Cyclic Dipeptides from Bacillus vallismortis BS07 Require Key Components of Plant Immunity to Induce Disease Resistance in Arabidopsis against Pseudomonas Infection

Metabolic Comparison and Molecular Networking of Antimicrobials in Streptomyces Species

Streptomyces are well-known for producing bioactive secondary metabolites, with numerous antimicrobials essential to fight against infectious diseases. Globally, multidrug-resistant (MDR) microorganisms significantly challenge human and veterinary diseases. To tackle this issue, there is an urgent need for alternative antimicrobials. In the search for potent agents, we have isolated four Streptomyces species PC1, BT1, BT2, and BT3 from soils collected from various geographical regions of the Himalayan country Nepal, which were then identified based on morphology and 16S rRNA gene sequencing. The relationship of soil microbes with different Streptomyces species has been shown in phylogenetic trees. Antimicrobial potency of isolates was carried out against Staphylococcus aureus American Type Culture Collection (ATCC) 43300, Shigella sonnei ATCC 25931, Salmonella typhi ATCC 14028, Klebsiella pneumoniae ATCC 700603, and Escherichia coli ATCC 25922. Among them, Streptomyces species PC1 showed the highest zone of inhibition against tested pathogens. Furthermore, ethyl acetate extracts of shake flask fermentation of these Streptomyces strains were subjected to liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis for their metabolic comparison and Global Natural Products Social Molecular Networking (GNPS) web-based molecular networking. We found very similar metabolite composition in four strains, despite their geographical variation. In addition, we have identified thirty-seven metabolites using LC-MS/MS analysis, with the majority belonging to the diketopiperazine class. Among these, to the best of our knowledge, four metabolites, namely cyclo-(Ile-Ser), 2-n-hexyl-5-n-propylresorcinol, 3-[(6-methylpyrazin-2-yl) methyl]-1H-indole, and cyclo-(d-Leu-l-Trp), were detected for the first time in Streptomyces species. Besides these, other 23 metabolites including surfactin B, surfactin C, surfactin D, and valinomycin were identified with the help of GNPS-based molecular networking.

Inhibitory effects of Bacillus vallismortis T27 against apple Valsa canker caused by Valsa mali

Apple Valsa canker caused by the pathogenic fungus Valsa mali, are one of the most destructive diseases of woody plants worldwide. One rhizosphere microbe strain, designated as T27 and subsequently identified as Bacillus vallismortis based on morphological and phylogenetic analyses, was studied as a potential biocontrol agent. Inoculation assay showed the B. vallismortis T27 suppressed the mycelial growth of V. mali with 81.33% antifungal effect on dual culture plates and caused hyphal deformities, wrinkles. The T27 fermentation broth significantly suppress the fungi's ability to acidify the surrounding environment. The addition of T27 cell-free supernatant (CFS) caused the pH of the fungal culture medium to increase from 3.60 to 5.10. B. vallismortis T27 showed the presence of Surfactin, IturinA and Bacilysin antimicrobial biosynthetic genes by the PCR assay. In addition, the B. vallismortis T27 was able to promote plant growth by producing siderophores and solubilizing phosphorus. The application of 2% fermentation broth of T27 resulted in a significant increase of 55.99% in the height of tomato plants and a 33.03% increase in the fresh weight of tomatoes. Under laboratory and field conditions, the B. vallismortis T27 exhibited strong antifungal activities on detached twigs and intact plants. The treatment of T27 resulted in a 35.9% reduction in lesion area on detached twigs. Furthermore, when applied to intact plants, T27 demonstrated a scar healing rate of 85.7%, surpassing the 77.8% observed in the treatment with tebuconazole. Comparative transcriptome analysis showed down-regulation of the genes associated with the fungal cell wall and cell membrane's synthesis and composition during V. mali treated with the B. vallismortis T27. In addition, gene transcription level analysis under treatment with B. vallismortis T27 revealed a significant increase in the expression levels of genes associated with diterpene biosynthesis, alanine, aspartic acid and glutamate metabolism, and plant hormone signaling in the apple, consistent with qRT-PCR and RNA-seq results. In this study, B. vallismortis T27 isolated from rhizosphere soil and identified as a novel biological control agent against apple Valsa canker. It exhibited effectively control over Valsa canker through multiple mechanisms, including disrupting the fungal cell membrane structure, altering the fungal growth environment, activating the plant MAPK pathway, and inducing upregulation of plant terpene biosynthetic genes. These findings highlight the potential of B. vallismortis T27 as a promising and multifaceted approach for managing apple Valsa canker.

Implications of Below-Ground Allelopathic Interactions of Camelina sativa and Microorganisms for Phosphate Availability and Habitat Maintenance

Toxic breakdown products of young Camelina sativa (L.) Crantz, glucosinolates can eliminate microorganisms in the soil. Since microorganisms are essential for phosphate cycling, only insensitive microorganisms with phosphate-solubilizing activity can improve C. sativa's phosphate supply. In this study, 33P-labeled phosphate, inductively coupled plasma mass spectrometry and pot experiments unveiled that not only Trichoderma viride and Pseudomonas laurentiana used as phosphate-solubilizing inoculants, but also intrinsic soil microorganisms, including Penicillium aurantiogriseum, and the assemblies of root-colonizing microorganisms solubilized as well phosphate from apatite, trigger off competitive behavior between the organisms. Driving factors in the competitiveness are plant and microbial secondary metabolites, while glucosinolates of Camelina and their breakdown products are regarded as key compounds that inhibit the pathogen P. aurantiogriseum, but also seem to impede root colonization of T. viride. On the other hand, fungal diketopiperazine combined with glucosinolates is fatal to Camelina. The results may contribute to explain the contradictory effects of phosphate-solubilizing microorganisms when used as biofertilizers. Further studies will elucidate impacts of released secondary metabolites on coexisting microorganisms and plants under different environmental conditions.

Draft Genome Sequence of Bacillus vallismortis Strain BL01, Isolated from Artemisia lerchiana Web. Roots

Some strains of Bacillus vallismortis have been reported to be efficient plant-growth-promoting bacteria as well as inducers of systemic resistance. Here, we report the draft genome sequence of Bacillus vallismortis strain BL01, isolated from the roots of Artemisia lerchiana Web.

Bacterial cyclodipeptides elicit Arabidopsis thaliana immune responses reducing the pathogenic effects of Pseudomonas aeruginosa PAO1 strains on plant development

Plants being sessile organisms are exposed to various biotic and abiotic factors, thus causing stress. The Pseudomonas aeruginosa bacterium is an opportunistic pathogen for animals, insects, and plants. Direct exposure of Arabidopsis thaliana to the P. aeruginosa PAO1 strain induces plant death by producing a wide variety of virulence factors, which are regulated mainly by quorum sensing systems. Besides virulence factors, P. aeruginosa PAO1 also produces cyclodipeptides (CDPs), which possess auxin-like activity and promote plant growth through activation of the target of the rapamycin (AtTOR) pathway. On the other hand, plant defense mechanisms are regulated through the production of phytohormones, such as salicylic acid (SA) and jasmonic acid (JA), which are induced in response to pathogen-associated molecular patterns (PAMPs), activating defense genes associated with SA and JA such as PATHOGENESIS-RELATED-1 (PR-1) and LIPOXYGENASE2 (LOX2), respectively. PR proteins are suggested to play critical roles in coordinating the Systemic Acquired Resistance (SAR). In contrast, LOX proteins (LOX2, LOX3, and LOX4) have been associated with the production of JA by producing its precursors, oxylipins. The activation of defense mechanisms involves signaling cascades such as Mitogen-Activated Protein Kinases (MAPKs) or the TOR pathway as a switch for re-directing energy towards defense or growth. In this work, we challenged A. thaliana (wild type, mpk6 or mpk3 mutants, and overexpressing TOR) seedlings with P. aeruginosa PAO1 strains to identify the role of bacterial CDPs in the plant immune response. Results showed that the pre-exposure of these Arabidopsis seedlings to CDPs significantly reduced plant infection of the pathogenic P. aeruginosa PAO1 strains, indicating that plants that over-express AtTOR or lack MPK3/MPK6 protein-kinases are more susceptible to the pathogenic effects. In addition, CDPs induced the GUS activity only in the LOX2::GUS plants, indicative of JA-signaling activation. Our findings indicate that the CDPs are molecules that trigger SA-independent and JA-dependent defense responses in A. thaliana; hence, bacterial CDPs may be considered elicitors of the Arabidopsis immune response to pathogens.

Plant-beneficial functions and interactions of Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 in co-culture by transcriptomics analysis

The development of mixed microbial agents can reduce the use of pesticides and fertilizers in agriculture. However, most previous studies focused only on the overall effects of mixed microbial agents and ignored the interactions between bacteria in mixed systems. In this study, Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 were used to explore the interactions between two different functional plant growth-promoting rhizobacteria (PGPR). The plant growth-promotion properties and inhibition rate of Rhizoctonia solani were determined, and the mechanism of the interactions under single and co-culture conditions was elucidated via transcriptomics analysis under single and co-culture conditions. Results showed that the co-culture was not conducive to B. subtilis SL-44 growth. Furthermore, the differentially expressed genes related to B. subtilis SL-44 developmental process and cell differentiation were downregulated by 82.7% and 84.8% respectively. Moreover, among the properties, only siderophore production by the mixed culture was higher than that of single cultures because of the upregulation of the siderophore-related genes of B. subtilis SL-44. In addition, results revealed the altruistic relationship between the two strains, and the chemical and non-chemical signals of their interaction. This study provides unique insights into PGPR interactions and offers guidance for the development and application of mixed microbial agents.

Isolation and identification of induced systemic resistance determinants from Bacillus simplex Sneb545 against Heterodera glycines

Heterodera glycines is one of the most destructive pathogens of soybean. Soybean seeds coated with Bacillus simplex Sneb545 have shown resistance to H. glycines as a result of induced systemic resistance (ISR) in the plants. In this study, we aimed to identify the resistance-inducing determinants from this B. simplex strain. Combining the ISR bioassay, six ISR-active compounds were isolated from a culture of B. simplex Sneb545 using organic solvent gradient extraction, silica gel column chromatography, Sephadex LH-20 column chromatography, and semi-preparative high-performance liquid chromatography (HPLC), and all systems were based on activity tracking. The compounds were determined as cyclic(Pro-Tyr), cyclic(Val-Pro), cyclic(Leu-Pro), uracil, phenylalanine, and tryptophan using 1H NMR and 13C NMR. In plants from seeds coated with Bacillus simplex Sneb545, these six ISR-active compounds delayed the development of H. glycines in soybean roots. Moreover, cyclic(Pro-Tyr), cyclic(Val-Pro), and tryptophan reduced the number of nematodes in soybean roots. The expression levels of defense-related genes with cyclic(Val-Pro), tryptophan and uracil treatment soybean analysed using Quantitative real-time PCR (qRT-PCR). The results indicate cyclic(Val-Pro), tryptophan and uracil induced the expression of defense-related genes involved in the SA- and JA-pathways to against H. glycines. Our research results provide new agents for the control of H. glycines.

Structural Identification, Synthesis and Biological Activity of Two Volatile Cyclic Dipeptides in a Terrestrial Vertebrate

Single substances within complex vertebrate chemical signals could be physiologically or behaviourally active. However, the vast diversity in chemical structure, physical properties and molecular size of semiochemicals makes identifying pheromonally active compounds no easy task. Here, we identified two volatile cyclic dipeptides, cyclo(L-Leu-L-Pro) and cyclo(L-Pro-L-Pro), from the complex mixture of a chemical signal in terrestrial vertebrates (lizard genus Sceloporus), synthesised one of them and investigated their biological activity in male intra-specific communication. In a series of behavioural trials, lizards performed more chemosensory behaviour (tongue flicks, lip smacks and substrate lickings) when presented with the synthesised cyclo(L-Pro-L-Pro) chemical blend, compared to the controls, the cyclo(L-Leu-L-Pro) blend, or a combined blend with both cyclic dipeptides. The results suggest a potential semiochemical role of cyclo(L-Pro-L-Pro) and a modulating effect of cyclo(L-Leu-L-Pro) that may depend on the relative concentration of both compounds in the chemical signal. In addition, our results stress how minor compounds in complex mixtures can produce a meaningful behavioural response, how small differences in structural design are crucial for biological activity, and highlight the need for more studies to determine the complete functional landscape of biologically relevant compounds.

A Diketopiperazine, Cyclo-(L-Pro-L-Ile), Derived From Bacillus thuringiensis JCK-1233 Controls Pine Wilt Disease by Elicitation of Moderate Hypersensitive Reaction

Pine wilt disease (PWD) caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus is one of the devastating diseases affecting pine forests worldwide. Although effective control measurements are still missing, induction of resistance could represent a possible eco-friendly alternative. In this study, induced resistance-based in vitro and in vivo screening tests were carried out for selection of bacteria with the ability to suppress PWD. Out of 504 isolated bacteria, Bacillus thuringiensis JCK-1233 was selected for its ability to boost pathogenesis-related 1 (PR1) gene expression, a marker of systemic acquired resistance. Moreover, treatment of pine seedlings with B. thuringiensis JCK-1233 resulted in increased expression of other defense-related genes, and significantly inhibited PWD development under greenhouse conditions. However, B. thuringiensis JCK-1233 showed no direct nematicidal activity against B. xylophilus. To identify the effective compound responsible for the induction of resistance in B. thuringiensis JCK-1233, several diketopiperazines (DPKs) including cyclo-(D-Pro-L-Val), cyclo-(L-Pro-L-Ile), cyclo-(L-Pro-L-Phe), and cyclo-(L-Leu-L-Val) were isolated and tested. Foliar treatment of pine seedlings with Cyclo-(L-Pro-L-Ile) resulted in suppression of PWD severity and increased the expression of defense-related genes similarly to B. thuringiensis JCK-1233 treatment. Interestingly, treatment with B. thuringiensis JCK-1233 or cyclo-(L-Pro-L-Ile) showed moderately enhanced expression of PR-1, PR-2, PR-3, PR-4, PR-5, and PR-9 genes following inoculation with PWN compared to that in the untreated control, indicating that they mitigated the burst of hypersensitive reaction in susceptible pine seedlings. In contrast, they significantly increased the expression levels of PR-6 and PR-10 before PWN inoculation. In conclusion, foliar spraying with either B. thuringiensis JCK-1233 culture suspension or DPKs could induce resistance in pine seedlings, thereby alleviating the serious damage by PWD. Taken together, this study supports aerial spraying with eco-friendly biotic or abiotic agents as a valuable strategy that may mark an epoch for the control of PWD in pine forests.

Comparison of Microbial Community Structure in Kiwifruit Pollens

Flowers of kiwifruit are morphologically hermaphroditic and survivable binucleate pollen is produced by the male flowers. In this study, we investigated microbial diversity in kiwifruit pollens by analyzing amplicon sequences of 16S rRNA. Four pollen samples were collected: 'NZ' was imported from New Zealand, 'CN' from China in year of 2014, respectively. 'KR13' and 'KR14' were collected in 2013' and 2014' in South Korea. Most of the identified bacterial phyla in the four different pollens were Proteobacteria, Actinobacteria and Firmicutes. However, the imported and the domestic pollen samples showed different aspects of microbial community structures. The domestic pollens had more diverse in diversity than the imported samples. Among top 20 OTUs, Pseudomonas spp. was the most dominant specie. Interestingly, a bacterial pathogen of kiwifruit canker, Pseudomonas syringae pv. actinidiae was detected in 'NZ' by the specific PCR. This study provides insights microbial distribution and community structure information in kiwifruit pollen.

Seed defense biopriming with bacterial cyclodipeptides triggers immunity in cucumber and pepper

Seed priming is to expose seeds to specific compounds to enhance seed germination. Few studies of plant immune activation through seed priming have been conducted. Here, we introduce an emerging technology that combines seed priming with elicitation of plant immunity using biologically active compounds. This technology is named 'seed defense biopriming' (SDB). We prepared heat-stable metabolites from 1,825 root-associated Bacillus spp. isolated from the rhizosphere in South Korea. These preparations were tested for their ability to induce SDB in cucumber and pepper seeds and trigger plant immunity. SDB with heat-stable metabolites of the selected Bacillus gaemokensis strain PB69 significantly reduced subsequent bacterial diseases under in vitro and field conditions and increased fruit yield. Transcriptional analysis of induced resistance marker genes confirmed the upregulation of salicylic acid, ethylene, and jasmonic acid signaling. Mortality of the insect pest Spodoptera litura increased when larvae fed on SDB-treated cucumber tissues. Analysis of the causative bacterial metabolites identified a leucine-proline cyclodipeptide and a commercially obtained leucine-proline cyclodipeptide induced similar results as treatment with the bacterial preparation. Our results indicate that SDB treatment with the heat-stable bacterial metabolite effectively elicited immunity and controlled disease in seedlings to whole plants, thereby increasing yield even under field conditions.