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Articles by Roman Stocker
Alteromonas macleodii breaches the diatom frustule triggering protoplast emergence and programmed necrosis-like death in Thalassiosira rotula
Abstract Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. Although bacteria are increasingly recognised as important drivers of algal mortality, the diversity of algicidal strategies remains understudied. Here we show that Alteromonas macleodii, a recurrent member of Thalassiosira rotula’s microbiome, breaches the diatom’s silica frustule, inducing >95% of cells to emerge from their shells within 72 h, exposing protoplasts to lysis and exploitation.
Metabolic feedbacks drive population dynamics and can lead to oscillations among leaf bacteria
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Abstract Metabolic interactions are fundamental to the assembly and function of microbiomes. Yet, our understanding of how specific interaction mechanisms can drive broader ecological outcomes and population dynamics remains limited. Here, we monitor interactions resulting from plant oligosaccharide degradation by leaf-associated bacteria using a microfluidic device that enables direct cell observation and quantitative metabolite detection.
By Alan R. Pacheco, Giovanni Stefano Ugolini, Simon H. Rüdisser, Miriam Bortfeld-Miller, Patrick Kiefer, Franziska Oschmann, Samuel Charlton, Michael Berger, Tommaso Redaelli, Miguel Salazar, Ilija Dukovski, Olga T. Schubert, Martin Ackermann, Roman Stocker, Julia A. Vorholt, Andrea Zamuner, Jan Roelof van der Meer
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Nature
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The ecology of bacterial attachment to phytoplankton
Abstract Phytoplankton are responsible for approximately half of Earth’s net primary production and, together with heterotrophic bacteria—the main consumers of organic matter—play a pivotal role in biogeochemical cycles. Their key ecological importance has led to growing interest in the interactions between these two groups. Yet, our understanding of the microscale mechanisms driving these interactions remains limited.
The geologic history of marine dissolved organic carbon from iron oxides - Nature
Abstract Dissolved organic carbon (DOC) is the largest reduced carbon reservoir in modern oceans1,2. Its dynamics regulate marine communities and atmospheric CO2 levels3,4, whereas 13C compositions track ecosystem structure and autotrophic metabolism5. However, the geologic history of marine DOC remains largely unconstrained6,7, limiting our ability to mechanistically reconstruct coupled ecological and biogeochemical evolution.
Space, the final frontier: The spatial component of phytoplankton–bacterial interactions
1 INTRODUCTION Belying their minute size, marine microorganisms have an enormous effect on large-scale processes. For example, marine phytoplankton, through their collective photosynthesis, are responsible for almost 50% of global primary productivity and oxygen production (Field et al., 1998). Importantly, phytoplankton do not exist in isolation and it is known that these microalgae encounter and interact with other microorganisms, such as bacteria.
Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes (Adv. Sci. 20/2024)
Graphical Abstract Multiscale Porosity Micromodel In natural porous media such as living tissues, geological or industrial substrates, porosity spans multiple scales. M. Mehdi Salek, Joaquin Jimenez-Martinez, and co-workers developed a novel multiscale porosity micromodel that incorporates hydrogel features for studying fundamental processes in porous media and advancing various applications, from understanding organ functioning to improving environmental remediation techniques.
Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes
1 Introduction Porous media frequently show a multimodal distribution of pore sizes (void volumes within the total volume), often characterized by both macropore and micropore regions.
Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting - Nature Communications
Abstract Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin.
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria - The ISME Journal
Abstract Polysaccharide breakdown by bacteria requires the activity of enzymes that degrade polymers either intra- or extra-cellularly. The latter mechanism generates a localized pool of breakdown products that are accessible to the enzyme producers themselves as well as to other organisms. Marine bacterial taxa often show marked differences in the production and secretion of degradative enzymes that break down polysaccharides.
Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria - Nature Microbiology
Abstract Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell–cell interactions might not be possible between some of the most abundant organisms in the ocean.
Chemotaxis shapes the microscale organization of the ocean’s microbiome - Nature
Abstract The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1,2,3, but has never been examined comprehensively in situ among natural microbial communities.
Publisher Correction: The ecological roles of bacterial chemotaxis - Nature Reviews Microbiology
Cite this article Keegstra, J.M., Carrara, F. & Stocker, R. Publisher Correction: The ecological roles of bacterial chemotaxis. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00734-9 Download citation Published: 01 April 2022 DOI: https://doi.org/10.1038/s41579-022-00734-9 Share this article Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article.
A microfluidic platform for characterizing the structure and rheology of biofilm streamers
A microfluidic platform for characterizing the structure and rheology of biofilm streamers† Giovanni Savorana, a Jonasz Słomka, a Roman Stocker,a Roberto Rusconi bc and Eleonora Secchi *a Abstract Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults.
Trophic Interactions and the Drivers of Microbial Community Assembly
Summary Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function.
Constrained optimal foraging by marine bacterioplankton on particulate organic matter
Significance Patch use theory predicts that organisms foraging in a heterogeneous resource landscape balance their residence time on a patch yielding diminishing returns with the sum of the metabolic, predation, and opportunity costs of foraging. By combining single-cell tracking with mathematical modeling, we show that bacteria foraging on seascapes of organic particles switch between attached and planktonic lifestyles and tune the time spent on particles to increase individual fitness.
Chemotaxis under flow disorder shapes microbial dispersion in porous media
Abstract Natural soils are host to a high density1 and diversity2 of microorganisms, and even deep-earth porous rocks provide a habitat for active microbial communities3. In these environments, microbial transport by disordered flows is relevant for a broad range of natural and engineered processes, from biochemical cycling to remineralization and bioremediation4,5,6,7.
On the collision of rods in a quiescent fluid
On the collision of rods in a quiescent fluid Jonasz Słomka, Roman Stocker Proceedings of the National Academy of Sciences Feb 2020, 201917163; DOI: 10.1073/pnas.1917163117
Chain formation can enhance the vertical migration of phytoplankton through turbulence
Abstract Many species of motile phytoplankton can actively form long multicellular chains by remaining attached to one another after cell division. While chains swim more rapidly than single cells of the same species, chain formation also markedly reduces phytoplankton’s ability to maintain their bearing.
The role of microbial motility and chemotaxis in symbiosis
Abstract Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis.
Biofilm disruption by an air bubble reveals heterogeneous age-dependent detachment patterns dictated by initial extracellular matrix distribution
We studied the formation and disruption of controlled Pseudomonas aeruginosa PA01 biofilm patches on the glass bottom of a microfluidic channel (Fig. 1a). Biofilm patches formed by the preferential adhesion of P.
Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics
Xie, L., Altindal, T., Chattopadhyay, S. & Wu, X.-L. Bacterial flagellum as a propeller and as a rudder for efficient chemotaxis . Proc. Natl Acad. Sci. USA 108, 2246–2251 (2011). This study reported the discovery of the 'flick', a new reorientation mechanism found among marine bacteria, which makes their motility drastically different from the run-and-tumble motility observed in E. coli. Zhao, K. et al. . Nature 497, 388–391 (2013).
Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens
MB medium was made similar to the commercial Marine Broth 2216 medium (BD Biosciences, #279110), but in comparison shows no precipitate. Chemicals [g/L]: Peptone 5.0, yeast extract 1.0, ferric acid citrate 0.1, MgCl 6H O 12.6, Na SO 3.24, NaCl 19.45, CaCl 2H O 2.38, KCl 0.55, NaHCO 0.16, Na HPO 2H O 0.01, agar 17.7 (for agar plates only).
The Microbial Olympics 2016
We can now go live to our correspondent at the white-water canoe slalom complex, for a report on the day's events: There you have it, ladies and gentle-microbes, the 2016 canoe slalom medallists. We've seen bacteria from all corners of our watery planet compete in this exceptionally tumultuous Olympic course. And my golly, amidst all the rumours of new strategies to be unveiled at these games, the field did not disappoint. Indeed, these novel adaptations led to surprising upsets.
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