Isolation and molecular characterization of antifungal metabolite producing actinomycete from mangrove soil

Actinomycete Potential as Biocontrol Agent of Phytopathogenic Fungi: Mechanisms, Source, and Applications

Synthetic fungicides have been the main control of phytopathogenic fungi. However, they cause harm to humans, animals, and the environment, as well as generating resistance in phytopathogenic fungi. In the last few decades, the use of microorganisms as biocontrol agents of phytopathogenic fungi has been an alternative to synthetic fungicide application. Actinomycetes isolated from terrestrial, marine, wetland, saline, and endophyte environments have been used for phytopathogenic fungus biocontrol. At present, there is a need for searching new secondary compounds and metabolites of different isolation sources of actinomycetes; however, little information is available on those isolated from other environments as biocontrol agents in agriculture. Therefore, the objective of this review is to compare the antifungal activity and the main mechanisms of action in actinomycetes isolated from different environments and to describe recent achievements of their application in agriculture. Although actinomycetes have potential as biocontrol agents of phytopathogenic fungi, few studies of actinomycetes are available of those from marine, saline, and wetland environments, which have equal or greater potential as biocontrol agents than isolates of actinomycetes from terrestrial environments.

Bio-priming with a consortium of Streptomyces araujoniae strains modulates defense response in chickpea against Fusarium wilt

Wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is one of the major diseases of chickpea affecting the potential yield significantly. Productivity and biotic stress resilience are both improved by the association and interaction of Streptomyces spp. with crop plants. In the present study, we evaluated two Streptomyces araujoniae strains (TN11 and TN19) for controlling the wilt of chickpea individually and as a consortium. The response of Foc challenged chickpea to inoculation with S. araujoniae TN11 and TN19 individually and as a consortium was recorded in terms of changes in physio-biochemical and expression of genes coding superoxide dismutase (SOD), peroxidase, and catalase. Priming with a consortium of TN11 and TN19 reduced the disease severity by 50–58% when challenged with Foc. Consortium primed-challenged plants recorded lower shoot dry weight to fresh weight ratio and root dry weight to fresh weight ratio as compared to challenged non-primed plants. The pathogen-challenged consortium primed plants recorded the highest accumulation of proline and electrolyte leakage. Similarly, total chlorophyll and carotenoids were recorded highest in the consortium treatment. Expression of genes coding SOD, peroxidase, and catalase was up-regulated which corroborated with higher activities of SOD, peroxidase, and catalase in consortium primed-challenged plants as compared to the challenged non-primed plants. Ethyl acetate extracts of TN11 and TN19 inhibited the growth of fungal pathogens viz., Fusarium oxysporum f. sp. ciceris. Macrophomina phaseolina, F. udum, and Sclerotinia sclerotiarum by 54–73%. LC–MS analyses of the extracts showed the presence of a variety of antifungal compounds like erucamide and valinomycin in TN11 and valinomycin and dinactin in TN19. These findings suggest that the consortium of two strains of S. araujoniae (TN11 and TN19) can modulate defense response in chickpea against wilt and can be explored as a biocontrol strategy.

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an “one strain many compounds” approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.

A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

Bioactive antifungal metabolites produced by Streptomyces amritsarensis V31 help to control diverse phytopathogenic fungi

Actinomycetes due to their unique repertoire of antimicrobial secondary metabolites can be an eco-friendly and sustainable alternative to agrochemicals to control plant pathogens. In the present study, antifungal activity of twenty different actinomycetes was evaluated via dual culture plate assay against six different phytopathogens, viz., Alternaria alternata, Aspergillus flavus, Fusarium oxysporum f. sp. lycopersici, Sarocladium oryzae, Sclerotinia sclerotiorum, and Rhizoctonia solani. Two potential isolates, Streptomyces amritsarensis V31 and Kribella karoonensis MSCA185 showing high antifungal activity against all six fungal pathogens, were further evaluated after extraction of bioactive metabolites in different solvents. Metabolite extracted from S. amritsarensis V31 in different solvents inhibited Rhizoctonia solani (7.5-65%), Alternaria alternata (5.5-52.7%), Aspergillus flavus (8-30.7%), Fusarium oxysporum f. sp. lycopersici (25-44%), Sarocladium oryzae (11-55.5%), and Sclerotinia sclerotiorum (29.7-40.5%); 1000 D diluted methanolic extract of S. amritsarensis V31 showed growth inhibition against R. solani (23.3%), A. flavus (7.7%), F. oxysporum (22.2%), S. oryzae (16.7%), and S. sclerotiorum (19.0%). Metabolite extracts of S. amritsarensis V31 significantly reduced the incidence of rice sheath blight both as preventive and curative sprays. Chemical profiling of the metabolites in DMSO extract of S. amritsarensis V31 revealed 6-amino-5-nitrosopyrimidine-2,4-diol as the predominant compound present. It was evident from the LC-MS analyses that S. amritsarensis V31 produced a mixture of potential antifungal compounds which inhibited the growth of different phytopathogenic fungi. The results of this study indicated that metabolite extracts of S. amritsarensis V31 can be exploited as a bio-fungicide to control phytopathogenic fungi.

In vitro biological properties of Streptomyces cangkringensis isolated from the floral rhizosphere regions

This context was investigated to determine in vitro antimicrobial, antioxidative, and anticancer traits of crude ethyl acetate extract of Streptomyces cangkringensis strain TSAS 04 isolated from soil sample of rhizosphere regions. The antimicrobial activity of ethyl acetate extract of strain TSAS 04 was determined against indicator pathogens using disc diffusion assay which exhibited maximum zones of inhibition of 20.6 ± 0.3 and 16.3 ± 0.6 mm against Bacillus subtilis and Trichoderma viride, respectively. In vitro antioxidant properties of the crude ethyl acetate extract were performed using standard methodologies. The extract revealed maximum DPPḢ and ABTS^•+ radical scavenging activities of 51.1 ± 0.39 and 81.25 ± 0.33%, respectively. Likewise, maximum phosphomolybdenum reduction and Fe³⁺ reduction of the crude ethyl acetate extract of strain TSAS 04 were estimated 76.18 ± 0.10 and 89.01 ± 0.44%, respectively. In vitro anticancer trait of the extract was determined against HeLa cell line using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay which showed anticancer activities in a dose dependent manner with an IC₅₀ value of 410.5 µg/mL. Fourier transform infrared spectroscopy (FT-IR) and Gas chromatography–mass spectrometry (GC-MS) analyses indicated the presence of distinct functional groups and bioactive components in the extract, respectively. In conclusion, S. cangkringensis strain TSAS 04 showed its effectiveness as ideal bioactive agent by exhibiting substantial antimicrobial, antioxidant, and anticancer properties.

Modulation of agriculturally useful rhamnolipid profile of Pseudomonas sp. K6 due to the supplementation with chitosan and gold nanoparticles

As rhizobacteria have extensively been studied for the production of compounds with biocontrol properties, methods to enhance its production are very important. In this study, nanotechnological method to modulate the rhamnolipid production by Pseudomonas sp. K6 has been demonstrated. For this, Pseudomonas sp. K6 was cultured with different concentrations of chitosan nanoparticles (CNPs) and gold nanoparticles (AuNPs). The rhamnolipid production was further analyzed by CTAB- methylene blue agar assay and also by LC-MS/MS analysis. From the LC-MS/MS result, induction of dirhamnolipid production in K6 could be confirmed when cultured with CNPs (1, 5 and 10 mg/mL) and AuNPs (10, 25, 50 and 100 µg/mL). The monorhamnolipid production by K6 was observed to get enhanced when the K6 culture was supplemented with 2.5 mg/mL CNPs and 10 µg/mL AuNPs. Also, in planta study confirmed the biocontrol ability of rhamnolipid as it suppressed the Sclerotium rolfsii infection in Vigna unguiculata plants. As the rhamnolipids have versatile applications in the agricultural field, the nano-based approach to enhance its production from the biocontrol organism is significant.