Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2

Streptomyces N2A, an endophytic actinobacteria that promotes soybean growth and increases yield and seed quality under field conditions

Sustainable agriculture based on the use of soil-beneficial microbes such as plant growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCA) is gaining great consideration to reduce the use of agrochemicals for crop production. With this aim, in this study, a total of 78 actinobacteria were isolated from the rhizosphere and endosphere of soybean roots. Based on in vitro compatibility with Bradyrhizobium japonicum, the ability to produce phytohormones, siderophores, exo-enzymes, antifungal compounds and phosphate solubilization (PGPR traits), two endophytic strains, named N2A and N9, were selected to evaluate their effects on plant growth and development at greenhouse and field conditions. Greenhouse trials showed significantly promoted seedling emergence compared to control and the conventional fungicide treatment. Analysis of growth and development associated parameters at reproductive stages and maturity at greenhouse, but also and most importantly, in field experiments showed significant improvements. Plant biomass, node number, pod number, and consequently yield, were higher in plants previously treated with N2A and co-inoculated with B. japonicum compared to the conventional seed treatment. Furthermore, a significant increase in health status and vigor was observed for seeds harvested from the N2A-treated plants in relation to seeds obtained from the conventional treatment. Thus, we demonstrated that Streptomyces sp. N2A can replace traditional chemical fungicides to protect the seed during germination, allowing good implantation, but also, stimulating the growth and development of soybean crop increasing yield and seed quality at field conditions. Altogether, this supports the potential use of Streptomyces N2A as a PGPR for soybean crop production more efficiently and sustainably.

Characterization and evaluation of actinomycete from the Protaetia brevitarsis Larva Frass

Protaetia brevitarsis larvae (PBL) are soil insects important for the soil organic carbon cycle, and PBL frass not only contains a large amount of humic acid but also affects the diversity, novelty, and potential functions of actinomycetes. Here, we characterized and assessed the actinomycete. The operational taxonomic unit (OTU) data showed that 90% of the actinomycetes cannot be annotated to species, and pure culture and genome analysis showed that 35% of the strains had the potential to be new species, indicating the novelty of PBL frass actinomycetes. Additionally, genome annotation showed that many gene clusters related to antifungal, antibacterial and insecticidal compound synthesis were identified, and confrontation culture confirmed the antifungal activities of the actinomycetes against soil-borne plant pathogenic fungi. The incubation experiment results showed that all isolates were able to thrive on media composed of straw powder and alkaline lignin. These results indicated that PBL hindgut-enriched actinomycetes could survive in soil by using the residual lignocellulose organic matter from plant residues, and the antibiotics produced not only give them a competitive advantage among soil microflora but also have a certain inhibitory effect on plant diseases and pests. This study suggests that the application of PBL frass can not only supplement soil humic acid but also potentially affect the soil microbiota of cultivated land, which is beneficial for the healthy growth of crops.

A Streptomyces species from the ginseng rhizosphere exhibits biocontrol potential

Plants and their associated microbes live in complicated, changeable, and unpredictable environments. They usually interact with each other in many ways through multidimensional, multiscale, and multilevel coupling manners, leading to challenges in the coexistence of randomness and determinism or continuity and discreteness. Gaining a deeper understanding of these diverse interaction mechanisms can facilitate the development of data-mining theories and methods for complex systems, coupled modeling for systems with different spatiotemporal scales and functional properties, or even a universal theory of information and information interactions. In this study, we use a "closed-loop" model to present a plant-microbe interaction system and describe the probable functions of microbial natural products. Specifically, we report a rhizosphere species, Streptomyces ginsengnesis G7, which produces polyketide lydicamycins and other active metabolites. Interestingly, these distinct molecules have the potential to function both as antibiotics and as herbicides for crop protection. Detailed laboratory experiments conducted in Arabidopsis (Arabidopsis thaliana), combined with a comprehensive bioinformatics analysis, allow us to rationalize a model for this specific plant-microbe interaction process. Our work reveals the benefits of exploring otherwise neglected resources for the identification of potential functional molecules and provides a reference to better understand the system biology of complex ecosystems.

Identification of Lydicamycins as Main Antioomycete Compounds from the Biocontrol Agent Streptomyces sp. NEAU-S7GS2

Oomycetes are well-known phytopathogens that seriously threaten many important crops worldwide. In this study, the endophytic actinobacterium Streptomyces sp. NEAU-S7GS2 demonstrated significant antagonistic activity against Phytophthora and Pythium and showed a potent biocontrol effect on suppression of soybean phytophthora root rot and pepper phytophthora blight. Two compounds were subsequently isolated as the main active components by bioassay-guided fractionation and identified as lydicamycins A and B. These two compounds showed high antioomycete activity against Phytophthora and Pythium with EC50 values of 0.73-2.67 μg/mL, which are equal to or lower than those of commercialized drug metalaxyl. In vivo bioassay using detached leaves demonstrated that lydicamycin A had a better control efficiency against soybean phytophthora root rot than metalaxyl. Taken together, these results suggest that the biocontrol agent Streptomyces sp. NEAU-S7GS2 and lydicamycins have the potential to be developed as promising pesticides to control diseases caused by oomycetes.

Streptomyces Strains and Their Metabolites for Biocontrol of Phytopathogens in Agriculture

Sustainable agriculture is increasingly linked to biological pesticides as alternatives to agro-chemicals. Streptomyces species suppress plant diseases through their unique traits and numerous metabolites. Although many Streptomyces strains have been developed into commercial products, their roles in the biocontrol of phytopathogens and mechanisms of functional metabolite synthesis remain poorly understood. In this review, biocontrol of plant diseases by Streptomyces is summarized on the basis of classification of fungal and bacterial diseases and secondary metabolites produced by Streptomyces that act on phytopathogenic microorganisms are discussed. The associated non-ribosomal peptide synthetases and polyketide synthetases responsible for biosynthesis of these secondary metabolites are also investigated, and advances in fermentation of Streptomyces are described. Finally, the need to develop precise and effective biocontrol methods for plant diseases is highlighted.

Antifungal Activity Enhancement of Cell-Free Streptomyces griseus Extract Obtained by Fermentation with Magnetic Manganese Ferrite Nanoparticles

The present study aims to obtain manganese ferrite nanoparticles functionalized with chitosan (C-MNP) or ethylenediamine (E-MNP) by coprecipitation and polyol one-step methods, characterize their interaction with S. griseus demonstrating cell immobilization, and evaluate the antimicrobial activity of the free cell extracts obtained from immobilized S. griseus fermentation in the presence of different concentrations of MNP. The adsorption isotherms were analyzed mathematically using Langmuir and Freundlich models. The highest coefficient of determination (R2) for the S. griseus cell adsorption isotherm with C-MNP was observed with a linear function of the Langmuir model. The adsorption isotherm of S. griseus cells with E-MNP was better fitted to the Freundlich model. Cell immobilization by adsorption on magnetic nanoparticles was demonstrated in both cases. Different concentrations of C-MNP and E-MNP were used in fermentations to prepare cell-free extracts with antifungal activity. The best results were obtained with E-MNP, with a 91.5% inhibition of radial fungal growth. Magnetic nanoparticles offer potential applications in different fields and easy biomass separation.

Micromonospora profundi TRM 95458 converts glycerol to a new osmotic compound

Plant growth and agricultural productivity was greatly limited by soil salinity and alkalization. The application of salt-tolerant rhizobacteria could effectively improve plant tolerance to saline-alkali stress. Micromonospora profundi TRM 95458 was obtained from the rhizosphere of chickpea (Cicer arietinum L.) as a moderate salt-tolerant rhizobacteria. A new osmotic compound (ABAGG) was isolated from the fermentation broth of M. profundi TRM 95458. The chemical structure of the new compound was elucidated by analyzing nuclear magnetic resonance (NMR) and high-resolution mass (HRMS) data. M. profundi TRM 95458 could convert glycerol into ABAGG. The accumulation of ABAGG varied depending on the amount of glycerol and glycine added to the fermentation medium. In addition, the concentration of NaCl affected the ABAGG content obviously. The highest yield of ABAGG was observed when the salt content of the fermentation medium was 10 g/L. The study indicated that salt stress led to the accumulation of ABAGG using glycerol and glycine as substrates, suggesting ABAGG might aid in the survival and adaptation of the strain in saline-alkaline environments as a new osmotic compound.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability

Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.

Rahnella aquatilis JZ-GX1 alleviates iron deficiency chlorosis in Cinnamomum camphora by secreting desferrioxamine and reshaping the soil fungal community

Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. Rahnella aquatilis JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in Cinnamomum camphora, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe²⁺ and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of C. camphora, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient C. camphora caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in C. camphora rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe²⁺ contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the C. camphora rhizosphere soil and increased the abundances of specific taxa, such as Glomus, Mortierella, Trichoderma, and Penicillium. Therefore, R. aquatilis JZ-GX1 application promoted iron absorption in C. camphora trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.

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.

Unraveling the tripartite interaction of volatile compounds of Streptomyces rochei with grain mold pathogens infecting sorghum

Sorghum is a major grain crop used in traditional meals and health drinks, and as an efficient fuel. However, its productivity, value, germination, and usability are affected by grain mold, which is a severe problem in sorghum production systems, which reduces the yield of harvested grains for consumer use. The organic approach to the management of the disease is essential and will increase consumer demand. Bioactive molecules like mVOC (volatile organic compound) identification are used to unravel the molecules responsible for antifungal activity. The Streptomyces rochei strain (ASH) has been reported to be a potential antagonist to many pathogens, with high levels of VOCs. The present study aimed to study the inhibitory effect of S. rochei on sorghum grain mold pathogens using a dual culture technique and via the production of microbial volatile organic compounds (mVOCs). mVOCs inhibited the mycelial growth of Fusarium moniliforme by 63.75 and Curvularia lunata by 68.52%. mVOCs suppressed mycelial growth and inhibited the production of spores by altering the structure of mycelia in tripartite plate assay. About 45 mVOCs were profiled when Streptomyces rochei interacted with these two pathogens. In the present study, several compounds were upregulated or downregulated by S. rochei, including 2-methyl-1-butanol, methanoazulene, and cedrene. S. rochei emitted novel terpenoid compounds with peak areas, such as myrcene (1.14%), cymene (6.41%), and ç-terpinene (7.32%) upon interaction with F. moniliforme and C. lunata. The peak area of some of the compounds, including furan 2-methyl (0.70%), benzene (1.84%), 1-butanol, 2-methyl-(8.25%), and myrcene (1.12)%, was increased during tripartite interaction with F. moniliforme and C. lunata, which resulted in furan 2-methyl (6.60%), benzene (4.43%), butanol, 2-methyl (18.67%), and myrcene (1.14%). These metabolites were implicated in the sesquiterpenoid and alkane biosynthetic pathways and the oxalic acid degradation pathway. The present study shows how S. rochei exhibits hyperparasitism, competition, and antibiosis via mVOCs. In addition to their antimicrobial functions, these metabolites could also enhance plant growth.

Streptomyces albidoflavus Strain CARA17 as a Biocontrol Agent against Fungal Soil-Borne Pathogens of Fennel Plants

Fennel crop is a horticultural plant susceptible to several soil-borne fungal pathogens responsible for yield losses. The control of fungal diseases occurring on fennel crops is very difficult with conventional and/or integrated means; although several chemical fungicides are able to contain specific fungal diseases, they are not registered for fennel crops. The intensive use of some fungicides causes public concern over the environment and human health. The main aims of this study were to assess the ability of a strain of Streptomyces albidoflavus CARA17 to inhibit the growth of fungal soil-borne pathogens, and to protect fennel plants against severe fungal soil-borne pathogens such as Athelia rolfsii, Fusarium oxysporum, Plectosphaerella ramiseptata, Sclerotinia sclerotiorum and Verticillium dahliae. This study confirmed that the CARA17 strain has been able to inhibit the mycelium growth of pathogens in vitro conditions with significant inhibition degrees, where S. sclerotiorum resulted in being the most controlled. The strain CARA17 was also able to significantly protect the fennel seedlings against fungal soil-borne pathogens used in vivo conditions, where the treatment with an antagonist strain by dipping resulted in being more effective at limiting the disease severity of each fungal soil-borne pathogen. Moreover, any treatment with the CARA17 strain, carried out by dipping or after transplanting, produced benefits for the biomass of fennel seedlings, showing significant effects as a promoter of plant growth. Finally, the results obtained showed that CARA17 is a valid strain as a biocontrol agent (BCA) against relevant fungal soil-borne pathogens, although further studies are recommended to confirm these preliminary results. Finally, this study allowed for first time worldwide the association of Plectosphaerella ramiseptata with fennel plants as a severe pathogen.

A Salt-Tolerant Streptomyces paradoxus D2-8 from Rhizosphere Soil of Phragmites communis Augments Soybean Tolerance to Soda Saline-Alkali Stress

Soil salinity and alkalization limit plant growth and agricultural productivity worldwide. The application of salt-tolerant plant growth-promoting rhizobacteria (PGPR) effectively improved plant tolerance to saline-alkali stress. To obtain the beneficial actinomyces resources with salt tolerance, thirteen isolates were isolated from rhizosphere saline and alkaline soil of Phragmites communis. Among these isolates, D2-8 was moderately halophilic to NaCl and showed 120 mmol soda saline-alkali solution tolerance. Moreover, the plant growth-promoting test demonstrated that D2-8 produced siderophore, IAA, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and organic acids. D2-8 showed 99.4% homology with the type strain Streptomyces paradoxus NBRC 14887T and shared the same branch, and, therefore, it was designated S. paradoxus D2-8. Its genome was sequenced to gain insight into the mechanism of growth-promoting and saline-alkali tolerance of D2-8. IAA and siderophore biosynthesis pathway, genes encoding ACC deaminase, together with six antibiotics biosynthesis gene clusters with antifungal or antibacterial activity, were identified. The compatible solute ectoine biosynthesis gene cluster, production, and uptake of choline and glycine betaine cluster in the D2-8 genome may contribute to the saline-alkali tolerance of the strain. Furthermore, D2-8 significantly promoted the seedling growth even under soda saline-alkali stress, and seed coating with D2-8 isolate increased by 5.88% of the soybean yield in the field. These results imply its significant potential to improve soybean soda saline-alkali tolerance and promote crop health in alkaline soil.

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.

Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung

A novel growth-promoting and indole acetic acid-producing strain, designated NEAU-LLB^T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, PR China. Cells of strain NEAU-LLB^T were Gram-stain-positive, non-motile, aerobic and non-spore-forming. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LLB^T belonged to the genus Microbacterium. Strain NEAU-LLB^T had high 16S rRNA sequence similarities of 98.81 and 98.41 % to Microbacterium paludicola DSM 16915^T and Microbacterium marinilacus DSM 18904^T, and less than 98 % to other members of the genus Microbacterium. Chemotaxonomic characteristics showed that MK-11 and MK-12 were detected as the predominant menaquinones. The peptidoglycan contained glutamic acid, aspartic acid, glycine, ornithine and a small amount of alanine, with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids were identified as anteiso-C_15 : 0, iso-C_16 : 0 and iso-C_17 : 0. The genomic DNA G+C content of strain NEAU-LLB^T was 70.2 mol%. In addition, the average nucleotide identity values between strain NEAU-LLB^T and its reference strains, M. paludicola DSM 16915^T, M. marinilacus DSM 18904^T and M. album SYSU D8007^T, were found to be 81.1, 79.4 and 78.7 %, respectively, and the level of digital DNA-DNA hybridization between them were 23.8, 22.6 and 21.8 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain NEAU-LLB^T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium stercoris sp. nov is proposed, with NEAU-LLB^T (=CCTCC AA 2018028^T=JCM 32660^T) as the type strain.

Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms

Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil

A novel protease-producing actinobacterium, designated strain NEAU-A11^T, was isolated from soil collected from Aohan banner, Chifeng, Inner Mongolia Autonomous Region, China, and characterised using a polyphasic approach. The hydrolytic enzymes, such as proteases, played critical roles in destruction of fungi by degrading the protein linkages to disrupt integrity in the cell wall. This suggested that the isolate could be a good biocontrol candidate against pathogens to control fungal diseases. On the basis of 16S rRNA gene sequence analysis, strain NEAU-A11^T was indicated to belong to the genus Actinoplanes and was most closely related to Actinoplanes rectilineatus JCM 3194 ^T (98.9%). Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were arabinose, xylose and glucose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. The predominant menaquinones were MK-9(H₄), MK-9(H₆) and MK-9(H₈). The major fatty acids were C_18:0, C_16:0, C_18:1 ω9c, C_17:0 and C_15:0. Genome sequencing revealed a genome size of 10,742,096 bp, a G + C content of 70.5% and 9,514 protein-coding genes (CDS), including 102 genes coding for protease. Moreover, Genome analysis showed that strain NEAU-A11^T contained 255 glycoside hydrolases (GHs), 152 glycosyl transferases (GTs), 40 carbohydrate esterases (CEs), 26 polysaccharide lyases (PLs), and 12 auxiliary activities (AAs) genes. Genome mining analysis using antiSMASH 5.0 led to the identification of 20 putative gene clusters responsible for the production of diverse secondary metabolites. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with A. rectilineatus JCM 3194 ^T in the genus Actinoplanes. Whole-genome phylogeny showed strain NEAU-A11^T formed a stable phyletic line with Actinoplanes lutulentus DSM 45883 ^T (97.6%). However, whole-genome average nucleotide identity value between strain NEAU-A11^T and its reference strains A. rectilineatus JCM 3194 ^T and A. lutulentus DSM 45883 ^T were found to be 81.1% and 81.6%, respectively. The levels of digital DNA-DNA hybridization between them were 24.6% (22.2-27.0%) and 24.8% (22.5-27.3%), respectively. The values were well below the criteria for species delineation of 70% for dDDH and 95-96% for ANI, suggesting that the isolate differed genetically from its closely related type strain. The content of G + C in genomic DNA was 70.5%, within the range of 67-76%. In addition, evidences from phenotypic, chemotaxonomic and genotypic studies indicated that strain NEAU-A11^T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes aureus sp. nov. is proposed, with NEAU-A11^T (= CCTCC AA 2019063 ^T = JCM 33971 ^T) as the type strain.

Isolation, Identification, Biocontrol Activity, and Plant Growth Promoting Capability of a Superior Streptomyces tricolor Strain HM10

Streptomyces is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local Streptomyces species, evaluate their capacity to biocontrol the selected phytopathogens, and promote the plant growth via siderophore and indole acetic acid (IAA) production and phosphate solubilization. Eleven isolates were obtained from local soil samples in Saudi Arabia via the standard serial dilution method and identified morphologically by scanning electron microscope (SEM) and 16S rRNA amplicon sequencing. The biocontrol of phytopathogens was screened against known soil-borne fungi and bacteria. Plant growth promotion capacity was evaluated based on siderophore and IAA production and phosphate solubilization capacity. From eleven isolates obtained, one showed 99.77% homology with the type strain Streptomyces tricolor AS 4.1867, and was designated S. tricolor strain HM10. It showed aerial hyphae in SEM, growth inhibition of ten known phytopathogens in in vitro experiments, and the production of plant growth promoting compounds such as siderophores, IAA, and phosphate solubilization capacity. S. tricolor strain HM10 exhibited high antagonism against the fungi tested (i.e., Colletotrichum gloeosporides with an inhibition zone exceeding 18 mm), whereas the lowest antagonistic effect was against Alternaria solani (an inhibition zone equal to 8 mm). Furthermore, the most efficient siderophore production was recorded to strain HM8, followed by strain HM10 with 64 and 22.56 h/c (halo zone area/colony area), respectively. Concerning IAA production, Streptomyces strain HM10 was the most effective producer with a value of 273.02 μg/ml. An autochthonous strain S. tricolor HM10 should be an important biological agent to control phytopathogens and promote plant growth.

The Impact of Growth-Promoting Streptomycetes Isolated from Rhizosphere and Bulk Soil on Oilseed Rape (Brassica napus L.) Growth Parameters

Inoculation of Streptomyces to improve oilseed rape (Brassica napus L.) yields and minimise the use of chemical fertilisers is a promising sustainable strategy. In this study, we isolated 72 actinobacterial strains from rhizosphere of oilseed rape and maize and from bulk soil for screening and characterising their antimicrobial activity. Nine promising strains, identified as Streptomyces sp. by morphology, physiological characteristics, and 16S rRNA gene sequencing, were selected for their plant growth-promoting traits and in planta experiments. The actinobacterial strains were positive for IAA production, siderophore production, and HCN production. In planta experiments were conducted by soaking the oilseed rape seeds in the actinobacterial suspension, followed by plant growth under controlled conditions in a cultivate chamber (22–28 °C, 8 h dark/16 h light, constant humidity 80%). We recorded root and shoot length (cm) and seedling fresh weight (g). For most of the abovementioned parameters, a significant enhancement was observed with strain KmiRC20A118 treatment. The length of the root increased by 53.14%, the shoot length increased by 65.6%, and the weight of the fresh plant by 60% compared to the control. The integrated application of PGPS (Plant Growth Promoting Streptomyces) from the rhizosphere of oilseed rape is a promising strategy to improve the growth of oilseed rape.

Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin

A novel actinobacterium, designated strain NEAU-HG-1^T, was isolated from soil collected from Harbin, Heilongjiang Province, Northeast China and characterised using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-HG-1^T belonged to the genus Micromonospora, and shared high sequence similarities with Micromonospora auratinigra DSM 44815^T (98.9%) and Micromonospora coerulea DSM 43143^T (98.7%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Micromonospora. Cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The polar lipid contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipid and phosphatidylinositol. The predominant menaquinones were MK-10(H₂), MK-10(H₄) and MK-10(H₆). The major fatty acids were C_17:0 cycle, iso-C_15:0, and iso-C_16:0. Furthermore, strain NEAU-HG-1^T displayed a DNA-DNA relatedness of 33.8 ± 2.2% with M. coerulea DSM 43143^T. The level of digital DNA-DNA hybridization between strain NEAU-HG-1^T and M. auratinigra DSM 44815^T was 27.2% (24.8-29.7%). The value was well below the criteria for species delineation of 70% for dDDH. Whole-genome average nucleotide identity analyses result also indicated that the isolate should be assigned to a new species under the genus Micromonospora. Therefore, it is concluded that strain NEAU-HG-1^T represents a novel species of the genus Micromonospora, for which the name Micromonospora rubida sp. nov. is proposed, with NEAU-HG-1^T (= CGMCC 4.7479^T = JCM 32386^T) as the type strain.

Changes in Bacterial Community Structure and Enriched Functional Bacteria Associated With Turfgrass Monoculture

There is increasing attention being paid to utilizing microbial communities to improve plant health while reducing management inputs. Thus, the objectives of this research were to assess changes in the rhizosphere bacterial community structure associated with long-term turfgrass monoculture and to demonstrate the feasibility of using functional bacteria as beneficial biocontrol agents. Large patch disease, caused by the fungal pathogen Rhizoctonia solani AG2-2, is a significant threat to turfgrass cultivation. Rhizosphere samples were collected from 2-, 13- and 25-year turfgrass (Zoysia japonica) monocultures. The 13-year monoculture field had a higher pathogen population density than both the 2- and 25-year monoculture fields. Analyses of the rhizosphere bacterial communities revealed that Streptomyces was dominant in the 2-year field and Burkholderia was enriched in the 25-year field. Based on the culturable rhizosphere bacteria, Streptomyces neyagawaensis J6 and Burkholderia vietnamiensis J10 were obtained from the 2- and 25-year fields, respectively. Application of S. neyagawaensis J6 and B. vietnamiensis J10 led to excellent inhibition of large patch disease as well as enhanced tolerance against drought and temperature stresses. The results showed that the selected bacteria could be developed as biocontrol and abiotic stress tolerance agents for turfgrass cultivation.

Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond

Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.

Draft genome sequences of two Streptomyces albidoflavus strains DEF1AK and DEF147AK with plant growth-promoting and biocontrol potential

Purpose

Bacteria belonging to the Streptomyces genus can be exploited in environmentally friendly approaches to food safety. Genome information can help to characterize bioactive strains opening the possibility to decipher their mechanisms of action.

Methods

The biocontrol and plant growth-promoting activity of two Streptomyces spp. strains, DEF1AK and DEF147AK, were assessed in vitro and in planta. The genome sequences were determined using the Illumina NextSeq sequencing system and were assembled using EvoCAT (Evogene Clustering and Assembly Toolbox).

Result

Streptomyces spp. DEF1AK and DEF147AK were able to improve seed germination and early plant development of maize, wheat, and tomato and inhibited the mycelium growth of diverse fungal plant pathogens in vitro. The genome sequence analysis identified both strains as S. albidoflavus (99% sequence identity). Both genomes were of 7.1-Mb length with an average GC content of 73.45%. AntiSMASH and MIBiG analyses revealed strain-specific sets of secondary metabolite gene clusters in the two strains as well as differences in the number and type of duplicated genes.

Conclusion

The combination of the biological activity and genomic data is the basis for in-depth studies aimed at the identification of secondary metabolites involved in plant growth-promoting and biocontrol activity of Streptomyces spp. The comparison of unique genomic features of the two strains will help to explain their diverse biocontrol and plant growth-promoting activities and warrant targeted functional genomics approaches to verify their mechanisms of action.

Characterization of a Novel Endophytic Actinomycete, Streptomyces physcomitrii sp. nov., and Its Biocontrol Potential Against Ralstonia solanacearum on Tomato

Bacterial wilt of tomato is a destructive disease caused by Ralstonia solanacearum throughout the world. An endophytic actinomycete with antagonistic activity, designated strain LD120^T, was isolated from moss (Physcomitrium sphaericum (Ludw) Fuernr). The biocontrol test demonstrated that co-inoculation by the isolate and the pathogen gave the greatest biocontrol efficiency of 63.6%. Strain LD120^T had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces. The diamino acid present in the cell wall was LL-diaminopimelic acid. Arabinose, glucose, rhamnose, and ribose occured in whole cell hydrolysates. The menaquinones detected were MK-9(H₄), MK-9(H₆), MK-9(H₈), and MK-9(H₂). The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylinositol. The major cellular fatty acids were found to be iso-C_16:0, iso-C_17:0, anteiso-C_15:0, and C_16:1 ω7c. The DNA G+C content of the draft genome sequence, consisting of 7.6 Mbp, was 73.1%. Analysis of the 16S rRNA gene sequence showed that strain LD120^T belongs to the genus Streptomyces, with the highest sequence similarity to Streptomyces azureus NRRL B-2655^T (98.97%), but phylogenetically clustered with Streptomyces anandii NRRL B-3590^T (98.62%). Multilocus sequence analysis based on five other house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) and the low level of DNA–DNA relatedness, as well as phenotypic differences, allowed strain LD120^T to be differentiated from its closely related strains. Therefore, the strain was concluded to represent a novel species of the genus Streptomyces, for which the name Streptomycesphyscomitrii sp. nov. was proposed. The type strain was LD120^T (=CCTCC AA 2018049^T = DSM 110638^T).

Siderophore production by Bacillus subtilis MF497446 and Pseudomonas koreensis MG209738 and their efficacy in controlling Cephalosporium maydis in maize plant

Late wilt disease, caused by Cephalosporium maydis in maize plant, is one of the main economical diseases in Egypt. Therefore, to cope with this problem, we investigated the potentiality of plant growth promoting rhizobacteria in controlling this disease. Six strains (Bacillus subtilis, B. circulance, B. coagulanse, B. licheniformis, Pseudomonas fluroscence and P. koreensis) were screened for siderophore production, and using dual plate culture method and greenhouse experiment, antagonistic activity against C. maydis was studied. Using two superior strains, single and dual inoculation treatments in maize were applied in field experiment during the 2018 and 2019 seasons. Results indicated that B. subtilis and P. koreensis strains had shown the most qualitative and quantitative assays for siderophore production and antagonistic activities. In greenhouse, the most effective treatments on the pre- and post-emergence damping off as well as growth promotion of maize were T3 treatment (inoculated with B. subtilis), and T8 treatment (inoculated with P. koreensis). In field experiment, T5 treatment (inoculated with a mixture of B. subtilis and P. koreensis) showed significant increases in catalase (CAT), peroxidase (POX) and polyphenol oxidase (PPO) activities, as well as total chlorophyll and carotenoids than control treatments during the two growing seasons. In the same way, the highest effect in reducing infection and increasing the thickness of the sclerenchymatous sheath layer surrounding the vascular bundles in maize stem was observed and these results were a reflection of the increase in yield and yield parameters.

Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential

This study was designed to investigate the cultivable actinobacteria associated with bryophytes and their plant growth promoting ability. Thirteen actinobacteria were isolated and tested for their ability to promote growth of plant in vitro and in planta. All isolates were able to produce IAA and siderophores. Six isolates were identified as members of the genus Micromonospora. Five isolates belonged to the genus Streptomyces and one each of Microbispora and Mycobacterium. Micromonospora sp. CMU55-4 was inoculated to rare moss [Physcomitrium sphaericum (C. Ludw.) Fürnr.] and could increase the amount of carotenoid, fresh weight, and dry weight of this moss. In addition, this strain promoted capsule production, and rescued P. sphaericum’s gametophytes during acclimatization to land. Strain CMU55-4 was identified as Micromonospora chalcea based on whole genome sequence analysis. Its plant growth promoting potential was further characterized through genome mining. The draft genome size was 6.6 Mb (73% GC). The genome contained 5,933 coding sequences. Functional annotation predicted encoded genes essential for siderophore production, phosphate solubilization that enable bacteria to survive under nutrient limited environment. Glycine-betaine accumulation and trehalose biosynthesis also aid plants under drought stress. M. chalcea CMU55-4 also exhibited genes for various carbohydrate metabolic pathways indicating those for efficient utilization of carbohydrates inside plant cells. Additionally, predictive genes for heat shock proteins, cold shock proteins, and oxidative stress such as glutathione biosynthesis were identified. In conclusion, our results demonstrate that bryophytes harbor plant growth promoting actinobacteria. A representative isolate, M. chalcea CMU55-4 promotes the growth of P. sphaericum moss and contains protein coding sequences related to plant growth promoting activities in its genome.