Related papers: Inferring resource competition in microbial commun…
Understanding the stability of complex communities is a central focus in ecology, many important theoretical advancements have been made to identify drivers of ecological stability. However, previous results often rely on the…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where…
The problem of natural selection in dispersal-structured populations consisting of individuals characterized by different diffusion coefficients is studied. The competition between the organisms is taken into account through the assumption…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Predicting species persistence within ecological communities is a fundamental challenge for both empirical and theoretical ecology. Existing methods span from mechanistic models, whose parameters are difficult to estimate from data, to…
An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…
Resource competition in heterogeneous environments is still an unresolved problem of theoretical ecology. In this article I analyze competition between two phytoplankton species in a deep water column, where the distributions of main…
Ecosystems are commonly organized into trophic levels -- organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic…
Community finding algorithms for networks have recently been extended to dynamic data. Most of these recent methods aim at exhibiting community partitions from successive graph snapshots and thereafter connecting or smoothing these…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Organisms shape their own environment, which in turn affects their survival. This feedback becomes especially important for communities containing a large number of species; however, few existing approaches allow studying this regime,…
Competition for a limited resource is the hallmark of many complex systems, and often, that resource turns out to be the physical space itself. In this work, we study a novel model designed to elucidate the dynamics and emergence in complex…
Microbial communities feature an immense diversity of species and this diversity is linked with outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple…
We present a spatial, individual-based predator-prey model in which dispersal is dependent on the local community. We determine species suitability to the biotic conditions of their local environment through a time and space varying fitness…
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion creates new niches and facilitates such diversity. Nonetheless, it…