Endophytic Nocardiopsis sp. from Zingiber officinale with both antiphytopathogenic mechanisms and antibiofilm activity against clinical isolates

An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes

Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.

A comprehensive review on soft rot disease management in ginger (Zingiber officinale) for enhancing its pharmaceutical and industrial values

Zingiber officinale L. Roscoe is a significant herb that possesses many medicinal and ethnomedicinal properties. Due to the presence of various bioactive compounds, it has immense healing capacity. However, ginger as a crop is susceptible to several fungal pathogens. Among all the fungal pathogens, Pythium and Fusarium spp. are of most concern, causing soft rot (rhizome rot) disease, majorly responsible for the downfall in its production by 50-90%. Pesticides and fungicides spray is generally recommended for the control of soft rot. Ample use of chemicals not only affects the quality of the crop but also disturbs ecological integrity. Therefore, biological methods of disease management involving suitable microbial agents such as Trichoderma harzianum, Pseudomonas spp., Bacillus subtilis, Streptomyces spp. and plant extracts are attracting and gaining importance as a part of integrated approaches (IPM) to manage the soft rot and sustainably enhance the production and improve the medicinal and pharmaceutical values of ginger. The present review is aimed to discuss various means of controlling soft rot disease by physical, chemical, biological, and nanotechnology-based methods. Moreover, various bioactive constituents of ginger and their pharmaceutical importance have been also discussed.

Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development

Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.

The Chemical Profiling, Docking Study, and Antimicrobial and Antibiofilm Activities of the Endophytic fungi Aspergillus sp. AP5

Growing data suggest that Aspergillus niger, an endophytic fungus, is a rich source of natural compounds with a wide range of biological properties. This study aimed to examine the antimicrobial and antibiofilm capabilities of the Phragmites australis-derived endophyte against a set of pathogenic bacteria and fungi. The endophytic fungus Aspergillus sp. AP5 was isolated from the leaves of P. australis. The chemical profile of the fungal crude extract was identified by spectroscopic analysis using LC-HRESIMS. The fungal-derived extract was evaluated for its antimicrobial activity towards a set of pathogenic bacterial and fungal strains including Staphylococcus aureus, Pseudomonas aeruginosa, Proteus vulgaris, Klebsiella sp., Candida albicans, and Aspergillus niger. Moreover, antibiofilm activity toward four resistant biofilm-forming bacteria was also evaluated. Additionally, a neural-networking pharmacophore-based visual screening predicted the most probable bioactive compounds in the obtained extract. The AP5-EtOAc extract was found to have potent antibacterial activities against S. aureus, E. coli, and Klebsiella sp., while it exhibited low antibacterial activity toward P. Vulgaris and P. aeruginosa and displayed anticandidal activity. The AP5-EtOAc extract had significant antibiofilm activity in S. aureus, followed by P. aeruginosa. The active metabolites’ antifungal and/or antibacterial activities may be due to targeting the fungal CYP 51 and/or the bacterial Gyr-B.

Anti-Biofilm Activity and Biocontrol Potential of Streptomyces Cultures Against Ralstonia solanacearum on Tomato Plants

Biological control of phytopathogen is a promising approach when compared to the use of chemical agents. In the present study, seven Streptomyces cultures showing promising anti biofilm activity against Ralstonia solanacearum was mixed individually with farmyard manure. All the Streptomyces fortified farmyard manure (SFYM) were screened for plant growth promotion and control of bacterial wilt caused by R. solanacearum on tomato. Further, the ability of SFYM on stimulating the production of defense-related enzymes in R. solanacearum-inoculated tomato plants was investigated. When compared to the control tomato plants, the SFYM-treated plants had longer shoot and root length along with higher fresh and dry weight. The maximum level of chlorophyll was observed in the plants treated with strain UP1A-1 (2.21 ± 0.18 mg g^-1). Strain UP1A-1 also showed maximum of 96.8 ± 1.4% biocontrol efficacy in tomato plants challenged with R. solanacearum. In addition, the UP1A-1 treated tomato plants showed maximum accumulation of total phenolics (3.02 ± 0.09 mg g^-1) after 6 days of pathogen inoculation (DPI). Similarly, tomato plants treated with UP1A-1 showed highest level of peroxides, polyphenol oxidase and phenylalanine ammonia lyase during 1-9 DPI. Findings of present study revealed that the Streptomyces culture UP1A-1 fortified farm yard manure could be applied as an eco-friendly alternative to synthetic agents for controlling bacterial wilt in tomato plants.

Biocontrol of Soil-Borne Pathogens of Solanum lycopersicum L. and Daucus carota L. by Plant Growth-Promoting Actinomycetes: In Vitro and In Planta Antagonistic Activity

Biotic stress caused by pathogenic microorganisms leads to damage in crops. Tomato and carrot are among the most important vegetables cultivated worldwide. These plants are attacked by several pathogens, affecting their growth and productivity. Fourteen plant growth-promoting actinomycetes (PGPA) were screened for their in vitro biocontrol activity against Solanum lycopersicum and Daucus carota microbial phytopathogens. Their antifungal activity was evaluated against Fusarium oxysporum f. sp. radicis-lycopersici (FORL) and Rhizoctonia solani (RHS). Antibacterial activity was evaluated against Pseudomonas syringae, Pseudomonas corrugata, Pseudomonas syringae pv. actinidiae, and Pectobacterium carotovorum subsp. carotovorum. Strains that showed good in vitro results were further investigated in vitro (cell-free supernatants activity, scanning electron microscope observations of fungal inhibition). The consortium of the most active PGPA was then utilized as biocontrol agents in planta experiments on S. lycopersicum and D. carota. The Streptomyces albidoflavus H12 and Nocardiopsis aegyptica H14 strains showed the best in vitro biocontrol activities. The diffusible and volatile compounds and cell-free supernatants of these strains showed both antifungal (in vitro inhibition up to 85%, hyphal desegregation and fungicidal properties) and antibacterial activity (in vitro inhibition >25 mm and bactericidal properties). Their consortium was also able to counteract the infection symptoms of microbial phytopathogens during in planta experiments, improving plant status. The results obtained highlight the efficacy of the selected actinomycetes strains as biocontrol agents of S. lycopersicum and D. carota.

Bioactivities of endophytic actinobacteria inhabiting Artemisia herba-alba emphasizing differences from free-living strains

The endophytic actinobacteria associated with Artemisia herba-alba (synonym: Seriphidium herba-alba) are highly diverse. This study aimed to illustrate the extent of their differences from the free-living actinobacteria in the surrounding environment. A selection of eighteen actinobacteria inhabiting A. herba-alba were compared with twenty and ten actinobatceria isolates from the surrounding desert and groundwater, respectively, representing six genera. Antagonistic and enzymatic activities, plant growth-promoting traits, and the occurrence of biosynthetic genes were compared among the isolates. Data were analyzed statistically using principal component analysis (PCA) and were visualized using heat map. Endophytic strains showed higher antimicrobial activity and production of plant growth promoters compared to desert and groundwater strains. Polyketide synthase and non-ribosomal peptide synthetase gene clusters were detected at higher frequencies in the endophytic strains (8 and 11 strains, respectively) than the desert strains (1 and 2 strains, respectively). In contrast, both gene clusters were not detected in the groundwater strains. The PCA revealed unique metabolic characteristics of the endophytes. The heatmap clustered the endophytic strains apart from the free-living strains, indicating distinctive qualitative and quantitative bioactivities. Analysis of 16S rRNA genes confirmed the chemotaxonomic identity of all but two strains, with > 94.5% similarity. Six endophytes displayed < 99.5% similarity with their closest type strains, which might indicate species novelty. This study provides an evidence of functional differences and possible species novelty of the endophytic actinobacteria inhabiting A. herba-alba, compared with the free-living species.

Beneficial Relationships Between Endophytic Bacteria and Medicinal Plants

Plants benefit extensively from endophytic bacteria, which live in host plant tissues exerting no harmful effects. Bacterial endophytes promote the growth of host plants and enhance their resistance toward various pathogens and environmental stresses. They can also regulate the synthesis of secondary metabolites with significant medicinal properties and produce various biological effects. This review summarizes recent studies on the relationships between bacterial endophytes and medicinal plants. Endophytic bacteria have numerous applications in agriculture, medicine, and other industries: improving plant growth, promoting resistance toward both biotic and abiotic stresses, and producing metabolites with medicinal potential. Their distribution and population structure are affected by their host plant's genetic characteristics and health and by the ecology of the surrounding environment. Understanding bacterial endophytes can help us use them more effectively and apply them to medicinal plants to improve yield and quality.

Bio-Guided Fractionation of Prenylated Benzaldehyde Derivatives as Potent Antimicrobial and Antibiofilm from Ammi majus L. Fruits-Associated Aspergillus amstelodami

Ammi majus L.; Family Apiaceae; is a plant indigenous to Egypt. Its fruits contain bioactive compounds such as furanocoumarins and flavonoids of important biological activities. An endophytic fungus was isolated from the fruits and identified as Aspergillus amstelodami (MK215708) by morphology, microscopical characterization, and molecular identification. To our knowledge this is the first time an endophytic fungus has been isolated from the fruits. The antimicrobial activity of the Ammi majus ethanol fruits extract (AME) and fungal ethyl acetate extract (FEA) were investigated, where the FEA showed higher antimicrobial activity, against all the tested standard strains. Phytochemical investigation of the FEA extract yielded five prenylated benzaldehyde derivative compounds isolated for the first time from this species: Dihydroauroglaucin (1), tetrahydroauroglaucin (2), 2-(3,6-dihydroxyhepta-1,4-dien-1-yl)-3,6-dihydroxy-5-(dimethylallyl)benzaldehyde (3), isotetrahydroauroglaucin )4), and flavoglaucin (5). Structure elucidation was carried out using (1H- and 13C-NMR). Fractions and the major isolated compound 1 were evaluated for their antimicrobial and antibiofilm activity. Compound 1 showed high antimicrobial activity against Escherichia coli with minimum inhibitory concentration (MIC) = 1.95 µg/mL, Streptococcus mutans (MIC = 1.95 µg/mL), and Staphylococcus aureus (MIC = 3.9 µg/mL). It exhibited high antibiofilm activity with minimum biofilm inhibitory concentration (MBIC) = 7.81 µg/mL against Staphylococcus aureus and Escherichia coli biofilms and MBIC = 15.63 µg/mL against Streptococcus mutans and Candida albicans and moderate activity (MBIC = 31.25 µg/mL) against Pseudomonas aeruginosa biofilm. This reveals that dihydroauroglaucin, a prenylated benzaldehyde derivative, has a broad spectrum antimicrobial activity. In conclusion, it was observed that the MICs of the FEA are much lower than that of the AME against all susceptible strains, confirming that the antimicrobial activity of Ammi majus may be due to the ability of its endophytic fungi to produce effective secondary metabolites.

Profile of the Intervention Potential of the Phylum Actinobacteria Toward Quorum Sensing and Other Microbial Virulence Strategies

The rapid dissemination of antimicrobial resistance amongst microorganisms and their deleterious effect on public health has propelled the exploration of alternative interventions that target microbial virulence rather than viability. In several microorganisms, the expression of virulence factors is controlled by quorum sensing systems. A comprehensive understanding into microbial quorum sensing systems, virulence strategies and pathogenesis has exposed potential targets whose attenuation may alleviate infectious diseases. Such virulence attenuating natural products sourced from the different phyla of bacteria from diverse ecosystems have been identified. In this review, we discuss chemical entities derived from the phylum Actinobacteria that have demonstrated the potential to inhibit microbial biofilms, enzymes, and other virulence factors both in vivo and in vitro. We also review Actinobacteria-derived compounds that can degrade quorum sensing signal molecules, and the genes encoding such molecules. As many Actinobacteria-derived compounds have been translated into pharmaceutically important agents including antibiotics, the identification of virulence attenuating compounds from this phylum exemplifies their significance as a prospective source for anti-virulent drugs.

Differential Modulation of Endophytic Microbiome of Ginger in the Presence of Beneficial Organisms, Pathogens and Both as Identified by DGGE Analysis

Endophytic microorganisms play a significant role in plants response to beneficial organisms and pathogens. In the current study, endophytic microorganisms from Zingiber officinale were screened for in vitro inhibition against Pythium myriotylum. From this, Burkholderia vietnamiensis ZoB74 was selected as an organism with remarkable antifungal effect. Further, the study focussed on analysis of in vivo changes in endophytic bacterial community of Z. officinale in presence of selected organisms and the pathogen P. myriotylum by PCR-DGGE. 16S rDNA sequencing of bacterial community after DGGE has resulted in the identification of a group of uncultured bacteria as the predominant microbial community of rhizome under various conditions of treatment. High frequency dominance of these endophytic bacteria suggests their role in disease resistance to soft rot in ginger. This also revealed the variation of endophytic microbiome of Z. officinale under biotic stress. Hence the study provides molecular insight into uncultured microbiome and its stress-inducible variation in ginger rhizome.

Effective management of soft rot of ginger caused by Pythium spp. and Fusarium spp.: emerging role of nanotechnology

Ginger (Zingiber officinale Rosc.) is a tropical plant cultivated all over the world due to its culinary and medicinal properties. It is one of the most important spices commonly used in food, which increases its commercial value. However, soft rot (rhizome rot) is a common disease of ginger caused by fungi such as Pythium and Fusarium spp. It is the most destructive disease of ginger, which can reduce the production by 50 to 90%. Application of chemical fungicides is considered as an effective method to control soft rot of ginger but extensive use of fungicides pose serious risk to environmental and human health. Therefore, the development of ecofriendly and economically viable alternative approaches for effective management of soft rot of ginger such diseases is essentially required. An acceptable approach that is being actively investigated involves nanotechnology, which can potentially be used to control Pythium and Fusarium. The present review is aimed to discuss worldwide status of soft rot associated with ginger, the traditional methods available for the management of Pythium and Fusarium spp. and most importantly, the role of various nanomaterials in the management of soft rot of ginger. Moreover, possible antifungal mechanisms for chemical fungicides, biological agents and nanoparticles have also been discussed.