Microbial Community Ecology and Physiology

Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS

This study uses BONCAT-FACS to identify translationally active microbial taxa in Guaymas Basin sediments, revealing heterotrophic communities involved in organic matter cycling.

A Novel Method to Simultaneously Estimate Bacterial Respiration and Growth from Oxygen Dynamics

This paper introduces a method to estimate bacterial respiration and growth rates simultaneously from oxygen dynamics, showing high accuracy and thermal response insights.

Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies

The paper predicts microbial community responses to disturbance using genome-resolved trait-based life-history strategies, showing alignment with disturbance regimes through functional trade-offs and genomic trait distributions.

Utilization and degradation of laminarin-based substrates by marine yeasts suggests their niche-specific role in microbial loop dynamics.

This study examines how marine yeasts degrade laminarin-based substrates, finding that yeast growth is negatively correlated with oligomer length and suggesting a niche role in microbial loop dynamics.

Molecular Tracking and Cultivation Reveal Ammonia-Oxidizing Archaea as Emerging Commensals of the Human Skin Microbiome

The paper identifies Nitrosocosmicus species as commensals in the human skin microbiome through cultivation and genomic analysis, showing their adaptation to skin environments.

Induced pathogenicity toward open-ocean diatoms by a newly isolated filterable bacterium Ekhidna algicida sp. nov.

A newly isolated bacterium from the Pacific Ocean kills diatoms, suggesting a pathogenic role in open-ocean ecosystems.

Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide

This paper introduces Absolute UniFrac, a beta-diversity metric that incorporates absolute microbial abundances, and demonstrates its utility through simulations and real datasets.

The probability and duration of immigration in microbial communities

The paper develops a method to estimate immigration probability and duration in microbial communities using the gamblers ruin equation and applies it to bioaugmentation, infection, and extinction scenarios.

Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean

The paper compares BONCAT-pic and microautoradiography to measure prokaryotic activity in the deep ocean, finding BONCAT-pic more sensitive and reliable.

Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers

This study investigates how multi-trophic microbial interactions influence pollutant biodegradation in rivers, revealing the roles of prokaryotic and eukaryotic communities in mediating environmental effects.

Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum

The study examines AAP bacterial communities across the DCM in the Atlantic Ocean, finding variations in diversity and structure linked to the DCM profile.

Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland

This study compares long-read and short-read 16S rRNA sequencing for microbial community analysis in sedimentary environments, finding long-reads offer better taxonomic resolution and capture rare taxa.

SIPdb: A stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using a reverse ecology approach

The paper introduces SIPdb, a database and analysis tool for linking microbial amplicon sequences to metabolic activity using SIP data, showing it recovers 70.1% of reported incorporators and validates known degraders.

Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community

This study shows pairwise microbial interactions predict community structure in sourdough starters, with improved accuracy when including nonequilibrium demography.

Symbiont diversity within Loripes orbiculatus and the case for multiple hosts

The paper compares symbiont diversity in lucinid bivalves and seagrass roots, finding shared bacterial species between the two hosts.

A Machine Learning Approach Elucidates Spatial Patterns of Environmental Properties Driving Microbial Composition Over Santos Basin, South Atlantic

This study uses machine learning to identify microbial assemblages in the Santos Basin, finding that environmental factors like temperature, salinity, and nutrients drive community structure across different depths.

Pseudoalteromonas is a novel symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis

This study identifies Pseudoalteromonas as a novel symbiont of marine invertebrates showing phylosymbiosis across multiple phyla and geographic regions.

Ecological processes shaping marine microbial assemblages diverge between equatorial and temperate time-series

This study compares microbial community dynamics in equatorial and temperate marine time-series, finding distinct ecological processes shaping their assembly and stability.

Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes

The paper investigates abundance-activity decoupling in sulfur-cycling bacteria in meromictic lakes, linking it to viral infection types and geochemical conditions.

Does ecological restoration align prokaryotic community structure with natural references across European coastal wetlands?

The paper assesses whether coastal wetland restoration aligns prokaryotic communities with natural references, finding rapid water community recovery but persistent sediment memory of altered conditions.

On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow

The paper develops a portable sequencing workflow for in situ microbial community analysis in rivers, combining autonomous sampling with field and lab sequencing to reduce costs and improve temporal resolution.

Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem

The paper investigates chemosynthesis in a marine cave ecosystem, finding that interior communities rely on chemosynthetic processes for carbon fixation and diversity, contrasting with entrance areas.

Global geography outweighs long-term dynamics in shaping marine microbial population structure

This study shows that geographic factors have a stronger impact on marine microbial population structure than long-term temporal changes, with taxon-specific responses to seasonal variation.

Ancient Roman saltworks drive the present-day microbial community profiles in a coastal aquifer

This study shows that ancient Roman saltworks continue to influence microbial communities and groundwater chemistry in a coastal aquifer through long-term salinization.

A balance between environmental filtering and competitive exclusion modulates the macroecology of alternative stable states in microbial communities

The paper shows that microbial community structure is shaped by state-dependent competitive exclusion, leading to alternative stable states and reciprocal prevalence patterns among phylogenetically close relatives.

Bacterial, fungal and protist communities affect differentially in succession stage of karst soil

This study examines how bacterial, fungal, and protist communities differ across succession stages in karst soil, showing variations in diversity and composition linked to vegetation and environmental factors.

The effects of host phylogenetic coverage and congruence metric on Monte Carlo-based null models of phylosymbiosis

This study evaluates how congruence metrics and host phylogenetic coverage affect Monte Carlo-based null models for detecting phylosymbiosis signals.

New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales

The paper describes 81 new SAR11 isolate genomes and identifies 29 monophyletic ecotypes within the Pelagibacterales, providing a classification system correlated with ecology and evolution.

Functional Unknomics of the SAR11 clade using bioinformatics approaches

This study investigates the function of the unknome in SAR11 clade bacteria, identifying genes involved in substrate uptake, nucleotide utilization, and antiviral defense, providing insights into their ecological success.

A duo of fungi and complex and dynamic bacterial community networks contribute to shape the Ascophyllum nodosum holobiont

This study characterizes the bacterial, archaeal, and fungal communities of Ascophyllum nodosum across multiple environmental factors, revealing dynamic bacterial interactions and stable fungal associations.