excavate_codes

This is the code to solve the Navier Stokes for foraging Excavate flagellates, as described in Foraging mechanisms in Excavate flagellates shed new light on the functional ecology of early eukaryotes to appear in PNAS.</p

Trade-offs in flagella propulsion, feeding and stealth*

Flagellates are key components of aquatic microbial food webs. Their flagella propel the cell through the water and generate a feeding current from which bacterial prey is harvested. However, the activity of the flagella also disturbs the ambient water, thereby attracting the flagellate’s flow-sensing predators. Here we use computational fluid dynamics to explore the optimality and fluid dynamics of the diverse arrangements, beat patterns, and external morphologies of flagella found among free-living flagellates in light of the fundamental propulsion-foraging-predation-risk trade-off. We examine 5-μm-sized representative model organisms with different resource acquisition modes: autotrophs relying on photosynthesis and uptake of nutrient molecules, phagotrophs that feed on bacteria, and mixotrophs that employ both strategies. For all types, the transport of inorganic molecules is diffusion dominated, and the flagellum in autotrophic species therefore mainly serves propulsion purposes. Flagellates with a single, naked flagellum found among non-foraging swarmer stages have a waveform (less than one wave) that is optimized for swimming and stealth but inefficient for feeding. Flagellates with a hairy flagellum typically have many waves, which optimizes swimming and stealth but is suboptimal for foraging, leading to a design trade-off. However, when compared with naked flagella, the presence of hairs allows an efficient feeding current, making these primarily phagotrophic flagellates the most efficient and dominant bacterivores in the ocean. Autotrophic biflagellates have wave patterns optimized for both propulsion and foraging but conflicting weakly with stealth. Finally, the mixotrophic haptophytes are optimized for foraging, conflicting with both stealth and propulsion. This is largely due to the long haptonema that improves prey collection but at the cost of stealth and propulsion

Hydrodynamics of Prey Capture and Transportation in Choanoflagellates

Choanoflagellates are unicellular microscopic organisms that are believed to be the closest living relatives of animals. They prey on bacteria through the act of the continuous beating of their flagellum, which generates a current through a crown-like filter. Subsequently, the filter retains bacterial particles from the suspension. The mechanism by which the prey is retained and transported along the filter remains unknown. We report here on the hydrodynamic effects on the transportability of bacterial prey of finite size using computational fluid dynamics. Here, the loricate choanoflagellate Diaphaoneca grandis serves as the model organism. The lorica is a basket-like structure found in only some of the species of choanoflagellates. We find that although transportation does not entirely rely on hydrodynamic forces, such forces positively contribute to the transportation of prey along the collar filter. The aiding effects are most possible in non-loricate choanoflagellate species, as compared to loricate species. As hydrodynamic effects are strongly linked to the beat and shape of the flagellum, our results indicate an alternative mechanism for prey transportation, especially in biological systems where having an active transport mechanism is costly or not feasible. This suggests an additional potential role for flagella in addition to providing propulsion and generating feeding currents