Role Of Secondary Metabolites Research Articles

Introducing Saffron and a few medicinal and high value plants for small farms and water deficit conditions of northern New Mexico

This document reviews the potential of cultivating saffron and other high-value medicinal and aromatic plants such as lavender, rosemary, thyme, chamomile, and Damask rose on small farms in northern New Mexico, particularly under water deficit conditions. Medicinal and aromatic plants, rich in secondary metabolites, are crucial to various industries including pharmaceuticals, cosmetics, and food. With an increasing global market for herbal products and a rising interest in traditional medicine, these plants offer economic benefits and sustainability for small-scale farmers. Northern New Mexico's diverse climate and soil conditions are suitable for growing a wide range of these plants, which are more lucrative and adaptable to dryland farming compared to traditional crops. Saffron (Crocus sativus), the most expensive herb globally, thrives in arid and semi-arid conditions and requires minimal resources. Its cultivation can enhance farm profitability through the integration of summer vegetable production. Lavender (Lavandula spp.), another high-value crop, is well-suited for the region and offers multiple uses in essential oils and personal care products. Rosemary (Rosmarinus officinalis) and thyme (Thymus vulgaris) are also highlighted for their drought tolerance and medicinal properties. Chamomile (Matricaria chamomilla) and Damask rose (Rosa damascena) are noted for their medicinal uses and potential in commercial production. The document underscores the importance of proper soil and water management, organic farming practices, and the role of secondary metabolites in enhancing crop quality under stressful conditions. Intercropping and the use of farm residues for soil conservation are also discussed. The review concludes that these high-value crops can diversify farm income, improve land use efficiency, and offer sustainable agricultural solutions for water-scarce regions in northern New Mexico.

Role of secondary metabolites in plant defense mechanisms: a molecular and biotechnological insights

Role of secondary metabolites in plant defense mechanisms: a molecular and biotechnological insights

Network pharmacology-based approach to elucidate the pharmacologic mechanisms of natural compounds from Dictyostelium discoideum for Alzheimer's disease treatment

Alzheimer's disease (AD) is increasingly becoming a major public health concern in our society. While many studies have explored the use of natural polyketides, alkaloids, and other chemical components in AD treatment, there is an urgent need to clarify the concept of multi-target treatment for AD. This study focuses on using network pharmacology approach to elucidate how secondary metabolites from Dictyostelium discoideum affect AD through multi-target or indirect mechanisms. The secondary metabolites produced by D. discoideum during their development were obtained from literature sources and PubChem. Disease targets were selected using GeneCards, DisGeNET, and CTD databases, while compound-based targets were identified through Swiss target prediction and Venn diagrams were used to find intersections between these targets. A network depicting the interplay among disease, drugs, active ingredients, and key target proteins (PPI network) was formed utilizing the STRING (Protein-Protein Interaction Networks Functional Enrichment Analysis) database. To anticipate the function and mechanism of the screened compounds, GO and KEGG enrichment analyses were conducted and visually presented using graphs and bubble charts. After the screening phase, the top interacting targets in the PPI network and the compound with the most active target were chosen for subsequent molecular docking and molecular dynamic simulation studies. This study identified nearly 50 potential targeting genes for each of the screened compounds and revealed multiple signaling pathways. Among these pathways, the inflammatory pathway stood out. COX-2, a receptor associated with neuroinflammation, showed differential expression in various stages of AD, particularly in pyramidal neurons during the early stages of the disease. This increase in COX-2 expression is likely induce by higher levels of IL-1, which is associated with neuritic plaques and microglial cells in AD. Molecular docking investigations demonstrated a strong binding interaction between the terpene compound PQA-11 and the neuroinflammatory receptor COX2, with a substantial binding affinity of −8.4 kcal/mol. Subsequently, a thorough analysis of the docked complex (COX2-PQA11) through Molecular Dynamics Simulation showed lower RMSD, minimal RMSF fluctuations, and a reduced total energy of −291.35 kJ/mol compared to the standard drug. These findings suggest that the therapeutic effect of PQA-11 operates through the inflammatory pathway, laying the groundwork for further in-depth research into the role of secondary metabolites in AD treatment.

A Role for Secondary Metabolites in Desiccation Tolerance in Lichens

In lichens, secondary metabolites have been shown to protect against biotic stresses such as pathogen attacks and grazing, and abiotic stresses such as ultraviolet (UV) and high photosynthetically active radiation (PAR). Lichen secondary metabolites are known to have strong antioxidant activity, and while theoretically they may have roles in tolerance to other abiotic stresses, these roles remain largely unclear. Here, we used the acetone rinsing method to harmlessly remove most of the secondary metabolites from the thalli of six lichen species. This enabled us to compare the effects of desiccation on thalli with and without the presence of secondary metabolites. Results showed that in general, the presence of lichen substances reduces the effects of desiccation stress. For all species, substances significantly improved the photosystem two (PSII) activity of the photobiont during either desiccation or rehydration. In the mycobiont, in four of the six species, the presence of substances reduced membrane damage, which was assessed by measuring ion leakage during rehydration following desiccation. However, in one species, secondary metabolites had no effect, while in another the presence of substances increased membrane damage. Nevertheless, it seems clear that in addition to their more established roles in protecting lichens against pathogen attacks and grazing, lichen substances can also play a role in aiding desiccation tolerance.

The role of secondary metabolites in the production of CuO nanoparticles by fungi: A physiological and metabolic approach

The role of secondary metabolites in the production of CuO nanoparticles by fungi: A physiological and metabolic approach

Current insights on rice (Oryza sativa L.) bakanae disease and exploration of its management strategies.

Bakanae is an emerging rice disease caused by the seed- and soil-borne pathogen Fusariumfujikuroi. It is becoming a more serious threat to sustainable rice production throughout rice-growing regions. Bakanae disease infection is responsible for high yield losses ranging from 3% to 95%, and disease incidence varies based on the region and cultivars. Hence, understanding the nature of the pathogen, its pathogenicity, disease epidemiology, symptoms, host‍-‍pathogen interaction, and the role of secondary metabolites in the disease cycle will be helpful in the development of effective and sustainable management strategies. However, very few comprehensive studies have described the details of rice bakanae disease. Thus, in this review we summarize and discuss in detail the information available from 1898 to 2023 on various critical facets of bakanae disease, and provide perspectives on future research.

Bioactive metabolites of plants and microbes and their role in agricultural sustainability and mitigation of plant stress

Primary metabolites are ubiquitous in nature and actively involved in growth while secondary metabolites (SMs) are involved in interaction with the environment. In plants terpenes are the largest group of secondary metabolites that play an important role in defense mechanisms against the herbivores and pathogens. Plant secondary metabolites such as alkaloids, phenolics and diterpenes have a great potential against many carcinogens. Carotenoids provide photoprotection and act as a pigment to absorb light during photosynthesis. Carotenoids are also efficient in the interaction with other organisms as they are phagostimulant and allelopathic agent. Flavonoids from the higher plants play a significant role in ultra-violet (UV) filtration, nitrogen fixation, floral pigmentation, and defense mechanisms against many diseases. These secondary metabolites provide protection to plants in a different type of biotic and abiotic stresses. Microorganisms also contain a high number of bioactive metabolites but not all of them. Marine microorganisms are a rich source of secondary metabolites such as alkaloids, terpenoids, polyketides, isoprenoids and non-isoprenoid and quinones amongst others. These metabolites are anti-inflammatory, anti-bacterial and anti-tumor in action. Secondary metabolites from fungi have a great therapeutic value as they have antifungal and antibacterial activity against many pathogens. Plant growth promoting rhizobacteria (PGPR) and Plant growth regulators (PGR) are the key biological entities to enhance the production of bioactive secondary metabolites in plants and can change the plant metabolome in response to various environmental stresses. This review paper will provide a new insight about the role of secondary metabolites in plant defense and the role of microorganisms in modulating the plant metabolome under various environmental stresses and their interactions with other microorganisms and plant growth regulators.

From Nature to Lab: A Review of Secondary Metabolite Biosynthetic Pathways, Environmental Influences, and In Vitro Approaches.

Secondary metabolites are gaining an increasing importance in various industries, such as pharmaceuticals, dyes, and food, as is the need for reliable and efficient methods of procuring these compounds. To develop sustainable and cost-effective approaches, a comprehensive understanding of the biosynthetic pathways and the factors influencing secondary metabolite production is essential. These compounds are a unique type of natural product which recognizes the oxidative damage caused by stresses, thereby activating the defence mechanism in plants. Various methods have been developed to enhance the production of secondary metabolites in plants. The elicitor-induced in vitro culture technique is considered an efficient tool for studying and improving the production of secondary metabolites in plants. In the present review, we have documented various biosynthetic pathways and the role of secondary metabolites under diverse environmental stresses. Furthermore, a practical strategy for obtaining consistent and abundant secondary metabolite production via various elicitation agents used in culturing techniques is also mentioned. By elucidating the intricate interplay of regulatory factors, this review paves the way for future advancements in sustainable and efficient production methods for high-value secondary metabolites.

Chemical composition and biological activity of metabolites of Rubus chamaemorus L.

The article describes the climatic conditions and the geographical zones of cloudberry (Rubus chamaemorus L.) growth. A trend towards cultural and semi-cultural cultivation of this species was noted. The current state of research on the chemical composition of various parts of cloudberry squat, growing in various environmental conditions, is highlighted. A systematic assessment of accumulation of biologically active substances (vitamins, fatty acids, flavonoids, anthocyanins, proanthocyanidins, phenolic acids) of this plant of northern and southern populations was carried out. The role of secondary metabolites in the formation of the biological potential of R. chamaemorus L. fruits and leaves is described. High antioxidant and antiradical activities of cloudberry fruit extracts in in vitro and in vivo model systems are also noted. The review presents the results of scientific works devoted to the study of the antimicrobial activity of fruits against Helicobacter pillory, Staphylococcus aureus, Staphylococcus epidermis, Bacillus subtilis, Campylobacter jejuni, Micrococcus luteus, Escherichia coli, Candida albicans. There is a lack of research of secondary metabolites of the plant on the southern border of the range. The biological significance of fruits and ground leaf mass, as well as the prospects for cultivation on the southern border of the range and their practical use in the pharmaceutical and food industries are highlighted.

The Role of Secondary Metabolites and Bark Chemistry in Shaping Diversity and Abundance of Epiphytic Lichens

Diversity of secondary lichen metabolites was studied in epiphytic lichens on six phorophytes—spruce, pine, birch, alder, aspen and poplar in the Middle Urals of Russia. Atranorin, usnic, fumarprotocetraric acid, zeorin, and gyrophoric acid were found in 31, 24, 23, 18, and 14 species, respectively, of 237 taxa collected. Seventy-seven species (i.e., 32% of total species documented) contained no secondary metabolites. Spectra of secondary metabolites of fruticose and foliose lichens varied on different phorophytes, while in crustose species the strong dependence on the tree species was not detected. This is different to the pH dependence of saxicolous lichens where crustose lichens were more susceptible to the rock chemistry. The results of Canonical Correspondence Analysis reveal the affinity of species containing depsides, depsidones or usnic acid to acidic substrata and those lacking secondary metabolites or containing terpenes and antraquinones to the pH-neutral bark. We suppose that phenolic compounds and flavonoids, as chemical constituents of bark, may interact with lichen symbioses and elements in phellem, and similarly to the lichen acids shape the affinity of species to the substrata.

The analysis of the biochemical diversity of the English oak vegetative sphere in the forest-steppe zone

The paper studies the biochemical diversity of the English oak trees growing in the protective forest strips of the forest-steppe zone in the Central Chernozem region. The features of accumulation of various groups of substances of secondary metabolism of phenolic nature in the leaves of model oak trees in seasonal dynamics are described. The role of secondary metabolites in the formation of adaptive mechanisms of resistance of individuals to adverse environmental factors is considered. It is proved that the content of substances of secondary metabolism of phenolic nature and their combination can serve as a criterion for the potential biochemical stability of trees when growing in unfavorable environmental conditions. The content of secondary metabolism substances was determined on oak leaf samples in early June and August. It was revealed that the quantitatively leading group of substances of secondary metabolism are flavonols. It was found that at the beginning of the growing season, the most significant fluctuations in the levels of accumulation of secondary metabolism substances occur in young oak leaf blades, and by the end of the growing season their content stabilizes. High rates of variation coefficients have been identified, which make it possible to ensure biochemical diversity in the population and a sufficient range of adaptability of traits. It is shown that the samples of control and experimental trees for flavonols are the most homogeneous.

Plant Secondary Metabolites as Defense Tools against Herbivores for Sustainable Crop Protection.

Plants have evolved several adaptive strategies through physiological changes in response to herbivore attacks. Plant secondary metabolites (PSMs) are synthesized to provide defensive functions and regulate defense signaling pathways to safeguard plants against herbivores. Herbivore injury initiates complex reactions which ultimately lead to synthesis and accumulation of PSMs. The biosynthesis of these metabolites is regulated by the interplay of signaling molecules comprising phytohormones. Plant volatile metabolites are released upon herbivore attack and are capable of directly inducing or priming hormonal defense signaling pathways. Secondary metabolites enable plants to quickly detect herbivore attacks and respond in a timely way in a rapidly changing scenario of pest and environment. Several studies have suggested that the potential for adaptation and/or resistance by insect herbivores to secondary metabolites is limited. These metabolites cause direct toxicity to insect pests, stimulate antixenosis mechanisms in plants to insect herbivores, and, by recruiting herbivore natural enemies, indirectly protect the plants. Herbivores adapt to secondary metabolites by the up/down regulation of sensory genes, and sequestration or detoxification of toxic metabolites. PSMs modulate multi-trophic interactions involving host plants, herbivores, natural enemies and pollinators. Although the role of secondary metabolites in plant-pollinator interplay has been little explored, several reports suggest that both plants and pollinators are mutually benefited. Molecular insights into the regulatory proteins and genes involved in the biosynthesis of secondary metabolites will pave the way for the metabolic engineering of biosynthetic pathway intermediates for improving plant tolerance to herbivores. This review throws light on the role of PSMs in modulating multi-trophic interactions, contributing to the knowledge of plant-herbivore interactions to enable their management in an eco-friendly and sustainable manner.

Secondary metabolites of six Siberian and Crimean Armillaria species and their in vitro phytotoxicity to pine, larch and poplar

Basidiomycetes Armillaria infect deciduous, coniferous and fruit trees, causing enormous economic damage. The role of secondary metabolites (tricyclic sesquiterpene aryl esters - melleolides) in the life cycle and pathogenesis of Armillaria is under active investigation. To date, not all species of Armillaria have been tested for the biosynthesis of melleolides. We investigated the secondary metabolite profiles of six root-pathogenic species of the genus Armillaria (A. borealis Marxmüller & Korhonen, A. cepistipes Velenovský, A. gallica Marxm, A. mellea (Vahl) P. Kummer, A. sinapina Bérubé & Dessur, A. ostoyae (Romagn.) Herink) distributed in Siberia (South Krasnoyarsk Krai, Republic of Tyva, Republic of Khakassia, Taimyr Peninsula), Russian Far East (Sikhote-Alin) and Crimea (Krymsky National Park, Chatyr-Dag Mountain Lower Plateau). A total of 15 compounds were identified in the metabolome profile. Two compounds (melleolide D and melledonal C) are synthesized by all investigated strains irrespective of their geographic location and host plant. The maximum spectrum of melleolides (7-8 compounds) was found in isolates of A. borealis, A. gallica, A. sinapina, A. ostoyae. In submerged culture, the maximum accumulation of melleolides varied from 2 up to 239 mg l-1. A mixture of melleolide D and melledonal C (1:1) synthesized by the most productive strain A. mellea Cr2-17 was first found to have a phytotoxic action on the growth parameters of the callus culture Populus balsamifera and 10-day-old conifer seedlings. A 0.5% concentration of melleolides caused a credible decrease of P. balsamifera callus raw biomass; a decrease of the viability of Larix sibirica and, which is especially significant, Pinus sylvestris seedlings; inhibition of stem and root growth processes; dechromation of foliage; loss of turgor. The occurrence of a broad range of melleolides in the metabolome profile and two common compounds in all investigated strains, with a phytotoxic action at their sufficiently high concentration, enables considering the synthesis of melleolides by Armillaria fungi as one of the possible mechanisms of their pathogenicity efficiently realized in strains characterized by overproduction of melleolides under natural conditions.

Fertilization Following Pollination Predominantly Decreases Phytocannabinoids Accumulation and Alters the Accumulation of Terpenoids in Cannabis Inflorescences.

In the last decades, growing evidence showed the therapeutic capabilities of Cannabis plants. These capabilities were attributed to the specialized secondary metabolites stored in the glandular trichomes of female inflorescences, mainly phytocannabinoids and terpenoids. The accumulation of the metabolites in the flower is versatile and influenced by a largely unknown regulation system, attributed to genetic, developmental and environmental factors. As Cannabis is a dioecious plant, one main factor is fertilization after successful pollination. Fertilized flowers are considerably less potent, likely due to changes in the contents of phytocannabinoids and terpenoids; therefore, this study examined the effect of fertilization on metabolite composition by crossbreeding (-)-Δ9-trans-tetrahydrocannabinol (THC)- or cannabidiol (CBD)-rich female plants with different male plants: THC-rich, CBD-rich, or the original female plant induced to develop male pollen sacs. We used advanced analytical methods to assess the phytocannabinoids and terpenoids content, including a newly developed semi-quantitative analysis for terpenoids without analytical standards. We found that fertilization significantly decreased phytocannabinoids content. For terpenoids, the subgroup of monoterpenoids had similar trends to the phytocannabinoids, proposing both are commonly regulated in the plant. The sesquiterpenoids remained unchanged in the THC-rich female and had a trend of decrease in the CBD-rich female. Additionally, specific phytocannabinoids and terpenoids showed an uncommon increase in concentration followed by fertilization with particular male plants. Our results demonstrate that although the profile of phytocannabinoids and their relative ratios were kept, fertilization substantially decreased the concentration of nearly all phytocannabinoids in the plant regardless of the type of fertilizing male. Our findings may point to the functional roles of secondary metabolites in Cannabis.

Potential Role and Involvement of Antioxidants and Other Secondary Metabolites of Wheat in the Infection Process and Resistance to Fusarium spp.

This article provides a summary of current knowledge about wheat metabolites that may affect resistance against Fusarium head blight (FHB). The mechanisms of resistance, the roles of secondary metabolites in wheat defense, and future directions for breeding are assessed. The soluble phenols play an important role in redox regulation in plant tissues and can act as antimicrobial compounds. The color of cereal hulls and grains is caused by such natural pigments as anthocyanins in the aleurone, endosperm, and pericarp layers of the grain. Phenolic acids, alkylresorcinols, and phytohormones actively participate in the defense system, whereas carotenoids show various effects against Fusarium species that are positively correlated with the levels of their mycotoxins. Pathogen infestation of vegetative tissues induces volatile organic compounds production, which can provide defensive functions to infested wheat. The efficient use of native resistance in the wheat gene pool, introgression of resistant alleles, and implementation of modern genotypic strategies to increase levels of native secondary metabolites with antifungal properties can enhance the FHB resistance of new varieties. Expanding the breeding interest in the use of forms with different grain color and plant organs can be a potential benefit for the creation of lines with increased resistance to various stresses.

The Intertwined Roles of Specialized Metabolites within the Bacillus subtilis Biofilm.

Bacteria produce specialized metabolites with a range of functions. In this issue of the Journal of Bacteriology, Schoenborn et al. study the production and role of secondary metabolites during biofilm development and sporulation in Bacillus subtilis (A. A. Schoenborn, S. M. Yannarell, E. D. Wallace, H. Clapper, et al., J Bacteriol 203:e00337-21, 2021, https://doi.org/https://doi.org/10.1128/JB.00337-21). Most metabolites studied are produced during differentiation, and six are required for the development of biofilms and/or spores. The authors propose a model for the timing of production and role in differentiation exerted by each secondary metabolite.

Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons

BackgroundEfficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions.ResultsIn this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101).ConclusionWith MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.

Biomedical Potential of Plant-Based Selenium Nanoparticles: A Comprehensive Review on Therapeutic and Mechanistic Aspects.

Selenium nanoparticles (SeNPs) have advantages over other nanomaterials because of the promising role of selenium in the stabilization of the immune system and activation of the defense response. The use of SeNPs and their supplements not only have pharmacological significance but also boost and prepare the body’s immune system to fight the pathogens. This review summarizes the recent progress in the biogenesis of plant-based SeNPs by using various plant species and the role of secondary metabolites on their biocompatible functioning. Phyto-synthesis of SeNPs results in the synthesis of nanomaterials of various, size, shape and biochemical nature and has advantages over other routine physical and chemical methods because of their biocompatibility, eco-friendly nature and in vivo actions. Unfortunately, the plant-based SeNPs failed to attain considerable attention in the pharmaceutical industry. However, a few studies were performed to explore the therapeutic potential of the SeNPs against various cancer cells, microbial pathogens, viral infections, hepatoprotective actions, diabetic management, and antioxidant approaches. Further, some of the selenium-based drug delivery systems are developed by engineering the SeNPs with the functional ligands to deliver drugs to the targeted sites. This review also provides up-to-date information on the mechanistic actions that the SeNPs adopt to achieve their designated tasks as it may help to develop precision medicine with customized treatment and healthcare for the ailing population.

Enantioselective effects of imazethapyr on the secondary metabolites and nutritional value of wheat seedlings

The secondary metabolism of plants is key for mediating responses to environmental stress, but few studies have examined how the relationship between secondary metabolism and the stress response of plants is affected by exposure to chiral herbicides. Here, we studied the enantioselective disturbance of the chiral herbicide imazethapyr (IM) on the secondary metabolism and nutrient levels of wheat seedlings. The bioactive enantiomer R-IM significantly increased the contents of major secondary metabolites, including phenolic acids, flavonoids, and carotenoids but greatly inhibited the production of benzoxazine. The antioxidant system also responded strongly to R-IM; specifically, the activities of SOD, CAT, and GPX enzymes were all significantly induced, and the GSH content initially increased but then decreased. Furthermore, the nutrient levels of wheat seedlings were also affected; dietary fiber content decreased, while the contents of the microelements Fe, Mn, and Zn increased. In sum, this study provides new insight into the phytotoxic effects of IM and raises new questions on the role of secondary metabolites and nutrients in mediating enantioselective effects.

Plant-associated Fungi: Methods for Taxonomy, Diversity, and Bioactive Secondary Metabolite Bioprospecting.

Plants harbor a large reservoir of fungal diversity, encompassing endophytic, epiphytic, phytopathogenic, and rhizosphere-associated fungi. Despite this diversity, relatively few fungal species have been characterized as sources of bioactive secondary metabolites. The role of secondary metabolites is still not fully understood; however, it is suggested that these metabolites play important roles in defense mechanisms and fungal interactions with other organisms. Hence, fungal secondary metabolites have potential biotechnological applications as prototype molecules for the development of therapeutic drugs. In this chapter, we describe the main methods used for routine fungi isolation, production of crude fungal extracts, and chemical characterization of bioactive compounds. In addition, explicative notes about the steps described are provided to explore the diversity of the endophytic, phytopathogenic, epiphytic, and rhizosphere fungi and to evaluate the biotechnological potential of each group.