The growing demand for sustainable solutions in agriculture, which are critical for crop productivity and food quality in the face of climate change and the need to reduce agrochemical usage, has brought biostimulants into the spotlight as valuable tools for regenerative agriculture. With their diverse biological activities, biostimulants can contribute to crop growth, nutrient use efficiency, and abiotic stress resilience, as well as to the restoration of soil health. Biomolecules include humic substances, protein lysates, phenolics, and carbohydrates have undergone thorough investigation because of their demonstrated biostimulant activities. Here, we review the process of the discovery and development of extract-based biostimulants, and propose a practical step-by-step pipeline that starts with initial identification of biomolecules, followed by extraction and isolation, determination of bioactivity, identification of active compound(s), elucidation of mechanisms, formulation, and assessment of effectiveness. The different steps generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to pilot-scale production in practical scenarios that are aligned with the prevailing regulatory frameworks.

CRISPR–Cas12a has been demonstrated to be activated for its trans-cleavage activity by single- and double-stranded DNA containing a protospacer adjacent motif (PAM), but other types of activators have remained undiscovered. In this work, we found that a hairpin-structured substrate can activate the trans-cleavage activity of Cas12a without a PAM, and the parameters of the hairpin loop obviously affect the activity. Cas12a exhibits sequence preference for proximal loops, preferring to recognize polyadenine hairpin loop activators. Molecular docking and dynamic calculations provide a theoretical basis for the activation of Cas12a by hairpin activators. Leveraging the efficient activation capability of the hairpin activator, we constructed an allosteric detection platform for non-nucleic acid targets, capable of sensitively and specifically detecting hypochlorous acid and calcium ions. This novel activator of Cas12a holds enormous potential for the development of multi-functional biological platforms.

The global crisis of plastic waste accumulation threatens wildlife and ecosystems. Catalytic processes that convert plastic waste into valuable chemicals and fuels offer promising solutions. Recycling or upcycling of real-life plastic mixtures is challenging owing to their diverse composition and structure. Here we propose a product-oriented strategy leveraging the orthogonality in reactivities of different functional groups in plastic mixtures to yield valuable products. This approach involves identifying functional groups followed by converting a selective component in the mixture to valuable products. We use mixtures of polystyrene, polylactic acid, polyurethane, polycarbonate, polyvinyl chloride, polyethylene terephthalate, polyethylene and polypropylene, as well as real-life plastics, to demonstrate the feasibility and effectiveness of the proposed strategy. The diverse physical and chemical properties of these components, which typically hinder direct recovery, offer opportunities for extraction and transformation with the proposed strategy. From a 20-g mixture of real-life plastics, including polystyrene foam, a polylactic acid straw, a polyurethane tube, a polycarbonate mask, a polyvinyl chloride bag, a polyethylene terephthalate bottle, a polyethylene dropper and a polypropylene bottle, we obtained more than 8 separate chemicals: 1.3 g of benzoic acid, 0.5 g of plasticizer, 0.7 g of alanine, 0.7 g of lactic acid, 1.4 g of aromatic amine salt, 2.1 g of bisphenol A, 2.0 g of terephthalic acid and 3.5 g of C3–C6 alkanes. This study reveals the potential for designing transformation strategies for complex plastic waste based on their chemical nature and opens paths for managing end-of-life plastic mixtures. A product-oriented strategy that leverages the reactivities of different functional groups in real-life plastic mixtures can be used to obtain valuable products, opening a path for managing end-of-life plastic mixtures.

Galactomannan oligosaccharides (GMOS), composed of 2–10 mannose units linked with β-1, 4 glycosidic bond as the main chain and galactose linked with α-1, 6 glycosidic bond as the side chain, are crucial for probiotic food synthesis due to their ability to promote the growth and activity of beneficial intestinal microbiota, enhance the host immune system, and improve nutrient digestion. GMOS is usually obtained by hydrolyzing plants such as locust bean gum and guar gum with mannanase. β-mannanase ManA from Alkaliphilic Bacillus sp. N16-5 can hydrolyze β-1, 4 glycosidic bond of galactomannan. In this study, an immobilization system was employed utilizing polyhydroxyalkanoate (PHA) biopolymers, which naturally have an affinity mainly mediated by hydrophobic interaction for PhaP protein. Fusion protein combining ManA with PhaP from Aeromonas hydrophila, was subsequently immobilized on PHA support to form a multi-enzyme complex, facilitating the hydrolysis of locust bean gum to generate GMOS. This immobilized enzyme enhances enzyme stability and reusability, can be reused up to 32 times while maintaining ~ 80% of its activity, offering substantial cost savings through in-situ enzyme and product separation. Additionally, the different PHA forms were developed to hydrolyze locust bean gum to produce GMOS, such as nano PHA particles, PHA electrospun materials, while these preliminary investigations show promise, further research is needed to optimize their performance and practical application.

Metabolomics, a critical tool for analyzing small-molecule metabolites, integrates with genomics, transcriptomics, and proteomics to provide a systems-level understanding of fungal biology. By mapping metabolic networks, it elucidates regulatory mechanisms driving physiological and ecological adaptations. In fungal pathogenesis, metabolomics reveals host-pathogen dynamics, identifying virulence factors like gliotoxin in Aspergillus fumigatus and metabolic shifts, such as glyoxylate cycle upregulation in Candida albicans. Ecologically, it highlights fungal responses to abiotic stressors, including osmolyte production like trehalose, enhancing survival in extreme environments. These insights highlight metabolomics’ role in decoding fungal persistence and niche colonization. In drug discovery, it aids target identification by profiling biosynthetic pathways, supporting novel antifungal and nanostructured therapy development. Combined with multi-omics, metabolomics advances insights into fungal pathogenesis, ecological interactions, and therapeutic innovation, offering translational potential for addressing antifungal resistance and improving treatment outcomes for fungal infections. Its progress shed light on complex fungal molecular profiles, advancing discovery and innovation in fungal biology.

Global agriculture stands at a critical juncture, facing the dual challenge of sustaining food production for a rapidly growing population while mitigating the environmental consequences of intensive farming. The overuse of chemical fertilizers and pesticides has accelerated soil degradation, biodiversity loss, and ecological imbalances, threatening long-term viability. Synthetic microbial communities (SynCom) have emerged as a promising approach to reshape plant-microbe interactions, offering a precise, scalable, and ecologically sustainable alternative to conventional agrochemicals. Unlike native microbial communities, which form naturally and vary with environmental conditions, SynComs are deliberately assembled consortium of multiple microbial strains selected for their complementary functions, ecological compatibility, and ability to perform targeted roles within a host or environment. By engineering microbes with targeted functional traits, SynComs enhance nutrient assimilation, bolster plant defence, and fortify resilience against biotic and abiotic stresses. The understanding of SynCom design, exploring their composition, functional dynamics, and mechanisms for optimizing plant health is crucial for effective synthesis and application, alongside cutting-edge computational tools and genomic databases that enable precision engineering of microbial communities. Despite their transformative potential, large-scale application of SynComs remains constrained by challenges related to field efficacy, regulatory frameworks, and long-term microbial persistence. Addressing these barriers through interdisciplinary research and policy innovation is imperative. As environmental microbiome moves towards sustainability-driven solutions, SynComs hold the key to revolutionizing farming practices, reducing chemical dependence, and ensuring global food security in an era of mounting environmental stressors.

The incorporation of non-canonical amino acids (ncAAs) enables customized chemistry to tailor protein functions. Genetic code expansion offers a general approach for ncAA encoding by reassigning stop codons as the ‘blank’ codon; however, it is not completely orthogonal to translation termination for cellular transcripts. Here, to generate more bona fide blank codons, we developed an RNA codon-expansion (RCE) strategy that introduces and decodes bioorthogonally assignable pseudouridine (Ψ) codons (ΨGA, ΨAA or ΨAG) on specified mRNA transcripts to incorporate ncAAs in mammalian cells. The RCE strategy comprises a programmable guide RNA, an engineered decoder tRNA, and aminoacyl-tRNA synthetase. We first developed the RCE(ΨGA) system, which incorporates functional ncAAs into proteins via the ΨGA codon, demonstrating a higher translatome-wide and proteomic specificity compared with the genetic code expansion system. We further expanded our strategy to produce the RCE(ΨAA) and RCE(ΨAG) systems, with all three Ψ codon:(Ψ codon)-tRNAPyl pairs exhibiting mutual orthogonality. Moreover, we demonstrated that the RCE system cooperates compatibly with the genetic code expansion strategy for dual ncAA encoding. In sum, the RCE method utilized Ψ as a post-transcriptional ‘letter’ to encode and decode RNA codons in specific mRNA transcripts, opening a new route for genetic alphabet expansion and site-specific ncAA incorporation in eukaryotic cells. An RNA codon-expansion strategy enables incorporation of non-canonical amino acids into proteins of interest orthogonally to existing methods by inserting pseudouridine codons into specific mRNA transcripts and using an engineered decoder tRNA.

Owing to advances in genome sequencing and editing, a genome can now be redesigned, synthesized and introduced into cells as desired. The field of synthetic genomics not only aims to provide deeper understanding of how the genome functions but can also be harnessed for a wide range of synthetic biology and bioengineering applications, from rapid evolution and screening for favorable strains to biotechnological and bioproduction tool development. Although genome synthesis has been carried out mainly in simple unicellular organisms, plants and animals are now also being investigated. Compared with animals, plants have unique advantages, such as fewer ethical concerns, simpler experimental operations and easier regeneration from cells to organisms. In this Review, we focus on genome synthesis in plants, discuss the current research landscape and assess possible future directions. Owing to advances in genome sequencing and editing, a genome can now be redesigned, synthesized and introduced into cells as desired. This Review discusses plant genome synthesis, highlighting bottom-up genome design, large-fragment assembly and site-directed targeting.

CRISPR–Cas genome editing technology is a cutting-edge strategy for crop breeding. However, the delivery of genome-editing reagents remains to be a technological bottleneck in monocot plants. Here we engineered barley yellow striate mosaic virus (BYSMV) into a negative-strand RNA virus-based vector system for delivery of both Cas9 and single guide RNA to achieve heritable gene editing in different wheat cultivars. We found that fusion of a mobile transfer RNA sequence to the Cas9 messenger RNA and single guide RNAs could deliver them into the growth points of axillary meristems to achieve gene editing before tiller generation. The resulting nascent tillers contained simultaneous mutations in the three homoeoalleles. Moreover, the progeny seedlings are virus-free and harbor bi-allelic or homozygous mutations. Given BYSMV infects 26 monocot species, the BYSMV delivery system could have wide applicability for achieving highly efficient, non-transgenic and less genotype-dependent heritable genome editing, thereby facilitating genomic studies and crops breeding. Efficient delivery systems are urgently needed for genome editing in monocot plants. Here, this study develops a system of virus-induced genome editing in tillers (ViGET) to achieve heritable editing in wheat bypassing transgene and tissue culture.