Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.

Anaerobic methanotrophic archaea (ANME) are crucial to planetary carbon cycling. They oxidise methane in anoxic niches by transferring electrons to nitrate, metal oxides, or sulfate-reducing bacteria. No ANMEs have been isolated, hampering the biochemical investigation of anaerobic methane oxidation.

Redox conduction facilitates direct interspecies electron transport in anaerobic methanotrophic consortia.

Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane. While direct interspecies electron transport is proposed to enable ANME/SRB symbiosis, its electrochemical properties remain uncharacterized. Here, using sediment-free enrichment cultures, we measured the electron transport capabilities of marine consortia under physiological conditions.

Genomic diversity and adaptation in Arctic marine bacteria.

Arctic marine bacteria experience seasonal changes in temperature, salinity, light, and sea ice cover. Time-series and metagenomic studies have identified spatiotemporal patterns in Arctic microbial communities, but a lack of complete genomes has limited efforts to identify the extent of genomic diversity in Arctic populations. We cultured and sequenced the complete genomes of 34 Arctic marine bacteria to identify patterns of gene gain, loss, and rearrangement that structure genomes and underlie adaptations to Arctic conditions.

Groundwater Nitrogen Fixation Is Associated with Methane and Sulfur Cycling.

Nitrogen fixation is an energy-intensive process critical for microbial survival in nitrogen-depleted environments. Groundwater, the Earth's largest accessible freshwater reservoir, is typically oligotrophic. However, recent studies have identified productive groundwater habitats where nitrogen fixation may become important to support the productivity.

Long-term impacts of straw and biochar applications on microbial diversity and soil functions in paddy soils.

The combined application of straw and biochar represents an established approach for soil improvement. However, its long-term effects on microbial diversity and soil functions remain poorly understood. In this decade-long field study, we evaluated the sustained impacts of straw and biochar amendments on microbial diversity and carbon/nitrogen-cycling functions in paddy soils.

Producing mixed linked xylooligosaccharides from red algae biomass through single-step enzymatic hydrolysis.

Background: The red alga Palmaria palmata is a rich source of sugar compounds, particularly mixed-linkage xylans present in the cell walls of the algae. In contrast to their terrestrial lignocellulosic counterparts, these xylans are more easily accessible. They can be hydrolyzed enzymatically into valuable xylooligosaccharides (XOS), known for their prebiotic, antioxidant, and immunomodulatory properties.

In Situ Metabolic Rates of Alkane-Degrading Sulphate-Reducing Bacteria in Hydrocarbon Seep Sediments Revealed by Combining CARD-FISH, NanoSIMS, and Mathematical Modelling.

Marine hydrocarbon seeps are hotspots for sulphate reduction coupled to hydrocarbon oxidation. In situ metabolic rates of sulphate-reducing bacteria (SRB) degrading hydrocarbons other than methane, however, remain poorly understood. Here, we assessed the environmental role of Desulfosarcinaceae clades SCA1, SCA2 for degradation of n-butane and clade LCA2 for n-dodecane.

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses from the Plant Viruses Subcommittee, 2025.

In March 2025, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote, newly proposed taxa were added to those under the mandate of the Plant Viruses Subcommittee. In brief, 1 new order, 3 new families, 6 new genera, 2 new subgenera and 206 new species were created. Some taxa were reorganized.

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.

This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species.

First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity.

Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition.

Gifting future scientists the past through well-preserved specimens of modern microbial ecosystems.

Historical specimens have enabled transformative insights across kingdoms and ecosystems with new technologies, yet microbes remain largely overlooked in preservation efforts. As we recognize microbial communities as fundamental drivers of planetary health, comprehensive microbial archiving becomes an urgent intergenerational responsibility.

Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.

Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. Here, we study dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction.

Dynamics of microbial communities in Western Antarctic Peninsula waters shaped primarily by the biological interactions.

Marine Antarctic microbial communities inhabit highly dynamic and extreme environments, characterized by deep vertical mixing, seasonal ice cover, and fluctuating light availability. Understanding the interplay between phytoplankton and bacterioplankton in such systems is critical to elucidate ecosystem function and biogeochemical cycling in the Southern Ocean. The current study presents a comprehensive three-year high-throughput analysis of phytoplankton-bacterioplankton interactions in the waters of Wilhelm Archipelago, elucidating interseasonal and interannual microbial dynamics.

Activity-Based Tracking of Glycan Turnover in Microbiomes.

Glycans shape microbiomes in the ocean and the gut, driving key steps in the global carbon cycle and human health. Yet, our ability to track microbial glycan turnover across microbiomes is limited, as identifying active degraders without prior genomic knowledge remains a key challenge. Here, we introduce an activity-based fluorescence resonance energy transfer (FRET) probe that enables direct visualization and quantification of glycan metabolism in complex microbial communities.

Using phenotyping to visualize and identify selfish bacteria: a methods guide.

Polysaccharides are dominant components of plant and algal biomass, whose degradation is typically mediated by heterotrophic bacteria. These bacteria use extracellular enzymes to hydrolyze polysaccharides to oligosaccharides that are then also available to other bacteria. Recently, a new mechanism of polysaccharide processing-"selfish" uptake-has been recognized, initially among gut-derived bacteria.

Glycan Annotation of Mass Spectrometry Data.

Carbohydrates are fundamental molecules of life that are involved in virtually all biological processes. The chemical diversity of glycans─carbohydrate chains─enables diverse functions but also challenges analytics. Annotation of glycans in mass spectrometry (MS) data relies heavily on experimental databases or manual calculations, hindering the discovery of novel glycan compositions and structures.

Characterizing organisms from three domains of life with universal primers from throughout the global ocean.

We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003-2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (>0.2 µm) seawater samples was amplified using the 515Y/926 R universal three-domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S.

From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics.

Spatial metabolomics is transforming our understanding of microbial systems by uncovering the localized molecular dynamics within complex microbial communities. By using advanced mass spectrometry imaging techniques, researchers can now visualize metabolites at the micron scale and show how microbes interact, form biofilms, and influence their environments at unprecedented levels of detail. These approaches not only provide molecular insights they also highlight the need of integrating activity measurements and temporal analyses to capture the dynamic nature of microbial assemblages.

Metaproteomic Dataset on Semi-Diurnal Variability of the Bacterioplankton Communities During a Spring Phytoplankton Bloom in the North Sea.

Phytoplankton blooms create a substrate-rich environment that supports the growth of bacterial planktonic heterotrophs. Previously, we studied the dynamics of such bacterioplankton at a long-term ecological research site near the coast of Helgoland Island (North Sea) once a day. Here, we present a novel dataset (available under the PRIDE-ID: PXD055396) indicating significant differences at the protein level in a semi-diurnal analysis.

Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae.

Background: Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these two microbial communities is limited due to the complexity of benthic microbiomes.

Results: Here, we used a long-reads (LRs) metagenomic approach to examine benthic microbiomes and compared them to the microbiomes in the overlaying water column and on particles, sampled at the same site and time off the island Heligoland in the North Sea.

Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans.

Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematode Caenorhabditis elegans and its microbiota isolate Pseudomonas fluorescens MYb115 that is known to protect against Bacillus thuringiensis (Bt) infection.

Exploring the potential of the COI gene marker for DNA barcoding of planktonic foraminifera.

Metabarcoding is a cornerstone of modern ecology, but its accuracy is dependent on the chosen gene marker. While the small subunit ribosomal DNA (SSU) is a powerful tool to describe protist diversity, its reliability in retrieving the composition of communities is less obvious. It is particularly challenging to obtain quantitative estimates of abundance in planktonic foraminifera, where the variability of the SSU gene copy number can span three orders of magnitude.

Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region.

Upwelling in the Tropical Eastern Pacific profoundly affects marine coastal ecosystems by driving drastic seasonal changes in water temperature, oxygen levels, and nutrient availability. These conditions serve as a natural experiment that provides a unique opportunity to study how marine animals and their associated microorganisms respond in the face of environmental change. Lucinid bivalves host chemosynthetic Thiodiazotropha symbionts equipped with diverse metabolic pathways for sulfur, carbon, and nitrogen use.

Provirus deletion from affects motility, stress resistance, and CRISPR RNA expression.

harbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3, and Halfvol4. In this study, we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain (∆Halfvol1-4) and a wild-type strain reveals an increase in archaella and chemotaxis gene expression, resulting in higher swarming motility in ∆Halfvol1-4.