Joël Wittmann awarded the ETH Medal 2023 for his Master thesis on hydropeaking impacts on fish larvae
Congratulations to Joël who has received the ETH Medal 2023 for his outstanding Master thesis Quantifying Pathway Suitability for Fish Escaping Rapid Flow Changes. He extended the Fish Escaping Route model, previously developed in the Stocker Lab, by assessing the capability of fish to follow spatial shifts in their habitat. The extended model was applied to identify critical areas and discharges for brown trout larvae in the hydropeaking Hasliaare River, Switzerland. With the extended model the impact of river morphology and hydropower operation on fish can be quantified as indicators, enabling various applications in hydropeaking research and mitigation. Joël’s work was developed in partnership with Kraftwerke Oberhasli AG, a Swiss hydropower company contributing to develop mitigation measures for hydropeaking.
PriME moves to the next phase!
Over five years ago, in collaboration with the MIT and other US universities, we started the Principles of Microbial Ecosystems (PriME) project with the goal of developing a quantitative synthesis of microbial ecology. Thanks to the further financial support provided by the Simons Foundation, we will be able to continue our effort towards the understating of how marine microbes form communities and how these communities function with the vision to develop a general blueprint for a similar quantitative understanding of microbes in other environments and ultimately for environmental microbiology at large.
Here is a recent article published by our ecohydraulics team in the Aqua Viva magazine
Led by Luiz, the article discusses global freshwater biodiversity decline and puts the Swiss context into it. It has been highlighted by the editors and made available for free download here.
Fish ecology becomes art
Robert investigates the influence of flow and temperature changes on the behavior of juvenile fish. Part of his scientific imagery is currently embedded into a film installation at the “ART SAFIENTAL – Biennale for Land and Environmental art”. His PhD project is jointly supervised by the Laboratory of Hydraulics, Hydrology and Glaciology (VAW) and our group. Learn more
Luiz Silva is the new President-elect of the International Fisheries Section
We’re happy to announce that Luiz has been elected the upcoming president of the International Fisheries Section (IFS) of the American Fisheries Society (AFS). He now joins the Executive Committee of IFS as President-elect and will serve the ExComm for a three years term. The IFS is a section of AFS with members from over 40 countries and more than 300 members. The aim of IFS is to promote awareness of education, research and science in the fish and fisheries realm across the globe. Best of luck to Luiz during his term serving IFS.
Our paper on the predator-prey interaction between Acanthamoeba and Listeria bacteria
Did you know that Acanthamoeba form backpacks of captured Listeria bacteria prior to phagocytosis? In a fruitful collaboration with the Laboratory of Food Microbiology, we characterized this fascinating predator-prey interaction and discovered that random encounters, enhanced by bacterial motility, and Acanthamoeba locomotion drive the predation and backpack formation of Listeria bacteria. Check it out in this PNAS publication. Many thanks and congratulations to everyone involved!
Our paper on encounters between elongated phytoplankton in turbulence
In our new work published in PNAS, we predict that cell elongation enhances encounter rates between phytoplankton cells and thus accelerates marine snow formation, a mechanism that potentially explains the rapid clearance of phytoplankton blooms. Thanks to the Wilczek lab for a very fruitful collaboration! Congratulations to everyone involved.
Every drop counts: Irrigation in the context of climate change
The project IRRIWAM, led by the Subsurface Environmental Processes group (SEP GROUP Eawag-ETH Zurich), showed that irrigation technology is crucial. It contributes more than climate change to how much water evaporates and groundwater accumulates.
This project was funded through the World Food System Center (Competitive Center of ETH Zurich) with support from Coop.
The next generation of scientists visit the StockerLab
Do you remember the first time you entered a scientific laboratory? Perhaps you recall the excitement, the fascination and a little bit of intimidation and shyness that came with it? For the majority of the girls of the Kangaroo goes Science event, it was the first time in a lab when they came to visit us. With the aim of giving the girls a taste of scientific work, we conducted an interactive workshop with a number of experiments related to our research topics and methods. Together with the girls, we mimicked the flow conditions of microbes in a flume, found the best shapes for slow sinking phytoplankton made of modelling clay models and spied on motile and non-motile phytoplankton to observe the different shapes that plankton species have and how some of them move. In the end, we hope to have given the girls a great first experience in a scientific laboratory and would love to see many of them again at ETH in couple of years!
SNF scientific imaging prize for Stefano’s leafscape
Stefano won a distinction prize for the image “Treellusion” related to the NCCR project. The image was awarded and exhibited at the Bienne festival of photography.
Another article is also available on SRF (German)
Every drop counts: irrigation research by the SEP group at the Mühlerama Museum
Dr. Joaquin Jimenez-Martinez and his group are participating at the exhibition “Science on Your Plate” at the Mühlerama Museum for Food Culture in Zurich, with their project “Understanding the effects of irrigation modernization in water resources management – citrus production in the Jucar river basin, Spain”.
Come and visit us on June 1st (from 18:00 until 21:00) at the event “Meet the Scientist”.
Motorious microbes escaping the lab!
It’s starting to be a tradition that we redirect our motions from the lab towards the SOLA relay race once a year. Inspired by our research activities, we headed to our starting lines as motorious microbes with a strong taxis (directed motion towards or away from a stimulus) towards the end line. No matter the environmental challenge we faced, whether we had to run under sunlight induced heat, we faced sudden water flow from above or we had to climb steep gradients, we remained motile and showed positive taxis towards the end line. And in the spirit of microbes being social organisms, we chemotaxed (directed motion towards a chemical gradient, i.e. food) to the potluck dinner to celebrate the successful day together.
(Text: Dorothee Kurz)
Our paper on the ecological roles of bacterial chemotaxis published in Nature Reviews Microbiology
A few days ago a review paper lead by Johannes and Francesco on the ecological roles of bacterial chemotaxis was published in Nature Reviews Microbiology. How chemotaxis is performed by bacteria is much better understood than why. In this review, the costs and benefits of chemotaxis are discussed, both for individual bacteria as well as whole populations. This reveals that the function of chemotaxis extends much beyond the traditional role of foraging and contributes to efficient colony expansion as well as microbial diversity. Congratulations to everyone involved.
Our paper on the role of eDNA in biofilm streamers formation published in PNAS
Our paper on the role of eDNA in biofilm streamers formation led by Eleonora was recently published in PNAS. It describes how extracellular DNA (eDNA) is essential to the mechanical stability of the streamers and under what conditions these biofilm structures are formed. Furthermore, it shows how, by controlling eDNA, it is possible to control streamers formation, a potentially relevant finding in the environmental and medical settings. Congratulations to everyone involved.
Luiz’s perspective about the hydropower and fish nexus hit the ETH News
Hydropower delivers renewable electricity, but comes with massive fish mortality – a global dilemma that can only be addressed by true compromises, says Luiz, and outlines how to find them.
Our paper on Raman microspectroscopy for microbiology published in Nature Reviews Methods Primers
Our paper on Raman microspectroscopy for microbiology led by Kang Soo and Zachary was recently published in Nature Reviews Methods Primers. This work was a collaborative effort with other Raman experts in the world. It describes technical aspects of Raman microspectroscopy in depth; best practice for measuring and analysing Raman data; useful applications in contemporary microbiology; and promises and future directions, covering from beginners to intermediates to experts in this technology. Congratulations to everyone involved.
Jeanette’s symposium proposal accepted by SICB
Proposed by Jeanette and Karen Chan (Swarthmore College, PA, USA) the symposium “Large-scale biological phenomena arising from small-scale biophysical processes” was selected for the Society of Integrative and Comparative Biology (SICB) Annual Meeting in January 2023, and was further selected to feature as a society-wide symposium. It will feature a cross-disciplinary slate of speakers on such topics as the organization of tissues and multicellularity, planktonic survival in patchy marine resource landscapes, and bacterial growth in soils and porous media.
Podcast aims at young women to inform and motivate them to get into engineering
The podcast aims at young women to inform and motivate them to get into engineering. If you are curious about why Dorothee studied Bioprocess engineering, why she chose to switch university for her Master degree or what in retrospect she would have done differently, listen in! For non-German speakers: The Podcast is in German – you can either practise your recent acquired German skills or Dorothee is happy to give you a short summary in English.
Elian Lüthy awarded the Culmann Fonds Award 2021 for her Master thesis on fish larvae and hydropeaking
Congratulations to Elian that has been granted the Culmann Fonds Award 2021 from ETH for her outstanding Master thesis entitled: “What are the Pathways? A method to assess habitat shifts for larvae during hydropeaking”. In this study, Elian developed a novel tool for modelling spatial and temporal shifts in suitable habitats for Brown trout larvae during hydropeaking events. This tool can serve as a complementary approach to the set of hydrological and ecological indicators available in the Swiss guidelines for hydropeaking mitigation. Elian’s work was developed in partnership with Kraftwerke Oberhasli AG (KWO), a Swiss hydropower company that has contributed to developing mitigation measures for hydropeaking impacts.
Robert gave a talk about the importance and the ecological costs associated with hydropower operation in Switzerland
In the scope of ETH Unterwegs, Robert was invited to discuss the relevance of his PhD with students at the cantonal school “Seetal” in Baldegg (canton Lucerne). In times of climate change, rising electricity demand and the Swiss decision to phase out nuclear power production, the role of storage hydropower is crucial, but comes at an ecological cost that is still poorly understood.
Our paper on sinking-enhanced degradation of marine particles published in Nature Geoscience
Our paper on the coupling between microbial degradation of marine particles and their sinking speed, led by Uria, was recently published in Nature Geoscience. This work demonstrates that particles that are sinking faster experience enhanced degradation due to the removal of degradation by-products by flow, letting bacterial enzymes focus on breaking down the particle material itself. A model developed by François showed that this coupling could play a significant role in setting the observed attenuation of carbon flux with depth in the marine environment. Article from ETH here. Also featured in Science News and Views. Congratulations to everyone involved!
Roman Stocker on C02 monitoring in the fight against Covid-19
Roman discusses the benefits of CO2 sensors against the spread of SARS-CoV-2 in classrooms and other indoor environments, in an SRF interview on 10vor10. Video: starting at 12:04-18:37
NCCR microbiomes at Scientifica 2021
For Scientifica 2021, the Stocker Lab put together a youth workshop on life at the microscale. Kids aged 12-16 got to participate in a range of hands-on activities which demonstrate how microorganisms swim, feed, and survive at scales smaller than the eye can see.
The workshop was organized under the umbrella of the NCCR Microbiomes program and was organized by Jeanette, Francois, Clara, and Juanita. The workshop volunteers were Jeanette, Juanita, Sophie, Sam, Robert, Dorothee, and Zach.
Event about fish mortality at hydropower plants
Luiz led the publication of a report that presented astonishing numbers about fish mortality events at hydropower plants in the Neotropical region. Hydropower operation has killed 128 tons of fish in the last ten years in Brazil, owing hundreds of millions of dollars in fines to the companies. The results were presented at the event “Fish Mortality at Hydropower Plants: identifying problems and co-creating solutions” on the 14th September 2020. The event had over 800 people registered from across the globe and aimed at initiating a discussion with multiple stakeholders to provide for well-informed decision-making processes and management actions. The report is available here and the recording of the event is accessible in this link.
Marie Skłodowska-Curie Fellowship
Sam was awarded a prestigious Marie Skłodowska-Curie Fellowship to investigate the biophysical processes controlling biofilm hydraulic resistance. Congratulations Sam!
Our paper on stress signaling by phytoplankton in turbulence published in PNAS
Our paper on phytoplankton in turbulence led by Francesco and former postdoc Anupam Sengupta(now at University of Luxembourg) was recently published in PNAS. This is a collaboration with former postdoc Lars Behrendt (now at Uppsala University) and Assaf Vardi at Weizmann Institute. Congratulations to everyone involved!
Roberto’s paper on sequential capillarity-assisted particle assembly was published in Lab on a Chip!
Roberto’s paper on sequential capillarity-assisted particle assembly (sCAPA) was published in Lab on a Chip! This microfluidic platform, a collaboration with the group of Lucio Isa, allows the placement of a precise spatial array of colloid particles and soon microorganisms. Congratulations to everyone involved!
Roman explains the role of aerosols in SARS-CoV-2 transmission on Swiss TV
Roman explains the role of aerosols in SARS-CoV-2 transmission on Swiss TV (10vor10), highlighting the risk posed by poorly ventilated indoor environments, particularly in case of prolonged exposure. See also SRF Espresso.
Let it snow! ETH showcases our work in a video on the breakdown of marine snow by bacteria
Our paper on optimal foraging by marine bacteria on particles published in PNAS
Estelle’s ISCA paper appeared in JoVE, the Journal of Visualized Experiments
Our paper on microbial transport in porous media published in Nature Physics
Luiz’s work published in Global Change Biology
Lars’s PhenoChip paper appeared in Science Advances
Lars’s paper describing PhenoChip, a platform for high-throughput phenotyping and selection of individual photosynthetic microorganisms exposed to physical and chemical gradients, was recently published in Science Advances.
Congratulations to everybody involved!
Marie Skłodowska-Curie Fellowship
Clara Martinez-Pérez was awarded a prestigious Marie Skłodowska-Curie Fellowship to work on syntrophic interactions between bacteria and diatoms – congratulations Clara!
One of our videos in The New York Times
One of our videos features in a fantastic article in The New York Times about predatory bacteria. They are fascinating organisms, much more common than most people realize, and currently being studied for their potential against disease-causing bacteria and their contribution to governing the microbiome.
New ETH Research Grant
The SEP group and the Stocker lab have been awarded an ETH Research Grant to work on microbial processes in soil, using microfluidics to create soil analogues. This award will support a PhD student and will strengthen the collaboration between the two groups.
Two newly awarded EU Innovative Training Network (ITN) grants
We’re part of two newly awarded EU Innovative Training Network (ITN) grants to collaborate with researchers across Europe: one involving the SEP group of Dr Jimenez-Martinez (Eawag and ETH Zurich) to work on the role of incomplete mixing in microbial behaviour, and one involving the Stocker group on the physics of microbial motility.
We look forward to further strengthening our links with colleagues across Europe and to contributing to the education of the next generation of PhD students in these fields.
Cherry’s Nature Communications article hit the ETH News
ETH researchers have analysed individual marine bacterial cells to show that metabolic processes inside them determine the amount of gas they release, which is involved in cloud formation.
Article published in Nature Communications
Corona video diary from the D-BAUG with Roman Stocker (29.4.2020)
Roman Stocker is a member of the “Swiss National COVID-19 Science Task Force”, which advises politicians and authorities in dealing with the coronavirus crisis. In the new corona video diary (in german) from D-BAUG, he emphasizes how important it is for science to sit at the table of decision makers and contribute its view of the pandemic.
Jen’s microfluidic device makes the cover
One of our collaborations with Uwe Sauer’s lab is highlighted as an article of significant interest in the current issue of AEM. Jen’s microfluidic device makes the cover!
Roman joins the ETH-Domain COVID task force
Roman joins the ETH-Domain COVID task force, launching a new platform for linking academic labs with hospitals for the supply of critically needed equipment, consumables, reagents and know-how.
Investigator Award from the Gordon and Betty Moore Foundation
Roman has received an Investigator Award from the Gordon and Betty Moore Foundation as part of their Symbiosis in Aquatic Systems Initiative. We’re very excited to have this opportunity to work for five years on the interactions of phytoplankton and marine bacteria, to understand how these marine microbes find each other, bond and exchange nutrients.
The Gordon and Betty Moore Foundation
Martin Polz inaugurates the LiMMat seminar series!
Our seminar series has officially started! On February 26th, Martin Polz from the University of Vienna talked about how interactions structure microbial diversity, attracting a large crowd from diverse institutions in Zurich. Some impressions from the seminar.
On the collision of rods in a quiescent fluid published in PNAS
Our article “On the collision of rods in a quiescent fluid”, with implications for the formation of marine snow by elongated phytoplankton as they sink, was published in PNAS. Congratulations Jonasz!
Ulrike featured on TV
Ulrike’s new research project on coral restoration with 3D-printed artificial reef elements was featured on Swiss TV “Schweiz aktuell” on 2nd December, together with the start of the Climate Change Conference COP25. [in German]
More here (clip starts at minute 16:55)
ETH Treffpunkt ScienceCity event
Roman gives a public lecture on the wonders and impacts of marine microorganisms at ETH Treffpunkt ScienceCity event [in German].
nanoTalks on Marine Microbiology
Johannes Keegstra, from our lab, will deliver an exciting public-audience lecture on the oceans, as part of the Zurich nanoTalks.
Congratulations, Dr. Nguyen and Dr. Norris!
The Stocker lab had two defenses back-to-back at MIT! Jen Nguyen successfully defended her thesis on bacterial growth in rapid nutrient fluctuations, and Noele Norris successfully defended her thesis on bacterial nutrient uptake strategies. Congratulations!!!
Visit of Prof. Tanvir Ahmed
The group’s first-ever PhD student, and author of many of our early publications on bacterial chemotaxis, Prof. Tanvir Ahmed, paid us a visit from Bangladesh. Great to see his involvement in so many important environmental topics! Keep up the good work Tanvir!
ETH Zürich Career Seed Grant for Jeanette and François
François and Jeanette just received an ETH Career Seed Grant for their joint-project on bacterial chemotaxis response to aerosol deposition: “Bacterial-aerosol interactions in the aquatic surface microlayer”. Congratulations!
Poster Award at RamanFest 2019 (Oxford UK)
Kang Soo Lee won the Poster Award at the seventh International Conference on Advanced Applied Raman Spectroscopy “RamanFest 2019” organized by HORIBA. Congratulations Kang!
A photo of airborne members won ETH photo contest
A photo of airborne members from STEP, Stocker and SEP groups studying the influence of variable gravity on bacterial anoxic hotspot in soils wins an ETH photo contest #coolestplaceateth.
New SNSF Sinergia grant
Together with colleagues Andrea Rinaldo (EPFL) and Arti Ahluwalia (Uni Pisa), our group will look into the scaling of metabolic rates with organism size, focusing on microorganisms from the ocean. An exciting new chapter of microscale visualization to understand the underpinnings of how our microbial oceans work!
The precision of chemotaxis in marine bacteria
Our latest paper – on the precision of chemotaxis in marine bacteria – just appeared in PNAS, with our image on the cover. The University of Melbourne (where our coauthors are based) published a great overview. Congratulations to all involved!
Prize for best presentation during the CSF Conference
Ben Lambert won the prize for best presentation during the CSF Conference “Marine Particles and Phycospheres”, held from May 19th to May 23rd 2019 on Monte Verita’ in Ascona. Congratulation!
Student Poster Award at InterPore 2019
Andres Velasquez (SEP group) received the Procter & Gamble Student Poster Award at InterPore 2019 (Valencia, Spain). Congratulations Andres!
Meeresbiologin mit Mission
Korallenriffe leiden unter dem Klimawandel. Ulrike Pfreundt will mit ökologisch sinnvollen Strukturen aus dem 3D-Drucker künstliche Riffe ermöglichen, die widerstandsfähigeren Korallen neuen Lebensraum bieten. More here
Microfluidic T-maze published in Nature Communications
Our article describing a microfluidic T-maze to quantify heterogeneity in the chemotactic performance of bacteria was published in Nature Communications. Congratulations to all involved!
Outreach event with ART LAB ZURICH
François, Jeanette and Jen recently completed an outreach event “ART LAB Zurich: Water World” in conjunction with Science Xplore Suisse, ETH Zurich and the University of Zurich. Among a week-long program of science and art activities, their module showed high school students how we spy on the diverse and complex lives of aquatic microorganisms.
Raman-based sorting platform published in Nature Microbiology
Kang published a blog on the Nature Research Microbiology Community to accompany our recent article describing Raman-activated microbial cell sorting in Nature Microbiology. Congratulations!
Review in Nature Reviews Microbiology
Our new article “The role of microbial motility and chemotaxis in symbiosis” reviews how the behaviour of microbial symbionts leads to their recruitment from the environment. Congratulations to all involved!
ETH Zürich Career Seed Grant for Ulrike
Ulrike just received an ETH Career Seed Grant for her new project on coral reef restoration: “Quantifying the impact of small-scale surface topography on coral larval settlement and metamorphosis for artificial coral reef substrates”. Congratulations!
Ulrike pitched her new project at one of the biggest StartUp Events in Europe – SLUSH Helsinki
Ulrike pitched her new project on engineered coral reefs in front of 1’200+ people at one of the biggest StartUp Events in Europe – SLUSH Helsinki. “It was an amazing experience to communicate a scientific project in 3 minutes to a large and broad audience! I really recommend to try it sometime”. Her 3-min pitch is available on youtube. More info here.
Picture credit: Vilja Pursiainen/Kaskas Media
Poster award for Mehdi
Mehdi received an award from ASME for the best poster presentation in the micro and nanotechnology forum at IMECE in Pittsburgh. Congratulations Mehdi! Award
Ulrike is one of eight finalists for the SKOLAR Award 2018
With her new project proposal to optimize the physical structure of artificial coral reefs, Ulrike made it to the finals of the SKOLAR research pitching competition and is in to win 100,000 € for her project. She will pitch her idea on the Slush stage in Helsinki on December 5th. More info: SKOLAR Award 2018
SNF PRIMA Grant – Doctoral Position
In the framework of the PRIMA Grant on biofilm in flow, awarded to Dr. Eleonora Secchi, the Stocker group is seeking a PhD student. More here
Eleonora has been awarded a SNF PRIMA Grant
Eleonora Secchi has been awarded a prestigious PRIMA Grant to work on biofilm formation in flow – congrats Eleonora!
Ulrike Pfreundt receives the Tom Brock Young Postdoctoral Award at ISME 2018
At the ISME17 meeting in Leipzig, Ulrike was awarded the Tom Brock Award 2018 for “Most innovative research by an early career scientist” in the field of Microbial Ecology. The award valued her work and talk on Trichodesmium aggregate behavior. Congratulations, Ulrike!
Zachary has been awarded a 3-year HFSP fellowship
Marie Curie Fellowship
François Peaudecerf was awarded a prestigious Marie Curie Fellowship to work on bacteria-bubble interactions – congrats François!
A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities
New ETH Grant
The Stocker group gets an ETH grant to work on a new single-cell technology tool with Lucio Isa’s group, to gain insights into the relation and interactions between individual microorganisms. The collaboration will be led by postdoc Eleonora Secchi.Doctoral position on “Sequential capillary assembly of microorganisms as a powerful new single-cell technology”
Collaborative work with Hardt group published in Nature
Joint work with Wolf-Dietrich Hardt’s group at ETH, for which the Stocker group performed mathematical modeling to quantify the effects of vaccines on bacterial growth, was published in Nature. More here
Stocker group co-leads large Simons-funded microbial collaborative
A research project by ETH Zurich, MIT with other US universities will receive 15 million US dollars in funding from the New York-based Simons Foundation. Over the next five years, researchers will investigate how microbial communities are organised and function, with a focus on the oceans. More here
Phytoplankton behavioral adaptation to turbulence published in Nature
Anupam and Francesco’s paper on shape-shifting phytoplankton in turbulence appears in Nature. Congratulations!
We visited CERN!
The Stocker lab visited CERN facility. It was very inspiring and influential – we all came back very impressed. Special thanks to Prof. Günther Dissertori for such a great tour and presentation.
Uria has been awarded a 2-year EMBO fellowship
To the space and back
A 5-member zero-gravity team from the lab (l to r: Francesco, Jeanette, Anupam, Ulrike and Roman) took to the skies on October 22, 2016 with the 2nd. Swiss Parabolic Flight Campaign. The team used this unique experimental opportunity – multiple cycles of hyper and microgravity conditions onboard the flight – to investigate the effect of gravity on phytoplankton migration. They have designed and used a two-pronged approach combining direct visualization of individual microscopic cells swimming, and molecular techniques to assess gene expression differences as a result of the changes in gravity.
Ulrike Pfreundt joined our group in October 2016
Uria Alcolombri joined our group in September 2016
The ISME Journal 2016 Cover Competition Award
At ISME-16 in Montreal, an image of bacterial chemotaxis in the phycosphere was selected to be the annual cover image for The ISME Journal. Congratulations to Steve and Vicente!
Eleonora Secchi joined our group in June 2016
Jeanette Wheeler joined our group in March 2016
Welcome Jeanette, our first female postdoc
Ocean Science Meeting
Ben Lambert and Steven Smriga each gave talks at the 2016 Ocean Sciences Meeting in New Orleans, USA.
Poster Award for Steven Smriga
Postdoc Steven Smriga won a best poster award at the EMBO/EMBL meeting on A New Age of Discovery for Aquatic Microeukaryotes held in Heidelberg, Germany in January 2016. Nice work Steven!
What we do: A 10 min video about our research
A 10 min video from KIKIM Media about research in the Stocker lab (sponsored by the Moore Foundation)
Review in Nature Reviews Microbiology
‘Live from under the lens’: Our review article on microbial motility and microfluidics appears in Nature Reviews Microbiology. Congratulations to Kwangmin and Doug!
Two new postdoc fellowships from ETH
We’re thrilled that both Eleonora Secchi and Jeanette Wheeler received a postdoc fellowship from ETH to come work with us. We look forward to welcoming you, Jeanette and Eleonora!
Young Scientists and the Future
Postdoc Anupam Sengupta was featured and interviewed by Nature in their documentary series Young Scientists and the Future. Anupam was selected by Nature as one of the brightest young researchers to address key scientific questions and to discuss ideas with Nobel laureates during the 65th Lindau Nobel Laureate Meeting in Germany. Congratulations Anupam!
Stocker lab moves to ETH Zürich, Switzerland!
We are very excited to start research in Europe!
Postdoc Francesco Carrara wins the 2014 Student Paper of the Year award from The American Naturalist.
Postdoc Francesco Carrara won the 2014 Student Paper of the Year award from The American Naturalist. This award is selected by the Editorial Board from all papers first-authored by students in the calendar year. Congratulations Francesco!
Jen wins 3rd place at the CEE video competition
Grad student Jen Nguyen won 3rd place and People’s Choice Award at the 2nd annual Department of Civil and Environmental Engineering video competition. Way to go Jen, you rock!
‘C’ Food selected for Koch Institute Image Award
The Koch Institute awarded Postdoc’s Steve Smirga and Vicente Fernandez for their striking image of a bacterial swarm accumulating around a diatom. Great job, Steve and Vicente!
Postdoc Anupam Sengupta invited to Lindau Meeting 2015
Anupam has received the official invitation to attend the 65th Lindau Nobel Laureate Meeting in the scenic town of Lindau, Germany from June 28 – July 3 2015. The annual meeting cycles between the themes of Nobel Prizes awarded in Physiology or Medicine, Physics and Chemistry. Every five years, as is the case for 2015, an interdisciplinary meeting is held. The meeting provides a globally recognised forum for the transfer of knowledge between Nobel Laureates and outstanding international talents. Anupam was nominated for this recognition by the International Human Frontier Science Program Organization as one of their most qualified young scientists. Congratulations Anupam !
3rd Annual Microscale Ocean Biophysics meeting was a success
The third edition of the Microscale Ocean Biophysics meeting in Aspen, Colorado, was a success! 90 scientists from different disciplines presented, discussed, and interacted for a week amidst winter activities. Congratulations to Kwangmin Son for receiving one of three best talk awards and to Steve (in close collaboration with Vicente) for receiving one of two best postdoc poster awards!
Postdoc Mehdi Salek wins Poster award
Postdoc Mehdi Salek’s poster “The mTm: A Microfluidic T-Maze for the Study of Chemotactic Decision Making in Microorganisms” was recently awarded 3rd place at the ASME International Mechanical Engineering Congress and Exposition in Montreal. Great job Mehdi!
Nikon Small World Photomicrography Competition
Postdoc Doug Brumley won 6th place in the Nikon Small World Photomicrography competition with his photo of the active fluid flow around a coral polyp. Congratulations Doug!
Anupam Sengupta wins the Glenn H. Brown Prize
Postdoc Anupam Sengupta wins the 2014 Glenn H. Brown Prize for pioneering contributions in the field of liquid crystals, specifically for his studies of liquid crystals in microfluidic environments. The prize is awarded every two years by the International Liquid Crystal Society. Anupam will deliver the award speech at Trinity College Dublin, Ireland, in July 2014. Congratulations Anupam!
Microscale Ocean Biophysics Meeting
Check out the third edition of the Microscale Ocean Biophysics meeting, to be held at the Aspen Center for Physics from Jan 12 to 16, 2015. More info can be found here:
Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations
New PNAS paper by the group demonstrates the importance of movement behavior in driving the differentiation of marine microbes.
Postdoc Anupam Sengupta awarded HFSP fellowship
Postdoc Anupam Sengupta has been awarded a 3-year fellowship from the Human Frontiers in Science Program (HFSP).
“Bacterial transport suppressed by fluid shear” published in Nature Physics
A new paper on the interplay between bacterial motility and fluid flow, with postdoc Roberto Rusconi as first author, just appeared in Nature Physics. Well done Roberto!
Image of coral flows appears on the cover of Science
A photograph taken by postdocs Vicente Fernandez and Orr Shapiro, illustrating the fascinating vortical flows that form on coral surfaces, won the NSF/AAAS Science and Technology Visualization Challenge and was featured on the cover of Science on Feb 7, 2014.
Postdoc Douglas Brumley receives the Block Award
Douglas attended the “Active Fluids: Bridging Complex Fluids and Biofluids” conference held at the Aspen Center for Physics, where he received the Block Award that is given to a promising young physicist. Well done, Douglas!
Gabriel Juarez gives talk at Aspen physics meeting
Gabe attended the Active Fluids: Bridging Complex Fluids and Biofluids where he gave a talk entitled “Life at the oil water interface: growth, colonization, and degradation of oil by microbes”.
Paper on turbulent fluid acceleration appears in Physical Review Letters
Article entitled “Turbulent Fluid Acceleration Generates Clusters of Gyrotactic Microorganisms” appeared in Physical Review Letters in the week ending January 31, 2014.
Congratulations Dr. Jang!
Hongchul Jang has successfully defended his thesis with a great presentation on bacterial biofilms! Hongchul is heading back to Korea, where he will be working for Samsung. Hongchul, we wish you and your family a happy move back home and good luck with the new start in Seoul!
Postdoc Vicente Fernandez attended the Sensory Transduction in Microorganisms Conference
Vicente recently participated as a Poster Presenter at the Gordon Research Seminars and the Gordon Research Conferences on Sensory Transduction in Microorganisms. Title of his presented poster was: Probing transient chemotactic responses in free-swimming bacterial populations.
Congratulations Dr. Barry!
Michael Barry has successfully defended his thesis with a very compelling presentation on phytoplankton motility! Mike will be working at Exponent in Massachusetts. Mike, we wish you all the best for your new responsibilities as an engineering consultant, and thanks for all the great contributions to the lab!
New Ph.D. Student Cherry Gao Joins the Lab
Welcome, Cherry! Cherry is a student in Biological Engineering, she is passionate about the environment (ask her about turtles!), and will look at genetically manipulating marine bacteria for optical reporting of DMSP degradation in a new generation of microfluidic devices.
Postdoc Anupam Sengupta Joins the Lab
Welcome on board, Anupam! Anupam is a mechanical engineer and physicist from India, he did his engineering degree at IIT Bombay, Ph.D. at the Max Planck Institute in Germany, and will be working on phytoplankton adaptations to physical cues, ordering and turbulence in in bacterial systems and will develop new microfluidic technology.
Paper on chemotaxis by coral pathogens appears in ISME Journal
A paper by the group, with postdoc Melissa Garren leading the charge, appeared in ISME Journal. The paper describes how coral pathogens can actively target coral hosts by chemotaxis, particularly for temperature-stressed hosts. We thank our collaborators from AIMS (Australia) and UTS (Sydney) for the joint work!
Postdoc Douglas Brumley Joins the Lab
Douglas is an applied mathematician from Australia, recently turned biophysicist! He did his Ph.D. at Cambridge University, and will be working on visualizing the flows generated by corals and how bacterial pathogens cope with the stormy environment on a coral surface. Welcome to MIT, Douglas!
Postdoc Kang Soo Lee Joins the Lab
Welcome, Kang! Kang is a mechanical engineer from Korea, he did his Ph.D. at Korea Advance Institute of Science and Technology (KAIST). He will be working on a new collaboration with Prof. Michael Wagner’s group at the University of Vienna on marrying microfluidics and Raman microscopy for cell sorting, as part of a U.S. Department of Energy Joint Genome Institute’s New Emerging Technologies Opportunity Grant.
Paper on phytoplankton in turbulence appears in Nature Communications
Who said that turbulence always mixes? Check out this paper showing that motility in turbulence can lead to un-mixing. Life looks pretty turbulent out there in the oceans! Congratulations to Mack Durham (former PhD student and now lecturer in Oxford) and Mike Barry, and to our collaborators in France and Italy.
Paper on flagellar buckling appears in Nature Physics
Kwangmin and Jeff’s paper in Nature Physics shows that marine bacteria reorient by causing the buckling of their flagellum. Pretty resourceful bugs out there in the Ocean!
We have a new lab manager: Welcome Becky!
Starting in August, we’ll have Rebecca Schilling taking good care of our lab: We’re thrilled by this new addition to the group!
Postdoc Gabriel Juarez wins first prize in MIT’s postdoc poster competition
Postdoc Gabriel Juarez wins first prize (and an iPad!) in MIT’s postdoc poster competition with an elegant, minimalistic poster on how marine bacteria find oil droplets. Gabe’s research aims to understand the biophysics of oil degradation.
Postdoc Filippo Menolascina to speak at the Cambridge Science Festival
Postdoc Filippo Menolascina will give a talk next Wednesday April, 17th on “What High School science should have been” in an event organized by the MIT Museum for the Cambridge Science Festival 2013.
Kick off time: 6pm. More info here. Go Filippo!
Postdoc Melissa Garren wins award at the École de Physique des Houches
Postdoc Melissa Garren wins the award for the best talk by a junior scientist at the second edition of the symposium on “Microscale Interactions in Aquatic Microenvironments”, held at the École de Physique des Houches, France. Melissa talked about the role of motility and chemotaxis in a coral pathogen.Congratulations Melissa!
Postdoc Gastón Miño joins the lab
Gastón is a physicist from Argentina and will be working in collaboration with Mimi Koehl and Nicole King, from the University of California Berkeley, on the role of motility and nutrient uptake in the evolution of multicellularity in choanoflagellats. Bienvenido Gastón!
Coral Work Appears in Physics Today
An image from our work on corals, showing the dramatic vertical flows produced by a coral’s cilia, appears on Physics Today “Backscatter”. Congratulations to Vicente Fernandez, Melissa Garren and Orr Shapiro.
Chemotaxis Review Paper Appears in MMBR
A comprehensive review of bacterial chemotaxis in the ocean by Roman Stocker and Justin Seymour appears in Microbiology and Molecular Biology Reviews. Justin is a former postdoc in the group and now a Senior Research Fellow at the University of Technology Sydney. An image of bacteria clustering around a diatom, by group members Steve Smriga, Kwangmin Son, Vicente Fernandez and Roman Stocker, appears on the cover.
Moore Foundation Selects Stocker as Research Investigator
Roman Stocker is selected as a Marine Microbiology Initiative Investigator by the Moore Foundation. This award will considerably enhance the lab’s abilities to investigate microbial processes in the Ocean over the next 5 years. Read full announcement.
NSF article on our work: ‘The Physics of the Ocean’s Tiniest Critters’
Roman answers NSF’s Jacqueline Conciatore’s questions on doing science, being inspired, and what to salvage if your lab goes up in flames.
Former PhD Student Mack Durham Delivers Acrivos Lecture at APS-DFD
Mack Durham delivers the Andreas Acrivos Dissertation Award lecture at the Division of Fluid Dynamics meeting in San Diego. This award recognizes “exceptional young scientists who have performed original doctoral thesis work of outstanding scientific quality and achievement in the area of fluid dynamics”. Mack’s thesis focused on “Phytoplankton in Flow” and he is now a lecturer at Oxford.
Lab Members attend APS Division of Fluid Dynamics Meeting
Seven from the Stocker group attends the American Physical Society Division of Fluid Dynamics meeting in San Diego, to present our work on bacterial motility and biophysical interactions among marine microbes.
Gabriel Juarez Wins Scholarship to Attend APS-DFD
Gabriel Juarez wins MIT postdoc travel scholarship to attend APS-DFD.
Ocean at MIT Website Features Stocker Lab
“Oceans at MIT” features a story on the lab’s focus on the hidden life of marine microbes.
“Marine microbes see a sea of gradients” Appears in Science
Roman’s review paper on microscale gradients appears in Science. The review, titled “Marine microbes see a sea of gradients”, highlights the importance of microscale processes in the ocean.
“Trade-Offs of Chemotactic Foraging in Turbulent Water” Appears in Science
John Taylor and Roman Stocker’s paper on the effects of turbulence on marine bacteria appears in Science. The paper, titled “Trade-offs of chemotactic foraging in turbulent water”, describes how turbulence affects the competition for nutrients among marine bacteria. John is a former postdoc and now a lecturer at Cambridge University.
Roman Participates in Ask An Engineer
Roman participates in “Ask an Engineer”, providing ideas for on how middle-school students can prepare for a career in Civil and Environmental Engineering
Roman Gives Squishy Physics Talk at Harvard
Roman gives Squishy Physics talk at Harvard on “Flagellar buckling and rheotaxis in bacteria”.
Postdoc Jeff Guasto to Join Faculty at Tufts University
Jeff Guasto secures a tenure-track faculty position in Mechanical Engineering at Tufts University, starting Sept 2013. Most deserved, Jeff: we will miss you, but are very excited for you!
Steve Smriga Awarded NSF Fellowship
Steve Smriga is awarded a 2-year Postdoctoral Research Fellowship from the Division of Ocean Sciences at NSF. We look forward to some exciting work together, Steve!
Lab Welcomes New PhD Student Bennett Lambert
Ph.D. student Bennett Lambert joins the lab. Ben is an Environmental Engineer from British Columbia and will be working on a collaboration with Rob Olson and Heidi Sosik at the Woods Hole Oceanographic Institution to design a microfluidic sorter and integrate it with the Imaging FlowCytobot, an automated submersible flow cytometer. Welcome, Ben!
Prof. Yvan Lagadeuc Joins the Lab
Prof. Yvan Lagadeuc from the University of Rennes, France, joins the lab for a one-year sabbatical, to work on luxury uptake in phytoplankton by integrating a new microfluidic approach and NanoSIMS imaging. Bienvenue Yvan!
Melissa Garren Wins the J.W. Costerton Award at ISME-14
Postdoc Melissa Garren wins the J.W. Costerton Award at ISME-14 in Copenhagen for “research that advances a new theory in microbial ecology that also has interdisciplinary significance”. Melissa’s poster was titled “The need for speed: A marine pathogen uses rapid chemotaxis and chemokinesis to target its host.” Well done, Melissa!
Yutaka Yawata Wins the Brock Postdoctoral Research Award at ISME-14
Postdoc Yutaka Yawata wins the Brock Postdoctoral Research Award at ISME-14 in Copenhagen for his talk “Mapping
genotypic diversity onto niche adaptation”. Omedetou, Yutaka!
Roman Gives Talk at ISME-14
Roman gives an invited talk at ISME-14 in Copenhagen on “Spying on the lives of marine microbes: The power of direct observation.”
Our new admin Ruth joins the group: welcome Ruth and we all look forward to working with you!
Orr Shapiro Wins Poster Award at Gordon Research Conference
Postdoc Orr Shapiro wins a poster award at the Gordon Research Conference on Marine Microbes at Il Ciocco, Tuscany, for his poster “Reef on a chip: Studying coral-pathogen interactions at the microscale”. Mazel tov, Orr!
Roman Gives Talk at Gordon Research Conference
Roman gives an invited talk at the Gordon Research Conference on Marine Microbes on “Bacterial Behavior in a sea of gradients.”
Our admin Roberta leaves us … grazie Roberta for all your help and buona fortuna for your new life in Italy!
Roman Gets Tenure
It’s been an exciting journey!!
Gabriel Juarez Joins the Lab
Gabriel Juarez joins the lab as a postdoc. Gabe is from Texas and studied physics. He will be working on bacteria-oil interactions.
Stocker Lab Gets a New Home
The Stocker lab gets a new home! We have moved and here is our new lab. We’re excited about this new space!
Swimming in Stratified Fluids Paper Appears in PNAS
Our paper on swimming in stratified fluids appears in PNAS. Roman collaborated with the group of Arezoo Ardekani, a former postdoc and now faculty at Notre Dame University.
Bacterial Rheotaxis Paper Appears in PNAS
Our paper on bacterial rheotaxis appears in PNAS. We show that hydrodynamic shear produced an unexpected torque on bacteria, making them drift across the flow due to the chirality of their flagella. This work was led by former Ph.D. student Marcos, now a faculty at NTU in Singapore, in collaboration with Henry Fu and Thomas Powers.
Melissa Garren Gives TedX Talk in Monterey
Postdoc Melissa Garren gives a TedX Talk in Monterey, California, on “The sea we have hardly seen”. Highly recommended!
Filippo Menolascina Joins the Lab
Postdoc Filippo Menolascina joins the lab. Filippo is a system biologist from Italy and will be working on bacterial chemotaxis, in a collaboration with Eduardo Sontag from Rutgers University. Benvenuto, Filippo!
Roman Co-organizes CEE Speed-Dating Event
Roman co-organizes the department’s research speed-dating event, the second episode of the Department of Civil and Environmental Engineering lightning-talks aimed at fostering research cross-fertilization. This year with jazz band!