Muhammad Asim

Botanical gardens are highly heterogeneous plant systems characterized by high taxonomic diversity, with numerous plant taxa represented within confined areas, and complex ecological interactions that create unique challenges for pest management. Conventional IPM strategies, designed for simplified agroecosystems, often fail to address complex pest pressures in curated environments. Microbial biostimulants have emerged as promising components of sustainable IPM strategies by enhancing plant defense responses, improving stress resilience, and reducing reliance on chemical inputs. This review synthesizes current knowledge on microbial biostimulants, including plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi and endophytic microorganisms, in modulating plant defense against insect herbivores. These beneficial microbes enhance plant resistance through multiple mechanisms. They activate induced systemic resistance and modulate key phytohormones, including jasmonic acid, salicylic acid, and ethylene. Additionally, they regulate calcium-dependent and reactive oxygen species-mediated defenses. Microbially induced changes in plant secondary metabolites and volatile organic compounds further influence herbivore behavior and trophic interactions. Emphasis is placed on integrating microbial biostimulants into IPM frameworks tailored to botanical gardens. This highlights compatibility with biological control agents and reduced reliance on synthetic pesticides. Despite promising advances, challenges remain, including context-dependent efficacy, host specificity and limited long-term validation. Overall, microbial biostimulants offer a promising tool for enhancing IPM in biodiversity-rich botanical gardens, although further long-term validation is needed to fully assess their sustainability and effectiveness.

Waterlogging (WL) stress severely affects the growth and productivity of fruit crops. Cytosolic calcium (Ca ²⁺ ) is recognized as a secondary messenger that initiates adaptive responses to environmental stresses. However, the mechanisms by which exogenously applied Ca ²⁺ enhances WL tolerance remain poorly understood. In this study, we investigated whether exogenous Ca ²⁺ , applied as calcium chloride (CaCl ₂ ) and calcium oxide nanoparticles (CaO-NPs), might mitigate WL-induced damage in peach ( Prunus persica ) seedlings. We found that both Ca ²⁺ formulations significantly alleviated WL-induced growth inhibition, restored photosynthetic efficiency, and maintained root system architecture and metabolic activity. Two Ca ²⁺ treatments markedly reduced intracellular superoxide (SOD) and hydrogen peroxide accumulation, thus attenuating membrane lipid peroxidation and electrolyte leakage. Hormonal profiling demonstrated that Ca ²⁺ suppressed excessive abscisic acid and salicylic acid accumulation while restoring jasmonate homeostasis under WL conditions. Furthermore, at the transcriptional level, Ca ²⁺ enhanced stress tolerance by upregulating the expression of genes encoding antioxidant ( PpSOD ; and peroxidase , PpPOD ), photosynthetic ( photosystem II subunit Q , PpPsbQ ; and photosystem I subunit K , PpPsaK ), and Ca ²⁺ ( CBL-interacting protein kinases , PpCIPK5 and PpCIPK11 ). In line with reduced oxidative stress, Ca ²⁺ also adaptively downregulated genes related to the fermentative pathway ( alcohol dehydrogenase , PpADH ; and lactate dehydrogenase , PpLDH ), indicating a shift away from anaerobic metabolism. Notably, comparative analysis revealed that ionic Ca ²⁺ and CaO-NP treatments resulted in largely similar outcomes under WL conditions, with only marginal differences in some parameters. Taken together, these results indicate that Ca ²⁺ -associated signaling is a putative regulatory network underlying adaptive responses to WL stress in woody fruit crops.

Loquat is a highly perishable, non-climacteric fruit that is prone to chilling injury, decay, and eating quality deterioration during cold storage. This study evaluates the effectiveness of tragacanth gum (TG) as a plant-based edible coating to mitigate postharvest chilling injury (CI) and preserve the eating quality of loquat fruit. Two commercial cultivars, ‘Sufaid’ and ‘Surkh’, were coated with 1% TG and stored at 4 ± 1 °C with 90 ± 5% relative humidity for 20 days, followed by 2 days at 20 °C ± 1 °C (specific focus on retail handling). TG-coated fruits exhibited significantly reduced weight loss and lower decay compared to controls. TG application alleviated CI symptoms and reduced respiration rates. TG-treated fruits maintained higher levels of titratable acidity, total soluble solids, and ascorbic acid. TG application also elevated phytochemical levels and antioxidant potential, reinforcing the fruit’s biochemical defenses against postharvest stress. Furthermore, TG treatment suppressed oxidative stress by lowering malondialdehyde and hydrogen peroxide levels and enhanced the activities of key antioxidant enzymes (SOD, CAT and APX). TG-coated fruits also showed improved taste, flavor, and consumer acceptability at shelf after storage. In conclusion, results indicate that application of TG coating represents a sustainable, eco-friendly strategy to alleviate CI and improve postharvest eating quality of commercial loquat cultivars, offering potential for broader adoption in the fresh fruit supply chain.

Hypoxic conditions caused by submergence or soil waterlogging constrain plant growth and productivity. To survive, plants coordinately reprogram both sugar metabolism and phytohormone signaling to trigger adaptive responses; yet, the integrative regulatory frameworks governing this interaction remain unresolved. Here, we synthesize current knowledge on how sugars, acting as both metabolites and signals, intersect with phytohormone networks to regulate growth and survival under low‐oxygen stress. Under hypoxia, ethylene and auxin reshape root architecture, while cytokinin mediates sugar‐dependent regulation of shoot branching to optimize resource allocation. The dynamic interplay between abscisic acid and sugars is central to maintaining energy balance under cyclic day–night hypoxia. This interaction modulates the stomatal aperture, facilitates controlled starch degradation, and coordinates sucrose transport to sustain metabolism. Furthermore, crosstalk between primary sugars, gibberellin, and brassinosteroid fine‐tunes critical developmental transitions, including seed germination and internode elongation. Although individual signaling pathways under hypoxia have been well studied, their integration via sugar–hormone crosstalk remains elusive. To address these issues, we propose integrating synthetic low‐oxygen sensors that initially detect hypoxic stress with engineered sugar–hormone balancing circuits that subsequently fine‐tune metabolic and hormonal responses, thereby creating closed‐loop feedback systems for adaptive stress resilience. Such systems could enable “Sensing, Metabolism, Adaptation, and Regulation Technology” (SMART) crops to autonomously sense and adapt to hypoxia stress. By synthesizing current knowledge and existing gaps, our work proposes future directions to advance the development of hypoxia‐resilient crops through optimizing growth and yield stability under stress.

High-throughput sequencing has generated massive DNA and RNA datasets, but extracting functional insight from raw sequences remains challenging. Deep learning provides a powerful framework to learn sequence representations directly from nucleotides, capturing complex and long-range dependencies that traditional methods often miss. This chapter summarizes major deep learning architectures and workflows for DNA/RNA sequence analysis and highlights key applications such as regulatory element prediction, splicing and isoform modeling, RNA–protein interactions, and variant effect prediction, along with current challenges and future directions.

Alpine ecosystems are distinguished by nutrient-poor soils and low temperatures, short growing seasons, and harsh environmental conditions that have strong influence on plant growth and survival. Soil nutrient dynamics, especially the cycling of carbon (C) and the nutrients (N), play a central role in controlling the productivity, diversity and resilience of alpine vegetation. Microbial communities are important mediators of nutrient transformations that influence nutrient availability under the conditions of limited decomposition and mineralization. This chapter discusses the role of soil microbes, nutrient constraints and biogeochemical processes in determining plant distribution in the alpine communities. It highlights how changes in C and N cycling with climate change affect vegetation resilience and ecosystem functioning. This chapter provides evidence-based insights into soil–plant interactions and the role of microbes in enhancing biodiversity and informing conservation strategies to improve nutrient stability in alpine landscapes.

Fungal endophytes are microorganisms that inhabit plant tissues without causing disease and emerge as critical mediators of plant stress tolerance, nutrient acquisition, and ecosystem resilience under diverse climate change scenarios. Their unique position within the host allows them to modulate physiological responses more closely than external microbiota. This review explores how endophytic fungi contribute to plant adaptation under climate-induced stresses such as heat, salinity, drought, pollution, and nutrient limitation, with a focus on molecular crosstalk, functional trait modules, and metabolic trade-offs. Key findings emphasize multilayered signaling systems, including MAMP/DAMP recognition, phytohormone regulation, immune tuning, ROS dynamics, and effector deployment, while emerging mechanisms such as cross-kingdom RNA and extracellular vesicle (EV)-mediated exchange are discussed as promising but currently limited in empirical validation within many endophytic systems. Endophytes also enhance nutrient exchange through conditional carbon-for-benefit trade and may shape rhizosphere microbiota and soil activities through plant-mediated inputs. Integrative multi-omics approaches provide predominantly correlational insights into the mechanistic basis of these effects, linking molecular function to ecosystem and community outcomes. These insights have potential applications in climate-resilient agriculture, phytoremediation, and ecosystem restoration; however, their large-scale implementation requires further field-based validation and context-specific assessment. Future priorities should focus on trait-based selection, ecological modeling, and biosafety evaluation to translate microbial functions into reliable field-level strategies that support sustainable crop performance under accelerating environmental stress.

Frequent changes in global climate enhance environmental cues, threaten agricultural systems, which jeopardizes food security, and impair the achievements of the United Nations Sustainable Development Goal 2 “Zero Hunger”. To achieve a sustainable path, use of biostimulants represents a new strategy to enhance plant resilience against abiotic stresses like drought, temperature, salt, waterlogging, and heavy metals. This review explores recent developments in biostimulant technologies, aiming to clarify the processes that underlie their ability to promote plant tolerance. We also highlight the versatile roles of small RNA, peptides, and hormones as emerging molecular regulators, thereby revealing their potential for use as natural biostimulants. Developing on this, transformative effects of microbial biostimulants that use microbiota to strongly regulate plant stress‐responsive modules are explored. Furthermore, AI‐driven early warning systems provide the opportunity to identify timely stress responses, thus enabling the discovery of multi‐omics network modules, allowing rational biostimulant design. These findings are then used to guide the metabolic engineering of tailored biostimulants, where the identified key regulators and network modules become direct targets for formulation or synthetic biology approaches. This review defines a roadmap for crop stress tolerance by clarifying the mechanisms of rationally designed biostimulants, thereby paving the way for climate‐resilient agriculture and sustainable food systems.