Presented By: Ecology and Evolutionary Biology
EEB Student Dissertation Defense - Microbial Diversity and Dynamics in Lake Food Webs: Species Interactions, Life History Strategies, and Community Reassembly
Nikesh Dahal, PhD Candidate, Denef Lab
Dissertation Abstract:
Understanding the processes involved in biodiversity maintenance and species coexistence is a central goal of community ecology. Lakes have long served as focal systems for exploring this puzzle, as they harbor high microbial diversity despite their relatively stable and homogeneous appearance—a paradox that challenges classical formulations in ecological theory. A significant body of work suggests that steady states are exceptions rather than the norm in natural lakes. This dissertation engages with this theme by investigating microbial community diversity and dynamics in the context of cross-scale species interactions, microbial life-history strategies, and ecological memory. Together, the chapters explore how general ecological principles play out in particular contexts—especially under heterogeneous environmental conditions and shifts in food web structures.
This is a hybrid event.
Join remotely: https://umich.zoom.us/j/99854884233
Meeting ID: 998 5488 4233
In Chapter 2, I examine the direct impacts of predation by introduced Dreissenid mussels on bacterial abundance, diversity, and composition in two regions of the Laurentian Great Lakes—Lake Erie’s western basin and Saginaw Bay in Lake Huron. While these mussels are known to exert strong top-down controls in lakes, including microbial communities, through filter-feeding, I find their impacts to be variable. In some cases, mussels significantly reduced microbial diversity; in others, their impacts were minimal or absent. Moreover, I find that resistance to predation was structured at a shallower phylogenetic depth than previously reported in the low-nutrient Lake Michigan. These results highlight the role of context dependency and natural history in shaping animal-microbe interactions beyond host-microbiome systems.
Chapter 3 explores whether the observed shifts in microbial community structure and diversity can be explained through growth-defense theory. This canonical theory in ecology assumes that organisms face fundamental trade-offs due to differences in allocation strategies under resource-limited conditions. Using metagenomic methods, I compare microbial populations resistant to mussel predation with those that are susceptible. I find no evidence for the emergence of resistance at the cost of growth. Instead, resistance emerges as a complex trait, shaped by varying patterns across phylogenetic, molecular, and broad functional levels. These results suggest that heterogenous environmental conditions in natural lakes may relax trade-off constraints in bacterial trait evolution, as trade-off frameworks often rely on a priori assumptions about the tendency of ecosystems to move toward steady-state conditions.
Chapter 4 turns toward ecological memory. Using a common garden mesocosm setup, which controls for the environmental differences between treatments by exposing them to the same background, I test whether the historical presence of mussels alters microbial community reassembly following environmental perturbation. I sampled six temperate lakes from southeast Michigan, three lakes with a history of mussel presence and three without. Microbial communities from lakes with and without mussels followed distinct reassembly trajectories. Moreover, shifts in community structure translated into shifts in function, indicating that the ecological memory of food web interactions leaves historical imprints with implications for broader ecosystem functioning.
Across chapters, my findings raise questions about the universality of equilibrium-based theories in ecology. These studies show that microbial diversity emerges from the dynamic interplay between context-dependency, functional traits, and historical imprints of species interactions. While grounded in experimental and genomic methods, this dissertation also critically engages with some foundational concepts in ecological theory (Chapters 1 and 5). In doing so, it gestures toward a broader philosophical tension in ecological thought: the inherent complexity of biodiversity and the challenges associated with its abstraction (Chapter 6).
Understanding the processes involved in biodiversity maintenance and species coexistence is a central goal of community ecology. Lakes have long served as focal systems for exploring this puzzle, as they harbor high microbial diversity despite their relatively stable and homogeneous appearance—a paradox that challenges classical formulations in ecological theory. A significant body of work suggests that steady states are exceptions rather than the norm in natural lakes. This dissertation engages with this theme by investigating microbial community diversity and dynamics in the context of cross-scale species interactions, microbial life-history strategies, and ecological memory. Together, the chapters explore how general ecological principles play out in particular contexts—especially under heterogeneous environmental conditions and shifts in food web structures.
This is a hybrid event.
Join remotely: https://umich.zoom.us/j/99854884233
Meeting ID: 998 5488 4233
In Chapter 2, I examine the direct impacts of predation by introduced Dreissenid mussels on bacterial abundance, diversity, and composition in two regions of the Laurentian Great Lakes—Lake Erie’s western basin and Saginaw Bay in Lake Huron. While these mussels are known to exert strong top-down controls in lakes, including microbial communities, through filter-feeding, I find their impacts to be variable. In some cases, mussels significantly reduced microbial diversity; in others, their impacts were minimal or absent. Moreover, I find that resistance to predation was structured at a shallower phylogenetic depth than previously reported in the low-nutrient Lake Michigan. These results highlight the role of context dependency and natural history in shaping animal-microbe interactions beyond host-microbiome systems.
Chapter 3 explores whether the observed shifts in microbial community structure and diversity can be explained through growth-defense theory. This canonical theory in ecology assumes that organisms face fundamental trade-offs due to differences in allocation strategies under resource-limited conditions. Using metagenomic methods, I compare microbial populations resistant to mussel predation with those that are susceptible. I find no evidence for the emergence of resistance at the cost of growth. Instead, resistance emerges as a complex trait, shaped by varying patterns across phylogenetic, molecular, and broad functional levels. These results suggest that heterogenous environmental conditions in natural lakes may relax trade-off constraints in bacterial trait evolution, as trade-off frameworks often rely on a priori assumptions about the tendency of ecosystems to move toward steady-state conditions.
Chapter 4 turns toward ecological memory. Using a common garden mesocosm setup, which controls for the environmental differences between treatments by exposing them to the same background, I test whether the historical presence of mussels alters microbial community reassembly following environmental perturbation. I sampled six temperate lakes from southeast Michigan, three lakes with a history of mussel presence and three without. Microbial communities from lakes with and without mussels followed distinct reassembly trajectories. Moreover, shifts in community structure translated into shifts in function, indicating that the ecological memory of food web interactions leaves historical imprints with implications for broader ecosystem functioning.
Across chapters, my findings raise questions about the universality of equilibrium-based theories in ecology. These studies show that microbial diversity emerges from the dynamic interplay between context-dependency, functional traits, and historical imprints of species interactions. While grounded in experimental and genomic methods, this dissertation also critically engages with some foundational concepts in ecological theory (Chapters 1 and 5). In doing so, it gestures toward a broader philosophical tension in ecological thought: the inherent complexity of biodiversity and the challenges associated with its abstraction (Chapter 6).
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