Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth. Benoit et al. present nanoMDBG, a scalable metagenome assembler for the latest ONT long reads, developed by adding error correction to metaMDBG. They demonstrate superior performance to the state-of-the-art and equivalent results to PacBio HiFi reads.

Plant hormones are essential small molecules that regulate plant growth, development, and systemic responses to environmental stimuli. These processes are mediated by complex signaling networks involving structurally diverse receptors, regulatory proteins, and dynamic protein–protein interactions. Advances in structural and functional biology over the past two decades have revealed how hormone receptors recognize their ligands and how they mediate responses from perception to signaling through transduction pathways and feedback regulation. In this review, we summarize the current knowledge of plant hormone receptors with experimentally determined structures and highlight their central roles in shaping plant biology. Finally, we discuss outstanding questions in the field and how emerging computational tools may help address these gaps.

Soils are the primary environmental reservoir of plant pathogens impacting food production and ecosystem productivity worldwide. Yet, some soils can also suppress pathogens through environmental and microbial regulation. Here we integrate 1602 soil metagenomes from 59 countries with a greenhouse experiment to identify 32 dominant pathogens, including Ralstonia solanacearum, Clavibacter michiganensis, and Streptomyces europaeiscabiei. Pathogen hotspots occur primarily in warm ecosystems and agricultural soils, whereas higher soil microbial diversity, increased soil organic carbon and colder climatic conditions are associated with lower pathogen prevalence. Non-pathogenic Streptomyces spp., arbuscular mycorrhizal fungi AMF, and biosynthetic gene clusters BGC encoding terpenes and polyketides are associated with reduced pathogen prevalence. Predictive modelling suggests that several dominant bacterial pathogens are likely to increase in prevalence under future climate scenarios, particularly in tropical and subtropical regions. By identifying global drivers of dominant pathogens and their suppression, this study provides a foundation for improved surveillance and management of plant disease risks under climate change. A global study of 1602 soil samples identifies dominant bacterial plant pathogens and reveals microbial traits, soil carbon and climate that promote natural suppression, while climate change may increase disease risks in many regional hotspots.

Conventional electronics are heavily dependent on fossil-based plastics, rare metals, ceramics and semiconductors, the production of which is too energy-intensive and polluting to be sustainable. Wood is a renewable natural resource with unique features that could help to meet the increasing need for environmentally friendly bio-based electronics.

CRISPR–Cas12a has transformative potential in molecular diagnostics owing to its robust signal amplification, but its sustained activity state severely limits temporal programmability and precise nuclease control in complex detection workflows. Here, we demonstrate that the conserved crRNA scaffold secondary structure itself can be repurposed as a reversible and programmable conformational switch to regulate Cas12a activity. By introducing short complementary DNA blockers of tunable length, we achieved length-dependent disruption and remodeling of scaffold secondary structure, shifting LbCas12a into an inactive conformation. Scaffold structure was subsequently reinstated through either single or cooperative strand displacement activation, enabling time-resolved and on-demand restoration of Cas12a activity. The conserved scaffold ensures intrinsic assay universality, while its programmable rewiring markedly improves SNVs discrimination and enables compatibility with one-pot isothermal amplification assays, delivering analytical sensitivity comparable to conventional two-step assays. This regulatory framework was further demonstrated in the detection of Klebsiella pneumoniae and Mycobacterium tuberculosis. By validating the crRNA scaffold as a practical and programmable switch for Cas12a activity control, this work establishes a universal and reversible framework for scaffold rewiring to modulate CRISPR nucleases and offers mechanistic insight to guide future assay engineering.

Food sustainability is a significant challenge for long-term space travel. Plants can provide fresh nutrition, reducing reliance on packaged foods. Using Lunar regolith simulant (LRS), we tested a methodology to create a productive growth medium for horticultural crops on the Moon. We leveraged chickpea (Cicer arietinum), Arbuscular Mycorrhizal Fungi, and Vermicompost (VC) to enhance plant stress tolerance, sequester contaminants, and improve substrate structure. Chickpeas were cultivated in LRS/VC mixtures, with or without AMF, under climate-controlled conditions. Plants seeded successfully in mixtures containing up to 75% LRS when inoculated with AMF. While the number of seeds declined with increasing LRS concentration, seed size remained stable. Higher LRS concentrations induced stress; however, plants grown in 100% LRS inoculated with AMF demonstrated an average extension of two weeks in survival compared to non-inoculated plants. AMF colonized roots across all mixtures, including 100% LRS, demonstrating the ability to establish symbioses under extreme conditions. We also observed improvement in the structural properties of LRS by forming aggregates capable of withstanding extreme conditions, potentially mitigating particle-related hazards. These results provide a baseline for chickpea establishment and yield in amended LRS while demonstrating biological improvements in regolith properties.

In this study, endospore-forming bacteria were isolated, screened, and characterized from samples collected in Tan Phu protection forest for potential use in biofertilizer application. Twelve endospore-forming bacteria showed the ability to produce indole-3-acetic acid were evaluated. Based on the relative enzyme activity, siderophore production, phosphate and potassium solubilization, strain CN12 was selected. Strain CN12 was identified as Bacillus amyloliquefaciens based on 16 S rRNA gene sequencing. The liquid culture medium using inexpensive substrates was optimized for increasing its endospore production. The medium consisted of 10% mung bean sprouts extract solution, 0.87% molasses, 0.12% urea, and 0.06% MgSO4 produced the spore yield of 5.53 ± 3.5 (× 108 CFU/mL) for strain CN12. Malabar spinach plants treated with strain CN12 showed significantly increases of 39.4 ± 8.9 to 77.6 ± 11.8 g in fresh weight, 17.1 ± 3.0 to 65.8 ± 17.2 cm in plant height, and 2.9 ± 0.9 to 6.8 ± 2.3 g in root weight compared to the control. These observations revealed that strain CN12 is a promising candidate for biofertilizer production.

The advent of spatial and quantitative biology has led to immense advances in understanding the complex inner workings of plants, down to the molecular scale. Functional imaging of live plants, which enables the spatial and quantitative mapping of biochemical cues, physicochemical properties of cellular structures, and the dynamics of physical and chemical signals with unprecedented resolution, has become a key technology for advancing the mechanistic understanding of plant cell biology. In this review, we highlight progress in live functional imaging in plants through the use and development of chemical fluorescent probes, which enable plant functional imaging without requiring genetic manipulation of the study object. We explain how probes sense, target, and report on functional features within the plant cell; discuss their limitations, including toxicity; and provide case studies to exemplify how these tools can complement biological studies to unravel the complex machinery that makes plants work. We conclude by outlining the expected future development of this field and identifying key challenges that lie ahead.

Marine viruses impact biogeochemical cycles through cell lysis, releasing organic matter and nutrients that fuel ocean productivity. Identifying and quantifying the specific viruses active in these processes remains a priority in the field. Here, we introduce a click-chemistry method to fluorescently label, sort, and sequence the genomes of newly produced viral particles (viral progeny) released from transcriptionally active host microbial cells, alongside the analysis of co-occurring inactive cells and pre-existing viruses in environmental samples. This approach, called viral BONCAT-FACS, combines biorthogonal non-canonical amino acid tagging (BONCAT) with environmental sample incubation, followed by single-virus and single-cell sorting by flow cytometry (FACS). Genomic analysis of translationally-active cells and new viral progeny in coastal seawater incubations confirmed BONCAT labelling and successful sorting of diverse marine bacteria, microeukaryotic cells, and virioplankton, with stark differences in the predicted turnover of specific groups of infecting viruses, including Pelagiphages, Methylophages, a Flavobacteriales-associated novel “Far-T4” clade, non-canonical DNA viruses of Naomiviridae using dU instead of dT, algae-infecting giant NCLDV viruses, and parasitic virophages. Sequenced BONCAT-active cells showed a strong enrichment in viral contigs relative to the inactive cell fraction, suggestive of a large proportion of translationally-active virocells. This study illustrates the effectiveness of viral BONCAT-FACS for uncovering genome-resolved virus-host dynamics. By providing a direct approach for tracking active viral infections in natural environments, this method enhances our ability to investigate behavior and interactions of these nanoscale predators, expanding our understanding of their role in ecosystem dynamics.

Asgard archaea played a key role in the origin of the eukaryotic cell, with extant genomes encoding relatives of diverse eukaryotic signature proteins (ESPs) involved in cellular organization. However, their often punctuated distribution and the absence of detectable homologues for many eukaryotic proteins limit our ability to reconstruct the cellular complexity of the Asgard archaeal ancestor of eukaryotes. Here we used de novo protein structure modelling and sequence similarity detection across an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome. We identified 908 ‘isomorphic’ ESPs—Asgard archaeal proteins with statistically enriched structural matches to eukaryotic proteins, often bridging deep sequence divergence. These isomorphic ESPs are enriched in information storage and processing roles and contain key components of the eukaryotic Vault (MVP) and Commander (COMMD) complexes, with potential roles in cellular compartmentalization and endosomal processing. These findings expand the repertoire of eukaryotic-like proteins in Asgard archaea and suggest a higher degree of eukaryote-like cellular complexity in the archaeal ancestor of eukaryotes. A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

The ShosTA system, a two-component toxin-antitoxin (TA) system consisting of the ShosT and ShosA proteins, has recently been shown to mediate antiphage defense. However, the molecular mechanisms underlying this system’s role in anti-phage defense remain elusive. Here, we first confirmed that ShosT functions as the toxic component that induces cell death, while ShosA acts as the antitoxin to neutralize these toxic effects. We then solved the crystal structures of apo-ShosT, ShosA, and the ShosT-PRPP (phosphoribosyl pyrophosphate) complex. The structural data reveal that while ShosT contains a PRTase (phosphoribosyl-transferase) domain, it possesses unique noncanonical features; furthermore, we demonstrate that its binding to PRPP is indispensable for its toxic activity. ShosA is a DprA-like protein that functions as a homodimer. Both its ssDNA-binding and dimerization abilities are essential for its antitoxin activity. Further biochemical and structural studies demonstrate that ShosA directly binds to RecA, an interaction that is essential for neutralizing ShosT. The ShosA–RecA interaction is sensitive to the presence of ssDNA, implying that ShosTA-mediated abortive infection (Abi) may be triggered by the invading phage DNA. Our studies uncovered the mechanisms of ShosT inducing cell death and ShosA antagonizing the toxic effects of ShosT in anti-phage defense.

Site-directed nuclease (SDN) classification into SDN-1, SDN-2 and SDN-3 outcomes is used for regulating genome-edited plant products in some countries. This reductive categorization system fails to cover the breadth of genome editing technologies developed over the past decade and their rapidly approaching commercial use. Here, we argue that, in the context of plant breeding, regulations should focus on the characteristics of the genome editing outcome, rather than specific methods used in the development process. Such a science-based, outcome-focused regulatory approach would future-proof the risk-proportionate oversight of plant breeding innovations and enable a more efficient delivery of improved crop varieties amidst growing concerns of climate change and evolving pests and diseases.