Uncovering the effect of waterlogging stress on plant microbiome and disease development: current knowledge and future perspectives

Waterlogging is a constant threat to crop productivity and ecological biodiversity. Plants face multiple challenges during waterlogging stress like metabolic reprogramming, hypoxia, nutritional depletion, reduction in gaseous exchange, pH modifications, microbiome alterations and disease promotion all of which threaten plants survival. Due to global warming and climatic change, the occurrence, frequency and severity of flooding has dramatically increased posing a severe threat to food security. Thus, developing innovative crop management technologies is critical for ensuring food security under changing climatic conditions. At present, the top priority among scientists is to find nature-based solutions to tackle abiotic or biotic stressors in sustainable agriculture in order to reduce climate change hazards to the environment. In this regard, utilizing plant beneficial microbiome is one of the viable nature based remedial tool for mitigating abiotic stressors like waterlogging. Beneficial microbiota provides plants multifaceted benefits which improves their growth and stress resilience. Plants recruit unique microbial communities to shield themselves against the deleterious effects of biotic and abiotic stress. In comparison to other stressors, there has been limited studies on how waterlogging stress affects plant microbiome structure and their functional traits. Therefore, it is important to understand and explore how waterlogging alters plant microbiome structure and its implications on plant survival. Here, we discussed the effect of waterlogging stress in plants and its microbiome. We also highlighted how waterlogging stress promotes pathogen occurrence and disease development in plants. Finally, we highlight the knowledge gaps and areas for future research directions on unwiring how waterlogging affects plant microbiome and its functional traits. This will pave the way for identifying resilient microbiota that can be engineered to promote their positive interactions with plants during waterlogging stress

DNA barcoding: a way forward to obtain deep insights about the realistic diversity of living organisms

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Advances in Nematode Identification: A Journey from Fundamentals to Evolutionary Aspects

Nematodes are non-segmented roundworms evenly distributed with various habitats ranging to approximately every ecological extremity. These are the least studied organisms despite being the most diversified group. Nematodes are the most critical equilibrium-maintaining factors, having implications on the yield and health of plants as well as well-being of animals. However, taxonomic knowledge about nematodes is scarce. As a result of the lack of precise taxonomic features, nematode taxonomy remains uncertain. Morphology-based identification has proved inefficacious in identifying and exploring the diversity of nematodes, as there are insufficient morphological variations. Different molecular and new evolving methodologies have been employed to augment morphology-based approaches and bypass these difficulties with varying effectiveness. These identification techniques vary from molecular-based targeting DNA or protein-based targeting amino acid sequences to methods for image processing. High-throughput approaches such as next-generation sequencing have also been added to this league. These alternative approaches have helped to classify nematodes and enhanced the base for increased diversity and phylogeny of nematodes, thus helping to formulate increasingly more nematode bases for use as model organisms to study different hot topics about human well-being. Here, we discuss all the methods of nematode identification as an essential shift from classical morphometric studies to the most important modern-day and molecular approaches for their identification. Classification varies from DNA/protein-based methods to the use of new emerging methods. However, the priority of the method relies on the quality, quantity, and availability of nematode resources and down-streaming applications. This paper reviews all currently offered methods for the detection of nematodes and known/unknown and cryptic or sibling species, emphasizing modern-day methods and budding molecular techniques

Transcription factors-golden keys to modulate the plant metabolism to develop salinity tolerance

Abiotic stressors such as drought, low temperature, heavy metals, waterlogging, nutrient imbalance, and salinity are major factors that affect the growth and development of crop plants, which, in turn, results in severe loss in production and yield of economically important crops. Current literature backs up the effect of high salinity on almost all crop plants. Thus, it can be concluded that salinity stress is amongst the most dominant abiotic stress factors in current farming systems, which counteract achieving the goal of “zero hunger.” Consequently, there is a dire need to improve crop plants to develop salinity tolerance for higher yield and production, even in salinity agricultural habitats. The last few decades have established a mechanistic understanding and have identified the molecular determinants favoring salinity tolerance in crop plants. Stress-responsive transcriptional control is the best strategy crop plants adapt to alleviate abiotic stressors, especially salinity stress. In crop plants, transcription factors (TFs) central to the regulation of salinity tolerance include bZIP, WRKY, NAC, AP2/ERFBP, bZIP, and MYB. Studying these TFs and their molecular mechanisms can facilitate their molecular modification at the genetic level to modify crop plants for stress tolerance. Collectively, these reports suggest that TFs enhance tolerance to salinity stress directly or indirectly through diverse signaling pathways. This review summarizes the recent developments in deciphering the mechanistic regulation of TFs in controlling the cellular process and gene expression under salinity stress. Finally, we highlight the way forward in applying genome editing technologies to modulate TFs as hallmark genes in circumventing salinity stress in crop plants

Plant beneficial microbiome a boon for improving multiple stress tolerance in plants

Beneficial microbes or their products have been key drivers for improving adaptive and growth features in plants under biotic and abiotic stress conditions. However, the majority of these studies so far have been utilized against individual stressors. In comparison to individual stressors, the combination of many environmental stresses that plants experience has a greater detrimental effect on them and poses a threat to their existence. Therefore, there is a need to explore the beneficial microbiota against combined stressors or multiple stressors, as this will offer new possibilities for improving plant growth and multiple adaptive traits. However, recognition of the multifaceted core beneficial microbiota from plant microbiome under stress combinations will require a thorough understanding of the functional and mechanistic facets of plant microbiome interactions under different environmental conditions in addition to agronomic management practices. Also, the development of tailored beneficial multiple stress tolerant microbiota in sustainable agriculture necessitates new model systems and prioritizes agricultural microbiome research. In this review, we provided an update on the effect of combined stressors on plants and their microbiome structure. Next, we discussed the role of beneficial microbes in plant growth promotion and stress adaptation. We also discussed how plant-beneficial microbes can be utilized for mitigating multiple stresses in plants. Finally, we have highlighted some key points that warrant future investigation for exploring plant microbiome interactions under multiple stressors

Saffron, a Potential Bridge between Nutrition and Disease Therapeutics: Global Health Challenges and Therapeutic Opportunities

Plants are an important source of essential bioactive compounds that not only have a beneficial role in human health and nutrition but also act as drivers for shaping gut microbiome. However, the mechanism of their functional attributes is not fully understood despite their significance. One such important plant is Crocus sativus, also known as saffron, which possesses huge medicinal, nutritional, and industrial applications like food and cosmetics. The importance of this plant is grossly attributed to its incredible bioactive constituents such as crocins, crocetin, safranal, picrocrocin, and glycosides. These bioactive compounds possess a wide range of therapeutic activities against multiple human ailments. Since a huge number of studies have revealed negative unwanted side effects of modern-day drugs, the scientific communities at the global level are investigating a large number of medicinal plants to explore natural products as the best alternatives. Taken into consideration, the available research findings indicate that saffron has a huge scope to be further explored to establish alternative natural-product-based drugs for health benefits. In this review, we are providing an update on the role of bioactive compounds of saffron as therapeutic agents (human disorders and antimicrobial activity) and its nutritional values. We also highlighted the role of omics and metabolic engineering tools for increasing the content of key saffron bioactive molecules for its mass production. Finally, pre-clinical and clinical studies seem to be necessary to establish its therapeutic potential against human diseases

Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

ABSTRACTDomestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises

Putting CRISPR-Cas system in action: a golden window for efficient and precise genome editing for crop improvement

ABSTRACTThe daunting task of feeding an ever-growing population is an immense challenge for the contemporary scientific community, especially in view of the rapidly changing climate throughout the world. Amidst these threatening crises, we witness rapid development in genome editing (GE) technologies, revolutionizing the field of applied genomics and molecular breeding. Various GE tools have been developed during the last two decades, but the CRISPR/Cas system has most recently made a significant impact on crop improvement. The major breakthroughs of this versatile toolbox are genomic modifications like single base-substitutions, multiplex GE, gene regulation, screening mutagenesis, and enhancing the breeding of wild crop plants. Previously, this toolbox was used to modify genes related to significant traits such as biotic/abiotic resistance/tolerance, post-harvest traits, nutritional regulation, and to address self-incompatibility analysis-related challenges. In the present review, we have demonstrated the functional dynamics of CRISPR-based GE and its applicability in targeting genes to accomplish novel editing of crops. The compiled knowledge will provide a solid foundation for highlighting the primary source for applying CRISPR/Cas as a toolbox for enhancing crops, to achieve food and nutritional security

Advances in Nematode Identification: A Journey from Fundamentals to Evolutionary Aspects

Nematodes are non-segmented roundworms evenly distributed with various habitats ranging to approximately every ecological extremity. These are the least studied organisms despite being the most diversified group. Nematodes are the most critical equilibrium-maintaining factors, having implications on the yield and health of plants as well as well-being of animals. However, taxonomic knowledge about nematodes is scarce. As a result of the lack of precise taxonomic features, nematode taxonomy remains uncertain. Morphology-based identification has proved inefficacious in identifying and exploring the diversity of nematodes, as there are insufficient morphological variations. Different molecular and new evolving methodologies have been employed to augment morphology-based approaches and bypass these difficulties with varying effectiveness. These identification techniques vary from molecular-based targeting DNA or protein-based targeting amino acid sequences to methods for image processing. High-throughput approaches such as next-generation sequencing have also been added to this league. These alternative approaches have helped to classify nematodes and enhanced the base for increased diversity and phylogeny of nematodes, thus helping to formulate increasingly more nematode bases for use as model organisms to study different hot topics about human well-being. Here, we discuss all the methods of nematode identification as an essential shift from classical morphometric studies to the most important modern-day and molecular approaches for their identification. Classification varies from DNA/protein-based methods to the use of new emerging methods. However, the priority of the method relies on the quality, quantity, and availability of nematode resources and down-streaming applications. This paper reviews all currently offered methods for the detection of nematodes and known/unknown and cryptic or sibling species, emphasizing modern-day methods and budding molecular techniques