Related papers: Functional universality in slow-growing microbial …
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…
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…
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…
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…
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…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a…
A packed community of exponentially proliferating microbes will spread in size exponentially. However, due to nutrient depletion, mechanical constraints, or other limitations, exponential proliferation is not indefinite, and the spreading…
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…
Photosynthetic microbes have evolved and successfully adapted to the ever-changing environmental conditions in complex microhabitats throughout almost all ecosystems on Earth. In the absence of light, they can sustain their biological…
Many microbes live in habitats below their optimum temperature. Retention of metabolic heat by aggregation or insulation would boost growth. Generation of excess metabolic heat may also provide benefit. A cell that makes excess metabolic…
Microbial communities routinely have several possible species compositions or community states observed for the same environmental parameters. Changes in these parameters can trigger abrupt and persistent transitions (regime shifts) between…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Microbes produce metabolic resources that are important for cell growth yet leak across membranes into the extracellular environment. Other microbes in the same environment can use these resources and adjust their own metabolic production…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
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…
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…