SAME13 - Keynote Lectures


In this page you may find the list of all the invited lectures, their abstracts, and a short biosketch of each presenter:

16:30. Opening Lecture by Farooq Azam
Microbial structuring of oceanic carbon cycle: from molecular interactions to global ecosystem connectivity

17:15. Opening Lecture by Sinead Collins
Plastic fantastic

9:00. Invited Lecture by Toshi Nagata
Embedding microbial foodwebs into ocean biogeochemical models: challenges towards a global synthesis

14:00. Invited Lecture by Dagmar Wöbken
N2 fixation in coastal microbial mats: from the process level to single cells

9:00. Invited Lecture by Jakob Pernthaler

Opening Pandora's Black Boxes: what have they done to our "active" bacteria?

11:15. Invited Lecture by Rachel Foster
A symbiotic advantage: diatoms and cyanobacteria work together to make the most in a nitrogen deplete ocean

14:00. Invited Lecture by Roberto Danovaro
New insights on the diversity of marine viruses and their impact of on the functioning of the global biosphere

9:00. Invited Lecture by Mary Ann Moran
Metatranscriptomic probing of microzones and interfaces

9:00. Invited Lecture by Josep M. Gasol
Patterns of microbe abundance and diversity in the deep ocean: the circumnavigation cruise Malaspina2010

14:00. Invited Lecture by Jay Lennon
Microbial seed banks: ecological and evolutionary implications of dormancy

9:00. Invited Lecture by Christopher Marx
Growth of multi-species communities in time and space: predictions from genome-scale models

11:15. Closing Lecture by Roman Stocker
Keep looking: the power of direct observation in microbial ecology



Opening Lectures

farooqProf. Farooq Azam
Marine Biology Research Division, Scripps Institution of Oceanography 
University of California - San Diego (USA)

MICROBIAL STRUCTURING OF OCEANIC CARBON CYCLE: FROM MOLECULAR INTERACTIONS TO GLOBAL ECOSYSTEM CONNECTIVITY. Discoveries during the last several decades have shown that microbes play major roles in global ocean carbon cycle, and genomic and related approaches have been uncovering an incredible wealth of microbial diversity and potential for biochemical expression. Despite these huge advances we cannot yet predict how ecosystem perturbation (e.g. climate change, ocean fertilization, eutrophication, overfishing, or oil spills) will affect the role microbes play in structuring the carbon cycle of the future ocean. In order to meet this challenge we must understand the underlying regulatory mechanisms of system function and resilience and explicitly appreciate the importance of in situ biology of the microbes. Complexity and habit scale are major challenges in microbial ecology and I will discuss some recent and novel conceptual and methodological approaches. The role of nanoscale to microscale interactions of microbes in ecosystem structuring would benefit from converging next-gen -omics with "next-gen imaging" of biogeochemical dynamics. I will discuss the hypothesis that microbial communities are a major structuring force for ecosystem connectivity and resilience through cumulatively diverse metabolic interactions with the organic matter continuum. Such molecular-level integrative and mechanistic view that explicitly considers the microbe's habitat can help formulate new hypotheses and models to better predict future ocean biogeochemical variability and response to climate change. It may also contribute to the development of a "new microbial ecology".

Farooq Azam studies marine microbial biogeochemistry. He and his students and postdocs have been contributing to the mechanistic understanding of microscale interactions of pelagic microbes with the ocean carbon cycle and their consequences for large scale ecosystem functioning and response to system stress.



sineadDr. Sinead Collins 
School of Biological Sciences, University of Edinburgh (UK)
PLASTIC FANTASTIC. Marine microbes are the small but mighty foundations of marine ecosystems, the tiny drivers of nutrient cycles, and fascinating in their own right. As the ocean changes, they have the capacity to evolve because of their large population sizes and short generation times, but most studies measure physiological responses of phytoplankton to ocean acidification. Can we use this data to learn how future microbial communities will differ from contemporary ones? What do plastic and epigenetic responses tell us about microevolution? I will show what adaptive plastic responses tell us about evolutionary responses in the globally-distributed picoplankton Ostreococcus tauri, and how this is relevant to understanding marine microbial responses to global change. I will also discuss the (many) challenges and benefits of using marine microbes for the nefarious purposes of "hardcore" experimental evolution, and the current explosion of "softcore" microbial experimental evolution studies using marine phytoplankton.

Her main area of research is how adaptive evolution occurs over hundreds or thousands of generations in large populations, where complex ecology or genetics have to be taken into account. She uses experimental evolution in microbes, and applies her work to understanding long-term responses of phytoplankton to (complex) global change.She received a B.Sc in biochemistry in 1999 and a PhD in biology in 2006 from McGill University in Montreal, Canada. Following a postdoctoral project at the Max Plank Institute for Plant Breeding in Cologne, Germany, she obtained a fellowship from the Natural Environment Research Council (UK) and moved to the Institute of Evolutionary Biology (IEB) at the University of Edinburgh in 2007. In 2010, she was awarded a Royal Society University Research Fellowship and a European Research Council starting grant. Dr. Collins has authored publications that use experimental evolution to build theory that is relevant to biological oceanography, including the first published experiment on microalgal evolution in response to elevated CO2, for which she won a Quebec Science discovery of the year in 2005. Experimental evolution and biological oceanography have historically had little communication between them, and Dr. Collins is dedicated to linking the two fields through shared research and discussions. In 2011, she was awarded a Petersen professorship, which lets her hang out and do just that from time to time at the IFM-Geomar in Kiel, Germany. Dr. Collins has also has a podcast called “Ask Science Dude” that discusses current topics (gender, global change, tattoos…) though the lens of evolutionary biology.


Plenary Presentations


toshiProf. Toshi Nagata 
Atmosphere and Ocean Research Institute, University of Tokyo (Japan)

EMBEDDING MICROBIAL FOOD WEBS INTO OCEAN BIOGEOCHEMICAL MODELS: CHALLENGES TOWARDS A GLOBAL SYNTHESIS. During the past three decades, studies have demonstrated that the processing (transformation and degradation) of organic matter (OM) by microbial food webs consisting of bacteria, protists and viruses plays a major role in the regulation of biogeochemical cycles in the oceans. However, there have been surprisingly few studies that have explicitly incorporated microbial food web - OM interactions into global biogeochemical models. The present talk introduces the results of our study using a global three-dimensional numerical model of the ocean general circulation and biogeochemistry to evaluate how microbial processes and OM interact with each other and affect global marine biogeochemical cycles and productivity. The initial analysis of this model, including the results of sensitivity analyses, is then used as a basis for identifying the major gaps in our knowledge regarding the key microbial processes. Finally, I discuss how complex microbial interactions could be effectively embedded into the global models in order to improve our ability to predict responses of ocean biogeochemical cycles and ecosystems to global change.


Toshi Nagata is a Professor in the Department of Chemical Oceanography at Atmosphere and Ocean Research Institute, The University of Tokyo. He has earned degrees at Tokyo Metropolitan University (B.S. 1980) and Kyoto University (M.S. 1982, D.S. 1987).He serves on the Section Editor of Fundamental and Applied Limnology, the Editorial Board of Microbes and Environments and Microbial Ecology, the Review Editor of Aquatic Microbial Ecology and the Contributing Editor of Aquatic Biology. His current study focuses on organic matter-microbe interactions and the role of bacteria, viruses and protists in the regulation of material cycling in marine environments. In order to achieve the research goal, he uses microbiological, molecular, biogeochemical and isotopic approaches. He also collaborates with theoreticians and modelers to explore fundamental features in microbial loop functions across scales.

dagmarDr. Dagmar Woebken 
NanoSIMS Group - Department of Microbial Ecology
University of Vienna (Austria)

N2 FIXATION IN COASTAL MICROBIAL MATS: FROM THE PROCESS LEVEL TO SINGLE CELLS. Photosynthetic microbial mats are laminated, self-sustaining ecosystems with vast phylogenetic and functional diversity that exhibit steep physico-chemical gradients on the millimeter scale. N2 fixation is a key process in these mats that supports the nitrogen demands associated with high primary production. This process has been intensively studied for decades by biogeochemical assays and molecular approaches, such as the sequencing of the functional gene for N2 fixation (dinitrogenase reductase, nifH). However, N2 fixation can be regulated from the transcriptional to the post-translational level, thus the gene distribution or even expression might not accurately reflect the groups actively contributing to N2 fixation. As such the identity of the active diazotroph(s) in these ecosystems remains unknown.
In my talk I will describe how a multi-disciplinary functional approach enabled us to identify members of the diazotroph community that actively contributed to N2 fixation along with their associated degree of activity. We investigated two mat ecosystems: Elkhorn Slough, California, USA, and Laguna Ojo de Liebre, Mexico. N2 fixation activity was determined by biogeochemical assays. Potential diazotroph bacteria were identified by targeted nifH gene and transcript sequencing, in addition to general metatranscriptome sequence analysis. The in situ activity of identified bacteria with the genetic potential to fix N2 was tested by 15N2 incubation experiments and subsequent single-cell isotope analysis through nanometer-scale secondary ion mass spectrometry (NanoSIMS). Thereby we were able to combine measurements on the process level down to the single-cell level. We identified a previously unknown cyanobacterium as the major cyanobacterial diazotroph in the mats at Elkhorn Slough. Previous nifH-based investigations of mats at Laguna Ojo de Liebre suggested that visually dominant Lyngbya spp.-related cyanobacteria did not contribute to N2 fixation, rather members of the delta-proteobacteria contributed to this process. Our combined results could not support this hypothesis, but instead identified cyanobacteria related to Lyngbya spp. as the most active N2 fixing microorganisms in this mat type. This work demonstrates that the combination of biogeochemical, molecular and single-cell techniques are powerful tools to define key functional populations in complex microbial communities.

Dagmar Woebken is the Head of the NanoSIMS Group in the Department of Microbial Ecology at the University of Vienna, Austria. During her PhD at the Max Planck Institute for Marine Microbiology in Bremen, Germany, she focused on marine anaerobic ammonium oxidizing bacteria (anammox bacteria). Upon completion of her PhD, she investigated diazotrophy in coastal microbial mats using biogeochemical and molecular techniques combined with single cell NanoSIMS analysis at Stanford University in collaboration with the NASA Ames Research Center and the Lawrence Livermore National Laboratory in California, USA, as a DFG postdoctoral fellow. Dagmar joined the Department of Microbial Ecology at the University of Vienna as a group leader in early 2012. Her research group investigates active participants in the N and C cycle across terrestrial and aquatic ecosystems using a wide array of methods, but focusing on stable isotope probing, NanoSIMS and single cell techniques.
jakobProf. Jakob Pernthaler
Limnological Station, University of Zurich (Switzerland)

OPENING PANDORA'S BLACK BOXES: WHAT HAVE THEY DONE TO OUR "ACTIVE" BACTERIA? The determination of the bulk activities and production of bacterioplankton assemblages has formed a backbone of traditional aquatic microbial ecology in the context of carbon cycling and microbial food webs. With the rise of molecular techniques to identify microbial genotypes and their specific traits, these community-level analyses (often derogatively termed "black box" approaches) have increasingly fallen into disgrace. Undoubtedly, the resulting forests of phylogenetic trees, the microphotographs of green and orange dots, and the arcane multivariate statistical biplots have greatly promoted our conceptual understanding of microbial diversity, of the various pro-and eukaryote players in pelagic habitats and of their respective interactions. However, there are also things we might have lost in the fire of enthusiasm for microbial community composition and individual taxa. While there is no going back to concepts that ignore the differences between sympatric bacterioplankton populations (such as the notion of the 'active bacterial fraction') it might nevertheless be profitable to apprehend their respective roles in the biogeochemical processes that microbial ecologists used to study decades ago. In other words, it might be rather dark inside the "black box" without a simultaneous appreciation of the specific interactions between pelagic bacteria and their abiotic environment, both in qualitative and quantitative terms. Unfortunately, important aspects of this environment seem to represent yet another "black box", e.g., the composition and turnover of organic matter. Moreover, that box seems to be predominantly of interest for (geo)chemists, whereas microbial ecologists of late have primarily been flirting with bioinformaticians. Is it, therefore, time for a ménage a trois in aquatic microbial ecology?



I investigate the role and fate of different water column bacteria in freshwater and marine habitats in the context of food web structure and substrate availability. I study the effects of predator-induced mortality on the composition of microbial assemblages, and in the potential adaptations of microbial species to compensate or to avoid such losses.


rachelDr. Rachel Foster
Department of Biogeochemistry
Max Planck Institute for Marine Microbiology - Bremen (Germany)
A SYMBIOTIC ADVANTAGE: DIATOMS AND CYANOBACTERIA WORK TOGETHER TO MAKE THE MOST IN A NITROGEN DEPLETE OCEAN. Hemiaulus spp. diatoms with associated cyanobacterial Richelia intracellularis symbionts are widely distributed in tropical and subtropical seas where nutrient concentrations are low or often undetectable. Since the symbionts are heterocystous, and therefore capable of nitrogen fixation, the function of the symbiont for the host was presumed to supply fixed N to the host, but the degree to which the symbiont supports the growth of the host and the benefit to the symbionts was unknown. We use imaging by nanometer scale secondary ion mass spectrometry (nanoSIMS) on field populations of symbiotic Diatoms incubated with 15N2 and 13-bicarbonate to better understand the basis of the relationship. In addition, we use eukaryotic protein inhibitor to resolve the function of the host for the symbiont. In parallel we also estimate transcript abundance and recently identified significant differences in both genome size and content in the Richelia genome, compared to another diatom symbiont, Calothrix. Combined, the results are allowing us a better understanding of the activity and nutrient exchanges in the partnerships. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems.

My primary research focuses on the distribution, activity and diversity of marine microorganisms and their overall roles in ecosystem function. More specifically, I focus on open ocean phytoplankton populations important to Nitrogen and Carbon cycling, with a strong emphasis on planktonic symbioses. Many unicellular cyanobacteria form symbioses with diverse unicellular eukaryotes, which are a unique system to study as most other marine symbioses involve multi-cellular host partners. We know that nitrogen, carbon, and other nutrients (i.e. phosphorus, iron, vitamins) are exchanged between organisms but we know very little about how that exchange occurs or is regulated between the individual partners of marine symbioses. To study the in situ activity of marine microorganisms I use a combination of microscopic techniques with targeted molecular biological and isotope tracer assays. My research attempts to cross relevant ecological scales, where on a micro-scale, I identify the metabolic exchanges, diversity, genome content, and distribution of individual cells, while on a larger scale, I determine the contributions of these populations to biogeochemical cycling in the world’s oceans. Most recently I have been using nanometer scale secondary ion mass spectrometry (nanoSIMS) to identify and measure metabolic interactions and the brevity of nutrient exchanges between planktonic symbiotic partners. In addition, I use nanoSIMS to investigate the variation in metabolic activity of free-living cyanobacteria as it relates to their life history or phenotype, i.e. colonial vs single cells.

cristopherProf. Christopher Marx
Department of Organismic and Evolutionary Biology - FAS Center for Systems Biology
Harvard University (USA)

GROWTH OF MULTI-SPECIES COMMUNITIES IN TIME AND SPACE: PREDICTIONS FROM GENOME-SCALE MODELS. To what extent can principles of optimality be used to predict the behavior and evolution of metabolic systems? I will discuss the use of a particular framework for modeling metabolism, Flux Balance Analysis (FBA), and first consider the degree to which it predicts how metabolic fluxes will redistribute over the course of 50,000 generations of adaptation of Escherichia coli to glucose minimal medium. Second, I will describe our work evolving synthetic, multi-species consortia in spatially-structured environments. Here we have learned about the genetic basis of the emergence of costly, cross-species cooperation and are beginning to use a new framework that embeds FBA into a spatial environment to make predictions about growth of communities in space and time.

My broad research goal is to develop a degree of predictability to future evolutionary trajectories or ecological states based upon the internal physiological function of the organisms present.

Mary AnnDr. Mary Ann Moran 
Department of Marine Sciences, University of Georgia (USA)

METATRANSCRIPTOMIC PROBING OF MICROZONES AND INTERFACES. The biogeochemistry that occurs in microzones and interfaces is hard to measure with bulk approaches, since these average across microenvironments and have low sensitivity to rapidly-cycling and low concentration compounds. Bacterial gene expression patterns, however, can provide an instantaneous assessment of the ecological conditions experienced by cells, capturing the processes that are difficult to detect at the bulk level yet are important at the ecosystem, and even global, scale. We are using metatranscriptomics to explore the biogeochemistry of microzones and interfaces. These include studies of the differential activities of marine free-living versus particle-associated bacterial cells, and phycosphere-scale interactions between bacteria and phytoplankton.

Mary Ann Moran is a Distinguished Research Professor in the Department of Marine Sciences at the University of Georgia. She has earned degrees at Colgate University (B.A. 1977), Cornell University (M.S. 1982), and the University of Georgia (Ph.D. 1987). Dr. Moran is a Moore Foundation Investigator in Marine Microbiologya fellow of the American Association for the Advancement of Science and the American Academy of Microbiology, and a recipient of the American Society for Microbiology’s D.C. White Research and Mentoring Award. She serves on the editorial board of Applied and Environmental Microbiology, Environmental Microbiology, and mBio. Moran's research program focuses on the genetic basis of bacterial sulfur and carbon cycling in the ocean, with the goal of understanding the role of marine bacteria in the productivity of the coastal ocean and the formation and flux of climatically active gases. Her research uses molecular microbial ecology and ecological genomics approaches to explore bacterial processes and their regulation in seawater.



pepDr. Josep M. Gasol 
Aquatic Microbial Ecology Group, CSIC Institute of Marine Sciences - Barcelona (Spain)

PATTERNS OF MICROBE ABUNDANCE AND DIVERSITY IN THE DEEP OCEAN: THE CIRCUMNAVIGATION CRUISE MALASPINA-2010. During a global circumnavigation cruise (Malaspina-2010) held between November 2010 and July 2011 we had the opportunity to sample the deep waters of the North and South Atlantic, North and South Pacific, and Indian Oceans. We measured vertical profiles of microbe abundance and heterotrophic activity, and we studied specifically the distribution of microbial diversity at the depth of ca. 4000 m all through the studied oceans by means of ARISA and 16S-DNA Illumina tags (iTags). Two fractions were considered: <0.8 µm and >0.8 and <20 µm. We describe here the variability around the characteristic depth decline of microbial abundance and activity, with clear variations in different oceans and high microbe abundance and activity in waters near the equatorial upwelling of the Pacific Ocean. We also describe a large variability in microbial characteristics at this specific depth, in which we could also enumerate heterotrophic nanoflagellates by flow cytometry to be in the 5-40 cells ml-1 range. We explore the factors determining microbe abundance in the deep. Free-living deep ocean prokaryotic communities had a greater richness (number of 97% similarity OTUs) and diversity (Shannon and Chao diversity estimators) than particle-attached counterparts. Individual samples had comparable richness values to those found in surface communities (ranging from more than 300 to less than 1000 OTUs at the sequencing effort of 9800 reads/sample). On the contrary the overall richness of the dataset (accumulating all the samples) was very low (less than 4000 OTUs at the same sequencing effort) indicating that deep ocean prokaryotic communities are highly homogeneous and many OTUs are shared between different samples. Particle-attached and free-living prokaryotes were seen to highly differ in community composition. Specific prokaryotic phyla were detected to be consistently enriched in both size-fractions indicating that particle association is a life-style conserved at broad phylogenetic scales. Besides the size-fraction effect (i.e. within each set of samples belonging to the same size fraction), the geographical distance between locations arises as the main factor explaining community compositional differences, pointing out that dispersal limitation has probably played a key role structuring prokaryotic communities in the deep ocean.

Microbes are microbes... whether they bath in freshwater or in the ocean. I did my PhD in the world's lake likely with more papers per unit surface (Lake Cisó, it's only 20 m diameter...) and then a postdoc at McGill University in Montréal (here they have so many lakes that you can’t write a paper about just one…). Then I had the opportunity to get more salty at the Institut de Ciències del Mar in Barcelona, and I've been there since, working mainly in the ocean but with some freshwater incursions and even some work at hypersaline environments. If the environment is nice (and visiting it includes some nice sight- and bird-seeing) then I'll try to work on its algae, protists, bacteria, archaea and -not much, they are too small- viruses. I was jealous of the physical oceanographers that came to cruises with just a bunch of CDs to record the data and didn’t do practically any wet work, and when I discovered a machine called flow cytometer I decided it was as similar as possible to the physicists work so I decided to learn about it and try to push its limits for work with microbes. Now that I think of it, maybe this is also the reason why I’m lately interested in high-throughput sequencing. Stop being wet…

J LennonProf. Jay Lennon 
Department of Biology - Indiana University (USA)

MICROBIAL SEED BANKS: ECOLOGICAL AND EVOLUTIONARY IMPLICATIONS OF DORMANCY. Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions, including energy limitation. Dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. Thus, microbial dormancy may help maintain biodiversity and influence the stability of ecosystem processes. After introducing a theoretical framework for microbial seed banks, I will present results from a meta-analysis on the prevalence of dormancy in a variety of ecosystems, including oceans, lakes, soils, and the human gut. In addition, I will discuss results demonstrating the importance of dormancy for the maintenance of microbial diversity and ecosystem functioning. Finally, I will present ongoing which focuses on the mechanisms of bacterial resuscitation, and the implications of these processes under global climate change scenarios.


My laboratory focusses on the biotic and abiotic factors that generate and maintain microbial biodiversity. In turn, we seek to understand the implications of microbial diversity for ecosystem functioning. We tackle these problems using a variety of tools including molecular biology, simulation modeling, laboratory experiments, field surveys, and more.



RobertoProf. Roberto Danovaro 
Marine Sciences Department - Politechnical University of Marche (Italy)
NEW INSIGHTS ON THE DIVERSITY OF MARINE VIRUSES AND THEIR IMPACT OF ON THE FUNCTIONING OF THE GLOBAL BIOSPHERE. Viruses are by far the most abundant "life forms" in the world's oceans (approximately 4x1030 viruses), exceeding prokaryotic abundance by at least one order of magnitude. Increasing evidence indicates that viral infection may be responsible for the high mortality of autotrophic and heterotrophic organisms in surface oceans, with cascading effects on carbon cycling and nutrient regeneration. Viral lysis of infected microbes transforms their cell contents and biomass into organic detritus, which can influence the pool of organic carbon in the ocean and the pathways of organic matter diagenesis (viral shunt). Recent studies reported that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Similar processes have been reported for different very common and "extreme" habitats all over the world. It is increasingly evident that prokaryote-virus interactions and viral infections of larger life forms can regulate can regulate ecosystems' metabolism and functioning. Available information also suggests that marine viruses can influence directly and indirectly biogeochemical cycles, carbon sequestration capacity of the oceans and the gas exchange between the ocean surface and the atmosphere. Here I will provide novel information about viral diversity in oceanic biomes and discuss how marine viruses can influence global biogeochemical cycles, and the overall functioning of our biosphere.


Roberto Danovaro was born in Genoa (Italy in 1966) where he obtained the degrees in Marine Biology in 1988. RD discussed the PhD in Marine Environmental Sciences at the University of Pisa in 1993.After specialization in the field of environmental microbiology and experiences (both during the PhD and the post-doc) in various EU countries including Ireland (Galway), France (Roscoff), Belgium (Gent), Greece (Crete), RD became Assistant Professor in 1994 (University of Ancona), Associate Professor in 1998 (University of Bari) and Full Professor in 2001 (Polytechnic University of Marche). From 2004 to 2011 has acted as Director of the Department of Marine Sciences at the Polytechnic University of Marche and is currently Director of the Dept. of Life and Environmental Sciences. RD holds courses in Marine Biology (8 ECTS), Marine Ecology (8 ECTS) and Environmental Ethics (7 ECTS). Present academic activities include the membership to the Doctorate in Marine biology and Ecology and Master degree in Marine Biology. RD has been President of the Master Courses on Environmental Bioremediation and Biotechnologies and is President of the Course of Environmental sustainability and civil protection. RD is Pro-Rector  of the Scientific Research at the Polytechnic University of Marche. RD research is focused on deep-sea biodiversity and ecology with a synecologic and interdisciplinary approach dedicated to the identification of the links between ecosystem functioning and the production of goods and services.


Closing Lecture (Friday 13th)


stockerProf. Roman Stocker 
Department of Civil and Environmental Engineering
Massachusetts Institute of Technology (USA)

KEEP LOOKING: THE POWER OF DIRECT OBSERVATION IN MICROBIAL ECOLOGY. At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment.
New technologies, including microfluidics, high-speed video-microscopy and image analysis, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology. I will illustrate this 'natural history approach to microbial ecology' by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) nanometer-resolution imaging at thousand frames per second to demonstrate that marine bacteria can exploit a buckling instability in their flagellum to actively steer, and (ii) microfluidic techniques and experiments to capture the dramatic chemotactic abilities of bacterial pathogens towards the roiling surface of coral hosts. Through these examples, I aim to convince you that direct visualization can foster a new layer of understanding in microbial ecology.
Leveraging his quantitative background in engineering and applied mathematics, Stocker has pioneered the use of microfluidics in microbial oceanography. By using microfluidics to generate carefully controlled nutrient landscapes and flow conditions, Stocker’s research has addressed a long-standing challenge in microbial oceanography: to study marine microbes in the context of their immediate microenvironment.Through the fundamental understanding of small-scale biophysical processes in the ocean – such as diffusion, settling, turbulence, and microbial motility – Stocker has introduced several microfluidic model systems that have allowed an unprecedented level of resolution in the study of the oceans’ microscale. This approach, suitably coupled with mathematical modeling, has enabled among others the first experimental study of particle plume utilization by marine bacteria (Stocker et al, PNAS 2008), a characterization of the chemical signaling effects of important sulfur compounds within the microbial loop (Seymour et al, Science 2010), and a new hypothesis for the formation of thin phytoplankton layers (Durham et al, Science 2009). By straddling fluid mechanics and microbial ecology, Stocker brings a new perspective – both experimental (microfluidics) and conceptual (modeling) – to the understanding of marine microorganisms and their interactions. His current research group, which mixes researchers with backgrounds in microbiology, oceanography, engineering and physics, focuses on microbial motility and chemotaxis, on innovative microfluidic methods, and on quantitative, high-resolution imaging approaches. Current areas of strong interest include the in situ application of microfluidics in the ocean and the pursuit of the powerful handshake between microfluidic technology and omic approaches. In his spare time, he studies the biophysics of lapping in cats (Reis et al, Science 2010).