Microbial Community Ecology and Physiology

Phylogenetic clustering of microbial communities as a biomarker for chemical pollution

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

Running against the clock: describing microbial diversity in an extremely endangered microbial oasis in the Chihuahuan desert

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

Genomic insights into polysaccharide substrate utilization and novel genera resource mining in macroalgal epiphytic bacteria

This study identifies novel bacterial genera and their polysaccharide utilization loci in macroalgal epiphytic bacteria, revealing their ecological roles in carbon cycling and potential for resource mining.

REPOP: bacterial population quantification from platecounts

REPOP reconstructs bacterial populations from platecounts by accounting for dilution and plating uncertainties, revealing hidden multimodality that standard methods obscure.

Genomic Characterization and New Species Identification of Winogradskyella with Comparative Analysis of Polysaccharide Utilization Loci

The paper identifies five new Winogradskyella species and characterizes their polysaccharide utilization loci, revealing their role in marine carbon cycling.

CABO-16S : A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples

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

The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions

This study links genome size to microbial prevalence and community structure in freshwater ecosystems, showing that streamlined genomes promote cosmopolitanism and interdependencies.

Microbial sedimentary DNA from a cultural landscape disentangles the impacts of humans and nature over the past 13.5 thousand years

This study uses sedimentary DNA from Lake Constance to analyze microbial changes over 13.5 thousand years, showing how both natural and human factors shaped microbial communities.

Year-round quantification, structure and dynamics of epibacterial communities from diverse macroalgae reveal a persistent core microbiota and strong host specificities

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

Fine-scale spatial patterns in hot springs mat bacterial communities

This study examines macroecological patterns in bacterial communities of hot springs mats at a fine spatial scale, finding sublinear species-area scaling and increasing abundance-occupancy trends.

Microbial strategies of environmental adaptation revealed by trait-environmental relationships

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

Seasonal cycles in a seaweed holobiont: A multiyear time series reveals repetitive microbial shifts and core taxa

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

Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system

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

A summer in the Greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

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

A uniform stress response of stream microbiomes in the hyporheic zone across North America

The paper analyzes hyporheic zone microbiomes across North America to show conserved stress responses and distinct metabolic activity in sediments versus surface water.

Phytoplankton recruitment of specific microbial assemblages and phylosymbiotic patterns

The paper investigates host-specific microbial assemblages in phytoplankton and identifies core microbial lineages shaping these assemblages through deterministic processes.

Impact of Soil Salinity on Microbial Community Composition in Coastal Agricultural lands of Bangladesh: A Metagenomic Approach

This study examines how soil salinity affects microbial communities in Bangladesh's coastal agricultural soils using metagenomics, finding reduced diversity and altered community composition in saline soils.

Microbial Partner (MiPner) Analysis

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

Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow

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

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

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

Increased Nutrient Levels Enhance the Bacterial Contribution to an Algal-Bacterial Extracellular Matrix

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

Residence time structures microbial communities through niche partitioning

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

Microbial functional guilds respond cohesively to rapidly fluctuating environments

The paper shows microbial functional guilds respond cohesively to rapid environmental fluctuations and competitively to slower ones, offering a framework for discovering guilds through nutrient perturbations.

An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota

The paper analyzes the genomic diversity and habitat preferences of Acidobacteriota across ecosystems, finding that phylogenetic affiliation shapes genomic traits more than habitat.

Psychromonas aestuarii sp. nov., a novel bacterial species isolated from estuarine surface sediment

The paper isolates and characterizes two bacterial strains from estuarine sediment, identifying them as a novel Psychromonas species based on molecular, phenotypic, and chemotaxonomic analyses.

Microbes under climatic refugia: Self-stabilizing subcommunity rank dynamics in large-river deltaic estuaries

The paper examines microbial subcommunity dynamics in large-river deltaic estuaries, finding that their rank structures are persistent and resilient to environmental changes.

From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment

The study examines how landscape design in a Tokyo museum affects microbial diversity and function, finding higher diversity but no consistent patterns in virulence or resistance genes.

Functional stability despite high taxonomic turnover characterizes the Ulva microbiome across a 2,000 km salinity gradient

The study examines the functional stability of Ulva-associated bacteria across a salinity gradient, finding limited functional variation despite high taxonomic turnover.

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

The paper links genomic traits like codon bias and genome size to bacterial growth and transcription rates in rewetted soil using metagenomic and metatranscriptomic data.

Overturning circulation structures the microbial functional landscape of the South Pacific

The paper uses genomic and hydrographic data to show that ocean circulation structures microbial diversity and function in the South Pacific.