Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improvements in scale and cost reduction. Nanopore sequencing has long held the promise for such progress, but has had limited market penetration. This is because efficient and accurate nanopore sequencing of nucleic acids has been challenged by fundamental signal-to-noise limitations resulting from the poor spatial resolution and molecular distinction of nucleobases. Here, we describe Sequencing by Expansion (SBX), a single-molecule sequencing technology that overcomes these limitations by using a biochemical conversion process to encode the sequence of a target nucleic acid molecule into an Xpandomer, a highly measurable surrogate polymer. Expanding over 50 times longer than the parent DNA templates, Xpandomers are engineered with high signal-to-noise reporter codes to enable facile, high-accuracy nanopore sequencing. We demonstrate the performance of SBX and present the specialized molecular structures, chemistries, enzymes and methods that enable it. The innovative molecular and systems engineering in SBX create a transformative technology to address the needs of existing and emerging sequencing applications. ### Competing Interest Statement Competing interests: Various authors are inventors on the following patents 7939259, 8349565, 8324360, 9920386, 9670526, 10851405, 11920184, 10457979, 10676782, 10301345, 10774105, 10745685, 11299725, 12037577, 12116570, 11530392, 11970731, 9771614, 8586301 and 10996213 held by Roche Sequencing Solutions, Inc. that cover SBX Technology. MK, RM, MN, AJ, MP, CC, KB, TL, JC, LM, ML, TR, CW, SB, AL, MK, RB, SM, BB, BK, ML, MW, AK, AA, MRP, SK, JL, MB are employees of Roche Sequencing Solutions, Inc. SBX, Xpandomer and XNTP are registered trademarks of Roche Sequencing Solutions, Inc.

Microbial growth curve data contain valuable information about microorganisms' physiology and metabolism. However, they are currently reported in various formats scattered across publications. A generic resource that allows querying and comparing microbial growth curve data is currently missing. For this reason, we developed μGrowthDB, an open repository designed to store, visualize, analyze, and share quantitative measurements of species abundances and metabolite profiles from monocultures and communities of known composition. μGrowthDB is designed to accommodate a range of experimental designs and measurement techniques. In addition to querying microbial growth curves by organism or metabolite, μGrowthDB supports comparative visualisation of growth curves and offers a guided data submission process intended to make data upload as easy as possible. μGrowthDB is available at: https://mgrowthdb.gbiomed.kuleuven.be/. ### Competing Interest Statement The authors have declared no competing interest.

Expansion of marine global oxygen minimum zones (OMZs) can have profound impacts on resident macrofauna. Less obvious is the influence OMZs will have on the diversity and abundance of planktonic microbes. This is particularly true in understudied OMZs such as the northern Benguela Upwelling System (nBUS). Here, we analyzed the influence of oxygen concentrations on the microbial community in the nBUS OMZ using 16S rRNA gene (iTag) sequence data. In the nBUS oxygen was a primary driver influencing microbial community structure and diversity. Diversity was highest in dysoxic samples and lowest in suboxic samples, which was primarily due to changes in community evenness in relationship to oxygen concentrations. For example, evenness decreased in suboxic samples due to oscillations in the abundance of microbial groups such as Thioglobaceae (SUP05), which was found to be the most abundant microbe in the nBUS OMZ and significantly increased in abundance as oxygen decreased. This finding prompted an analysis of 217 publicly available medium to high quality Thioglobaceae genomes, including cultured representatives, from the nBUS and other OMZs. Genome annotation of these Thioglobaceae indicated important roles in carbon cycling, sulfur oxidation and denitrification. Importantly, few Thioglobaceae possess the genetic potential to carry out complete denitrification, as most lack the gene that codes for nitrous oxide reductase (NosZ), which converts nitrous oxide (N2O), a potent greenhouse gas, to nitrogen gas. As OMZs expand in size and severity, decreasing microbial diversity and a concomitant increase in Thioglobaceae abundances, could lead to enhanced N2O production through incomplete denitrification.

Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we question this view by demonstrating cross-communication between distinct arbitrium systems. Using prototypical arbitrium phages, we demonstrate that AimP peptides bind and repress unrelated AimR receptors, promoting lysogeny and reducing prophage induction. Structural and binding assays reveal conserved residues enabling cross-recognition while preserving specificity. In mixed lysogenic cultures, these interactions shape induction outcomes, demonstrating ecological relevance. We extent these findings to infection contexts, showing that arbitrium signalling influences outcomes in cells harbouring prophages with compatible communicating systems. These findings reveal that phages engage in cross-species communication, a trait restricted to more complex life forms, challenging our understanding of how these elements reshape microbial communities. ### Competing Interest Statement The authors have declared no competing interest. Spanish Government (Ministerio de Ciencia e Innovación), PID2022-137201NB-I00 Valencian Government, CIPROM/2023/30 European Commission NextGenerationEU fund, (EU 2020/2094) European Research Council Grant, 101118890 (TalkingPhages) Medical Research Council (UK), MR/X020223/1, MR/M003876/1, MR/V000772/1 Biotechnology and Biological Sciences Research Council (BBSRC, UK), BB/V002376/1, BB/V009583/1 Engineering and Physical Sciences Research Council (EPSRC, UK), EP/X026671/1

In this Review, Weingarth and colleagues discuss both recently discovered compounds and established envelope-targeting antibiotics, including compounds that target Gram-positive bacteria, more complex Gram-negative bacteria and mycobacterial pathogens, with a particular focus on their drug–target interactions.

Abstract. Nitrogen and iron are essential yet often limiting nutrients in many ecosystems. Microbial nitrogen fixation by diazotrophs and dissimilatory fer

Abstract. In complex ecosystems, the loss of certain species can trigger a cascade of secondary extinctions and invasions. However, our understanding of th

Abstract. Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA d

Giant double-stranded DNA viruses infecting microalgae often interact with polinton-like viruses (PLVs), yet their dynamics within natural hosts remain poorly understood. Here, we report the isolation of a new Tetraselmis striata giant virus (Allomimiviridae) from Mediterranean coastal waters, which we designate Oceanusvirus lionense (TetV-2). From the same sample, we co-isolated a PLV, Tsa-S2b, that replicates concomitantly with TetV-2. Remarkably, TetV-2 infection also reactivates at least two additional PLVs integrated into the host genome. We show that these PLVs exert a virophage-like effect, reducing the fitness of the giant virus. Comparative genomics reveals that these virophagic PLVs are related to the autonomous lytic PLV TsV-N1, sharing structural but not replication-associated genes. This newly described pathosystem provides a unique model to investigate the evolution of PLVs and the parasitic mechanisms underlying virophage-giant virus interactions. ### Competing Interest Statement The authors have declared no competing interest. European FEDER Fund, project 1166-39417 Excellence Initiative of Aix-Marseille University – A*MIDEX

Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Here we identify Hib, a previously unrecognized family of archaeal hibernation factors. Genetic, structural and biochemical analyses show that Hib binds ribosomal subunits, blocking the mRNA channel and tRNA sites to inactivate translation. Deletion of hib in Thermococcus barophilus delays recovery from stationary phase and reduces 70S ribosome pools, establishing its role in ribosome preservation. Hib displays a unique modular architecture, combining a bacterial-like HPF module with tandem CBS domains. Cryo-EM structures reveal conformational heterogeneity of Hib:ribosome complexes, consistent with dynamic engagement, and the CBS-containing N-terminal domain binds adenine nucleotides, suggesting a link between hibernation and energy status. These findings define Hib as a key archaeal hibernation factor and provide a framework for understanding ribosome dormancy and adaptation across all domains of life. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-25-CE12-4161

Abstract. While resequencing Microcystis aeruginosa (PCC7806) and its nontoxigenic mutant (PCC7806 ΔmcyB), we discovered identical unreported plasmids in b

Peptidoglycan (PG) is a crucial biopolymer in the bacterial cell wall that has been the subject of intense study since it was first isolated in the early 1950s (1, 2). Over the last 70 years, extensive research has expanded our understanding of the structure and function of this microbial biopolymer. Recent advances in mass spectrometry and bioinformatics have revolutionized PG analysis, enabling a comprehensive detection of individual components and their global composition within bacterial cells. Like genomics, transcriptomics, and proteomics, peptidoglycomics is the non-targeted, non-biased detection of all elements that comprise the overall PG structure. Peptidoglycomic analyses can identify and monitor hundreds of potential compositional changes that occur within the PG structure of a cell. By comparison, traditional methods of analyzing PG composition only distinguish a relatively limited number of PG components. Therefore, peptidoglycomic approaches produce a detailed global overview of the PG structural elements and give unprecedented insight into the physiological function of this biopolymer within the bacterial cell.

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...