Secondary metabolites produced by endophytic fungi and bacteria with antimicrobial activity (2010–2020).
Antibiotic-resistant pathogens are a public health threat that has rapidly spread over decades due to continuous and uncontrolled administration of antimicrobial medicines, becoming an ever-increasing worldwide concern. Since the past decade, no significant innovations have been made, so the search for new compounds that face multidrug-resistant pathogens is critically important. Plant-symbiont microorganisms are capable of producing a variety of bioactive natural products, making it possible to treat several infectious diseases. Biotechnological processes using microorganisms have been increasing in recent years since the discovery of Paclitaxel, an important antimitotic produced by the endophyte Taxomyces andreanae. It was isolated for the first time from the native tree of Pacific Taxus brevifolia. Several studies have demonstrated the isolation and characterization of promising and potent substances capable of inhibiting these pathogens. In addition, both rhizospheric and endophytic communities represent an unexplored reserve of unique chemical structures for drug development. This chapter focuses on the potential of plant-derived microorganisms as a source of bioactive substances and the perspectives for further studies and their application.
- antimicrobial resistance
- natural products
- Streptomyces spp.
The discovery of medicines in the treatment of infectious diseases represents one of the most significant accomplishments of humankind. The introduction of antibiotics made it possible to treat previously incurable diseases.
Major classes of antibiotics were discovered between the 1940s and 1960s, where soil-derived actinobacteria produced most of them. However, several decades passed without significant innovations until the discovery and development of oxazolidinones in 2010 (Figure 1). Moreover, the continuous uncontrolled use of these medicines favored the rapid spread of resistant pathogens, where new compounds were discovered, and their introduction into clinical practice was not fast enough [1, 2, 3, 4, 5].
The CDC (Centers for Disease Control and Prevention) has recognized the emerging antibiotic resistance as a significant threat to public health . Superbugs, such as Methicillin-resistant
Therefore, the search for compounds and the exploration of niches that harbor microorganisms that produce bioactive metabolites are critically important [11, 12, 13]. Several studies have shown that plant tissues represent a rich source of natural products for pharmaceutical and biotechnological interest. Most of these compounds are produced by microorganisms that live in intimate interaction with the host plant without causing damage; therefore, they are known as endophytes [11, 14, 15].
In the same context, the rhizosphere’s microbiome can exert profound direct and indirect effects on plant growth, nutrition, and health in natural ecosystems. Its micro-community (bacteria, oomycetes, viruses, archeas, fungi and arbuscular mycorrhizae) is attracted and fed by nutrients, exudates, border cells and mucilage that are released by the root of the plant .
Relevant studies have reported potent antimicrobial compounds, such as teixobactin, isolated from the non-cultivable bacterium
In the study by , endophytic fungi were isolated from the medicinal plant
Herein, we address a review topic concerning the potential of rhizospheric and endophytic microorganisms as producers of antimicrobial compounds.
2. Endophytes: an overview
In 1866, de Bary outlined the first distinction between endophytes and plant pathogens. These microorganisms (typically fungi or bacteria) colonize the plant’s internal tissues and live part of its life or its entire life cycle without causing apparent damage, establishing a mutualistic interaction with the host plant. Moreover, endophytes are capable of producing beneficial substances, such as alkaloids, enzymes, antibiotics and other compounds that protect and help the plant under stress conditions in exchange for nutrients and protection provided by the host plant [14, 15, 20, 21, 22].
In this context, plants have served humanity for centuries and led to the discovery of novel bioactive compounds. However, concerns regarding biodiversity and conservation, as well as large quantities of plant tissue, are required to produce sufficient yields of compounds . According to , paclitaxel isolation requires about 10,000 kg of
Fungi are skilled producers of natural products, including antitumor agents, cholesterol-lowering agents, immunosuppressants and antibiotics [25, 26]. The study by  detected potent antimicrobial properties of the natural product extract (NPE) of endophytic fungi associated with
Therefore, the emerging use of endophytes in the research and development of new drugs represents the most successful example of bioactive natural products in medicine, pharmaceutical and biotechnological applications. Table 1 provides an idea of some secondary metabolites of endophytic fungi and bacteria tested against resistant and multidrug-resistant microorganisms.
|Endophyte||Host plant||Compound||Target strain||Reference|
|4-(2,4,7-trioxa-bicyclo[4.1.0]heptan-3-yl) phenol (1)|||
|(22E,24R)-stigmasta-5,7,22-trien-3-β-ol; Aspernolide F|||
|Diphenyl ethers derivates|||
|Eudesmene-type sesquiterpenes (kandenols)|||
|Polyketides (2-hydroxy-5-((6-hydroxy-4-oxo-4H-pyran-2-yl) methyl) -2- propylchroman-4 one)|||
|S.aureus MRSA (ATCC 33591)|
|1-Monolinolein, bafilomycin D; nonactic acid; daidzein|||
3. Rhizospheric microorganisms: an overview
The term rhizosphere was first used in 1904 by agronomist and plant physiologist Lorenz Hiltner to describe the interface between plant roots and the soil inhabited by a unique microbial community, which is influenced by the chemical release from plant roots . In recent years, based on the relative proximity and influence to the root, the rhizosphere definition has been refined to include three zones: (i) endorhizosphere, which includes portions of the cortex and endoderm, where microorganisms and mineral ions occupy free space between cells (apoplastic space); (ii) rhizoplane, a middle zone adjacent to the root’s epidermal cells and mucilage; and (iii) ectorhizosphere, which extends from the rhizoplane out into the bulk soil and is colonized by the microorganisms that are either free-living or non-symbionts [50, 51].
The rhizosphere is a complex and dynamic region, where bacteria (including Plant Growth-Promoting Rhizobacteria—PGPR), fungi (including Arbuscular Mycorrhizal Fungi – AMF), oomycetes, viruses and archaea are attracted by chemical compounds (sugars, proteins, fatty acids, organics acids, vitamins, and other cellular components) released in the vicinity of the plant roots [16, 52, 53]. These rhizodeposits are used as carbon sources by microorganisms and represent an essential source of carbon allocated to the roots and available to plants through photosynthesis .
The establishment of the symbiotic plant-PGPR interaction in the rhizosphere can favor the plant growth through direct and indirect mechanisms. The first one includes the fixation of atmospheric nitrogen , phosphate solubilization  or any other process capable of supplying the plant with some of its previously unavailable nutrients. Many PGPRs also produce phytohormones, such as auxins (Indole-3-acetic acid) and cytokinin, which exert strong effects on root and shoot growth, respectively [59, 60, 61]. The indirect mechanisms of plant growth prevent the deleterious effects of pathogens and include competition for nutrients and niches, induction of systemic resistance (Jasmonic acid (JA), and ethylene), and lytic enzymes (chitinase, pectinase, cellulase, glucanase, protease, xylanase), siderophore, bacteriocins and antibiotics production  (Figure 2).
The phyla of PGPR commonly found in the rhizosphere are Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes; among the main genera,
Due to its fundamental function in suppressing pathogens, as well as endophytes, rhizospheric fungi and bacteria, these microorganisms have attracted the attention of researchers as a new source of valuable bioactive metabolites with antimicrobial activity [71, 72, 73]. Since antibiotic resistance is a serious global health concern , exploring the potential of these microorganisms to discover novel medicine is also of great urgency. In this way, in recent years, secondary metabolites partially or totally identified from microorganisms that inhabit the rhizosphere have been shown to possess antimicrobial activities against important pathogen agents. Table 2 provides an overview of selected studies that represent significant advances in the search for secondary metabolites produced from rhizospheric fungi and bacteria tested against resistant and multidrug-resistant microorganisms.
|Rhizospheric microorganism||Compound/extracts||Target strains||Reference|
|Ethanol and ethyl acetate extracts|||
|Bacteriocin-like inhibitory substance (BLIS)|||
|Ethyl acetate extract|||
|3,6,18-trione, 9,10-dihydro-12 -hydroxyl-2methyl-5-(phenyl methyl)(5-alpha, 10- alpha)-dihydroergotamine (C3) and dipropyl—S-propyl ester (C4)|||
|Ethyl acetate fraction|
|- Ethyl acetate extract; − FT-IR included aldehydes, alkynes, 2 aromatic rings, alkanes and alkynes|||
|1-Octadecane and 1-nonadecanol|||
|Ethyl acetate extract|||
|(1,1-Dichloropentane (DCP) (76%) - major compound in partial purification)|
Therefore, these and other studies emphasize the vital importance of continuing scientific research to find new antimicrobials and other compounds produced from rhizosphere microorganisms for other biotechnological purposes.
4. Actinobacteria and natural antimicrobial products
Actinobacteria phyla have a high G + C DNA content and share both the characteristics of bacteria and fungi. These Gram-positive filamentous bacteria belong to one of the largest taxonomic groups recognized in the Bacteria domain, widely distributed across ecosystems [86, 87, 88].
In terms of metabolite production, the
The development of biofilm inhibitors has become a priority in recent years. Bacterial biofilms can tolerate antibiotics and host defense systems, leading to the emergence of drug-resistant and totally drug-resistant infections. As previously mentioned,
Other studies report different strategies to successfully induce secondary metabolism and, subsequently, produce compounds that are not produced under usual growing conditions. Cryptic genes consist of silent sequences of DNA that are not expressed during the life cycle of a microorganism and can occur through mutations and recombination processes in a few members of a population [98, 99, 100]. In this context, cultured actinobacteria combined with mycolic acid-containing bacteria (
Caraballo-Rodríguez  tested the endophytic actinobacteria
As already mentioned, the process of antibiotic resistance is spreading rapidly in relation to the discovery of new compounds and their introduction into clinical practice. The CDC classifies pathogens such as
5. Natural products and endophytic fungi
The scientific interest in fungal natural products gained notoriety after the paclitaxel discovery . Endophytic fungi exhibit the ability to synthesize plant-derived compounds by mimicking the metabolic pathways of the host plant, which confers multifaceted applications in the fields of agriculture, medicine, and pharmaceuticals .
The medicinal plant barbatimão (
Although toxic to humans and animals, mycotoxins are secondary metabolites known for their cytotoxic effect against malignant cells . Several species of
The superbug methicillin-resistant
Saponins exhibit a wide range of biological activities, such as antifungal, hemolytic, antiviral, and immunomodulatory. These compounds represent an alternative to overcome multidrug-resistant microorganisms since they can act synergistically with antibiotics. Moreover, medicines that were once considered ineffective due to resistance problems might be effective for resistant microbes [122, 123]. Nevertheless, as reported by , saponin from
6. Concluding remarks
Antibiotic-resistant microbes represent a severe threat to the public health system worldwide. Furthermore, multidrug-resistant ‘ESKAPE’ organisms (
In this chapter, we highlighted the strategies of antimicrobial drug discovery produced by endophytes and rhizospheric microorganisms, since enormous untapped resources remain. The use of such microbes in biotechnological processes has increased in recent years, as they are skilled producers of natural bioactive products that can be used as pharmaceuticals to face this ever-increasing threat.
Conflict of interest
The authors declare no conflict of interest.
This manuscript was financially supported by Sao Paulo State Research Support Foundation (FAPESP) through project number 2016/13423-5.