RMH

Soil-borne diseases hinder crop yield and quality. Liu et al. found that organic fertilizer induces tomato roots to secrete specific microRNAs (miRNAs) likely via exosome-like extracellular vesicles (EVs) to regulate rhizosphere microbiomes and enhance soil disease resistance, revealing a new mechanism and informing sustainable agriculture.

Below every step we take there is groundwater. Out-competing rivers, lakes and wetlands in terms of water quantity and quality, shallow aquifers are an essential reservoir of freshwater for the human population. At the same time, they represent the largest freshwater biome on earth, forming a responsive but vulnerable interface between the highly dynamic surface aquatic and terrestrial ecosystems and the environmentally static deeper zones of the subsurface. Shallow aquifers are home to a vast phylogenetic and functional microbial diversity, regularly surpassing those of surface environments. Predominantly colonized by microorganisms, key drivers of community composition and biogeochemical cycles are the hydrogeological settings, availability of energy and prevailing redox conditions, as well as climate and local to regional anthropogenic activities. Although there is steadily growing knowledge on microbial biodiversity and their potential functions, quantitative data on active key processes, such as carbon cycling, are scarce. We do have a very incomplete idea of the abundances and distribution of viruses, protists and fungi and their ecological role in groundwater. In this Review, we discuss current and future pressures to shallow groundwater ecosystems in terms of microbial community dynamics particularly in light of global and climate change, that is, groundwater pollution and warming. In this Review, Karwautz and Griebler examine the microbial communities found in shallow groundwater and aquifers, exploring their diversity, functional roles and dynamic interactions with adjacent terrestrial and aquatic ecosystems, as well as the influence of global change and anthropogenic pressures on these microorganisms.

CRISPR-Cas systems have revolutionized microbial genome engineering, yet counter-selection strategies typically rely on targeted DNA cleavage, where the severe cytotoxicity of double-strand breaks restricts transformation efficiency and clonal recovery. Here, we present an innovative strategy, SuCas12a2-Universal Recombination Editing (SURE), that circumvents these limitations by repurposing the RNA-targeting CRISPR-Cas12a2 system. Instead of directly attacking the genome, SURE utilizes Cas12a2’s RNA-triggered collateral activity to induce an abortive infection-like state, providing a potent yet recoverable selective pressure. This strategy increases transformation efficiency by up to 1,000-fold compared to Cas9- or Cas12-based systems while achieving over 90% editing efficiency for gene knockout, insertion, and replacement in E. coli MG1655. We validate the SURE platform’s broad utility by extending it to diverse species, including Bacillus subtilis BSZR and Shewanella oneidensis MR-1. Mechanistically, we identify collateral double-stranded DNA degradation as the decisive factor for driving efficient selection. Finally, we apply this system to engineer E. coli MG1655 for efficient assimilation of the plastic monomer ethylene glycol, demonstrating its practical utility. Collectively, this work establishes a universal and robust RNA-guided editing framework that resolves the toxicity-efficiency trade-off inherent to the conventional DNA-targeting methods. Microbial genome engineering is often limited by toxicity from existing selection methods. Here, the authors develop a Cas12a2-based RNA-guided editing strategy that improves efficiency and reduces cellular damage, providing a robust tool for microbial engineering.

Outer membrane vesicles (OMV) contribute to bacterial adaptation and persistence, yet the metabolic triggers of vesiculation remain poorly understood. Here, we show that clinical Acinetobacter baumannii strains vary in their capacity for glucose oxidation, with only oxidation-positive strains exhibiting acidification and enhanced OMV biogenesis. Comparative genomics revealed variable distributions of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase homologs among isolates. In strain NCCP 16011, glucose supplementation induced acidification, biofilm formation, membrane remodeling, and enhanced OMV production. Introduction of the PQQ biosynthetic gene cluster into PQQ-deficient ATCC 17978 conferred glucose-dependent acidification and increased vesiculation. Electron microscopy and fluorescence recovery after photobleaching analyses revealed periplasmic expansion, protein accumulation, and reduced protein mobility, consistent with envelope stress. The adhesin Ata and the β-lactamase BlaOXA-51 were enriched in glucose-induced OMVs, consistent with their respective roles in cell aggregation and β-lactam resistance. Together, these findings identify glucose oxidation-driven acidification as a metabolic trigger of envelope instability and OMV biogenesis in A. baumannii, linking glucose metabolism to envelope remodeling.

Microorganisms facilitate both the synthesis and breakdown of bio-based biodegradable plastics, which positions them as central players in the development of a future circular plastics economy. However, advances in microbial production and biodegradation of plastics are often considered in isolation, limiting our ability to integrate these processes into viable circular systems. In this Review, we discuss the contributions of microorganisms across the life cycle of key bio-based polymers, focusing on polyhydroxyalkanoates, bacterial nanocellulose, and the monomers of polylactic acid and polyethylene furanoate, and we critically assess the extent to which current microbial capabilities can support polymer synthesis and degradation. Although the genetic capacity for these processes is widespread, this does not necessarily translate into efficient synthesis or biodegradation in industrial or environmental conditions. Microbial synthesis remains constrained by low volumetric productivity, carbon inefficiencies and downstream processing challenges, whereas biodegradation is highly dependent on material properties and environmental conditions, with efficient biodegradation often limited to managed settings. Thus, achieving an effective circular bio-based plastic economy requires the integration of microbial engineering, polymer chemistry, material science and other disciplines to optimize both production and end-of-life management. In this Review, O’Connor and colleagues discuss the contributions of microorganisms across the life cycle of key bio-based polymers and assess the current role, the potential and limitations of microbial production and degradation of bio-based polymers as well as the implications for integration of microbiological processes into a circular bioeconomy.

Human tumor-associated microbes – the tumor microbiome – have demonstrated an increasingly important role in human health due to their relevance to cancer progression and treatment response. While the metabolism at the host-microbiota interface, such as in the human gut, has been extensively investigated in recent years, the specialized metabolites from the tumor microbiome remain uncharted territory. To address this knowledge gap, we report a survey of the biosynthetic potential of the human tumor microbiome. Utilizing high-quality microbial metagenome-assembled genomes from 3,526 human tumor tissue samples, we identify 528 biosynthetic gene clusters with the potential to encode specialized metabolites relevant to tumor pathology. We reveal that the tumor microbiome encodes known and unknown metabolites spanning multiple biosynthetic classes. From this diverse biosynthetic landscape, we express a conserved family of biosynthetic genes from the genus Fusobacterium, which has a well-established role in cancer, and discover distinct families of long-chain fatty acyl amides. We subsequently find that one of these fatty acyl amides, oleoyl γ-aminobutyric acid, has immunomodulatory and G-protein-coupled receptor partial agonist activities, potentially supporting the influence of Fusobacterium in tumor pathology. The findings of our investigation lay a foundation for further research into the roles of tumor microbe-derived metabolites in cancer. Here, Pulliam and colleagues characterize the metabolites encoded by tumor-inhabiting microbes and their potential role in cancer pathology.

Advances in synthetic biology now offer spatiotemporal, conditional, and precise control of plant metabolism, enabling engineering of pathways that have resisted constitutive approaches. Plant cell wall biosynthesis and metabolite glycosylation are industrially valuable pathways that are also acutely sensitive to constitutive perturbation. We use these pathways as a lens to examine the potential impact of emerging programmable tools, including synthetic, tissue-specific, and inducible promoter design; RNA-, protein-, and pathway-level regulatory switches; and CRISPR-based systems. We then examine how these tools are overcoming barriers in cell wall engineering, production of glycosylated therapeutics, and emerging applications in signalling and herbicide tolerance. Together, these advances move plant metabolic engineering from static modification toward self-regulating, precise metabolic control, with complex glycosylation emerging as both a significant test and a key beneficiary of these advances.