those organisms out, and possibly use this to determine protein turnover times. These questions are not typically tractable with uncultured organisms in the environment." Orphan's lab is also now using BONCAT on samples of deep-sea sediment in which mixed groups of bacteria and archaea catalyze the anaerobic oxidation of methane.

Why sample the Caltech lily pond? Roland Hatzenpichler, a postdoctoral scholar in Orphan's lab, explains: "When I started applying BONCAT on environmental samples, I wanted to try this new approach on samples that are both interesting from a microbiological standpoint, as well as easily accessible. Samples from the lily pond fit those criteria." Hatzenpichler is lead author of a study describing BONCAT that appeared as the cover story of the August issue of the journal Environmental Microbiology.

The work is supported by the Gordon and Betty Moore Foundation Marine Microbiology Initiative.

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Measuring Earthquake Shaking with the Community Seismic Network

In 2011, the Community Seismic Network (CSN) began taking data from small, inexpensive accelerometers in the greater Pasadena area. Able to measure both weak and strong ground movement along three axes, these accelerometers promise to provide very high-resolution data of shaking produced by seismic activity in the region. "We have quite a large deployment of these accelerometers, about 400 sensors now, in people's homes but also in schools and businesses, and in some high-rise buildings downtown," says Julian Bunn, principal computational scientist for Caltech's Center for Advanced Computing Research. "We run client software on each sensor that sends data up into Google's cloud. From there we can analyze the data from all these sensors."

The CSN is the brainchild of Professor of Geophysics Rob Clayton, Professor of Engineering Seismology Tom Heaton, and Simon Ramo Professor of Computer Science, Emeritus, K. Mani Chandy, and a collaboration among Caltech's seismology, earthquake engineering, and computer science departments. It has successfully detected the many earthquakes that have occurred since its establishment. In addition, the CSN currently assists in damage assessment by generating maps of peak ground acceleration before accurate measurements of the earthquake epicenter or magnitude are known.

However, the CSN could provide further assistance in damage assessment if it were also able to produce an immediate estimation of the magnitude. "Right now we only detect an event," says Bunn. "We don't estimate the magnitude." This is where Caltech junior Kevin Li comes in. Li has been spending his 10-week Summer Undergraduate Research Fellowship (SURF) trying to develop a machine-learning system that can accurately estimate the magnitude of an earthquake within seconds of its detection.

Of course, the USGS already accurately measures earthquake magnitudes, but it does so by means of highly sophisticated—and expensive—seismometers that are located several miles apart from one another. Post-quake "ShakeMaps" are then constructed by extrapolating from this data to estimate shaking between seismometer stations. The problem, as recent quakes in California have shown, is that shaking can vary widely even from block to block—as can damage and potential injuries. The CSN proposes to capture this variation and provide an important resource for first responders during major earthquakes, pinpointing areas likely to have the most damage. Should this pilot study prove fruitful, says Bunn, it could "provide better hazard mitigation in parts of the world where they can't afford these very expensive installations."

"Seismic networks like the USGS use really fine sensors," explains Li. "However, the CSN sensors sacrifice fine measurement precision for low-cost efficiency. The sensors record particularly noisy data, far noisier than what the USGS system is used to. As a result, we cannot just adopt the algorithms from USGS. We need to develop our own system."

So far, says Li, the work is going well. "I'm currently still in week nine of my 10 weeks, but I have a system that seems like it can give a magnitude estimate that is within 1 unit of magnitude. For instance, if the estimation is 5.4, then the real magnitude should be somewhere between 4.4 and 6.4. If we can get to better precision than that, even better."

Li notes that his system has so far only been evaluated using USGS magnitudes for previous seismic events over the past two years. "I have yet to test it on a new event. Perhaps I can test it on the data from the recent earthquake in Napa once Caltech has finished processing it."

CSN is supported by funding from the Gordon and Betty Moore Foundation.

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Measuring Earthquake Shaking
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GPS Names a New Division Chair

John Grotzinger, the Fletcher Jones Professor of Geology, has been named the new chair of the Division of Geological and Planetary Sciences (GPS). With his selection formally approved by the Board of Trustees earlier this year, Grotzinger took the helm of the division on September 1. He will replace current division chair Ken Farley, the W. M. Keck Foundation Professor of Geochemistry.

Grotzinger, who had previously served as both a visiting associate professor at Caltech in 1996 and a Moore Distinguished Scholar in 2004, joined the faculty and the division in 2005. His research is focused on the early environmental evolution of both Earth and Mars. By working to understand the chemical and physical conditions of the early oceans and atmosphere on our planet, Grotzinger's group has been able to determine the influence of those conditions on microbial evolution and the emergence of animals. He also works as the project scientist of the Mars Science Laboratory mission, whose Curiosity rover has been exploring the Red Planet since 2012, gaining insights into how water was involved in the early history of Mars and what its potential role might have been in supporting microbial habitability, had life ever originated there.

"I'm thrilled John Grotzinger has been selected as the new GPS chair—he's a uniquely broad-based scientist who's brought his keen geological insight to bear on solving problems in fields that span nearly the entire breadth of GPS, from geobiology to planetary science, geophysics and geochemistry," says Michael Gurnis, John E. and Hazel S. Smits Professor of Geophysics and director of the Seismological Laboratory, who was the chair of the search committee. "Combined with his enormous experience leading MSL, I can see that John will be a superb chair of the Division of Geological and Planetary Sciences.

As chair, Grotzinger says he wants to help the faculty and students in GPS to achieve their goals in research and education. "I look forward to supporting the unique excellence that distinguishes our division from its peers at other universities, and I will especially enjoy interacting with the students—and the outstanding young faculty members we've hired over the past few years," Grotzinger says.

"GPS excels at crossing traditional barriers, and I am curious to see how we might continue to catalyze new research opportunities," he adds. "So in addition to maintaining the existing excellence of our programs, I also want to find ways to develop the future by fostering creative interactions and finding new mechanisms to support this emerging research."

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