Interactions between organisms, sediment, and microbial communities in coastal environments

Interactions between benthic and infaunal organisms, sediment, and microbial communities have shaped marine environments throughout Earth’s history. Bioturbation is the disturbance and reworking of sediment by living organisms. The field of ichnology studies these processes through trace fossils and their modern analogues, revealing how environmental factors like salinity, oxygenation, sedimentation rates, and substrate consistency influence the distribution and behaviour of infaunal and benthic organisms. Conversely, these organisms also often act as ecosystem engineers, modifying the physicochemical properties of their habitats through their activities, driving ecological and evolutionary innovation. The central theme of this thesis is the intersection between microbial mats, sediments, and bioturbating organisms. Microbial mats were among the earliest life forms, blanketing Precambrian shallow marine environments and driving the oxygenation of Earth’s atmosphere. Subsequently, the agronomic revolution marked the advent of penetrative bioturbation and the debut of the mixed layer, fundamentally altering marine substrates, facilitating new ecological niches, and leading to biogeochemical consequences. In this thesis, these themes are explored through distinct facets of these interaction through time. In Chapter 2, a new ichnogenus, Aratichnus, is described. Aratichnus is a horizontal, epichnial furrow ranging from simple straight to curved grooves to more complex serial furrows. It is documented in the lower Eocene-aged tidally reworked sandstone, the Baronia Formation, in Spain. This ichnogenus is interpreted as an interface deposit feeding exploiting the patchy food resources of an ancient intertidal environment. Chapter 3 is a comprehensive review of biostabilization in shallow marine siliciclastic environments. In this chapter, experiments aiming to quantify this effect are compiled and compared with the Shields’ diagram, measured and modelled values of shear stress in shallow marine environments, and occurrences of microbially induced sedimentary structures in marine environments in the rock record. The results show that this effect is considerably variable, ranging from 0.1 orders of magnitude beyond the Sheilds’ curve, to 4. This chapter demonstrated the complexity of biostabilization. Chapter 4 investigates the interactions between microbial mats and thalassinid shrimp on the tidal flats of northern Willapa Bay, Washington, USA, integrating geochemistry and spatial analysis. A high-resolution orthophotomosaic of the study area is generated from a 3D model constructed using aerial imagery captured by an unmanned aerial vehicle (UAV), enabling precise mapping of microbial mat distribution and shrimp burrow openings. A transect of four sites is established, spanning a continuum from fully bioturbated substrates to undisturbed, mat-covered sediments, with two intermediate zones exhibiting mixed biogenic and microbial signatures. At each site, sedimentological and ichnological characteristics are documented in situ, while porewater samples are collected using Rhizon samplers. The geochemical composition of these porewater samples is analyzed via inductively coupled plasma mass spectrometry (ICP-MS), providing insights into elemental composition. DNA sequencing of microbial mat samples identifies key taxa and metabolic pathways, linking community structure to environmental parameters. Spatial statistics reveal non-random distributions of shrimp burrows relative to mat boundaries, suggesting selective colonization behaviors. Results indicate that shrimp preferentially occupy transitional zones adjacent to microbial mats, a pattern interpreted as a trade-off between accessing mat-derived organic matter (enhancing food availability), exploiting biostabilized sediment (reducing burrow collapse), and avoiding mat-associated chemical stressors. These findings demonstrate the interplay between ecosystem engineering by thalassinid shrimp and the physicochemical legacy of microbial mats, offering a modern analogue for understanding historical shifts in benthic ecosystems during pivotal events like the agronomic revolution. Chapter 5 investigates the distribution of surface textures and ichnological features in the Bay of Fundy, Canada using UAV-derived orthomosaics. High-resolution aerial imagery enables quantitative analysis of sediment surface patterns, biogenic structures, and the spatial organization of benthic habitats across tidal environments. The study reveals distinct zones characterized by varying types of bioturbation and sediment texture and relates these patterns to environmental gradients such as salinity and hydrodynamic regime. This work demonstrates the power of remote sensing in advancing ichnological research and understanding the spatial ecology of modern trace-making communities. Together, these studies advance our understanding of how biogenic structures interact with structures sedimentary in both the modern and the geological record. By integrating methodologies, this thesis provides a multifaceted perspective on the feedback between biology and sedimentology, with broad implications for paleoenvironmental reconstruction, the interpretation of trace fossils, and the management of contemporary coastal ecosystems in a changing world.

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