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Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Soil microorganisms shape global element cycles in life and death. Living soil
microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil …
microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil …
Genomes OnLine Database (GOLD) v. 8: overview and updates
S Mukherjee, D Stamatis, J Bertsch… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) is a manually
curated, daily updated collection of genome projects and their metadata accumulated from …
curated, daily updated collection of genome projects and their metadata accumulated from …
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …
prescribed drugs. Designing precision medicine approaches that incorporate microbial …
Life history strategies of soil bacterial communities across global terrestrial biomes
The life history strategies of soil microbes determine their metabolic potential and their
response to environmental changes. Yet these strategies remain poorly understood. Here …
response to environmental changes. Yet these strategies remain poorly understood. Here …
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns
Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders
of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth …
of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth …
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Many microorganisms are auxotrophic—unable to synthesize the compounds they require
for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a …
for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a …
Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress
Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations
with plants to provide host resilience to drought stress. Here we synthesize the emerging …
with plants to provide host resilience to drought stress. Here we synthesize the emerging …
Inferring microbiota functions from taxonomic genes: a review
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to
global change. High-throughput sequencing at the individual or community level has …
global change. High-throughput sequencing at the individual or community level has …
Building a genome-based understanding of bacterial pH preferences
The environmental preferences of many microbes remain undetermined. This is the case for
bacterial pH preferences, which can be difficult to predict a priori despite the importance of …
bacterial pH preferences, which can be difficult to predict a priori despite the importance of …
Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical
models, microbial genome data can be leveraged to infer key functional traits. By integrating …
models, microbial genome data can be leveraged to infer key functional traits. By integrating …