Understanding the role and dynamics of endosymbionts within host organisms is crucial in various fields including ecology, evolutionary biology, and biotechnology. Traditional PCR-based methods have significandy contributed to this understanding, but they often pose limitations such as the inability to distinguish between live and dead cells or the requirement for prior knowledge of target sequences. Non-PCR-based approaches offer innovative solutions to overcome these challenges and provide deeper insights into the ecology and physiology of endosymbionts. Fluorescence In Situ Hybridization (FISH) and Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH), flow cytometry and cell sorting, and DNA microarray technology are some of the important non-PCR-based techniques. FISH and CARD-FISH allow for the visualization and localization of specific endosymbionts within host tissues or environmental samples, enabling researchers to examine spatial relationships and quantify cellular abundances with high resolution. Flow cytometry, coupled with cell sorting, facilitates the isolation and purification of endosymbiont-containing cells based on their physical and chemical properties, thus enabling downstream genomic or proteomic analyses. DNA microarrays provide a high -throughput method to analyze the genetic diversity and functional capabilities of endosymbiont communities by simultaneously detecting multiple genetic targets.

Isolating fungal endosymbionts is crucial for understanding their roles in various ecosystems, agriculture, and biotechnology. Fungal endosymbionts residing within plant tissues play essential roles in enhancing plant growth, stress tolerance, and disease resistance. However, their isolation presents several challenges, including host specificity, non-culturable nature, and contamination risks. Traditional methods, such as morphological identification, are often supplemented or replaced with molecular techniques, including DNA sequencing of conserved regions like the ITS and 18S rRNA genes, which provide accurate identification of endosymbionts. Recent advancements have enabled the isolation of diverse endosymbiotic fungi, such as Epichloe festucae, Piriformospora indica, Trichoderma harzianum, Fusarium oxysporum, and Penicillium chrysogenum, each of which offers unique benefits, ranging from biocontrol to antibiotic production. This book chapter highlights the importance of combining traditional and molecular approaches to overcome the challenges of isolation, ensuring a deeper understanding of fungal endosymbionts and their potential applications across various fields.

Micro- and nano-plastics (MNPs) are emerging contaminants in soil ecosystems that influence microbial communities and key ecological processes through complex physicochemical and biological interactions. This review synthesizes current knowledge on MNP-microbe interactions, highlighting the central role of the eco-corona, which governs particle bioavailability and mediates interactions with microbial cells in realistic soil environments. At the nanoscale, MNPs exhibit distinct molecular mechanisms, including surface charge-driven interactions, hydrophobic insertion into lipid bilayers, and cellular internalization, leading to oxidative stress and membrane disruption. The formation of plastisphere biofilms is identified as a critical factor shaping microbial community dynamics and acting as a hotspot for antibiotic resistance gene (ARG) enrichment and horizontal gene transfer (HGT). In addition, the impacts of weathered plastics, additive leaching, and co-contaminant transport are discussed in relation to their enhanced ecological risks. The review also adopts a critical perspective on microbial degradation, distinguishing superficial surface modifications from true biodegradation involving polymer depolymerization and mineralization, and highlights the limited evidence for effective degradation of conventional plastics. Despite recent advances, significant knowledge gaps remain regarding long-term environmental behavior, standardized analytical approaches, and realistic soil conditions, underscoring the need for more integrated and mechanistic research to better understand the ecological implications of MNP contamination.

The macropores of biochar provide a suitable habitat for microbial growth, and its high carbon content serves as an energy source for beneficial microbes. This study evaluated the potential of biochar as a carrier for Trichoderma in managing Sclerotinia sclerotiorum in chickpeas. Biochar application reduced plant disease severity by 36.5% and increased plant root mass by 23.3%. For this, three types of biochar, wheat straw, organic kitchen waste, and hardwood were tested with Trichoderma, analyzing such as organic C, total N, P, K, Mg, and Ca; pH, and ash content. Trichoderma populations were monitored with biochar carrier of different mesh sizes (250, 150, 75, and 45 µm) for up to 6 weeks after inoculation. Hardwood biochar at 150 µm supported the highest Trichoderma population, reaching 33.5 × 105 CFU·g−1 after 6 weeks. Hardwood biochar also achieved the maximum disease suppression compared to other biochar types. This research highlights the dual role of biochar in enhancing plant growth and controlling disease, contributing to the standardization of biochar use in agricultural practices.

The current study was carried out to assess the alkaloid-enriched constituents of Prosopis juliflora (Fabaceae) against bacterial blight of pomegranate. Utilising plant extracts for disease management offers an eco-friendly approach. In vitro assessment of the minimum inhibitory concentration (MIC) for alkaloid-enriched fractions from the leaves and inflorescence of P. juliflora revealed a 14 mm zone of inhibition, with the lowest MIC value being 30 mg/mL. Untargeted metabolomics analysis of alkaloid-rich fractions (ARF) from four different tissues of P. juliflora, subjected to LC-MS for alkaloid identification, detected a total of 1489 peaks in positive mode and 240 peaks in negative mode. The highest peaks were detected in the leaves, where 47 metabolites and 9 alkaloids were identified. Ellipticine and ormosanine were found in relatively high concentrations across all four tissues, as indicated by their peak areas. The inflorescence had significantly high concentrations of sparteine, solanidine-I and puberanidine compared with other parts. Additionally, acetylsolanine was more abundant in the inflorescence, while solasodine-I was more prevalent in the leaves. A substantial amount of strictosidine was also found in the inflorescence.

Phytopathogens are one of the major detrimental agents which cause significant yield loss and affect crop productivity and food security. Diagnosis of phytopathogen in the initial stages of disease development is essential for accurate field-level management. The disease can be currently diagnosed early from the field more precisely because of the development of precise, quick, and sensitive technologies. This is especially true today, when variables like climate change may drive infections to arise in regions where they were unanticipated in the past. The traditional identification methods largely relied on the cultural characteristics of pathogens, the symptomatic expression of plants infected, or based on the signs present in infected plants. These methods largely involved skilled experts and it is time-consuming. On the other hand, the recent developments in DNA-based diagnosis methods have become popular in the diagnosis of phytopathogen. Advanced molecular methods such as PCR-based methods, isothermal amplification-based methods, probe-based methods, post-amplification techniques, next-generation sequencing, and approaches grounded on the analysis of volatile compounds are being used in the detection of several phytopathogen owing to their sensitivity and reliability. Further, these techniques have the advantage of their applicability to non-culturable pathogens. The current review aims to explore some of the potential methods and advances in the field of real-time detection of plant pathogens and how these methods may alter farmers and pathologists in diagnosing plant diseases.

Nowadays, scientists and researchers are combining their efforts for establishing a resilient and stable sustainable agriculture, which will help preserve the environment and the ecosystems, leading, especially, to a long-term higher plant productivity. Endophytic bacteria are associated with the above-ground habitat, that is, they colonize the aerial part of and thrive inside host plant, especially in leaves, stems, flowers, and fruits, and impart protection to the host under favorable as well as unfavorable conditions. Little is known about the diversity of bacterial endophytes; thus, there is a need to advance fundamental knowledge of their dynamics in association with phyllosphere. Plant growth-promoting phyllosphere endophytic bacterial colonizers may positively influence agricultural production, and thereby be useful in decreasing the activity of phytopathogenic microbes. The chapter gathers information on bacterial diversity for the most common classes of Alphaproteobacteria and Gammaproteobacteria in the phylum Pseudomonadota, formerly known as proteobacteria, and the two following phyla, namely Actinobacteria and Bacteroidetes, and regarding specific factors controlling phyllosphere endophytes and their major biotechnological applications as bioagents, plant growth-promoting compound, bioactive metabolite prime producers, and plant abiotic stress tolerance mechanism-potential providers. This chapter also accentuates the understand of the functioning of phyllosphere, types of endophyte transmission in plants, and recent research trends that may improve plant-endophyte bacterial association. Here, we also summarize the knowledge regarding the ecological significance of phyllospheric helpful and potentially harmful bacteria.

The bacterial blight of pomegranate caused by Xanthomonas axonopodispv. Punicae has become a conceivably dangerous infection. Though, the chemical management is efficient, their hazardous effects restrict them for their usage. In this context use of different parts of Prosopis juliflora extract along with antibiotics has become the alternative strategy for management of disease. Detection of secondary metabolites from different parts of the P. juliflorausing specific test indicated the presence of various secondary metabolites. However, leaf extract exhibited high concentration metabolites compared to green pod, yellow pod and inflorescence. Management of this disease utilizing plant extracts is an eco-friendly approach. Alkaloid rich fractions obtained from the different parts of Prosopis juliflora in combination with bactericides were found compatible. Leaf ARF with streptocycline @ 500 ppm showed maximum inhibition of 40.66 mm. Wherein combination with copper hydroxide @ 0.25% ppm and 2-bromo-2-nitro propane-1,3-diol @ 500 ppm showed inhibition of 25.00 mm and 36.98 mm whereas copper oxychloride @ 0.3% showed inhibition of 28.19 mm. These fundings can be used as an effective, eco friendly management strategy against the disease and a feasible solution for antibiotic resistance.

Metagenomics is the most prominent and powerful tool for understanding the genetic variability of microorganisms communities in different complex ecosystems. In recent years, several studies have been carried out in this research field. Genome-level validation through high-throughput next-generation sequencing technologies and bioinformatics tools leads to the independent assessment of microbial communities. Application of high-throughput sequencing and metagenomics studies opened a new window into metabolic diversity in the microbial communities, phylogenetic analysis, the origin of the microorganism, expression of genes at diverse environmental conditions, recovery of novel biomolecules, and identification of new isolates. These microbes are involved in numerous biogeochemical cycles and decomposition. Integrating metagenomics with bioinformatic tools helps better monitor and understand various environmental and ecological strategies for microbial diversity, evolution, and adaptation in multiple ecosystems.

Fungi are among the least understood life forms on the planet, and bioluminescence suggests that hundreds of species may still exist. A natural light-emitting process called bioluminescence phenomenon has been observed in 71 out of the 100,000 documented species in the kingdom of fungi. When an enzyme, namely luciferase, catalyzes the oxidation of an organic molecule called luciferin, energy from a chemical process is released as light, resulting in bioluminescence. Understanding the chemistry of molecules that produce natural light has resulted in new instruments that have numerous beneficial applications. Beyond their ecological roles, bioluminescent fungi have sparked interest in their potential applications in various fields. In biotechnology, the unique light-producing capability of these fungi could be harnessed for imaging purposes, enabling non-invasive tracking of biological processes in living organisms. These bioluminescent fungi are used in biotechnological processes including heavy metal extraction, luciferase reporter gene systems in genetic engineering, bioluminescence imaging, and many other things. Moreover, the study of bioluminescent fungi may contribute to advancements in environmental monitoring and conservation efforts, providing insights into the health of ecosystems. As researchers delve deeper into understanding the molecular mechanisms behind fungal bioluminescence, the future may see these captivating organisms become valuable tools in both scientific research and innovative technologies.

Rhizobacteria are one of the ecofriendly strategies which can be used in enhancing agriculture productivity. They are rhizosphere-inhibiting bacteria that are directly and indirectly involved in encouraging plant growth and development by producing various chemicals in the rhizosphere. Under both normal and stressful conditions, the use of plant growth–promoting bacteria has been shown to improve the health and productivity of several plant species, by producing exopolysaccharides phytohormones, 1-aminocyclopropane -1-carboxylate (ACC) deaminase, volatile compound, induced accumulation of osmolytes, antioxidant, upregulating or downregulating stress-responsive genes, and altering root morphology. These advantageous microorganisms colonize the rhizosphere and endo-rhizosphere of plants and impart drought tolerance. Additionally, these microorganisms can increase crop resistance to abiotic stress like salinity, heat, and drought. The management of a sustainable agriculture system will be made easier by recent advancements in the understanding of the diversity of rhizobacteria in the rhizosphere, their capacity to colonize and their mode of action in reducing biotic stress. In future, it may be possible and perhaps practical to use these rhizobacteria as biofertilizers and biopesticides which have least adverse effects on the environment.

Mushrooms are classified into different categories on different basis but here we are classifying them into edible, poisonous and medicinal based on their effect on human body after their ingestion. They have difference in their morphology and their nutrient content also which is the major reason for their effect on humans. We need to identify the differences between edible and poisonous mushroom in order to prevent accidental poisoning which have become one of the great concerns of modern world. On the other hand, there are some medicinal mushrooms which are boon to the society and human life, they are used to make a lot of life saving drugs to increase life expectancy. Bio fortified edible mushrooms also play an important role in this society of hidden hunger people.

The region between a plant's root system and the soil around it is known as the rhizosphere. The rhizosphere's microbiome, which is made up of all the microbes that live there, is a complex microbial ecosystem that supports the terrestrial biosphere. Archaea, bacteria, fungi, picoeukaryotes, and viruses are just a few of the microbial species that interact with their plant hosts directly in this intricate biological system. An integrated multiomics approach can be used to reveal the composition of the rhizospheric microbiome through 16S ribosomal amplicons and metagenomics. The functional characteristics of the microbiome through metatranscriptomics, metaproteomics, transcriptomics and proteomics, and the signaling network within the rhizosphere enable the complexity of the rhizosphere. A number of bioinformatics tools and softwares are available for the statistical analysis and visualizing omics data. Specific bioinformatic workflows to cover large eukaryotic genomes get around the resource constraints on genome databases is essential to understand the diversity of rhizosphere microbiome.

Chilli is one of the most significant spice crops cultivated with numerous culinary, medicinal, and industrial applications. Colletotrichum has a wide host range, causing anthracnose disease in various crops, whereas in chilli, anthracnose caused by Colletotrichum capsici is the major constraint in chilli production. Under severe environmental conditions, the symptoms appear all over the plant, including the fruit, which leads to complete crop damage. The particular disease has a huge economic impact on yield reduction and also debars the export criteria due to the lower quality of the chilli crop. Management of the disease is difficult under field conditions, and the majority of the management strategies are highly dependent on the use of chemicals. Solely relying on chemicals is harmful to the environment and human health, so an integrated disease management approach can help in managing the disease at the initial stage. Detection and identification of pathogens play a major role in pathogen management. Early identification and detection of the pathogen based on conventional and molecular methods are very important to reduce yield loss under field conditions. The current review consists of a detailed understanding of the pathogen, its identification, detection and diagnosis, as well as the most recent research updates.

Chilli is one of the most significant spice crops cultivated with numerous culinary, medicinal, and industrial applications. Colletotrichum have a wide host range causing anthracnose disease in various crops whereas in chili anthracnose caused by Colletotrichum capsici is the major constraint in chili production. Under severe environmental conditions, the symptoms appear all over the plant including fruit which lead to complete crop damage. The particular disease has a huge economic impact on yield reduction and also debars the export criteria due to the less quality of chili crop. Management of the disease is difficult under field conditions and majority of the management strategies are highly dependent on the use of chemicals. Solely rely on chemicals is harmful to environmental and human health so integrated disease management approach can help to manage the disease at the initial stage. Detection and identification of pathogen play a major role in pathogen management. Early identification and detection of the pathogen based on conventional and molecular methods are very important to reduce yield loss under field conditions. The current review consists of a detailed understanding of the pathogen, identification, detection and diagnosis, and the most recent research updates.