Integrating viral metagenomics into an ecological framework
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses,
within both environmental (eg, terrestrial and aquatic) and host-associated (eg, plants and …
within both environmental (eg, terrestrial and aquatic) and host-associated (eg, plants and …
Current status of and future perspectives in bacterial degradation of benzo [a] pyrene
Benzo [a] pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight
PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important …
PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important …
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
Background Winter carbon loss in northern ecosystems is estimated to be greater than the
average growing season carbon uptake and is primarily driven by microbial decomposers …
average growing season carbon uptake and is primarily driven by microbial decomposers …
Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems
The growth and physiology of soil microorganisms, which play vital roles in biogeochemical
cycling, are shaped by both current and historical soil environmental conditions. Here, we …
cycling, are shaped by both current and historical soil environmental conditions. Here, we …
Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of an agricultural soil
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-
products which can promote interactions with noncellulolytic organisms. We hypothesized …
products which can promote interactions with noncellulolytic organisms. We hypothesized …
Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation
Stable isotope probing (SIP) is a powerful tool to study microbial community structure and
function in both nature and engineered environments. Coupling with advanced genomics …
function in both nature and engineered environments. Coupling with advanced genomics …
Genomic features predict bacterial life history strategies in soil, as identified by metagenomic stable isotope probing
SE Barnett, R Egan, B Foster, EA Eloe-Fadrosh… - MBio, 2023 - Am Soc Microbiol
Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial
dynamics in soil that govern carbon (C) cycling are not well understood. Life history …
dynamics in soil that govern carbon (C) cycling are not well understood. Life history …
Measurement error and resolution in quantitative stable isotope probing: implications for experimental design
Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of
individual microbes and can link microbial biodiversity and biogeochemistry in complex …
individual microbes and can link microbial biodiversity and biogeochemistry in complex …
Ecological stoichiometry as a foundation for omics-enabled biogeochemical models of soil organic matter decomposition
EB Graham, KS Hofmockel - Biogeochemistry, 2022 - Springer
Coupled biogeochemical cycles drive ecosystem ecology by influencing individual-to-
community scale behaviors; yet the development of process-based models that accurately …
community scale behaviors; yet the development of process-based models that accurately …
MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment
DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to
sequencing data. Every SIP dataset captures distinct information about microbial community …
sequencing data. Every SIP dataset captures distinct information about microbial community …