Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere

Evaluation of Streptomyces sporoverrucosus B-1662 for biological control of red pepper anthracnose and apple bitter rot diseases in Korea

Fungi are the prominent phytopathogens that have significant impact on the productivity of agriculture worldwide. Streptomyces species have been extensively studied for the production of various bioactive metabolites. These metabolites have been used as biocontrol agents for the management of diseases caused by phytopathogenic fungi. The purpose of this investigation is to assess the efficacy of Streptomyces sporoverrucosus B-1662, an antagonistic agent in the control of red pepper anthracnose caused by Colletotrichum acutatum KACC 42403 and apple anthracnose caused by Colletotrichum siamense CGCP6 (GYUN-10348). On the basis of the morphological, and molecular characterization using 16S rRNA, the strain B-1662 was determined to be S. sporoverrucosus. The strain B-1662 exhibited antagonistic activity against seven fungal phytopathogens, including C. acutatum KACC 42403 and C. siamense CGCP6. The culture filtrates (CF) from B-1662 showed antifungal activity against all seven fungal pathogens with greater inhibition rate (%) in comparison with a control. The bacterial suspensions of B-1662 showed an excellent biological control effect on the red pepper anthracnose and apple bitter rot using an in planta assay. The anthracnose disease rate (%) was controlled by over 90% with B-1662 cell suspensions at 105 to 107 CFU/mL. Compared to a control, the strain B-1662 played a more effective role in controlling the anthracnose disease in field conditions in both years 2022 and 2023. From the effective solvent fractions, the effect compound (dibutoxybutane) has been isolated exhibiting with antifungal effect. The genetic base underlying the biocontrol traits of B-1662 was characterized using the whole-genome sequence of B-1662, which was compared with closely related strains. Consequently, these results collectively suggest that S. sporoverrucosus B-1662 can aid in the management of red-pepper anthracnose.

Interference with sexual mating of Sporisorium scitamineum by verrucarin A isolated from Paramyrothecium sp

Sugarcane smut, caused by Sporisorium scitamineum, poses a significant global threat, leading to substantial economic losses. The pathogenic process involves haploid spores engaging in sexual mating to produce diploid mycelia, which then initiates the disease by penetrating sugarcane tissues. Targeting the mating process has thus emerged as the Achilles' heel in controlling sugarcane smut. In this study, we isolated a fungus designated as P-6 from a bryophyte, which impeded the mycelia formation of S. scitamineum. Phylogenetic and morphological analyses classified the strain P-6 within the genus Paramyrothecum. Through ethyl acetate extraction, subsequent separation, and nuclear magnetic resonance (NMR) analysis, we identified the active compound responsible for inhibiting the mating process as verrucarin A (Ver-A). Specifically, Ver-A inhibited the sexual mating of S. scitamineum by modulating the gene expression of loci a and b. Greenhouse pot experiments underscored the efficacy of strain P-6's fermentation products in reducing the incidence of sugarcane smut. These findings lay a robust groundwork for the development and application of P-6 as a novel biocontrol strain against sugarcane smut.

Streptomyces improves sugarcane drought tolerance by enhancing phenylalanine biosynthesis and optimizing the rhizosphere environment

Drought stress is a common hazard faced by sugarcane growth, and utilizing microorganisms to enhance plant tolerance to abiotic stress has become an important method for sustainable agricultural development. Several studies have demonstrated that Streptomyces chartreuses WZS021 improves sugarcane tolerance to drought stress. However, the molecular mechanisms underlying tolerance at the transcriptional and metabolomic levels remain unclear. We comprehensively evaluated the physiological and molecular mechanisms by which WZS021 enhances drought tolerance in sugarcane, by performing transcriptome sequencing and non-targeted metabolomics; and examining rhizosphere soil properties and plant tissue antioxidant capacity. WZS021 inoculation improved the rhizosphere nutritional environment (AP, ammonia, OM) of sugarcane and enhanced the antioxidant capacity of plant roots, stems, and leaves (POD, SOD, CAT). Comprehensive analyses of the transcriptome and metabolome revealed that WZS021 mainly affects plant drought tolerance through phenylalanine metabolism, plant hormone signal transduction, and flavonoid biosynthesis pathways. The drought tolerance signaling molecules mediated by WZS021 include petunidin, salicylic acid, α-Linoleic acid, auxin, geranylgeraniol and phenylalanine, as well as key genes related to plant hormone signaling transduction (YUCCA, amiE, AUX, CYPs, PAL, etc.). Interestingly, inoculation with WZS021 during regular watering induces a transcriptome-level response to biological stress in sugarcane plants. This study further elucidates a WZS021-dependent rhizosphere-mediated regulatory mechanism for improving sugarcane drought tolerance, providing a theoretical basis for increasing sugarcane production capacity.

Molecular mechanisms of growth promotion and selenium enrichment in tomato plants by novel selenium-doped carbon quantum dots

Selenium (Se)-doped nanoparticles as novel Se fertilizers have a promising potential in the agricultural application. Here, the effects of two novel Se-doped carbon quantum dots (Se-CQDs1 and Se-CQDs2, prepared using co-cracking and adsorption-reduction methods, respectively) on the growth and Se enrichment of tomato plants were studied, where the promoting molecular mechanisms were explored in terms of the related genes expression and soil microbial composition. The results indicated that the soil application of 2.5 mg kg-1 Se-CQDs1 more significantly increased the root growth, plant biomass, and fruit yield than that of Se-CQDs2 and Na2SeO3 treatments (control). Specifically, Se-CQDs1 treatment was more effective to up-regulate the expressions of aquaporin gene (i.e., PIP) and growth hormone synthesis gene (i.e., NIT) than Se-CQDs1 and Na2SeO3 treatments. The expressions of Se methyltransferase gene (smt) and methionine methyltransferase gene (mmt) induced by Se-CQDs1 were 1.45 and 1.18 times higher than that by Se-CQDs2 as well as 1.82 and 2.17 times higher than that by Na2SeO3. Also, Se-CQDs1 more greatly increased the diversity and relative abundance of soil bacterial communities, especially the Actinobacteria phylum, which was beneficial to increase plant growth-promoting substances. These outstanding promoting effects of Se-CQDs1 were mainly ascribed to its higher hydrophilicity and content of the stable doped-Se. The overall results demonstrated that Se-CQDs would be a promising candidate for nano-fertilizer to increase crop growth and development (e.g., tomato plants), where the synthesis modes of Se-CQDs play a critical role in regulating the utilization efficiency of Se.

The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis

This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome

Environmental pollutants from different chemical families may reach the gut microbiome, where they can be metabolized and transformed. However, how our gut symbionts respond to the exposure to environmental pollution is still underexplored. In this observational, cohort study, we aim to investigate the influence of environmental pollution on the gut microbiome composition and potential activity by shotgun metagenomics. We select as a case study a population living in a highly polluted area in Campania region (Southern Italy), proposed as an ideal field for exposomic studies and we compare the fecal microbiome of 359 subjects living in areas with high, medium and low environmental pollution. We highlight changes in gut microbiome composition and functionality that were driven by pollution exposure. Subjects from highly polluted areas show higher blood concentrations of dioxin and heavy metals, as well as an increase in microbial genes related to degradation and/or resistance to these molecules. Here we demonstrate the dramatic effect that environmental xenobiotics have on gut microbial communities, shaping their composition and boosting the selection of strains with degrading capacity. The gut microbiome can be considered as a pivotal player in the environment-health interaction that may contribute to detoxifying toxic compounds and should be taken into account when developing risk assessment models. The study was registered at ClinicalTrials.gov with the identifier NCT05976126.

Effect of endogenous sodium and potassium ions in plants on the quality of alfalfa silage and bacterial community stability during fermentation

This study investigated the impact of endogenous sodium and potassium ions in plants on the quality of alfalfa silage, as well as the stability of bacterial communities during fermentation. Silage was produced from the fermented alfalfa, and the chemical composition, fermentation characteristics, and microbiome were analyzed to understand their interplay and impact on silage fermentation quality. The alfalfa was cultivated under salt stress with the following: (a) soil content of <1‰ (CK); (b) 1‰-2‰ (LP); (c) 2‰-3‰ (MP); (d) 3‰-4‰ (HP). The results revealed that the pH of silage was negatively correlated with the lactic acid content. With the increase of lactic acid (LA) content increased (26.3-51.0 g/kg DM), the pH value decreased (4.9-5.3). With the increase of salt stress, the content of Na+ in silage increased (2.2-5.4 g/kg DM). The presence of endogenous Na+ and K+ ions in plants significantly affected the quality of alfalfa silage and the dynamics of bacterial communities during fermentation. Increased salt stress led to changes in microbial composition, with Lactococcus and Pantoea showing a gradual increase in abundance, especially under high salt stress. Low pH inhibited the growth of certain bacterial genera, such as Pantoea and Pediococcus. The abundance of Escherichia-Shigella and Comamonas negatively correlated with crude protein (CP) content, while Enterococcus and Lactococcus exhibited a positive correlation. Furthermore, the accumulation of endogenous Na+ in alfalfa under salt stress suppressed bacterial proliferation, thereby reducing protein degradation during fermentation. The pH of the silage was high, and the LA content was also high. Silages from alfalfa under higher salt stress had higher Na+ content. The alpha diversity of bacterial communities in alfalfa silages showed distinct patterns. Desirable genera like Lactococcus and Lactobacillus predominated in silages produced from alfalfa under salt stress, resulting in better fermentation quality.

Promoting plant resilience against stress by engineering root microenvironment with Streptomyces inoculants

Plant growth is directly influenced by biotic and abiotic stress factors resulting from environmental changes. Plant growth-promoting rhizobacteria (PGPR) have become a crucial area of research aimed at addressing these challenges. However, a knowledge gap exists regarding how PGPR impacts the microenvironments surrounding plant roots. The purpose of this study is to elucidate the effects of two distinct PGPR strains, Streptomyces griseorubiginosus BTU6 (known for its resistance to smut disease) and S. chartreusis WZS021, on sugarcane roots. Additionally, we compare the resultant modifications in the physicochemical characteristics of the rhizospheric soil and root architecture. The results reveal that following the inoculation of S. chartreusis WZS021, there was a significant increase in the active chemicals associated with nitrogen metabolism in sugarcane roots. This enhancement led to a substantial enrichment of nitrogen-cycling microbes like Pseudomonas and Gemmatimona. This finding supports earlier research indicating that S. chartreusis WZS021 enhances sugarcane's capacity to utilize nitrogen effectively. Furthermore, after treatment with S. chartreusis, Aspergillus became the predominant strain among endophytic fungi, resulting in alterations to their community structure that conferred drought resistance. In contrast, the relative abundance of Xanthomonas in the root environment decreased following inoculation with S. griseorubiginosus. Instead, Gemmatimona became more prevalent, creating a favorable environment for plants to bolster their resistance against disease. Notably, inoculations with S. chartreusis WZS021 and S. griseorubiginosus BTU6 led to substantial changes in the chemical composition, enzymatic activity, and microbial community composition in the soil surrounding sugarcane roots. However, there were distinct differences in the specific alterations induced by each strain. These findings enhance plant resilience to stress by shedding light on PGPR-mediated modifications in root microenvironments.

Characterization and biocontrol mechanism of Streptomyces olivoreticuli as a potential biocontrol agent against Rhizoctonia solani

Rhizoctonia solani is a widespread and devastating plant pathogenic fungus that infects many important crops. This pathogen causes tobacco target spot, a disease that is widespread in many tobacco-growing countries and is destructive to tobacco. To identify antagonistic microorganisms with biocontrol potential against this disease, we isolated Streptomyces strains from forest inter-root soil and screened a promising biocontrol strain, ZZ-21. Based on in vitro antagonism assays, ZZ-21 showed a significant inhibitory effect on R. solani and various other phytopathogens. ZZ-21 was identified as Streptomyces olivoreticuli by its phenotypic, genetic, physiological and biochemical properties. Complete genome sequencing revealed that ZZ-21 harbored numerous antimicrobial biosynthesis gene clusters. ZZ-21 significantly reduced the lesion length in detached inoculated leaf assays and reduced the disease index under greenhouse and field conditions. Based on an in vitro antagonistic assay of ZZ-21 culture, the strain exhibited an antifungal activity against R. solani in a dose-dependent manner. The culture filtrate could impair membrane integrity, possibly through membrane lipid peroxidation. ZZ-21 could secrete multiple extracellular enzymes and siderophores. According to a series of antifungal assays, the extracellular metabolites of ZZ-21 contained antimicrobial bioactive compounds composed of proteins/peptides extracted using ammonium sulfate precipitation, which were stable under stress caused by high temperature and protease K. The EC50 value for ammonium sulfate precipitation was determined to be 21.11 μg/mL in this study. Moreover, the proteins/peptides also exhibited biocontrol ability and were observed to alter the plasma membrane integrity of R. solani which were evaluated by biocontrol efficacy assays on detached tobacco leaves and PI staining. Overall, strain ZZ-21 shows the potential to be developed into a biopesticide against tobacco target spot disease.

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.

Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis

The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool

Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.

Complete genome analysis of sugarcane root associated endophytic diazotroph Pseudomonas aeruginosa DJ06 revealing versatile molecular mechanism involved in sugarcane development

Sugarcane is an important sugar and bioenergy source and a significant component of the economy in various countries in arid and semiarid. It requires more synthetic fertilizers and fungicides during growth and development. However, the excess use of synthetic fertilizers and fungicides causes environmental pollution and affects cane quality and productivity. Plant growth-promoting bacteria (PGPB) indirectly or directly promote plant growth in various ways. In this study, 22 PGPB strains were isolated from the roots of the sugarcane variety GT42. After screening of plant growth-promoting (PGP) traits, it was found that the DJ06 strain had the most potent PGP activity, which was identified as Pseudomonas aeruginosa by 16S rRNA gene sequencing. Scanning electron microscopy (SEM) and green fluorescent protein (GFP) labeling technology confirmed that the DJ06 strain successfully colonized sugarcane tissues. The complete genome sequencing of the DJ06 strain was performed using Nanopore and Illumina sequencing platforms. The results showed that the DJ06 strain genome size was 64,90,034 bp with a G+C content of 66.34%, including 5,912 protein-coding genes (CDSs) and 12 rRNA genes. A series of genes related to plant growth promotion was observed, such as nitrogen fixation, ammonia assimilation, siderophore, 1-aminocyclopropane-1-carboxylic acid (ACC), deaminase, indole-3-acetic acid (IAA) production, auxin biosynthesis, phosphate metabolism, hydrolase, biocontrol, and tolerance to abiotic stresses. In addition, the effect of the DJ06 strain was also evaluated by inoculation in two sugarcane varieties GT11 and B8. The length of the plant was increased significantly by 32.43 and 12.66% and fresh weight by 89.87 and 135.71% in sugarcane GT11 and B8 at 60 days after inoculation. The photosynthetic leaf gas exchange also increased significantly compared with the control plants. The content of indole-3-acetic acid (IAA) was enhanced and gibberellins (GA) and abscisic acid (ABA) were reduced in response to inoculation of the DJ06 strain as compared with control in two sugarcane varieties. The enzymatic activities of oxidative, nitrogen metabolism, and hydrolases were also changed dramatically in both sugarcane varieties with inoculation of the DJ06 strain. These findings provide better insights into the interactive action mechanisms of the P. aeruginosa DJ06 strain and sugarcane plant development.

A Rhizobacterium, Streptomyces albulus Z1-04-02, Displays Antifungal Activity against Sclerotium Rot in Mungbean

Sclerotium rot causes damping-off and stem rot in seedlings and mature mungbeans, which negatively impacts cultivation. The use of a rhizobacterium to control soil-borne diseases is an alternative method to the excess use of synthetic fungicides; therefore, this study aims to screen rhizosphere actinobacteria with fungicidal activities against Sclerotium rolfsii, the pathogen that causes sclerotium rot in mungbeans. Primary screening showed that the Streptomyces sp. isolate Z1-04-02 displayed the highest effectiveness against S. rolfsii in dual culture plates, with a percentage inhibition of 74.28%. An assay containing enzymes that degrade cell walls, of the cell-free culture filtrate (CF) of Z1-04-02, showed that the activities of chitinase and β-1,3-glucanase were 0.0209 and 1.0210 U/mL, respectively, which was significantly higher than that of the control (media alone). The cell-free CF of Z1-04-02, incubated at 37 °C and 100 °C, using agar well diffusion, effectively inhibited the growth of S. rolfsii with inhibition percentages of 37.78% and 27.78%, respectively. Solid-phase microextraction (SPME) was applied to trap volatiles released from Z1-04-02 and gas chromatography-mass spectrometry (GC/MS); volatile antifungal compounds were tentatively identified as bicyclic monoterpene (1R)-(-)-myrtenal. The application of the cell-free CF, and the spore suspension of Z1-04-02, showed disease severity indexes (DSIs) of 12.5% and 8.25%, respectively, which were significantly lower than those showing inoculation by S. rolfsii alone. The identification of this strain by morphology, biochemistry tests, and 16s rDNA sequences revealed that Z1-04-02 was Streptomyces albulus. This finding revealed that S. albulus Z1-04-02 displayed diverse fungicidal activities against S. rolfsii, and it has the potential to act as a biological control agent in terms of inhibiting sclerotium rot in mungbeans.

Biological control and plant growth promotion properties of Streptomyces albidoflavus St-220 isolated from Salvia miltiorrhiza rhizosphere

Root rot disease caused by Fusarium oxysporum is a devastating disease of Salvia miltiorrhiza and dramatically affected the production and quality of Sa. miltiorrhiza. Besides the agricultural and chemical control, biocontrol agents can be utilized as an additional solution. In the present study, an actinomycete that highly inhibited F. oxysporum was isolated from rhizosphere soil and identified as based on morphological and molecular characteristics. Greenhouse assay proved that the strain had significant biological control effect against Sa. miltiorrhiza root rot disease and growth-promoting properties on Sa. miltiorrhiza seedlings. To elucidate the biocontrol and plant growth-promoting properties of St-220, we employed an analysis combining genome mining and metabolites detection. Our analyses based on genome sequence and bioassays revealed that the inhibitory activity of St-220 against F. oxysporum was associated with the production of enzymes targeting fungal cell wall and metabolites with antifungal activities. Strain St-220 possesses phosphate solubilization activity, nitrogen fixation activity, siderophore and indole-3-acetic acid production activity in vitro, which may promote the growth of Sa. miltiorrhiza seedlings. These results suggest that St. albidoflavus St-220 is a promising biocontrol agent and also a biofertilizer that could be used in the production of Sa. miltiorrhiza.

Streptomyces can be an excellent plant growth manager

Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.