The authors developed a screen to find compounds that modulate intracellular Staphylococcus aureus metabolism and discovered KL1, which sensitizes persisters to antibiotics by reversing host-induced tolerance.

Surbhi et al. report that a conserved AAA+ ATPase, IncA, whose production is enhanced in nutrient-poor conditions, is required to inhibit DNA replication progression by delocalizing the β-sliding clamp DnaN in Caulobacter. Deletion of IncA increases mutation frequency, underscoring its role in maintaining genomic integrity under nutrient scarcity.

Abstract. SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smal

The adaptive oxidative stress response allows bacteria to adapt to hostile environmental conditions. We explored how the evolution of cellular ROS in oxidative stress triggers physiological and genetic changes in multiple pathogenic species. Our study posits that growth-survival tradeoffs under oxidative stress enact a diverse array of genetic and physiological changes resulting in cross-resistance to acid, antimicrobial resistance, and metabolic reprogramming in bacteria. ### Competing Interest Statement The authors have declared no competing interest.

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

Abstract. SMART (Simple Modular Architecture Research Tool, https://smart.embl.de) is a web-based platform for identifying and annotating protein domains a

Abstract. Phase separation (PS) is a fundamental principle driving the formation of membraneless organelles (MLOs), which are critical for various cellular

Structural analysis reveals how a phage protein blocks a lipid II flippase to prevent bacterial cell wall synthesis.

Abstract. The deep biosphere encompasses life beneath the Earth’s surface and constitutes a substantial portion of the planet’s microbial biomass. This stu

The genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.

A two-phase machine-learning-based tool making use of high-throughput experimentation is introduced to examine the connections between chemical and protein sequence space and predict productive biocatalytic reactions among substrate and enzyme pairs.

Extracellular ATP acts as a signal regulating physiology and immunity in eukaryotes and is elevated during intestinal infection or damage. Tronnet et al. show that extracellular ATP reprograms the transcriptional and metabolic landscapes of gut bacteria, impacting biofilm formation, production of bioactive metabolites, bacterial envelope composition, antimicrobial resistance, and virulence.

Identification of the core microbiome from clear water lakes in the Arctic reveals non-unique members when compared with a conceptually similar lake from a more temperate region. Biogeographic assign...

We report the isolation and genomic sequencing of nine Actinomycetota obtained from both cave biofilms and trogloxenic Ceuthophilus (cave crickets). Strains were isolated from samples via actinomycetota-selective media and sequenced using nanopore sequencing. Provisional taxonomic inference of strains was performed by whole genome phylogenetic analysis, revealing a broad range of genera, with most strains clustering with known genera with digital DNA-DNA hybridization values less than 70%, and one strain not clustering with known genera. An analysis of secondary metabolism reveals the quantity and diversity of secondary metabolism in cave Actinomycetota. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, https://ror.org/01cwqze88, CA226833

Circadian rhythms, driven by endogenous clocks and synchronized with environmental cues, are fundamental to life on Earth. While extensively studied in diverse organisms, their influence on viral ecology remains largely unexplored. This study takes the temporal dynamics of viruses in Daya Bay as an example to uncover the rhythmic control of viral replication and activity. Using a high-resolution time-series dataset collected every 2 hours over a 3-day period, we identified a total of 22,151 viral operational taxonomic units (vOTUs) and 414 Nucleocytoplasmic Large DNA Virus (NCLDV) genomes. Our analysis revealed significant diel fluctuations, with 14.48% of vOTUs exhibiting diel patterns in metagenomic abundance and 1.97% showing diel transcriptional activity. We found that these abundant diel viruses infect hosts across the domains of life, including cyanobacteria, pelagibacteria, Marine Group II (MGII) archaea and protists, all known for their diel metabolism. The expanded spectrum of host diversity with diel viral interactions significantly broadens our understanding of virus-host rhythmic dynamics in natural environmental settings. A strong positive correlation was detected between the transcriptional activities of these diel viruses and their respective hosts. Contrary to bacteriophages, which mostly peaked during the day, we demonstrated that NCLDVs showed nocturnal diel abundance with a co-fluctuating diel transcriptomic activity pattern tightly hitched to their hosts, peaking at night and declining during the day. Furthermore, we identified a rich compendium of viral genes with significant diel expression patterns, including those related to structural protein production, DNA replication, and stress response. Notably, several essential viral genes involved in stress response and repair were found to be diel transcribed for the first time, including UV-endonuclease (UvdE), peroxidase, chaperones, and early light-induced protein (ELIP). Our findings suggest that viruses across host domains actively synchronize with environmental cues to optimize their replication and transmission, despite their dependence on host metabolism. This study provides novel insights into the rhythmic control of viral communities and their intricate interactions with hosts, with profound implications for microbial community succession and biogeochemical cycles. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 2476109, 42276163, 42406144 the Shenzhen Science, Technology and Innovation Commission Program, JCYJ20220530115401003 SUSTech Education Reform Programme, SJZLGC202437 grant from the Deutsche Forschungsgemeinschaft, SPP 2330 project number 464976318

Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

AbstractSummary. Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic c

Intrinsically disordered proteins and regions (IDRs) lack stable 3D structures, posing challenges for interaction prediction. We present SpatPPI, a geometric deep learning model tailored for IDPPI prediction. SpatPPI leverages structural cues from folded domains to guide the dynamic adjustment of IDRs via geometric modeling, adaptive conformation refinement, and a two-stage decoding mechanism. It captures spatial variability without requiring supervised input and achieves state-of-the-art performance on benchmark datasets. Molecular dynamics simulations further validate its high adaptability to conformational changes in IDRs and strong capacity to generate distinct and structure-aware embeddings. A freely accessible server is available at http://liulab.top/SpatPPI/server .

R6K plasmids are commonly used for a wide range of genome engineering applications due to their ability to support transient delivery of genetic cargoes in many hosts. The maintenance of R6K plasmids requires specific strains. Unfortunately, many of these have obscure backgrounds, limited availability and were not built for efficient cloning. To address this issue, we present the construction and characterisation of a series of Pir E. coli strains called SHARK that are built from the DH10B derivative, Marionette-Clo. All SHARK strains have a genome encoded Pir gene for stable R6K plasmid maintenance and a λCI gene for tight unconditional repression of specific genes on plasmids. We show that SHARK strains are >100-fold more efficient than a commercial Pir strain for large and complex cloning reactions. SHARK is intended to help facilitate the cloning of large and complex R6K plasmids for challenging genome engineering projects, with all strains and genetic tools for their assembly being made publicly available. ### Competing Interest Statement The authors have declared no competing interest. Biotechnology and Biological Sciences Research Council, BB/Y007638/1 Royal Society, https://ror.org/03wnrjx87, URF\R\221008

Tertiary plastids derived from diatoms in “dinotom” dinoflagellates offer a rare view of organellogenesis in action, while the genomic and metaboli...

Desiccated cells lose over 85% of their water content and experience widespread biomolecular dysfunction. Romero-Pérez et al. show that the yeast proteome contains a subset of proteins that are desiccation tolerant and possess specific surface chemistries. Moreover, resistant proteins show a functional bias that can facilitate recovery upon rehydration.

Transcription attenuation fine-tunes biosynthetic gene expression in bacteria via premature termination upon metabolic signals. In transcription initiation-controlled bacterial systems, promoter architecture and transcription factor binding sets the size of transcriptional bursts at σ70 promoters, while distal enhancer elements and associated transcriptional activators modulate burst frequency at σ54 promoters. Using the tryptophan biosynthesis operon as a model, we show that transcription attenuation, acting post-initiation and alongside transcriptional repression, simultaneously modulates both burst size and frequency from a σ70 promoter. This challenges the view that frequency modulation requires distal enhancer input and reveals that post-initiation mechanisms can shape divergent transcriptional bursting. We also uncover that bacteria use cross-feeding as a previously unrecognised strategy for controlling cell-to-cell variation in gene expression, with implications for metabolic coordination among cells. These findings redefine transcription dynamics within cell populations and suggest new principles by which bacteria regulate gene expression to adapt to environmental change. ### Competing Interest Statement The authors have declared no competing interest. Leverhulme Trust, RPG-2021-050 Biotechnology and Biological Sciences Research Council, BB/W019698/1

Thioredoxins are ubiquitous redox proteins that are found in all domains of life. These conserved proteins are also found in many phages, including marine cyanophages that infect the ecologically important marine cyanobacteria. However, their role in phage infection is not known. Cyanophages also carry many small genes lacking homology to known functional domains. Whether these have a functional role or not remains unknown. Here, we explore the distribution and role of a cyanophage thioredoxin (trxA), and that of a small gene directly downstream of it (g26), in phage infection. For this we used the T7-like cyanophage, Syn5, which infects an open-ocean marine Synechococcus strain, WH8109. We found that thioredoxin genes are common in phage genomes, including in cyanophages. The g26 gene, however, is restricted in it distribution to the cyanophages. The cyanophage thioredoxin is catalytically active and it increases phage DNA replication, progeny production and competitive fitness. It also negatively impacts host growth. The g26 gene product is translationally coupled to, and thus dependent on, translation of the thioredoxin gene. This gene itself significantly increases phage virulence and fitness, yet reduces burst size. Our findings demonstrate that cyanophage thioredoxins impact phage fitness and infection physiology and that small viral genes with no homology to known genes can play an important role in the infection process. These findings provide insights into the importance of unusual genes in phage genomes and show that they are likely to play an important role in the interactions between abundant cyanobacteria and cyanophages in ocean ecosystems. ### Competing Interest Statement The authors have declared no competing interest.

The structural integrity of bacterial cells is traditionally attributed to the peptidoglycan cell wall, and more recently to the outer membrane, with the cytoplasmic membrane assumed to be mechanically passive. Cells lacking filaments of the actin homolog MreB are more bendable, suggesting a role for the cytoskeleton in cell stiffness. Here, we show that MreB does not stiffen the envelope directly, but instead mechanically couples the cell wall to the cytoplasmic membrane through its role in peptidoglycan synthesis, increasing resistance to bending. Under hyperosmotic stress, MreB relocalized to the poles, forming linkages that prevent membrane detachment from the cell wall and attenuate cytoplasmic contraction. Disruption of MreB filament formation, nutrient starvation, or inactivation of glycan elongation factors abolished or reduced this coupling, revealing that peptidoglycan biosynthesis actively mediates stress distribution across surface layers. Our findings redefine the bacterial envelope as a mechanically integrated composite, with the cytoplasmic membrane having substantial load-bearing capacity. ### Competing Interest Statement The authors have declared no competing interest.

Abstract. Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate.