The Causative Agent of Soft Rot in Plants, the Phytopathogenic Bacterium Pectobacterium carotovorum subsp. carotovorum: A Brief Description and an Overview of Methods to Control It

Abstract

This review presents information obtained over the past 10 years on the methods to control the widespread worldwide phytopathogen Pectobacterium carotovorum subsp. carotovorum (Pcc). This bacterium is among the ten most dangerous phytopathogens; it affects a wide range of cultivated plants: vegetables, ornamental and medicinal crops, both during vegetation and during the storage of fruits. Symptoms of Pcc damage include the wilting of plants, blackening of vessels on leaves, stems and petioles. At the flowering stage, the stem core gradually wilts and, starting from the root, the stem breaks and the plant dies. Pcc is a rod-shaped, non-capsule and endospore-forming facultative anaerobic Gram-negative bacterium with peritrichous flagellation. Pcc synthesizes bacteriocins—carocins. The main virulence factors of Pcc are the synthesis of N-acyl-homoserine lactone (AHL) and plant cell wall-degrading enzymes (PCWDEs) (pectinases, polygalacturonases, cellulases, and proteases). Diagnostic methods for this phytopathogen include polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), multilocus genotyping of strain-specific genes and detection of unique volatile organic compounds (VOCs). The main methods to control this microorganism include the use of various chemicals (acids, phenols, esters, salts, gases), plant extracts (from grasses, shrubs, trees, and algae), antagonistic bacteria (Bacillus, Pseudomonas, Streptomyces, and lactic acid bacteria), viruses (including a mixture of bacteriophages), and nanomaterials based on metals and chitosan.

1. Introduction

Pectobacterium carotovorum (Pc), specifically Pectobacterium carotovorum subsp. carotovorum (formerly Erwinia carotovora subsp. carotovora) (Pcc) is a Gram-negative motile phytopathogenic bacterium [1]. Pc and P. atrosepticum, originally classified as Erwinia carotovora subspecies carotovora and subspecies atroseptica, respectively, are among the top ten most dangerous bacteria for plants in molecular plant pathology and cause serious yield losses during cultivation and storage [2]. This pathogen, Pc or Pcc, causes infectious soft rot disease in various crop species, including vegetables during the growing season and post-harvest processing, such as Chinese cabbage Bok choy (Brassica rapa var. Chinensis (L.) Kitam.) [3,4,5], lettuce (Lactuca sativa L.) [6], radish (Raphanus sativus L.) [7], eggplant (Solanum melongena L.) [8], potato (Solanum tuberosum L.) [9], tomatoes (Solanum lycopersicum L.) [1], onions (Allium cepa L.) [10], turnips (Brassica rapa L.) [11], chili peppers (Capsicum annuum L.) [12], and the tropical perennial plant Amorphophallus spp. [13]. In trees, Pc causes bark cracking disease in jackfruit (Artocarpus heterophyllus Lam.) [14]. Among ornamental crops, the disease occurs in poinsettia (Euphorbia pulcherrima Willd. ex Klotzsch) [15], golden calla (Zantedeschia elliotiana (H. Knight) Engl.) [16], perennial bulbous herbaceous plants of the genus Ornithogalum [17,18], chicory and orchids [19]. Among medicinal plants, Pc infects Pinellia ternata (Thunb.) Breit [20]. In potatoes, Pc causes blackleg disease, which leads to the wilting of the entire plant, as well as blackening and necrosis of the stem [9].

Despite the high prevalence of Pc or Pcc worldwide and the large economic losses resulting from its activity, there are no recent review articles summarizing the data devoted to the characteristics of this pathogen and the methods of regulating its numbers. Over the past 10 years, there have been no review articles that include information on the comprehensive characteristics of Pc or Pcc (but see [21]). A few reviews devoted to this phytopagen have been published earlier [22,23,24,25]. Pc/Pcc is often used only as an object for testing new compounds along with other microorganisms. In this regard, the purpose of this work is to analyze the literature data published over the past 10 years and devoted to the characteristics of the soft rot disease and the bacteria that cause it, as well as to summarize the methods of regulating the numbers of Pc/Pcc. This review will also present the characteristics of the phytopathogen Pc/Pcc itself—its systematic position, morphological and physiological–biochemical characteristics, and virulence factors. Attention will also be paid to the symptoms of plant damage by soft rot, methods for diagnosing the pathogen, the plant’s protective response to infection, and methods for combating Pc/Pcc.

2. Systematic Position, Morphological, and Physiological–Biochemical Characteristics of Pectobacterium carotovorum

Pectobacterium spp. are plant-pathogenic necrotrophic bacteria belonging to the family Pectobacteriaceae (formerly the family Enterobacteriaceae). The genus Pectobacterium was denominated in 1945; it is characterized by high genetic heterogeneity and includes several species and subspecies. The taxonomic structure of Pectobacterium spp. has been classified into 19 recognized and described species and subspecies [26]. The species P. carotovorum has been divided as well into several subspecies and putative subspecies, including subsp. carotovorum, atrosepticum, betavasculorum, odoriferum, and wasabiae. More recently, the latter have been elevated to the species rank [27,28,29] in addition to a new species P. polaris [30]. In 2019, the taxonomic status of some representatives of the species also changed: Pectobacterium carotovorum subsp. odoriferum was elevated to species level as Pectobacterium odoriferum sp. nov., Pectobacterium actinidiae sp. nov., and Pectobacterium brasiliense sp. nov. were proposed to emend the description of Pectobacterium carotovorum, and a novel species, Pectobacterium versatile sp. nov., which includes the strains previously described as ‘Candidatus Pectobacterium maceratum’, was also proposed [29]. Their current taxonomic classification according to the NCBI GenBank taxonomy is presented in Figure 1.

The taxonomic data were obtained from the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy, accessed on 15 May 2025) using R program taxize v.4.5.1 (https://github.com/ropensci/taxize, accessed on 15 May 2025), and the taxonomic tree was generated using R program ggtree (https://rdrr.io/bioc/ggtree, accessed on 15 May 2025). The identified members of the Pectobacterium Genus include 23 species. Other members of the Pectobacteriaceae family include Brenneria, Dickeya, Lonsdalea, Musicola, Prodigiosinella, Affinibrenneria, Acerihabitans, and Samsonia genera. The taxonomic tree presented in Figure 1 is not strictly phylogenetic but rather reflects taxonomic names and the taxonomy of the sequences submitted to the NCBI GenBank. The phylogeny of the Pectobacterium Genus is continuously developing and improving, and the detailed phylogenetic analysis is beyond the scope of our review, but the most recent phylogenetic trees can be seen, for instance, in [28,29,31].

According to the most recent review by Oulghazi et al. [32], four subspecies are distinguished in the taxonomy of the species Pc: Pcc, P. carotovorum subsp. odoriferum, P. carotovorum subsp. actinidiae, and P. carotovorum subsp. brasiliense (see references there). However, several genomic comparisons have suggested that Pc represents a species complex that requires new taxonomic classification [28]. For instance, Portier et al. [31] found that most of the 27 former Pcc strains should be split between Pc (12/27) and P. versatile (8/27). Moreover, they suggested that based on dnaX-leuS-recA phylogeny and genome analysis, all studied Pectobacterium species and subspecies could be reduced to 18 species (see Figure 4 in [31]), although, according to [26] or [32], there are 19 or 22 species of Pectobacterium, respectively, and no subspecies. Therefore, we admit that the taxonomic status of Pcc could be controversial, and the subspecies designation can even lack current formal recognition in the modern taxonomic frameworks, but we used it in our review considering that it is still commonly used by many authors. We keep referring to Pc or Pcc depending on the names that were used by the authors of the papers cited in this review. In any case, this uncertainty should not affect the observations presented in the review, and most traits are shared by both Pc and Pcc.

Pc is a rod-shaped, non-encapsulated, non-endospore-forming, facultative anaerobic Gram-negative bacterium with a size of 0.6–1.8 × 1.7–5.1 μm. The bacteria are motile due to peritrichous flagella. The isolates can be plated and developed on an agar medium using either the spot or streak isolation method. The morphology of the colonies can then be examined to determine their dorsal appearance, height, edge shape, and color [33]. The external structure of Pcc colonies growing on potato agar is oval or round, with smooth edges; the colonies are convex, 1 to 3 mm in diameter, with a smooth texture, and have a shiny yellowish-cream color [34]. When examined microscopically, they appear mainly as single or paired rods, sometimes in short chains [35]. The optimal temperature for growth is 27–30 °C. This microorganism is grown on potato agar; bacterial growth is noticeable within 1–2 days. Meat-peptone agar with different glucose concentrations (0.5, 1.0, 1.5, 2.0, 2.5, or 3.0%) is also used. Photos of bacterial colonies and Pcc cells cultured on meat-peptone agar and a schematic representation of the basic data on Pcc are presented in Figure 2.

Bacteria of this species catabolize carbohydrates to produce acid and gas [36]. Isolation, detection, identification, and characterization of Pectobacterium species are also achieved using a selective medium containing pectate. An example of such a medium is crystal violet pectate (CVP), a semi-selective medium containing pectin [37]. CVP is actively used in various studies to identify the phytopathogen under study. However, in recent years it has been considered that selective media including pectate do not allow for the qualitative separation of Pc from other bacterial strains. Therefore, new media for identification are being developed [38]. The pathogenicity test is carried out by inoculating bacteria into potato tubers. As a result of Pcc pathogenesis, maceration of plant tissues is observed. Experiments are usually carried out on slices of potato tubers or radish fruits. Biochemical and physiological traits of the strains are characterized using tests that are usually used to differentiate Pectobacterium species. In particular, gelatin liquefaction, litmus milk reduction (individual strains peptonize), hydrogen sulfide, and ammonia release, indole formation, and starch hydrolysis are analyzed (Pcc do not form indole and do not hydrolyze starch). In general, Pcc are citrate- and catalase-positive, and oxidase-negative. They are capable of fermenting glucose, reducing nitrate to nitrite, producing ß-galactosidase, utilizing L-rhamnose, L-arabinose, D-galactose, D-glucose, glycerol, D-mannose, D-ribose, and sucrose, but are unable to utilize dextrin, produce urease and acid from adonitol. Isolates are negative for indole and phosphatase [34,35,39,40].

General methods used to isolate phytopathogenic bacteria from soil and plant samples can also be used for these bacteria [28]. However, not all Pectobacterium species in this group can be distinguished using general tests traditionally used for bacteria and the Pectobacteriaceae family, and, thus, without genetic analysis there may be uncertainty in their taxonomic classification.

Thus, the development of genetic methods allows a more accurate study of similarities and differences among isolates of the Pectobacteriaceae family. For the correct identification of the microorganism, the availability of selective media is also important, since molecular genetic methods may not always be readily available to the agronomists. Currently, a number of nutrient and selective media are offered for the cultivation of Pcc. However, these media require improvement, so the development and improvement of media for the cultivation of Pcc is constantly underway.

Bacteriocins

Since Pc/Pcc is a necrotrophic phytopathogenic bacterium and has to compete for nutrients with other microorganisms, it has special antimicrobial compounds in its arsenal that help it successfully exist in its ecological niche. Pc/Pcc is capable of producing a wide range of bacteriocins—proteins that suppress or kill other bacteria. Such bacteriocins include pectocins and carocins. The genes encoding bacteriocins are often located on a plasmid. Pectocin is a protein toxin involved in intraspecific competition [41]. In Pectobacterium spp., two types of pectocins have been found: M1 and M2 [42]. Pectocins consist of a cytotoxic domain and a horizontally acquired plant-like ferredoxin, which is necessary for binding to the receptor and translocation into the cell [42]. Pectocin blocks the bacteria’s use of plant iron-containing proteins because it has a ferredoxin domain that allows it to exploit the FusA ferredoxin uptake system of plants [43]. FusA is an outer membrane receptor belonging to the TonB-dependent receptor (TBDR) family and responsible for the import of ferredoxin and pectocin into Pectobacterium spp. [44]. FusA belongs to a special type of outer membrane receptors of the family TonB-dependent Pectobacterium spp. These receptors bind microbial iron-retaining siderophores and host iron-containing proteins. Thanks to them, Pectobacterium spp. are also able to use plant ferredoxins as an iron source [44].

Pcc is capable of producing another type of low-molecular-weight bacteriocins—carocins [45]. These are small peptides similar to E. coli colicin. Currently, information on the functioning of Pcc carocins is very limited and much remains unclear. Pcc carocins have deoxyribonuclease or ribonuclease activity [45]. The crp gene, encoding the synthesis of the cyclic adenosine monophosphate (AMP) receptor protein, is involved in the synthesis of carocins. Deletion of crp was shown to inhibit genes involved in extracellular bacteriocin export via the flagellar type III secretion system and affected the production of many low molecular weight bacteriocins [46]. The dgc gene is recognized as responsible for the synthesis of low-molecular bacteriocins (carocin S2, carocin S3, carocin S4), and it also affects the genes of the flagellar type III secretion system, which exports bacteriocins from the cell and therefore, is an important virulence mechanism for Pcc [47]. The mechanism of secretion of Pcc bacteriocins is carried out through the bacterial flagellum type III secretion system (T3bSS), which uses the bacterial flagellum for extracellular secretion. It was found that the translocation-associated type III secretion system (T3aSS)-associated proteins, SctT, SctU, and SctV, act as flagellar T3SS chaperones in the secretion of Pcc bacteriocins for their extracellular export. The authors call this type of secretion a hybrid of the injectisome and flagellar secretion systems [48]. It has been shown that the expression of carocin genes is regulated by ultraviolet radiation [46].

It is important to briefly review the existing information on several important types of carocins synthesized by Pcc. Carocin S1 is a low molecular weight protein with nuclease activity [49]. Carocin S2 was found in Pcc strain 3F3 [46]. This protein is encoded by two genes, caroS2K and caroS2I, inhibits the growth of closely related strains due to the presence of ribonuclease activity, and is induced by ultraviolet radiation [50]. Carocin S2 is a ribonuclease responsible for binding sites between immune cells and killer proteins [46]. Other carocin proteins, Carocin S3K and Carocin S3I, have antagonistic activity against each other. Moreover, Carocin S3K had more pronounced antimicrobial and specific antimicrobial activity for Pcc along with nuclease activity than Carocin S3I. Moreover, Carocin S3I at high concentrations had DNA nuclease properties, and Carocin S3K inhibited its activity [45]. The low-molecular-weight bacteriocin CaroS4K (killer protein) and CaroS4I (immunity protein) encoded by the caroS4K and caroS4I genes were also detected [51]. CaroS4K is a deoxyribonuclease, as it has 23% and 85% homology with CaroS1K and CaroS3K, respectively. Moreover, CaroS4K is capable of hydrolyzing not only genomic DNA, but also plasmid DNA. CaroS4K is 90% homologous to CaroS2K, but has a different mechanism of action, since the latter is a ribonuclease [51]. Carocin D, which is imported by a unique colicin-like bacteriocin translocation system, was also detected [52].

Some E. carotovora Er isolates produce high-molecular-weight bacteriocins such as carotovoricin Er, which have similar structures to bacteriophages [53]. This bacteriocin has a morphology similar to the tail of the Myoviridae phage, with a contractile sheath and multiple tail fibers [54]. This bacteriocin has nuclease activity [55] and is synthesized by the bacterium in response to DNA-damaging agents [56].

Thus, Pcc are Gram-negative, motile, facultatively anaerobic bacteria that synthesize a wide range of low-molecular bacteriocins—pectocins and carocins, as well as high-molecular bacteriocins, which scientists have yet to characterize in more detail.

3. Plant Damage Symptoms, Virulence Factors and Effect of Temperature on Pathogenesis

3.1. Symptoms of the Disease

Pc has a strong survival rate, is widely distributed, and can remain in the soil or plants as saprophytes for more than a year [57]. Symptoms of Pcc damage include the wilting of plants, blackening of vessels on leaves, stems and petioles, through which the pathogen spreads. Pcc penetrates host cells through natural openings or wounds, and the bacteria then destroy the plant cell walls, causing them to soften [58]. Softening occurs due to the extracellular enzymes pectinase, cellulase, and protease, which in some studies are called maceration enzymes [59]. At the flowering stage, a gradual wilting of the stem core begins, starting from the root. This leads to stem breakage and death of crop plants [60]. It is important to consider in more detail the symptoms of soft rot damage to some vegetable crops. The symptoms of soft rot are briefly listed in Figure 2.

In potatoes, at the beginning of the growing season, the underground parts of the stolons can be affected by the Pc pathogen, which leads to slow growth and gradual death of the tops. In the middle of the growing season, the disease manifests itself as blackening and necrosis of the basal part of the stems, accompanied by wilting and yellowing of the leaves. The affected stems usually die before the tubers are fully ripe, which prevents the formation of a high-quality crop. Tubers collected from affected plants are often infected with the pathogen, which is noted during the storage period. When such tubers are planted, soft rot symptoms develop on the plants during the growing season [8].

In cabbage, the disease caused by Pc/Pcc is observed in the form of slimy bacteriosis. The first signs of the disease are noted in the second part of the growing season during the formation of heads. Blurry oily spots are observed on the affected leaves. These spots quickly spread to the entire leaf blade. Over time, such leaves darken, become slimy and rot. The affected stump softens and is initially creamy, and later turns into light gray. During the slow rotting of the stump, the infection can reach a growing point, but the disease remains unnoticed for a long time. With severe damage, such heads of cabbage break in the field. When the internally infected heads of cabbage end up in storage, they rot completely [2,4,61].

In peppers, bacteria, having penetrated the tissues, secrete the enzyme protopectinase, which dissolves the cell walls, so depressed watery spots appear on the stem, in the root collar area and on the fruits. They grow, the tissues soften, macerate, and a slimy mass with an unpleasant odor remains in their place. The fleshy parts of plants with mechanical damage are most severely affected. When the stem and root system are affected, the manifestation of the disease will coincide with root rot or wilting [12].

In onions in the field, infected leaves wither and dry out prematurely. A large, softened, light or slightly pinkish spot forms around the neck of the bulbs. In such bulbs, the outer layer of juicy scales is healthy, and the next two layers acquire a yellow-brown color and soften. When cutting an affected bulb, it is clear that the juicy scales and core are yellow-brown and slimy. The disease, starting from the neck, reaches the bottom of the bulb after 1.5–2 months. Affected bulbs acquire a sharp, unpleasant odor [10].

In turnips, infection begins with damage to underground organs. Infected tissues of the turnip root become soft, mushy, and watery. The lower leaves of the bush wither, curl and turn yellow; if the root is severely damaged, the stem may break. Mucous masses of bacteria flow out of cracks in the root tissue. In six days, the root can rot completely, appearing as a cream, brown or black mass with a putrid odor [11].

3.2. Methods of Plant Infection

High air humidity, droplet moisture, and temperatures above 15 °C promote the spread of the pathogen. During storage, wet rot from affected tubers, bulbs and fruits can spread to neighboring individuals. Bacteria penetrate through damage caused by heavy rain, hail, and early cutting of leaves or through damage caused by insects (onion fly, wireworm, mites). Tubers can also become infected through affected stolons or lenticels when bacteria from an affected mother tuber enter the root zone. Other sources of bacterial infection include infected plant debris and stumps, irrigation water, the rhizosphere of vegetables and some weeds. The pathogen penetrates the cabbage plant through damage to the outer leaves or through the stump from the soil. Bacteria survive in the soil on plant debris. During the growing season and fruit harvesting, bacteria are carried by water, wind, and during plant care and fruit harvesting—by hands and equipment. Primary infection of fruits occurs in the field, secondary—during storage [62].

Experiments were conducted on the widely distributed ornamental poinsettia plant Euphorbia pulcherrima to study the transmission of the Pc pathogen by cuttings. It was found that the transmission of Pc among unrooted cuttings through the dipping process is relatively low, depending on the susceptibility of the cultivars and the bacterial titer [15].

It is quite possible to infect plants with the soft rot pathogen when applying organic fertilizers. An interesting study was conducted by Sledz et al. [63], who showed that phytopathogenic bacteria are capable of growing on animal manure. Thus, it was shown that phytopathogenic bacteria Ralstonia solanacearum, Pectobacterium atrosepticum, Xanthomonas campestris pv. Campestris, and Pcc are capable of growing on cattle manure. Moreover, the growth rate of Pcc and P. atrosepticum on manure was higher than that of other phytopathogenic bacteria [63].

3.3. Virulence Factors

The successful infection of host plants depends on the interaction between the virulence factors of the phytopathogen and their transmission within the host plant organism [64]. The main virulence factors of E. carotovora ssp. carotovora (Ecc) include the synthesis of acyl-homoserine lactone and plant cell wall-degrading enzymes (PCWDEs)—pectinases, polygalacturonases, cellulases, and proteases. In addition, a number of new genes and proteins responsible for Ecc virulence have been identified in recent years [65]. Many bacterial phytopathogens, including Pc, use quorum sensing (QS)-based mechanisms for the expression of virulence genes, manifestation of pathogenicity, and regulation of PCWDEs [66]. It is important to consider in detail the virulence mechanisms of Pcc. The following key virulence proteins were identified in the Pc strain ICMP5702 isolated from potato: pectate lyase and metalloprotease enzymes, as well as plant cell wall-degrading PCWDEs, which disrupt flagellar motility, cell membrane structure, and the type III secretion systems of the AvrE family [67]. The main factors of Pcc virulence are schematically presented in Figure 2.

Pcc is a necrotrophic phytopathogen that secretes PCWDEs that cause soft rot in various crops. Maceration of plant tissue is caused by the production of various PCWDEs by Pc, including pectinases (an enzyme that breaks down pectin, a polysaccharide), polygalacturonase (an enzyme that degrades pectin), cellulases (an enzyme that catalyzes the hydrolysis of cellulose to form glucose or the disaccharide cellobiose), and protease (an enzyme that catabolizes proteins) [57]. It has been shown that maceration induced by Pcc S1 is due to the suppression of callose deposition in the plant and the superlytic capacity of pectinolytic enzymes produced in Pcc S1 [68]. These exoenzymes are secreted through the type II secretion system (T2SS) under the control of the QS system, which involves a complex interaction of transcription factors and post-transcriptional regulators and depends on N-acyl homoserine lactones (AHLs) [64,69]. The type II secretion system (T2SS) transports fully folded proteins across the outer membrane of Gram-negative bacteria. The Pel3 Pc pectinase is secreted outward through several distant and structurally flexible loop regions in the membrane. These loop regions act together as an integral mechanism of the secretion system [70]. Pectate lyases (EC 4.2.2.2), also called trans-eliminases, catalyze the cleavage of pectate via a β-elimination reaction to form 4,5-unsaturated oligogalacturonates [71]. The studied bacterium also has other pectate lyases, for example, an extracellular pectate lyase (PL, EC 4.2.2.2) produced by Pcc BR1, which has a high affinity for polygalacturonic acid [72]. There are even commercial preparations based on Pcc pectate lyase, for example, pectate lyase 2A (PcPel2A), which is an endo-1,4-α-polygalacturonic acid lyase (https://www.nzytech.com/en/pectate-lyase-2a-pectobacterium-carotovorum-pl2, accessed on 25 March 2025). It is interesting that the pectate lyase activity of some Pcc isolates correlates with the ambient temperature. Thus, it was shown that the highest pectate lyase activity of isolate ZT0505 was detected at 28 °C, while the standard temperature for Pcc existence is 14–17 °C [73]. The diversity of pectate lyases is presented in [68], where the results of transcriptome analysis of PccS1 recovered from Zantedeschia odorata P.L. Perry were presented. In the PccS1 genome, 27 genes encoding pectinases were found, of which 13 encode pectate lyase, and six of them were induced upon plant infection.

The type III secretion system (T3SS) is used by many pathogenic Gram-negative bacteria to deliver virulence proteins (known as effector proteins) into plant cells. Once inoculated, the effector proteins suppress the plant’s defense mechanisms and promote the proliferation of the plant pathogen. Unlike many other bacterial plant pathogens, the Pc T3SS appears to secrete only one effector protein, DspE [74].

An important virulence factor of Pcc is biofilm formation. Due to the ability to attach and form a biofilm, Pc effectively infects plant tissues, and also acquires resistance and survives in various field conditions [75]. Biofilm formation in bacteria is also based on QS. In Pcc, AHLs are responsible for this process, which regulate the expression of virulence factors in Pcc by influencing QS [76]. The synthesis and recognition of AHLs signaling molecules that coordinate cellular activity in the population of these Gram-negative bacteria is regulated by ExpI and ExpR proteins [64,66]. In Pectobacterium spp., the ExpI protein is directly involved in the synthesis of AHLs. The ExpR protein functions as an activator that binds to the promoter, turns it on, and initiates the transcription of virulence-associated genes [66,77]. According to the type of AHLs, there are two QS classes: QS class II-1 strains producing N-(3-oxooctanoyl)-L-homoserine lactone (3-oxo-C8-HSL) and QS class II-1 strains producing N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) [78]. In the bacterial suspension of Pcc, the maximum content of N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) was observed at the end of the logarithmic growth phase. During the stationary growth phase, OHHL was destroyed and its amount decreased further during the cell death phase [79]. PCWDEs and the ability to form biofilms of the bacterium are virulence factors that contribute to the ability of the bacterium to macerate plant organs and tissues [3]. Importantly, due to the production of biofilms, this pathogen is more resistant to physical and chemical treatments, making it more resistant than free-living bacteria in various environments even under unfavorable conditions [3].

Several researchers have identified genes encoding proteins with various functions that can influence Pcc virulence. These genes include svx, cpxR, wcaG, and hfq [80,81,82,83]. The proteins encoded by these genes are secreted by phytopathogenic bacteria into the cell wall of the host plant. One of the main virulence factors of almost all representatives of the genus Pectobacterium are Svx proteins [83]. In the Pc-related species P. atrosepticum, it was shown that these proteins encoded by the svx gene are glycopeptidase capable of cleaving α-glycosylated proteins, which are represented in the plant cell wall by extensin proteins involved in cell signaling and ensuring its rigidity [84]. Svx proteins in P. atrosepticum and Dickeya solani were shown to be glucocorticoid metallopeptidases with conserved tertiary structures and had phytoimmunosuppressive properties, inducing ethylene-sensitive plant responses that play a critical role in disease caused by these pathogens [83].

The cpxR gene was found in the Pc genome, encoding a cytoplasmic response regulator that affects virulence, biofilm formation, chemotaxis, and antimicrobial resistance [82]. Pcc PC1 mutants with a deletion in the cytR gene (ΔcytR), homologous to the cpxR gene, and the fliC genes (ΔfliC), encoding flagellin, and motA (ΔmotA), encoding a membrane protein required for flagellar rotation, as well as mutants with an insertion of the Tn5 transposon in the flhD gene (flhD::Tn5), encoding a protein included in the FlhD/FlhC complex that serves as a master regulator for flagellar synthesis and motility in bacteria, produced thin and fragile biofilms with a lower cellulose content compared to the control [85].

Using celery slices and carrot discs, it was shown that wcaG, encoding a NAD-dependent epimerase/dehydratase, is involved in the biosynthesis of the exopolysaccharide, colanic acid Pc [81]. Colanic acid promotes biofilm formation, the creation of a capsule and mucus layer around Enterobacteriaceae bacterial cells [86]. The hfq gene, encoding the RNA chaperone Pc, affects the virulence of the bacterium and the activity of the enzyme that degrades the plant cell wall [80]. Mutants in this gene were characterized by reduced biofilm formation, bacterial motility, and reduced secretion of hemolysin coregulated protein (Hcp) [80].

Pc is capable of synthesizing expansins, protein mediators of pH-dependent cell wall stretching. Expansins are proteins involved in loosening the plant cell wall. The Pc expansin Exl1 is located in the intercellular spaces between xylem vessels and adjacent plant xylem cells and binds primarily to tracheal elements using pectin, cellulose, and hemicellulose polymers [87].

The results presented in this section demonstrate the diversity of Pcc virulence factors. Despite the constant discoveries in this field, there are still many “blank spots” to date, for example, the diversity, structure, and function of all PCWDEs, effector proteins of secretion systems, and expansin proteins are still insufficiently studied.

3.4. Effect of Temperature on Virulence

Although Pcc is very resistant to environmental factors, its virulence can be affected by ambient temperature. Saha et al. [79] investigated the effect of elevated temperatures (24, 26, 28, 30, 33, 35, and 37 °C) on the intensity of Pcc synthesis of the essential molecule for QS, OHHL. The highest OHHL synthesis and maximum disease severity were detected at 33 °C. At 35 and 37 °C, OHHL was not detected at all, and tomato plants were not affected by soft rot [79]. Su et al. [88] also showed that the pathogenicity of Pc increased with increasing temperature at 20, 25, 28, and 32 °C. Jee et al. [89] evaluated the virulence of different Pectobacterium species at 24, 28, 32, and 37 °C. Most of them showed more virulence at 28 °C and 32 °C than at 24 °C and weak activity at 37 °C. Pectolytic, protease, cellulase, and polygalacturonase activities decreased with increasing temperature. Pectate lyase activity was not significantly affected by temperature. The inability of isolated Pectobacterium to soften host tissues at 37 °C was attributed to decreased motility and PCWDE activity [89].

Thus, the symptoms of soft rot disease are associated with the wilting of plant stems during the growing season with the subsequent death of the plant, as well as with the maceration of tuber and bulb tissues during storage. Infection can occur during the growing season through wounds, when applying fertilizers, from an affected mother plant, through harvesting equipment, and during storage from neighboring infected plants. The main virulence factors of Pc include the synthesis of acylgomoserine lactone, as well as enzymes and other proteins that destroy the plant cell wall. Although elevated temperatures negatively affect the viability of Pc, global warming in recent years has not yet slowed down the spread of Pc; on the contrary, an expansion of the spread of Pc to northern and eastern territories is observed [90].

4. Diagnosis of the Disease

Diagnostic methods for Pcc include reverse transcription quantitative real-time PCR (RT-qPCR), loop-mediated isothermal amplification (LAMP), multilocus sequence typing (MLST), and detection of unique volatile organic compounds (VOCs). The main methods of Pcc diagnostics are schematically presented in Figure 2.

Test systems for RT-qPCR operating in a unified Pc amplification mode have been developed. The test systems (including polymerase and reverse transcriptase) are immobilized and lyophilized in miniature microreactors (1.2 μL) on silicon DNA/RNA microarrays [91]. A real-time PCR method for diagnosing Pc in potato tissues has been developed based on the Pcar1F/R primer pair for a variable segment of 16S rRNA and intergenic spacer allowing efficient discrimination of different Pectobacterium species [92]. There is a multiplex PCR protocol for the simultaneous detection of R. solanacearum and Pcc in potato tubers [93]. Since the titer of Pcc cells at the early stages of plant infection is low, enrichment methods and efficient separation of pathogens are desirable for sensitive monitoring. For this purpose, it is proposed to pre-treat fresh produce to concentrate the pathogen prior to real-time PCR using silicon-coated magnetic nanoparticles (NPs) [94].

LAMP is a rapid test that detects Pc with high specificity [95]. LAMP typically targets a unique genomic region and, when combined with lateral flow immunoassay (LFA), allows visualization of Pcc [96]. In potato and Chinese cabbage, this method was able to detect Pcc at titers of 1.57 × 10² CFU/g and 1.29 × 10² CFU/g, respectively [96]. In affected plants, the presence of Pc can be detected using MLST of the dnaX, mdh, icdA, and proA genes [97].

Phytopathogens are capable of influencing the qualitative and quantitative composition of plant VOCs [98]. Ray et al. [99] proposed using the detection of unique VOCs as markers of Pcc infection of potato tubers. Using gas chromatography-mass spectrometry, they found differences in 27 VOCs between the control and Pcc-infected potatoes. In addition, the content of peroxide and methyl jasmonate increased in infected tissues [99]. Using the same method, but already on cabbage, it was shown that when infected with Pcc, plants release specific volatile substances with an odor [100]. Thus, 4-ethyl-5-methylthiazole and 3-butenyl isothiocyanate were found in uninfected cabbage, and 2,3-butanediol and ethyl acetate were found in cabbage infected with Pcc [100]. Other researchers have also paid great attention to VOCs in the pathogenesis of potato soft rot during the period of tuber curing [101]. Thus, infection with Pc leads to the detection of 130 compounds in the tissues of infected potatoes using the HS-SPME-GC-MS method, including sesquiterpenes, dimethyl disulfide, 1,2,4-trimethylbenzene, 2,6,11-trimethyldodecane, benzothiazole, 3-octanol and 2-butanol [101]. Kate et al. [102] also proposed the use of VOCs to identify plants affected by Pcc. They considered 1-butanol and 1-hexanol to be biomarkers of bacterial spoilage of potato tubers by Pc during storage [102].

A substrate with surface Raman amplification was created for the rapid and accurate detection of Pcc in kimchi cabbage, where silver nanospheres, silver nanowires and nanosembles are combined on a polydimethylsiloxane platform [58]. The substrate yielded strong Raman signals at Pcc concentrations ranging from 10¹ to 10⁶ CFU/mL [58].

The information presented above indicates that standard effective methods for detecting the Pcc pathogen in plant tissues have now been developed. In addition to the classical methods, new methods for detecting this phytopathogen are emerging. However, due to global climate change, which leads to the expansion of the range of phytopathogens, new isolates of Pcc are constantly being discovered and studied. Therefore, methods for identifying such a pathogen must be constantly improved.

5. Plant Defense Reaction

The plant defense response to Pcc infection is associated with both changes at the gene expression and metabolomic levels. Such changes lead to a specific plant response to biotic stress. Micro RNAs are also involved in this process. In addition, Pcc infection leads to shifts in the qualitative and quantitative composition of the plant microbiome. These responses are discussed in more detail below. The main plant defense reactions to infection by Pcc are schematically presented in Figure 2.

5.1. Gene Expression in Plant Tissues During Pcc Infection

When tomato (Solanum lycopersicum L.) was infected with Pcc, the expression of Myb transcription factor, ethylene response element binding protein EREBP (stress-related factors), CytP450, hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase HQT (resistance biomarker), pathogenesis-related proteins PR3 and PR6, and resistance protein CC-NBS-LRR genes significantly increased in plant tissues after 24 h of inoculation [103].

The expression of 13 key inducible defense response genes in Chilli pepper (Capsicum annuum L.) showed that at 24 h following bacterium inoculation with Pcc, the expression profiles of all the genes including Myb (MYB transcriptor factor), EREBP (ethylene response element-binding protein), SGT1 (suppressor of the G2 allele of Skp1), CytP450 (cytochrome P450), SAR1-GTPase (small Sar1 GTPase), HQT (hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase), PR1 (pathogenesis-related protein 1a), PR2 (endo-1,3-b-glucanase), PR3 (chitinase), PR6 (proteinase inhibitor), PR12 (defensin), CC–NBS–LRR (oiled-coil-nucleotide-binding site-leucine-rich repeat), and PAL (phenylalanine ammonia lyase) genes were significantly upregulated, with a maximum expression of 10-fold observed for CC–NBS–LRR. At 72 h, the qPCR results showed that only the expression profile of CytP450 was significantly downregulated by 10-fold compared with the control sample following inoculation with Pcc [12].

One of the strategies for the plant control of soft rot pathogen is the ectopic expression of the plant ferredoxin-like protein (PFLP) gene pflp [104]. PFLP enhanced pathogen-associated molecular pattern-trigger immunity, promoted rapid H₂O₂ formation, callose deposition, and hypersensitive response, affected the expression of the FLG22-induced receptor kinase 1 gene, which is part of the mitogen-activated protein kinase (MAPK) pathway, and increased the expression of PR1 and PDF1.2 genes in tissues of transgenic plants [104].

The ERF96 gene of Arabidopsis thaliana (L.) Heynh. is an ethylene sensitivity factor. Its overexpression increased resistance to necrotrophic pathogens, including Pc, by enhancing the expression of the defense genes encoding the hormones jasmonic acid and ethylene, as well as genes for resistance to biotic stress PR-3 and PR-4 [105].

To identify the mechanisms of Pcc pathogenesis, a model experiment was conducted on mosses. Physcomitrium patens (Hedw.) Mitt. was treated with Pc elicitors, and gene expression was analyzed [106]. In total, 239 differentially expressed genes (DEGs) were found, including genes associated with the shikimate, phenylpropanoid, and oxylipin pathways, and the synthesis of cinnamic acid and auxins increased. Strengthening of the cell wall due to the deposition of phenolic compounds and callose in the moss was also noted [106].

In the medicinal plant Pinellia ternata (Thunb.) Makino, transcriptome analysis showed that external signs of plant wilting 20 h after Pc infection were reflected in gene expression [107]. It was accompanied by the increased expression of genes encoding cell wall proteins, receptor kinases, and enzymes and proteins involved in defense mechanisms during biotic stress (cationic peroxidase, chitinase, EP3-like endochitinase, thaumatin-like protein). In addition, activation of calcium and phospholipid transporters, ATPases, was noted 20 h after infection. At the same time, the reduced expression of pectate lyase, expansin, PR1, and RPS2 genes was noted [107].

In chili pepper, it was also shown that Pcc infection resulted in a decrease in the levels of acetylcarnitine, adenosine, adenosine-3′,5′-cyclic monophosphate, guanosine-3′,5′-cyclic monophosphate, and inosine in leaf tissues [12].

To identify the mechanisms of Pcc plant damage and the genes responsible for this process, experiments with mutant strains are actively being carried out. Thus, studies of the M29 mutant (transposon insertion mutation in the metC gene encoding cystathionine β-lyase that catalyzes cystathionine to homocysteine at the penultimate step in methionine biosynthesis) showed a reduction in disease symptoms in Chinese cabbage and potatoes [108]. It was shown that the pre-treatment of Chinese cabbage plants with OHHL leads to the accumulation of jasmonic acid, which increased the plant’s resistance to Pc [109].

During the pathogenesis of Pcc, reactive oxygen species (ROS) are formed, which leads to the induction of cyanide-resistant respiration in potato tubers, suppressing the production of H₂O₂ [110]. It was shown that during the development of infection in potato tubers, the proportion of alternative respiration increased in plant cells, which was accompanied by an increase in the potential of the mitochondrial membrane [111].

It has been shown in A. thaliana that the archaea Nitrosocosmicus oleophilus MY3 is able to colonize the plant root surface, release volatiles, and enhance resistance to phytopathogens, including Pc, through salicylic acid-independent signaling pathways [112]. It has also been shown that defensins, cysteine-rich proteins with fungicidal activity, may also play a role in A. thaliana resistance to Pcc [113].

5.2. Small RNAs

In the process of plant-microbe interactions, plants are able to suppress gene expression at the transcript and post-transcriptional levels by small RNAs in response to pathogenesis [114]. In a model experiment, changes in the expression profile of some stress-sensitive miRNAs and the differential expression pattern of a number of target genes were investigated in A. thaliana inoculated with Pcc [115]. It has been shown that the infection of A. thaliana with Pcc results in the overexpression of six miRNAs at 24, 48, and 72 h and the downregulation of their target genes, while the expression of two miRNAs did not affect their target genes [115].

5.3. Impact of Pcc Infection on Plant Microbiome

Infection of plants with Pcc also affects the microbiome of the plant. It was shown that bacterial and fungal communities of the rhizosphere changed in two plant species of the genus Amorphophallus—Amorphophallus muelleri Blume and Amorphophallus konjac K. Koch infected by Pcc [116]. It was found that the changes depended on the species. Thus, the number of microorganisms of the phyla Actinobacteria, Chloroflexi, Acidobacteria, Firmicutes, and the genera Bacillus and Lysobacter was lower in the infected A. konjac plants than in the healthy plants, but on the contrary, it was higher in the infected A. muelleri plants than in the healthy plants. The number of fungi of the phylum Ascomycota and the genus Fusarium in the rhizosphere of the infected A. konjac plants was significantly higher than in healthy plants, but it was lower in infected A. muelleri plants than in healthy plants. A completely opposite result was demonstrated for the presence of Penicillium fungi [116]. The number of saprophytic fungi Cladosporium increased upon infection in both plant species, with this effect being more pronounced in A. muelleri than in A. konjac [13]. In another study using the same plant, the qualitative and quantitative composition of soil microflora was analyzed when A. konjac was grown in the field, where plants were affected by soft rot to varying degrees [117]. Damage severity increased with increasing the amount of organic matter and available N, P, and K in the soil. Higher damage severity was associated with decreased soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). Bacteria of the phylum Proteobacteria dominated in all studied soil samples. In soil unaffected by Pc, representatives of the genera Pseudomonas, Bacillus, Rhizobium, and Streptomyces were widespread. Pc and Serratia spp. predominated in soils with severe and moderate damage. At the same time, the diversity and number of rhizosphere bacteria were higher in areas with unaffected soil. The authors associate this with a change in the content of available potassium in the soil, the activity of sucrase and urease [117].

The danger of Pcc development on crop plants is also associated with the possible colonization of affected fruits by other bacteria pathogenic to humans and animals. Thus, George et al. [118] report that when plants are affected by Pc, they can be colonized by Salmonella spp. that experiences a metabolic shift in the current situation, which affects the mobility of the bacterium, its synthesis of nucleotides and amino acids. Salmonella enterica has been shown to be able to successfully survive in plant media, and Pc increases its survival [119].

5.4. Resistance of Different Plant Varieties and Hybrids

Different crop varieties may have different resistance to soft rot. Agronomists recommend growing mainly resistant varieties to combat this disease. Therefore, it is very important to study the varietal specificity of plants when infected with different Pcc strains. Thus, Lee et al. [7] tested four radish varieties for resistance to different Pc strains. They found that Pc strains exhibited different virulence in susceptible varieties. The intensity of disease progression positively correlated with the virulence of the strains, and the number of resistant varieties decreased with the increasing virulence of Pc strains [7]. At the same time, differences in resistance were observed both between varieties of the same species and between closely related species. Yang et al. [13] studied the response of resistant A. muelleri and susceptible A. konjac species of konjac to infection with Pcc. At the transcript and metabolite level, the plant responses were similar, with differences noted only in the change in the qualitative and quantitative composition of the plant endophytic microflora [13]. Experiments were carried out on plants of the same genus to study DEGs and differentially accumulated metabolites associated with phytohormones, biosynthesis of phenylpropanoids, and other alkaloids [117]. The involvement of the genes of the phenylpropane biosynthesis pathway (PAL, CYP73A16, CCOAOMT1), an oxidative stress-related gene (RBOHD) and a calcium ion channel-related gene (CDPK20), in the response of konjac to Pcc was found [120]. Luo et al. [20] compared the transcriptome of Pcc-resistant and susceptible Pinellia ternata Breit. It was found that 33 zinc finger proteins (ZFP) genes were differentially expressed upon Pc infection. In plant tissues of the resistant variety, some of these genes were increased 24 h after infection and increased further after 48 h [20]. Interspecific hybridization between Ornithogalum thyrsoides (Chincherinchee) and O. dubium Houtt. produced hybrids with increased resistance to Pectobacterium infection [18].

Thus, Pcc infection leads to standard reactions of a plant organism to a necrotrophic phytopathogenic bacterium. Plants have been noted to have increased expression of genes involved in cell protection under stress, in particular PR genes. In addition, the expression of genes responsible for hormone synthesis and antioxidant enzyme activity increased. A change in the expression profile of some stress-sensitive miRNAs was noted as well during soft rot pathogenesis. Such events led to the accumulation of jasmonic acid and the induction of cyanide-resistant respiration, and affected both the qualitative and quantitative composition of the plant microbe. Varieties and hybrids characterized by increased resistance to soft rot have been created.

6. Methods to Control Pcc

6.1. Agrotechnical Methods

To regulate the number of phytopathogen Pcc, a number of agricultural practices are recommended. It is recommended to choose fields with structured drained soil for planting crops, which does not allow water to accumulate. Increased soil moisture is especially dangerous during the period from the beginning of bulb or tuber formation until harvesting. During the growing season, it is important to use the rational application of nitrogen fertilizers and mechanically remove diseased plants from the field. It is necessary to protect plantings from receiving injuries from hail and rain. It is better to harvest onions when at least one third of the plants are naturally lodging. During storage, it is necessary to maintain optimal temperature and humidity in vegetable storage facilities, so the bulbs should be stored in dry and cool conditions (at a temperature of 0–2 °C). Storage conditions for cabbage heads also affect the development of this infection during the winter. Low temperatures (−1–+2 °C) slow down the decay processes to a significant extent [62].

Pcc is characterized by high resistance to external factors. Pesticides used in agriculture are usually aimed at combating phytopathogenic fungi and are often useless in relation to phytopathogenic bacteria. In addition to agricultural techniques for regulating the number of phytopathogen Pcc, the use of chemicals of various nature and plant extracts have been actively studied in the last decade; the influence of other bacteria, fungi and viruses on Pcc has been studied and reviewed below, respectively.

6.2. Chemical Substance

Pcc is actively used in various studies to test the presence of antimicrobial activity of various substances with pesticide potential. Among the chemicals studied for the viability and pathogenicity of Pcc are acids (salicylic acid, phenylacetic acid, linolenic fatty acid hydroperoxide), phenols, esters, salts (sodium hypochlorite, potassium tetraborate tetrahydrate, sodium salt of nalidixic acid), gaseous substances (ozone, chlorine), and ozonated water.

Salicylic acid is a well-known plant signaling molecule that mediates defense against biotic stress [121]. Salicylic acid at high doses of 800 and 1200 mg L⁻¹ was shown to inhibit the growth of Pcc bacteria [122]. Ethyl N^α-lauroyl arginate ester (LAE) resulted in increased membrane permeability, decreased membrane potential of Pcc and damaged organelles in bacteria [123]. Phenylacetic acid promoted plant growth and induced systemic resistance in tobacco (Nicotianum tabacum L. cv. Xanthi) against Pcc [124]. Víchová et al. [125] showed that treatment of potato slices by cinnamaldehyde (0.5 μL mL⁻¹), l-menthone (2.5 μL mL⁻¹ and carvacrol (5–10 μL mL⁻¹) did not cause rotting on slices of potato tubers [125]. Hong et al. [3] demonstrated that the treatment of knifes by sodium hypochlorite (NaOCl) when harvesting Chinese cabbage delayed the development of disease symptoms of soft rot and also affected the expression of PG10, PG12-1, PG12-3, WRKY 33, MPK3, ACO1, and ACO2 genes [3]. Potassium tetraborate tetrahydrate at a concentration of 100 mM caused complete inhibition of Pc growth in tomato as a result of the destruction of the bacterial membrane [126]. In addition, the authors suggest immersing fruits in potassium tetraborate tetrahydrate for 5–10 min to avoid the development of soft rot [126]. Bacteriostatic and biocidal effects in relation to Pc at a concentration of 0.075 mg mL⁻¹ were demonstrated by ZnAl-NADS, in which the sodium salt of nalidixic acid (NADS) is bound to the layered double hydroxide ZnAl-NO₃ (LDH) used as a nanocarrier [127]. Çetinkaya et al. [128] proposed treating plants with gaseous ozone (O₃) and ozonated water to combat Pcc on the bulbs of cultivated plants [128]. Linolenic fatty acid hydroperoxide has a dose-dependent effect on Pc by influencing the bacterial membrane and causing rearrangements in it [129]. To prevent tomato fruit infection with soft rot, Bartz et al. [130] proposed treating them with chlorine. Model experiments demonstrated that such chlorine treatment of artificially inoculated fruits 1 h after infection was effective [130].

It is also proposed to treat potato tubers with antibiotics to combat Pc [131,132]. However, there are antibiotic-resistant strains of Pcc [133]. To solve this problem, it is proposed to use a combination of plant treatments with antibiotics and other chemicals. Thus, streptomycin is used with carvacrol, which disrupts the permeability of the pathogen’s cell membrane and the integrity of the cell wall. This reduces the severity of the disease and inhibits the motility and secretion of extracellular hydrolase Pcc [133].

Table 1. Effect of chemical substance on Pcc and soft rot disease.

Substance	Effects	Reference
salicylic acid	inhibit the growth of Pcc bacteria	[122]
ethyl Nα-lauroyl arginate ester (LAE)	increased membrane permeability, decreased membrane potential of Pcc and damaged organelles in bacteria	[123]
phenylacetic acid	induced systemic resistance in tobacco against Pcc	[124]
cinnamaldehyde, l-menthone and carvacrol	blocking disease development symptoms on potato slices	[125]
NaOCl	delayed the development of disease symptoms of soft rot and also affected gene expression in plant tissues	[3]
potassium tetraborate tetrahydrate	destruction of bacterial membrane, inhibition of bacterial growth	[126]
ZnAl-NADS	bacteriostatic and biocidal effects	[127]
O3, ozonated water	recovering plant bulbs from soft rot	[128]
linolenic fatty acid hydroperoxide	rearrangements in the bacterial membrane	[129]
Cl	improving tomato resistance to soft rot infection	[130]
antibiotics	antibacterial action	[131,132,133]

briefly summarizes the published data on the effect of chemical substance on Pcc and soft rot disease.

The study of chemical agents that can control the number of Pcc and suppress the development of soft rot disease is a promising direction of modern science, which can reduce crop losses. However, when developing such compounds, it is necessary to take into account the danger of potential environmental pollution and the impact on the plant organism.

6.3. Plant Extracts

The influence of extracts of different plants—herbs, shrubs, trees and algae—on the Pcc is actively studied and reviewed below in detail.

6.3.1. Herbaceous Plants

Extract of rhubarb (Rheum tanguticum Maxim. ex Balf.) inhibited the synthesis of bacterial beta-lactam resistance proteins, the two-component system, and the phosphotransferase system in Pcc [134]. Visually, it was manifested as a decrease in the motility of bacterial flagella and affected the motility of Pcc cells [134]. Cai et al. [135] found that essential oil of Polygonum orientale L. destroyed the Pcc at a concentration of 0.625 mg mL⁻¹ due to increasing permeability of the cell membrane and a decrease in the membrane potential, as well as influence on bacterial enzymes [135]. Park et al. [136] showed the synergistic antimicrobial activity of palmarosa (Cymbopogon martini (Roxb.) W.Watson) nanoemulsion and citric acid against Pc. They affected the membrane integrity and led to intracellular ATP depletion [136]. Ethanol extract of Salsola kali demonstrated high antibacterial activity against Pc due to the presence of several polyphenolic compounds in the extract: gallic acid, caffeic acid, cinnamic acid, chlorogenic acid, quercetin, and hesperetin [137]. Essential oil of Mentha piperita at a concentration of 3 μL mL⁻¹ effectively inhibited the viability of Pcc [138]. Extract of Datura stramonium L. seeds and Urtica dioica L. leaves demonstrated both antibacterial activity against Pcc and a reduction in the development of disease symptoms after their treatment of potato tubers [139]. Antibacterial effect against Pcc was also detected in extracts of some ornamental crops, such as leaf extract of Duranta plumieri Jacq. and Lantana camara L. [140]. Ethanol extract of seeds and berry peel of silverleaf nightshade Solanum elaeagnifolium Cav. at a concentration of 100 μg mL⁻¹ exerted a pronounced bactericidal effect on E. carotovora [141].

Rhapontigenin, which is produced in some plant tissues (e.g., rhubarb), is able to inhibit QS of bacteria by inhibiting violacilin production [142]. Rhapontigenin showed significant inhibition of motility, exopolysaccharides (EPS) production, biofilm formation, virulence–exoenzyme synthesis, and AHL production by Pcc. Li et al. [4] reported that rhapontigenin could help to extend the shelf life of vegetables by reducing the incidence of soft rot symptoms [4]. An extract of the flowering plant Falcaria vulgaris reduced the maceration intensity of Pcc plant tissues due to the presence of QS inhibitors (QSIs)—oleic acid, n-hexadecanoic acid, cytidine, and linoleic acid [143]. Crude extract of barnyard grass Echinochloa crus-galli (L.) P. Beauv. contained phenolic compounds that exerted antibacterial effects on Pcc [144].

6.3.2. Shrubs and Trees

Methanolic extracts of rosemary Salvia rosmarinus L. are able to inactivate pectate lyase 1 and endo-polygalacturonase of Pcc [145]. Methanolic extract from the shrub Salsola imbricata (Forssk.) Moq. demonstrated high antimicrobial activity against Pc due to the high content of gallic, syringic, and caffeic acids [146]. Grapevine extract reduced the adhesive properties of Pc [147]. The leaf extract of the tropical shrub Lantana camara L. contains 5,8-diethyl-dodecane, pyrimidin-2-one, 4-[N-methylureido]-1-[4-methylaminocarbonyloxymethyl, oleic acid, 3-(octadecyloxy)propyl ether and has pronounced antimicrobial activity against Pc [140]. The essential oil of the perennial herbaceous fern Pteridium aquilinum L. contains linalool, carvacrol, benzaldehyde, 2-undecanone, and cuminaldehyde, and has a potent antimicrobial effect against Pcc at a concentration of 2.50 μL mL⁻¹ [148].

Cinnamaldehyde extracted from cinnamon bark essential oil obtained from bark of Cinnamomum verum J. Presl, 1825 affected the expression of 1907 genes in Pc BP201601 treated with 500 μg mL⁻¹ cinnamaldehyde [149]. For post-harvest preservation of potato crops, it is proposed to cover tubers with a film of carboxymethyl cellulose with green tea extract [150]. It was found that oak bark extract reduced the synthesis of acyl-HSL Pc, which also led to a decrease in bacterial cellulolytic and protease activity, and inhibition of genes associated with QS, in particular the expR/expI genes [151]. Potato tubers treated with oak bark extract were resistant to the disease. This biological activity of oak bark extracts is associated with the presence of the following active substances: n-hexadecanoic acid, 2,6-di-tert-butyl-4-methylphenol, butylated hydroxytoluene, gamma-sitosterol, and lupeol [151]. Citrus peel polyphenols have antimicrobial activity against Pc [152]. Butanol extract of Callistemon viminalis (Sol. ex Gaertn.) G. Don ex Loudon (1830) flowers (active ingredients: palmitic acid, 2-hydroxymyristic acid, 5-hydroxymethylfurfural, and shikimic acid) and butanol extract of Eucalyptus camaldulensis Dehnh., 1832 bark (active ingredients of the extract: methyl ester of 8-nonynic acid, camphor, menthol, and 1,8-cineole) inhibited the growth of Pc [153]. Punica granatum L. fruit peel extract at a concentration of 50 mg inhibited the growth of Pcc (inhibition zone 0.92 cm) [154]. Published data on the effect of plant extracts on Pcc and soft rot disease are briefly summarized in

Table 2. Brief summary of published data on the effects of plant extracts on Pcc and soft rot disease.

Species	Substance	Antimicrobial Effects on Pcc	Reference
Herbaceous plants
Rheum tanguticum	extract	decreased motility of Pcc bacterial flagella	[134]
		inhibition of QS Pcc	[142]
Polygonum orientale	essential oil	increase in the surface potential of the Pcc cell and its hydrophobicity, damage to the cell wall, destruction of the integrity and permeability of the cell membrane, suppression of the activity of bacterial enzymes pyruvate kinase, succinate dehydrogenase and adenosine triphosphatase	[135]
Cymbopogon martini	nanoemulsions and citric acid	effects on membrane integrity and intracellular ATP depletion	[136]
Salsola kali	ethanol extract	antibacterial activity (well method)	[137]
Mentha piperita	essential oil	antibacterial activity (well method)	[138]
Datura stramonium Urtica dioica	seed extract leaf extract	antibacterial activity (well method), reduction of disease symptoms development after potato tubers treatment	[139]
Falcaria vulgaris	extract	inhibition of QS Pcc	[143]
Echinochloa crus-galli	crude extract	antibacterial activity (well method)	[144]
Solanum elaeagnifolium	ethanol extract	antibacterial activity (well method)	[141]
Shrubs and Trees
Salvia rosmarinus	methanol extract	inactivation of pectate lyase 1 and endopolygalacturonase	[145]
Salsola imbricata	methanol extract	antibacterial activity (well method)	[146]
Vitis vinifera	extract	reduced the adhesive properties of Pcc	[147]
Duranta plumieri Lantana camara	leaf extract	antibacterial activity (well method)	[140]
Pteridium aquilinum	essential oil	antibacterial activity (well method)	[148]
Cinnamomum cassia	bark	impaired aerobic respiration of Pc, effects on nitrate reductase activity and regulation of the citrate cycle	[149]
Camellia sinensis	film of carboxymethylcellulose with extract of leaves	reducing tuber infection during storage	[150]
Quercus sp. cortex	bark extract	decreased acyl-HSL Pc synthesis, decreased bacterial cellulolytic and protease activity, inhibition of QS-related genes	[151]
Callistemon viminalis Eucalyptus camaldulensis	butanol extract from flowers; bark	antibacterial activity (well method)	[153]
Punica granatum	fruit peel extract	antibacterial activity (well method)	[154]

.

6.3.3. Seaweed

A hexane extract of the microalga Dunaliella salina had antimicrobial activity against Pcc, and its treatment of candied fruit and tomato plants significantly reduced the development of soft rot [155].

Thus, the data presented in Section 6.3. demonstrate that the studies of extracts of various plants that suppress Pcc are actively underway. Pronounced effects on the viability of the bacterium and the pathogenesis of soft rot are detected due to the presence of compounds with high biological activity in plant extracts. However, it is a challenge to determine the right quantities of active substances for use in real field conditions which at the same time have no negative effect on plants, since plant extracts are often obtained on the basis of unsafe chemicals.

7. Competition and Interaction of Pcc with Bacteria, Fungi, Bacteriophages

Bacteria are able to compete with each other by synthesizing a whole arsenal of antibacterial compounds. There are many studies devoted to the use of bacteria to regulate the number of Pcc, as this method seems to be an environmentally friendly alternative to chemicals. Among the most frequently used microorganisms for this purpose are representatives of the genera Bacillus, Pseudomonas, lactic acid bacteria, and streptomycetes.

7.1. Bacillus spp.

Bacillus velezensis CE 100 suppressed the growth of Pc, reduced its damage to cucumbers, and stimulated plant growth and development [156]. Free cell lysate of the endophytic B. thuringiensis strain KMCL07 was shown to attenuate Pcc virulence by suppressing the QS system [59]. The lysate inhibited the production of extracellular enzymes (pectate lyase, cellulose, and proteinase) that cause Pcc virulence [59]. It was found that Bacillus sp. OA10 isolated from the purple sponge Haliclona sp. suppressed the QS of bacteria, reduced the virulence of Pc, and reduced the maceration of potato tissues [66]. The mechanisms of action of Bacillus sp. are the inhibition of PCWDE and disruption of the production of Pc BR1 carbapenems. In this case, acyl serine lactones are not destroyed, but their synthesis is inhibited [66]. In the study of Yamchi et al. [157], two genes responsible for the synthesis of acyl homoserine lactonase (AiiA), which disrupts the QS of Pc, and isolated from Bacillus sp. A24 (aiiAA24) and Bacillus sp. DMS133 (aiiADMS133) were inserted into plasmids that transformed Pc. The transformed bacteria had reduced motility and biofilm formation ability and significantly decreased expression of the peh and hrpL genes [157]. Inoculation of Chinese cabbage seedlings with B. amyloliquefaciens KC-1 reduced the survival of Pcc in the rhizosphere and prevented the spread of bacteria along the stem [158]. Cell-free filtrate of B. velezensis inhibited the growth of Pcc in vitro and in vivo and increased the resistance of eggplant to soft rot by increasing the activity of antioxidant enzymes [159]. The endophytic bacterium Bacillus sp. EBS9, isolated from the medicinal plant Tecomella undulata, synthesizes diketopiperazines, L,L-Cyclo (leucylprolyl), and Cyclo (L-Phe-L-Pro), which are antagonists of AHLs [160]. Treatment of Pcc-infected radish slices with this bacterium reduced maceration of plant tissues and stimulated plant growth and development [160]. B. aryabhattai H26-2 and B. siamensis H30-3, isolated from Chinese cabbage, increased resistance to soft rot due to active colonization of the rhizosphere and an increase in the content of abscisic acid in leaves [161]. The bacterium B. brevis synthesizes the enzyme BbMomL, which causes the degradation of AHLs Pcc. This enzyme also significantly reduced the secretion of pathogenic factors and the pathogenicity of Pcc [162]. Bacteria of the genus Bacillus are capable of synthesizing antibiotics. Thus, B. subtilis strains UMAF6614, UMAF6639 synthesized lipopeptide antibiotics—surfactins, iturins, and fengycins, which had a negative effect on the plasma membrane of Pcc, causing the death of the bacterium [163].

7.2. Pseudomonas

The Pseudomonas multiresinivorans strain QL-9a degraded AHLs using AHL acylase within 48 h, in particular degrading 98.2% of N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) within 48 h [164]. Some Pseudomonas spp. synthesize the secondary metabolite 2,4-diacetylphloroglucinol, which leads to an increase in bacterial membrane permeability and suppresses AHL biosynthesis in Pc in a dose-dependent manner [165]. P. segetis P6 bacteria, isolated from the herbaceous plant Salicornia europaea of the Amaranth family, belong to plant growth-promoting (PGP) bacteria and have enzymatic activity against a wide range of AHLs, including AHL Pc [166].

7.3. Lactic Acid Bacteria

Lactic acid bacteria (LAB) Lactobacillus pentosus and Leuconostoc fallax in combination with chitosan inhibit the development of soft rot caused by Pcc [167]. Also, LAB Lactobacillus paracasei WX322 secrete the bacteriocin parocin, which reduced the incidence of soft rot in green pepper [168]. EPS of LAB inhibited the growth of Pcc after 3–6 h of cultivation and had antibiofilm activity against Pc [169].

7.4. Streptomycetes

Endophytic bacteria Streptomyces sp. of potato from Chile inhibited the growth of Pcc bacteria and reduced maceration of potato tuber tissues [170]. Streptomyces sp. AN090126 bacteria isolated from soil synthesized various VOCs, including dimethyl sulfide and trimethyl sulfide, which inhibited the growth of streptomycin-resistant Pcc [171]. Streptomyces microbes isolated from honeycombs exerted an antimicrobial effect on P. carotovorum [172]. A new oligosaccharide obtained from Streptomyces californicus demonstrated antibacterial activity against P. carotovorum [173]. Treatment of cultivated plants with the antibiotic paromomycin, which is synthesized by Streptomyces sp. AG-P 1441, is recommended in [132]. It was shown that the use of paromycin (1.0 μg mL⁻¹) on chili pepper plants reduced the number of soft rot zones. At the same time, a phytoprotective effect was observed due to the increased expression of the PR1, PR4 and PR10 genes [132].

7.5. Other Types of Bacteria

The bacterium Ochrobactrum intermedium D-2 has been shown to be able to synthesize an AHL-lactonase called AidF [174]. This lactonase degrades AHLs: N-hexanoyl-L-homoserine lactone (C6HSL), N-(3-oxohexanoyl)-L-homoserine lactone (3OC6HSL), N-(3-oxooctanoyl)-L-homoserine lactone (3OC8HSL), and N-(3-oxododecanoyl)-L-homoserine lactone (3OC12HSL), and reduces Pcc maceration on radish and potato slices [174]. The bacterial strain Mesoflavibacter zeaxanthinifaciens XY-85 from Onchidium sp. has an AHL-lactonase (MzmL), which significantly reduces the virulence of Pcc, inhibits biofilm formation and the synthesis of cellulalytic enzymes, and as a result, reduces the development of soft rot on potato slices [175]. The soil bacterium Lysinibacillus sp. Gs50 produces lactonase capable of cleaving AHLs of Pcc [176]. Four strains of Stenotrophomonas maltophilia isolated from marine invertebrates are also capable of degrading AHLs of Pc [177]. The nitrogen-fixing bacterium Paraburkholderia sabiae isolated from the root nodule of Mimosa caesalpiniifolia in Brazil protected potato tubers from soft rot due to the presence of the type VI secretion system (T6SS) [178]. The bacterium Pediococcus sp. M21F004, isolated from the intestine of starry flounder, synthesizes oleic acid and, through it, has an antimicrobial effect on Pcc, reducing the intensity of soft rot development on tomatoes and kim chi [179]. The bacterium Acidovorax sp. MR-S7 synthesizes AHL acylase, which degrades AHLs of Pc and leads to the suppression of QS in bacteria [180]. The grapevine crown gall pathogen Allorhizobium vitis is able to degrade AHLs by ring hydrolysis [181]. The AHL-lactonase homologue gene aiiV was cloned into E. coli, and the AiiV-expressing plasmid was then transformed into Pcc NBRC 3830. This resulted in decreased AHL synthesis and decreased maceration of plant tissues [181]. Bacteria of the genus Reyranella synthesize lactonases capable of cleaving AHLs Pc [182]. Bacteria from turf soil Delftia sp. VM4 synthesize AHL acylase, which suppresses the accumulation of AHLs and the production of virulence-determining enzymes of Pcc BR1 [183]. Acinetobacter sp. XN-10 isolated from contaminated agricultural soil efficiently degraded by hydrolysis and dehydroxylation N-(3-oxohexanoyl)-L-homoserine lactone (OHHL), N-hexanoyl-L-homoserine lactone (C6HSL), N-(3-oxododecanoyl)-L-homoserine lactone (3OC12HSL), and N-(3-oxooctanoyl)-L-homoserine lactone (3OC8HSL), all of which belong to the family of AHLs responsible for the QS of Pcc. Strain XN-10, significantly attenuated the pathogenicity of Pcc by inhibiting tissue maceration in carrot, potato, and Chinese cabbage [184]. Paenibacillus polymyxa KH-19 bacteria secreted the lysophosphatidyl esterase protein, which has antimicrobial activity against Pc [185]. Eight strains of phosphate-solubilizing bacteria isolated from the rhizosphere of poplar growing in urban conditions near a road were shown to inhibit the growth of Pc TP1 [186]. The entomopathogenic bacterium Xenorhabdus nematophila secretes the antibiotic benzylideneacetone (trans-4-phenyl-3-buten-2-one) into the culture medium, which has a pronounced antimicrobial effect against Pcc [187]. The bacterium Pantoea agglomerans, which can live in soil, plants, and excrement, causes infections of soft tissues, bones, and joints in humans and also has antibacterial activity against Pcc [188].

7.6. Fungi

Emodin, produced by the fungus Trichoderma asperellum, acts as an inhibitor of the QS system in bacteria such as Pcc. It competes with the Pcc proteins ExpR and ExpI, which are key components of the QS. ExpI is responsible for the synthesis of AHLs, and ExpR is responsible for their recognition and activation of virulence-related genes. Emodin binds to ExpR and ExpI, interfering with their normal functioning in Pcc and, thus, weakening the QS and repressing the expression of genes responsible for enzymes that degrade the plant cell wall [64]. In addition, emodin reduced the activities of pectinase, cellulase, and protease in Pcc by 50–70% compared to the control. The lesions of Chinese cabbage, carrot, and cherry tomato after Pcc infection were reduced by 10.02–68.57%, 40.17–88.56%, and 11.36–86.17%, respectively, under the influence of emodin [64]. In addition, soil-borne Trichoderma fungi possess AHL-lactonase, which catalyzes the ring opening of AHLs by hydrolyzing them in Pcc [189]. T. viride and T. virens reduced soft rot symptoms on inoculated potato tuber slices when applied simultaneously with or 2 h before pathogen inoculation [190]. Aqueous, butanol, and ethyl acetate extracts of the mushrooms Hericium erinaceus, Lentinula edodes, Grifola frondosa, and Hypsizygus marmoreus also demonstrated high antibacterial activity and enhanced the expression of the induced systemic resistance genes PR1 and β-1,3-glucanase in tomato plants [191]. Based on the mushrooms Ganoderma colossus, selenium-containing biocomposites were synthesized that had pronounced antimicrobial activity against Pc [192].

7.7. Bacteriophages

Bacteriophages are actively studied as an alternative to chemicals for the purpose of controlling Pcc. Bacterial viruses are specific; they penetrate and lyse bacterial cells of a particular species, thereby effectively reducing the population density of bacteria [193], releasing many progeny viruses into the environment, without having a direct negative effect on plant cells. Under favorable environmental conditions, the action of bacteriophages is long-lasting due to the release of large numbers of virions from each infected cell, which again lyse new host cells and gives them an advantage in the fight against phytopathogenic bacteria compared to other control methods [194]. However, their specificity requires the search for effective phages for each specific population of phytopathogens. In addition, the stability of bacteriophages is affected by various environmental factors, including temperature and pH [195]. Any interaction of a phage with a phytopathogen, including Pcc, begins with specific adsorption of the phage onto receptors on the bacterial surface of the host cell. These receptors in Pc include exopolysaccharides (colanic acid) and lipopolysaccharides (LPS) of the bacterial cell wall, as well as flagella, a mucus layer (capsule) [196]. After successful adsorption, phage DNA is injected and subsequently replicates inside the Pcc cell, after which bacteria are lysed and many progeny viruses are released into the environment [195].

For example, four Pectobacterium-specific phages (P. atrosepticum phages phiTE and CB7 and Pectobacterium phages DU_PP_I and DU_PP_IV) have been described [197]. The isolated bacteriophage PP1, belonging to the Podoviridae family, had lytic activity against Pcc in liquid medium over a wide pH range [198]. Phages φPD10.3 and φPD23.1 demonstrated rapid adsorption (70–83% within 20 min of exposure) on Pcc bacterial cells with subsequent release of 82 to 102 phage particles per infected cell, resulting in a more than 80% reduction in maceration of potato tuber tissue. Analysis of the genomes of phages φPD10.3 and φPD23.1 revealed the absence of genes encoding toxins, transposases or integrases [199]. The vB_PcaM_P7_Pc phage, obtained from Pcc-infected carrots, is capable of the lysis of Pcc cells and one strain of P. aroidearum. This phage is characterized by the absence of antibiotic resistance, toxicity, and lysogeny [197]. The bacteriophage POP72, which belongs to the Podoviridae family, specifically infected Pcc. It was found that colanic acid, as one of the types of extracellular polysaccharides of Pcc, functioned as a new phage receptor for POP72. Phage POP72 protects Chinese cabbage from Pcc infection [200]. The Pcc phage isolate Pc1 is able to increase its infectivity under the influence of calcium chloride, magnesium chloride, and copper sulfate (from 0.1 to 0.5 mM) and decrease it under the influence of zinc chloride at similar doses [201]. Pectobacterium phage Wc5r demonstrated activity against two phage-resistant P. carotovorum strains [194]. Phage phiPccP-2, belonging to the Myoviridae family, effectively destroys Pc due to colanic acid and lipopolysaccharides [196]. Bacteriophage vB_PcaP_PP2 (PP2), belonging to the Podoviridae family, effectively infects Pcc [202]. Bacteriophage PPWS1 of the Pod-oviridae family was isolated from the rhizome of Japanese horseradish with soft rot and is effective against Pc [203]. Effective suppression of the development of bacterial infection caused by Pcc both in vitro and in planta was reported for the phage PP16. This phage belongs to a separate phylogenetic branch of the genus Phimunavirus, subfamily Autographivirinae [204].

The use of individual phages has a number of limitations, such as a narrow host range and easy development of bacterial resistance [205]. To protect plants from Pcc, it is advisable to use a mixture of bacteriophages, which can be used to combat either one species or even a strain of bacteria, or several types of bacteria at once [206]. Methods have been developed to control Pcc using several phages (cocktails), which expand the spectrum of phage activity and prevent the emergence of phage-resistant variants. Thus, a phage cocktail was developed with three lytic phages that recognize colanic acid (phage POP12) and flagella (phages POP15 and POP17) as phage receptors [207]. Under in vitro conditions, the phage cocktail was shown to effectively suppress the emergence of phage-resistant Pcc strains. In addition, the use of the cocktail inhibited the development of soft rot disease symptoms on Chinese cabbage [207]. Bacteriophage suspensions (Ds3CZ + Ds20CZ and PcCB7V + PcCB251) slowed the delay in the development of the disease both in whole tubers and on potato slices [208]. Vu et al. [209] found that two virulent phages (phiPccP-2 and phiPccP-3) belonging to the Myoviridae and Siphoviridae families inhibited the growth of phage-resistant Pcc bacteria compared to monovariant phage treatment in vitro experiments, preventing the development of soft rot symptoms in mature leaves of Chinese cabbage. The addition of a third phage phiPccP-1 (Autographivirinae family) to this cocktail increased the biocontrol efficacy against a mixture of Pectobacterium strains on Chinese cabbage seedlings. No genes associated with toxins, antibiotic resistance, or lysogenicity were detected in the genomes of phages phiPccP-2 and phiPccP-3. These phages showed stability under environmental conditions [209].

A schematic representation of the comparative effectiveness of phages on the Pcc is shown in Figure 3.

Published data suggest that the development of phage cocktails is an effective approach for the biocontrol of soft rot caused by Pcc strains in crops compared to single phage treatment. However, the use of bacteriophages for Pcc biocontrol should be considered on a case-by-case basis.

Table 3. A brief summary of the published data on the effects of bacteria, fungi, and viruses on Pcc and soft rot disease.

Species	Effects on Pcc and Plants	Reference
Bacteria
Bacillus
B. velezensis CE 100	Pc growth inhibition; cytoprotective effect on cucumber plants	[156]
B. thuringiensis KMCL07	suppression of QS Pcc; inhibition of extracellular Pcc enzymes cellulase, pectate lyase and proteinase	[59]
Bacillus sp. OA10	suppression of QS Pc (inhibition of acylserine lactone synthesis); reduction of potato tissue maceration	[66]
Bacillus sp. A24 Bacillus sp. DMS133	inhibition of QS Pc by acylhomoserine lactonase	[157]
B. amyloliquefaciens KC-1	reducing colonization of Chinese cabbage plants by Pcc	[158]
B. velezensis	inhibition of Pcc growth; phytoprotective effect on eggplant plants due to increased activity of antioxidant enzymes	[159]
Bacillus sp. EBS9	suppression of QS Pcc by synthesis of N-acyl homoserine lactone antagonists; phytoprotective effect on radish plants	[160]
B. aryabhattai H26-2 B. siamensis H30-3	phytoprotective effect on Chinese cabbage plants by reducing the colonization of the rhizosphere by Pcc and increasing the content of abscisic acid in leaves	[161]
B. brevis	suppression of QS Pcc due to the synthesis of the enzyme BbMomL, which degrades N-acyl homoserine lactones; reduction of secretion of virulence factors Pcc	[162]
B. subtilis UMAF6614, UMAF6639	destruction of the bacterial plasma membrane Pcc under the influence of lipopeptide antibiotics Bacillus spp.: surfactins, iturins, and fengycins	[163]
Pseudomonas
Ps. multiresinivorans QL-9a	suppression of QS Pc by N-(-3-oxohexanoyl)-L-homoserine lactone acylase cleavage	[164]
Pseudomonas spp.	increased permeability of the bacterial membrane Pc; suppression of biosynthesis of acyl homoserine lactones Pc	[165]
P. segetis P6	suppression of QS Pc by cleavage of N-acyl homoserine lactones	[166]
Lactic acid bacteria
Lactobacillus pentosus, Leuconostoc fallax	inhibition of disease symptom development on radish	[167]
Lactobacillus paracasei WX322	phytoprotective effect on pepper plants due to the synthesis of bacteriocin parocin	[168]
exopolysaccharides of bacteria of the genera Leuconostoc, Pediococcus, and Lactobacillus	bacteriostatic and antibiofilm effect on Pc	[169]
Streptomyces
Streptomyces spp.	bacteriostatic effect on Pcc; inhibition of potato tuber tissue maceration	[170]
Streptomyces sp. AN090126	antimicrobial effect against Pcc due to the synthesis of volatile organic compounds (VOCs)	[171]
Streptomyces sp.	antibacterial activity (well method)	[172]
S. californics	antibacterial activity (well method)	[173]
Streptomyces sp. AG-P 1441	reduction of soft rot symptoms development on the plant due to the antibiotic paromomycin; phytoprotective effect due to the increased expression of PR genes	[132]
Other types of bacteria
Cedecea sp., Cellulosimicrobium sp., Delftia sp., Ensifer sp., Paenibacillus sp., Pantoea sp., Phyllobacterium sp., Pseudomonas sp., Rhizobium sp., Sinorhizobium sp., Staphylococcus sp.	inhibition of Pc growth	[186]
Paenibacillus polymyxa KH-19	inhibited the growth of Pc by synthesizing the enzyme lysophosphatidyl esterase	[185]
Ochrobactrum intermedium D-2	suppression of QS Pcc by AHL-lactonase synthesis; reduction of maceration on radish and potato slices	[174]
Mesoflavibacter zeaxanthinifaciens XY-85	reduction of Pcc virulence, inhibition of biofilm formation, and synthesis of cellulolytic enzymes	[175]
Lysinibacillus sp. Gs50	suppression of QS Pcc by lactonase synthesis	[176]
Stenotrophomonas maltophilia	suppression of QS Pc by cleavage of N-acyl homoserine lactones	[177]
Paraburkholderia sabiae	cytoprotective effect on potato plants	[178]
Pediococcus sp. M21F004	antimicrobial effect on Pcc through oleic acid synthesis; phytoprotective effect on kim chi and tomato plants	[179]
Acidovorax sp. MR-S7	suppression of QS Pc by AHL-lactonase synthesis	[180]
Allorhizobium vitis	suppression of QS Pcc by cleavage of N-acyl homoserine lactones	[181]
Reyranella sp.	suppression of QS Pc by lactonase synthesis	[182]
Delftia sp. VM4	suppression of QS Pcc by lactonase synthesis	[183]
Acinetobacter sp. XN-10	suppression of QS Pcc by cleaving N-acyl homoserine lactones and inhibition of tissue maceration in carrot, potato, and Chinese cabbage	[184]
Xenorhabdus nematophila	inhibition of Pcc viability by the antibiotic benzylideneacetone (trans-4-phenyl-3-buten-2-one)	[187]
Pantoea agglomerans	antibacterial activity (well method)	[188]
Fungi
Trichoderma asperellum	suppression of PCWDE and QS Pcc enzyme synthesis by emodin synthesis; phytoprotective effect on cabbage, carrot and cherry tomato plants	[64]
Trichoderma sp.	suppression of QS Pcc by lactonase synthesis	[189]
T. viride, T. virens	suppression of maceration of potato tuber tissues	[190]
Hericium erinaceus, Lentinula edodes, Grifola frondosa, Hypsizygus marmoreus	antimicrobial effect against Pcc; phytoprotective effect on tomato plants due to the development of induced systemic resistance	[191]
Ganoderma colossus	antibacterial activity (well method) and bacteriostatic effect against Pc of selenium biocomposites obtained on the basis of fungal culture medium	[192]
Bacteriophages
PP1	lytic activity against Pcc in liquid medium	[198]
φPD10.3; φPD23.1	reduction by >80% of maceration of potato tuber tissues	[199]
vB_PcaM_P7_P	Pc cell lysis	[197]
POP72	protection of Chinese cabbage from Pcc infection	[200]
Wc5r	suppression of phage-resistant strains	[194]
phiPccP-2	lytic activity against Pc/Pcc	[196]
vB_PcaP_PP2 (PP2)		[202]
PPWS1		[203]
PP16	suppression of infection caused by Pcc in vitro and in planta	[204]
POP12 + POP15 + POP17	in vitro suppression of phage-resistant Pcc isolates and development of soft rot symptoms on Chinese cabbage	[207]
Ds3CZ + Ds20CZ; PcCB7V + PcCB251	slowing down the development of the disease both in whole tubers and on potato slices	[208]
phiPccP-2 + phiPccP-3	suppression of phage-resistant strains, prevention of development of soft rot symptoms in mature leaves of Chinese cabbage	[209]
phiPccP-1 + phiPccP-2 + phiPccP-3	suppression of a mixture of Pectobacterium strains on Chinese cabbage seedlings

provides a brief summary of the published data on the effects of bacteria, fungi, and viruses on Pcc and soft rot disease.

Thus, the published data presented in Section 7. demonstrate that an active search is underway for environmentally safe methods of controlling Pcc using other microorganisms. Studies on the suppression of the viability of Pcc by other bacteria are especially popular. However, it remains quite difficult to identify the most effective organisms limiting the development of the studied phytopathogen, since Pcc has a number of mechanisms for effective survival in a competitive environment on necrotrophic material. In addition, many studies are based on identifying the fact of inhibition of bacterial growth by Pcc, without delving into the mechanisms of this process. The scope of application of bacteriophages in relation to Pcc has not been sufficiently developed and studied, probably due to the methodological difficulties of research.

8. Using Nanomaterials to Control Pcc

Nanomaterials are being actively introduced into various areas of the economy, including in the field of plant protection from phytopathogens [210]. Research interest in the use of new and environmentally friendly nanoparticles (NPs) is increasing. These agents are considered as a means of reducing the bacterial load on the plant.

8.1. Chitosan Nanoparticles (NPs)

Chitosan is an aminopolysaccharide obtained from crustacean shells [211]. Pcc was incubated with chitosan NPs enriched with thyme essential oil Thymus vulgaris L. for up to 48 h [212]. Then, cellular changes and viability were assessed using a transmission electron microscope (TEM) and two colorimetric assays 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Alamar blue. Incubation time and addition of a secondary metabolite to the NP preparation were key factors in cell damage and their inhibitory effect on Pc. TEM observation parameters on treated bacteria showed cell surface changes. The agglomeration of NPs outside and inside the cells leads to deformation, lysis of the cell wall and plasma membrane of the bacteria [213]. Cell viability was reduced by about 80% (based on the MTT assay) and 100% (based on the Alamar blue assay) by the application of chitosan-enriched thyme essential oil NPs. After 48 h of incubation, complete cell inhibition was shown starting from 6 h of incubation. TEM micrographs and cell viability assays provided sufficient evidence for the antimicrobial activity of the nanostructured formulations compared to the control where no damage was observed [213]. Similar work was conducted on the application of chitosan NPs and thyme essential oil on green bell pepper for the treatment of soft rot. The treatment reduced the incidence of peppers by 15% and preserved the marketable appearance of the fruits [214]. Chitosan NPs were also studied in combination with Athyrium sinense Rupr. essential oil [215]. These essential oils contained n-hexadecanoic acid, linoleic acid, phytol, phytone, α-linolenyl alcohol, isophytol, and methyl hexadecanoic acid. Such NPs had a pronounced antimicrobial effect against Pcc [215]. Chitosan NPs were synthesized using Streptomyces sp. strain NEAE-83, and these NPs exhibited antibacterial activity against Pc [216].

8.2. Chalcogen-Containing NPs

Sulfur (S) NPs are proposed to combat soft rot of lettuce caused by Pc [6]. In an experiment with plants, it was shown that S NPs, in addition to the antibacterial effect, stimulate the tricarboxylic acid cycle in the plant, trigger systemic induced resistance in lettuce tissues due to the synthesis of jasmonic and salicylic acids, which enhanced the expression of PR genes and the activity of antioxidant enzymes [6]. Chemically synthesized selenium (Se) NP compounds with the natural polysaccharide arabinogalactan (AG)—Se nanocomposites (Se/AG NCs)—had bactericidal, bacteriostatic, and antibiofilm effects on Pc, and also reduced the activity of dehydrogenases in bacterial cells [217]. The phytoprotective effect of Se/AG NCs has been demonstrated. Thus, the treatment of Glycine max L. soybean seeds infected with Pc with Se/AG NCs increased seed germination and eliminated the negative effect of infection on the biometric and biochemical characteristics of seedlings [217]. In addition, in vitro treatment of potato plants with these NCs reduced the negative effect of infection, promoting an increase in potato biomass and reducing the intensity of plant colonization by Pc [218].

8.3. Metal-Containing NPs

Metal-containing NPs of copper (Cu), iron (Fe), cobalt (Co), and zinc (Zn), obtained by green synthesis with the enzyme nitrate reductase from bacteria Enterococcus thailandicus, Pseudomonas putida, Marinobacter carbonoclasticus, and P. geniculata isolated from water in Egypt, showed a high antagonistic effect against Pc [219]. In this study, Fe NPs were the most effective, followed by Cu NPs, and then Zn NPs [219]. Green synthesis of ZnO NPs was carried out using extracts of Japanese mashmallow Eriobotrya japonica in [220]. These NPs were found to have antibacterial activity at a concentration of 5 μg mL⁻¹ against Pc [220]. Analysis of the antibacterial mechanism of NPs showed that CuS NPs could increase ROS and lipid peroxidation (LPO) levels [221]. CuS NPs disrupted the structure of bacterial cells observed by scanning electron microscopy and Fourier transform infrared spectroscopy. These NPs could also inhibit the motility of Pcc. CuS NPs effectively killed Pc by inducing oxidative stress in the bacterial cell, enhancing LPO, and ultimately leading to the destruction of the bacterial cell [221]. Chemically synthesized CuO and Mn(OH)₂ NPs with AG—Cu/AG NCs and Mn/AG NCs reduced the negative effects of in vitro infection of potato plants with the bacterium Pc, exerting a stimulating effect on the biometric and biochemical parameters of plants [218]. The antibacterial effect of Cu NPs against Pc and a decrease in tuber maceration after potato treatment with them, obtained by green synthesis using citrus peel, were also shown [222].

Ag NPs have high antimicrobial activity against Pc, which is higher than Cr₂O₃ and ZnO NPs have [223]. The antimicrobial activity of Ag NPs was even higher than that of the antibiotic chloramphenicol [223]. Ag NPs at 8 μg mL⁻¹ completely inhibited the growth of Pcc, reduced their tolerance to 0.25 mM H₂O₂, and also significantly suppressed the colony formation of bacteria after 1 h of incubation [224]. The use of Ag NPs resulted in the destruction of bacterial cell membrane and inhibition of biofilm formation [224]. To combat Pc in the post-harvest period of potatoes, it is proposed to use cotton bags impregnated with Ag NPs for their storage, which reduced their infection with soft rot by 12% [225]. Antimicrobial Ag NPs were also synthesized using extractive enzymes of the entamopathogenic fungi Beauveria bassiana and Metarhizium anisopliae and exhibited high antibacterial activity against Pc [226]. AgNPs synthesized using Fusarium culmorum JTW1 exerted an antibiofilm effect against Pc at a concentration of 0.25 μg mL⁻¹ [227]. The antibacterial effect of Ag NPs against Pc and the complete absence of maceration of tubers after treating potatoes with them, obtained by green synthesis using citrus peel, were shown [222].

Ag NPs synthesized using an aqueous extract of Ficus sycomorus leaves demonstrated antibacterial activity against Pc [228]. Studies have shown that Ag NPs attach to the cell wall of Pcc bacteria and alter the membrane permeability [229]. Moreover, the damaged membrane permeability impairs transport across the plasma membrane and ultimately leads to cell death [230]. The Pcc membrane is composed of lipopolysaccharides (LPS) in the outer membrane, which serves as an effective permeability barrier. The interaction of Ag NPs with LPS disrupts its integrity and affects other membrane proteins. Consequently, the permeability or even degradation of the membrane structure is impaired [231]. Ag NPs obtained by the “green method” with Fusarium oxysporum exhibit antibacterial activity against Pcc [232]. Ag NPs obtained using Mhonia fortunei extracts had pronounced antimicrobial activity against Pc at a concentration of 500 μg mL⁻¹, the cell membrane of bacteria was destroyed, and biofilm formation was impaired [224]. Synthesis of Ag NPs using exudates from Quercus oak fruits had a pronounced inhibition of plant tissue maceration: a 22% decrease was observed in potato, 19.8% in zucchini, 21.5% in carrot, and 18.5% in eggplant [233]. Ag NPs were synthesized using Laurus nobilis L. leaf extract. The treatment of peppers with these NPs reduced the incidence of soft rot by 15%, exerting a stimulating effect on plants [231].

The information presented in this section demonstrates that various methods for controlling the phytopathogen Pcc have been developed to date. They include agrotechnical methods, as well as the use of chemicals of various natures and compounds, including those produced by different organisms—plants, bacteria, viruses, fungi. Most of these substances highlight virulence factors as their target in Pcc—the AHL production system, biofilm formation and enzymes that destroy the plant cell wall. In addition, many compounds affect the integrity of the bacterial membrane, leading to changes in its permeability and subsequent destruction. Bacteria are capable of synthesizing a number of antibacterial substances effective against Pcc, while some bacteria are also capable of having a phytoprotective effect. The direction of research into the biological activity of NPs in relation to reducing the viability of the phytopathogen Pcc is actively developing. Many studies have shown that NPs of chalcogens, metals, and chitosan are effective in regulating the number of Pcc, while having a stimulating effect on the resistance of plants to soft rot. However, the effectiveness of nanocompounds in relation to Pcc requires further study, since bacteria are able to develop resistance to NPs. The presented data encourage agronomists with the prospects for effective methods of combating Pcc, which, due to its high resistance to environmental factors and formed resistance to antibiotics, causes high economic losses.

9. Conclusions

Thus, the presented literature review demonstrates that pathogenic Pcc bacteria are able to quickly colonize susceptible plants of various species, including those of great economic importance. High pathogenicity of Pcc is associated with its virulence factors, which are enzymes that destroy the cell wall of plants, various virulence proteins that cause necrosis, the secretion system of types II and III (T2SS and T3SS), and the ability of bacteria to form biofilms due to the synthesis of AHL. Soft rot caused by Pcc causes global economic losses in crop production. In this regard, it is extremely important to expand the knowledge about the mechanisms of Pcc virulence, which are not yet fully known. In addition, it is necessary to improve existing and develop new identification methods, including plant cultivation on selective media. It is promising to develop effective strategies for protecting crops from this phytopathogen. Currently, special attention is paid to the search for alternatives to pesticides, since many phytopathogenic pests have developed resistance to traditional pesticides. For this purpose, plant extracts, substances synthesized by bacteria, fungi, and viruses are tested, and a variety of chemical compounds and nanomaterials are used. However, effective methods and substances for controlling Pcc on a large scale have not yet been developed, which is still a challenge for scientific research in this area.