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

Exploring the dynamics of ISR signaling in maize upon seed priming with plant growth promoting actinobacteria isolated from tea rhizosphere of Darjeeling

Plant growth-promoting rhizobacteria (PGPR) offer an eco-friendly alternative to agrochemicals for better plant growth and development. Here, we evaluated the plant growth promotion abilities of actinobacteria isolated from the tea (Camellia sinensis) rhizosphere of Darjeeling, India. 16 S rRNA gene ribotyping of 28 isolates demonstrated the presence of nine different culturable actinobacterial genera. Assessment of the in vitro PGP traits revealed that Micrococcus sp. AB420 exhibited the highest level of phosphate solubilization (i.e., 445 ± 2.1 µg/ml), whereas Kocuria sp. AB429 and Brachybacterium sp. AB440 showed the highest level of siderophore (25.8 ± 0.1%) and IAA production (101.4 ± 0.5 µg/ml), respectively. Biopriming of maize seeds with the individual actinobacterial isolate revealed statistically significant growth in the treated plants compared to controls. Among them, treatment with Paenarthrobacter sp. AB416 and Brachybacterium sp. AB439 exhibited the highest shoot and root length. Biopriming has also triggered significant enzymatic and non-enzymatic antioxidative defense reactions in maize seedlings both locally and systematically, providing a critical insight into their possible role in the reduction of reactive oxygen species (ROS) burden. To better understand the role of actinobacterial isolates in the modulation of plant defense, three selected actinobacterial isolates, AB426 (Brevibacterium sp.), AB427 (Streptomyces sp.), and AB440 (Brachybacterium sp.) were employed to evaluate the dynamics of induced systemic resistance (ISR) in maize. The expression profile of five key genes involved in SA and JA pathways revealed that bio-priming with actinobacteria (Brevibacterium sp. AB426 and Brachybacterium sp. AB440) preferably modulates the JA pathway rather than the SA pathway. The infection studies in bio-primed maize plants resulted in a delay in disease progression by the biotrophic pathogen Ustilago maydis in infected maize plants, suggesting the positive efficacy of bio-priming in aiding plants to cope with biotic stress. Conclusively, this study unravels the intrinsic mechanisms of PGPR-mediated ISR dynamics in bio-primed plants, offering a futuristic application of these microorganisms in the agricultural fields as an eco-friendly alternative.

Identification and Aggressiveness of Fusarium Species Associated with Onion Bulb (Allium cepa L.) during Storage

Plant pathogens present a major challenge to crop production, leading to decreased yield and quality during growth and storage. During long-term storage, healthy onions can develop diseases from latent pathogen infections. This poses a challenge for onion growers because infected bulbs without visible symptoms can lead to significant crop losses during the growing season. In this study, we aimed to isolate and identify Fusarium species from yellow onion bulbs (Allium cepa L.) that developed disease symptoms during storage. The aggressiveness of these strains against onion bulbs and seedlings was also evaluated. The isolated strains were further subjected to morphological and molecular differentiation. The results revealed that all 16 isolated strains belonged to the Fusarium complex species incarnatum-equiseti and Fusarium fujikuroi, namely, F. proliferatum (98%), F. oxysporum (1%), and Fusarium sp. (1%). Koch's postulate analysis of isolated strains revealed varying aggressiveness on onion bulbs and plants depending on fungal species. Disease symptoms developed more slowly on plants than on onion bulb plants according to Koch's postulates. Moreover, the results revealed that Fusarium strains that can infect onion plants were less pathogenic to onion bulbs and vice versa. In addition, three isolates were found to be non-pathogenic to onions. Furthermore, the in vitro control of Fusarium species through Bacillus velezensis KS04-AU and Streptomyces albidoflavus MGMM6 showed high potential for controlling the growth of these pathogenic fungi. These results may contribute to the development of environmentally friendly approaches for controlling onion spoilage caused by pathogens during storage.

Medium Optimization and Fermentation Kinetics for Antifungal Compounds Production by an Endophytic Paenibacillus polymyxa DS-R5 Isolated from Salvia miltiorrhiza

An endophytic bacterium Paenibacillus polymyxa DS-R5 which can effectively inhibit the growth of pathogenic fungi was isolated from Salvia miltiorrhiza in our previous study. By using hydrochloric acid precipitation, methanol extraction, silica gel column isolation, dextran gel chromatography column, and HPLC, 3 compounds with antifungal activity were isolated. To further improve the production of antifungal compounds produced by this strain, fermentation medium was optimized using one-factor-at-a-time, Plackett-Burman design, and Box-Behnken design experiments. Through statistical optimization, the optimal medium composition was determined to be as follows: 14.7 g/l sucrose, 20.0 g/l soluble starch, 7.0 g/l corn steep liquor, 10.0 g/l (NH4)2SO4, and 0.7 g/l KH2PO4. In this optimized medium, the highest titer of antifungal compounds reached 3452 U/ml, which was 123% higher than that in the initial medium. In addition, in order to guide scale-up for production, logistic and Luedeking-Piret equations were proposed to predict the cell growth and antifungal compounds production. The fermentation kinetics and empirical equations of the coefficients (X0, Xm, μm, α, and β) for the two models were reported, which will aid the design and optimization of industrial processes. The degrees of fit between calculated values of the model and the experimental data were 0.989 and 0.973, respectively. The results show that the cell growth and product synthesis models established in this study may better reflect the dynamic process of antifungal compounds production and provide a theoretical basis for further optimization and on-line monitoring of the fermentation process.

Genomic Insights into the Microbial Agent Streptomyces albidoflavus MGMM6 for Various Biotechnology Applications

Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways that have significant biotechnological potential. Genome mining revealed that MGMM6 consists of a linear chromosome of 6,932,303 bp, with a high G+C content of 73.5%, lacking any plasmid contigs. Among the annotated genes, several are predicted to encode enzymes such as dye peroxidase, aromatic ring-opening dioxygenase, multicopper oxidase, cytochrome P450 monooxygenase, and aromatic ring hydroxylating dioxygenases which are responsible for the biodegradation of numerous endogenous and xenobiotic pollutants. In addition, we identified genes associated with heavy metal resistance, such as arsenic, cadmium, mercury, chromium, tellurium, antimony, and bismuth, suggesting the potential of MGMM6 for environmental remediation purposes. The analysis of secondary metabolites revealed the presence of multiple biosynthesis gene clusters responsible for producing compounds with potent antimicrobial and metal-chelating activities. Furthermore, laboratory tests conducted under controlled conditions demonstrated the effectiveness of MGMM6 in inhibiting phytopathogenic microbes, decolorizing and degrading aromatic triphenylmethane dyes, particularly Blue Brilliant G250, from wastewater by up to 98 ± 0.15%. Overall, the results of our study highlight the promising biotechnological potential of S. albidoflavus MGMM6.

Whole genome analysis of Bacillus amyloliquefaciens TA-1, a promising biocontrol agent against Cercospora arachidicola pathogen of early leaf spot in Arachis hypogaea L

BACKGROUND

Early leaf spot disease, caused by Cercospora arachidicola, is a devastating peanut disease that has severely impacted peanut production and quality. Chemical fungicides pollute the environment; however, Bacillus bacteria can be used as an environmentally friendly alternative to chemical fungicides. To understand the novel bacterial strain and unravel its molecular mechanism, De novo whole-genome sequencing emerges as a rapid and efficient omics approach.

RESULTS

In the current study, we identified an antagonistic strain, Bacillus amyloliquefaciens TA-1. In-vitro assay showed that the TA-1 strain was a strong antagonist against C. arachidicola, with an inhibition zone of 88.9 mm. In a greenhouse assay, results showed that the TA-1 strain had a significant biocontrol effect of 95% on peanut early leaf spot disease. De novo whole-genome sequencing analysis, shows that strain TA-1 has a single circular chromosome with 4172 protein-coding genes and a 45.91% guanine and cytosine (GC) content. Gene function was annotated using non-redundant proteins from the National Center for Biotechnology Information (NCBI), Swiss-Prot, the Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups of proteins, gene ontology, pathogen-host interactions, and carbohydrate-active enZYmes. antiSMASH analysis predicted that strain TA-1 can produce the secondary metabolites siderophore, tailcyclized peptide, myxochelin, bacillibactin, paenibactin, myxochelin, griseobactin, benarthin, tailcyclized, and samylocyclicin.

CONCLUSION

The strain TA-1 had a significant biological control effect against peanut early leaf spot disease in-vitro and in greenhouse assays. Whole genome analysis revealed that, TA-1 strain belongs to B. amyloliquefaciens and could produce the antifungal secondary metabolites.

Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide

Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430T (99.72%) and Streptomyces polychromogenes NBRC 13072T (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC50) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.

Plant-beneficial Streptomyces dioscori SF1 potential biocontrol and plant growth promotion in saline soil within the arid and semi-arid areas

Environmental challenges like salinity, drought, fungal phytopathogens, and pesticides directly or/and indirectly influence the environment and agricultural yields. Certain beneficial endophytic Streptomyces sp. can ameliorate environmental stresses and be utilized as crop growth promoters under adverse conditions. Herein, Streptomyces dioscori SF1 (SF1) isolated from seeds of Glycyrrhiza uralensis tolerated fungal phytopathogens and abiotic stresses (drought, salt, and acid base). Strain SF1 showed multifarious plant growth promotion characteristics, including the production of indole acetic acid (IAA), ammonia, siderophores, ACC deaminase, extracellular enzymes, the ability of potassium solubilization, and nitrogen fixation. The dual plate assay showed that strain SF1 inhibited 63.21 ± 1.53%, 64.84 ± 1.35%, and 74.19 ± 2.88% of Rhizoctonia solani, Fusarium acuminatum, and Sclerotinia sclerotiorum, respectively. The detached root assays showed that strain SF1 significantly reduced the number of rotten sliced roots, and the biological control effect on sliced roots of Angelica sinensis, Astragalus membranaceus, and Codonopsis pilosula was 93.33%, 86.67%, and 73.33%, respectively. Furthermore, the strain SF1 significantly increased the growth parameters and biochemical indicators of adversity in G. uralensis seedlings under drought and/or salt conditions, including radicle length and diameter, hypocotyl length and diameter, dry weight, seedling vigor index, antioxidant enzyme activity, and non-enzymatic antioxidant content. In conclusion, the strain SF1 can be used to develop environmental protection biological control agents, improve the anti-disease activity of plants, and promote plant growth in salinity soil within arid and semi-arid regions.

Stress-Resistance and Growth-Promoting Characteristics and Effects on Vegetable Seed Germination of Streptomyces sp. Strains Isolated from Wetland Plant Rhizospheres

Wetlands are the most biologically diverse ecosystems on Earth. The isolation of Streptomyces strains from wetlands is helpful to study their diversity and functions in such habitats. In this study, six strains of Streptomyces were isolated from the rhizosphere soil of three plant species in the Huaxi Wetland at Guiyang and were identified as Streptomyces galilaeus, S. avidinii, S. albogriseolus, S. albidoflavus, S. spororaveus, and S. cellulosae, respectively. The six strains all solubilized phosphate, fixed nitrogen, and produced ACC deaminase and siderophores, and four strains also secreted indole-3-acetic acid. The six strains had the ability to resist to certain degrees of salinity, drought, and acidic/alkaline pH stress. In addition, the S. avidinii WL3 and S. cellulosae WL9 strains significantly promoted seed germination of mung bean, pepper, and cucumber, especially the WL3 strain. A pot experiment further showed that WL3 significantly promoted the growth of cucumber seedlings. Thus, strains of six species of Streptomyces with multiple plant growth-promoting characteristics were isolated from the wetland. These results lay a foundation for their potential use as microbial agents for seed-coating treatments.

Bacillus paralicheniformis RP01 Enhances the Expression of Growth-Related Genes in Cotton and Promotes Plant Growth by Altering Microbiota inside and outside the Root

Plant growth-promoting bacteria (PGPB) can promote plant growth in various ways, allowing PGPB to replace chemical fertilizers to avoid environmental pollution. PGPB is also used for bioremediation and in plant pathogen control. The isolation and evaluation of PGPB are essential not only for practical applications, but also for basic research. Currently, the known PGPB strains are limited, and their functions are not fully understood. Therefore, the growth-promoting mechanism needs to be further explored and improved. The Bacillus paralicheniformis RP01 strain with beneficial growth-promoting activity was screened from the root surface of Brassica chinensis using a phosphate-solubilizing medium. RP01 inoculation significantly increased plant root length and brassinosteroid content and upregulated the expression of growth-related genes. Simultaneously, it increased the number of beneficial bacteria that promoted plant growth and reduced the number of detrimental bacteria. The genome annotation findings also revealed that RP01 possesses a variety of growth-promoting mechanisms and a tremendous growth-promoting potential. This study isolated a highly potential PGPB and elucidated its possible direct and indirect growth-promoting mechanisms. Our study results will help enrich the PGPB library and provide a reference for plant-microbe interactions.

Streptomyces beihaiensis sp. nov., a chitin-degrading actinobacterium, isolated from shrimp pond soil

A Gram-stain-positive actinobacterium, designated strain GXMU-J5^T, was isolated from a sample of shrimp pond soil collected in Tieshangang Saltern, Beihai, PR China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. The organism formed an extensively branched substrate mycelium, with abundant aerial hyphae that differentiated into spores. Phylogenetic analysis of 16S rRNA gene sequences showed that strain GXMU-J5^T was most related to Streptomyces kunmingensis DSM 41681^T (similarity 97.74 %) and Streptomyces endophyticus YIM 65594^T (similarity 96.80 %). However, the values of digital DNA-DNA hybridization, average nucleotide identity and evolutionary distance of multilocus sequence analysis between strain GXMU-J5^T and its closest relatives indicated that it represented a distinct species. Strain GXMU-J5^T contained ll-diaminopimelic acid and the major whole-cell hydrolysates were xylose and galactose. The predominant menaquinones of strain GXMU-J5^T were revealed as MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The predominant cellular fatty acids were iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16 : 0, iso-C_17 : 0 and anteiso-C_17 : 0. The whole genome size of strain GXMU-J5^T was 6.79 Mbp with a 71.39 mol% G+C content. Genomic analysis indicated that strain GXMU-J5^T had the potential to degrade chitin. On the basis of these genotypic and phenotypic data, it is supported that strain GXMU-J5^T represents a novel species of the genus Streptomyces, for which the name Streptomyces beihaiensis sp. nov. is proposed. The type strain is strain GXMU-J5^T (=MCCC 1K08064^T=JCM 35629^T).

Diversity of actinomycete and their metabolites isolated from Howz Soltan Lake, Iran

Saline environments are largely unexplored sources of actinomycetes with the potential to produce biologically active secondary metabolites. A total of 34 actinomycete isolates from water, sediments and mostly rhizosphere (82%) were collected from different sites at Howz Soltan Lake in Iran. Based on phylogenetic analysis, the isolates belonged to the genera Streptomyces, Nocardia and Saccharomonospora. Cytotoxic assay revealed extract from isolate act9 as the most potent (19.716±5.72 µg/ml) against the MDA-MB-231 human breast cancer cell. Also, 38% of the isolates showed antimicrobial activity against some of the test microorganisms. The ethyl-acetate extract of isolate act18 showed the strongest antibacterial effect against Staphylococcus aureus and MRSA, and was further analyzed by GC/MS. Ar-tumerone (26.41%) and butyl isodecyl phthalate (21.77 %) were the main constituents detected in the extract. This is the first time Ar-tumerone is being detected in a prokaryote. Isolate act18 showed a high 16S rRNA sequence similarity to that of Streptomyces youssoufiensis DSM 41920. In addition, a number of the isolates produced different enzymes including lipase, amylase, protease, gelatinase, urease and lecithinase. Some of the isolates belonging to the genera Streptomyces and Nocardia exhibited plant growth promoting activity such as increased seed germination, stem length and the number of Echium leaves during the 20 days. Findings from this study indicated the diversity and biosynthetic potential of actinomycetes from saline environment.

Screening, and Optimization of Fermentation Medium to Produce Secondary Metabolites from Bacillus amyloliquefaciens, for the Biocontrol of Early Leaf Spot Disease, and Growth Promoting Effects on Peanut (Arachis hypogaea L.)

A novel Bacillus amyloliquefaciens BAM strain, with novel fermentation nutrient mediums and compositions, could produce potent antifungal secondary metabolites, as the existing strains face resistance from fungus pathogens. In the current study, we introduced two novel nutrient mediums for the fermentation process, semolina and peanut root extract, as carbon and nitrogen sources in order to maximize the antifungal effects of B. amyloliquefaciens against Cercaspora arachidichola to control early leaf spot disease in peanuts. Based on a single-factor test and the central composite design of response surface methodology, the optimum fermentation medium for Bacillus amyloliquefaciens antagonistic substance was determined, containing 15 gm/L of semolina flour, 12.5 gm/L of beef extract, and 0.5 gm/L of magnesium sulfate, which inhibited the fungal growth by 91%. In vitro, antagonistic activity showed that the fermentation broth of B. amyloliquefaciens BAM with the optimized medium formulation had an inhibition rate of (92.62 ± 2.07)% on the growth of C. arachidichola. Disease control effects in pot experiments show that the pre-infection spray of B. amyloliquefaciens BAM broth had significant efficiency of (92.00 ± 3.79)% in comparison to post-infection spray. B. amyloliquefaciens BAM broth significantly promoted peanut plant growth and physiological parameters and reduced the biotic stress of C. archidechola. Studies revealed that B. amyloliquefaciens BAM with a novel fermentation formulation could be an ideal biocontrol and biofertilizer agent and help in early disease management of early leaf spots in peanuts.