The global soil community and its influence on biogeochemistry
BACKGROUND Soil is the largest repository of organic matter on land, storing~ 1500 Gt
carbon, which is at least as much as the vegetation (~ 560 Gt) and atmosphere (~ 750 Gt) …
carbon, which is at least as much as the vegetation (~ 560 Gt) and atmosphere (~ 750 Gt) …
Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
Geobacter: the microbe electric's physiology, ecology, and practical applications
Geobacter species specialize in making electrical contacts with extracellular electron
acceptors and other organisms. This permits Geobacter species to fill important niches in a …
acceptors and other organisms. This permits Geobacter species to fill important niches in a …
Applications of genome‐scale metabolic reconstructions
The availability and utility of genome‐scale metabolic reconstructions have exploded since
the first genome‐scale reconstruction was published a decade ago. Reconstructions have …
the first genome‐scale reconstruction was published a decade ago. Reconstructions have …
Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of
microbial communities. This raises the question of whether ecosystem-level behavior of …
microbial communities. This raises the question of whether ecosystem-level behavior of …
Explicitly representing soil microbial processes in Earth system models
Microbes influence soil organic matter decomposition and the long‐term stabilization of
carbon (C) in soils. We contend that by revising the representation of microbial processes …
carbon (C) in soils. We contend that by revising the representation of microbial processes …
Expanding the role of reactive transport models in critical zone processes
Abstract Models test our understanding of processes and can reach beyond the spatial and
temporal scales of measurements. Multi-component Reactive Transport Models (RTMs) …
temporal scales of measurements. Multi-component Reactive Transport Models (RTMs) …
Synthetic ecology of microbes: mathematical models and applications
As the indispensable role of natural microbial communities in many aspects of life on Earth
is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions …
is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions …
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
The advent of rapid complete genome sequencing, and the potential to capture this
information in genome-scale metabolic models, provide the possibility of comprehensively …
information in genome-scale metabolic models, provide the possibility of comprehensively …
Mathematical modeling of microbial community dynamics: a methodological review
Microorganisms in nature form diverse communities that dynamically change in structure
and function in response to environmental variations. As a complex adaptive system …
and function in response to environmental variations. As a complex adaptive system …