William M. Durham

Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers

Thin layers of phytoplankton are important hotspots of ecological activity that are found in the coastal ocean, meters beneath the surface, and contain cell concentrations up to two orders of magnitude above ambient concentrations. Current interpretations of their formation favor abiotic processes, yet many phytoplankton species found in these layers are motile. We demonstrated that layers formed when the vertical migration of phytoplankton was disrupted by hydrodynamic shear. This mechanism, which we call gyrotactic trapping, can be responsible for the thin layers of phytoplankton commonly observed in the ocean. These results reveal that the coupling between active microorganism motility and ambient fluid motion can shape the macroscopic features of the marine ecological landscape.

Biofilm Formation As a Response to Ecological Competition

Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us. Biofilm formation is commonly viewed as a cooperative enterprise, where strains and species work together for a common goal. Here we explore an alternative model: biofilm formation is a response to ecological competition. We co-cultured a diverse collection of natural isolates of the opportunistic pathogen Pseudomonas aeruginosa and studied the effect on biofilm formation. We show that strain mixing reliably increases biofilm formation compared to unmixed conditions. Importantly, strain mixing leads to strong competition: one strain dominates and largely excludes the other from the biofilm. Furthermore, we show that pyocins, narrow-spectrum antibiotics made by other P. aeruginosa strains, can stimulate biofilm formation by increasing the attachment of cells. Side-by-side comparisons using microfluidic assays suggest that the increase in biofilm occurs due to a general response to cellular damage: a comparable biofilm response occurs for pyocins that disrupt membranes as for commercial antibiotics that damage DNA, inhibit protein synthesis or transcription. Our data show that bacteria increase biofilm formation in response to ecological competition that is detected by antibiotic stress. This is inconsistent with the idea that sub-lethal concentrations of antibiotics are cooperative signals that coordinate microbial communities, as is often concluded. Instead, our work is consistent with competition sensing where low-levels of antibiotics are used to detect and respond to the competing genotypes that produce them.

Turbulent fluid acceleration generates clusters of gyrotactic microorganisms.

The motility of microorganisms is often biased by gradients in physical and chemical properties of their environment, with myriad implications on their ecology. Here we show that fluid acceleration reorients gyrotactic plankton, triggering small-scale clustering. We experimentally demonstrate this phenomenon by studying the distribution of the phytoplankton Chlamydomonas augustae within a rotating tank and find it to be in good agreement with a new, generalized model of gyrotaxis. When this model is implemented in a direct numerical simulation of turbulent flow, we find that fluid acceleration generates multifractal plankton clustering, with faster and more stable cells producing stronger clustering. By producing accumulations in high-vorticity regions, this process is fundamentally different from clustering by gravitational acceleration, expanding the range of mechanisms by which turbulent flows can impact the spatial distribution of active suspensions.

Microbial alignment in flow changes ocean light climate

The growth of microbial cultures in the laboratory often is assessed informally with a quick flick of the wrist: dense suspensions of microorganisms produce translucent “swirls” when agitated. Here, we rationalize the mechanism behind this phenomenon and show that the same process may affect the propagation of light through the upper ocean. Analogous to the shaken test tubes, the ocean can be characterized by intense fluid motion and abundant microorganisms. We demonstrate that the swirl patterns arise when elongated microorganisms align preferentially in the direction of fluid flow and alter light scattering. Using a combination of experiments and mathematical modeling, we find that this phenomenon can be recurrent under typical marine conditions. Moderate shear rates (0.1 s−1) can increase optical backscattering of natural microbial assemblages by more than 20%, and even small shear rates (0.001 s−1) can increase backscattering from blooms of large phytoplankton by more than 30%. These results imply that fluid flow, currently neglected in models of marine optics, may exert an important control on light propagation, influencing rates of global carbon fixation and how we estimate these rates via remote sensing.

Microbial competition in porous environments can select against rapid biofilm growth

Significance The overwhelming majority of bacteria live in porous environments, like soil, aquifers, and sediments, where they facilitate many important processes. Despite their importance, we understand little about how these complex environments shape the composition of the microbial communities that live within them. Here, we combine two diverse bodies of theory—fluid dynamics and game theory—to shed light on how bacteria evolve in these habitats. We show that bacteria in porous environments face a fundamental dilemma: they rely on flow for nutrients and dispersal; however, as cells grow, they tend to reduce their access to flow. A fast growing strain can, therefore, choke off its own nutrient supply, diverting it instead to competitors. In contrast with classical theory, our results suggest that cells within a biofilm can obtain a competitive advantage by growing more slowly. Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow–biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.

Tumbling for Stealth

A green alga changes its flagellar beating patterns to create a run-and-tumble motion that may help it escape predation. One of the most remarkable and pervasive feats in the microscopic world is the coordination of flagella, the slender, whiplike structures that protrude from many types of cells. The collective motion of flagella (also known as cilia when they occur in large numbers in eukaryotes) drives fluid transport (1), and permits individuals to save energy through cooperation (2). Because the internal structure of cilia is highly conserved among eukaryotes from algae to humans, free-swimming organisms like Chlamydomonas (see the first figure, panel A) have long been powerful model systems (3). On page 487 of this issue, Polin et al. (4) show how synchronization of the flagella in Chlamydomonas reinhardtii governs the movement of this green alga through water, a key determinant of its ecological fitness.

Single-cell twitching chemotaxis in developing biofilms

Significance Bacterial biofilms affect many aspects of our lives, from causing disease to promoting health and shaping many key processes in the environment. Despite this, surface-attached cells in biofilms are often portrayed as static and sluggish, a stark contrast to the energetic swimming they exhibit in liquid. Here we use microfluidic devices and automated cell tracking to challenge this view: We find that individual cells will actively move toward nutrients within a developing biofilm. This ability not only allows cells to seek out favored positions on a surface but our analyses show that they can regulate their movement with remarkable submicron precision. Our findings suggest we can systematically engineer biofilms by manipulating the movement of the cells from which they are founded. Bacteria form surface-attached communities, known as biofilms, which are central to bacterial biology and how they affect us. Although surface-attached bacteria often experience strong chemical gradients, it remains unclear whether single cells can effectively perform chemotaxis on surfaces. Here we use microfluidic chemical gradients and massively parallel automated tracking to study the behavior of the pathogen Pseudomonas aeruginosa during early biofilm development. We show that individual cells can efficiently move toward chemoattractants using pili-based “twitching” motility and the Chp chemosensory system. Moreover, we discovered the behavioral mechanism underlying this surface chemotaxis: Cells reverse direction more frequently when moving away from chemoattractant sources. These corrective maneuvers are triggered rapidly, typically before a wayward cell has ventured a fraction of a micron. Our work shows that single bacteria can direct their motion with submicron precision and reveals the hidden potential for chemotaxis within bacterial biofilms.

Microfluidics with fluid walls.

Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method — Freestyle Fluidics — that overcomes many key limitations. In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications — triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.

Division by fluid incision: Biofilm patch development in porous media

Division by fluid incision: Biofilm patch development in porous media W. M. DURHAM1,2*, O. TRANZER1,3, A. LEOMBRUNI1,4,5, K. Z. COYTE6 AND R. STOCKER1 1 Department of Civil and Environmental Engineering, MIT, Cambridge, Massachusetts, USA (*correspondence: william.durham@zoo.ox.ac.uk) 2 Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK 3 Ecole Polytechnique, 91128 Palaiseau, France 4 DIIAR SEZIONE C.I.M.I., Politecnico di Milano, 20133 Milano, Italy 5 Regenesis Ltd, Bath BA1 5BB, UK 6 Centre for Mathematical Biology, Mathematical Institute, University of Oxford, OX1 3LB

Correction: Biofilm Formation As a Response to Ecological Competition

Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us. Biofilm formation is commonly viewed as a cooperative enterprise, where strains and species work together for a common goal. Here we explore an alternative model: biofilm formation is a response to ecological competition. We co-cultured a diverse collection of natural isolates of the opportunistic pathogen Pseudomonas aeruginosa and studied the effect on biofilm formation. We show that strain mixing reliably increases biofilm formation compared to unmixed conditions. Importantly, strain mixing leads to strong competition: one strain dominates and largely excludes the other from the biofilm. Furthermore, we show that pyocins, narrow-spectrum antibiotics made by other P. aeruginosa strains, can stimulate biofilm formation by increasing the attachment of cells. Side-by-side comparisons using microfluidic assays suggest that the increase in biofilm occurs due to a general response to cellular damage: a comparable biofilm response occurs for pyocins that disrupt membranes as for commercial antibiotics that damage DNA, inhibit protein synthesis or transcription. Our data show that bacteria increase biofilm formation in response to ecological competition that is detected by antibiotic stress. This is inconsistent with the idea that sub-lethal concentrations of antibiotics are cooperative signals that coordinate microbial communities, as is often concluded. Instead, our work is consistent with competition sensing where low-levels of antibiotics are used to detect and respond to the competing genotypes that produce them.