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Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in…
Explaining biodiversity in nature is a fundamental problem in ecology. An outstanding challenge is embodied in the so-called Competitive Exclusion Principle: two species competing for one limiting resource cannot coexist at constant…
Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level…
Microbial populations exhibit a broad spectrum of nutrient utilization strategies, ranging from strategies utilizing diverse nutrients, called "generalists," to those being highly adapted to specific nutrients, called "specialists." The…
There has been a long-standing and at times fractious debate whether complex and large systems can be stable. In ecology, the so-called `diversity-stability debate' arose because mathematical analyses of ecosystem stability were either…
We consider a model for a population in a heterogeneous environment, with logistic type local population dynamics, under the assumption that individuals can switch between two different nonzero rates of diffusion. Such switching behavior…
Explaining biodiversity is a fundamental issue in ecology. A long-standing puzzle lies in the paradox of the plankton: many species of plankton feeding on a limited variety of resources coexist, apparently flouting the competitive exclusion…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…
The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
A novel mathematical framework is proposed to describe the ecological and evolutionary consequences of consumer--resource interactions. Both the consumer and resource are assumed to consist of several (sub)species, which interact between…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative…
The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological…
Relations among species in ecosystems can be represented by complex networks where both negative (competition) and positive (mutualism) interactions are concurrently present. Recently, it has been shown that many ecosystems can be cast into…
Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species,…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Cooperative mutualism is a major force driving evolution and sustaining ecosystems. Although the importance of spatial degrees of freedom and number fluctuations is well-known, their effects on mutualism are not fully understood. With range…