Rapid quality assessment and multiple assembly comparison are essential steps while assembling new genomes or re-sequencing known ones. Many available tools used for assembly evaluation produce global metrics, representing assembly quality or overall features, most of them working as command line tools that typically act on large data files and produce long detailed result files, where it is not always easy to identify regions of similarity or difference among different chromosome assemblies. ChromoMapperWeb is a new web tool that takes as input nucmer or QUAST output files, quickly identifies similarities and differences between the compared assemblies, and displays them using both table visualizations and pre-arranged or custom graphics. Graphical displays are interactive and allow progressive zoom levels which, in a few steps, move from full genome to very enlarged views, where even small alignment blocks are easily identified. The program, freely accessible through the web server https://chromomapperweb.ceinge.unina.it/, provides an easy-to-use graphical interface, used for experiment planning and interactive evaluation of the results, which include tables and graphical representations of whole genomes, chromosomes, or single blocks.

Microbe Decoder is a web server that predicts functional traits of microbes in microbiome sequencing datasets. Sequencing has revealed thousands of organisms in most ecosystems, but the functional traits of many organisms remain unclear. Existing tools can predict names of organisms or their genes, but they rarely predict concrete biological functions (e.g. fermentation or anaerobic growth). Microbe Decoder fills this gap using three complementary tools relying on taxonomy, metabolic networks, or machine learning. These tools accept either names or gene functions as inputs and are integrated into an easy-to-use web app. When tested against data for microbial isolates, Microbe Decoder showed good predictive performance (e.g. balanced accuracy of 0.85). When applied to datasets from the gut, sediment, and sea, it predicted shifts in functional traits over space and time. Microbe Decoder is designed for use with prokaryotes, with the goal of including eukaryotes in the future. By revealing functional traits of microbes in biological systems, Microbe Decoder will advance biology, medicine, and environmental science. Microbe Decoder is available at https://www.microbe-decoder.org/.

Fungi are a key component of the microbial community in soils, forming species-rich assemblages in soils of natural ecosystems and managed soils. Their unique physiology, absorptive nutritional mode and growth form as spore-producing filamentous eukaryotes enables them to make specific contributions to a wide range of ecological roles as potent decomposers, versatile mutualists and also destructive pathogens. Fungi have important roles in biogeochemical cycles, for example, in nutrient mineralization, plant nutrient uptake and carbon storage. Positioned at the basis of the soil food web, they are one of the pillars of the flow of carbon and energy through the soil food web. As bottom-up controlled organisms in the soil, largely controlled by their resources, they react sensitively to a range of anthropogenic factors, including climate change and other factors of global environmental change, such as chemical pollution. By influencing the food system and via their role as pathogens and in antifungal resistance, fungi are key players in One Health and planetary health. In this Review, Rillig explores the diversity of fungi in the soil ecosystem, their ecological interactions and diverse ecological roles in terrestrial ecosystems as well as anthropogenic factors that affect soil fungi.

Biomolecular condensates have emerged as versatile regulators of plant cellular processes, offering a dynamic and reversible mechanism to coordinate development, stress response, and spatial organization. Through phase separation, these condensates spatially and temporally modulate biochemical reactions, sequester or activate specific proteins and RNAs, and reshape cellular architecture. This review presents a comprehensive and multidimensional framework for understanding biomolecular condensates in plant biology, from their biophysical properties and ensemble dynamics to their roles across diverse cellular compartments, including plasma membranes, cytoskeleton, intracellular compartments, and chromatin. We highlight their functions in growth, environmental sensing, and defense and discuss current challenges in studying their composition, material properties, and context-dependent behaviors. Understanding plant condensates not only deepens our knowledge of plant cell organization and adaptability but also opens new avenues for biotechnological innovation in agriculture.

RNA interference (RNAi) has emerged as a promising approach to sustainable crop protection. Extensive proof-of-concept studies have led to the approval of the first sprayable plant protection products in the United States and China, with Europe currently evaluating them. Although gene silencing mechanisms are among the most extensively studied processes in molecular biology, with two Nobel Prizes recognizing their discovery, the optimization of delivery systems and field performance remains an area currently undergoing extensive development. The uptake, stability, and efficacy of double-stranded RNA (dsRNA) are influenced by species-specific and environmental factors, introducing variability that must be understood in order to select robust targets, design effective dsRNA, and assess risk. Although these knowledge gaps remain, they are increasingly addressed through systematic experimental and technological advances. This review summarizes the current knowledge on RNAi mechanisms in plants, fungi, and insects, emphasizing the differences in dsRNA uptake and processing between species. We highlight advances in formulations and delivery technologies, discuss how regulatory and ecological questions are being systematically investigated, and present examples of approved products that demonstrate the approach's feasibility and safety. Finally, we outline how remaining uncertainties can be addressed through targeted research and risk-mitigation strategies and how RNAi technologies can be incorporated into comprehensive pest and disease management systems.

lthough protein engineering and laboratory evolution have been used to optimize prime editors, we show that previous changes that improve prime editor efficiency also compromise protein stability and expression level, limiting performance. To address these limitations, we apply structure-informed artificial intelligence-guided methods such as the inverse-folding network ProteinMPNN to redesign the reverse transcriptase (RT)domains of engineered and evolved prime editors while preserving regions essential for catalysis. Redesigned RTs are extensively mutated, with 30–163 amino acid substitutions, and exhibit enhanced folding stability and soluble expression and up to twofold higher intracellular prime editor protein levels following mRNA delivery. Redesigned PE8 prime editors demonstrate enhanced editing efficiencies across multiple ex vivo contexts, including in several human primary cell types and via several delivery modalities. In mice, editing efficiency is up to 2.9-fold higher than that of state-of-the-art PE6, PE7 and PEmax prime editors. These findings demonstrate a generalizable approach for augmenting laboratory evolution to improve genome editing agents. A computational redesign strategy improves evolved prime editors.

Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, microbiologists are confronted with numerous algorithms that must be carefully chosen and parameterized to achieve optimal tracking for their experiments. We present an automated methodology to determine optimal tracking configurations for microbiological applications. It is based on TrackMate 8, a novel version of the TrackMate Fiji plugin extended with microbiology-specific tools. Our approach systematically evaluates algorithm-parameter combinations optimizing biologically relevant metrics (e.g., cell-cycle accuracy, bacterial morphology) and includes: (1) integration of deep-learning algorithms (Omnipose, YOLO, Trackastra) adequate for bacterial images in TrackMate; (2) a TrackMate-Helper extension for parameter optimization; and (3) a tracking and segmentation editor for tracking ground-truth generation. We demonstrate the effectiveness of the methodology on two use cases showing its adaptability to diverse experimental conditions. This methodology enables microbiologists with a widely applicable, automated framework to optimize tracking pipelines, facilitating quantitative analysis in bacterial imaging.

Orfamide A, a lipopeptide produced by Pseudomonas protegens Pf-5, is a key determinant of its biocontrol properties. In this study, we investigated the regulatory interactions among the GacS/A two-component system, small RNAs (sRNAs), repressor proteins, and two LuxR-type transcription factors in orfamide A biosynthesis. We found that GacS/A indirectly regulates orfamide A production by enhancing transcription of three sRNAs (RsmX, RsmY, and RsmZ). RsmY and RsmZ synergistically relieve repression by RsmA and RsmE, while RsmX plays a lesser role, likely counteracting only one repressor. LuxR-type transcription factors, LuxR1 and LuxR2, which positively regulate orfamide A synthesis, are directly repressed by RsmA and RsmE via binding to their 5′ untranslated regions, linking them to the Gac–Rsm signaling cascade. We further demonstrated that LuxR2 activates luxR1 expression, which in turn facilitates orfamide A production by binding to the promoter of the orfamide A biosynthetic gene cluster. Importantly, we showed that this entire regulatory cascade operates in the rhizosphere and directly influence biocontrol efficacy. These findings provide a comprehensive understanding of the Gac–Rsm–LuxR pathway in orfamide A biosynthesis and offer valuable insights for the development of biocontrol agents based on Pseudomonas strains.

The rise in antimicrobial resistance underscores the need for innovative strategies to combat gastrointestinal infections. Probiotics such as E. coli Nissle 1917 (EcN) offer promising options, but the molecular mechanisms underlying their protective effects remain unclear. We introduce a G66R point mutation in FimH, creating a high-binding EcN variant that more effectively prevents Salmonella Typhimurium attachment and induces a distinct host transcriptional profile, shifting toward adaptive rather than innate inflammatory signaling. In vivo, EcNG66R pretreatment significantly reduced intestinal colonization, fecal shedding, and systemic spread, and prevented splenic enlargement compared with EcNWT. Protection was associated with a marked expansion of CD4+ and CD8+ T cells, essential for clearing intracellular pathogens. EcNG66R further enhanced “readiness” in the spleen under non-infected conditions, without adverse effects on host physiology. EcNG66R thus functions as a dual-action probiotic—improving competitive exclusion while priming cytotoxic T-cell-mediated protection—and provides a promising platform for developing next-generation microbe-based therapies.

The twin-arginine translocation (Tat) system is the only general pathway for the transport of folded proteins across energized biological membranes. It is found in the bacterial or archaeal cytoplasmic membrane, the plant thylakoid membrane or the inner membrane of plant mitochondria. The biological importance of this translocation system can be exemplified by the fact that all bacterial or plant photosynthesis and photosynthetic oxygen evolution on earth requires this system. Despite many biochemical and biophysical studies, the Tat mechanism has been puzzling since the system was discovered in the 1990ies. Important characteristics of the Tat system could not be explained, and also recent high resolution structures of the Tat system’s core with bound substrate has not led to a general transport mechanism yet. In this integrative review, we attempted to answer the key open questions relevant to the Tat mechanism and thereby developed an in its molecular detail new comprehensive explanation of how folded proteins are translocated across membranes by the Tat system.