Microbial Community Ecology and Physiology

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

The paper investigates the relationship between co-occurrence and horizontal gene transfer (HGT) in marine bacteria, finding a significant association independent of phylogeny.

A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts

The paper presents a high-resolution multi-omics dataset of surface ocean metagenomes, metatranscriptomes, and tRNA transcripts collected over 48 hours to study microbial responses to environmental change.

Microflora Danica: the atlas of Danish environmental microbiomes

Microflora Danica compiles 10,686 shotgun metagenomes and 449 rRNA datasets to create an atlas of Danish environmental microbiomes, revealing hidden homogeneity and novel nitrifiers.

Distribution of carbon monoxide-oxidizing microorganisms along a chronosequence on Piton De La Fournaise volcano

This study examines CO-oxidizing microbial communities in volcanic soils of different ages, finding increased activity in older soils and shifts in microbial phyla.

Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs

The paper analyzes 653 MAGs and SAGs of the Roseobacter group to assess their phylogeny, genomic features, and global biogeography, revealing novel clusters and functional adaptations.

Microbial communities in Phragmites australis biofilms from Masurian lakes (Poland) with varying trophic states

The paper examines microbial communities in Phragmites australis biofilms and planktonic fractions across lakes with different trophic states, finding distinct biofilm communities with unique core microbiomes and higher physiological activity.

Hierarchical taxonomic constraints shape bacterial nitrogen cycling across functional and molecular scales

The paper quantifies how taxonomic identity influences nitrogen cycling functions across bacterial genomes, revealing hierarchical constraints and ecological strategies.

National-scale biogeography and function of river and stream bacterial biofilm communities

This study assesses bacterial diversity and function in river biofilms across England, revealing taxonomic novelty and environmental drivers of community composition.

Oligotrophy and organic carbon dissipation as trophic strategy in chernozem rare and uncultured taxa

This study identifies trophic strategies of rare and uncultured soil bacteria using genomic and functional traits, revealing oligotrophy and copiotrophy as distinct ecological adaptations.

Biological insights and methodological challenges learned from working with a diverse heterotrophic marine bacterial library

The paper establishes and characterizes a marine bacterial library, identifying genetic variations, growth patterns, and methodological challenges in strain maintenance and analysis.

Transcriptomic and Proteomic Analysis Reveals Nitrogen Recycling as a Core Mechanism for Prochlorococcus Prolonged Survival

This study uses transcriptomics and proteomics to show that Prochlorococcus survives nitrogen limitation through a mutualistic relationship with Alteromonas, which recycles nitrogen via organic matter degradation.

BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

The paper isolates the first cultured strain of the deep-branching phylum Candisdatus Bipolaricaulota from a serpentinite-hosted ecosystem and describes its hydrocarbon metabolism and morphology.

Microbial metabolism of complex organic matter across diverse deep-sea ecosystems

This study investigates how deep-sea microbes metabolize complex organic matter across different ecosystems, identifying specialized adaptations in the PVC superphylum for polysaccharide degradation.

Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries

This study characterizes Actinobacteriota in two estuaries, showing their abundance, functional potential, and environmental drivers, with emphasis on secondary metabolite production and ecological roles.

Four Potential Mechanisms Underlying Phytoplankton-Bacteria Interactions Assessed Using Experiments and Models

The paper assesses four mechanisms of phytoplankton-bacteria interactions using models and experiments, finding two distinct modes of interaction and highlighting the need for additional mechanisms like allelopathy.

Evolutionary stasis and homogeneous selection structure microbial communities in the deep subseafloor sedimentary biosphere

This study analyzes microbial communities in deep subseafloor sediments, finding evolutionary stasis driven by homogeneous selection and environmental stability over 480 kyr.

Rainwater-driven transport of matter and microbes from phyllosphere to soil in a temperate beech forest

The paper quantifies microbial transport via rainwater in a temperate forest and shows bacteria contribute significantly to organic matter fluxes.

Facilitation-competition tradeoffs structure microbial niches and nitrogen cycling

This study uses a trait-based model to show how microbial facilitation and competition shape nitrogen cycling and biogeochemical outcomes in marine environments.

Unlocking River Biofilm Microbial Diversity: A Comparative Analysis of Sequencing Technologies

This study compares Illumina short-read and PacBio long-read sequencing for microbial diversity in river biofilms, finding that PacBio provides higher taxonomic resolution while both methods yield similar community structures.

Cultivating microbial communities from the serpentinite-hosted Prony Bay Hydrothermal Field on different carbon sources in hydrogen-fed bioreactors

The paper cultivates microbial communities from the Prony Bay hydrothermal field using different carbon sources in hydrogen-fed bioreactors and finds that non-glycine substrates support diverse taxa, including aerobic genera.

On Copiotrophy and Temperature: Controls on Microbial Maximum Growth Rate Versus Translation Rate Optimization

The paper examines how temperature affects microbial growth optimization and shows that genomic signatures of growth optimization better predict ecological roles than maximum growth rates.

River biofilm bacteria as sentinels of national-scale freshwater ecosystems

The paper uses river biofilm bacterial communities to monitor freshwater ecosystem health by analyzing 16S rRNA gene sequences and identifying ecological thresholds.

Drivers of diversity within and between microbialcommunities during stochastic assembly

The paper develops a stochastic model to explain diversity patterns in microbial communities based on dispersal and division rates, validates it with simulations and equations, and applies metrics to experimental data.

From microbial diversity to function; evaluating dimensionality reduction methods

The paper evaluates dimensionality reduction methods for microbial oceanography data, finding that Self Organizing Maps (SOM) better identify functionally distinct microbial ecotypes than Principal Coordinate Analysis (PCoA).

Global pattern of nitrogen metabolism in marine prokaryotes

The paper uses global marine metagenomic data and machine learning to map the biogeography of nitrogen metabolism pathways in marine prokaryotes, revealing distinct patterns linked to environmental conditions and taxa.

Assembly of skin microbiomes is more neutral than gut microbiomes in multiple animal species

The paper compares neutral and selective processes in shaping skin and gut microbiomes across species, finding skin microbiomes are more influenced by neutral processes.

Metabolic and Population Profiles of Active Subseafloor Autotrophs in Young Oceanic Crust at Deep-Sea Hydrothermal Vents

This study identifies active subseafloor autotrophs at deep-sea hydrothermal vents using RNA-SIP and metatranscriptomics, revealing their metabolic strategies and population dynamics.

Dissolved oxygen concentrations influence microbial diversity, abundance and dominant players in an oxygen minimum zone

The paper examines how dissolved oxygen affects microbial diversity and abundance in the northern Benguela Upwelling System OMZ, identifying Thioglobaceae as a dominant group with implications for nitrous oxide production.

Small- and large-scale patches shape benthic microbial community structure and function in streams at the subcontinental scale

The paper investigates how small- and large-scale environmental factors shape benthic microbial communities in streams across the USA, finding that local conditions and water quality both influence microbial structure and function at different scales.