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.
Proposed by Jeanette Wheeler 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.
The podcast aims at young women to inform and motivate them to get into engineering. If you are curious about why Dorothee Kurz 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 Lüthy 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 Naudascher 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 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 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
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.
Luiz G. M. Silva 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.
Sam Charlton was awarded a prestigious Marie Skłodowska-Curie Fellowship to investigate the biophysical processes controlling biofilm hydraulic resistance. Congratulations Sam!
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 (10vor10), highlighting the risk posed by poorly ventilated indoor environments, particularly in case of prolonged exposure. See also SRF Espresso.
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!
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 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.
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.
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.
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.
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.
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
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.
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!
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!!!
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!
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!
Kang Soo Lee won the Poster Award at the seventh International Conference on Advanced Applied Raman Spectroscopy “RamanFest 2019” organized by HORIBA. Congratulations Kang!
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!
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!
Andres Velasquez (SEP group) received the Procter & Gamble Student Poster Award at InterPore 2019 (Valencia, Spain). Congratulations Andres!
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!
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.
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 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
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
Eleonora Secchi has been awarded a prestigious PRIMA Grant to work on biofilm formation in flow – congrats Eleonora!
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!
François Peaudecerf was awarded a prestigious Marie Curie Fellowship to work on bacteria-bubble interactions – congrats François!
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”
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
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
Anupam and Francesco’s paper on shape-shifting phytoplankton in turbulence appears in Nature. Congratulations!
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.
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.
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!
Welcome Jeanette, our first female postdoc
Ben Lambert and Steven Smriga each gave talks at the 2016 Ocean Sciences Meeting in New Orleans, USA.
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!
A 10 min video from KIKIM Media about research in the Stocker lab (sponsored by the Moore Foundation)
‘Live from under the lens’: Our review article on microbial motility and microfluidics appears in Nature Reviews Microbiology. Congratulations to Kwangmin and Doug!
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!
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!
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!
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 !
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’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!
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!
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 has been awarded a 3-year fellowship from the Human Frontiers in Science Program (HFSP).
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!
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.
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!
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”.
Article entitled “Turbulent Fluid Acceleration Generates Clusters of Gyrotactic Microorganisms” appeared in Physical Review Letters in the week ending January 31, 2014.
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!
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.
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!
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.
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.
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!
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!
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.
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.
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!
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 (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 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 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!
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!
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.
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.
Roman answers NSF’s Jacqueline Conciatore’s questions on doing science, being inspired, and what to salvage if your lab goes up in flames.
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.
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.
“Oceans at MIT” features a story on the lab’s focus on the hidden life of marine microbes.
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.
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.
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 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!
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 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!
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!
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!
Our new admin Ruth joins the group: welcome Ruth and we all look forward to working with you!
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 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!
It’s been an exciting journey!!
Gabriel Juarez joins the lab as a postdoc. Gabe is from Texas and studied physics. He will be working on bacteria-oil interactions.
The Stocker lab gets a new home! We have moved and here is our new lab. We’re excited about this new space!
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.
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.
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!