Antimicrobials from endophytes as novel therapeutics to counter drug-resistant pathogens

The rapid increase in antimicrobial resistance (AMR) projects a "global emergency" and necessitates a need to discover alternative resources for combating drug-resistant pathogens or "superbugs." One of the key themes in "One Health Concept" is based on the fact that the interconnected network of humans, the environment, and animal habitats majorly contribute to the rapid selection and spread of AMR. Moreover, the injudicious and overuse of antibiotics in healthcare, the environment, and associated disciplines, further aggravates the concern. The prevalence and persistence of AMR contribute to the global economic burden and are constantly witnessing an upsurge due to fewer therapeutic options, rising mortality statistics, and expensive healthcare. The present decade has witnessed the extensive exploration and utilization of bio-based resources in harnessing antibiotics of potential efficacies. The discovery and characterization of diverse chemical entities from endophytes as potent antimicrobials define an important yet less-explored area in natural product-mediated drug discovery. Endophytes-produced antimicrobials show potent efficacies in targeting microbial pathogens and synthetic biology (SB) mediated engineering of endophytes for yield enhancement, forms a prospective area of research. In keeping with the urgent requirements for new/novel antibiotics and growing concerns about pathogenic microbes and AMR, this paper comprehensively reviews emerging trends, prospects, and challenges of antimicrobials from endophytes and their effective production via SB. This literature review would serve as the platform for further exploration of novel bioactive entities from biological organisms as "novel therapeutics" to address AMR.

Weapons against Themselves: Identification and Use of Quorum Sensing Volatile Molecules to Control Plant Pathogenic Fungi Growth

Quorum sensing (QS) is often defined as a mechanism of microbial communication that can regulate microbial behaviors in accordance with population density. Much is known about QS mechanisms in bacteria, but fungal QS research is still in its infancy. In this study, the molecules constituting the volatolomes of the plant pathogenic fungi Fusarium culmorum and Cochliobolus sativus have been identified during culture conditions involving low and high spore concentrations, with the high concentration imitating overpopulation conditions (for QS stimulation). We determined that volatolomes emitted by these species in conditions of overpopulation have a negative impact on their mycelial growth, with some of the emitted molecules possibly acting as QSM. Candidate VOCs related to QS have then been identified by testing the effect of individual volatile organic compounds (VOCs) on mycelial growth of their emitting species. The antifungal effect observed for the volatolome of F. culmorum in the overpopulation condition could be attributed to ethyl acetate, 2-methylpropan-1-ol, 3-methylbutyl ethanoate, 3-methylbutan-1-ol, and pentan-1-ol, while it could be attributed to longifolene, 3-methylbutan-1-ol, 2-methylpropan-1-ol, and ethyl acetate for C. sativus in the overpopulation condition. This work could pave the way to a sustainable alternative to chemical fungicides.

HPLC-PDA-ESI-MS/MS Profiling and Anti-Biofilm Potential of Eucalyptussideroxylon Flowers

The development of multidrug-resistant bacterial strains is a worldwide emerging problem that needs a global solution. Exploring new natural antibiofilm agents is one of the most important alternative therapies in combating bacterial infections. This study aimed at testing the antimicrobial potential of Eucalyptus sideroxylon flowers extract (ESFE) against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Candida albicans prior to testing the antibiofilm activity against S. aureus, P. aeruginosa and C. albicans. ESFE demonstrated antimicrobial activity and promising inhibition activity against methicillin-resistant S. aureus (MRSA) biofilm formation up to 95.9% (p < 0.05) at a concentration of 0.05 mg/mL and eradicated C. albicans biofilm formation up to 71.2% (p < 0.05) at a concentration of 0.7 mg/mL. LC-MS analysis allowed the tentative identification of eighty-three secondary metabolites: 21 phloroglucinol, 18 terpenes, 16 flavonoids, 7 oleuropeic acid derivatives, 7 ellagic acid derivatives, 6 gallic acid derivatives, 3 phenolic acids, 3 fatty acids and 2 miscellaneous. In conclusion, E. sideroxylon is a rich source of effective constituents that promote its valorization as a promising candidate in the management of multidrug-resistant bacterial infections.

The architecture of a mixed fungal-bacterial biofilm is modulated by quorum-sensing signals

Interkingdom communication is of particular relevance in polymicrobial biofilms. In this work, the ability of the fungus Ophiostoma piceae to form biofilms individually and in consortium with the bacterium Pseudomonas putida, as well as the effect of fungal and bacterial signal molecules on the architecture of the biofilms was evaluated. Pseudomonas putida KT2440 is able to form biofilms through the secretion of exopolysaccharides and two large extracellular adhesion proteins, LapA and LapF. It has two intercellular signalling systems, one mediated by dodecanoic acid and an orphan LuxR receptor that could participate in the response to AHL-type quorum sensing molecules (QSMs). Furthermore, the dimorphic fungus O. piceae uses farnesol as QSM to control its yeast to hyphae morphological transition. Results show for the first time the ability of this fungus to form biofilms alone and in mixed cultures with the bacterium. Biofilms were induced by bacterial and fungal QSMs. The essential role of LapA-LapF proteins in the architecture of biofilms was corroborated, LapA was induced by farnesol and dodecanol, while LapF by 3-oxo-C6-HSL and 3-oxo-C12-HSL. Our results indicate that fungal signals can induce a transient rise in the levels of the secondary messenger c-di-GMP, which control biofilm formation and architecture.

Enhancement of exopolysaccharide production from Ganoderma lucidum using a novel submerged volatile co-culture system

Based on the impact of volatile organic compounds (VOCs) on secondary metabolite pathways, a novel submerged volatile co-culture system was constructed, and the effects of thirteen fungal and bacterial VOCs were investigated on Ganoderma lucidum exopolysaccharides production. The results demonstrated at least a 2.2-fold increase in exopolysaccharide (EPS) specific production yield in 6 days submerged volatile co-culture of G. lucidum with Pleurotus ostreatus. Therefore, P. ostreatus was selected as a variable culture, and the effects of agitation speed, inoculum size, initial pH, and co-culture volume on EPSs production were investigated using a Taguchi L₉ orthogonal array. Finally, the highest concentration of EPSs (3.35 ± 0.22 g L^-1) was obtained under optimized conditions; initial pH 5.0, inoculum size 10%, 150 rpm, and 3:1 volume ratio of variable culture to main culture.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

Farnesol altered morphogenesis and induced oxidative burst-related responses in Rhizoctonia solani AG1-IA

Farnesol induces morphological changes characteristic of apoptosis in filamentous fungi. Growth-inhibitory effect and induced features of apoptosis on Rhizoctonia solani AG1-IA were observed in our study by addition of exogenous farnesol to the culture. The obtained results implied that farnesol triggered apoptosis-like features, such as production of reactive oxygen species (ROS), in R. solani AG1-IA and that there was increased superoxide dismutase (SOD) activity in the presence of farnesol, as well as decreased fungal biomass. Light microscopic analysis showed that farnesol disrupted the cytoplasm and deformed the hyphae of R. solani AG1-IA. The diameter of the hyphal cross-section in the fungus treated with farnesol decreased compared with control. Transmission electron microscopy (TEM) showed marked alternations in the cell wall, cell membrane, parenthesome, septum, and septal pore of the fungal cells. The findings of this work suggest that farnesol is deleterious to R. solani and has potential for use as an antifungal compound against this destructive phytopathogenic fungus.

In Silico Analysis of the Quorum Sensing Metagenome in Environmental Biofilm Samples

Quorum sensing (QS) is a sophisticated cell to cell signaling mechanism mediated by small diffusible molecules called “autoinducers.” This phenomenon is well studied in bacteria, where different QS systems are described that differ between Gram-negative and Gram-positive bacteria. However, a common system to these groups was discovered, the autoinducer 2. QS has implications in biofilm formation, where the application of metagenomic techniques to study these phenomena may be useful to understand the communication networks established by the different components of the community, and to discover new targets for microbial control. Here we present an in silico screening of QS proteins in all publicly available biofilm metagenomes from the JGI database. We performed sequence, conserved motifs, phylogenetic, and three-dimensional structure analyses of the candidates, resulting in an effective strategy to search QS proteins in metagenomes sequences. The number of QS proteins present in each sample, and its phylogenetic affiliation, was clearly related to the bacterial diversity and the origin of the biofilm. The samples isolated from natural habitats presented clear differences with those from artificial habitats. Interesting findings have been made in the abundance of LuxR-like proteins finding an unbalanced ratio between the synthases and the receptor proteins in Bacteroidetes bacteria, pointing out the existence of “cheaters” in this group. Moreover, we have shown the presence of the LuxI/R QS system in bacteria from the Nitrospira taxonomic group. Finally, some undescribed proteins from the HdtS family have been found in Gamma-proteobacteria.

Fungal Biofilms: Targets for the Development of Novel Strategies in Plant Disease Management

The global food supply has been facing increasing challenges during the first decades of the 21st century. Disease in plants is an important constraint to worldwide crop production, accounting for 20-40% of its annual harvest loss. Although the use of resistant varieties, good water management and agronomic practices are valid management tools in counteracting plant diseases, there are still many pathosystems where fungicides are widely used for disease management. However, restrictive regulations and increasing concern regarding the risk to human health and the environment, along with the incidence of fungicide resistance, have discouraged their use and have prompted for a search for new efficient, ecologically friendly and sustainable disease management strategies. The recent evidence of biofilm formation by fungal phytopathogens provides the scientific framework for designing and adapting methods and concepts developed by biofilm research that could be integrated in IPM practices. In this perspective paper, we provide evidence to support the view that the biofilm lifestyle plays a critical role in the pathogenesis of plant diseases. We describe the main factors limiting the durability of single-site fungicides, and we assemble the current knowledge on pesticide resistance in the specific context of the biofilm lifestyle. Finally, we illustrate the potential of antibiofilm compounds at sub-lethal concentrations for the development of an innovative, eco-sustainable strategy to counteract phytopathogenic fungi. Such fungicide-free solutions will be instrumental in reducing disease severity, and will permit more prudent use of fungicides decreasing thus the selection of resistant forms and safeguarding the environment.

Fungal Volatiles Can Act as Carbon Sources and Semiochemicals to Mediate Interspecific Interactions Among Bark Beetle-Associated Fungal Symbionts

Mountain pine beetle (Dendroctonus ponderosae) has killed millions of hectares of pine forests in western North America. Beetle success is dependent upon a community of symbiotic fungi comprised of Grosmannia clavigera, Ophiostoma montium, and Leptographium longiclavatum. Factors regulating the dynamics of this community during pine infection are largely unknown. However, fungal volatile organic compounds (FVOCs) help shape fungal interactions in model and agricultural systems and thus may be important drivers of interactions among bark beetle-associated fungi. We investigated whether FVOCs can mediate interspecific interactions among mountain pine beetle's fungal symbionts by affecting fungal growth and reproduction. Headspace volatiles were collected and identified to determine species-specific volatile profiles. Interspecific effects of volatiles on fungal growth and conidia production were assessed by pairing physically-separated fungal cultures grown either on a carbon-poor or -rich substrate, inside a shared-headspace environment. Fungal VOC profiles differed by species and influenced the growth and/or conidia production of the other species. Further, our results showed that FVOCs can be used as carbon sources for fungi developing on carbon-poor substrates. This is the first report demonstrating that FVOCs can drive interactions among bark beetle fungal symbionts, and thus are important factors in beetle attack success.

Diversity in yeast-mycelium dimorphism response of the Dutch elm disease pathogens: the inoculum size effect

Dutch elm disease (DED) is caused by the dimorphic fungi Ophiostoma ulmi, Ophiostoma novo-ulmi, and Ophiostoma himal-ulmi. A cell population density-dependent phenomenon related to quorum sensing was previously shown to affect the reversible transition from yeast-like to mycelial growth in liquid shake cultures of O. novo-ulmi NRRL 6404. Since the response to external stimuli often varies among DED fungal strains, we evaluated the effect of inoculum size on 8 strains of the 3 species of DED agents by determining the proportion of yeast and mycelium produced at different spore inoculum concentrations in defined liquid shake medium. The results show that not all DED fungi strains respond similarly to inoculum size effect, since variations were observed among strains. It is thus possible that the different strains belonging to phylogenetically close species use different signalling molecules or molecular signalling pathways to regulate their growth mode via quorum-sensing mechanisms.