Habitat filtering at multiple scales : a case study with crab-associated microbial communities

Local diversity is the result of colonization from a species pool and local habitat filters. The relative contribution of these processes delineates our ability to predict changes in biodiversity, key in a changing world. Although theory suggests that these interactions are critical for the maintenance of biodiversity, empirical work has been restricted by limitations of studies across biogeographical regions and laboratory microcosms. Alternatively, host-associated microbial communities represent discrete, tractable and replicable assemblages. Hosts provide distinct habitat patches with different habitat filters and are surrounded by environmental bacteria that determine the regional species pools. My dissertation focuses on colonization and habitat filtering processes driving species composition of microbial communities associated with coastal crabs. First, I investigated colonization from the water column and filtering associated with the striped shore crab (Pachygrapsus transversus). Using a field experiment I asked whether species pool size interacts with habitat filters to structure microbial communities. Results indicated that the carapace was a stronger filters than the surrounding surfaces and are thus less influenced by changes in the regional species pool. Next, I examined whether the temporal scale of convergence and divergence in community composition was habitat dependent. In a mesocosm experiment, gut communities converged in community composition while carapace communities converged at day 8 and diverged thereafter. These findings indicate that the gut represents a strong filter when compared to carapace habitats, whose communities were driven by species interactions during biofilm formation. Second, I investigated whether multiple colonist pools can influence microbial communities. In a field study, I found that surface and burrow sediment colonize fiddler crab gut and carapace communities To better understand the interaction between multiple colonist pools and habitat filters, I used a mesocosm experiment where I manipulated sediment bacteria. While carapace communities were influenced by burrow sediment, removing bacteria from the surface also impacted carapace microbial composition. In contrast, gut communities responded weakly to colonist pool manipulations suggesting strong filtering. These findings highlight complex interactions between local communities and colonist pools. Importantly, identifying when multiple colonist pools or habitat filters drives community composition should lead to a more predictive community ecology.Ecology, Evolution and Behavio

Data from: A shift from exploitation to interference competition with increasing density affects population and community dynamics

Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of protozoa and bacteria under different combinations of protozoan density and basal resource availability. We then solved a dynamic predator–prey model for parameters of the functional response using population growth rates measured in our experiment. As population density increased, competition shifted from exploitation to interference, and competition was less dependent on resource levels. Surprisingly, the effect of resources was weakest when competition was the most intense. We found that at low population densities, competition was largely exploitative and resource availability had a large effect on population growth rates, but the effect of resources was much weaker at high densities. This shift in competitive mechanism could have implications for interspecific competition, trophic interactions, community diversity, and natural selection. We also tested whether this shift in the mechanism of competition with protozoa density affected the structure of the bacterial prey community. We found that both resources and protozoa density affected the structure of the bacterial prey community, suggesting that competitive mechanism may also affect trophic interactions

InterferenceExploitative_Experiment

Contains treatment metadata (resource availability in mg and initial Colpidium density in cells/mL) as well as final Colpidium density in cells/mL. Also indicates which samples were randomly selected for 16S rRNA gene sequencing ("y"=yes, sample was sequenced; "n"=no, sample was not sequenced)

Spatiotemporal patterns of rhizosphere microbiome assembly : From ecological theory to agricultural application

There is urgency in optimizing agricultural production in light of climate uncertainty, human population growth and resource limitations. The rhizosphere microbiome is a promising genetic resource, yet it is poorly understood. Additionally, research into rhizosphere microbial community assembly (MCA) lacks a consistent ecological framework that incorporates the dynamics of the occurring interactions. We explore the ecological principles that guide community establishment as they pertain to the rhizosphere while reviewing relevant research and highlighting the gaps in knowledge. We propose a conceptual model for studying the rhizosphere, and argue for higher resolution characterizations of the rhizosphere, under a framework of root and microbial traits that will determine its resulting composition. For this, we borrow concepts from ecological theory to chronologically describe MCA as a function of colonization, distribution and succession under changing plant-imposed filters. We argue that there is a need to consider the temporal and spatial scale of rhizosphere processes in a manner that is relevant to its microbial components. Finally, we discuss strategies for managing the rhizosphere microbiome for agriculture and the remaining gaps in knowledge that impede their application. Synthesis and applications. We aim to initiate a comprehensive conversation on ecological processes and plant and microbial traits that affect rhizosphere assembly. Rhizosphere microbiome research is relatively new and highly multidisciplinary. The use of a shared vocabulary and ecological theory will facilitate the development and advances in this discipline.</p

Reciprocal Inhibition and Competitive Hierarchy Cause Negative Biodiversity-Ecosystem Function Relationships

The relationship between biodiversity and ecosystem function (BEF) captivates ecologists, but the factors responsible for the direction of this relationship remain unclear. While higher ecosystem functioning at higher biodiversity levels (‘positive BEF’) is not universal in nature, negative BEF relationships seem puzzlingly rare. Here, we develop a dynamical consumer-resource model inspired by microbial decomposer communities in pitcher plant leaves to investigate BEF. We manipulate microbial diversity via controlled colonization and measure their function as total ammonia production. We test how niche partitioning among bacteria and other ecological processes influence BEF in the leaves. We find that a negative BEF can emerge from reciprocal interspecific inhibition in ammonia production causing a negative complementarity effect, or from competitive hierarchies causing a negative selection effect. Absent these factors, a positive BEF was the typical outcome. Our findings provide a potential explanation for the rarity of negative BEF in empirical data