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

In vitro antifungal activity analysis of Streptomyces sp. strain 196 against Candida albicans and Aspergillus flavus

Numerous bioactive compounds have been reported to be produced by the members of the genus Streptomyces. During our previous studies, Streptomyces sp. strain 196 was tested for its antimicrobial activity, and bioactive compounds produced by this strain were characterized LC-MS and 1H NMR. To examine the antifungal potential of strain 196 is the goal of the current investigation. Present investigation is focused on exploring antifungal activity of extract of strain 196 (196EA) on membrane disruption potential against two fungi Candida albicans ATCC 90028 and Aspergillus flavus ITCC 5599. Results revealed that the MIC value is higher for A. flavus than for C. albicans which is 450 µg/mL and 250 µg/mL, respectively. Disc diffusion and spot assay also correspond to the values of the MIC for their respective pathogen. In growth curve analysis, lag and log phase are significantly affected by the extract of strain 196. The effects of extract from strain 196 on plasma membrane disruption of Candida albicans and Aspergillus flavus were analyzed in terms of ergosterol quantification assay, cellular leakage, proton efflux measurement (PM-ATPase), plasma membrane integrity assay (PI), and DNA damage assay (DAPI). Results shown that the extract of strain 196 has the potential to inhibit the cell membrane of the both pathogenic fungi which was further confirmed with the help of scanning electron microscopic (SEM) studies.

Biocontrol of Mycotoxigenic Fungi by Actinobacteria

Actinobacteria are well known for their production of metabolites of interest. They have been previously studied to identify new antibiotics in medical research and for their ability to stimulate plant growth in agronomic research. Actinobacteria represents a real source of potential biocontrol agents (BCAs) today. With the aim of reducing the use of phytosanitary products by 50% with the different Ecophyto plans, a possible application is the fight against mycotoxin-producing fungi in food matrices and crops using BCAs. To deal with this problem, the use of actinobacteria, notably belonging to the Streptomyces genus, or their specialized metabolites seems to be a solution. In this review, we focused on the impact of actinobacteria or their metabolites on the development of mycotoxigenic fungi and mycotoxin production on the one hand, and on the other hand on their ability to detoxify food matrices contaminated by mycotoxins.

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Holomics - a user-friendly R shiny application for multi-omics data integration and analysis

An organism's observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other 'omics' disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.

Why Do We Need Alternative Methods for Fungal Disease Management in Plants?

Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides-if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.

Mechanistic insights into the role of actinobacteria as potential biocontrol candidates against fungal phytopathogens

Worldwide mounting demand for better food production to nurture exasperating population emphasizes on reduced crop losses. The incidence of pathogens into the agricultural fields has tend to dwindle plethora of cereal, vegetable, and other fodder crops. This, in turn, has seriously impacted the economic losses on global scale. Apart from this, it is quite challenging to feed the posterity in the coming decades. To counteract this problem, various agrochemicals have been commercialized in the market that no doubt shows positive results but along with adversely affecting the ecosystem. Therefore, the excessive ill-fated use of agrochemicals to combat the plant pests and diseases highlights that alternatives to chemical pesticides are need of the hour. In recent days, management of plant diseases using plant-beneficial microbes is gaining interest as safer and potent alternatives to replace chemically based pesticides. Among these beneficial microbes, actinobacteria especially streptomycetes play considerable role in combating plant diseases along with promoting the plant growth and development along with their productivity and yield. The mechanisms exhibited by actinobacteria include antibiosis (antimicrobial compounds and hydrolytic enzymes), mycoparasitism, nutrient competition, and induction of resistance in plants. Thus, in cognizance with potential of actinobacteria as potent biocontrol agents, this review summarizes role of actinobacteria and the multifarious mechanisms exhibited by actinobacteria for commercial applications.

Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil

Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.

Effect of Streptomyces roseolus Cell-Free Supernatants on the Fungal Development, Transcriptome, and Aflatoxin B1 Production of Aspergillus flavus

Crop contamination by aflatoxin B1 (AFB1), an Aspergillus-flavus-produced toxin, is frequently observed in tropical and subtropical regions. This phenomenon is emerging in Europe, most likely as a result of climate change. Alternative methods, such as biocontrol agents (BCAs), are currently being developed to reduce the use of chemicals in the prevention of mycotoxin contamination. Actinobacteria are known to produce many bioactive compounds, and some of them can reduce in vitro AFB1 concentration. In this context, the present study aims to analyze the effect of a cell-free supernatant (CFS) from Streptomyces roseolus culture on the development of A. flavus, as well as on its transcriptome profile using microarray assay and its impact on AFB1 concentration. Results demonstrated that in vitro, the S. roseolus CFS reduced the dry weight and conidiation of A. flavus from 77% and 43%, respectively, and was therefore associated with a reduction in AFB1 concentration reduction to levels under the limit of quantification. The transcriptomic data analysis revealed that 5198 genes were differentially expressed in response to the CFS exposure and among them 5169 were downregulated including most of the genes involved in biosynthetic gene clusters. The aflatoxins' gene cluster was the most downregulated. Other gene clusters, such as the aspergillic acid, aspirochlorine, and ustiloxin B gene clusters, were also downregulated and associated with a variation in their concentration, confirmed by LC-HRMS.

Ecotoxicological implications of residual pesticides to beneficial soil bacteria: A review

Optimization of crop production in recent times has become essential to fulfil food demands of constantly increasing human populations worldwide. To address this formidable challenge, application of agro-chemicals including synthetic pesticides in intensive farm practices has increased alarmingly. The excessive and indiscriminate application of pesticides to foster food production however, leads to its exorbitant deposition in soils. After accumulation in soils beyond threshold limits, pesticides harmfully affect the abundance, diversity and composition and functions of rhizosphere microbiome. Also, the cost of pesticides and emergence of resistance among insect-pests against pesticides are other reasons that require attention. Due to this, loss in soil nutrient pool cause a substantive reduction in agricultural production which warrant the search for newer environmentally friendly technology for sustainable crop production. Rhizosphere microbes, in this context, play vital roles in detoxifying the polluted environment making soil amenable for cultivation through detoxification of pollutants, rhizoremediation, bioremediation, pesticide degradation, and stress alleviation, leading to yield optimization. The response of soil microorganisms to range of chemical pesticides is variable ranging from unfavourable to the death of beneficial microbes. At cellular and biochemical levels, pesticides destruct the morphology, ultrastructure, viability/cellular permeability, and many biochemical reactions including protein profiles of soil bacteria. Several classes of pesticides also disturb the molecular interaction between crops and their symbionts impeding the overall useful biological processes. The harmful impact of pesticides on soil microbes, however, is poorly researched. In this review, the recent findings related with potential effects of synthetic pesticides on a range of soil microbiota is highlighted. Emphasis is given to find and suggest strategies to minimize the chemical pesticides usage in the real field conditions to preserve the viability of soil beneficial bacteria and soil quality for safe and sustainable crop production even in pesticide contaminated soils.

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.