Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Hub metabolites at the root-microbiome interface: unlocking plant drought resilience

Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.

Self-authenticating genomic materials in Escherichia coli via advanced genome signatures

The authenticity and integrity of synthetic genomic materials containing valuable intellectual property are essential for advancing scientific knowledge and enhancing biosafety. Nevertheless, existing DNA tags and watermarks have limited efficacy due to low mutation tolerance and inadequate digital encoding capacity. Here, we present "Genome Signature", a biochemically stable and tamper-resistant DNA labeling system that enables the creation of self-authenticating genomes. Central to this system is a Golomb-ruler-derived Genome-Comb, which efficiently maps extensive nucleotide sequences onto limited codons within endogenous genes, significantly improving error correction and data encoding across millions of nucleotides. Using our labeling system, we successfully recorded a 4.5-million-nucleotide genome in living E. coli. The Genome Signature effectively encodes data within codon orders, and autonomously identifies and corrects mutations in our computing test, ensuring genome integrity and authenticity. Furthermore, it allows precise tracking of coded sequences across different cells, potentially advancing the development of reliable genomic materials in synthetic biology.

Deciphering the rhizosphere microbiota composition of nature farming soybean (Glycine max L.) with different nodulation phenotypes

BACKGROUND

Nature farming, a sustainable agricultural method which avoids agrochemicals and untreated organic amendments, promotes both agricultural productivity and ecological conservation. This system may foster unique plant-microbiota interactions for growth and fitness; however, the microbiota of nature-farmed plants remains largely unexplored. Second, root nodule symbiosis (RNS) is crucial for nitrogen fixation in legumes; however, its broader impact on rhizosphere microbiota assembly is not well understood. This study examined the dynamics between impaired nodule symbiosis, soil management, and the rhizosphere microbiota composition and growth of soybean (Glycine max L.).

RESULTS

We evaluated the growth and characterized the rhizosphere bacterial and fungal communities of soybean by comparing wildtype soybeans (Enrei) with the non-nodulating mutants (En1282) across four soils under conventional and nature farming, including fumigated and unfumigated conditions. We found that the non-nodulating soybean mutants (En1282) exhibited reduced growth compared with wild-type (Enrei) plants, especially in untreated soils. Soil fumigation decreased microbial diversity and reshaped rhizosphere community composition with a significant reduction in plant growth and nodulation in all soils. Restriction in RNS increased bacterial diversity in untreated soils, possibly as a compensatory mechanism for nitrogen acquisition, whereas fungal diversity remained relatively stable. Nature farming promoted beneficial microbes like Rhizobium, Trichoderma, and Chloridium, whereas conventional soil plants favored Bacillus and Aspergillus. Notably, differential enrichment analysis identified distinct associations for each nodulation phenotype, with Enrei predominantly enriched for Pseudomonas, and En1282 associated primarily with oligotrophic microbes.

CONCLUSION

Our study sheds light on the complex interplay between legume symbiosis and rhizosphere microbiota assembly and highlights the significance of eco-friendly farming methods like nature farming in cultivating a healthy rhizosphere for plant growth. The results paves way for future strategies to manipulate rhizosphere microbiota, ultimately promoting robust and sustainable farming systems that reduce reliance on chemical inputs.

Symbiotic microalgae and microbes: a new frontier in saline agriculture

With the growing human population worldwide, innovative agricultural development is needed to meet food security needs. However, this has inadvertently led to problematic irrigation practices and overuse of agrochemicals. Such practices can exacerbate soil salinization, which prevents plant growth. As a progressively widespread and escalating problem, soil salinization poses a major threat to global food security. Compared with the traditional use of microalgae or microorganisms that act on plant growth, microalgae-microorganism symbiosis has significant advantages in promoting plant growth. Microalgae and microorganisms can work together to provide a wide range of nutrients required by plants, and they exhibit nutrient complementarity, which supports plant growth. Here, the development potential of microalgae-microbial symbiosis for enhancing plant salt tolerance was investigated. Our review demonstrated that the metabolic complementarity between microalgae and microorganisms can enhance plant salt tolerance. The diversity of a microalgae-microorganism symbiotic system can improve ecosystem stability and resistance and reduce the incidence of plant disease under salt stress. These systems produce bioactive substances (e.g., phytohormones) that promote plant growth, which can improve crop yield, and they can improve soil structure by increasing organic matter and improving water storage capacity and soil fertility. Exploiting the synergistic effects between microalgae and beneficial microorganisms has biotechnological applications that offer novel solutions for saline agriculture to mitigate the deleterious effects of soil salinity on plant health and yield. However, there are several implementation challenges, such as allelopathic interactions and autotoxicity. To make microalgae-bacteria consortia economically viable for agricultural applications, optimal strains and species need to be identified and strategies need to be employed to obtain sufficient biomass in a cost-effective manner. By elucidating the synergistic mechanisms, ecological stability, and resource utilization potential of microalgae-microbial symbiotic systems, this review clarifies salt stress responses and promotes the shift of saline-alkali agriculture from single bioremediation to systematic ecological engineering.

Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose

Engineering enzymes to degrade solid substrates, such as crystalline cellulose from paper sludge or microplastics in sewage sludge, presents challenges for high-throughput screening (HTS), as solid substrates are not readily accessible in cell-based biosensor systems. To address this challenge, we developed a cell-free cellobiose-detectable biosensor (CB-biosensor) for rapid characterization of cellobiohydrolase (CBH) activity, enabling direct detection of hydrolysis products without cellular constraints. The CB-biosensor demonstrates higher sensitivity than conventional assays and distinguishes between CBH subtypes (CBHI and CBHII) based on their modes of action. Integration with the Echo 525 liquid handler enables precise and reproducible sample processing, with fluorescence signals from automated preparations comparable to manual experiments. Furthermore, assay volumes can be reduced to just a few microlitres-impractical with manual methods. This cell-free CB-biosensor with Echo 525 minimizes reagent consumption, accelerates testing, and facilitates reliable large-scale screening. These findings highlight its potential to overcome current HTS limitations, advancing enzyme screening and accelerating the Design-Build-Test-Learn cycle for sustainable biomanufacturing.

Integrating microbial communities into algal biotechnology: a pathway to enhanced commercialization

Microalgae are increasingly recognized for their potential in wastewater treatment and the sustainable production of feedstock for fuel, feed, food, and other bioproducts. Like conventional agricultural systems, algal cultivation involves complex microbial communities. However, despite their pivotal role in cultivation outcomes, especially at the commodity-scale, the critical interactions between microalgae and their microbiomes are often overlooked. Here we synthesize current knowledge on the taxonomic diversity, ecological roles, and biotechnological potential of algal microbiomes, with a focus on their interactions with algal hosts through nutrient exchange, growth modulation, pathogen defense, and environmental conditioning. We also examine how environmental factors such as nutrient availability, salinity, and temperature influence these interactions. Advances in microbiome engineering, including synthetic biology and ecological approaches, offer opportunities to enhance beneficial algal-microbiome interactions, thereby improving growth, resilience, and yield. These advancements could lead to more sustainable and economically viable microalgae cultivation, with far-reaching implications for environmental management and biotechnological innovation. By addressing key economic and environmental barriers, microbiome engineering holds transformative potential to revolutionize large-scale algae cultivation and provide sustainable solutions to global challenges.

Unravelling the Molecular Dialogue of Beneficial Microbe-Plant Interactions

Plants are an intrinsic part of the soil community, which is comprised of a diverse range of organisms that interact in the rhizosphere through continuous molecular communications. The molecular dialogue within the plant microbiome involves a complex repertoire of primary and secondary metabolites that interact within different liquid matrices and biofilms. Communication functions are likely to involve membrane-less organelles formed by liquid-liquid phase separation of proteins and natural deep eutectic solvents that play a role as alternative media to water. We discuss the chemistry of inter-organism communication and signalling within the biosphere that allows plants to discriminate between harmful, benign and beneficial microorganisms. We summarize current information concerning the chemical repertoire that underpins plant-microbe communication and host-range specificity. We highlight how the regulated production, perception and processing of reactive oxygen species (ROS) is used in the communication between plants and microbes and within the communities that shape the soil microbiome.

Synthetic Biology Strategies and Tools to Modulate Photosynthesis in Microbes

The utilization of photosynthetic microbes, such as cyanobacteria and microalgae, offers sustainable solutions to addressing global resource shortages and pollution. While these microorganisms have demonstrated significant potential in biomanufacturing, their industrial application is limited by suboptimal photosynthetic efficiency. Synthetic biology integrates molecular biology, systems biology, and engineering principles to provide a powerful tool for elucidating photosynthetic mechanisms and rationally optimizing photosynthetic platforms. This review summarizes recent advancements in regulating photosynthesis in cyanobacteria and microalgae via synthetic biology, focusing on strategies to enhance light energy absorption, optimize electron transport chains, and improve carbon assimilation. Furthermore, we discuss key challenges in translating these genetic modifications to large-scale bioproduction, highlighting specific bottlenecks in strain stability, metabolic burden, and process scalability. Finally, we propose potential solutions, such as AI-assisted metabolic engineering, synthetic microbial consortia, and next-generation photobioreactor designs, to overcome these limitations. Overall, while synthetic biology holds great promise for enhancing photosynthetic efficiency in cyanobacteria and microalgae, further research is needed to refine genetic strategies and develop scalable production systems.

Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly

Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.

From glycans to green biotechnology: exploring cell wall dynamics and phytobiota impact in plant glycopathology

Filamentous plant pathogens, including fungi and oomycetes, pose significant threats to cultivated crops, impacting agricultural productivity, quality and sustainability. Traditionally, disease control heavily relied on fungicides, but concerns about their negative impacts motivated stakeholders and government agencies to seek alternative solutions. Biocontrol agents (BCAs) have been developed as promising alternatives to minimize fungicide use. However, BCAs often exhibit inconsistent performances, undermining their efficacy as plant protection alternatives. The eukaryotic cell wall of plants and filamentous pathogens contributes significantly to their interaction with the environment and competitors. This highly adaptable and modular carbohydrate armor serves as the primary interface for communication, and the intricate interplay within this compartment is often mediated by carbohydrate-active enzymes (CAZymes) responsible for cell wall degradation and remodeling. These processes play a crucial role in the pathogenesis of plant diseases and contribute significantly to establishing both beneficial and detrimental microbiota. This review explores the interplay between cell wall dynamics and glycan interactions in the phytobiome scenario, providing holistic insights for efficiently exploiting microbial traits potentially involved in plant disease mitigation. Within this framework, the incorporation of glycobiology-related functional traits into the resident phytobiome can significantly enhance the plant's resilience to biotic stresses. Therefore, in the rational engineering of future beneficial consortia, it is imperative to recognize and leverage the understanding of cell wall interactions and the role of the glycome as an essential tool for the effective management of plant diseases.

Sustainable pollution removal and resources recovery from electroplating wastewater by coagulation, advanced oxidation coupling with bioaugmentation

Electroplating wastewater contains high concentrations of dissolved organic matter, heavy metal ions (HMs), refractory organic compounds (ROC), and the complicated composition of effluents. Bioaugmentation presents an efficient strategy for eliminating pollution and recycling resources from electroplating effluent. In this study, simultaneous removal of pollution and sustainable resources recovery from electroplating wastewater were conducted by polyferric sulfate (PFS)-based coagulation, ultraviolet (UV)-activated persulfate (PS) (UV-APS)-based advanced oxidation coupling with bioaugmentation. To reduce carbon emissions and achieve carbon neutrality, genetically engineered Vibrio natriegens with an aerobic sulfate reduction pathway (GeVin) was introduced to remove sulfate, organics, and HMs, which further promoted generation of metal sulfides. The results of coagulation by PFS eliminated 34.68% of chemical oxygen demand (COD), 38.56% of ammonia nitrogen (NH4-N), 36.30% of ROC, and 16.67% of HMs. The rest of refractory contaminants in the effluent of coagulation were oxidatively degraded by UV-APS to improve biodegradability index. The bioaugmentation using immobilized GeVin (IMGevin) coupled with membrane bioreactor (MBR) (IMGevin-MBR) significantly removed 98.25% of COD, 96.23% of NH4-N, 99.42% of biochemical oxygen demand (BOD), 97.85% of sulfate, and 97.68% of HMs. Mechanism analysis indicated that sulfate derived from PFS-based coagulation and UV-APS provided more electron acceptors to generate H2S metabolized by GeVin, contributing to HMs removal via sulfate reduction pathway. Furthermore, IMGeVin-MBR decreased startup phase, hydraulic retention time (HRT), increased the microbial activity, functional microbial community and abundances of genes related to sulfate metabolism, resulting in improvement of systemic stability. Meanwhile, IMGeVin-MBR decreased the total treatment cost, sludge yields, and greenhouse gas (GHG) emissions for treatment of electroplating wastewater. In conclusion, this study provides a sustainable pollution removal and resources recovery strategy for treating electroplating wastewater.

Recombinant DNA: unlocking untapped microbial potential for innovation in crop agriculture

The Asilomar Conference on Recombinant DNA, held in 1975, established guidelines for recombinant DNA (rDNA) research and laid the foundation for biotechnology regulations. While rDNA has driven significant advancements in pharmaceutical and crop biotechnology, the commercialization of plant-beneficial microbials developed using rDNA has lagged behind. This disparity may be attributed to a cumbersome regulatory framework shaped by the perception that rDNA products pose biosafety risks. To unlock the full potential of rDNA technology in addressing global challenges, regulatory reform for rDNA-derived microbial products for crop plants that reduce reliance on chemical fertilizers and pesticides is essential. Streamlining these barriers will enable greater societal benefits from microbial solutions in agriculture and beyond.

A mechanistic overview on green assisted formulation of nanocomposites and their multifunctional role in biomedical applications

The importance of nanocomposites constantly attains attention because of their unique properties all across the fields especially in medical perspectives. The study of green-synthesized nanocomposites has grown to be extremely fascinating in the field of research. Nanocomposites are more promising than mono-metallic nanoparticles because they exhibit synergistic effects. This review encapsulates the current development in the formulation of plant-mediated nanocomposites by using several plant species and the impact of secondary metabolites on their biocompatible functioning. Phyto-synthesis produces diverse nanomaterials with biocompatibility, environment-friendliness, and in vivo actions, characterized by varying sizes, shapes, and biochemical nature. This process is advantageous to conventional physical and chemical procedures. New studies have been conducted to determine the biomedical efficacy of nanocomposites against various diseases. Unfortunately, there has been inadequate investigation into green-assisted nanocomposites. Incorporating phytosynthesized nanocomposites in therapeutic interventions not only enhances healing processes but also augments the host's immune defenses against infections. This review highlights the phytosynthesis of nanocomposites and their various biomedical applications, including antibacterial, antidiabetic, antiviral, antioxidant, antifungal, anti-cancer, and other applications, as well as their toxicity. This review also explores the mechanistic action of nanocomposites to achieve their designated tasks. Biogenic nanocomposites for multimodal imaging have the potential to exchange the conventional methods and materials in biomedical research. Well-designed nanocomposites have the potential to be utilized in various biomedical fields as innovative theranostic agents with the subsequent objective of efficiently diagnosing and treating a variety of human disorders.

Metagenomic insights into the development of microbial communities of straw and leaf composts

Introduction

Soil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.

Methods

Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.

Results

In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.

Discussion

Our study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

Groundbreaking Technologies and the Biocontrol of Fungal Vascular Plant Pathogens

This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture.

Whole-genome sequencing and secondary metabolite exploration of the novel Bacillus velezensis BN with broad-spectrum antagonistic activity against fungal plant pathogens

The utilization of chemical pesticides recovers 30%-40% of food losses. However, their application has also triggered a series of problems, including food safety, environmental pollution, pesticide resistance, and incidents of poisoning. Consequently, green pesticides are increasingly seen as viable alternatives to their chemical counterparts. Among these, Plant Growth-Promoting Rhizobacteria (PGPR), which are found within plant rhizosphere, stand out for their capacity to stimulate plant growth. Recently, we isolated a strain, BN, with broad-spectrum antimicrobial activity from the rhizosphere of Lilium brownii. Identification revealed that this strain belongs to the species Bacillus velezensis and exhibits significant inhibitory effects against various fungal plant pathogens. The complete genome sequence of B. velezensis BN consists of a circular chromosome with a length of 3,929,791 bp, includes 3,747 protein-coding genes, 81 small RNAs, 27 rRNAs, and 86 tRNAs. Genomic analysis revealed that 29% of the genes are directly involved in plant growth, while 70% of the genes are indirectly involved. In addition, 12 putative biosynthetic gene clusters were identified, responsible for the synthesis of secondary metabolites, such as non-ribosomal peptides, lanthipeptides, polyketides, siderophores, and terpenes. These findings provide a scientific basis for the development of efficient antimicrobial agents and the construction of biopesticide production platforms in chassis cells.

Harnessing the plant microbiome for sustainable crop production

Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.

The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization

Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.

Prospects for synthetic biology in 21st Century agriculture

Plant synthetic biology has emerged as a transformative field in agriculture, offering innovative solutions to enhance food security, provide resilience to climate change, and transition to sustainable farming practices. By integrating advanced genetic tools, computational modeling, and systems biology, researchers can precisely modify plant genomes to enhance traits such as yield, stress tolerance, and nutrient use efficiency. The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges. Here, we highlight recent advancements and applications of plant synthetic biology in agriculture, focusing on key areas such as photosynthetic efficiency, nitrogen fixation, drought tolerance, pathogen resistance, nutrient use efficiency, biofortification, climate resilience, microbiology engineering, synthetic plant genomes, and the integration of artificial intelligence (AI) with synthetic biology. These innovations aim to maximize resource use efficiency, reduce reliance on external inputs, and mitigate environmental impacts associated with conventional agricultural practices. Despite challenges related to regulatory approval and public acceptance, the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems, contributing to global food security and environmental sustainability. Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.

Biotechnological advances in plant growth-promoting rhizobacteria for sustainable agriculture

The rhizosphere, the soil zone surrounding plant roots, serves as a reservoir for numerous beneficial microorganisms that enhance plant productivity and crop yield, with substantial potential for application as biofertilizers. These microbes play critical roles in ecological processes such as nutrient recycling, organic matter decomposition, and mineralization. Plant growth-promoting rhizobacteria (PGPR) represent a promising tool for sustainable agriculture, enabling green management of crop health and growth, being eco-friendly alternatives to replace chemical fertilizers and pesticides. In this sense, biotechnological advancements respecting genomics and gene editing have been crucial to develop microbiome engineering which is pivotal in developing microbial consortia to improve crop production. Genome mining, which involves comprehensive analysis of the entire genome sequence data of PGPR, is crucial for identifying genes encoding valuable bacterial enzymes and metabolites. The CRISPR-Cas system, a cutting-edge genome-editing technology, has shown significant promise in beneficial microbial species. Advances in genetic engineering, particularly CRISPR-Cas, have markedly enhanced grain output, plant biomass, resistance to pests, and the sensory and nutritional quality of crops. There has been a great advance about the use of PGPR in important crops; however, there is a need to go further studying synthetic microbial communities, microbiome engineering, and gene editing approaches in field trials. This review focuses on future research directions involving several factors and topics around the use of PGPR putting special emphasis on biotechnological advances.

Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice

Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including Hormiactis, Emericellopsis, Ceriosporopsis, Dirkmeia, and Moesziomyces predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as Desulfoprunum and Hydrogenophaga exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the "two-component system", "sulfur metabolism", and "microbial metabolism in diverse environments". The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like Ceriosporopsis and Dirkmeria, along with bacteria such as Desulfoprunum, Rippkaea, and Bellilinea, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions.

Beyond correlation: Understanding the causal link between microbiome and plant health

Understanding the causal link between the microbiome and plant health is crucial for the future of crop production. Established studies have shown a symbiotic relationship between microbes and plants, reshaping our knowledge of plant microbiomes' role in health and disease. Addressing confounding factors in microbiome study is essential, as standardization enables precise identification of microbiome features that influence outcomes. The microbiome significantly impacts plant development, necessitating holistic investigation for maintaining plant health. Mechanistic studies have deepened our understanding of microbiome structure and function related to plant health, though much research still needs to be carried out. This review, therefore, discusses current challenges and proposes advancing studies from correlation to causation and translation. We explore current knowledge on the microbiome and plant health, emphasizing multi-omics approaches and hypothesis-driven research. Future studies should focus on developing translational research for producing probiotics and prebiotics from biomarkers that regulate the microbiome-plant health connection, promoting sustainable crop production through microbiome applications.

Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato

For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.

Exploring and exploiting the rice phytobiome to tackle climate change challenges

The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.

Phosphorus dynamics and sustainable agriculture: The role of microbial solubilization and innovations in nutrient management

Phosphorus (P) is an essential element for plant growth, playing a crucial role in various metabolic processes. Despite its importance, phosphorus availability in soils is often restricted due to its tendency to form insoluble complexes, limiting plant uptake. The increasing demand for phosphorus in agriculture, combined with limited global reserves of phosphate rock, has created challenges for sustainable plant production. Additionally, the overuse of chemical phosphorus fertilizers has resulted in environmental degradation, such as eutrophication of water bodies. Increasing agronomic phosphorus (P) efficiency is crucial because of population growth and increased food demand. Hence, microorganisms involved in the P cycle are a promising biotechnological strategy that has gained global interest in recent decades. Microorganisms' solubilization of phosphate rock (PR) is an environmentally sustainable alternative to chemical processing for producing phosphate fertilizers. Phosphorus-solubilizing microorganisms (PSMs), including bacteria and fungi, and their enzymatic processes offer an eco-friendly and sustainable alternative to chemical inputs by converting insoluble phosphorus into forms readily available for plant uptake. Integrating PSMs into agricultural systems presents a promising strategy to reduce dependence on chemical fertilizers, enhance soil health, and contribute to the transition toward more sustainable and resilient agricultural practices. It can be an alternative that reduces the loss of phosphorus in the environment, especially the eutrophication of aquatic systems. This paper explores the challenges of phosphorus availability in agriculture and the potential of microbial phosphorus solubilization as a sustainable alternative to conventional practices.

Observing root growth and signalling responses to stress gradients and pathogens using the bi-directional dual-flow RootChip

Plants respond to environmental stressors with adaptive changes in growth and development. Central to these responses is the role of calcium (Ca2+) as a key secondary messenger. Here, the bi-directional dual-flow RootChip (bi-dfRC) microfluidic platform was used to study defence signalling and root growth. By introducing salinity as sodium chloride (NaCl) treatment via a multiplexed media delivery system (MMDS), dynamic gradients were created, mimicking natural environmental fluctuations. Signal analysis in Arabidopsis thaliana plants showed that the Ca2+ burst indicated by the G-CaMP3 was concentration dependent. A Ca2+ burst initiated in response to salinity increase, specifically within the stele tissue, for 30 seconds. The signal then intensified in epidermal cells directly in contact with the stressor, spreading directionally towards the root tip, over 5 minutes. Inhibition of propidium iodide (PI) stain transport through the xylem was observed following salinity increase, contrasting with flow observed under control conditions. The interaction of Phytophthora capsici zoospores with A. thaliana roots was also studied. An immediate directional Ca2+ signal was observed during early pathogen recognition, while a gradual, non-directional increase was observed in Orp1_roGFP fluorescent H2O2 levels, over 30 min. By adjusting the dimensions of the bi-dfRC, plants with varying root architectures were subjected to growth analysis. Growth reduction was observed in A. thaliana and Nicotiana benthamiana roots when exposed to salinity induced by 100 mM NaCl, while Solanum lycopersicum exhibited growth increase over 90 minutes at the same NaCl concentration. Furthermore, novel insights into force sensing in roots were gained through the engineering of displaceable pillars into the bi-dfRC channel. These findings highlight the vital role of controlling fluid flow in microfluidic channels in advancing our understanding of root physiology under stress conditions.

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress

Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.

Identification of putative genes for caffeoylated flavonoid glycoside biosynthesis in Pseudognaphalium affine

Pseudognaphalium affine (D. Don) Anderberg, commonly found in East Asia, has extensive applications as both a traditional medicine and a vegetable in China. The caffeoylated flavonoid glycosides produced by P. affine exhibit remarkable anti-complement activities. Although these compounds have potential therapeutic value, the biosynthetic pathway responsible for their production remains largely unknown. To elucidate the key catalytic steps involved in caffeoylated flavonoid glycoside biosynthesis, we conducted a comprehensive analysis of the full-length transcriptome of P. affine. Further phylogenetic tree analysis predicted potential UDP glycosyltransferase (UGT) and BAHD acyltransferase (BAHD-AT) related with caffeoylated flavonoid glycoside biosynthesis. Subsequently, enzyme assay led to the discovery of PaUGT23 as a key enzyme responsible for the glycosylation of hydroxy groups in flavonoids, resulting in the formation of luteolin-4'-O-glucoside, luteolin-7-O-glucoside, quercetin-4'-O-glucoside, quercetin-7-O-glucoside, and apigenin-7-O-glucoside, while PaBAHD21 was found to catalyze the caffeoylation of flavonoid glycosides, resulting in the formation of luteolin 4'-O-β-D-(6″-E-caffeoyl)-glucopyranoside, quercetin 4'-O-β-D-(6″-E-caffeoyl)-glucopyranoside, apigenin 4'-O-β-D-(6″-E-caffeoyl)-glucopyranoside and apigenin 7-O-β-D-(6″-E-caffeoyl)-glucopyranoside. Moreover, their catalytic activities were verified in vivo by transient transfection experiment. This study presents the first comprehensive analysis of the full-length transcriptome in P. affine, providing significant insights into the biosynthesis and accumulation mechanisms of bioactive caffeoylated flavonoid glycosides.

Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology

Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.

Drought stress mitigation through bioengineering of microbes and crop varieties for sustainable agriculture and food security

Climate change and agriculture are intrinsically connected and sudden changes in climatic conditions adversely impact global food production and security. The climate change-linked abiotic stressors like drought and high temperatures are resulting in crop failure. The most severe abiotic stress drought significantly affect the stomatal closure, production of reactive oxygen species, transpiration, photosynthesis or other physiological processes and plant morphology, and adversely affect plant growth and crop yield. Therefore, there is an exigent need for cost effective and eco-friendly modern technologies to induce drought tolerance in crop plants leading to climate-adapted sustainable agricultural practices for sustained food production. Among many options being pursued in this regard, the use of plant growth promoting microbes (PGPMs) is the most sustainable approach to promote drought stress resilience in crop plants leading to better plant growth and crop productivity. These PGPMs confer drought resistance via various direct or indirect mechanisms including production of antioxidants, enzymes, exopolysaccharides, modulation of phytohormones level, osmotic adjustment by inducing the accumulation of sugars, along with increases in nutrients, water uptake and photosynthetic pigments. However, several technological and ecological challenges limit their use in agriculture and sometimes treatment with plant beneficial microbes fails to produce desired results under field conditions. Thus, development of synthetic microbial communities or host mediated microbiome engineering or development of transgenic plants with the capacity to express desired traits may promote plant survival and growth under drought stress conditions. The present review critically assesses research evidence on the plant growth and stress resilience promoting potentials of PGPMs and their genes as an approach to develop drought resilient plants leading to increased crop productivity. Effective collaboration among scientific communities, policymakers and regulatory agencies is needed to create strong frameworks that both promote and regulate the utilization of synthetic microbial communities and transgenic plants in agriculture.

Promoting salt tolerance, growth, and phytochemical responses in coriander (Coriandrum sativum L. cv. Balady) via eco-friendly Bacillus subtilis and cobalt

In plant production, evaluation of salt stress protectants concerning their potential to improve growth and productivity under saline stress is critical. Bacillus subtilis (Bs) and cobalt (Co) have been proposed to optimize salt stress tolerance in coriander (Coriandrum sativum L. cv. Balady) plants by influencing some physiological activities. The main aim of this work is to investigate the response of (Bs) and (Co) as eco-safe salt stress protectants to resist the effect of salinity, on growth, seed, and essential oil yield, and the most important biochemical constituents of coriander produced under salt stress condition. Therefore, in a split-plot factorial experiment design in the RCBD (randomized complete block design), four levels of salinity of NaCl irrigation water (SA) were assigned to the main plots; (0.5, 1.5, 4, and 6 dS m-1); and six salt stress protectants (SP) were randomly assigned to the subplots: distilled water; 15 ppm (Co1); 30 ppm (Co2); (Bs); (Co1 + Bs); (Co2 + Bs). The study concluded that increasing SA significantly reduced coriander growth and yield by 42.6%, which could be attributed to ion toxicity, oxidative stress, or decreased vital element content. From the results, we recommend that applying Bs with Co (30 ppm) was critical for significantly improving overall growth parameters. This was determined by the significant reduction in the activity of reactive oxygen species scavenging enzymes: superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) and non-enzyme: proline by 5, 11.3, 14.7, and 13.8% respectively, while increasing ascorbic acid by 8% and preserving vital nutrient levels and enhancing plant osmotic potential to buffer salt stress, seed yield per plant, and essential oil yield increased by 12.6 and 18.8% respectively. The quality of essential oil was indicated by highly significant quantities of vital biological phytochemicals such as linalool, camphor, and protein which increased by 10.3, 3.6, and 9.39% respectively. Additional research is suggested to determine the precise mechanism of action of Bs and Co's dual impact on medicinal and aromatic plant salt stress tolerance.

Phytocytokine StPep1-Secreting Bacteria Suppress Potato Powdery Scab Disease

Powdery scab is an important potato disease caused by the soilborne pathogen Spongospora subterranea f. sp. subterranea. Currently, reliable chemical control and resistant cultivars for powdery scab are unavailable. As an alternative control strategy, we propose a novel approach involving the effective delivery of a phytocytokine to plant roots by the rhizobacterium Bacillus subtilis. The modified strain is designed to secrete the plant elicitor peptide StPep1. In our experiments employing a hairy root system, we observed a significant reduction in powdery scab pathogen infection when we directly applied the StPep1 peptide. Furthermore, our pot assay, which involved pretreating potato roots with StPep1-secreting B. subtilis, demonstrated a substantial decrease in disease symptoms, including reduced root galling and fewer tuber lesions. These findings underscore the potential of engineered bacteria as a promising strategy for safeguarding plants against powdery scab.

Growth and protein response of rice plant with plant growth-promoting rhizobacteria inoculations under salt stress conditions

Soil salinity has been one of the significant barriers to improving rice production and quality. According to reports, Bacillus spp. can be utilized to boost plant development in saline soil, although the molecular mechanisms behind the interaction of microbes towards salt stress are not fully known. Variations in rice plant protein expression in response to salt stress and plant growth-promoting rhizobacteria (PGPR) inoculations were investigated using a proteomic method and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Findings revealed that 54 salt-responsive proteins were identified by mass spectrometry analysis (LC-MS/MS) with the Bacillus spp. interaction, and the proteins were functionally classified as gene ontology. The initial study showed that all proteins were labeled by mass spectrometry analysis (LC-MS/MS) with Bacillus spp. interaction; the proteins were functionally classified into six groups. Approximately 18 identified proteins (up-regulated, 13; down-regulated, 5) were involved in the photosynthetic process. An increase in the expression of eight up-regulated and two down-regulated proteins in protein synthesis known as chaperones, such as the 60 kDa chaperonin, the 70 kDa heat shock protein BIP, and calreticulin, was involved in rice plant stress tolerance. Several proteins involved in protein metabolism and signaling pathways also experienced significant changes in their expression. The results revealed that phytohormones regulated the manifestation of various chaperones and protein abundance and that protein synthesis played a significant role in regulating salt stress. This study also described how chaperones regulate rice salt stress, their different subcellular localizations, and the activity of chaperones.

Revisiting the current and emerging concepts of postharvest fresh fruit and vegetable pathology for next-generation antifungal technologies

Fungal infections of fresh fruits and vegetables (FFVs) can lead to safety problems, including consumer poisoning by mycotoxins. Various strategies exist to control fungal infections of FFVs, but their effectiveness and sustainability are limited. Recently, new concepts based on the microbiome and pathobiome have emerged and offer a more holistic perspective for advancing postharvest pathogen control techniques. Understanding the role of the microbiome in FFV infections is essential for developing sustainable control strategies. This review examines current and emerging approaches to postharvest pathology. It reviews what is known about the initiation and development of infections in FFVs. As a promising concept, the pathobiome offers new insights into the basic mechanisms of microbial infections in FFVs. The underlying mechanisms uncovered by the pathobiome are being used to develop more relevant global antifungal strategies. This review will also focus on new technologies developed to target the microbiome and members of the pathobiome to control infections in FFVs and improve safety by limiting mycotoxin contamination. Specifically, this review stresses emerging technologies related to FFVs that are relevant for modifying the interaction between FFVs and the microbiome and include the use of microbial consortia, the use of genomic technology to manipulate host and microbial community genes, and the use of databases, deep learning, and artificial intelligence to identify pathobiome markers. Other approaches include programming the behavior of FFVs using synthetic biology, modifying the microbiome using sRNA technology, phages, quorum sensing, and quorum quenching strategies. Rapid adoption and commercialization of these technologies are recommended to further improve the overall safety of FFVs.

Synthetic microbial communities: Novel strategies to enhance the quality of traditional fermented foods

Consumers are attracted to traditional fermented foods due to their unique flavor and nutritional value. However, the traditional fermentation technique can no longer accommodate the requirements of the food industry. Traditional fermented foods produce hazardous compounds, off-odor, and anti-nutritional factors, reducing product stability. The microbial system complexity of traditional fermented foods resulting from the open fermentation process has made it challenging to regulate these problems by modifying microbial behaviors. Synthetic microbial communities (SynComs) have been shown to simplify complex microbial communities and allow for the targeted design of microbial communities, which has been applied in processing traditional fermented foods. Herein, we describe the theoretical information of SynComs, particularly microbial physiological processes and their interactions. This paper discusses current approaches to creating SynComs, including designing, building, testing, and learning, with typical applications and fundamental techniques. Based on various traditional fermented food innovation demands, the potential and application of SynComs in enhancing the quality of traditional fermented foods are highlighted. SynComs showed superior performance in regulating the quality of traditional fermented foods using the interaction of core microorganisms to reduce the hazardous compounds of traditional fermented foods and improve flavor. Additionally, we presented the current status and future perspectives of SynComs for improving the quality of traditional fermented foods.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

A century of studying plant secondary metabolism-From "what?" to "where, how, and why?"

Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

A pilot oral history of plant synthetic biology

The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.

AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria

Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.

Programming Dynamic Division of Labor Using Horizontal Gene Transfer

The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils

Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Fungi beyond limits: The agricultural promise of extremophiles

Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges.

Growth regulation by apyrases: Insights from altering their expression level in different organisms

Apyrase (APY) enzymes are nucleoside triphosphate (NTP) diphosphohydrolases that can remove the terminal phosphate from NTPs and nucleoside diphosphates but not from nucleoside monophosphates. They have conserved structures and functions in yeast, plants, and animals. Among the most studied APYs in plants are those in Arabidopsis (Arabidopsis thaliana; AtAPYs) and pea (Pisum sativum; PsAPYs), both of which have been shown to play major roles in regulating plant growth and development. Valuable insights on their functional roles have been gained by transgenically altering their transcript abundance, either by constitutively expressing or suppressing APY genes. This review focuses on recent studies that have provided insights on the mechanisms by which APY activity promotes growth in different organisms. Most of these studies have used transgenic lines that constitutively expressed APY in multiple different plants and in yeast. As APY enzymatic activity can also be changed post-translationally by chemical blockage, this review also briefly covers studies that used inhibitors to suppress APY activity in plants and fungi. It concludes by summarizing some of the main unanswered questions about how APYs regulate plant growth and proposes approaches to answering them.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism

The aromatic amino acids (AAAs) phenylalanine, tyrosine, and tryptophan are basic protein units and precursors of diverse specialized metabolites that are essential for plant growth. Despite their significance, the mechanisms that regulate AAA homeostasis remain elusive. Here, we identified a cytosolic aromatic aminotransferase, REVERSAL OF SAV3 PHENOTYPE 1 (VAS1), as a suppressor of arogenate dehydrogenase 2 (adh2) in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses determined that VAS1 uses AAAs as amino donors, leading to the formation of 3-carboxyphenylalanine and 3-carboxytyrosine. These pathways represent distinct routes for AAA metabolism that are unique to specific plant species. Furthermore, we show that VAS1 is responsible for cytosolic AAA biosynthesis, and its enzymatic activity can be inhibited by 3-carboxyphenylalanine. These findings provide valuable insights into the crucial role of VAS1 in producing 3-carboxy AAAs, notably via recycling of AAAs in the cytosol, which maintains AAA homeostasis and allows plants to effectively coordinate the complex metabolic and biosynthetic pathways of AAAs.