Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia.

Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.

Genetic Loci of Plant Pathogenic Dickeya solani IPO 2222 Expressed in Contact with Weed-Host Bittersweet Nightshade (Solanum dulcamara L.) Plants.

Dickeya solani, belonging to the Soft Rot Pectobacteriaceae, are aggressive necrotrophs, exhibiting both a wide geographic distribution and a wide host range that includes many angiosperm orders, both dicot and monocot plants, cultivated under all climatic conditions. Little is known about the infection strategies D. solani employs to infect hosts other than potato (Solanum tuberosum L.). Our earlier study identified D. solani Tn5 mutants induced exclusively by the presence of the weed host S. dulcamara. The current study assessed the identity and virulence contribution of the selected genes mutated by the Tn5 insertions and induced by the presence of S. dulcamara. These genes encode proteins with functions linked to polyketide antibiotics and polysaccharide synthesis, membrane transport, stress response, and sugar and amino acid metabolism. Eight of these genes, encoding UvrY (GacA), tRNA guanosine transglycosylase Tgt, LPS-related WbeA, capsular biosynthesis protein VpsM, DltB alanine export protein, glycosyltransferase, putative transcription regulator YheO/PAS domain-containing protein, and a hypothetical protein, were required for virulence on S. dulcamara plants. The implications of D. solani interaction with a weed host, S. dulcamara, are discussed.

An iron fist in a velvet glove: The cooperation of a novel pyoverdine from Pseudomonas donghuensis P482 with 7-hydroxytropolone is pivotal for its antibacterial activity.

Pseudomonas donghuensis P482 exhibits broad antimicrobial activity against phytopathogens, including the soft rot bacteria of the Dickeya genus. Here, we report that under limited nutrient availability, the antibacterial activity of P. donghuensis P482 against Dickeya solani requires the reciprocal action of two iron scavengers: 7-hydroxytropolone (7-HT) and a newly characterized pyoverdine (PVDP482 ) and is quenched in the iron-augmented environment. Further, we show that the biosynthesis of pyoverdine and 7-HT is metabolically coordinated, and the functional BV82_4709 gene involved in 7-HT synthesis is pivotal for expressing the BV82_3755 gene, essential for pyoverdine biosynthesis and vice versa. The synthesis of both scavengers is under the control of Gac/Rsm, but only PVD is controlled by Fur. The isoelectric focusing profile of the P482 siderophore differs from that of the other Pseudomonas spp. tested. This finding led to the unveiling of the chemical structure of the new pyoverdine PVDP482 . To summarize, the antibacterial activity of P. donghuensis P482 is attributed to 7-HT and PVDP482 varies depending on the nutrient and iron availability, highlighting the importance of these factors in the competition between P482 and D. solani.

Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts.

Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.

Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize.

Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.

Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

Lytic bacteriophages able to infect and kill Dickeya spp. can be readily isolated from virtually all Dickeya spp. containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Two spontaneous D. solani IPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 (ΦD5) were identified in this study that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptible D. solani IPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (in mutant DsR34) and elongation factor Tu (EF-Tu) (in mutant DsR207) were altered in these strains. These mutations impacted the DsR34 and DsR207 proteomes. Features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, production of plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulence in planta were assessed. Compared to the wild-type strain, D. solani IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants.

Crystal violet-based assay for the assessment of bacterial biofilm formation in medical tubing.

Crystal violet-based assay is widely used to evaluate the early stages of bacterial biofilm formation. Here, we modified it to study biofilm formation in medical tubing. While cost-effective and requiring no sophisticated equipment, our method provided quantitative and qualitative distinctions between the ability of four bacterial strains to colonize PVC catheters.

High-Quality Complete Genome Resource of Tomato Rhizosphere Strain Pseudomonas donghuensis P482, a Representative of a Species with Biocontrol Activity Against Plant Pathogens.

Strain P482 was isolated from a tomato rhizosphere and classified as Pseudomonas donghuensis. The P. donghuensis species was first established in 2015 and currently consists of only four strains: P482, HYST, SVBP6, and 22G5. P. donghuensis strains antagonize plant pathogens, including bacteria, fungi, and oomycetes, and, therefore, are of high interest regarding their biological control potential to combat plant diseases. The antimicrobial activity of P. donghuensis P482 is based on the production of iron-scavenging compound 7-hydroxytropolone, antifungal volatile organic compounds, and as-yet-unidentified secondary metabolites. Here, we report a complete genome resource for P. donghuensis strain P482. The genome consists of a single chromosome (5,656,185 bp) with 5,258 open reading frames (5,158 protein-coding genes, 74 transfer RNAs, 22 ribosomal RNAs, 3 noncoding RNAs, and 1 transfer-messenger RNA) and no plasmid. We believe that information on the first high-quality, complete genome of P. donghuensis will provide resources for analyses targeting the biological control potential of this species and understanding the traits essential for plant-microbe interaction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides Are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato (Solanum tuberosum L.) Plants.

Pectobacterium parmentieri is a Gram-negative plant-pathogenic bacterium able to infect potato (Solanum tuberosum L.). Little is known about lytic bacteriophages infecting P. parmentieri and how phage-resistance influences the environmental fitness and virulence of this species. A lytic phage vB_Ppp_A38 (ϕA38) has been previously isolated and characterized as a potential biological control agent for the management of P. parmentieri. In this study, seven P. parmentieri SCC 3193 Tn5 mutants were identified that exhibited resistance to infection caused by vB_Ppp_A38 (ϕA38). The genes disrupted in these seven mutants encoded proteins involved in the assembly of O-antigen, sugar metabolism, and the production of bacterial capsule exopolysaccharides. The potential of A38-resistant P. parmentieri mutants for plant colonization and pathogenicity as well as other phenotypes expected to contribute to the ecological fitness of P. parmentieri, including growth rate, use of carbon and nitrogen sources, production of pectinolytic enzymes, proteases, cellulases, and siderophores, swimming and swarming motility, presence of capsule and flagella as well as the ability to form biofilm were assessed. Compared to the wild-type P. parmentieri strain, all phage-resistant mutants exhibited a reduced ability to colonize and to cause symptoms in growing potato (S. tuberosum L.) plants. The implications of bacteriophage resistance on the ecological fitness of P. parmentieri are discussed.

The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482.

Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

High-Quality Complete Genome Resource of Plant-Pathogenic Bacterium Dickeya solani IPO 2019, Isolated from Hyacinthus orientalis.

Dickeya solani is an emerging plant-pathogenic bacterium causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date, a number of D. solani genomes have been sequenced and characterized; the great majority of these genomes have, however, come from D. solani strains isolated from potato (Solanum tuberosum L.) and not from other plant hosts. Herewith, we present the first complete, high-quality genome of D. solani IPO 2019 (LMG 25990), isolated from the ornamental plant Hyacinthus orientalis. The genome of D. solani IPO 2019 consists of one chromosome of 4,919,542 bp, with a GC content of 56.2% and no plasmids. The genome contains 4,502 annotated features, 22 ribosomal RNA genes, 73 transfer RNA genes, and one CRISPR. We believe that the information on this high-quality, complete, closed genome of D. solani strain isolated from a host plant different from potato (i.e. hyacinth) will provide resources for comparative genomic studies and for analyses targeting adaptation and ecological fitness mechanisms present in Dickeya solani species.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol.

Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.

Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara.

Dickeya solani is a Gram-negative bacterium able to cause disease symptoms on a variety of crop and ornamental plants worldwide. Weeds including Solanum dulcamara (bittersweet nightshade) growing near agricultural fields have been reported to support populations of soft rot bacteria in natural settings. However, little is known about the specific interaction of D. solani with such weed plants that may contribute to its success as an agricultural pathogen. The aim of this work was to assess the interaction of D. solani with its crop plant (Solanum tuberosum) and an alternative (S. dulcamara) host plant. From a collection of 10,000 Tn5 transposon mutants of D. solani IPO2222 carrying an inducible, promotorless gusA reporter gene, 210 were identified that exhibited plant tissue-dependent expression of the gene/operon into which the Tn5 insertion had occurred. Thirteen Tn5 mutants exhibiting the greatest plant tissue induction of such transcriptional units in S. tuberosum or S. dulcamara as measured by qRT-PCR were assessed for plant host colonization, virulence, and ability to macerate plant tissue, as well as phenotypes likely to contribute to the ecological fitness of D. solani, including growth rate, carbon and nitrogen source utilization, motility, chemotaxis toward plant extracts, biofilm formation, growth under anaerobic conditions and quorum sensing. These 13 transcriptional units encode proteins involved in bacterial interactions with plants, with functions linked to cell envelope structure, chemotaxis and carbon metabolism. The selected 13 genes/operons were differentially expressed in, and thus contributed preferentially to D. solani fitness in potato and/or S. dulcamara stem, leaf, and root tissues.

The chemical structure of polysaccharides isolated from the Ochrobactrum rhizosphaerae PR17T.

The bacteria from Ochrobactrum genus are commonly found in the soil and association with the roots of plants. The O-polysaccharide and the glucan were isolated from the Ochrobactrum rhizosphaerae PR17T strain. Purified polysaccharides were analysed using chemical methods and NMR spectroscopy. Sugar and absolute configuration assignment combined with NMR data revealed the chemical structure of the repeating unit of the O.

The Great Five-an artificial bacterial consortium with antagonistic activity towards Pectobacterium spp. and Dickeya spp.: formulation, shelf life, and the ability to prevent soft rot of potato in storage.

"The Great Five" (GF) is an artificial bacterial consortium developed to protect potato tubers from soft rot caused by Pectobacterium spp. and Dickeya spp. To investigate the commercialization potential of the GF, we developed liquid and powder formulations of the consortium and of each of the comprising strains (Serratia plymuthica strain A294, Enterobacter amnigenus strain A167, Rahnella aquatilis strain H145, Serratia rubidaea strain H440, and S. rubidaea strain H469). To form powders, the cells were lyophilized using a newly developed lyoprotectant: Reagent PS. The shelf life of the formulations stored at 8 and 22 °C was monitored for a period of 12 months. The longest shelf life was obtained for formulations stored at 8 °C; however, the viability of all formulations was negatively affected at 22 °C. For the consortium, a 2.5 log10 cfu (colony forming units) drop in cell number was recorded for the liquid formulation after 6 months, while in case of powders, the drop remained below 1 log10 cfu following 12 months. The ability of the powder formulations to preserve biocontrol activity of the consortium was tested on potato tubers treated with the formulations and a mixture of the soft rot pathogens. The inoculated tubers were stored for 6 months at 8 °C to mimic commercial storage conditions. Soft rot severity and incidence on potato tubers treated with formulations were significantly reduced (62-75% and 48-61%, respectively) in comparison to positive control with pathogens alone. The potential use of the newly developed formulations of "The Great Five" for the biocontrol of soft rot is discussed. KEY POINTS : • An innovative reagent to protect bacterial cells during lyophilization was developed. • Powder formulations of "The Great Five" prolonged its shelf life. • The powder-formulated "The Great Five" was active against soft rot bacteria on potato tubers.

Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR.

Reverse transcription quantitative PCR (RT-qPCR), a method of choice for quantification of gene expression changes, requires stably expressed reference genes for normalization of data. So far, no reference genes were established for the Alphaproteobacteria of the genus Ochrobactrum. Here, we determined reference genes for gene expression studies in O. quorumnocens A44. Strain A44 was cultured under 10 different conditions and the stability of expression of 11 candidate genes was evaluated using geNorm, NormFinder and BestKeeper. Most stably expressed genes were found to be rho, gyrB and rpoD. Our results can facilitate the choice of reference genes in the related Ochrobactrum strains. O. quorumnocens A44 is able to inactivate a broad spectrum of N-acyl homoserine lactones (AHLs) - the quorum sensing molecules of many Gram-negative bacteria. This activity is attributed to AiiO hydrolase, yet it remains unclear whether AHLs are the primary substrate of this enzyme. Using the established RT-qPCR setup, we found that the expression of the aiiO gene upon exposure to two AHLs, C6-HLS and 3OC12-HSL, does not change above the 1-fold significance threshold. The implications of this finding are discussed in the light of the role of quorum sensing-interfering enzymes in the host strains.

Compatible Mixture of Bacterial Antagonists Developed to Protect Potato Tubers from Soft Rot Caused by Pectobacterium spp. and Dickeya spp.

Possibilities to protect potato tubers from rotting caused by Soft Rot Pectobacteriaceae (SRP) under disease favoring conditions were investigated using compatible mixtures of bacterial antagonists and tested with a newly developed stepwise efficacy-based screening protocol. Twenty-two bacterial antagonists were evaluated against a combination of five Pectobacterium and Dickeya strains representing species and subspecies most often associated with potato soft rot in Europe. To enable potential synergistic activity, the antagonists were initially tested against the combination of pathogens in 15 random mixtures containing up to 5 antagonists each. Three mixtures (M2, M4, and M14) out of 15 tested reduced tuber tissue maceration due to soft rot. The individual antagonists derived from M2, M4, and M14 mixtures were tested on potato slices and whole tuber injection assays. These five strains (S. plymuthica strain A294, E. amnigenus strain A167, R. aquatilis strain H145, S. rubidaea strain H440, and S. rubidaea strain H469) were combined to develop a tailored biological control mixture against potato soft rot. The new mixture, designated the Great Five (GF), was tested on seed potato tubers vacuum infiltrated with antagonists and subsequently with the combination of five SRP pathogens. In these experiments, the GF mixture provided stable protection of inoculated potato tubers, reducing soft rot by 46% (P = 0.0016) under high disease pressure conditions. The A294, A167, H145, H440, and H469 antagonists were characterized for features important for viable commercial applications including growth at different temperatures, resistance to antibiotics, and potential toxicity toward Caenorhabditis elegans. The implications for control of soft rot caused by SRP with the use of the GF mixture of antagonists are discussed.

Correction: Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.

[This corrects the article DOI: 10.1371/journal.pone.0210874.].

Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.

Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50-66% of each individual genome. Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).