28 February 2019

Cold World Explorers


by Fatima Husain

Story Image: Traveling by snowmobile, Emily Matys and her colleagues dragged sleds deep into the field laden with drills and equipment to melt holes in the thick Antarctic ice to obtain samples of the marine microbes living beneath. As evidence of the extreme environment, in the background is a red “apple”—a type of portable shelter common around polar research sites to protect researchers in the case of inclement weather. Image courtesy Emily Matys.

Throughout their journeys in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS), students and researchers alike investigate the mysteries of the planet. Fieldwork, a critical component of geological study, takes some researchers to the ends of the Earth, and occasionally to some of the coldest, most remote environments known to humankind. 

Emily Matys PhD ’18 from the EAPS Summons Lab, spent part of the 2018 southern hemisphere summer at McMurdo Station, the United States Antarctic research center located in McMurdo Sound. Matys works in geobiology and astrobiology—fields that sometimes look for life in extreme and ancient environments. She specializes in studying life in cold locations—from microbial mats at lake bottoms to the organisms that live in icy surface waters.  

“For the most part, we were interested in looking at what lives underneath the ice, and what lives in the open ocean,” Matys says. Matys had traveled to Antarctica to learn how to study life on the continent as part of the National Science Foundation Antarctic Biology Training Program. 

“People wonder if microbial communities [in Antarctica] are present because they’re selected for by the cold or just able to deal with the cold,” Matys says. To investigate this, Matys and her peers drilled or melted holes through thick layers of ice to access the waters and microbes of interest. Then, they’d characterize the water, measuring components such as temperature and conductivity, or collect samples to bring back to the station’s lab and culture them. There, they analyzed how Antarctic environmental conditions support life. “We took them from a very cold environment and exposed them to warmer temperatures or colder temperatures to see how they behaved. We found that they were actually able to grow a little bit better when exposed to warmer temperatures.” 

Story Image: Emily Matys in Antarctica. Image courtesy Emily Matys.

Matys and her colleagues’ finding challenged the research community’s perception about life in the cold. “The conventional thought was that all of the organisms that live down there are best suited for the cold, and it’s not necessarily the case. They’re just tolerant of the cold,” she says. 

When they weren’t out in the field or in the lab, Matys and the other researchers spent time in lectures about current and historical research topics on the base.

For Matys, Antarctica was a place to learn how to do fieldwork in variable and challenging conditions—and a springboard for potential future research studying life on icy moons. 

On the other side of the globe, Lauren Kipp, an MIT-WHOI Joint Program graduate based in EAPS, spent nearly two months in 2015 aboard the U.S. Coast Guard’s icebreaker Healy tracking sediment transport from continental shelves into the Arctic Ocean. During this GEOTRACES research cruise—examining biogeochemical cycles and large-scale distribution of trace elements in the marine environment—Kipp and the team measured oceanic radium-228, a naturally occurring radioactive element in sediment. Using it as a chemical tracer, she investigated whether climate change via its effects on continental shelves could alter the chemistry of ocean water.

“It’s one of the regions of the world that’s being most affected by climate change, and so I like being able to study this really pressing and pertinent issue and all the ways that it’s going to affect the ocean,” Kipp says.

In the Arctic, shallow continental shelves cover more than half of the ocean; here, sediments accumulate and release compounds like radium into the sea. Ice melt and turbulent waters help to erode the coast and stir sediment up containing the saltwater soluble radium. 

To understand and investigate how radium-228 traveled from Arctic coasts to the waters of the North Pole, Kipp measured radium in water samples along 69 stops as Healy broke through ice-laden waters. “We filtered what we wanted out of the seawater at depth and then brought those filters and cartridges back onto the deck,” Kipps says. “Then we analyzed those cartridges back in the lab at Woods Hole Oceanographic Institution (WHOI).” By the end of her cruise, Kipp says she filtered an estimated 286,868 liters of seawater, looking for changes in water chemistry and land-sea interactions due to climate change. 

Her Arctic research revealed the unexpected. “Radium has a [continental] shelf source, so we expected it to be highest near the shelf. However, we were really surprised to see such high levels in the center of the ocean because that’s as far away as you can get from [the shelf],” Kipp says. The radium being transported rapidly into the central Arctic was about twice that seen during a previous GEOTRACES cruise in the region in 2007.

To explain the observations, Kipp turned to global ocean circulation maps. “It started to come together, because I realized there is this strong surface current [called the Transpolar Drift] that carries water from the shelf seas north of Russia across to the central Arctic, near the North Pole, where we measured it,” Kipp says. “The radium that we saw [in the ocean] was coming from that shelf,” Kipp says, not the Chukchi shelf that the Healy crossed earlier in the trip. 

What could cause the doubling of radium levels over such a short period of time? Climate change. Kipp found that ice shelves in Russia were experiencing rapid and strong warming due to rising air and sea temperatures. The resultant loss of sea ice allowed winds and waves to increase water turbulence on the shelf and coastal erosion in the region. These factors ultimately added more sediments, including radium, to the ocean.

Kipp’s experience during the cruise ignited her fascination with the Arctic due to the territory’s susceptibility to climate change. “I think that’s a really great opportunity to increase public opinion about how climate change is currently affecting Earth’s oceans,” Kipp says. 

2 January 2019

Archiving Experiences in Science


by Fatima Husain

In December, Summons Lab members Ainara Sistiaga and Fatima Husain conducted invited talks and activities for the semesterly Science and Us high school student workshop held at MIT, which brings approximately fifty students from around Massachusetts to campus for science enrichment activities.

Student artwork produced at the workshop.

Sistiaga and Husain both shared their experiences in science, and discussed the importance of preserving impressions and memories in science in an effort to support diversity and inclusion efforts across STEAM fields. Sistiaga and Husain discussed with the students how social media tools such as Twitter could be used to archive impressions in science, and created a brand-new Twitter account that serves solely to archive student-produced STEAM artwork. The account, @ArchiveScience, contains pictures of all the STEAM artwork produced by the workshop participants.

The Twitter account created from the workshop.
6 December 2018

How to survive in one of Earth’s most extreme environments


New research finds that a unique component of cell membranes in an archaea species conveys protection against acidic surroundings

by Fatima Husain

Even in Earth’s most inhospitable environments, life has taken hold. Extremophiles, the organisms most well-known for withstanding extreme temperatures, pHs, salinity, and even nutrient-starvation, have evolved special mechanisms that enable them to survive in their environments — but getting to the bottom of that resilience requires targeted and methodical interrogation.

At Yellowstone National Park and similar sites, extremophiles reside in environments such as acid hot springs or thermal acid soils. Here, they are exposed, often intermittently, to some of the lowest naturally-occurring pHs on Earth and temperatures nearing the boiling point of water. To survive in these rapidly fluctuating conditions, organisms protect themselves with complex membranes, composed of interlocked lipids linked to their backbones with strong ether bonds, rather than the ester bonds most commonly found in eukaryotes and bacteria.

In Sulfolobus acidocaldarius, an archaeon that lives in high-acid, high-temperature environments that are common in Yellowstone, cellular membrane lipids called glycerol dialkyl glycerol tetraether (GDGTs) are linked to an uncommon sugar-like molecule called calditol. This week, a group of scientists published findings in the Proceedings of the National Academy of Sciences (PNAS) identifying how calditol is made in the cell and how, specifically, it is responsible for acid-tolerance in these organisms — helping scientists get steps closer to understanding how life evolved to survive in extreme environments.

Story Caption: Grand Prismatic Spring at Yellowstone National Park. Credit: Jim Peaco, National Park Service

Roger Summons, the Schlumberger Professor of Geobiology in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS) and one of the authors of the study, credits advances in molecular biology, bioinformatics, and targeted gene deletion strategies for enabling this discovery.

“The era of genomics has brought a range of new tools to advance lipid biomarker research,” Summons says. Paula Welander, a former EAPS postdoctoral researcher in the Summons Lab and now Assistant Professor in the Department of Earth System Science at Stanford, directed the study that was conducted by Zhirui Zeng and Jeremy H. Wei at Stanford, and Xiao-lei Liu, an Assistant Professor of Organic Geochemistry at the University of Oklahoma.

“This study is an excellent example of how an interdisciplinary approach, including microbial physiologists and organic geochemists, can address outstanding questions regarding lipid biomarkers,” Welander says.

To identify calditol’s role in the Sulfolobus acidocaldarius membranes, the researchers used tools in comparative genomics, gene deletion, and lipid analysis to zero in on a particular protein within the class of radical S-andenosylmethionine (SAM) enzymes that is required to synthesize calditol. When they searched for what coded that protein in calditol-producing archaeal genomes, they found just a few candidate genes. To test the protein’s importance for acid tolerance, the researchers created mutants —with the membrane-related genes deleted — and analyzed their lipids. By subjecting the calditol-free mutant to highly acidic conditions, the researchers were able to confirm the true function of the calditol component of the membrane. Only the naturally-occurring, calditol-producing Sulfolobus and the mutant strain with the radical-SAM gene restored, were able to grow after a significant drop in pH.

“While Welander and colleagues have demonstrated the presence of radical-SAM lipid biosynthesis genes in bacteria, this is the first time one has been unambiguously identified in archaea,” Summons says. “Calditol-linked to membrane lipids in these organisms confer significant protective effects.”

Welander adds: “Researchers have hypothesized for many years that producing calditol would provide this type of protective effect, but this has not been demonstrated directly. Here we finally show this link directly.”

Even further, the fact that a radical SAM protein is involved in linking calditol to the membranes might help scientists better understand the chemistry and evolution of membrane lipids from a wide variety of environments across the planet.

“What this result speaks to is the possible presence of a variety of other radical chemistries to modify membrane lipids once they’ve been synthesized,” Summons says. “In turn, this could help us better understand the biosynthesis of other archaea-specific lipids and help us write the evolutionary history of these strikingly distinctive membranes.”

The study was supported by the Simons Foundation Collaboration on the Origins of Life.

22 November 2018

Roger Summons on Proof


Over the summer, Roger Summons was interviewed for Proof, America’s Test Kitchen’s podcast. His interview appears in the episode “Beanboozled.” The whole podcast episode is fun, and Roger appears between minutes 27 and 32.

Listen in here!

21 November 2018

Mars 2020 landing site offers unique opportunity to study ancient Martian history and search for ancient life


EAPS Professors Summons, Bosak and Weiss provide insight and advise on landing site potential.

by Fatima Husain

Credits: NASA/JPL-Caltech/MSSS/JHU-APL

In 2020, NASA’s next rover will launch from Cape Canaveral Air Force Station in Florida and head to Jezero crater on Mars. The location, which NASA Science Mission Directorate associate administrator Thomas Zurbuchen announced this week, was selected from among sixty candidates for its rich geology dating back to 3.6 to 3.9 billion years. The crater was once home to an ancient lake-delta system, which could have captured and preserved evidence of ancient life as well as information on the Red Planet’s evolution.

The decision was many years in the making. Before the site was selected, scientists from around the world gathered in Glendale, California to lend their expertise on the four final candidate landing sites at the last of four Mars 2020 Landing Site Workshops. One of those scientists was Tanja Bosak, an associate professor in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). Her work uses experimental geobiology to explore modern biogeochemical and sedimentological processes in microbial systems. For Bosak, Jezero crater is the ideal landing site for learning about the potential habitability of early Mars.

“Jezero crater’s geology is very obvious [from orbit], and it is clear that the environment was habitable in the past. It is older than any sedimentary environment preserved in the rock record from Earth,” Bosak says. “Jezero crater preserves some of the most ideal rock types that we use to look for past life on Earth.”

Within these rocks are clays and carbonates — minerals known to facilitate the preservation of fossils on Earth. Bosak’s work as an Investigator in the Simons Collaboration on the Origins of Life (SCOL) contributed to a talk at the October workshop titled “A Search for Prebiotic Signatures with the Mars 2020 Rover,” given by David Catling. Catling is a professor in Earth and Space Sciences at the University of Washington and is also a SCOL Investigator.

In his talk, Catling argued that even if life never emerged on Mars in the first place, scientists could focus on whether prebiotic precursors were ever present in the Martian environment — information that is important for discerning the conditions necessary for life to occur. Roger Summons, the Schlumberger Professor of Geobiology in EAPS and SCOL Investigator also contributed to the presentation. As PI of the MIT NASA Astrobiology Institute team Foundations of Complex Life and as a member of the Sample Analysis on Mars instrument team using NASA’s Curiosity rover, Summons’s work focuses on the preservation of organic matter from different environments on Earth and Mars.

“We know from our efforts to find traces of the earliest life on the Earth that the best chance for finding convincing and credible evidence will come from studies of well-preserved, fine-grained layered rocks that were deposited under bodies of standing water,” Summons says.

Earlier in the year, both Bosak and Summons contributed to “A Field Guide to Finding Fossils on Mars,” a review article published in the Journal of Geophysical Research which summarized the strategies behind the search for ancient biosignatures among the different potentially habitable Martian environments. The authors of the review mentioned the favorability of sedimentary environments much like those found at Jezero crater, because analogs to those environments on Earth, like river deltas and lakes, have the highest potential to collect and preserve both molecular fossils and body fossils of microbes.

In fact, organic matter was recently detected in 3 billion-year-old mudstones at the site of an ancient lake at Gale Crater, the research site of the Mars Curiosity Rover. The findings, published in Science, fueled heightened interests in potential organic matter preservation at other landing sites on Mars — including Jezero crater. This is because the Mars 2020 mission, unlike previous missions to Mars, will not only perform measurements in the Martian environment, but will also collect and cache sediment cores from sites of interest to be returned to Earth during a later mission.

“While much can be learned from using the imaging and spectroscopic tools that can be operated remotely on spacecraft, nothing compares to the sensitivity and specificity with the rapidly advancing chemical instrumentation we can access in laboratories around the world,” Summons says. “This has been shown over and over again by what has been learned during the almost fifty years of studies of rocks that were returned to Earth during the Apollo era of moon exploration.”

Bosak is most excited about the images and data the rover will collect during its mission to Jezero crater. The mission could shed light on whether carbonates present on the rim of the crater “precipitated out of the lake, just like limestones do.” On Earth, “limestones from the early Earth can have shapes that record microbial interactions with sediments and microbially-stimulated precipitation of minerals,” Bosak says.

Ben Weiss, professor of planetary sciences in EAPS, also attended the Mars 2020 Landing Site Workshop and presented with co-author Anna Mittelholz, a graduate student at the University of British Columbia, on potential studies of Mars’ magnetic field. “Jezero will also be an extremely exciting place to obtain samples for understanding the history of the ancient Martian magnetic field,” Weiss says. In the summer, Mittelholz and Weiss published a paper in the journal Earth and Space Science, “The Mars 2020 Candidate Landing Sites: A Magnetic Field Perspective,” which details the findings they presented at the workshop.

Sometime during the Martian planetary evolution, Mars lost its global magnetic field and much of its early atmosphere, which could have drastically altered the Martian environment. Planetary magnetic fields are generated by the movement of metallic fluids deep in planetary interiors in a process known as the dynamo. For example, Earth’s magnetic field is generated and sustained from its molten, iron-rich core.

“The most important issue is to determine when the [Martian] dynamo turned off. This would help determine if the transition from a warmer, wetter early Mars to the current cold and dry state was caused by the loss of the dynamo field,” Weiss says. “Jezero is an excellent place to test this hypothesis because it contains rocks and minerals with ages spanning the time we suspect that the dynamo turned off.”

All in all, rover exploration and sample collection at Jezero crater may refine scientific knowledge across disciplines. “Jezero crater will make a great place for understanding the contribution of the dynamo to protecting the early atmosphere, and the habitability of early Mars,” Weiss says — information that could also contribute to our understanding on how and why life took hold on our own planet.

“I think that this is as good as it gets,” Bosak says.

24 October 2018

Addressing the Possibility of Life on Mars


Mars expert John Grotzinger tells the story of exploration and the search for ancient life on the red planet at the 2018 Carlson Lecture.

by Fatima Husain

Story Image: John Grotzinger’s research focuses on interactions between life and environment, and tectonic and climatic regimes. (Vicki McKenna)

In 2018, millions around the world caught glimpses of the planet Mars, discernible as a bright red dot in the summer’s night skies. Every 26 months or so, the red planet reaches a point in its elliptical orbit closest to Earth, setting the stage for exceptional visibility. This proximity also serves as an excellent opportunity for launching Mars missions, the next of which will occur in 2020 when a global suite of rovers will take off from Earth.

While Mars hid behind the drizzling Boston sky on October 11th, 2018, an audience gathered at the New England Aquarium for the 8th annual John Carlson Lecture featuring Mars expert John Grotzinger, the Fletcher Jones Professor of Geology at the California Institute of Technology and a former professor in the MIT Department of Earth, Atmospheric and Planetary Sciences (EAPS). In his talk, Grotzinger gave audiences a different perspective of Mars, taking them through a journey of its geologic history as well as the current search for life on the planet.

Specializing in sedimentology and geobiology, Grotzinger has made significant contributions to understanding the early environmental history of the Earth and Mars and their habitability. In addition to involvement with the Mars Exploration Rover (MER) mission and the High Resolution Science Experiment (HiRISE) onboard the Mars Reconnaissance Orbiter (MRO), Grotzinger served as project scientist of the Mars Science Laboratory mission, which operates the Curiosity roving laboratory. Curiosity explores the rocks, soils and air of Gale Crater to find out whether Mars ever hosted an environment that was habitable for microbial life in its nearly 4.6-billion-year history. “What I’d like to do is give you a very broad perspective of how we as scientists go about exploring a planet like Mars, with the rather audacious hypothesis that there could have been once life there,” he said. “This is a classic mission of exploration where a team of scientists heads out into the unknown.”

“Simple one-celled microorganisms we know have existed on Earth for the last three-and-a-half billion years — a long time. They originated, they adapted, they evolved, and they didn’t change very much until you had the emergence of animals just 500 million years ago,” Grotzinger said. “For basically 3 billion years, the planet was pretty much alone with microbes. So, the question is: Could Mars have done something similar?”

Part of the research concerning whether or not Mars ever hosted ancient life involves identifying the environmental characteristics necessary for the survival of living organisms, including liquid water. Currently, the thin atmosphere around Mars prevents the accumulation of a standing body of water, but that may not always have been the case. Topographic features documented by orbiters and landers suggest the presence of ancient river channels, deltas and possibly even an ocean on Mars, “just like we see on Earth,” Grotzinger said. “This tells us that, at least, for some brief period of time if you want to be conservative, or maybe a long period of time, water was there [and] the atmosphere was denser. This is a good thing for life.”

To describe how scientists search for evidence of the past habitability on Mars, Grotzinger told the story of stratigraphy — a discipline within geology that focuses on the sequential deposition and layering of sediments and igneous rocks. The changes that occur layer-to-layer indicate shifts in the environmental conditions under which different layers were deposited. In that manner, interpreting stratigraphic records is simple: “It’s like reading a book. You start at the bottom and you get to the first chapter, and you get to the top and you get to the last chapter,” Grotzinger said. “Sedimentary rocks are records of environmental change…What we want to do is explore this record on Mars.”

While Grotzinger and Curiosity both continue their explorations of Mars, scientists from around the world are working on pinpointing new landing sites for future Mars rovers which will expand the search for ancient life. This past summer, the SAM (Sample Analysis on Mars) instrument aboard the Curiosity rover detected evidence of complex organic matter in Gale Crater, a discovery which further supports the notion that Mars may have been habitable once.

“We know that Earth teems with life and we have enough of a fossil record to know that it’s been that way since we get to the oldest, well-preserved rocks on Earth. But yet, when you go to those rocks, you almost never find evidence of life,” Grotzinger said, leaving space for hope. “And that’s because, in the conversion of the sedimentary environment to the rock, there are enough mineralogic processes that are going on that the record of life gets erased. And so, I think we’re going to have to try over and over again.”

Following the lecture, members and friends of EAPS attended a reception in the main aquarium that featured some of the research currently taking place in the department. Posters and demonstrations were arranged around the aquarium’s cylindrical 200,000-gallon tank simulating a Caribbean coral reef, and attendees were able to chat with presenters and admire aquatic life while learning about current EAPS projects. EAPS graduate student, postdoc and research scientist presenters included Tyler Mackey, Andrew Cummings, Marjorie Cantine, Athena Eyster, Adam Jost, and Julia Wilcots from the Bergmann group; Kelsey Moore and Lily Momper from the Bosak group; Eric Beaucé, Ekaterina Bolotskaya, and Eva Golos from the Morgan group; Jonathan Lauderdale and Deepa Rao from the Follows group; Sam Levang from the Flierl group; Joanna Millstein and Kasturi Shah from the Minchew group; and Ainara Sistiaga, Jorsua Herrera, and Angel Mojarro from the Summons group.

The John H. Carlson Lecture series communicates exciting new results in climate science to general audiences. Free of charge and open to the general public, the annual lecture is made possible by a generous gift from MIT alumnus John H. Carlson to the Lorenz Center in the Department of Earth, Atmospheric and Planetary Sciences, MIT.

To join the invitation list for next year’s Carlson Lecture, please contact Angela Ellis: aellis@mit.edu.

21 October 2018

The Power of Persistence and the Scientific Method


Researchers identify a unique molecular fossil that tracks multicellular animal evolution.

Credit: Roger Summons

by Fatima Husain

Evidence of ancient life on Earth is scattered around the globe. The most obvious examples of past life include visible fossils, preserved in sedimentary rocks in the geologic record, viewable in museums and paleontology laboratories alike. But the visible fossil record doesn’t fully reflect the diversity of life on ancient Earth — for that, researchers focus on the microscopic. They also search for molecular fossils, compounds that resist significant biological and thermal degradation on geologic timescales.

This past Monday, researchers at the University of California (UC), Riverside, identified evidence for some of the earliest animal life on Earth using molecular fossils diagnostic for multicellular animals called demosponges, which encompass over eight thousand different species of sponge — including the common bath sponge. Their findings were published in the journal Nature Ecology & Evolution.

Roger Summons, the Schlumberger Professor of Geobiology in the MIT Department of Earth, Atmospheric and Planetary Sciences (EAPS) co-authored the paper along with scientists from California Institute of Technology, Geoscience Australia, Central Michigan University, Uppsala University and Stanford University.

The researchers identified a previously unknown sterane molecule (a degraded and saturated steroid), called 26-methylstigmastane, in rocks sampled from the Huqf Supergroup of the South Oman Salt Basin, a particularly well-preserved sedimentary sequence with extensive sample availability due to the long history of petroleum exploration there. The ages of the rocks span the Cryogenian through early Cambrian periods — from over 635 million years ago to approximately 540 million years ago. The chemical structure of this sterane was determined by rigorous comparisons with the carbon skeletons of sterols present in some modern-day demosponges.

The research was first-authored by graduate student J. Alex Zumberge in the UC research group of Gordon D. Love, a former EAPS postdoctoral research fellow from 2003 to 2006. While at MIT, Love researched molecular fossils from the Proterozoic eon as well as from the end-Permian mass extinctions in the Summons Lab.

For a number of years now, Love has been a strong proponent of the sponge marker hypothesis: the hypothesis that another molecular fossil, sterane 24-isopropylcholestane, can be a diagnostic tool for sponges. But evidence of 24-isopropylcholestane has also been found at trace levels in some algae today, complicating its use for tracking sponge evolutionary history. Love’s identification of 26-methylstigmastane doesn’t have that problem: its sterol precursor is only found in demosponges.

“He has continued to find creative ways to test the sponge biomarker hypothesis,” Summons says, “and now, with his student Alex Zumberge and colleagues with expertise in sponge biology, has discovered a carbon skeleton in ancient sedimentary rocks that is unique to demosponges.”

Through their research, the researchers estimate that demosponges were ecologically prominent in marine environments well-prior to the Cambrian explosion, known for its rich fossil records of diverse animal clades. These estimates line up with current molecular clock predictions, which make use of the genomic histories contained in the genes of living organisms and their ancient fossil counterparts.

“The sponge biomarker hypothesis will continue to be controversial because presently, it cannot be reconciled with the record of fossilized sponge spicules,” Summons says. Spicules, structural support elements in sponges, are also preserved in the fossil record for some demosponges — but none so far date back to the ages in which the 26-methlystigmastane was found. However, a 2010 study suggests that siliceous sponge spicules existed in the Precambrian — as the presence of 26-methlystigmastane would suggest — but were not preserved. “Ultimately, the outcome of this work shows the power of persistence and the scientific method,” Summons says.

This research was supported, in part, by the NASA Astrobiology Institute (NAI), Foundations of Complex Life based at MIT, NAI’s Alternative Earths, NASA Exobiology, the National Science Foundation’s Frontiers in Earth Systems Dynamics, as well as the Agouron Institute and the SponGES project.

12 October 2018

Studying the Hotbed of Horizontal Gene Transfers


Global Microbiome Conservancy’s preliminary results reveal new insights into human gut microbiomes

by Fatima Husain

Story caption: A farming scene in rural Rwanda
Credit: Christopher Corzett

For over 200,000 years, humans and their gut microbiomes have coevolved into some of the most complex collections of living organisms on the planet. But as human lifestyles vary from the urban to rural, so do the bacterial diversities of gut microbiomes.

A global, non-profit collaboration of over 70 scientists has been working for the past two years to interrogate and preserve that diversity of gut microbiomes from populations around the world. They’re racing against the proliferation of antibiotic overuse and Western-style diets, which are known to contribute to a decrease in gut bacterial diversity. The Global Microbiome Conservancy, launched in 2016, already has some surprising insights that further shed light on the black box of gut bacterial diversity and human digestion.

A set of MIT-based scientists who founded the conservancy come from a disparate set of disciplines: biological engineering, evolutionary biology, organic geochemistry, and biomedical research. But such collaborations may allow for interdisciplinary innovation that stands to improve the understanding of the science within our guts. Mathilde Poyet, a postdoctoral researcher in the Department of Biological Engineering’s Alm Lab, believes the interdisciplinary nature of the collaboration promotes the conservancy’s goals, which she says are to “preserve the full biodiversity of the human gut microbiome before it is lost, and to advance our understanding of the origins and functions of the human gut microbiomes,” within a “robust research ecosystem.” As part of the efforts, the conservancy establishes long-term collaborations with local populations and researchers for sampling and analysis — and the participants themselves maintain ownership of their samples.

Poyet and fellow MIT-based postdoctoral researchers Mathieu Groussin, who also works in the Alm Lab, and Ainara Sistiaga, a Marie Curie postdoctoral fellow in the Department of Earth, Atmospheric and Planetary Sciences (EAPS) Summons Lab, presented the preliminary results of their work at the first MIT Microbiome Club meeting of the 2018-19 academic year. At the meeting, Poyet, Groussin, and Sistiaga spoke about their research progress as well as what’s surprised them most so far.

In addition to biobanking and characterizing bacterial isolates collected from fecal samples from around the world, Poyet focuses on the horizontal exchange of genetic materials between living organisms, known as horizontal gene transfer (HGT). Unlike vertical transfers, horizontal gene transfers are acquisitions of genetic material from non-parental lineages.

“Transfers of genes are known to be crucial for bacterial evolution and the human gut microbiome is an important hotbed for horizontal gene transfers,” Poyet says. “But all previous studies fell short at characterizing the timescale of these HGT events.”

With the collection of bacterial isolates and genomes she built, Poyet is now able to identify evidence of very recent horizontal gene transfers, supporting the notion that these transfers frequently occur during the human lifetime. The effects of highly active horizontal gene transfers mean that gut bacteria could experience a sort of turnover of genetic material over time, which the conservancy hopes to study further as they collect more data.

From additional preliminary analysis, Poyet and Groussin have found that in industrialized populations, which tend to have less gut bacterial diversity, meaning the rate of gene exchange through horizontal gene transfer is greater. “As HGT is a mechanism frequently used by bacteria to rapidly adapt to changing environments, this result suggests that an industrialized lifestyle imposes a stronger selective pressure on the gut microbiome of individual people, possibly as a result of the high consumption of antibiotics,” Poyet says.

Ainara Sistiaga has been zeroing in on a dietary element that could also have implications for gastrointestinal bacteria and human health: lipids. Lipids, the hydrophobic biomolecules often referred to as fats, are unexplored in the gut microbiome. Sistiaga aims to change that.

With fecal samples collected through the conservancy, Sistiaga performs lipid analysis — a series of chemistry-rooted procedures that help researchers characterize which lipids are present as well as their abundances.

One lipid of particular interest is cholesterol, a molecule widely implicated in heart disease and stroke. As meat-heavy diets increase in popularity around the world, global cholesterol intake is set to rise as well. Theoretically, in most humans, some of the cholesterol that reaches the gut should undergo a bacterial conversion into a byproduct that the body cannot reabsorb and would be excreted. But Sistiaga finds that all gut microbiomes execute metabolic functions differently. “What we have observed is that most of the participants in rural populations are performing this conversion much more efficiently than Western donors,” Sistiaga says. So, in order to describe and understand how such processes work within the gut, Sistiaga hopes to use methods informed from organic geochemistry to characterize the fate of cholesterol in humans from around the world.

After the presentation, the MIT researchers fielded questions from the audience. “People were interested in all aspects of the presentation — traveling, how to get involved, the science, the preliminary results, the potential outcomes of this project,” Sistiaga says. “Even after the Q&A, a lot of people approached us for more specific questions.”

Within the next two years, the Global Microbiome Conservancy is set to increase their global coverage. Currently, the microbiome studies conducted focus on samples collected from 19 distinct populations sampled worldwide from Arctic regions, Sub-Saharan countries & North America, but they’ll soon be complemented with samples from Malaysia and Peru. Poyet adds, “We anticipate [samples from Asia and South America] will yield novel and unique microbial communities that must be preserved.”

“It’s been exciting to unveil the microbiome of these underrepresented communities, and I think we are just seeing the tip of the iceberg,” Sistiaga says. “Everything we’ve observed so far confirms how important and truly urgent this work is.”

Story caption: A woman in Ghana collects fish
Credit: Mathieu Groussin

30 July 2018

From simple separations to complex questions


Using demonstrations in geobiology and astrobiology to educate and empower

Campers separated different ink colors on coffee filters. Photo Credit: Alina Husain

Each summer, groups of girls from around Groton, New Hampshire gather near the scenic Spectacle Pond to take part in the Circle Program, a program which provides girls from low-income backgrounds with year-round mentorship and a summer camp experience. Throughout the summer, girls camp for weeks at a time, building friendships and the skills to face the academic, social, and cultural challenges in their lives.

Part of the regular camp programming for all the girls involves science. Camp counselors and staff encourage girls to pursue their curiosities in STEM and regularly integrate aspects of the scientific method into camp activities.

Over the past weekend, EAPS Summons Lab member and MIT science writing graduate student Fatima Husain traveled to Groton to meet with 19 middle school girls attending the camp. During her visit, Husain took the students on a journey through geologic time, displaying rocks samples that spanned billions of years of Earth’s history. Some of the samples contained visible fossils, such as trilobites, while other samples contained subtler cues of ancient Earth, like stromatolites. To take their conversation to space, Husain also brought in small meteorites and a tektite formed by meteor impacts. Through the samples, Husain and the girls discussed how Earth evolved since its formation.

To introduce the fields of geochemistry, geobiology, and astrobiology, Husain led the girls through a basic chromatography demonstration to simplify the concept of chemical separation. In the Summons lab, Husain studies ancient lipids, or fats, that contain information about Earth’s past climate. To purify and examine the lipids for analysis, Husain uses many different types of chromatography. While her separations in the lab require advanced techniques and instrumentation, the scientific concepts behind them can be readily illustrated in a STEAM (science, technology, engineering, art, and mathematics) activity. In natural environments, she says, most samples of interest exist as complex mixtures, and separations are performed based on the particular characteristics of the components of interest.

Husain tests out the chromatography demonstration using non-toxic materials in the Summons Lab before visiting the camp. Photo Credit: Alina Husain

Using low-cost, accessible materials, Husain showed the girls how to separate colors in washable markers with coffee filters and water — to create art while doing science. Dissolved ink traveled up each filter, captivating some girls, who watched deep blues separate into shades of purple, red, green, and yellow. Others performed the demonstration before in school — and for those girls, Husain added a challenge to the mix: comparing how well different solvents separated colors.

Over talks with small groups, Husain queried the girls for unexpected results and hypotheses, and encouraged them to ask questions during and after the demonstration.

Some students opted to keep their completed separations for decorating their rooms at home. Photo credit: Alina Husain 

By the time the demo and discussion finished, some groups of girls had separated ten marker colors, and some began to create their own color mixtures to separate. One pair of girls commented that they looked forward to continuing the demonstration after the camp and decorating their rooms with the colorful filters.

In the future, Husain hopes to help plan more science activities for girls of all ages with Circle Program staff.

This outreach activity was supported with funding from the NASA Astrobiology Institute MIT Team.

Additional photos of campers enjoying their demonstrations, courtesy of Hannah Holmes at the Circle Program:

30 July 2018

Gateway to Antarctica


Summons lab member Emily Matys searches around the globe to reveal the secrets of microbial life
by Fatima Husain

Matys in Antarctica. Photo Credit: Emily Matys

To reveal the complex secrets of microbial life, MIT EAPS PhD candidate and Summons lab member Emily Matys travels around the globe. Matys analyzes lipids — oils, waxes, and fats that living organisms produce in order to store energy and respond to environmental changes.

During her time at MIT, Matys has ventured to Mexico, Germany, Chile, and, most recently, New Zealand to learn innovative lab techniques and to study within different cultures and environments with the support of grants from MIT International Science and Technology Initiatives (MISTI).

“I am the biggest supporter of MISTI,” Matys says. “The grants provide MIT affiliates with an incredible opportunity to interact and collaborate with diverse groups of researchers from around the world.”

By working directly with scientists around the world, Matys gained a global perspective on geobiological research. In Mexico, Matys learned the microbiological methods necessary to understand the modification of cellular lipids in response to environmental conditions. During her time in Chile, Matys analyzed lipids produced by organisms that live in an oxygen minimum zone (OMZ) off the coast of northern Chile. More recently, Matys has collaborated with a group of researchers from Germany. Together, they hope to develop analytical methods that will enable the spatial analysis of lipids in natural samples.

In 2016, Matys traveled to New Zealand to meet with three other scientists from around the world who study life in cold environments. “It’s rare that a group of four scientists can get together, sit down, talk, and discuss the details and common themes of their research.”

From the conversations in New Zealand, the scientists published a perspectives paper in the journal Geobiologyin 2018 titled “The ‘Dirty Ice’ of the McMurdo Ice Shelf: Analogues for biological oases during the Cryogenian.”

“It describes the McMurdo Ice Shelf in Antarctica, and how it can help us to understand how life may have persisted throughout the Neoproterozoic Snowball Earth events,” Matys says.

But that’s not all Matys gained from her visit to New Zealand. During a discussion about Antarctic research, two of the scientists recommended Matys apply for the National Science Foundation Antarctic Biology Training Program, an approximately month-long research experience based out of McMurdo Station, Antarctica. Matys applied, and, in January 2018, she completed the training program and added Antarctica to her list of travels.

“I certainly did not expect to gain so many amazing international colleagues during my graduate education, but I am exceedingly grateful for the opportunities that have enabled me to do so,” Matys says.