Session L01: Focus Session: Ecological Fluid Mechanics

Ecological Fluid Mechanics - Interactions among Organisms and their Fluid Environment

The presentation will introduce the focus session and define the topic of "Ecological Fluid Mechanics", which broadly is the study of how fluid motion and scalar transport mediate and influence the ecology of organisms. The session specifically addresses the role that fluid motion, flow gradients, and chemical stirring play in shaping organism behavior, interactions, recruitment, reproduction, and community structure. Relevant studies address a broad range of taxonomic groups and span topics of biomechanics, transport and settling, propulsion, and sensory ecology. Themes include the influence of instantaneous flow patterns, the influence of extreme physical events, the influence of scale on biological-physical coupling, and biological/ecological advantages mediated by flow and chemical transport. Methods span experimental, modeling, and computational efforts with flow regimes spanning creeping, laminar, unsteady, wavy, and turbulent flows.   

Microbial Navigation and Ecology in Flow Networks

Bacteria often thrive in flow networks, including branched microchannels, vascular systems, tissues, foams, and porous media. Instead of being advected downstream, microbes can swim upstream to reach nutrient sources and colonize favorable habitats. Here, we study experimentally and theoretically how bacteria navigate in these structured environments and actively construct niches surrounded by flows. First, we nanofabricated microfluidic networks with branching and looping architectures. Subsequently, we inoculated these devices with E. coli bacteria and mapped out their dynamics using single-cell tracking. We reveal that bacteria accumulate in specific areas of the network, governed by the currents in the surrounding network segments. By tuning these currents using flow network theory, we can control the bacterial motion and guide their population dynamics. Finally, we explore the ecology of multiple bacterial species in these flow networks and reveal how different architectures affect microbial coexistence, cooperation, and competition. Hence, we achieve programmable control for various functions, including species-specific depletion and accumulation, species sorting, structured community biofilm formation, and biomedical contamination prevention.   

Bacterial chemotaxis and dispersion in crowded environments

Swimming bacteria can adapt their swimming in the face of environmental cues and stresses. In response to nutrient gradients, bacteria lower their tumbling frequency when going up the gradients, leading to a net drift toward the nutrient source. In the presence of flows and in crowded environments, however, bacterial swimming patterns change. They get trapped near surfaces due to flow shear, and around obstacles due to hydrodynamic/steric interactions. While bacteria often live in such complex environments, our understanding of bacterial chemotaxis has mostly remained limited to simple environments with 1D steady nutrient gradients. Here, using microfluidic experiments and numerical simulations, we probe the role of chemotaxis in dynamic environments in the presence of flows and obstacles on bacterial colonization of nutrient sources. We discuss the implications of our observations for bacterial colonization of marine snow in the oceans and nutrient hotspots in the soil.    

Bacterial streamers formation and hydrodynamics of a rising oil droplet with natural seawater samples using ecology-on-a-chip (eChip) microfluidics

During the Deepwater Horizon oil spill, dispersant has been used to break up oil into small droplets within the water column, resulting in the generation of substantial quantities of submillimeter/submicron oil droplets. Most research focus on the transport and fate of pristine droplets. Recent studies reveal that bacteria is capable of forming extracellular polymeric substances (EPS) aggregates around individual droplet to increase its drag. However, the mechanism’s implications and the effect of dispersants in the real world scenario remains unclear. Here, we use eChip microfluidic that enables the observation of EPS streamer formation by natural microbial consortium on a rising oil droplet using natural seawater samples. By applying a layer-by-layer hydrophilic functionalization methodology, a single oil droplet can be pinned in the microfluidic channel, and natural seawater is flowed through the channel. Flow field around the oil droplet with streamers is obtained by micro-PIV with natural seeding. Control volume analysis provides instantaneous drag.   

How fluid flow influences colony formation and migration of cyanobacteria

Cyanobacterial colonies frequently cause toxic blooms in many freshwater bodies around the world. These suspended bacterial aggregates rely on their large size to achieve fast, density-regulated migration. Yet, the interaction between colony migration and hydrodynamics remains elusive. This study investigates how colony size and shape affect their movement and how fluid flow may induce fragmentation and aggregation of these colonies. We performed flotation velocity experiments on field samples of cyanobacterial colonies and showed that the colony settling factor and density are correlated with their size and morphology. Furthermore, cone-and-plate shear experiments were conducted on colonies to measure variations in size distribution under various flow stresses. Experiments are complemented by a theoretical formulation, where a two-category population model captured well the measured size distributions. Our results provide useful guidelines for prediction models and control techniques for toxic cyanobacterial blooms.   

Diatoms' Response to Quantified Turbulent Environments

Diatoms play important roles in the health of ocean ecosystems and carbon and nutrient cycling.  These unicellular phytoplankton absorb CO₂ and begin its transport from the atmosphere to the deep ocean through sinking. Diatoms likely sink to regulate a balance between sunlight absorption and access to nutrient uptake in the water. Previous studies of sinking behavior have shown that variables in their natural habitat affect diatoms’ sinking behavior, suggesting cells have the ability to respond to the environment around them. This study investigates the response of the diatom Coscinodiscus to different turbulent conditions to increase understanding of diatom behavior. Treatments mimic four natural environments: surf, inlet/estuaries, continental shelf, and open ocean. We will utilize a variety of methods adapted from studies that replicated natural turbulence to observe effects of hydrodynamic forces. Additionally, this study will build on previous research that identified significant differences in diatom sinking behavior after uncharacterized turbulence. Quantifying turbulence using dissipation rate and acceleration is essential to apply these results to larger oceanographic models and to better understand diatom sinking in the greater context of marine ecosystems.   

Plankton active response to turbulence suggests surfing strategy

Despite predominantly being thought to drift with the ocean currents, plankton may be able to enhance their transport in their swimming direction by taking advantage of certain flow features. For example, Monthiller et al., Phys. Rev. Lett. 129, 064502 (2022) recently theorized a “surfing’’ strategy, where plankton preferentially sample upwelling areas of the flow by simply sensing and reorienting in response to the local velocity gradients. Here, we present experimental evidence that suggests real plankton may in fact be able to surf turbulence. We study a planktonic larval snail as our model organism. By observing these plankton in a jet-stirred turbulence tank, we find that they have complex responses to velocity gradients, and that they tend to actively oppose the flow’s rotation. This is the opposite of what would be expected from passively rotating bottom-heavy plankton. This active orientational response is similar to the behavior of simulated surfing plankton, and suggests that real plankton may be able to surf turbulence.   

Spatial distribution of depth-directed swimmers within shallow flows

We investigate the behavior of swimming particles in a 3D shallow flow by numerical simulations and Lagrangian tracking. The particles swim vertically to reach a specific depth, either close to the bottom or the surface. This behavior is like that of bottom-dwelling zooplankton in shallow environments. In the horizontal, they strictly follow the flow which is confined to a thin fluid layer bounded vertically by rigid boundaries. The flow has a horizontal extent much larger than the layer depth and consists of several shallow vortices with updrafts in their cores and downdrafts at their peripheries. Statistics of particle positions and velocities reveal distinctive distribution patterns. The swimmers aiming to reach the lower depth accumulate in the updrafts, while the swimmers aiming to reach the upper depth accumulate in the downdrafts. The swimmers in the updrafts form tree-like structures that extend in the vertical direction, whereas swimmers in the downdrafts form thin structures that are elongated in the horizontal direction. The distribution patterns are a result of the interaction of the underlying flow features and the swimming capability of the particles, and they are reproduced using an idealized kinematic flow allowing us to explain the governing dynamics.   

Enhanced feeding with structural coordination of ciliary band and oral apparatus

Oceanic single-cell organisms, particularly ciliates, have specialized oral structures that facilitate nutrient absorption through phagocytosis. These organisms use ciliary bands around their oral surface to generate flow currents, driving nutrients toward their mouths. We previously showed that ciliary currents in both "swimming" and "sessile" organisms can be equally advantageous for feeding. But what are the advantages of having specialized oral structures? If a larger mouth, implying a larger absorbing surface, results in a greater nutrient encounter area, why do ciliates have specialized oral apparatuses occupying relatively small fraction of the cell surface? To address this question, we developed a mathematical model and systematically analyzed the feeding rates of ciliates with various oral apparatus and ciliary band sizes. Our model is based on Blake's envelope model and incorporates an advection-diffusion process of nutrient transport around the model ciliate. Our findings reveal that the feeding rate is enhanced when the ciliary band is positioned adjacent to the oral apparatus. Furthermore, we identified that the optimal designs maximizing feeding rates differ between sessile and motile ciliates. By integrating these results with intracellular nutrient transport mechanisms, our analysis bridges the understanding of outer and inner food transport mechanisms in single-celled ciliates. This study provides insights into the evolution of specialized functions and structures in eukaryotes, highlighting the collaborative adaptation of external and internal mechanisms for efficient nutrient acquisition.   

Thin-layer formation of spheroidal motile micro-swimmers in unsteady flow

Several meters below the ocean surface, thin layers of concentrated motile phytoplankton are ubiquitous and are responsible for high ecological activities. Gyrotactic trapping has been proposed as a potential mechanism for the layer formation of bottom-heavy swimming cells. Prior research has often simplified these active particles as small (~10 microns) spheres, thereby ignoring the influence of the size and the shape of the cell. Three open questions remain. First, how does the size of the swimmer affect the gyrotactic trapping? Second, how does the shape affect the gyrotactic trapping? Third, how does the transient trapping process interact with the time-varying background flow? In this study, we proposed a model that considers the effects of spheroidal shape on the competition between gravitational torque and viscous torque. Based on this model, we numerically investigated gyrotactic trapping in shear flow. Linear stability analysis was utilized to reveal a characteristic timescale of trapping. Subsequently, in time-varying shear flow, we identified three different regimes of thin layer formation. In sum, our findings highlight the importance of spheroidal shape for motile phytoplankton in flow and reveal that there are three mechanisms for thin layer formation in time-varying background flow.   

Zooplankton Aggregations Induced by a 2D Laboratory Model of Langmuir Circulation

Langmuir Circulation is a widespread form of wind shear-driven turbulence at the ocean surface made up of a series of counterrotating vortex pairs. The upwellings and downwellings within Langmuir circulation may concentrate vertically moving particles or plankton. In particular, upwards swimming zooplankton (e.g., copepods, daphniids, and mysids) matching the downwelling flow speed may be trapped and form aggregations within regions known as Stommel Retention Zones (SRZs). Here we investigate SRZ formation by mysids (Americamysis bahia) and daphniids (Daphnia magna) within a laboratory facility which creates a two-dimensional model of Langmuir circulation. Using light to induce upwards swimming, we measured zooplankton spatial distribution and swimming characteristics in simulated Langmuir Circulation of various flow strengths. At flow speeds which do not exceed their swimming capabilities, the mysids and daphniids aggregated in the downwelling, forming SRZs. At higher flow speeds, the zooplankton were more uniformly distributed as they were primarily advected by the flow. In order to investigate how Langmuir Circulation may affect trophic interactions, we also describe how the spatial distribution of the mysid is altered by the presence of prey.