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Background Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading enzymes is usually critical for Pectobacterium infection. However, other virulence factors and the mechanisms of genetic adaptation still need to be studied in detail. Results In this study, the complete genome of P. carotovorum subsp. brasiliense strain SX309 isolated from cucumber was compared with eight other pathogenic bacteria belonging to the Pectobacterium genus, which were isolated from various host plants. Genome comparison revealed that most virulence genes are highly conserved in the Pectobacterium strains, especially for the key virulence determinants involved in the biosynthesis of extracellular enzymes and others including the type II and III secretion systems, quorum sensing system, flagellar and chemotactic genes. Nevertheless, some variable regions of the T6SS and the CRISP-Cas immune system are unique for P. carotovorum subsp. brasiliense . Conclusions The extensive comparative genomics analysis revealed highly conserved virulence genes in the Pectobacterium strains. However, several variable regions of type VI secretion system and two subtype Cas mechanism-Cas immune systems possibly contribute to the process of Pectobacterium infection and adaptive immunity.

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.

Bacterial pathogens from the genus Pectobacterium cause soft rot in various plants, and result in important economic losses worldwide. We understand much about how these pathogens digest their hosts and protect themselves against plant defences, as well as some regulatory networks in these processes. However, the spatiotemporal expression of genome‐wide infection of Pectobacterium remains unclear, although researchers analysed this in some phytopathogens. In the present work, comparing the transcriptome profiles from cellular infection with growth in minimal and rich media, RNA‐Seq analyses revealed that the differentially expressed genes (log2‐fold ratio ≥ 1.0) in the cells of Pectobacterium carotovorum subsp. carotovorum PccS1 recovered at a series of time points after inoculation in the host in vivo covered approximately 50% of genes in the genome. Based on the dynamic expression changes in infection, the significantly differentially expressed genes (log2‐fold ratio ≥ 2.0) were classified into five types, and the main expression pattern of the genes for carbohydrate metabolism underlying the processes of infection was identified. The results are helpful to our understanding of the inducement of host plant and environmental adaption of Pectobacterium. In addition, our results demonstrate that maceration caused by PccS1 is due to the depression of callose deposition in the plant for resistance by the pathogenesis‐related genes and the superlytic ability of pectinolytic enzymes produced in PccS1, rather than the promotion of plant cell death elicited by the T3SS of bacteria as described in previous work. In Pectobacterium PccS1 infection, transcriptomic analysis using a two‐control gene expression experiment reveals more differentially expressed genes with different expression change types, which are related to virulence, adaptation, and host response.

Pectobacterium carotovorum and Pectobacterium aroidearum represent the primary pathogens causing variable soft rot disease. However, the fundamental defense responses of Pinellia ternata to pathogens remain unclear. Our investigation demonstrated that the disease produced by P. carotovorum is more serious than P. aroidearum . RNA-seq analysis indicated that many cell wall-related genes, receptor-like kinase genes, and resistance-related genes were induced by P. aroidearum and P. carotovorum similarly. But many different regulatory pathways exert a crucial function in plant immunity against P. aroidearum and P. carotovorum , including hormone signaling, whereas more auxin-responsive genes were responsive to P. carotovorum , while more ethylene and gibberellin-responsive genes were responsive to P. aroidearum . 12 GDSL esterase/lipase genes and 3 fasciclin-like arabinogalactan protein genes were specifically upregulated by P. carotovorum , whereas 11 receptor-like kinase genes and 8 disease resistance genes were up-regulated only by P. aroidearum . Among them, a lectin gene (part1transcript/39001) was induced by P. carotovorum and P. aroidearum simultaneously. Transient expression in N. benthamiana demonstrated that the lectin gene improves plant resistance to P. carotovorum . This study offers a comprehensive perspective on P. ternata immunity produced by different soft rot pathogens and reveals the importance of lectin in anti-soft rot of P. ternata for the first time.

Pectobacterium actinidiae is one of the primary pathogens that causes summer canker disease in kiwifruit, yet its pathogenic mechanisms remain unknown. The exopolysaccharide PCAP‐1a, isolated from the fermentation broth of P. actinidiae strain GX1, exhibits notable cytotoxicity and acts as a virulence factor facilitating host infection. Genome‐wide analysis revealed a 21‐gene cluster responsible for the biosynthesis of exopolysaccharides in GX1. Homologous recombination was used to systematically knock out these genes, which led to the identification of RmlA as a key protein in the synthesis of the PCAP‐1a precursor. The deletion of the rmlA gene significantly affected the yield of PCAP‐1a and resulted in a direct reduction in GX1 pathogenicity. Further studies revealed that mutations in the substrate binding site of RmlA weakened its capacity to bind G‐1‐P and dTTP, which led to markedly reduced pathogenicity in the corresponding complemented strains. This study indicates that the exopolysaccharide PCAP‐1a serves as a virulence factor in the pathogenesis of GX1, and its biosynthesis depends on the polysaccharide synthesis gene rmlA and the substrate binding activity of its encoded protein. Deletion of the rmlA gene negatively affected PCAP‐1a yield, structure and directly diminished GX1 pathogenicity. Furthermore, mutations within RmlA's substrate binding site impaired its ability to bind G‐1‐P and dTTP.

Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymerase amplification (RPA) combined with a lateral flow device (LFD) was developed for specific detection of Pectobacterium sp. directly from infected plant materials with no need for DNA isolation. The specificity of RPA-LFD was tested with 26 Pectobacterium sp. strains and 12 non- Pectobacterium species and no false positive or false negative outcomes were observed. RPA primers and probe for host control were also developed to detect the host genome for enhanced reliability and accuracy of the developed assay. The detection limit of 10 fg was obtained with both sensitivity and spiked sensitivity assays. No inhibitory effects were observed on the RPA assay when targets (pathogen and host) were directly detected from infected potato and tomato sap. The developed RPA assay has numerous applications from routine diagnostics at point-of-care, biosecurity, surveillance and disease management to epidemiological studies. In addition, this tool can also be used to discover reservoir hosts for Pectobacterium species.

Expansins are encoded by some phytopathogenic bacteria and evidence indicates that they act as virulence factors for host infection. Here we analysed the expression of exl1 by Pectobacterium brasiliense and Pectobacterium atrosepticum . In both, exl1 gene appears to be under quorum sensing control, and protein Exl1 can be observed in culture medium and during plant infection. Expression of exl1 correlates with pathogen virulence, where symptoms are reduced in a Δexl1 mutant strain of P. atrosepticum . As well as Δexl1 exhibiting less maceration of potato plants, fewer bacteria are observed at distance from the inoculation site. However, bacteria infiltrated into the plant tissue are as virulent as the wild type, suggesting that this is due to alterations in the initial invasion of the tissue. Additionally, swarming from colonies grown on MacConkey soft agar was delayed in the mutant in comparison to the wild type. We found that Exl1 acts on the plant tissue, probably by remodelling of a cell wall component or altering the barrier properties of the cell wall inducing a plant defence response, which results in the production of ROS and the induction of marker genes of the JA, ET and SA signalling pathways in Arabidopsis thaliana . Exl1 inactive mutants fail to trigger such responses. This defence response is protective against Pectobacterium brasiliense and Botrytis cinerea in more than one plant species.

The presence of bacteria from the Dickeya spp. and Pectobacterium spp. in farmlands leads to global crop losses of over $420 million annually. Since 1982, the scientists have started to suspect that the development of disease symptoms in crops might be inhibited by bacteria present in the soil. Here, we characterized in terms of physicochemical properties and the composition of bacterial soil microbiota two fields differing, on the basis of long-term studies, in the occurrence of Dickeya spp.- and Pectobacterium spp.-triggered infections. Majority, i.e. 17 of the investigated physicochemical features of the soils collected from two fields of either low or high potato blackleg and soft rot diseases incidences turned out to be similar, in contrast to the observed 4 deviations in relation to Mg, Mn, organic C and organic substance contents. By performing microbial cultures and molecular diagnostics-based identification, 20  Pectobacterium spp. strains were acquired from the field showing high blackleg and soft rot incidences. In addition, 16S rRNA gene amplicon sequencing followed by bioinformatic analysis revealed differences at various taxonomic levels in the soil bacterial microbiota of the studied fields. We observed that bacteria from the genera Bacillus , Rumeliibacillus , Acidobacterium and Gaiella turned out to be more abundant in the soil samples originating from the field of low comparing to high frequency of pectinolytic bacterial infections. In the herein presented case study, it is shown for the first time that the composition of bacterial soil microbiota varies between two fields differing in the incidences of soft rot and blackleg infections.

Pectobacterium species are necrotrophic bacterial pathogens that cause soft rot diseases in potatoes and several other crops worldwide. Gene expression data identified Pectobacterium carotovorum subsp. carotovorum budB, which encodes the α-acetolactate synthase enzyme in the 2,3-butanediol pathway, as more highly expressed in potato tubers than potato stems. This pathway is of interest because volatiles produced by the 2,3-butanediol pathway have been shown to act as plant growth promoting molecules, insect attractants, and, in other bacterial species, affect virulence and fitness. Disruption of the 2,3-butanediol pathway reduced virulence of P. c. subsp. carotovorum WPP14 on potato tubers and impaired alkalinization of growth medium and potato tubers under anaerobic conditions. Alkalinization of the milieu via this pathway may aid in plant cell maceration since Pectobacterium pectate lyases are most active at alkaline pH.

The carbon-use-efficiency (CUE) of microorganisms is an important parameter in determining ecosystem-level carbon (C) cycling; however, little is known about how variance in resources affects microbial CUE. To elucidate how resource quantity and resource stoichiometry affect microbial CUE, we cultured four microorganisms - two fungi (Aspergillus nidulans and Trichoderma harzianum) and two bacteria (Pectobacterium carotovorum and Verrucomicrobium spinosum) - under 12 unique C, nitrogen (N) and phosphorus (P) ratios. Whereas the CUE of A. nidulans was strongly affected by C, bacterial CUE was more strongly affected by mineral nutrients (N and P). Specifically, CUE in P. carotovorum was positively correlated with P, while CUE of V. spinosum primarily depended on N. This resulted in a positive relationship between fungal CUE and resource C : nutrient stoichiometry and a negative relationship between bacterial CUE and resource C : nutrient stoichiometry. The difference in the direction of the relationship between CUE and C : nutrient for fungi vs. bacteria was consistent with differences in biomass stoichiometry and suggested that fungi have a higher C demand than bacteria. These results suggest that the links between biomass stoichiometry, resource demand and CUE may provide a mechanism for commonly observed temporal and spatial patterns in microbial community structure and function in natural habitats.