Abstract
Marine biofluidics is the study of how organisms interact with their fluid environments at the intersection of biology and fluid physics. An integrative field, it addresses fundamental and applied questions about the feedbacks that connect physical and biological characteristics of the ocean, and how these interact with other processes such as chemical cycling. The research described in this dissertation advances both fundamental understanding and practical application of marine biofluidics. Specifically, I studied how burrowing organisms pump oxygenated water through burrows change the chemical characteristics of coastal sediments, and how this mediated by water temperature. I also studied how biofilm growth creates drag on aquatic surfaces, with an emphasis on ship hulls for which this drag has enormous economic consequences.
Burrowing organisms play a central role in shaping the chemical characteristics of coastal sediments by pumping oxygenated water through burrows into what would otherwise be an anoxic environment. In cohesive sediments, oxygenated burrow water allows for the diffusive flux of oxygen across the burrow wall and into the sediment, where it is consumed. In a series of laboratory experiments, I used particle image velocimetry (PIV), planar optodes, and a transparent mud analog that I developed to measure the water movements and oxygenation patterns in and around the burrows of a common coastal polychaete, the nereid Alitta succinea.
The polychaete ventilates its burrows through undulatory pumping, but this activity is periodic, resulting in pulses of oxygen flux across the burrow wall and into the sediments. The frequency and magnitude of pumping (and hence oxygen pulses) depends strongly on water temperature. I found that the volume of oxygenated sediment, as well as the pattern of oxygenation that sediment experiences, vary substantially due to seasonal shifts in water temperature, but that total oxygen flux remains relatively uniform. Collectively, my results demonstrate that animal behavior can cause dramatic changes in the chemical environment of sediments and that these processes are tied to environmental parameters such as water temperature, which is changing in many regions across the planet.
Biofilms are bacterial and algal cells that form a thin layer on most aquatic surfaces including streambeds, coral reefs, and ship hulls. Biofilms are known to impact the dynamics of the fluid environment, for example increasing skin friction on surfaces, but the processes contributing to this are poorly quantified. In this dissertation, I studied the impact of biofilm fouling on boundary layer flow structure at moderate, ship-relevant Reynolds numbers. Specifically, I measured the characteristics of the turbulent boundary layer over diatomaceous-slime-fouled plates using high resolution PIV. The mean velocity profile over biofilm has a large downward shift due to momentum extracted from the flow, and higher friction velocity and drag coefficient compared to a control plate with no biofilm. Due to the complex nature of the biofilm’s topography, the Reynolds shear stress, turbulence production, and dispersive stress is highly heterogeneous in the streamwise direction. The strength of instantaneous turbulent events also increased, enhancing vertical momentum transport to and from the biofilm, and the bed, if exposed. Collectively, these processes increase the effective roughness of a surface significantly more than the physical thickness of the biofilm. Patchy biofilms have the greatest increase in near- bed turbulence production, dispersive stresses, and rotational flow, compared with a uniform biofilm or a sparse biofilm. Uniform biofilm, however, increases the drag coefficient of the bed more than patchy biofilms. These results contribute to understanding the mechanisms that fuel biofilm growth on diverse surfaces by bringing nutrients to and removing metabolites from the organism. They also have immediate importance for understanding biofouling impacts on ships and autonomous underwater vehicles. Specifically, my results show that percent cover of a biofilm is a good indicator of the effect of a biofilm on ship performance and could be used to schedule optimal cleaning frequencies.
