Search

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security. [ABSTRACT FROM AUTHOR]

Over the past decade, advances in nutritional science have led to the development of food-based nutraceuticals as personalized therapeutic agents. Finger millet (Eleusine coracana), an under-explored crop with significant nutraceutical potential, stands out from more commonly consumed cereals. As nutritional security becomes increasingly critical, harnessing the benefits of finger millet could establish it as an alternative functional food, improving global well-being through biofortification and integration into staple crops. The dominance of staple crops like rice, wheat, maize, and potatoes provides essential carbohydrates but lacks key amino acids and minerals, posing a risk to food security. Finger millet, with its high levels of calcium, iron, dietary fiber, protein, phytates, and essential amino acids like riboflavin, thiamine, leucine, and isoleucine, presents a valuable opportunity for enhancing nutritional security. Despite its advantages, finger millet has not been a major focus of genetic improvement efforts. Recent advancements in omics and molecular breeding technologies offer promising opportunities to accelerate its genetic enhancement. This review explores how these biotechnological advancements can enrich the nutritional value of finger millet and their implications for nutritional science and future research. [ABSTRACT FROM AUTHOR]

Table olives are widely produced and consumed in the Mediterranean area. The production of table olives is mainly based on spontaneous fermentations, which may have several drawbacks (e.g., the development of undesirable microorganisms; organoleptic defects) compared to fermentative processes driven by starter cultures (typically lactic acid bacteria, yeasts, or their combinations). Studies on the effect of starter cultures have been mainly focused on some technological traits (e.g., acidifying capability, the degradation of phenolic compounds, metabolite production) and, to a lesser extent, on the dynamics of olive microbiota during fermentation. Recently, the application of Amplicon Targeted—High-Throughput Sequencing (AT–HTS) has enabled improvement of the knowledge on the composition and evolution of microbial communities during fermentations, including the role of starter cultures. The AT–HTS approaches used so far, however, have several constraints (e.g., poor investigation of mycobiota and metabolically active microorganisms) that do not allow a full understanding of the complex microbial interactions occurring in fermented olives. The aim of this review is to provide insights into the role of starter cultures in fermented olives and highlight the need to apply, as for other fermented foods, integrated "omics" approaches to predict and exploit their metabolic potential to improve the final properties of products. [ABSTRACT FROM AUTHOR]

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients’ cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature’s untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.

Sophisticated analytical instruments are used for quality evaluation and scientific validation to compliance the market demands. Recently, increase in demand of Curcuma longa has led to a high swing in small and medium food industry. The present review is devoted to an in-depth information on metabolite database of C. longa from different analytical techniques such as high-performance thin-layer chromatography (HPTLC), liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry and nuclear magnetic resonance. This work highlights different extraction methods, phytochemistry along with structure activity relationship, nutritional profiling, market viability and pharmacology of C. longa. The bioactives of C. longa depends on various factors such as plants growth, temperature, humidity, soil type, collection, drying and extraction process. These factors can contribute in quality evaluation of the food supplements if need to be included. The introduction of omics approaches can helpful to explore the quality and identification of potential lead of C. longa. The results could play an essential role in the area of food-phyto based profiling. Further, metabolomics techniques may provide an analytical platform by combination of different “omics” data sources for future research to food and herbal based products.

The interaction between biochar application and calcium ions (Ca2+) in plants, in terms of activating plant defense mechanism would be useful to improve plant resilience and sustainable agriculture. This review aims to highlight the possible connection between biochar-induced changes in soil physicochemical properties, microbial interactions, and Ca2+ dynamics, ultimately leading to promote the plant defense mechanisms. We are also interested to discuss the role of Ca2+ signaling in coordinating plant responses to various biotic and abiotic stresses such as pathogen and insects attacks, cold or heat stress and drought stress as well as how Ca2+ fluxes, calcium-binding proteins, and ion channels are influenced by biochar application in the soil environment. Furthermore, we examine the impact of biochar on plant Ca2+ signaling pathways and how it can prime defense genes and strengthen call wall barriers to improve plant immunity. Despite significant progress, there is a need for interdisciplinary collaboration to fully sort out the mechanism of Ca2+ signaling in plants and induction of Ca2+ ions by biochar induction in soil environment. Advanced imaging techniques, proteomics and omics approaches could be helpful to unlock the complex interaction between biochar application and Ca2+ signaling. Overall, this review contributes substantially to the literature by describing the relationship between biochar and Ca2+ signaling and providing insights into novel approaches for enhancing plant defense mechanisms and development of sustainable agricultural solutions.

Globally, pest-induced crop losses ranging from 20% to 40% have spurred the extensive use of pesticides, presenting a double-edged sword that threatens not only human health but also our environment. Amidst various remediation techniques, bioremediation stands out as a compelling and eco-friendly solution. Recently, the phytomicrobiome has garnered increasing attention as endophytic microbes, colonizing plants from their roots, not only foster plant growth but also enhance the host plant's resilience to adverse conditions. Given the persistent demand for high crop yields, agricultural soils often bear the burden of pesticide applications. Biodegradation, the transformation of complex pesticide compounds into simpler forms through the activation of microbial processes and plant-based enzymatic systems, emerges as a pivotal strategy for restoring soil health. Manipulating the phytomicrobiome may emerge as a viable solution for this purpose, offering a native metabolic pathway that catalyzes pollutant degradation through enzymatic reactions. This review delves into the pivotal role of phytomicrobiomes in the degradation of diverse pesticides in soil. It explores contemporary innovations and paves the way for discussions on future research directions in this promising field. [ABSTRACT FROM AUTHOR]

This editorial published in the journal Frontiers in Plant Science discusses recent advancements in genomics and genetics of horticultural crops and their contribution to breeding efforts. The editorial highlights various research studies on topics such as selenium accumulation in tea cultivars, fern gametophytes' response to light, proteomics and metabolomics analysis of kale cultivars, genome-wide identification of gene families in mangrove species and pineapple, and the development of a single primer enrichment technology panel for lettuce. The text also mentions a study on genome editing in cabbage and a review paper on breeding for secondary metabolites content in horticultural crops. The editorial provides information on the progress made in breeding for higher accumulation of phenolic acids and flavonoids in popular vegetables such as pepper, tomato, and eggplant, using genetic and genomic technologies to discover enzymes, genes, and QTLs involved in the biosynthesis and accumulation of these compounds. The text also discusses the assembly and annotation of non-nuclear genomes, specifically the mitochondrial and chloroplastic genomes of the wax apple and three wild perennial Hordeum species, respectively. These genome studies provide insights into plant biology, phylogenetic evolution, and genetic diversity, and offer valuable information for molecular breeding and genetic improvement. [Extracted from the article]

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments. [ABSTRACT FROM AUTHOR]

This document is an editorial published in the journal Frontiers in Endocrinology. It discusses the role of gut microbiota-derived metabolites in obesity and metabolic disorders. The editorial highlights the use of omics approaches, such as metabolomics and proteomics, to study the relationship between gut microbiota and host metabolism. The document also provides an overview of the pathogenesis of obesity and outlines potential risk factors for metabolic disorders. The editorial includes several research articles and a review that explore various aspects of this topic, including the impact of obesity on non-alcoholic fatty liver disease, the relationship between adolescent obesity and hypertension, and the role of gut microbiota in obesity and type 2 diabetes. The authors emphasize the need for a better understanding of disease mechanisms to develop effective diagnostics and therapeutic strategies for obesity. [Extracted from the article]

Plants are frequently subjected to heavy metal (HM) stress that impedes their growth and productivity. One of the most common harmful trace metals and HM discovered is chromium (Cr). Its contamination continues to increase in the environment due to industrial or anthropogenic activities. Chromium is severely toxic to plant growth and development and acts as a human carcinogen that enters the body by inhaling or taking Cr-contaminated food items. Plants uptake Cr via various transporters, such as sulfate and phosphate transporters. In nature, Cr is found in various valence states, commonly Cr (III) and Cr (VI). Cr (VI) is soil's most hazardous and pervasive form. Cr elevates reactive oxygen species (ROS) activity, impeding various physiological and metabolic pathways. Plants have evolved various complex defense mechanisms to prevent or tolerate the toxic effects of Cr. These defense mechanisms include absorbing and accumulating Cr in cell organelles such as vacuoles, immobilizing them by forming complexes with organic chelates, and extracting them by using a variety of transporters and ion channels regulated by various signaling cascades and transcription factors. Several defense-related proteins including, metallothioneins, phytochelatins, and glutathione-S-transferases aid in the sequestration of Cr. Moreover, several genes and transcriptional factors, such as WRKY and AP2/ERF TF genes, play a crucial role in defense against Cr stress. To counter HM-mediated stress stimuli, OMICS approaches, including genomics, proteomics, transcriptomics, and metallomics, have facilitated our understanding to improve Cr stress tolerance in plants. This review discusses the Cr uptake, translocation, and accumulation in plants. Furthermore, it provides a model to unravel the complexities of the Cr- plant interaction utilizing system biology and integrated OMICS approach. [ABSTRACT FROM AUTHOR]

Heat stress (HS) is a major threat to crop productivity and is expected to be more frequent and severe due to climate change challenges. The predicted increase in global temperature requires us to understand the dimensions of HS experienced by plants, particularly during reproductive stages, as crop productivity is majorly dependent on the success of plant reproduction. The impact of HS on crop productivity is relatively less-studied than the other abiotic stresses, such as drought and salinity. Plants have evolved diverse mechanisms to perceive, transduce, respond, and adapt to HS at the molecular, biochemical, and physiological levels. Unraveling these complex mechanisms underlying plant HS response and tolerance would facilitate designing well-informed and effective strategies to engineer HS tolerance in crop plants. In this review, we concisely discuss the molecular impact of HS on plant reproductive processes and yield, with major emphasis on transcription factors. Moreover, we offer vital strategies (encompassing omics studies, genetic engineering and more prominently gene editing techniques) that can be used to engineer transcription factors for enhancing heat tolerance. Further, we highlight critical shortcomings and knowledge gaps in HS tolerance research that should guide future research investigations. Judicious studies and a combination of these strategies could speed up the much-needed development of HS-resilient crop cultivars. [ABSTRACT FROM AUTHOR]

Solanaceous crops act as a source of food, nutrition and medicine for humans. Soil salinity is a damaging environmental stress, causing significant reductions in cultivated land area, crop productivity and quality, especially under climate change. Solanaceous crops are extremely vulnerable to salinity stress due to high water requirements during the reproductive stage and the succulent nature of fruits and tubers. Salinity stress impedes morphological and anatomical development, which ultimately affect the production and productivity of the economic part of these crops. The morpho-physiological parameters such as root-to-shoot ratio, leaf area, biomass production, photosynthesis, hormonal balance, leaf water content are disturbed under salinity stress in Solanaceous crops. Moreover, the synthesis and signalling of reactive oxygen species, reactive nitrogen species, accumulation of compatible solutes, and osmoprotectant are significant under salinity stress which might be responsible for providing tolerance in these crops. The regulation at the molecular level is mediated by different genes, transcription factors, and proteins, which are vital in the tolerance mechanism. The present review aims to redraw the attention of the researchers to explore the mechanistic understanding and potential mitigation strategies against salinity stress in Solanaceous crops, which is an often-neglected commodity. [ABSTRACT FROM AUTHOR]

Driven by a surge in global interest in natural products, macroalgae or seaweed, has emerged as a prime source for nutraceuticals and pharmaceutical applications. Characterized by remarkable genetic diversity and a crucial role in marine ecosystems, these organisms offer not only substantial nutritional value in proteins, fibers, vitamins, and minerals, but also a diverse array of bioactive molecules with promising pharmaceutical properties. Furthermore, macroalgae produce approximately 80% of the oxygen in the atmosphere, highlighting their ecological significance. The unique combination of nutritional and bioactive attributes positions macroalgae as an ideal resource for food and medicine in various regions worldwide. This comprehensive review consolidates the latest advancements in the field, elucidating the potential applications of macroalgae in developing nutraceuticals and therapeutics. The review emphasizes the pivotal role of omics approaches in deepening our understanding of macroalgae's physiological and molecular characteristics. By highlighting the importance of omics, this review also advocates for continued exploration and utilization of these extraordinary marine organisms in diverse domains, including drug discovery, functional foods, and other industrial applications. The multifaceted potential of macroalgae warrants further research and development to unlock their full benefits and contribute to advancing global health and sustainable industries. [ABSTRACT FROM AUTHOR]

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO. [ABSTRACT FROM AUTHOR]

Candida albicans is an opportunistic fungal pathogen that can cause superficial and invasive infections. Seventy-five percent of women suffer from vaginal candidiasis at least once in their lifetime, 372 million women are currently suffering from recurrent vulvovaginal candidiasis, and 700 000 cases of invasive candidiasis are reported yearly, with an associated mortality of 30–40%. Bacteria from the gut and vaginal microbiota can control C. albicans growth by the release of antifungal metabolites, modulation of the host immune response, and/or competition for nutrients, niches, and adhesion sites. Cutting-edge OMICs-based pipelines, relying on metagenomics and/or metabolomics, have permitted the identification of bacterial species and metabolites with potential antifungal activities. The development of experimental platforms has allowed the validation and screening of new anti- C. albicans bacteria. In silico and experimental approaches have allowed an ever-growing understanding of the interactions within the microbiota. For instance, recently acquired data have increased knowledge of the mechanisms that support, in the gut and vaginal microbiota, the resistance to colonization by Candida albicans , an opportunistic fungal pathogen whose overgrowth can initiate severe infections in immunocompromised patients. Here, we review how bacteria from the microbiota interact with C. albicans. We show how recent OMICs-based pipelines, using metagenomics and/or metabolomics, have identified bacterial species and metabolites modulating C. albicans growth. We finally discuss how the combined use of cutting-edge OMICs-based and experimental approaches could provide new means to control C. albicans overgrowth within the microbiota and prevent its consequences. [ABSTRACT FROM AUTHOR]

The stability of ecosystem and the well-being of humans have been significantly impacted by the contamination of heavy metals and pesticides, primarily due to their resistance, persistence, and high toxicity. Consequently, this paper attempts to provide a comprehensive elucidation of the bioremediation capabilities of microorganisms, considering the current environmental and health risks posed by these pollutants. This review has systematically discussed and analyzed the recent reports (2012–2023) on the applications of microbes for removal of heavy metals and degradation of pesticides, with the objective of understanding the underlying mechanisms associated with microbial behavior in diverse habitats. The study advocated the utilization of specific microorganisms, namely Pseudomonas aeruginosa, Jeotgalicoccus sp., Aspergillus sp., Penicillium chrysogenum, and Chlorella vulgaris for the remediation of cadmium, arsenic, chromium, lead, copper, mercury, and nickel. Similarly, Bacillus sp., Aspergillus sydowii, Pseudomonas putida, and Cordyceps militaris have demonstrated significant potential for remediating cypermethrin, organo-phosphate, chlorpyrifos, profenofos, and trichlorodibenzofuran. In addition, a brief explanation of molecular methods that aid in the bioremediation process has also been discussed. The paper also highlights the importance of evaluating the efficacy of microbial remediation methods and summarizes the existing assessment approaches. In conclusion, this paper highlights the importance of a universally designed assessment framework to support decisions and actions aimed at reducing environmental pollution. It emphasizes that such a framework is crucial in preventing unintentional worsening of environmental concerns.Highlights: Microbe exertion is a promising tool in environmental remediation. Pseudomonas aeruginosa bioaccumulate Cu, Pb, Zn, Cd and Ni. Bacillus aryabhattai degrades chlorpyrifos and parathion pesticides. Chlorella sp. reveals higher biosorption for Cu, Cr, Cd, Hg and Zn. Omics-based methods enhance bioremediation mechanisms of microbes. [ABSTRACT FROM AUTHOR]

Microbial endophytes are microorganisms that reside within plant tissues without causing any harm to their hosts. These microorganisms have been found to confer a range of benefits to plants, including increased growth and stress tolerance. In this review, we summarize the recent advances in our understanding of the mechanisms by which microbial endophytes confer abiotic and biotic stress tolerance to their host plants. Specifically, we focus on the roles of endophytes in enhancing nutrient uptake, modulating plant hormones, producing secondary metabolites, and activating plant defence responses. We also discuss the challenges associated with developing microbial endophyte-based products for commercial use, including product refinement, toxicology analysis, and prototype formulation. Despite these challenges, there is growing interest in the potential applications of microbial endophytes in agriculture and environmental remediation. With further research and development, microbial endophyte-based products have the potential to play a significant role in sustainable agriculture and environmental management. [ABSTRACT FROM AUTHOR]

Globally, pest-induced crop losses ranging from 20% to 40% have spurred the extensive use of pesticides, presenting a double-edged sword that threatens not only human health but also our environment. Amidst various remediation techniques, bioremediation stands out as a compelling and eco-friendly solution. Recently, the phytomicrobiome has garnered increasing attention as endophytic microbes, colonizing plants from their roots, not only foster plant growth but also enhance the host plant’s resilience to adverse conditions. Given the persistent demand for high crop yields, agricultural soils often bear the burden of pesticide applications. Biodegradation, the transformation of complex pesticide compounds into simpler forms through the activation of microbial processes and plant-based enzymatic systems, emerges as a pivotal strategy for restoring soil health. Manipulating the phytomicrobiome may emerge as a viable solution for this purpose, offering a native metabolic pathway that catalyzes pollutant degradation through enzymatic reactions. This review delves into the pivotal role of phytomicrobiomes in the degradation of diverse pesticides in soil. It explores contemporary innovations and paves the way for discussions on future research directions in this promising field.

Simple Summary: Freshwater ecosystems face various threats, especially in recent decades, that pose unprecedented challenges to human health, water supply, agriculture, forestry, ecology, and biodiversity. Although progress has been made in biomonitoring techniques tailored to specific countries and communities, significant constraints exist in assessing and quantifying biodiversity and its interaction with detrimental factors. The incorporation of modern techniques into biomonitoring is challenging, with multiple perspectives. This review aims to provide a comprehensive overview of contemporary advancements in freshwater biomonitoring, focusing on omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. Additionally, this work highlights the need for modernization by presenting case studies, examining studied organisms, and evaluating the benefits and drawbacks of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a departure from conventional practices, necessitating a significant shift. The contributions of omics techniques to biological quality elements (BQEs) and their interpretations of ecological problems are crucial for biomonitoring programs. These contributions identify interactions between different levels of biological organization and their responses to specific critical conditions. Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions. [ABSTRACT FROM AUTHOR]

Salinity is one of the significant abiotic stresses that negatively affect plant production processes, growth, and development, which ultimately reduce yield. Plants adapt specific mechanisms to withstand saline conditions and activate diverse salt tolerance genes to counter osmotic and oxidative stresses induced by salinity. Genetic development in salinity tolerance is quite complex, while advancement has made less progress than expectation over the past few decades. Generating an explosion of genetics- and genomics-related information and technology in recent decades pledge to deliver innovative and advanced resources for the potential production of tolerant genotypes. Despite considerable progress in defining the primary salinity tolerance mechanisms, main obstacles are yet to be solved in the translation and incorporation of the resulting molecular knowledge into the plant breeding activities. Diverse approaches are proposed to enhance plant breeding efficacy to increase plant productivity in saline environments. Understanding the genetics of salt tolerance is a difficult task because multiple genes and pathways are involved. Important advances in tools and methods for updating and manipulating plant genomics knowledge provide detailed insights and dissect the salinity tolerance mechanism accomplished by the breeding goals. Genome-wide analyses (GWA) identify SNP variations and functional effects that appear to be the way of the future for developing salinity-tolerant plants. Gene discovery to manipulate the molecular mechanisms which underlie the complex phenotype of salinity tolerance methods, identification of genes, QTL, association mapping, linkage, and functional genomics, such as transcript identifying and proteins related to salinity, is necessary. The present analysis also discussed some of the opportunities and challenges, focusing on molecular breeding strategies used in conjunction with other crop development approaches to growing elite salt-tolerant lines. [ABSTRACT FROM AUTHOR]

Pesticides are a well-known family of chemicals that have contaminated water systems globally. Four common subfamilies of pesticides include organochlorines, organophosphates, pyrethroids, and carbamate insecticides which have been shown to adversely affect the human nervous system. Studies have shown a link between pesticide exposure and decreased viability, proliferation, migration, and differentiation of murine neural stem cells. Besides human exposure directly through water systems, additional factors such as pesticide bioaccumulation, biomagnification and potential synergism due to co-exposure to other environmental contaminants must be considered. A possible avenue to investigate the molecular mechanisms and biomolecules impacted by the various classes of pesticides includes the field of -omics. Discovery of the precise molecular mechanisms behind pesticide-mediated neurodegenerative disorders may facilitate development of targeted therapeutics. Likewise, discovery of pesticide biodegradation pathways may enable novel approaches for water system bioremediation using genetically engineered microorganisms. In this mini-review, we discuss recently established harmful impacts of various categories of pesticides on the nervous system and the application of -omics field for discovery, validation, and mitigation of pesticide neurotoxicity. [ABSTRACT FROM AUTHOR]

Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential. [ABSTRACT FROM AUTHOR]

The 36th Malaysian Society of Pharmacology and Physiology (MSPP) Annual Scientific Meeting was hosted in collaboration with the Faculty of Medicine and Health Sciences, Universiti Putra Malaysia from the 7th to 8th of August 2023 at Bangi Resort Hotel in Bangi, Malaysia. The event focused on the theme "Pharmacology & Physiology Post-Millenial Era: Challenges & Opportunities". This platform is one of the suitable avenues to facilitate the exchange of scientific endeavors and enhance networking among scientists, academicians, clinicians, and postgraduate students involved in the fields of pharmacology and physiology, as well as multidisciplinary areas such as drug discovery, omics approaches, stem cells, and regenerative medicine. The primary objective of the special issue is to revitalize recent advances and breakthroughs in pharmacology and physiology to enhance opportunities and vanquish challenges in the post-millenial era, especially in the wake of the COVID-19 pandemic. In light of this, the special issue compiles the conference proceeding, to provide opportunities for knowledge integration of research and innovations.

Heat stress (HS) is a major threat to crop productivity and is expected to be more frequent and severe due to climate change challenges. The predicted increase in global temperature requires us to understand the dimensions of HS experienced by plants, particularly during reproductive stages, as crop productivity is majorly dependent on the success of plant reproduction. The impact of HS on crop productivity is relatively less-studied than the other abiotic stresses, such as drought and salinity. Plants have evolved diverse mechanisms to perceive, transduce, respond, and adapt to HS at the molecular, biochemical, and physiological levels. Unraveling these complex mechanisms underlying plant HS response and tolerance would facilitate designing well-informed and effective strategies to engineer HS tolerance in crop plants. In this review, we concisely discuss the molecular impact of HS on plant reproductive processes and yield, with major emphasis on transcription factors. Moreover, we offer vital strategies (encompassing omics studies, genetic engineering and more prominently gene editing techniques) that can be used to engineer transcription factors for enhancing heat tolerance. Further, we highlight critical shortcomings and knowledge gaps in HS tolerance research that should guide future research investigations. Judicious studies and a combination of these strategies could speed up the much-needed development of HS-resilient crop cultivars.

Driven by a surge in global interest in natural products, macroalgae or seaweed, has emerged as a prime source for nutraceuticals and pharmaceutical applications. Characterized by remarkable genetic diversity and a crucial role in marine ecosystems, these organisms offer not only substantial nutritional value in proteins, fibers, vitamins, and minerals, but also a diverse array of bioactive molecules with promising pharmaceutical properties. Furthermore, macroalgae produce approximately 80% of the oxygen in the atmosphere, highlighting their ecological significance. The unique combination of nutritional and bioactive attributes positions macroalgae as an ideal resource for food and medicine in various regions worldwide. This comprehensive review consolidates the latest advancements in the field, elucidating the potential applications of macroalgae in developing nutraceuticals and therapeutics. The review emphasizes the pivotal role of omics approaches in deepening our understanding of macroalgae’s physiological and molecular characteristics. By highlighting the importance of omics, this review also advocates for continued exploration and utilization of these extraordinary marine organisms in diverse domains, including drug discovery, functional foods, and other industrial applications. The multifaceted potential of macroalgae warrants further research and development to unlock their full benefits and contribute to advancing global health and sustainable industries.

New approaches based on -omics technologies can identify biomarkers and processes regulated in response to xenobiotics, and thus support toxicological risk assessments. This is vital to meet the challenges associated with “cocktail effects”, i.e. combination effects of chemicals present simultaneously in a product, our environment, and/or our body. For plant protection products (PPPs), investigations largely focus on active ingredients such as herbicides and fungicides. In this study, we have analyzed agricultural chemicals, two surfactants (poly(oxy-1,2-ethanediyl), alpha-sulfo-omega-[2,4,6-tris(1-phenylethyl)phenoxy]-, ammonium salt, POL; N,N-dimethylcapramide, NND), and one preservative, 1,2-benzisothiazol-3(2 H)-one (BEN) used as adjuvants in PPPs, and further three fungicide PPPs, Proline EC 250, Shirlan, Folicur Xpert, containing the adjuvants, and other major individual constituents (fluazinam (FLU), prothioconazole (PRO), tebuconazole (TEB)) as well as defined mixtures (“mixes”) thereof using several in vitro approaches. All investigated single agricultural chemicals were predicted as skin sensitizers using an in vitro transcriptomic assay based on a dendritic cell model. For selected chemicals and mixes, also skin sensitization potency was predicted. The preservative BEN induced significant changes in cytokine secretion and dendritic cell activation marker CD86 expression. The surfactant NND changed cytokine secretion only and the POL only affected CD86 expression. Proteomic analyses revealed unique response profiles for all adjuvants, an oxidative stress pattern response in BEN-treated cells, and differentially abundant proteins associated with cholesterol homeostasis in response to POL. In summary, we find responses to agricultural chemicals and products consistent with the dendritic cell model reacting to chemical exposure with oxidative stress, ER stress, effects on autophagy, and metabolic changes especially related to cholesterol homeostasis. After exposure to certain mixes, novel proteins or transcripts were differentially expressed and these were not detected for any single constituents, supporting the occurrence of cocktail effects. This indicates that all chemicals in a PPP can contribute to the toxicity profile of a PPP, including their skin sensitizing/immunotoxic properties.

Abstract Background Women with uterine adenomyosis seeking assisted reproduction have been associated with compromised endometrial receptivity to embryo implantation. To understand the mechanisms involved in this process, we aimed to compare endometrial transcriptome profiles during the window of implantation (WOI) between women with and without adenomyosis. Methods We obtained endometrial biopsies LH-timed to the WOI from women with sonographic features of adenomyosis (n=10) and controls (n=10). Isolated RNA samples were subjected to RNA sequencing (RNA-seq) by the Illumina NovaSeq 6000 platform and endometrial receptivity classification with a molecular tool for menstrual cycle phase dating (beREADY®, CCHT). The program language R and Bioconductor packages were applied to analyse RNA-seq data in the setting of the result of accurate endometrial dating. To suggest robust candidate pathways, the identified differentially expressed genes (DEGs) associated with the adenomyosis group in the receptive phase were further integrated with 151, 173 and 42 extracted genes from published studies that were related to endometrial receptivity in healthy uterus, endometriosis and adenomyosis, respectively. Enrichment analyses were performed using Cytoscape ClueGO and CluePedia apps. Results Out of 20 endometrial samples, 2 were dated to the early receptive phase, 13 to the receptive phase and 5 to the late receptive phase. Comparison of the transcriptomics data from all 20 samples provided 909 DEGs (p

The recent outbreak of the emerging pathogenic races of Fusarium wilt and early blight causing pathogens capable of infecting numerous commercial tomato varieties/cultivars highlights the need for robust disease resistance in crop plants. To breed plants with increased and robust disease resistance using quantitative disease resistance genes and resistance gene pyramids is being used to combat Fusarium wilt and early blight resistance, but broader acceptance of these methods is required to maintain resistance effectiveness. A greater understanding of the molecular basis of plant disease resistance at host levels offers further possibilities for Fusarium wilt and early blight resistance using omics approaches, such as genomics, transcriptomics, proteomics, and metabolomics. These omics technologies are delivering us many candidate genes that might lead to increased disease resistance through genetic engineering. There are several strategies for manipulating these genes, which can come from plants, pathogens, or other organisms. However, truly durable tomato cultivars with Fusarium wilt and early blight resistance appear a doubtful prospect in the face of frequently evolving virulent populations of associated pathogens. This article discusses recent developments and future perspectives for improving tomato plants resistant to Fusarium wilt and early blight.

Drought intensity that has increased as a result of human activity and global warming poses a serious danger to agricultural output. The demand for ecologically friendly solutions to ensure the security of the world's food supply has increased as a result. Plant growth-promoting rhizobacteria (PGPR) treatment may be advantageous in this situation. PGPR guarantees the survival of the plant during a drought through a variety of processes including osmotic adjustments, improved phytohormone synthesis, and antioxidant activity, among others and these mechanisms also promote the plant's development. In addition, new developments in omics technology have improved our understanding of PGPR, which makes it easier to investigate the genes involved in colonizing plant tissue. Therefore, this review addresses the mechanisms of PGPR in drought stress resistance to summarize the most current omics-based and molecular methodologies for exploring the function of drought-responsive genes. The study discusses a detailed mechanistic approach, PGPR-based bioinoculant design, and a potential roadmap for enhancing their efficacy in combating drought stress. [ABSTRACT FROM AUTHOR]

Abiotic stressors are major constraints that affect agricultural plant physio-morphological and biochemical attributes, resulting in a loss of normal functioning and, eventually, a severe decline in crop productivity. The co-occurrence of different abiotic stresses, rather than a specific stress situation, can alter or trigger a wide range of plant responses, such as altered metabolism, stunted growth, and restricted development. Therefore, systematic and rigorous studies are pivotal for understanding the impact of concurrent abiotic stress conditions on crop productivity. In doing so, this review emphasizes the implications and potential mechanisms for controlling/managing combined abiotic stresses, which can then be utilized to identify genotypes with combined stress tolerance. Furthermore, this review focuses on recent biotechnological approaches in deciphering combined stress tolerance in plants. As a result, agronomists, breeders, molecular biologists, and field pathologists will benefit from this literature in assessing the impact of interactions between combined abiotic stresses on crop performance and development of tolerant/resistant cultivars. [ABSTRACT FROM AUTHOR]