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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…
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…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
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…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
From a purely operational standpoint, the existence of microbes that can grow under extreme conditions, or "extremophiles", leads to the question of how the molecules making up these microbes can maintain both their structure and function.…
It has been argued that the limited set of proteins used by life as we know it could not have arisen by the process of Darwinian selection from all possible proteins. This probabilistic argument has a number of implicit assumptions that may…
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…
Studies by microbiologists from the 1970s provided robust estimates for the energy supply and demand of a prokaryotic cell. The amount of ATP needed to support growth was calculated from the chemical composition of the cell and known…
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…
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…
Populations evolving in fluctuating environments face the fundamental challenge of balancing adaptation to current conditions against preparation for uncertain futures. Here, we study microbial evolution in partially predictable…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
With the characterisations of potentially habitable planetary atmospheres on the horizon, the search for biosignatures is set to become a major area of research in the coming decades. To understand the atmospheric characteristics that might…