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 …

Interactions between bacterial and phage communities in natural environments

A Chevallereau, BJ Pons, S van Houte… - Nature Reviews …, 2022 - nature.com
We commonly acknowledge that bacterial viruses (phages) shape the composition and
evolution of bacterial communities in nature and therefore have important roles in ecosystem …

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

S Roux, AP Camargo, FH Coutinho, SM Dabdoub… - PLoS …, 2023 - journals.plos.org
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

J Guo, B Bolduc, AA Zayed, A Varsani… - Microbiome, 2021 - Springer
Background Viruses are a significant player in many biosphere and human ecosystems, but
most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to …

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M Shaffer, MA Borton, BB McGivern… - Nucleic acids …, 2020 - academic.oup.com
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the
specific reactions catalyzed by these biological engines are hard to decode due to the …

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

S Nayfach, AP Camargo, F Schulz… - Nature …, 2021 - nature.com
Millions of new viral sequences have been identified from metagenomes, but the quality and
completeness of these sequences vary considerably. Here we present CheckV, an …

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 …

Soil microbiomes and climate change

JK Jansson, KS Hofmockel - Nature Reviews Microbiology, 2020 - nature.com
The soil microbiome governs biogeochemical cycling of macronutrients, micronutrients and
other elements vital for the growth of plants and animal life. Understanding and predicting …

[HTML][HTML] Scientists' warning to humanity: microorganisms and climate change

R Cavicchioli, WJ Ripple, KN Timmis, F Azam… - Nature Reviews …, 2019 - nature.com
In the Anthropocene, in which we now live, climate change is impacting most life on Earth.
Microorganisms support the existence of all higher trophic life forms. To understand how …

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

K Kieft, Z Zhou, K Anantharaman - Microbiome, 2020 - Springer
Background Viruses are central to microbial community structure in all environments. The
ability to generate large metagenomic assemblies of mixed microbial and viral sequences …