Population genomics of plant viruses: the ecology and evolution of virus emergence

MJ McLeish, A Fraile, F García-Arenal - Phytopathology®, 2021 - Am Phytopath Society
The genomics era has revolutionized studies of adaptive evolution by monitoring large
numbers of loci throughout the genomes of many individuals. Ideally, the investigation of …

Contribution of single-cell omics to microbial ecology

S Mauger, C Monard, C Thion… - Trends in Ecology & …, 2022 - cell.com
Micro-organisms play key roles in various ecosystems, but many of their functions and
interactions remain undefined. To investigate the ecological relevance of microbial …

Seasonal niche differentiation among closely related marine bacteria

A Auladell, A Barberán, R Logares, E Garcés… - The ISME …, 2022 - academic.oup.com
Bacteria display dynamic abundance fluctuations over time in marine environments, where
they play key biogeochemical roles. Here, we characterized the seasonal dynamics of …

A multi-omics approach to solving problems in plant disease ecology

SG Crandall, KM Gold, MM Jiménez-Gasco… - PLoS …, 2020 - journals.plos.org
The swift rise of omics-approaches allows for investigating microbial diversity and plant-
microbe interactions across diverse ecological communities and spatio-temporal scales. The …

Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

R Maddamsetti, Y Yao, T Wang, J Gao… - Nature …, 2024 - nature.com
Horizontal gene transfer (HGT) and gene duplication are often considered as separate
mechanisms driving the evolution of new functions. However, the mobile genetic elements …

Gene flow and introgression are pervasive forces shaping the evolution of bacterial species

A Diop, EL Torrance, CM Stott, LM Bobay - Genome Biology, 2022 - Springer
Background Although originally thought to evolve clonally, studies have revealed that most
bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the …

Prochlorococcus have low global mutation rate and small effective population size

Z Chen, X Wang, Y Song, Q Zeng, Y Zhang… - Nature ecology & …, 2022 - nature.com
Prochlorococcus are the most abundant free-living photosynthetic carbon-fixing organisms
in the ocean. Prochlorococcus show small genome sizes, low genomic G+ C content …

The active free-living bathypelagic microbiome is largely dominated by rare surface taxa

M Sebastián, CR Giner, V Balagué… - ISME …, 2024 - academic.oup.com
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent
findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic …

Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome

CR Strachan, XA Yu, V Neubauer, AJ Mueller… - Nature …, 2023 - nature.com
The activities of different microbes in the cow rumen have been shown to modulate the
host's ability to utilize plant biomass, while the host–rumen interface has received little …

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand

AS Noble, S Noe, MJ Clearwater, CK Lee - PLoS One, 2020 - journals.plos.org
The phyllosphere microbiome is increasingly recognised as an influential component of
plant physiology, yet it remains unclear whether stable host-microbe associations generally …