Microbial Community Ecology and Physiology

MicroEcoTools provides an R package for testing ecological theories in microbial communities using null models and functional trait analysis.

This study compares the metatranscriptomes of two Candidatus Altiarchaeum populations in different subsurface ecosystems, identifying gene expression differences related to metabolism and defense mechanisms.

This study examines how multiple global change factors affect soil microbial communities using metagenomics, finding that combined factors select for distinct microbial communities and functional traits not seen with individual factors.

This study uses spectral methods to infer resource competition in microbial communities from time series data, showing they outperform simple correlations.

This study examines how low salinity affects the bacterial communities of Saccharina latissima and its surrounding environment, finding that low salinity reduces core bacterial abundance and increases community dissimilarity.

The paper identifies a risk-reward trade-off in motility endurance among copiotrophic marine bacteria, revealing two distinct strategies with genomic predictors.

The paper synthesizes genetic data with a marine ecosystem model to analyze functional biogeography of marine heteroprokaryotes, identifying key ecological factors shaping their distribution.

This study analyzes the virulome and resistome of deep-sea cold seeps, finding minimal public health risks due to low abundance of high-risk genes and non-pathogenic functions.

This study shows river sediment microbiomes are highly sensitive to reduced flow velocity, leading to altered community compositions and stress responses that recover after two weeks.

This study identifies a bacterium that contributes to diatom population collapse in outdoor algal ponds and explores its interactions with other microbes.

This study examines nitrogen cycling in an Arctic microbial community during a phytoplankton bloom, showing a shift from chemolithotrophy to chemoorganotrophy as the bloom progresses.

The paper examines how microbial community composition in mangrove sediments changes with degradation levels and seasonal flooding, identifying shifts in dominant taxa and potential for ecosystem restoration.

This study shows Beggiatoa spp. can survive extreme phosphate starvation and rapidly uptake phosphate, suggesting they play a key role in phosphate buffering in marine sediments.

The paper develops a pipeline called Tabigecy to predict metabolic functions from metabarcoding data and integrate them into biogeochemical cycle representations.

The paper examines microbial community diversity in a uranium-contaminated aquifer, finding reduced taxonomic and phylogenetic diversity but stable functional diversity.

This study examines how chemical stressors affect microbiomes across different food chain components, finding component-specific responses and shifts in microbial composition and stability.

The paper shows that microbial community phylogenetic clustering can indicate chemical pollution, using the net relatedness index as a monitoring tool.

The paper investigates microbial connectivity and diversity loss in the Cuatro Cienegas Basin, finding core microbial genera and declining diversity linked to groundwater overexploitation.

CABO-16S improves 16S rRNA-based identification of prokaryotes and eukaryotes by integrating bacterial, archaeal, and organelle sequences, enhancing classification of environmental samples.

The paper quantifies and analyzes epibacterial communities on macroalgae over a year, revealing a persistent core microbiome and strong host-specific associations.

The paper identifies microbial functional traits linked to environmental adaptation and develops an index to quantify species-level adaptive capacity across different stress gradients.

The paper refines a marker-gene-based method to quantify multifunctional redundancy in prokaryotic communities by incorporating non-random extinction scenarios and applying it to aquatic ecosystems.

This study tracks seasonal microbial shifts in a seaweed holobiont over three years, revealing predictable functional changes and core taxa.

The paper identifies potential microbial producers of branched GDGTs in anoxic marine environments using lipid analysis and metagenomic data.

This study examines how trophic status affects prokaryotic community structure and functional potential in nine peri-urban lakes around Paris over a summer season.

The paper develops a method to identify bacterial pairs through cell-cell binding, enriching for specific genera and revealing dependencies between strains.

The paper develops a standardized bioinformatic workflow and database for analyzing nifH amplicon data to study marine diazotroph biogeography and diversity.

The paper examines seasonal dynamics of an Arctic pelagic microbiome, revealing modular patterns in taxonomic and functional composition across four years.

The paper shows that increased nutrient levels boost bacterial EPS production, contributing to algal-bacterial aggregation in marine environments.

This study shows that residence time affects microbial community structure by promoting niche partitioning, with short- and long-residence-time specialists forming distinct clusters.