相关论文: Representation of Dormant and Active Microbial Dyn…

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…

We present models of dormancy in a planktonic culture and in biofilm, and examine the relative advantage of short dormancy versus long dormancy times in each case. Simulations and analyses indicate that in planktonic batch cultures and in…

Dormancy is a widespread adaptive strategy that enables populations to persist in fluctuating environments, yet how its benefits depend on the temporal structure of environmental variability remains unclear. We examine how dormancy…

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…

Microbial dormancy is an evolutionary trait that has emerged independently at various positions across the tree of life. It describes the ability of a microorganism to switch to a metabolically inactive state that can withstand unfavorable…

The factors contributing to the persistence and stability of life are fundamental for understanding complex living systems. Organisms are commonly challenged by harsh and fluctuating environments that are suboptimal for growth and…

Researchers puzzle over questions as to how rare species survive extinction, and why a significant proportion of microbial taxa are dormant. Computational simulation modeling by a genetic algorithm provides some answers. First, a…

Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…

Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…

We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated…

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…

Mathematical modelling of the evolution of the size-spectrum dynamics in aquatic ecosystems was discovered to be a powerful tool to have a deeper insight into impacts of human- and environmental driven changes on the marine ecosystem. In…

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…

Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and…

One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…

In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…