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A central question in ecology is to understand the ecological processes that shape community structure. Niche-based theories have emphasized the important role played by competition for maintaining species diversity. Many of these insights…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
This chapter defines and presents different kinds of software ecosystems. The focus is on the development, tooling and analytics aspects of software ecosystems, i.e., communities of software developers and the interconnected software…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
The changes on abiotic features of ecosystems have rarely been taken into account by population dynamics models, which typically focus on trophic and competitive interactions between species. However, understanding the population dynamics…
Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has…
Rising interest in the resilience of ecological systems has spawned diverse interpretations of the term's precise meaning. This paper classifies and explores definitions of resilience from the ecological literature using a dynamical systems…
We develop a theoretical framework to understand the persistence and coexistence of competitive species in a spatially explicit metacommunity model with a heterogeneous dispersal kernel. Our analysis, based on methods from the physics of…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be…
Understanding the quantitative patterns behind scientific disciplines is fundamental for informed research policy. While many fields have been studied from this perspective, Urban Science (USc) and its subfields remain underexplored. As…
The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant…
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…
Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". It is not always clear to what extent the intuition derived…
Many studies have been performed to characterize the dynamics and stability of the microbiome across a range of environmental contexts [Costello et al., 2012, Faust et al., 2015]. For example, it is often of interest to identify time…
Patterns in a semiarid ecosystem are important because they directly and indirectly affect ecological processes, biodiversity, and ecosystem resilience. Understanding the causes and effects of these patterns is critical for long-term land…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
The harsh environment imposes a unique set of challenges on networking strategies. In such circumstances, the environmental impact on network resources and long-time unattended maintenance has not been well investigated yet. To address…