Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

Most of our knowledge about bacterial functional roles in microbiomes comes from bulk measurements. Yet microbial communities are complex ecosystems in which functionally distinct bacterial subpopulat...

biorxiv.org

Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities - Nature Communications

Profiling soil viral communities is challenging due to the inherent complexity of soil samples. In this study, the authors show that soil sample preparation strongly shapes which DNA and RNA viruses a...

nature.com

Declining coccolithophore blooms in the North Atlantic and Western Barents Sea

Satellite observations reveal substantial decreases in coccolithophore blooms across the North Atlantic and Barents Sea.

science.org

The need for standardization and improved open (meta)data practices in metaproteomics - Microbiome

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization...

link.springer.com

Evolutionary trajectory of microbial sulfur oxidation pathways recapitulates Earth’s oxygenation history - Nature Communications

Microorganisms have long driven Earth’s oxidative sulfuric cycle using complex sulfur-oxidizing systems. This study shows that this molecular machinery first originated in the anoxic Archean eon and g...

nature.com

onlinelibrary.wiley.com

Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources

Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...

enviromicro-journals.onlinelibrary.wiley.com

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients - Molecular Systems Biology

Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we c...

link.springer.com

Ideas and perspectives: Nitrite turnover controls nitrogen fate across redox gradients

Abstract. Reactive nitrogen fate in natural systems remains difficult to predict because pathway partitioning occurs at the stage of nitrite turnover, where rapid and tightly coupled production and co...

bg.copernicus.org

Oxygen dependent nitric oxide (NO) and nitrous oxide (N2O) dynamics during aerobic ammonia oxidation

Ammonia-oxidizing microorganisms (AOM) produce atmospherically active gases, such as nitric oxide (NO) and nitrous oxide (N₂O), as intermediates and b…

sciencedirect.com

Black Sea picocyanobacteria exploit ancestral traits for energy and chlorophyll production in dark anoxia

Abstract. Picocyanobacteria, typically associated with oxygenated waters, thrive also in oxygen minimum zones (OMZs) and anoxic environments. The extent to

academic.oup.com

Increased nutrient diversity can induce loss of microbial diversity through enhanced resource uptake - Nature Ecology & Evolution

Increasing nutrient diversity is expected to promote microbial diversity. This study shows that more complex environments can enhance resource uptake, intensify competition and lead to microbial biodi...

nature.com

Thermoregulation of functional amyloid Fap-dependent biofilm formation via cyclic diguanosine monophosphate signaling in Pseudomonas fluorescens | Applied and Environmental Microbiology

The persistence of bacteria in various biofilms frequently leads to food spoilage and foodborne illnesses. Pseudomonas fluorescens is widely recognized as one of the most prevalent spoilage organisms,...

journals.asm.org

Evolution-guided engineering of an ancient nitrogenase interface enhances enzyme activity and stability

Nitrogenase is the only enzyme capable of biological nitrogen fixation and a major target for sustainable agricultural engineering, yet its functional and structural complexity has made it difficult t...

biorxiv.org

The dynamic mesoscale sink and source niches for eukaryotic phytoplankton in a subtropical gyre | PNAS

By tracking the water mass histories of genetic samples, we investigated the biophysical dynamics shaping eukaryotic phytoplankton populations in a...

pnas.org

Deep-sea anaerobic microbial communities couple degradation of insoluble chitin to extracellular electron transfer

Abstract. Chitin, a major structural component of arthropod exoskeletons, is an abundant carbon and nitrogen source in marine ecosystems. While its degrada

academic.oup.com

Enhanced marine burial of terrestrial organic carbon through the Palaeocene–Eocene Thermal Maximum - Nature Geoscience

The burial of terrestrially derived organic carbon in coastal marine sediments greatly increased during the Palaeocene–Eocene Thermal Maximum, probably helping to draw down a large portion of carbon r...

nature.com

Major contribution of anaplerosis to inorganic carbon fixation in the dark ocean - Nature Geoscience

While most newly formed organic carbon in the dark ocean is derived from chemolithoautotrophic microorganisms, 17% also comes from an alternative pathway called anaplerosis that is related to the tric...

nature.com

Mapping the soil microbiome functions shaping wetland methane emissions | mSystems

Soil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond “single-lever” strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.

journals.asm.org