Field efficacy of nonpathogenic Streptomyces species against potato common scab

Discovery and Biosynthesis of Streptolateritic Acids A-D: Acyclic Pentacarboxylic Acids from Streptomyces sp. FXJ1.172 with Promising Activity against Potato Common Scab

Potato common scab (PCS) is a widespread plant disease that lacks effective control measures. Using a small molecule elicitor, we activate the production of a novel class of polyketide antibiotics, streptolateritic acids A-D, in Streptomyces sp. FXJ1.172. These compounds show a promising control efficacy against PCS and an unusual acyclic pentacarboxylic acid structure. A gene cluster encoding a type I modular polyketide synthase is identified to be responsible for the biosynthesis of these metabolites. A cytochrome P450 (CYP) and an aldehyde dehydrogenase (ADH) encoded by two genes in the cluster are proposed to catalyze iterative oxidation of the starter-unit-derived methyl group and three of six branching methyl groups to carboxylic acids during chain assembly. Our findings highlight how activation of silent biosynthetic gene clusters can be employed to discover completely new natural product classes able to combat PCS and new types of modular polyketide synthase-based biosynthetic machinery.

Biological control of potato common scab and growth promotion of potato by Bacillus velezensis Y6

Potato common scab, caused mainly by Streptomyces scabies, causes surface necrosis and reduces the economic value of potato tubers, but effective chemical control is still lacking. In this study, an attempt was made to control potato common scab by inoculating potatoes with Bacillus velezensis (B. velezensis) and to further investigate the mechanism of biological control. The results showed that B. velezensis Y6 could reduce the disease severity of potato common scab from 49.92 ± 25.74% [inoculated with Streptomyces scabies (S. scabies) only] to 5.56 ± 1.89% (inoculated with S. scabies and Y6 on the same day) and increase the potato yield by 37.32% compared with the control under pot experiment in this study. Moreover, in the field trial, it was found that Y6 could also significantly reduce disease severity from 13.20 ± 1.00% to 4.00 ± 0.70% and increase the potato yield from 2.07 ± 0.10 ton/mu to 2.87 ± 0.28 ton/mu (p < 0.01; Tukey's test). Furthermore, RNA-seq analysis indicated that 256 potato genes were upregulated and 183 potato genes were downregulated in response to B. velezensis Y6 inoculation. In addition, strain Y6 was found to induce the expression of plant growth-related genes in potato, including cell wall organization, biogenesis, brassinosteroid biosynthesis, and plant hormone transduction genes, by 1.01-4.29 times. As well as up-regulate hydroquinone metabolism-related genes and several transcription factors (bHLH, MYB, and NAC) by 1.13-4.21 times. In summary, our study will help to understand the molecular mechanism of biological control of potato common scab and improve potato yield.

Biocontrol Effect of Bacillus subtilis YPS-32 on Potato Common Scab and Its Complete Genome Sequence Analysis

Potato common scab is caused by Streptomyces, which resides in soil and has become a serious disease in potato planting areas worldwide. In this study, we obtained a Bacillus subtilis YPS-32 strain by natural screening, and atmospheric and room-temperature plasma (ARTP) mutagenesis and field trial results showed that B. subtilis YPS-32 has a control efficacy of 83.70% against potato common scab. The complete genome of B. subtilis YPS-32 was sequenced, and multiple genes related to the synthesis of antibiotics and plant growth promoters were detected. Based on the genomic information for B. subtilis YPS-32, the sfp gene-inactivated (related to the synthesis of secondary metabolites) mutant strain B. subtilis YPS-32Δsfp was constructed. Analysis of crude extract metabolites using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) techniques revealed that strain YPS-32 encodes antagonists, such as surfactin and fengycin, which have antimicrobial effects. This study clarifies the mode of action by which B. subtilis YPS-32 antagonizes Streptomyces scabies and provides a reference for further research on antibacterial genes in the future.

Plant Natural Products as Antimicrobials for Control of Streptomyces scabies: A Causative Agent of the Common Scab Disease

The common scab disease caused by Streptomyces scabies, a soil-dwelling Gram-positive bacterium, is an economically important disease of potatoes and other tuber crops. The lack of effective treatments against this disease accounts for large economic losses globally. Plant extracts were screened to find several that effectively inhibited Streptomyces scabies growth in culture. Seven tinctures showed the greatest inhibition of S. scabies growth by reducing pathogen growth in culture by 75% or more. These extracts were myrrh, garlic, cayenne, barberry, frankincense, wild indigo root, and lavender. Myrrh extract from Commiphora myrrha, a resin made from tree sap, showed strong antibacterial activity by reducing the growth of S. scabies to 13% of the control. Additionally, a flavonoid library was screened to identify several compounds that were effective to control the pathogen growth. The flavonoids that showed the greatest inhibition of Streptomyces scabies growth were sophoraflavanone G, jaceosidin, baicalein, and quercetin. Minimum inhibitory concentrations for the effective flavonoids were calculated to be 6.8 ± 0.4 μM, 100.0 ± 2.1 μM, 202.9 ± 5.3 μM, and 285.2 ± 6.8 μM, respectively. The mean lethal doses for these flavonoids against Streptomyces scabies were 2.0 ± 0.1 μM, 22.6 ± 0.5 μM, 52.9 ± 1.3 μM, and 37.8 ± 1.0 μM, respectively. A live/dead assay showed complete cell death in the presence of sophoraflavanone G indicative of a bactericidal mechanism for flavonoid action on Streptomyces scabies. Scanning electron and transmission electron microscopy imaging showed damaged cell membrane morphologies when Streptomyces scabies was exposed to these flavonoids. Mycelia appeared as flat and deflated structures with contents seen as spewing from branching hyphae with numerous holes and tears in the membrane structure indicative of cell death. Sophoraflavanone G showed the greatest potency and potential as a natural antibiotic from the library of tested flavonoids. These results suggest that these plant compounds act on the pathogen through a bactericidal mechanism involving cell membrane destabilization and disruption leading to cell death.

Bioactive Streptomycetes from Isolation to Applications: A Tasmanian Potato Farm Example

The genus Streptomyces constitutes approximately 50% of all soil actinomycetes, playing a significant role in the soil microbial community through vital functions including nutrient cycling, production of bioactive metabolites, disease-suppression and plant growth promotion. Streptomyces produce many bioactive compounds and are prime targets for industrial and biotechnological applications. In addition to their agrobiological roles, some Streptomyces spp. can, however, be phytopathogenic, examples include, common scab of potato that causes economic losses worldwide. Currently used chemical control measures can have detrimental effect to environmental and human health as a result alternative methods to chemical disease control are being investigated. One alternative is the use of streptomycete specific phages to remove this pathogenic bacterium before it can cause the disease on potatoes. However, due to co-existence of non-common scab-causing species belonging to the genus Streptomyces, phage treatment is likely to affect a wide range of non-target streptomycete species including the beneficial ones in the soil. Therefore, before such treatment starts the host range of the phages within the targeted family of bacteria should be determined. In a study conducted using soil samples from a Tasmanian potato farm, streptomycetes were isolated and tested against streptomycete-specific phages. Their antifungal activity was also determined using multiple assays against selected phytopathogens. The four strongest antifungal activity-displaying isolates were further tested for their persistent antifungal activity using wheat and Fusarium solani in a pot trial. A second pot trial was also conducted to evaluate whether the beneficial streptomycetes were affected by streptophage treatment and whether their removal via the phage battery would cause opportunistic fungal infections to plants in soil. The streptomycetes prevented the reduction in wheat shoot weight caused by F. solani indicating their disease suppressive effect. However, when phages were added into the pots, the growth of wheat was detrimentally impacted. This finding might suggest that the reduced presence of antifungal streptomycetes via phage-induced lysis might encourage opportunistic fungal infections in plants.

Development of Anti-Virulence Therapeutics against Mono-ADP-Ribosyltransferase Toxins

Mono-ADP-ribosyltransferase toxins are often key virulence factors produced by pathogenic bacteria as tools to compromise the target host cell. These toxins are enzymes that use host cellular NAD⁺ as the substrate to modify a critical macromolecule target in the host cell machinery. This post-translational modification of the target macromolecule (usually protein or DNA) acts like a switch to turn the target activity on or off resulting in impairment of a critical process or pathway in the host. One approach to stymie bacterial pathogens is to curtail the toxic action of these factors by designing small molecules that bind tightly to the enzyme active site and prevent catalytic function. The inactivation of these toxins/enzymes is targeted for the site of action within the host cell and small molecule therapeutics can function as anti-virulence agents by disarming the pathogen. This represents an alternative strategy to antibiotic therapy with the potential as a paradigm shift that may circumvent multi-drug resistance in the offending microbe. In this review, work that has been accomplished during the past two decades on this approach to develop anti-virulence compounds against mono-ADP-ribosyltransferase toxins will be discussed.

A Novel Streptomyces sp. Strain PBSH9 for Controlling Potato Common Scab Caused by Streptomyces galilaeus

Potato common scab is an important soilborne disease worldwide that can significantly reduce the quality and economic values of potato. The disease is caused by multiple species of Streptomyces, which are not well controlled due to lack of effective strategies. Streptomyces galilaeus has been recently identified as a dominant species causing potato common scab in Inner Mongolia, China. This study was focused on screening and characterizing antagonists for biological control against pathogenic S. galilaeus. Bacterial strain PBSH9 was isolated from a potato tuber. PBSH9 was identified as a Streptomyces sp. on the basis of morphological, physiological, and biochemical characteristics, as well as DNA sequence analysis. PBSH9 inhibited S. galilaeus with a diameter of inhibitory zone of 19.8 mm on agar plates. The extracellular filtrate of PBSH9 also inhibited S. galilaeus growth with a diameter of inhibition zone of 10.0 mm. Furthermore, PBSH9 promoted potato sprouting and emergence. Disease control was up to 81.88% in greenhouse trials, and from 47.64 to 73.97% in 3-year field trials. Among the tested inoculation methods, seed treatment was more effective than soil drenching for PBSH9 application. PBSH9 not only effectively controlled potato common scab but also increased potato growth. Thus, it can be a potential candidate for biocontrol agent.

Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities

Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.

Evolution and expression of genes encoding TCP transcription factors in Solanum tuberosum reveal the involvement of StTCP23 in plant defence

Background

The plant-specific Teosinte branched1/Cycloidea/Proliferating cell factor (TCP) family of transcription factors is involved in the regulation of cell growth and proliferation, performing diverse functions in plant growth and development. In addition, TCP transcription factors have recently been shown to be targets of pathogenic effectors and are likely to play a vital role in plant immunity. No comprehensive analysis of the TCP family members in potato (Solanum tuberosum L.) has been undertaken, however, and whether their functions are conserved in potato remains unknown.

Results

To assess TCP gene evolution in potato, we identified TCP-like genes in several publicly available databases. A total of 23 non-redundant TCP transcription factor-encoding genes were identified in the potato genome and subsequently subjected to a systematic analysis that included determination of their phylogenetic relationships, gene structures and expression profiles in different potato tissues under basal conditions and after hormone treatments. These assays also confirmed the function of the class I TCP StTCP23 in the regulation of plant growth and defence.

Conclusions

This is the first genome-wide study including a systematic analysis of the StTCP gene family in potato. Identification of the possible functions of StTCPs in potato growth and defence provides valuable information for our understanding of the classification and functions of the TCP genes in potato.

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

BACKGROUND

Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS.

RESULTS

The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence.

CONCLUSIONS

The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.

Biological control of potato common scab by Bacillus amyloliquefaciens Ba01

Potato common scab, which is caused by soil-borne Streptomyces species, is a severe plant disease that results in a significant reduction in the economic value of potatoes worldwide. Due to the lack of efficacious pesticides, crop rotations, and resistant potato cultivars against the disease, we investigated whether biological control can serve as an alternative approach. In this study, multiple Bacillus species were isolated from healthy potato tubers, and Bacillus amyloliquefaciens Ba01 was chosen for further analyses based on its potency against the potato common scab pathogen Streptomyces scabies. Ba01 inhibited the growth and sporulation of S. scabies and secreted secondary metabolites such as surfactin, iturin A, and fengycin with potential activity against S. scabies as determined by imaging mass spectrometry. In pot assays, the disease severity of potato common scab decreased from 55.6 ± 11.1% (inoculated with S. scabies only) to 4.2 ± 1.4% (inoculated with S. scabies and Ba01). In the field trial, the disease severity of potato common scab was reduced from 14.4 ± 2.9% (naturally occurring) to 5.6 ± 1.1% after Ba01 treatment, representing evidence that Bacillus species control potato common scab in nature.

Dynamics of Scabin toxin. A proposal for the binding mode of the DNA substrate

Scabin is a mono-ADP-ribosyltransferase enzyme and is a putative virulence factor produced by the plant pathogen, Streptomyces scabies. Previously, crystal structures of Scabin were solved in the presence and absence of substrate analogues and inhibitors. Herein, experimental (hydrogen-deuterium exchange), simulated (molecular dynamics), and theoretical (Gaussian Network Modeling) approaches were systematically applied to study the dynamics of apo-Scabin in the context of a Scabin·NAD⁺·DNA model. MD simulations revealed that the apo-Scabin solution conformation correlates well with the X-ray crystal structure, beyond the conformation of the exposed, mobile regions. In turn, the MD fluctuations correspond with the crystallographic B-factors, with the fluctuations derived from a Gaussian network model, and with the experimental H/D exchange rates. An Essential Dynamics Analysis identified the dynamic aspects of the toxin as a crab-claw-like mechanism of two topological domains, along with coupled deformations of exposed motifs. The “crab-claw” movement resembles the motion of C3-like toxins and emerges as a property of the central β scaffold of catalytic single domain toxins. The exposure and high mobility of the cis side motifs in the Scabin β-core suggest involvement in DNA substrate binding. A ternary Scabin·NAD⁺·DNA model was produced via an independent docking methodology, where the intermolecular interactions correspond to the region of high mobility identified by dynamics analyses and agree with binding and kinetic data reported for wild-type and Scabin variants. Based on data for the Pierisin-like toxin group, the sequence motif R_β1–R_La–N_Lc–STT_β2–W_PN–W_ARTT–(QxE)_ARTT emerges as a catalytic signature involved in the enzymatic activity of these DNA-acting toxins. However, these results also show that Scabin possesses a unique DNA-binding motif within the Pierisin-like toxin group.

Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase

Scabin was previously identified as a novel DNA-targeting mono-ADP-ribosyltransferase (mART) toxin from the plant pathogen 87.22 strain of Streptomyces scabies Scabin is a member of the Pierisin-like subgroup of mART toxins, since it targets DNA. An in-depth characterization of both the glycohydrolase and transferase enzymatic activities of Scabin was conducted. Several protein variants were developed based on an initial Scabin·DNA molecular model. Consequently, three residues were deemed important for DNA-binding and transferase activity. Trp128 and Trp155 are important for binding the DNA substrate and participate in the reaction mechanism, whereas Tyr129 was shown to be important only for DNA binding, but was not involved in the reaction mechanism. Trp128 and Trp155 are both conserved within the Pierisin-like toxins, whereas Tyr129 is a unique substitution within the group. Scabin showed substrate specificity toward double-stranded DNA containing a single-base overhang, as a model for single-stranded nicked DNA. The crystal structure of Scabin bound to NADH - a competitive inhibitor of Scabin - was determined, providing important insights into the active-site structure and Michaelis-Menten complex of the enzyme. Based on these results, a novel DNA-binding motif is proposed for Scabin with substrate and the key residues that may participate in the Scabin·NAD(+) complex are highlighted.

Repeated Applications of a Nonpathogenic Streptomyces Strain Enhance Development of Suppressiveness to Potato Common Scab

Potato common scab caused by several Streptomyces spp. is an important disease with no effective methods of control. Suppressiveness against common scab can develop in soil as a result of long-term potato monoculture and has been associated with nonpathogenic Streptomyces spp. To determine whether the development of scab suppressiveness could be enhanced, the effect of repeated applications of an antagonistic Streptomyces strain on common scab was investigated in a long-term field trial over 5 years. Streptomyces strain 272 applied annually at planting consistently suppressed development of common scab symptoms. On scab-susceptible potato cultivar Bintje, strain 272 reduced disease severity, on average, by 43%; whereas, on the scab-tolerant Nicola, the strain reduced both disease incidence and severity by 43 and 59%, respectively. Regardless of disease pressure, the combined use of strain 272 and the tolerant cultivar reduced the scab coverage to a negligible level. After a single application of strain 272, efficient disease suppression did not persist in the soil to the following growing season. However, when strain 272 was applied in three or more consecutive years, the soil remained suppressive to scab for at least 2 years beyond the last application, suggesting that, with repeated applications, it may be possible to enhance development of scab suppression in soil.

Community Analysis of Root- and Tuber-Associated Bacteria in Field-Grown Potato Plants Harboring Different Resistance Levels against Common Scab

Eight genotypes of potato plants with different resistance levels against common scab were grown in a field infested with Streptomyces turgidiscabies. DNA was extracted from the roots, tubers, and rhizosphere soils of each of the eight genotypes at the flowering stage, and the quantity of S. turgidiscabies genomic DNA was assessed by real-time PCR using a TaqMan probe. The results obtained showed that the different potato genotypes had significant impacts on the population levels of S. turgidiscabies between resistant and susceptible genotypes in the tubers, but not in the roots or rhizosphere soils. Clone analyses of 16S rRNA gene libraries from the eight potato genotypes identified three phyla (Proteobacteria, Firmicutes, and Actinobacteria) as dominant taxa in root and tuber clone libraries, while a clustering analysis identified 391 operational taxonomic units (OTUs) at the species level. Eleven OTUs closely related to Aquicella siphonis, Arthrobacter nicotinovorans, Streptomyces rishiriensis, Rhodococcus baikonurensis, Rhizobium radiobacter, Rhizobium etli, Phyllobacterium myrsinacearum, Paenibacillus pabuli, Paenibacillus alginolyticus, and Bacillus halmapalus were detected in the root or tuber libraries of all the potato genotypes examined. Furthermore, an abundance of OTUs related to Aquicella and Rhodococcus was observed in the rhizospheres of resistant and susceptible potato genotypes, respectively. Based on this ecological information, an efficient survey may be conducted for biological agents from the potato rhizosphere.

Pseudomonas fluorescens LBUM223 Increases Potato Yield and Reduces Common Scab Symptoms in the Field

Common scab of potato, caused by pathogenic Streptomyces spp., is an important disease not efficiently controlled by current methods. We previously demonstrated that Pseudomonas fluorescens LBUM223 reduces common scab development under controlled conditions through phenazine-1-carboxylic (PCA) production, leading to reduced thaxtomin A production by the pathogen, a key pathogenicity and virulence factor. Here, we aimed at determining if LBUM223 is able to increase potato yield and control common scab under field conditions, while characterizing the biocontrol mechanisms involved. We investigated if a reduction in pathogen soil populations, activation of induced systemic resistance in potato, and/or changes in txtA gene expression, involved in thaxtomin A biosynthesis in pathogenic Streptomyces spp. were involved in common scab control by LBUM223. Common scab symptoms were significantly reduced and total tuber weight increased by 46% using biweekly applications of LBUM223. LBUM223 did not reduce pathogen soil populations, nor was potato systemic defense-related gene expression significantly altered between treatments. However, a significant down-regulation of txtA expression occurred in the geocaulosphere. This is the first demonstration that a Pseudomonas strain can directly alter the transcriptional activity of a key pathogenesis gene in a plant pathogen under field conditions, contributing to disease control.