Life and death in the soil microbiome: how ecological processes influence biogeochemistry

NW Sokol, E Slessarev, GL Marschmann… - Nature Reviews …, 2022 - nature.com
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 …

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 …

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

A Heinken, J Hertel, G Acharya, DA Ravcheev… - Nature …, 2023 - nature.com
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …

Life history strategies of soil bacterial communities across global terrestrial biomes

G Piton, SD Allison, M Bahram, F Hildebrand… - Nature …, 2023 - nature.com
The life history strategies of soil microbes determine their metabolic potential and their
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

JL Weissman, S Hou, JA Fuhrman - … of the National Academy of Sciences, 2021 - pnas.org
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 …

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

J Ramoneda, TBN Jensen, MN Price… - Nature …, 2023 - nature.com
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 …

Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress

H Liu, J Li, BK Singh - Nature Plants, 2024 - nature.com
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 …

Inferring microbiota functions from taxonomic genes: a review

C Djemiel, PA Maron, S Terrat, S Dequiedt… - …, 2022 - academic.oup.com
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to
global change. High-throughput sequencing at the individual or community level has …

Building a genome-based understanding of bacterial pH preferences

J Ramoneda, E Stallard-Olivera, M Hoffert… - Science …, 2023 - science.org
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 …

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

GL Marschmann, J Tang, K Zhalnina, U Karaoz… - Nature …, 2024 - nature.com
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 …