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 …
Soil viral diversity, ecology and climate change
JK Jansson, R Wu - Nature Reviews Microbiology, 2023 - nature.com
Soil viruses are highly abundant and have important roles in the regulation of host dynamics
and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems …
and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems …
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
Carbohydrate active enzymes (CAZymes) are made by various organisms for complex
carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis …
carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis …
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
Wildfire-dependent changes in soil microbiome diversity and function
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and
rhizosphere processes. Wildfire season length, and the frequency and size of severe fires …
rhizosphere processes. Wildfire season length, and the frequency and size of severe fires …
Soil microbiome engineering for sustainability in a changing environment
Recent advances in microbial ecology and synthetic biology have the potential to mitigate
damage caused by anthropogenic activities that are deleteriously impacting Earth's soil …
damage caused by anthropogenic activities that are deleteriously impacting Earth's soil …
eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale
CP Cantalapiedra, A Hernández-Plaza… - Molecular biology …, 2021 - academic.oup.com
Even though automated functional annotation of genes represents a fundamental step in
most genomic and metagenomic workflows, it remains challenging at large scales. Here, we …
most genomic and metagenomic workflows, it remains challenging at large scales. Here, we …
Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species
Z Zhou, C Zhang, P Liu, L Fu, R Laso-Pérez, L Yang… - Nature, 2022 - nature.com
The methanogenic degradation of oil hydrocarbons can proceed through syntrophic
partnerships of hydrocarbon-degrading bacteria and methanogenic archaea,–. However …
partnerships of hydrocarbon-degrading bacteria and methanogenic archaea,–. However …
Interrogating the viral dark matter of the rumen ecosystem with a global virome database
The diverse rumen virome can modulate the rumen microbiome, but it remains largely
unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create …
unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create …
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
S Saheb Kashaf, DM Proctor, C Deming, P Saary… - Nature …, 2022 - nature.com
Human skin functions as a physical barrier to foreign pathogen invasion and houses
numerous commensals. Shifts in the human skin microbiome have been associated with …
numerous commensals. Shifts in the human skin microbiome have been associated with …