Phytopathogenic Bacteria

Last updated: September 22, 2026

1. Bacterioses — an Underestimated Threat

1.1. Why Are Bacterioses Underestimated?

In phytopathology, historically, the main attention has been paid to fungal and fungus-like pathogens. This is reflected in summary lists of diseases: fungi account for approximately 50–65% of named diseases, viruses for 10–20%, and bacteria for only 5–10% (Sigee, 1993). However, this quantitative ratio does not mean that bacterioses are less dangerous. On the contrary, the underestimation of bacterial pathogens is associated with several reasons: they are more difficult to isolate and identify by classical methods, symptoms are often nonspecific, and latent infections remain unnoticed for a long time (Sigee, 1993; Czajkowski et al., 2015).

Bacteria as a group possess a number of biological features that make them especially dangerous when they enter favorable conditions. They multiply rapidly, are capable of reaching enormous densities in host tissues, and causing epiphytotics in a short time. Although bacteria do not form spores, do not have a powerful chitinous protection, and cannot independently penetrate intact cuticle, they use natural openings—stomata, hydathodes, lenticels—and wounds caused by insects, wind, hail, or agricultural machinery (Sigee, 1993; Agrios, 2005). In addition, many phytopathogenic bacteria are transmitted with seeds, tubers, cuttings, and planting material, which ensures their latent movement over long distances (Czajkowski et al., 2015; EPPO, 2023).

1.2. Economic Damage from Bacterioses

On a global scale, annual losses from diseases, pests, and weeds are estimated at 31–42% of potential yield. Of these, diseases account for an average of about 14.1%, insects for 10.2%, and weeds for 12.2% (Agrios, 2005). This means that diseases alone cause annual losses of products worth about USD 220 billion. Additionally, 6–12% of the harvest is lost after harvest, especially in developing tropical countries, where refrigeration capacity and modern storage systems are often lacking (Agrios, 2005). Although these figures include all pathogens, bacterioses make a substantial and often poorly accounted contribution to them.

One of the most striking examples is bacterial wilt caused by members of the Ralstonia solanacearum complex. On potato, this pathogen causes annual damage of about USD 1 billion, affecting about 3 million farming families on an area of 1.5 million ha in approximately 80 countries worldwide (Charkowski et al., 2020). The disease leads not only to direct yield losses but also to indirect costs: bans on export of products, quarantine restrictions, the need for prolonged fallow and replacement of planting material (Charkowski et al., 2020; Vailleau and Genin, 2023).

Another major group is soft rots and blackleg of potato caused by Pectobacterium spp. and Dickeya spp. These pathogens are among the top 10 bacterial phytopathogens and annually cause damage of USD 50–100 million on vegetable, fruit, and ornamental crops (Arif et al., 2022). Losses occur both in the field and during storage, and latent infection of tubers makes visual assessment of seed potato lots practically impossible (Czajkowski et al., 2015; EPPO, 2023).

Fire blight, caused by Erwinia amylovora, is considered one of the most destructive bacterial diseases of apple and pear. It can destroy entire orchards, and its control requires annual multiple treatments, pruning, and uprooting of affected trees (EPPO, 2022; Pedroncelli and Puopolo, 2024). In the United Kingdom in 1958–1969, losses from fire blight amounted to about 20 thousand pear trees, 20 thousand hawthorns, 15 thousand cotoneasters, and 2 thousand pyracanthas (Agrios, 2005). In the USA and Europe, this disease remains a constant threat to commercial horticulture (Pedroncelli and Puopolo, 2024).

Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis, can lead to yield losses of 30% or more, and in some years in certain regions up to 70–85% (Akhatov et al., 2013). The pathogen is seed-borne, survives in plant residues, and can spread during plant care, which makes it especially dangerous for greenhouse operations (Akhatov et al., 2013).

One cannot fail to mention Candidatus Liberibacter solanacearum, the causal agent of zebra chip disease of potato. This disease causes multi-million losses in North America, Mexico, and New Zealand, reducing tuber quality and making them unsuitable for processing (Charkowski et al., 2020). The pathogen is transmitted by the potato psyllid, and its control requires vector management and the use of tolerant cultivars.

Indirect losses from bacterioses are often no less than direct ones. For example, the elimination of a citrus canker outbreak in the USA required the destruction of more than a quarter of a million fruit-bearing trees and more than 3 million seedlings, as well as multi-million costs and 20 years of quarantine measures (Agrios, 2005). Quarantine restrictions, seed certification, and bans on the movement of plant material all place an additional burden on producers and trade (EPPO, 2025).

1.3. Difficulties in Diagnosing Bacterioses

Diagnosis of bacterioses is difficult for several reasons. First, symptoms are often nonspecific and resemble fungal, viral, or abiotic damage. For example, fire blight can be confused with damage caused by Erwinia pyrifoliae, Erwinia piriflorinigrans, Pseudomonas syringae pv. syringae, as well as with fungal and even physiological disorders (EPPO, 2022). Bacterial canker of tomato externally resembles fusarium wilt, necrosis of the stem pith, and other vascular diseases (Akhatov et al., 2013).

Second, many bacterioses are latent. Ralstonia solanacearum can persist in tubers, water, and host plants without visible symptoms; strain PIIB1 is especially dangerous because it is adapted to moderate temperatures and can spread with seed potato (Charkowski et al., 2020). Pectobacterium and Dickeya are also often present on tubers asymptomatically, and visual inspection of lots does not give a reliable result (Czajkowski et al., 2015; EPPO, 2023).

Third, bacteria can enter the VBNC (viable but non-culturable) state. Erwinia amylovora after treatment with copper or chlorine, as well as during starvation, may not grow on nutrient media but remain pathogenic (EPPO, 2022; Pedroncelli and Puopolo, 2024). This leads to false-negative results during isolation on media.

Fourth, the titer of the pathogen in tissues may be low, and its distribution uneven. In such cases, enrichment, selective media, serological methods (ELISA, latex agglutination), or molecular methods are necessary: PCR, qPCR, LAMP, sequencing (Czajkowski et al., 2015; Yang et al., 2025; Venbrux et al., 2023). Modern diagnostics increasingly relies on metagenomics and CRISPR systems, but their introduction into routine practice requires trained personnel and equipment (Venbrux et al., 2023; Yang et al., 2025).

Finally, taxonomic rearrangements create additional difficulties. Many familiar names have changed: Erwinia carotovora has been divided into Pectobacterium spp., Erwinia chrysanthemi into Dickeya spp., and part of Agrobacterium has been transferred to Rhizobium. Diagnostic kits, quarantine lists, and scientific literature must track these changes; otherwise, errors in identification and legal conflicts are possible (Mousavi and Young, 2023; Bansal et al., 2023; EPPO, 2023).

1.4. Difficulties in Controlling Bacterioses

Control of bacterioses is substantially more difficult than control of many fungal diseases. There is no equally broad arsenal of systemic fungicides against bacteria. Copper-containing preparations and antibiotics (streptomycin, oxytetracycline) are used to a limited extent: they are poorly effective against latent infections, cause resistance, and antibiotics are prohibited on commercial products in many countries (Agrios, 2005; EPPO, 2022; Charkowski et al., 2020). Biological control currently occupies a niche but does not provide complete protection (Sigee, 1993; Pedroncelli and Puopolo, 2024).

Breeding for resistance is also difficult. For many bacterioses, resistance is polygenic, race-specific, and unstable under different conditions. For example, for Ralstonia solanacearum, there are still no commercial cultivars with complete resistance; existing sources of resistance are often associated with undesirable traits (Charkowski et al., 2020; Vailleau and Genin, 2023). For Pectobacterium and Dickeya, there are practically no resistant potato cultivars, although differences in tolerance exist (Czajkowski et al., 2015; EPPO, 2023).

Quarantine and certification of planting material remain key measures. For potato, certification schemes with zero tolerance to Clavibacter sepedonicus and Ralstonia spp. in microplants are in force; for seed potato, tolerance levels to Pectobacterium and Dickeya have been recommended (EPPO, 2023). However, the cost of testing and quarantine measures is high, and latent infections reduce the effectiveness of even the strictest schemes (Czajkowski et al., 2015).

1.5. Examples Worth Knowing

Blackleg and soft rot of potato. The causal agents are Pectobacterium spp. and Dickeya spp. They were previously assigned to the genus Erwinia, but modern taxonomy has divided them into several genera and species. The disease manifests as blackening of the stem base, wilting, and rotting of tubers in the field and during storage. The pathogens are transmitted with seed tubers, survive in plant residues, soil, and water. Control is based on healthy seed material, sanitation, avoiding tuber injury, proper storage, and crop rotation (Charkowski et al., 2020; Czajkowski et al., 2015; EPPO, 2023).

Bacterial canker of tomato. The causal agent is Clavibacter michiganensis subsp. michiganensis. The pathogen is seed-borne and systemic; it causes wilting, unilateral yellowing of leaves, vascular necrosis, stem cankers, and characteristic “bird’s-eye” spots on fruits. Losses can reach 30% or more. Control measures: seed disinfection, phytosanitary measures, removal of diseased plants, limited use of copper and antibiotics during the seedling period. Diagnosis: PCR, ELISA, LAMP (Akhatov et al., 2013; EPPO, 2025).

Fire blight. The causal agent is Erwinia amylovora. It affects apple, pear, and other Rosaceae. Symptoms: “shepherd’s crook” on shoots, blackening of leaves, bacterial exudate, cankers. The disease is quarantine-regulated in many countries. Control includes pruning and burning of affected branches, copper preparations, antibiotics during flowering, forecasting, and resistant cultivars. Diagnosis is regulated by EPPO PM 7/20 (EPPO, 2022; Pedroncelli and Puopolo, 2024).

Bacterial wilt (southern bacterial wilt). The causal agent is the Ralstonia solanacearum species complex. It affects more than 250 plant species, including potato, tomato, and banana. Symptoms: sudden wilting, vascular browning, bacterial exudate. The pathogen persists in soil, water, and plant residues, and is transmitted with tubers and cuttings. It is a quarantine organism. Control: certified planting material, crop rotation, resistant cultivars, sanitation (Charkowski et al., 2020; Vailleau and Genin, 2023; EPPO, 2025).

Zebra chip disease of potato. The causal agent is Candidatus Liberibacter solanacearum; the vector is the potato psyllid. Losses are associated with deterioration of tuber quality and reduced yield. Measures: vector control, tolerant cultivars, monitoring (Charkowski et al., 2020).

2. Major Genera of Phytopathogenic Bacteria

2.1. Introduction: Taxonomic Diversity of Phytopathogenic Bacteria

Phytopathogenic bacteria do not form a single taxonomic group. They are distributed across several major branches of the domain Bacteria, primarily among Gram-negative proteobacteria, and also among Gram-positive actinobacteria (Agrios, 2005; Sigee, 1993). Historically, the idea of five main groups of phytopathogenic bacteria developed: Agrobacterium, Erwinia, Pseudomonas, Xanthomonas, and coryneform bacteria (Clavibacter, Curtobacterium, Rhodococcus, etc.) (Sigee, 1993). However, modern systematics based on molecular data has substantially expanded and restructured this picture. New genera have appeared—Pectobacterium, Dickeya, Ralstonia, Xylella, Candidatus Liberibacter—and the boundaries of many traditional genera have been refined (Arif et al., 2022; Charkowski et al., 2020; Bansal et al., 2023).

In this lecture, we will consider the major genera of phytopathogenic bacteria, their modern nomenclature, type species, diseases caused, and taxonomic features. It is important to understand that bacterial systematics is dynamic: as genomic data accumulate, names and boundaries of taxa change, and this directly affects diagnosis, quarantine, and breeding (Mousavi and Young, 2023; Bansal et al., 2023).

2.2. Genus Pseudomonas

Pseudomonas is one of the largest and most diverse genera of Gram-negative bacteria. Among phytopathogenic representatives, the most significant is Pseudomonas syringae, a complex species including more than 50 pathovars that differ in host range and symptoms (Agrios, 2005; Sigee, 1993). P. syringae causes leaf spots, blights, necroses, cankers, rots, and wilts in many crops: tomato, bean, soybean, fruit trees, cereals, and ornamental plants. Pathovars P. syringae pv. tabaci (wildfire of tobacco), pv. phaseolicola (halo blight of bean), pv. tomato (bacterial speck of tomato), and pv. syringae (bacterial canker of stone fruits) are classical examples (Agrios, 2005; Akhatov et al., 2013).

Pseudomonas savastanoi (formerly P. syringae subsp. savastanoi) causes olive knot and bacterial canker of oleander. The pathogen affects olive, ash, forsythia, and oleander, causing hyperplastic outgrowths on branches and trunks (Agrios, 2005). Some strains of P. savastanoi produce phytohormones, which leads to tissue proliferation.

Among other phytopathogenic pseudomonads are P. marginalis (soft rot of vegetables), P. fluorescens (can cause rots in weakened plants), and P. cichorii (leaf spot of vegetables and ornamental crops). It is important to note that Pseudomonas in the modern understanding is a composite group; genomic studies have shown that some species previously assigned to Pseudomonas should be transferred to other genera, and the genus itself requires revision (Bansal et al., 2023). For example, P. solanacearum has been transferred to the genus Ralstonia, and P. savastanoi has been separated as a distinct species.

2.3. Genus Xanthomonas

Xanthomonas is a genus of Gram-negative bacteria whose characteristic feature is the production of the yellow pigment xanthomonadin. It is one of the most economically significant genera of phytopathogenic bacteria. The type species is Xanthomonas campestris, which includes many pathovars affecting crucifers, tomatoes, peppers, citrus, cereals, and ornamental plants (Agrios, 2005; Chuang et al., 2025).

Xanthomonas campestris pv. campestris causes black rot of cabbage and other crucifers—a disease leading to significant losses in vegetable production. X. campestris pv. vesicatoria (now X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, X. vesicatoria) causes bacterial spot of tomato and pepper (Chuang et al., 2025; Akhatov et al., 2013). Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight of rice, one of the most destructive diseases of this crop in Asia. Xanthomonas citri pv. citri (formerly X. campestris pv. citri) is the causal agent of citrus canker, a quarantine disease whose control requires destruction of trees and strict phytosanitary measures (Agrios, 2005).

The taxonomy of Xanthomonas is actively being revised. Based on genomic data, the genus has been divided into several species, and many pathovars have received the status of separate species or have been transferred to other species. For example, X. axonopodis pv. citri is now X. citri pv. citri; X. campestris pv. phaseoli is X. phaseoli pv. phaseoli (Chuang et al., 2025; Bansal et al., 2023). Recent studies propose including Xylella, Stenotrophomonas, and some Pseudomonas in the genus Xanthomonas, but these proposals have not yet been officially accepted (Bansal et al., 2023). For diagnosis, it is important to consider that different Xanthomonas species can cause similar symptoms but differ in quarantine status and control measures (Chuang et al., 2025).

2.4. Genus Agrobacterium and Modern Nomenclature of Rhizobia and Agrobacteria

Agrobacterium is a genus of Gram-negative soil bacteria that cause hyperplastic diseases in plants. The type species is Agrobacterium tumefaciens, the causal agent of crown gall—tumors on roots and stems of many dicotyledons, especially fruit, berry, and ornamental crops. Pathogenicity is due to the presence of the Ti plasmid (tumor-inducing), which transfers part of its DNA (T-DNA) into the plant cell, causing uncontrolled division and synthesis of opines (Agrios, 2005; Sigee, 1993). This mechanism made A. tumefaciens a natural genetic engineer and the basis of plant biotechnology.

Agrobacterium rhizogenes causes “hairy root” disease, in which a mass of roots forms instead of tumors. Pathogenicity is associated with the Ri plasmid (root-inducing). A. rubi causes galls on raspberry and blackberry. A. vitis affects grapevine, causing crown gall and necrosis.

Modern systematics of rhizobia and agrobacteria has undergone significant changes. Based on genomic comparisons, many Agrobacterium species have been transferred to the genus Rhizobium: A. tumefaciens → Rhizobium radiobacter, A. rhizogenes → Rhizobium rhizogenes, A. vitis → Allorhizobium vitis (Mousavi and Young, 2023). However, in phytopathological literature and diagnostic protocols, the old names are often retained. The Subcommittee on the Taxonomy of Rhizobia and Agrobacteria recommends using modern names but recognizes that the transition period may take years (Mousavi and Young, 2023). For diagnosis, this means the need to check synonyms and update databases.

2.5. Genus Ralstonia and the Ralstonia solanacearum Complex

Ralstonia is a genus of Gram-negative bacteria in the family Burkholderiaceae. The most significant phytopathogen is the Ralstonia solanacearum species complex (RSSC), which causes bacterial wilt (southern bacterial wilt) in more than 250 plant species, including potato, tomato, banana, tobacco, geranium, ginger, and peanut (Charkowski et al., 2020; Vailleau and Genin, 2023). The disease manifests as sudden wilting, vascular browning, and bacterial exudate; on potato tubers, vascular ring browning and rot occur (brown rot).

RSSC was long considered a single species with four phylotypes (I–IV) corresponding to geographic origin: I—Asia, II—America, III—Africa, IV—Southeast Asia. Based on genomic data, the complex has been divided into three species: R. solanacearum (phylotype II), R. pseudosolanacearum (phylotypes I and III), and R. syzygii (phylotype IV) (Safni et al., 2014; Prior et al., 2016; Charkowski et al., 2020). R. syzygii includes three subspecies: subsp. syzygii (carnation), subsp. celebesensis (banana blood disease), and subsp. indonesiensis (potato, tomato, pepper). Strain PIIB1 (phylotype IIB, sequevar 1) is the most dangerous for potato in temperate latitudes, capable of latent infection and transmitted with seed tubers (Charkowski et al., 2020).

Within RSSC, races (by host range) and biovars (by biochemical traits) are distinguished. Race 1 affects many species, race 2 affects banana and Heliconia (Moko disease), and race 3 affects potato and tomato. Biovars 1–5 differ in the utilization of carbohydrates and alcohols. For diagnosis and quarantine, it is important to accurately identify the species, phylotype, and race, since control measures depend on this (Vailleau and Genin, 2023; Charkowski et al., 2020).

2.6. Genus Erwinia and Fire Blight

Erwinia is a genus of Gram-negative bacteria in the family Erwiniaceae. The type species is Erwinia amylovora, the causal agent of fire blight—one of the most destructive diseases of apple and pear. The disease also affects quince, cotoneaster, hawthorn, rowan, pyracantha, and other Rosaceae (EPPO, 2022; Pedroncelli and Puopolo, 2024). Symptoms: blackening and drying of flowers, leaves, and shoots, the characteristic “shepherd’s crook,” bacterial exudate, and cankers on branches and trunks. E. amylovora is a quarantine organism on the EPPO A2 list (EPPO, 2025).

Besides E. amylovora, the genus Erwinia includes E. pyrifoliae (bacterial blight of Asian pear), E. piriflorinigrans (necrosis of pear flowers), E. uzenensis (pear blight in Japan), and E. tasmaniensis (nonpathogenic or weakly pathogenic). Some Erwinia species cause soft rots, but most pectolytic “erwinias” have been transferred to the genera Pectobacterium and Dickeya (Arif et al., 2022; Czajkowski et al., 2015). Diagnosis of E. amylovora is regulated by EPPO PM 7/20 and includes isolation, serology, PCR, LAMP, and pathogenicity testing (EPPO, 2022).

2.7. Genera Pectobacterium and Dickeya: Soft Rots and Blackleg

Until 1998, pectolytic erwinias were assigned to the genus Erwinia: E. carotovora (with subspecies) and E. chrysanthemi. Based on 16S rDNA and genomic data, they were separated into distinct genera: Pectobacterium and Dickeya (Hauben et al., 1998; Samson et al., 2005; Arif et al., 2022). Currently, Pectobacterium includes 19 species and Dickeya 12 species (Arif et al., 2022). The most important for potato are P. atrosepticum, P. carotovorum, P. brasiliense, P. parmentieri, P. polaris, P. punjabense; D. dianthicola, D. solani, D. dadantii, D. zeae, and D. chrysanthemi (Czajkowski et al., 2015; EPPO, 2023; Charkowski et al., 2020).

These bacteria cause blackleg—necrosis of the stem base, soft rot of tubers, fruits, and vegetables during storage, as well as aerial stem rot. Pathogenicity is associated with the secretion of pectolytic enzymes via T2SS, as well as T3SS, toxins, and regulators (Arif et al., 2022; Charkowski et al., 2020). Pectobacterium and Dickeya differ in temperature optima: P. atrosepticum is psychrophilic, D. solani is more thermophilic. Species differ in aggressiveness, host range, and geographic distribution. For diagnosis, species-specific PCR, qPCR, and LAMP have been developed (Czajkowski et al., 2015; EPPO, 2023; Yang et al., 2025).

2.8. Genus Clavibacter and Bacterial Canker of Tomato

Clavibacter is a genus of Gram-positive coryneform bacteria in the family Microbacteriaceae. The type species is Clavibacter michiganensis, which includes several subspecies: subsp. michiganensis (bacterial canker of tomato), subsp. sepedonicus (ring rot of potato), subsp. insidiosus (wilt of alfalfa), subsp. nebraskensis (wilt of corn), subsp. phaseoli (wilt of bean), and subsp. tesselarius (spot of wheat) (Akhatov et al., 2013; Charkowski et al., 2020). Some authors propose elevating the subspecies to species: C. sepedonicus, C. insidiosus, C. nebraskensis (Charkowski et al., 2020).

C. michiganensis subsp. michiganensis causes bacterial canker and wilt of tomato—a disease widespread in all growing regions. The pathogen is seed-borne and systemic; symptoms include unilateral wilting of leaves, vascular necrosis, stem cankers, and “bird’s-eye” spots on fruits. Losses can reach 30–70% (Akhatov et al., 2013). Diagnosis includes isolation on selective media, ELISA, PCR, and LAMP (Akhatov et al., 2013; EPPO, 2025). C. michiganensis subsp. sepedonicus is the causal agent of ring rot of potato, a quarantine organism; it causes browning of the vascular ring of tubers, wilting, and bacterial exudate (Charkowski et al., 2020; EPPO, 2023).

2.9. Genus Streptomyces and Potato Scab

Streptomyces is a genus of Gram-positive mycelial actinobacteria, inhabitants of soil. Most species are saprophytes, but some cause plant diseases, in particular common scab of potato. The main causal agents are Streptomyces scabiei (formerly S. scabies), S. acidiscabiei, S. turgidiscabiei, S. europaeiscabiei, S. caviscabiei, and others (Charkowski et al., 2020). Pathogenicity is associated with the phytotoxin thaxtomin, which inhibits cellulose synthesis and causes cell hypertrophy. Pathogenicity genes are located on mobile pathogenicity islands, which promotes horizontal transfer (Charkowski et al., 2020).

Scab manifests as superficial, raised, or pitted lesions on tubers, reducing marketability. The disease is widespread wherever potato is grown. Control includes crop rotation, maintenance of low pH, irrigation, resistant cultivars, and biological control (Charkowski et al., 2020). Diagnosis is based on isolation on selective media, PCR detection of thaxtomin genes (txtAB), and species identification (Charkowski et al., 2020; EPPO, 2023).

2.10. Candidatus Liberibacter: Citrus HLB and Zebra Chip

Candidatus Liberibacter is a genus of Gram-negative, phloem-limited, unculturable bacteria transmitted by psyllids. The name “Candidatus” indicates that the organisms have not been isolated in pure culture and their taxonomic status is preliminary (Charkowski et al., 2020). The best-known species are Candidatus Liberibacter asiaticus, Ca. L. africanus, and Ca. L. americanus—causal agents of Huanglongbing (HLB, citrus greening)—the most destructive citrus disease in the world. Ca. L. solanacearum is the causal agent of zebra chip of potato and diseases of tomato, pepper, carrot, and celery; it is transmitted by the potato psyllid (Bactericera cockerelli) (Charkowski et al., 2020).

HLB manifests as yellowing of veins, mottling, leaf deformation, small fruits with a bitter taste, and rapid tree decline. The disease is incurable; control is aimed at vector management, use of healthy planting material, and resistant cultivars (Charkowski et al., 2020). Zebra chip of potato causes darkening of flesh when fried, reduced yield and quality; measures include psyllid control, tolerant cultivars, and monitoring (Charkowski et al., 2020). Diagnosis of Candidatus Liberibacter is based on PCR, qPCR, LAMP, and sequencing, since cultivation is impossible (Charkowski et al., 2020; Yang et al., 2025).

2.11. Other Important Genera and Groups

In addition to those listed, the following are important in phytopathology:

Xylella fastidiosa — a Gram-negative, xylem-limited, slow-growing bacterium, causal agent of Pierce’s disease of grapevine, citrus variegated chlorosis, leaf scorch of coffee, oleander, oak, and almond. It is transmitted by leafhoppers. It is a quarantine organism (Charkowski et al., 2020; Bansal et al., 2023). Some researchers propose including Xylella in the genus Xanthomonas (Bansal et al., 2023), but this has not yet been accepted.

Curtobacterium flaccumfaciens pv. flaccumfaciens — a Gram-positive bacterium, causal agent of wilt of bean. It is a quarantine organism on the EPPO A2 list (EPPO, 2025).

Rathayibacter spp. — causal agents of toxicoses of cereals, associated with nematodes.

Pantoea stewartii subsp. stewartii — causal agent of Stewart’s wilt of corn, transmitted by flea beetles. It is a quarantine organism (EPPO, 2025).

Mollicutes (phytoplasmas and spiroplasmas) — although formally not bacteria but a separate group of prokaryotes without a cell wall, they cause many diseases: stolbur of Solanaceae, aster yellows, apple proliferation, and lethal yellowing of coconut palm. Diagnosis: PCR, microscopy, sensitivity to tetracyclines (Charkowski et al., 2020; Vailleau and Genin, 2023).

2.12. Conclusion

The major genera of phytopathogenic bacteria cover a wide range of taxonomic groups: from Gram-negative proteobacteria (Pseudomonas, Xanthomonas, Ralstonia, Erwinia, Pectobacterium, Dickeya, Agrobacterium, Xylella, Candidatus Liberibacter) to Gram-positive actinobacteria (Clavibacter, Streptomyces, Curtobacterium). Each genus is characterized by certain symptoms, mechanisms of pathogenicity, ecology, and diagnostic methods. Modern systematics actively revises the boundaries of genera and species based on genomic data, which requires plant protection specialists to constantly track nomenclatural changes. In the next lecture, we will examine taxonomic rearrangements and their practical consequences in detail.

3. Taxonomic Rearrangements of Phytopathogenic Bacteria

3.1. Introduction: Why Bacterial Systematics Is Unstable

Bacterial systematics is one of the most dynamic areas of biology. Unlike the systematics of higher plants and animals, where morphological characters often allow species to be distinguished relatively stably, bacterial morphology is extremely poor: most are rods or cocci, with differences that are minimal to the naked eye or even under a light microscope (Sigee, 1993). That is why bacterial classification was long based on physiological and biochemical characters and, especially important for phytopathology, on pathogenicity. If a bacterium caused disease in a particular host plant, it was often described as a new species—even if biochemically it was almost identical to an already known species (Sigee, 1993). This approach, called “new host—new species,” led to an enormous number of described species: by 1957, about 60 species of Xanthomonas were recognized, and by 1974, more than 200 (Chuang et al., 2025).

However, beginning in the 1960s–1970s, and especially from the 1980s–1990s, molecular methods entered bacterial systematics. First came determination of G+C content, then DNA-DNA hybridization (DDH), then 16S rRNA sequencing, and in the 21st century, whole-genome sequencing and genome comparison (Mousavi and Young, 2023; Bansal et al., 2023). These methods showed that many traditional species and genera of phytopathogenic bacteria are not monophyletic groups, and some names are synonyms. As a consequence, the systematics of phytopathogenic bacteria has undergone and continues to undergo profound rearrangements. Understanding these rearrangements is necessary for diagnosis, quarantine, breeding, and scientific communication (Mousavi and Young, 2023; Bansal et al., 2023; Czajkowski et al., 2015).

3.2. Causes of Taxonomic Rearrangements

Molecular Data and the Polyphasic Approach

Modern bacterial systematics is based on a polyphasic approach that combines phenotypic, genotypic, and phylogenetic data (Bansal et al., 2023). Key roles are played by:

16S rRNA sequencing — a universal marker for phylogenetic reconstructions. However, for closely related species, the resolving power of 16S rRNA is often insufficient, so multilocus sequence analysis (MLSA) of several housekeeping genes is additionally used: atpD, dnaK, gyrB, recA, rpoB, etc. (Chuang et al., 2025; Mousavi and Young, 2023).

DNA-DNA hybridization (DDH) — long considered the gold standard for delimiting species. A threshold of 70% DDH was considered species-level, but the method is laborious and not always reproducible (Bansal et al., 2023).

Average nucleotide identity (ANI) — a modern computational analogue of DDH. A threshold of 95–96% ANI usually corresponds to the species boundary (Bansal et al., 2023; Chuang et al., 2025).

Average amino acid identity (AAI) and percentage of conserved proteins (POCP) — used to delimit genera. An AAI threshold of about 65–68% is often accepted for genus (Bansal et al., 2023).

Phylogenomics — construction of trees based on hundreds of conserved genes (e.g., PhyloPhlAn 3.0, PIRATE) allows identification of monophyletic groups and verification of whether proposed taxa correspond to evolutionary history (Bansal et al., 2023).

Rejection of Pathogenicity as the Main Species Criterion

Historically, pathogenicity was the main criterion for describing species of phytopathogenic bacteria. If a strain caused disease in a new host, it was described as a new species or pathovar. However, molecular data showed that pathogenicity is often determined by mobile genetic elements—plasmids, pathogenicity islands, prophages—which can be transmitted horizontally between unrelated strains (Sigee, 1993; Arif et al., 2022). For example, pathogenicity genes of Agrobacterium are located on Ti or Ri plasmids; loss of the plasmid makes the strain avirulent but does not change its species affiliation. Similarly, thaxtomin genes in Streptomyces are located on mobile pathogenicity islands (Charkowski et al., 2020). Therefore, modern systematics strives to classify bacteria by their evolutionary relatedness (phylogeny), not by pathogenicity. Pathovars and races are retained as infrasubspecific categories, but not as species (Mousavi and Young, 2023; Chuang et al., 2025).

Horizontal Gene Transfer and Mosaic Genomes

Horizontal gene transfer (HGT) is another cause of taxonomic instability. Bacterial genomes may contain regions acquired from unrelated organisms, which complicates phylogenetic reconstruction based on individual genes. For example, in Pectobacterium and Dickeya, pathogenicity genes (pectinases, T3SS, T6SS) are often located on pathogenicity islands and could have been acquired independently by different lineages (Arif et al., 2022). This means that phenotypic similarity (e.g., the ability to cause soft rot) does not necessarily reflect close relatedness. Phylogenomic analysis based on conserved genes allows vertical inheritance to be separated from horizontal transfer and a more reliable classification to be constructed (Arif et al., 2022; Bansal et al., 2023).

3.3. Key Examples of Taxonomic Rearrangements

Erwinia → Pectobacterium, Dickeya, Brenneria, Pantoea

One of the best-known examples is the reorganization of the genus Erwinia. Until 1998, pectolytic erwinias causing soft rots and blackleg were assigned to the species Erwinia carotovora (with subspecies carotovora, atroseptica, betavasculorum, odorifera, wasabiae) and Erwinia chrysanthemi (with pathovars). Based on 16S rDNA and genomic data, Hauben et al. (1998) proposed separating them into the genus Pectobacterium, and Samson et al. (2005) into the genus Dickeya (Arif et al., 2022; Czajkowski et al., 2015). Later, Pectobacterium was divided into many species: P. atrosepticum, P. carotovorum, P. brasiliense, P. parmentieri, P. polaris, P. punjabense, P. peruviense, P. versatile, P. wasabiae, P. odoriferum, P. aroidearum, P. betavasculorum, P. cacticida, P. zantedeschiae, etc. (Arif et al., 2022; EPPO, 2023). The genus Dickeya includes D. dianthicola, D. solani, D. dadantii, D. zeae, D. chrysanthemi, D. paradisiaca, D. aquatica, D. fangzhongdai, D. lacustris, D. undicola, D. oryzae, and D. parazeae (Arif et al., 2022; EPPO, 2023).

Other former Erwinia species have been transferred to the genera Brenneria (causal agents of tree diseases), Pantoea (causal agent of Stewart’s wilt of corn, P. stewartii), Samsonia, and Lonsdalea (Arif et al., 2022; EPPO, 2023). The genus Erwinia in the narrow sense now includes E. amylovora, E. pyrifoliae, E. piriflorinigrans, E. uzenensis, E. tasmaniensis, and some others (EPPO, 2022). For diagnosis, this means that old names such as Erwinia carotovora or Erwinia chrysanthemi are no longer used in official nomenclature, although they may occur in literature and databases. Modern EPPO diagnostic protocols (2023) use the names Pectobacterium spp. and Dickeya spp.

Agrobacterium → Rhizobium, Allorhizobium

The genus Agrobacterium traditionally included species causing crown gall (A. tumefaciens), hairy root (A. rhizogenes), raspberry galls (A. rubi), and grapevine canker (A. vitis). Based on phylogenomic analysis of rhizobia and agrobacteria, it was proposed to transfer these species to the genus Rhizobium and Allorhizobium: A. tumefaciens → Rhizobium radiobacter, A. rhizogenes → Rhizobium rhizogenes, A. rubi → Rhizobium rubi, A. vitis → Allorhizobium vitis (Mousavi and Young, 2023). In addition, new species Agrobacterium burrii and A. shirazense have been described (Mousavi and Young, 2023), and A. vaccinii from blueberry (Mousavi and Young, 2023). The Subcommittee on the Taxonomy of Rhizobia and Agrobacteria recommends using modern names but recognizes that the transition period may be long (Mousavi and Young, 2023). For diagnosis and quarantine, this means the need to check synonyms: for example, Rhizobium radiobacter and Agrobacterium tumefaciens are the same organism.

It is important to note that not all strains of Rhizobium radiobacter are pathogenic: virulence depends on the presence of the Ti plasmid. Strains without the plasmid are saprophytes or weak opportunists (Mousavi and Young, 2023). This once again confirms that taxonomy should be based on the genome, not on pathogenicity.

Pseudomonas → Ralstonia, Burkholderia, Acidovorax

The genus Pseudomonas in the traditional understanding was a composite group. Based on 16S rRNA and genomic data, the following were separated from it:

Ralstonia — R. solanacearum (formerly Pseudomonas solanacearum), R. pseudosolanacearum, R. syzygii (Safni et al., 2014; Prior et al., 2016; Charkowski et al., 2020).
Burkholderia — B. cepacia and related species, some of which are phytopathogenic or opportunistic for humans.
Acidovorax — A. citrulli (causal agent of bacterial fruit blotch of watermelon), A. avenae (cereal diseases) (Agrios, 2005; Charkowski et al., 2020).
Ralstonia pickettii, R. mannitolilytica — opportunistic human pathogens, but not plant pathogens.

Pseudomonas syringae remains in the genus Pseudomonas, but its taxonomy is also being revised: many pathovars have been elevated to species or transferred to other species (Bansal et al., 2023). For example, P. syringae pv. savastanoi is now P. savastanoi; P. syringae pv. phaseolicola is P. savastanoi pv. phaseolicola (according to some classifications). This creates confusion in literature and diagnosis.

Xanthomonas: Splitting and Reclassification

The genus Xanthomonas has undergone particularly strong changes. Based on DDH, AFLP, MLSA, and whole-genome sequencing, it was shown that many “species” described by host are pathovars within several large species: X. campestris, X. axonopodis, X. citri, X. euvesicatoria, X. hortorum, X. oryzae, X. phaseoli, X. vasicola, X. arboricola, X. sacchari, X. fragariae, X. albilineans, X. hyacinthi, X. theicola, X. populi, X. bromi, X. cucurbitae, X. melonis, X. pisi, X. translucens, etc. (Chuang et al., 2025; Bansal et al., 2023).

For example, X. campestris pv. campestris (black rot of crucifers) remains in X. campestris; X. campestris pv. vesicatoria (bacterial spot of tomato and pepper) has been divided into X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria (Chuang et al., 2025; Akhatov et al., 2013). X. campestris pv. citri → X. citri pv. citri; X. campestris pv. phaseoli → X. phaseoli pv. phaseoli; X. campestris pv. manihotis → X. phaseoli pv. manihotis; X. campestris pv. oryzae → X. oryzae pv. oryzae (Chuang et al., 2025).

For strains affecting Araceae and Araliaceae, reclassification has been carried out: X. axonopodis pv. dieffenbachiae → X. phaseoli pv. dieffenbachiae; X. campestris pv. syngonii → X. phaseoli pv. syngonii; X. campestris pv. zantedeschiae → X. arboricola pv. zantedeschiae; X. campestris pv. amorphophalli → X. euvesicatoria pv. amorphophalli; X. campestris pv. aracearum → X. citri pv. aracearum (Chuang et al., 2025). New species X. hawaiiensis and Stenotrophomonas aracearum, S. oahuensis have been described (Chuang et al., 2025). Bansal et al. (2023) proposed an even more radical revision, including the genera Xylella, Stenotrophomonas, Pseudoxanthomonas, Lysobacter, Luteimonas, Thermomonas, and Vulcanibacterium in the genus Xanthomonas, but this proposal has not yet been officially accepted.

Ralstonia solanacearum Species Complex → Three Species

Ralstonia solanacearum was long considered a single species with four phylotypes (I–IV). Based on ANI, DDH, and phylogenomics, the complex has been divided into three species: R. solanacearum (phylotype II), R. pseudosolanacearum (phylotypes I and III), and R. syzygii (phylotype IV) (Safni et al., 2014; Prior et al., 2016; Charkowski et al., 2020). R. syzygii includes three subspecies: subsp. syzygii, subsp. celebesensis, and subsp. indonesiensis. Strain PIIB1 (phylotype IIB, sequevar 1), formerly known as race 3/biovar 2, remains in R. solanacearum and is the most dangerous for potato in temperate latitudes (Charkowski et al., 2020). For quarantine and diagnosis, this means that tests must distinguish these species, since their quarantine status and control measures may differ (EPPO, 2025; Vailleau and Genin, 2023).

Clavibacter: Subspecies → Species

The genus Clavibacter includes C. michiganensis with subspecies michiganensis, sepedonicus, insidiosus, nebraskensis, phaseoli, and tesselarius. Some authors propose elevating them to species: C. sepedonicus, C. insidiosus, C. nebraskensis (Charkowski et al., 2020). This is due to genomic differences and different ecology. For diagnosis, this means the need to use species-specific tests, not only subspecies-specific ones (EPPO, 2023; Akhatov et al., 2013).

3.4. The Problem of Synonyms in Diagnosis and Quarantine

Taxonomic rearrangements create serious practical problems.

Old and New Names in Literature

Scientific literature, diagnostic kits, databases, and quarantine lists often use different names for the same organism. For example:

Erwinia carotovora subsp. carotovora = Pectobacterium carotovorum subsp. carotovorum = Pectobacterium carotovorum (Arif et al., 2022).
Erwinia chrysanthemi = Dickeya chrysanthemi = Dickeya dadantii = Dickeya solani (depending on strain) (Arif et al., 2022).
Agrobacterium tumefaciens = Rhizobium radiobacter (Mousavi and Young, 2023).
Pseudomonas solanacearum = Ralstonia solanacearum = Ralstonia pseudosolanacearum (depending on phylotype) (Safni et al., 2014; Charkowski et al., 2020).
Xanthomonas campestris pv. vesicatoria = X. euvesicatoria pv. euvesicatoria = X. vesicatoria = X. hortorum pv. gardneri = X. euvesicatoria pv. perforans (Chuang et al., 2025; Akhatov et al., 2013).
Xanthomonas campestris pv. citri = X. citri pv. citri = X. axonopodis pv. citri (Chuang et al., 2025).
Clavibacter michiganensis subsp. sepedonicus = C. sepedonicus (Charkowski et al., 2020).

This creates a risk of errors when searching for information, choosing diagnostic tests, interpreting results, and making quarantine decisions.

EPPO Quarantine Lists

EPPO (European and Mediterranean Plant Protection Organization) regularly updates the A1 and A2 lists of quarantine organisms. The A1 list (absent in the region) and A2 list (present but limited) indicate modern names, but synonyms are often given in parentheses or notes (EPPO, 2025). For example:

Xanthomonas citri subsp. citri (A1) — formerly X. campestris pv. citri (EPPO, 2025).
Xanthomonas citri subsp. aurantifolii (A1) — formerly X. campestris pv. citrumelo (EPPO, 2025).
Xanthomonas euvesicatoria pv. euvesicatoria (A2), X. euvesicatoria pv. perforans (A2), X. vesicatoria (A2), X. cynarae pv. gardneri (A2) — formerly all were X. campestris pv. vesicatoria (EPPO, 2025).
Xanthomonas phaseoli pv. phaseoli (A2), X. citri pv. fuscans (A2) — formerly X. campestris pv. phaseoli and X. phaseoli var. fuscans (EPPO, 2025).
Xanthomonas phaseoli pv. dieffenbachiae (A2) — formerly X. axonopodis pv. dieffenbachiae (EPPO, 2025).
Ralstonia solanacearum (A2), R. pseudosolanacearum (A2), R. syzygii (A1) — formerly the single R. solanacearum (EPPO, 2025).
Clavibacter sepedonicus (A2) — formerly C. michiganensis subsp. sepedonicus (EPPO, 2025).
Dickeya dianthicola (A2) — formerly Erwinia chrysanthemi pv. dianthicola (EPPO, 2025).
Erwinia amylovora (A2) — name unchanged (EPPO, 2025).
Curtobacterium flaccumfaciens pv. flaccumfaciens (A2) — formerly Corynebacterium flaccumfaciens (EPPO, 2025).
Pantoea stewartii subsp. stewartii (A2) — formerly Erwinia stewartii (EPPO, 2025).

For quarantine specialists, this means the need to check synonyms when identifying, preparing phytosanitary documents, and communicating with colleagues from other countries (EPPO, 2025; Czajkowski et al., 2015).

Diagnostic Protocols

EPPO develops and publishes diagnostic protocols (PM 7 series) that contain modern names, methods of isolation, serology, PCR, LAMP, sequencing, and pathogenicity (EPPO, 2022; EPPO, 2023; Yang et al., 2025). For example, PM 7/20 (3) Erwinia amylovora (EPPO, 2022), PM 7/155 (1) Pectobacterium spp. and Dickeya spp. (EPPO, 2023), PM 7/21 Ralstonia solanacearum (EPPO, 2025). These protocols are regularly revised taking taxonomic changes into account. However, not all laboratories and countries update their methods in a timely manner, which can lead to incorrect identification and, consequently, incorrect quarantine measures (Czajkowski et al., 2015; Venbrux et al., 2023).

Databases

LPSN (List of Prokaryotic names with Standing in Nomenclature), NCBI Taxonomy, EzBioCloud, and GTDB (Genome Taxonomy Database) are the main sources of modern names. However, they are not always synchronized with each other, and many sequence databases (GenBank, EMBL) contain records with old names. When working with databases, it is necessary to check synonyms and dates of renaming (Mousavi and Young, 2023; Bansal et al., 2023). For example, a sequence deposited as Erwinia carotovora may now correspond to Pectobacterium carotovorum or P. brasiliense; without additional analysis, this is not always obvious (Arif et al., 2022).

3.5. Why It Is Important to Track Name Changes

For Diagnosis

Accurate identification of the pathogen is the basis for choosing a diagnostic method. If a laboratory uses primers developed for Xanthomonas campestris pv. vesicatoria, but the pathogen belongs to X. euvesicatoria pv. perforans, the test may fail or give a false-positive result (Chuang et al., 2025; Akhatov et al., 2013). Similarly, tests for Erwinia carotovora may not detect Pectobacterium parmentieri or Dickeya solani (Czajkowski et al., 2015; EPPO, 2023). Therefore, diagnostic protocols must be regularly updated taking new taxonomic data into account.

For Quarantine

Quarantine lists operate with specific names. If an organism has been renamed but the old name remains in national legislation, legal conflicts are possible: the pathogen may not be recognized as quarantine, although in fact it is the same organism. For example, Ralstonia pseudosolanacearum (phylotypes I and III) may not be mentioned in old quarantine lists, where only R. solanacearum is listed (Safni et al., 2014; EPPO, 2025). Similarly, Xanthomonas citri subsp. citri may not be listed in lists where X. campestris pv. citri appears (Chuang et al., 2025). For effective quarantine, harmonization of nomenclature at the international level is necessary (EPPO, 2025; Czajkowski et al., 2015).

For Breeding

Breeding for resistance requires knowledge of races and pathovars of the pathogen. If a species has been renamed but its race composition remains the same, breeders must use modern names to avoid confusion in publications and exchange of genetic material (Vailleau and Genin, 2023; Charkowski et al., 2020). For example, Xanthomonas campestris pv. vesicatoria has been divided into several species, each of which may have its own races and its own resistance genes in plants (Chuang et al., 2025; Akhatov et al., 2013). For the Ralstonia solanacearum species complex, different species and phylotypes differ in aggressiveness and cultivar resistance (Charkowski et al., 2020; Vailleau and Genin, 2023).

For Scientific Communication

Unified nomenclature is the basis of scientific communication. If one author writes Erwinia carotovora, another Pectobacterium carotovorum, and a third P. brasiliense, it is difficult for the reader to understand which organism is meant. Therefore, international committees (ICSP, Subcommittee on Taxonomy of Rhizobia and Agrobacteria, EPPO Panel on Diagnostics) recommend using modern names and indicating synonyms at first mention (Mousavi and Young, 2023; EPPO, 2025).

3.6. Conclusion

Taxonomic rearrangements of phytopathogenic bacteria are not an end in themselves but a reflection of the accumulation of new knowledge about the genomes, phylogeny, and ecology of these organisms. They affect almost all major genera: Erwinia, Pectobacterium, Dickeya, Agrobacterium, Rhizobium, Pseudomonas, Ralstonia, Xanthomonas, Clavibacter, Streptomyces, and Candidatus Liberibacter. For plant protection specialists, this means the need to constantly track nomenclatural changes, check synonyms, update diagnostic protocols and quarantine lists. Accurate identification of a pathogen is impossible without understanding modern systematics, and effective plant protection is impossible without accurate identification. In the next lecture, we will consider the concepts of pathovar and pathotype, as well as their significance for breeding, quarantine, and diagnosis.

4. The Concept of Pathovar and Pathotype

4.1. Introduction: Why Infrasubspecific Categories Are Needed

In previous lectures, we examined the major genera of phytopathogenic bacteria and the taxonomic rearrangements their systematics is undergoing. However, for practical phytopathology it is often insufficient to know only the species or even subspecies of a pathogen. Within one species, there may be groups of strains that differ in the range of affected plants, in virulence to certain cultivars, or in biochemical properties. To designate such groups, infrasubspecific categories are used: pathovar, pathotype, race, biovar, serovar, lysotype, and others (Sigee, 1993; Agrios, 2005). These categories do not have official status in the International Code of Nomenclature of Prokaryotes (ICNP), but they are widely used in phytopathology, breeding, quarantine, and diagnosis. Without them, it is impossible to describe pathogen diversity, predict epiphytotics, and create resistant cultivars.

In this lecture, we will examine in detail the concepts of pathovar and pathotype, their relationship with other infrasubspecific categories, examples, and practical significance.

4.2. Pathovar: Definition and History of the Concept

What Is a Pathovar

Pathovar (pathovar, pv.) is an infrasubspecific category that unites strains of one species (or subspecies) of bacteria characterized by a common host range and causing similar symptoms on those hosts (Sigee, 1993; Agrios, 2005). A pathovar is designated by the abbreviation “pv.” after the species name: for example, Xanthomonas campestris pv. campestris, Pseudomonas syringae pv. tabaci, Xanthomonas citri pv. citri.

A pathovar is not a taxonomic category in the strict sense but a practical grouping based on pathogenicity. Strains of one pathovar may be genetically heterogeneous but phenotypically similar in their ability to affect certain plants. Conversely, strains of different pathovars may be genetically close but differ in host range due to the presence or absence of mobile genetic elements—plasmids, pathogenicity islands, prophages (Sigee, 1993; Arif et al., 2022).

Historical Context

The concept of pathovar was introduced in 1978 by the International Committee on Systematics of Bacteria (ICSB) to replace the informal categories “variant” and “special form” (Sigee, 1993). Before that, many phytopathogenic bacteria were described as separate species based on their pathogenicity: if a bacterium affected a new host plant, it was called a new species. This approach led to an enormous number of described species: by 1957, about 60 species of Xanthomonas, and by 1974, more than 200 (Chuang et al., 2025). However, biochemical and physiological differences between these “species” were often minimal or absent. The introduction of pathovar allowed species names to be retained for genetically distinct groups, while intraspecific diversity in pathogenicity was designated by pathovars (Sigee, 1993; Chuang et al., 2025).

Pathovar and Species: Relationship

A pathovar is always within a species or subspecies. For example, Pseudomonas syringae includes more than 50 pathovars: pv. syringae, pv. tabaci, pv. phaseolicola, pv. tomato, pv. lachrymans, pv. pisi, pv. glycinea, pv. coronafaciens, pv. atrofaciens, pv. maculicola, pv. morsprunorum, and many others (Agrios, 2005; Sigee, 1993). Xanthomonas campestris traditionally included more than 140 pathovars, but after genomic revisions many of them have been transferred to other species: X. euvesicatoria, X. hortorum, X. citri, X. phaseoli, X. oryzae, X. arboricola, X. vasicola, X. sacchari, etc. (Chuang et al., 2025; Bansal et al., 2023).

It is important to understand that a pathovar is not a genetic but a pathogenetic category. Strains of one pathovar may be genetically heterogeneous, and strains of different pathovars may be genetically close. For example, Xanthomonas citri pv. citri and X. citri pv. aurantifolii are genetically close but differ in host range and symptoms (Chuang et al., 2025). Similarly, X. phaseoli pv. phaseoli and X. phaseoli pv. dieffenbachiae may be genetically similar, but the first affects bean and the second affects aroids (Chuang et al., 2025; Constantin et al., 2016).

Rules for Nomenclature of Pathovars

The nomenclature of pathovars is regulated by the International Society for Plant Pathology (ISPP) and follows the rules set out in “International Standards for Naming Pathovars of Phytopathogenic Bacteria” (Dye et al., 1980). The main rules:

A pathovar is designated in lowercase letters after the species epithet: Xanthomonas campestris pv. campestris.
The name of a pathovar usually derives from the name of the host plant or genus: pv. campestris (from Brassica campestris), pv. phaseoli (from Phaseolus), pv. oryzae (from Oryza), pv. citri (from Citrus), pv. dieffenbachiae (from Dieffenbachia), pv. syngonii (from Syngonium), pv. zantedeschiae (from Zantedeschia), pv. amorphophalli (from Amorphophallus), pv. aracearum (from Araceae) (Chuang et al., 2025; Sigee, 1993).
If a pathovar is transferred to another species, the pathovar name is retained: for example, X. axonopodis pv. dieffenbachiae → X. phaseoli pv. dieffenbachiae (Constantin et al., 2016; Chuang et al., 2025).
Pathovars do not have type strains in the same sense as species; instead, reference strains (pathotype strains) are used, which are deposited in international collections (Sigee, 1993).

Pathovars in Different Genera

Pathovars have been described in several genera of phytopathogenic bacteria:

Xanthomonas — the largest number of pathovars. X. campestris (more than 140 pathovars), X. citri, X. euvesicatoria, X. hortorum, X. phaseoli, X. oryzae, X. arboricola, X. vasicola, X. sacchari, X. fragariae, X. albilineans, X. hyacinthi, X. theicola, X. populi, X. bromi, X. cucurbitae, X. melonis, X. pisi, X. translucens, etc. (Chuang et al., 2025; Bansal et al., 2023; Sigee, 1993).
Pseudomonas — P. syringae (more than 50 pathovars), P. savastanoi (pv. savastanoi, pv. phaseolicola, pv. glycinea, etc.), P. marginalis, P. cichorii (Sigee, 1993; Agrios, 2005).
Erwinia — E. amylovora (has no pathovars but has strains differing in hosts), E. pyrifoliae, E. piriflorinigrans (EPPO, 2022).
Pectobacterium — has no pathovars in the strict sense but has biovars and serovars (Czajkowski et al., 2015; EPPO, 2023).
Dickeya — has biovars (biovar 1, 2, 3, 7, etc.), which previously corresponded to pathovars of E. chrysanthemi (Samson et al., 2005; Czajkowski et al., 2015).
Clavibacter — has no pathovars but has subspecies and pathotypes (Akhatov et al., 2013; Charkowski et al., 2020).
Curtobacterium — C. flaccumfaciens pv. flaccumfaciens, pv. oortii, pv. poinsettiae, pv. beticola (Sigee, 1993; EPPO, 2025).
Ralstonia — has no pathovars but has races (race 1, 2, 3) and biovars (biovar 1–5) (Charkowski et al., 2020; Vailleau and Genin, 2023).

4.3. Pathotype: Definition and Relationship with Pathovar

What Is a Pathotype

Pathotype is a group of strains within a pathovar (or species) characterized by the same virulence to a certain set of differential cultivars (Sigee, 1993; Agrios, 2005). A pathotype is a narrower category than a pathovar. If a pathovar differs in host range (e.g., affects bean but not soybean), then a pathotype differs in virulence to cultivars within one host species (e.g., affects cultivar A but not cultivar B).

Pathotype is often used interchangeably with the term “race” or “physiological race.” However, there is a nuance: “race” usually designates a group of strains differing in virulence to a set of differential cultivars, and this concept is applied to both fungi and bacteria. “Pathotype” is a more general term that can designate any group of strains with the same pathogenicity, including races (Sigee, 1993; Agrios, 2005).

Pathotype and Race: Relationship

In phytopathology, the terms “pathotype” and “race” are often used as synonyms, but there are nuances:

Race — a group of strains differing in virulence to certain differential cultivars. Races are designated by numbers or letters: race 1, race 2, race 3; race 0, race 1, race 2, etc. (Sigee, 1993; Akhatov et al., 2013).
Pathotype — a broader concept that may include races, biovars, serovars, and other infrasubspecific groups united by pathogenicity. For example, a pathotype may designate a group of strains affecting a certain host species but not differing by cultivar (Sigee, 1993).

In resistance breeding practice, the term “race” is more often used, while in diagnosis and quarantine, “pathovar” and “pathotype” are used (Agrios, 2005; Chuang et al., 2025).

Examples of Pathotypes and Races

A classic example is Pseudomonas syringae pv. phaseolicola (causal agent of halo blight of bean). This pathovar is divided into several races (race 1, race 2, race 3, race 4, race 5, race 6, race 7, race 8, race 9) based on the reaction of bean cultivars Canadian Wonder, Red Mexican, Tendergreen, and others (Sigee, 1993; Agrios, 2005). Race 1 affects Canadian Wonder and Tendergreen but not Red Mexican; race 2 affects Red Mexican and Tendergreen but not Canadian Wonder; race 3 affects all three cultivars; etc. (Sigee, 1993). Knowledge of races is necessary for breeding resistant cultivars: if race 1 predominates in a region, a cultivar with the resistance gene to race 1 will be resistant but may be susceptible to race 2.

Another example is Xanthomonas campestris pv. vesicatoria (now X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, X. vesicatoria) — the causal agent of bacterial spot of pepper and tomato. In pepper, races 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 have been described, which differ in virulence to cultivars with resistance genes Bs1, Bs2, Bs3, etc. (Akhatov et al., 2013). Gene Bs1 provides resistance to race 1 but not to race 2; gene Bs2 to races 1 and 2 but not to race 3; etc. (Akhatov et al., 2013). For breeding, this means the need to pyramid resistance genes or use cultivars with broad resistance.

In the Ralstonia solanacearum species complex, races (race 1, 2, 3) are distinguished by host range and biovars (biovar 1–5) by biochemical traits. Race 1 affects many species, race 2 affects banana and Heliconia (Moko disease), and race 3 affects potato and tomato (Charkowski et al., 2020; Vailleau and Genin, 2023). Biovars differ in the utilization of carbohydrates and alcohols: biovar 1, 2, 3, 4, 5. Strain PIIB1 (phylotype IIB, sequevar 1) — race 3, biovar 2 — is the most dangerous for potato in temperate latitudes (Charkowski et al., 2020).

In Pectobacterium and Dickeya, races and pathotypes are not used to the same extent as in Xanthomonas and Pseudomonas. Instead, biovars (biovar 1–7 in Dickeya), serovars, and genotypes are used (Czajkowski et al., 2015; EPPO, 2023). For example, D. dianthicola — biovar 1 and 7; D. solani — biovar 3; D. dadantii — biovar 1, 2, 3; D. zeae — biovar 1, 2, 3 (Samson et al., 2005; Czajkowski et al., 2015).

4.4. Biovars, Serovars, and Other Infrasubspecific Categories

In addition to pathovars and pathotypes, other infrasubspecific categories are used in phytopathology:

Biovar — a group of strains differing in biochemical or physiological traits: utilization of carbohydrates, alcohols, organic acids, acid production, hydrolysis of esculin, gelatin, etc. (Sigee, 1993; Czajkowski et al., 2015). Biovars are widely used in Ralstonia, Dickeya, Pectobacterium, and Agrobacterium (Mousavi and Young, 2023; Charkowski et al., 2020).
Serovar (serotype) — a group of strains differing in antigenic properties: lipopolysaccharides (O antigens), flagellar antigens (H antigens), capsular antigens (K antigens). Serovars are used for epidemiological studies and diagnosis (Sigee, 1993; Czajkowski et al., 2015). For example, 8 serogroups have been described in Pectobacterium atrosepticum; 9 serogroups in Dickeya (Czajkowski et al., 2015).
Lysotype (phagotype) — a group of strains differing in sensitivity to bacteriophages. Lysotyping has been used to differentiate Xanthomonas campestris pv. oryzae (5 lysotypes), X. citri (groups A, B, C, E), Pectobacterium, and others (Sigee, 1993).
Symbiovar — a category analogous to pathovar but for symbiotic bacteria (rhizobia). Symbiovars differ in the range of host plants with which they form nodules (Mousavi and Young, 2023). The Subcommittee on the Taxonomy of Rhizobia and Agrobacteria recommends developing minimum standards for defining symbiovars, including the level of sequence similarity and host specificity data (Mousavi and Young, 2023).
Genotype — a group of strains differing in genetic markers: RFLP, AFLP, REP-PCR, MLST, ANI, whole-genome sequencing. Genotypes are used for phylogenetic studies, epidemiology, and diagnosis (Czajkowski et al., 2015; EPPO, 2023; Chuang et al., 2025).

4.5. Significance of Pathovars and Pathotypes for Breeding Resistant Cultivars

Gene-for-Gene Interaction

Plant resistance to bacteria often follows the gene-for-gene model proposed by Flor in 1946 for rust fungi and later confirmed for many bacterioses (Agrios, 2005; Sigee, 1993). The essence of the model: each resistance gene (R) in the plant corresponds to an avirulence gene (avr) in the pathogen. If the plant has gene R and the pathogen has the corresponding avr, the plant is resistant; if the pathogen loses avr (mutation, deletion, horizontal transfer), it becomes virulent and the plant is affected (Agrios, 2005; Sigee, 1993).

For breeding, this means that knowledge of races and pathovars of the pathogen is necessary for choosing resistance genes. If race 1 predominates in a region, gene R1 is sufficient; if race 2 appears, gene R1 loses effectiveness, and gene R2 or pyramiding of R1 + R2 is needed (Agrios, 2005; Akhatov et al., 2013).

Examples

Pepper and Xanthomonas. Genes Bs1, Bs2, and Bs3 provide resistance to different races of X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria (Akhatov et al., 2013; Chuang et al., 2025). Gene Bs2 provides resistance to races 1, 2, and 3 but not to race 4; gene Bs3 to races 1, 2, 3, and 4 but not to race 5; etc. (Akhatov et al., 2013). Breeders combine these genes for broad resistance.
Tomato and Xanthomonas. In tomato, resistance genes Xv1, Xv2, Xv3, and Xv4 have been described, which correspond to different races of X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria (Chuang et al., 2025).
Bean and Pseudomonas syringae pv. phaseolicola. Races 1–9 differ in virulence to cultivars with genes R1–R9 (Sigee, 1993; Agrios, 2005). Breeding for resistance requires knowledge of the race composition in the region.
Potato and Ralstonia. Resistance to R. solanacearum is polygenic and race-specific; different phylotypes and sequevars differ in aggressiveness, and cultivar resistance may be unstable under different conditions (Charkowski et al., 2020; Vailleau and Genin, 2023).

Problems of Breeding

Breeding for resistance to bacterioses is complicated by several factors:

Polygenic resistance. Many resistance genes have small effects, and their pyramiding requires time and resources (Vailleau and Genin, 2023; Charkowski et al., 2020).
Dynamic race composition of the pathogen. The appearance of new races can quickly overcome cultivar resistance (Agrios, 2005; Akhatov et al., 2013).
Horizontal gene transfer. Pathogens can acquire new virulence genes through plasmids, pathogenicity islands, and prophages, which accelerates overcoming resistance (Arif et al., 2022; Charkowski et al., 2020).
Lack of resistance in cultivated cultivars. For many bacterioses (e.g., Pectobacterium and Dickeya on potato), there are no resistant commercial cultivars, and breeding is limited to tolerance (Czajkowski et al., 2015; EPPO, 2023).

4.6. Significance of Pathovars and Pathotypes for Quarantine

Quarantine Lists and Pathovars

Quarantine lists of EPPO, EU, and national lists often indicate not only the species but also the pathovar or pathotype. For example:

Xanthomonas citri subsp. citri (A1) — citrus canker; formerly X. campestris pv. citri (EPPO, 2025).
Xanthomonas citri subsp. aurantifolii (A1) — formerly X. campestris pv. citrumelo (EPPO, 2025).
Xanthomonas euvesicatoria pv. euvesicatoria (A2), X. euvesicatoria pv. perforans (A2), X. vesicatoria (A2), X. cynarae pv. gardneri (A2) — formerly all were X. campestris pv. vesicatoria (EPPO, 2025).
Xanthomonas phaseoli pv. phaseoli (A2), X. citri pv. fuscans (A2) — formerly X. campestris pv. phaseoli and X. phaseoli var. fuscans (EPPO, 2025).
Xanthomonas phaseoli pv. dieffenbachiae (A2) — formerly X. axonopodis pv. dieffenbachiae (EPPO, 2025).
Curtobacterium flaccumfaciens pv. flaccumfaciens (A2) — formerly Corynebacterium flaccumfaciens (EPPO, 2025).
Pantoea stewartii subsp. stewartii (A2) — formerly Erwinia stewartii (EPPO, 2025).

For quarantine, it is important to know exactly which pathovar or pathotype is present in a country or region, since control measures depend on this: some pathovars may be quarantine-regulated, others not. For example, X. campestris pv. campestris (black rot of crucifers) is not quarantine-regulated in EPPO, while X. citri pv. citri (citrus canker) is (EPPO, 2025).

Problem of Identifying Pathovars

Identification of pathovars requires pathogenicity tests: inoculation of a set of host plants and differential cultivars. This is laborious and requires greenhouses, phytotrons, and qualified personnel (Sigee, 1993; EPPO, 2022; EPPO, 2023). Molecular methods (PCR, qPCR, LAMP, sequencing) allow rapid species determination but not always pathovar or race. For pathovars that differ by the presence of certain virulence genes, PCR for these genes can be used (e.g., avrBs2, avrBsT, avrRpt2), but for many pathovars such markers are lacking (Chuang et al., 2025; EPPO, 2023).

Harmonization of Nomenclature

For effective quarantine, harmonization of nomenclature at the international level is necessary. EPPO, EU, NAPPO, IPPC, and other organizations update lists and protocols, but not always synchronously. For example, Ralstonia pseudosolanacearum (phylotypes I and III) may not be mentioned in old quarantine lists, where only R. solanacearum is listed (Safni et al., 2014; EPPO, 2025). Similarly, X. euvesicatoria pv. perforans may not be listed in lists where X. campestris pv. vesicatoria appears (Chuang et al., 2025). For quarantine specialists, this means the need to check synonyms and update the regulatory framework (EPPO, 2025; Czajkowski et al., 2015).

4.7. Significance of Pathovars and Pathotypes for Diagnosis

Choice of Diagnostic Method

Knowledge of pathovar and pathotype determines the choice of diagnostic method:

For species identification, PCR, qPCR, LAMP, sequencing, and serology are sufficient (Czajkowski et al., 2015; Yang et al., 2025).
For pathovar identification, pathogenicity tests or PCR for virulence genes are necessary (Chuang et al., 2025; EPPO, 2023).
For race identification, inoculation on differential cultivars is necessary (Akhatov et al., 2013; Sigee, 1993).

Latent Infection and Pathovars

Latent infection can be caused by any pathovar, but some pathovars are more prone to latent course. For example, R. solanacearum PIIB1 can persist in tubers without symptoms, and X. citri pv. citri can be present in citrus leaves without visible lesions (Charkowski et al., 2020; Chuang et al., 2025). For diagnosis, this means the need to use sensitive methods (qPCR, LAMP, metagenomics) and enrichment (Czajkowski et al., 2015; Venbrux et al., 2023).

Mixed Infections

In the field and in greenhouses, mixed infections are common: several pathovars or even bacterial species on one plant. For example, Pectobacterium and Dickeya may be present simultaneously in tubers; X. euvesicatoria pv. euvesicatoria and X. euvesicatoria pv. perforans on tomato; R. solanacearum and R. pseudosolanacearum on potato (Czajkowski et al., 2015; Chuang et al., 2025; Charkowski et al., 2020). For diagnosis, this means the need for multiplex tests, metagenomics, and sequencing (Venbrux et al., 2023; Yang et al., 2025).

4.8. Problems and Limitations of the Pathovar System

Pathovar Is Not Always a Monophyletic Group

Pathovars may be polyphyletic: strains of one pathovar may descend from different ancestors and acquire pathogenicity independently through horizontal gene transfer (Arif et al., 2022; Chuang et al., 2025). For example, X. campestris pv. campestris may include strains genetically closer to other pathovars than to each other. This creates problems for phylogenetic reconstructions and taxonomy (Bansal et al., 2023; Chuang et al., 2025).

Pathovar Is Not Always a Stable Category

A pathovar may lose or acquire pathogenicity upon loss or acquisition of a plasmid, pathogenicity island, or prophage. For example, Agrobacterium without the Ti plasmid is avirulent but genetically identical to a virulent strain (Mousavi and Young, 2023; Sigee, 1993). Pectobacterium without pectinase genes does not cause soft rot but remains the same species (Arif et al., 2022). This means that pathovar is not always a reliable criterion for identification and classification.

Problem of Intermediate Forms

Some pathovars have intermediate forms that are difficult to assign to one or another pathovar. For example, Pseudomonas syringae pv. syringae and pv. morsprunorum both affect stone fruits but differ in hosts and ecology; in South Africa, mixed populations with intermediate forms occur (Sigee, 1993). For diagnosis, this means the need to use several methods and careful interpretation of results.

Transition to Genomic Taxonomy

Modern systematics increasingly relies on genomic data (ANI, AAI, phylogenomics), which allow monophyletic species and genera to be delimited but do not always correspond to traditional pathovars (Bansal et al., 2023; Mousavi and Young, 2023). For example, X. campestris pv. campestris may be divided into several species, and some pathovars may be merged into one species. This creates tension between the traditional pathovar system and modern genomic taxonomy (Chuang et al., 2025; Bansal et al., 2023). For practice, this means the need for a gradual transition to genomic identification methods and updating nomenclature (Mousavi and Young, 2023; EPPO, 2025).

4.9. Conclusion

Pathovar and pathotype are key concepts in phytopathology that allow intraspecific diversity of bacteria to be described by pathogenicity. A pathovar unites strains by host range, and a pathotype (race) by virulence to differential cultivars. These categories do not have official taxonomic status but are widely used in breeding, quarantine, diagnosis, and epidemiology. They allow:

prediction of disease development and selection of resistant cultivars;
determination of quarantine measures and restrictions on the movement of plant material;
choice of diagnostic methods and interpretation of results;
understanding of pathogen evolution and adaptation to hosts.

However, the pathovar system has limitations: pathovars may be polyphyletic, unstable, and difficult to identify. Modern genomic taxonomy is gradually replacing traditional pathovars with monophyletic species and subspecies, but the full transition will take time. For plant protection specialists, it is important to combine classical pathogenicity methods with modern molecular and genomic approaches to ensure accurate identification and effective plant protection.

5. The Role of Systematics in Developing Protection Methods

5.1. Introduction: Why Systematics Has Practical Significance

In previous lectures, we examined the major genera of phytopathogenic bacteria, taxonomic rearrangements, and infrasubspecific categories—pathovars and pathotypes. It may seem that systematics is a purely academic discipline, interesting only to a narrow circle of specialists. However, this is a deeply mistaken idea. Accurate identification of a pathogen is the basis of the entire plant protection system. The choice of control strategy and methods, the effectiveness of chemical and biological preparations, quarantine measures and restrictions on the movement of plant material, breeding of resistant cultivars, and forecasting of epiphytotics depend on which species, subspecies, pathovar, or race the causal agent belongs to (Agrios, 2005; Sigee, 1993; Czajkowski et al., 2015).

As Sigee (1993) noted, “it is impossible to control a disease without knowing its causal agent.” Systematics gives us the language to describe pathogens and their diversity, as well as tools for their identification. In this lecture, we will examine how systematic knowledge is applied in practice—from the choice of bactericide to the development of quarantine lists and breeding programs.

5.2. Accurate Identification as the Basis for Choosing a Protection Strategy

Species and Pathovar Determine Control Methods

Different species and pathovars of phytopathogenic bacteria have different biology, ecology, and sensitivity to control agents. Therefore, the first step in developing a protection strategy is accurate identification of the pathogen (Czajkowski et al., 2015; EPPO, 2023).

Example 1: Pectobacterium and Dickeya. Both genera cause soft rots and blackleg of potato but differ in temperature optima and aggressiveness. Pectobacterium atrosepticum is active at temperatures below 18 °C, P. carotovorum at temperatures above 18 °C, and Dickeya dianthicola and D. solani at temperatures above 25 °C (Charkowski et al., 2020; EPPO, 2023). This means that different pathogens predominate in different climatic zones and seasons. The protection strategy must take this into account: for example, in cool regions, focus should be on P. atrosepticum, and in warm regions on Dickeya (Czajkowski et al., 2015; EPPO, 2023). In addition, species differ in resistance to disinfectants and antibiotics, which affects the choice of treatments (Czajkowski et al., 2015).

Example 2: Ralstonia solanacearum species complex. Different species and phylotypes of the complex differ in host range, temperature preferences, and aggressiveness. Strain PIIB1 (R. solanacearum, phylotype IIB, sequevar 1) is adapted to moderate temperatures and poses a particular danger to potato in Europe; it is capable of latent infection and is transmitted with seed tubers (Charkowski et al., 2020). Other phylotypes, for example phylotype I (R. pseudosolanacearum), are more thermophilic and are distributed in the tropics and subtropics. Quarantine measures and control strategies must take these differences into account (Vailleau and Genin, 2023; EPPO, 2025).

Example 3: Xanthomonas. Different species and pathovars of Xanthomonas cause different diseases and require different approaches. X. citri pv. citri (citrus canker) is a quarantine organism requiring destruction of trees and strict phytosanitary measures; X. euvesicatoria pv. euvesicatoria (bacterial spot of tomato and pepper) is not quarantine but is an economically significant pathogen controlled by copper preparations, antibiotics, and resistant cultivars (Chuang et al., 2025; Akhatov et al., 2013; EPPO, 2025). If a laboratory mistakenly identifies X. euvesicatoria as X. citri, this can lead to unjustified quarantine measures and economic losses (Chuang et al., 2025).

Pathovar and Race Determine Choice of Cultivar and Pesticide

Pathovars and races differ in virulence to plant cultivars. This means that the same pesticide or the same resistant cultivar may be effective against one race but not another (Sigee, 1993; Agrios, 2005).

Example 1: Pseudomonas syringae pv. phaseolicola. This pathovar is divided into several races differing in virulence to bean cultivars. Race 1 affects Canadian Wonder and Tendergreen but not Red Mexican; race 2 affects Red Mexican and Tendergreen but not Canadian Wonder; race 3 affects all three cultivars (Sigee, 1993). If race 1 predominates in a region, cultivar Red Mexican will be resistant, and Canadian Wonder susceptible. The breeder must know the race composition of the pathogen to choose the correct resistance genes (Agrios, 2005).

Example 2: Xanthomonas euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, X. vesicatoria. In pepper, races 1–11 have been described, differing in virulence to cultivars with genes Bs1, Bs2, Bs3, etc. (Akhatov et al., 2013). Gene Bs1 provides resistance to race 1 but not to race 2; gene Bs2 to races 1 and 2 but not to race 3; etc. (Akhatov et al., 2013). For breeding, this means the need to pyramid resistance genes or use cultivars with broad resistance. For diagnosis, it means the need to determine the race of the pathogen to recommend the correct cultivar (Chuang et al., 2025; Akhatov et al., 2013).

Example 3: Ralstonia solanacearum. Races 1, 2, and 3 differ in host range: race 1 affects many species, race 2 affects banana and Heliconia (Moko disease), and race 3 affects potato and tomato (Charkowski et al., 2020; Vailleau and Genin, 2023). Biovars 1–5 differ in biochemical traits. Strain PIIB1 — race 3, biovar 2 — is the most dangerous for potato in temperate latitudes. If a cultivar is resistant to race 1 but not to race 3, it will be affected in regions where race 3 predominates (Charkowski et al., 2020). Breeding for resistance requires knowledge of the race and biovar composition of the pathogen in a particular region (Vailleau and Genin, 2023).

5.3. Differences in Sensitivity to Antibiotics and Bactericides

Species and Pathovar Determine Sensitivity to Chemical Agents

Different species and pathovars of bacteria have different sensitivity to antibiotics and bactericides. This is due to differences in cell wall structure, the presence of enzymes degrading preparations, and efflux pumps removing toxins from the cell (Sigee, 1993; Agrios, 2005).

Example 1: Copper-containing preparations. Copper-based bactericides (Bordeaux mixture, copper oxychloride, copper hydroxide) are effective against many bacteria, but some strains acquire resistance. For example, copper resistance has been described in Xanthomonas citri pv. citri, X. euvesicatoria, Pseudomonas syringae pv. syringae, and Erwinia amylovora (Agrios, 2005; EPPO, 2022; Chuang et al., 2025). This means that in regions where copper is used for a long time, the effectiveness of preparations may decrease, and alternative agents are needed (EPPO, 2022; Chuang et al., 2025).

Example 2: Antibiotics. Streptomycin and oxytetracycline are used against Erwinia amylovora, Xanthomonas spp., and Pseudomonas spp. However, resistance to streptomycin has been described in E. amylovora, P. syringae pv. papulans, X. campestris pv. vesicatoria, and others (Agrios, 2005; EPPO, 2022). In the EU, antibiotics are prohibited for use on commercial products, which limits their use (EPPO, 2022; Charkowski et al., 2020). For effective use of antibiotics, it is necessary to know which species and pathotype the pathogen belongs to and whether it has resistance genes (Agrios, 2005; Sigee, 1993).

Example 3: Biological control. Biological agents (antagonists, bacteriophages, endophytes) are also species-specific. For example, Agrobacterium radiobacter strain K84 controls crown gall caused by A. tumefaciens but is ineffective against other Agrobacterium species (Sigee, 1993; Mousavi and Young, 2023). Bacillus subtilis is effective against many fungal and bacterial pathogens, but its effectiveness depends on the species and strain of the pathogen (Akhatov et al., 2013; Charkowski et al., 2020). Bacteriophages used to control Erwinia amylovora are specific to this species and do not act on other bacteria (Pedroncelli and Puopolo, 2024). To choose a biological agent, it is necessary to accurately identify the pathogen (Sigee, 1993; Pedroncelli and Puopolo, 2024).

Pathogen-Specific and Broad-Spectrum Preparations

Some preparations have a broad spectrum of action, others narrow. For example, copper-containing preparations are effective against many bacteria and fungi but poorly effective against Candidatus Liberibacter (Charkowski et al., 2020). Antibiotics (streptomycin, tetracycline) have a narrower spectrum but can be highly effective against specific pathogens (Agrios, 2005; EPPO, 2022). Biological agents are often species-specific (Sigee, 1993; Pedroncelli and Puopolo, 2024). Systematics allows determination of the species of the pathogen and selection of a preparation with maximum effectiveness and minimal side effects (Czajkowski et al., 2015; Charkowski et al., 2020).

5.4. Quarantine Measures and Systematics

A1 and A2 Quarantine Lists

EPPO (European and Mediterranean Plant Protection Organization) publishes A1 lists (quarantine organisms absent in the region) and A2 lists (present but limited in distribution). These lists contain modern names of species, subspecies, and pathovars, as well as synonyms (EPPO, 2025). For example:

Xanthomonas citri subsp. citri (A1) — formerly X. campestris pv. citri (EPPO, 2025).
Xanthomonas citri subsp. aurantifolii (A1) — formerly X. campestris pv. citrumelo (EPPO, 2025).
Xanthomonas euvesicatoria pv. euvesicatoria (A2), X. euvesicatoria pv. perforans (A2), X. vesicatoria (A2), X. cynarae pv. gardneri (A2) — formerly all were X. campestris pv. vesicatoria (EPPO, 2025).
Xanthomonas phaseoli pv. phaseoli (A2), X. citri pv. fuscans (A2) — formerly X. campestris pv. phaseoli and X. phaseoli var. fuscans (EPPO, 2025).
Ralstonia solanacearum (A2), R. pseudosolanacearum (A2), R. syzygii (A1) — formerly the single R. solanacearum (EPPO, 2025).
Clavibacter sepedonicus (A2) — formerly C. michiganensis subsp. sepedonicus (EPPO, 2025).
Dickeya dianthicola (A2) — formerly Erwinia chrysanthemi pv. dianthicola (EPPO, 2025).
Erwinia amylovora (A2) — name unchanged (EPPO, 2025).
Curtobacterium flaccumfaciens pv. flaccumfaciens (A2) — formerly Corynebacterium flaccumfaciens (EPPO, 2025).
Pantoea stewartii subsp. stewartii (A2) — formerly Erwinia stewartii (EPPO, 2025).

For quarantine, it is important to know exactly which species, subspecies, or pathovar is present in a country or region, since control measures depend on this. For example, X. campestris pv. campestris (black rot of crucifers) is not quarantine-regulated in EPPO, while X. citri pv. citri (citrus canker) is (EPPO, 2025). If a laboratory mistakenly identifies a non-quarantine pathogen as quarantine, this can lead to unjustified measures and economic losses (Chuang et al., 2025; EPPO, 2025).

Harmonization of Nomenclature for Quarantine

EPPO Diagnostic Protocols

PM 7/20 (3) Erwinia amylovora (EPPO, 2022).
PM 7/155 (1) Pectobacterium spp. and Dickeya spp. (EPPO, 2023).
PM 7/21 Ralstonia solanacearum (EPPO, 2025).
PM 7/161 (1) Xanthomonas phaseoli pv. phaseoli and X. citri pv. fuscans (EPPO, 2025).

These protocols are regularly revised taking taxonomic changes into account. However, not all laboratories and countries update their methods in a timely manner, which can lead to incorrect identification and, consequently, incorrect quarantine measures (Czajkowski et al., 2015; Venbrux et al., 2023).

5.5. Breeding for Resistance: Knowledge of Races and Pathovars

Gene-for-Gene Interaction and Its Practical Application

Examples of Breeding Programs

Pepper and Xanthomonas. Genes Bs1, Bs2, and Bs3 provide resistance to different races of X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria (Akhatov et al., 2013; Chuang et al., 2025). Gene Bs2 provides resistance to races 1, 2, and 3 but not to race 4; gene Bs3 to races 1, 2, 3, and 4 but not to race 5; etc. (Akhatov et al., 2013). Breeders combine these genes for broad resistance.

Tomato and Xanthomonas. In tomato, resistance genes Xv1, Xv2, Xv3, and Xv4 have been described, which correspond to different races of X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria (Chuang et al., 2025).

Bean and Pseudomonas syringae pv. phaseolicola. Races 1–9 differ in virulence to cultivars with genes R1–R9 (Sigee, 1993; Agrios, 2005). Breeding for resistance requires knowledge of the race composition in the region.

Potato and Ralstonia. Resistance to R. solanacearum is polygenic and race-specific; different phylotypes and sequevars differ in aggressiveness, and cultivar resistance may be unstable under different conditions (Charkowski et al., 2020; Vailleau and Genin, 2023). Breeding for resistance to Ralstonia is a difficult task, and there are currently no commercial cultivars with complete resistance (Charkowski et al., 2020; Vailleau and Genin, 2023).

Potato and Pectobacterium / Dickeya. There are practically no resistant commercial cultivars, although differences in tolerance exist. Breeding is limited by the polygenic nature of resistance and high variability of pathogens (Czajkowski et al., 2015; EPPO, 2023; Charkowski et al., 2020).

Gene Pyramiding and Multiline Cultivars

For long-term resistance, breeders use pyramiding (combining several resistance genes in one cultivar) and multiline cultivars (mixtures of lines with different resistance genes). These strategies reduce the probability of resistance being overcome by the pathogen, since the pathogen would need to acquire several virulence genes simultaneously (Agrios, 2005; Vailleau and Genin, 2023). However, pyramiding requires knowledge of the race composition of the pathogen and the availability of resistance genes (Agrios, 2005; Akhatov et al., 2013).

Problems of Breeding for Resistance to Bacterioses

Breeding for resistance to bacterioses is complicated by several factors:

Polygenic resistance. Many resistance genes have small effects, and their pyramiding requires time and resources (Vailleau and Genin, 2023; Charkowski et al., 2020).
Dynamic race composition of the pathogen. The appearance of new races can quickly overcome cultivar resistance (Agrios, 2005; Akhatov et al., 2013).
Horizontal gene transfer. Pathogens can acquire new virulence genes through plasmids, pathogenicity islands, and prophages, which accelerates overcoming resistance (Arif et al., 2022; Charkowski et al., 2020).
Lack of resistance in cultivated cultivars. For many bacterioses (e.g., Pectobacterium and Dickeya on potato), there are no resistant commercial cultivars, and breeding is limited to tolerance (Czajkowski et al., 2015; EPPO, 2023).

5.6. Forecasting Epiphytotics and Systematics

Disease Modeling

Modern epiphytotic forecasting systems take into account the biology of the pathogen, its race composition, weather conditions, and cultivar resistance. For example, for potato late blight, the BLITECAST model has been developed, which predicts infection risk based on temperature and humidity (Agrios, 2005). For bacterioses, such models are less developed, but for some pathogens (e.g., Erwinia amylovora) forecasting systems exist based on temperature, humidity, and host plant phenology (EPPO, 2022; Pedroncelli and Puopolo, 2024).

For accurate forecasting, it is necessary to know which species, pathovar, or race of the pathogen is present in the region, since different pathogens have different temperature optima, development cycles, and humidity requirements (Czajkowski et al., 2015; Charkowski et al., 2020). For example, P. atrosepticum is active at low temperatures, Dickeya at high temperatures; R. solanacearum PIIB1 is adapted to moderate temperatures, and phylotype I to tropical temperatures (Charkowski et al., 2020; Czajkowski et al., 2015). An error in identification can lead to an incorrect forecast and incorrect recommendations (Czajkowski et al., 2015; EPPO, 2023).

Monitoring and Decision Support Systems

Modern monitoring and decision support systems (DSS) include:

Molecular diagnostics (PCR, qPCR, LAMP, metagenomics) for rapid pathogen identification (Czajkowski et al., 2015; Yang et al., 2025; Venbrux et al., 2023).
Remote sensing (hyperspectral and thermal imaging, machine learning) for detecting symptoms and presymptomatic changes over large areas (Venbrux et al., 2023).
Geographic information systems (GIS) for mapping pathogen distribution and forecasting epiphytotics (Venbrux et al., 2023; Charkowski et al., 2020).
Epiphytotic modeling based on weather data, plant phenology, and pathogen biology (Agrios, 2005; EPPO, 2022).

All these systems require accurate taxonomic identification of the pathogen, since different species and pathovars have different model parameters (Czajkowski et al., 2015; Venbrux et al., 2023).

5.7. Integrated Plant Protection and Systematics

Concept of Integrated Protection

Integrated pest management (IPM) is a strategy that combines different control methods (cultural, biological, chemical, genetic) to minimize losses and reduce pesticide load (Agrios, 2005; Charkowski et al., 2020). IPM requires accurate identification of the pathogen, knowledge of its biology and ecology, and monitoring of its populations (Czajkowski et al., 2015; EPPO, 2023).

Examples of IPM for Bacterioses

Potato. For control of Pectobacterium and Dickeya, a complex of measures is recommended: use of certified seed material, sanitation, avoiding tuber injury, proper storage, crop rotation, and resistant cultivars (Czajkowski et al., 2015; EPPO, 2023; Charkowski et al., 2020). For control of Ralstonia—certification, quarantine, crop rotation, resistant cultivars, and sanitation (Charkowski et al., 2020; Vailleau and Genin, 2023).

Apple and pear. For control of Erwinia amylovora—pruning and burning of affected branches, copper preparations, antibiotics during flowering, forecasting, resistant cultivars, and biological control (EPPO, 2022; Pedroncelli and Puopolo, 2024).

Tomato. For control of Clavibacter michiganensis subsp. michiganensis—seed disinfection, phytosanitary measures, removal of diseased plants, limited use of copper and antibiotics during the seedling period, and resistant cultivars (Akhatov et al., 2013; EPPO, 2025).

Citrus. For control of X. citri pv. citri—quarantine, destruction of affected trees, vector control, copper preparations, and resistant cultivars (Chuang et al., 2025; EPPO, 2025).

Role of Systematics in IPM

Systematics plays a key role in IPM:

Accurate identification of the pathogen determines the choice of control methods (Czajkowski et al., 2015; EPPO, 2023).
Knowledge of pathogen biology (temperature optima, development cycles, ecology) is necessary for forecasting and choosing treatment times (Charkowski et al., 2020; Czajkowski et al., 2015).
Knowledge of race composition is necessary for choosing resistant cultivars and pyramiding genes (Agrios, 2005; Akhatov et al., 2013).
Monitoring of pathogen populations requires molecular and serological methods based on taxonomic data (Czajkowski et al., 2015; Yang et al., 2025; Venbrux et al., 2023).

5.8. Economic Aspects: The Cost of Identification Errors

Errors in pathogen identification can have serious economic consequences:

Unjustified quarantine measures. If a non-quarantine pathogen is mistakenly identified as quarantine, this can lead to destruction of the crop, ban on export of products, loss of markets and reputation (Chuang et al., 2025; EPPO, 2025).
Ineffective treatments. If the pathogen is identified incorrectly, the chosen pesticides or biological agents may be ineffective, leading to yield losses and additional costs (Czajkowski et al., 2015; Charkowski et al., 2020).
Loss of cultivar resistance. If the breeder does not know the race composition of the pathogen, the chosen resistance genes may not protect the plants, leading to an epiphytotic and economic losses (Agrios, 2005; Akhatov et al., 2013).
Diagnostic delay. If a laboratory uses outdated methods or names, diagnosis may take longer, leading to spread of the disease and additional losses (Czajkowski et al., 2015; Venbrux et al., 2023).

The cost of accurate diagnosis and taxonomic research is many times repaid by prevented losses and effective control measures (Czajkowski et al., 2015; Charkowski et al., 2020; EPPO, 2025).

5.9. Conclusion

Systematics of phytopathogenic bacteria is not an abstract science but a practical tool for plant protection. Accurate identification of a pathogen to species, subspecies, pathovar, or race determines:

the choice of strategy and control methods;
the effectiveness of chemical and biological preparations;
quarantine measures and restrictions on the movement of plant material;
breeding of resistant cultivars and gene pyramiding;
forecasting of epiphytotics and integrated plant protection.

Modern systematics is actively developing, using molecular, genomic, and phylogenomic methods. For plant protection specialists, this means the need to constantly track nomenclatural changes, update diagnostic protocols and quarantine lists, and integrate classical pathogenicity methods with modern molecular approaches. Only in this way can accurate pathogen identification and effective plant protection be ensured in a changing world.

6. Diagnosis of Phytopathogenic Bacteria

6.1. Introduction: Goals and Objectives of Diagnosis

Diagnosis of phytopathogenic bacteria is a complex of methods aimed at detecting, identifying, and confirming the pathogenicity of the causal agent. Accurate diagnosis is necessary for:

choosing effective control measures;
quarantine measures;
breeding of resistant cultivars;
forecasting epiphytotics;
scientific research (Agrios, 2005; Czajkowski et al., 2015).

Unlike fungal and viral diseases, bacterioses are often diagnosed later, when symptoms become nonspecific and the pathogen has already spread. This is due to the latent course of many bacterioses, low pathogen titer in tissues, transition of bacteria to the viable but non-culturable state (VBNC), and similarity of symptoms to fungal, viral, and abiotic damage (Czajkowski et al., 2015; EPPO, 2022; Venbrux et al., 2023). Therefore, modern diagnostics combines classical microbiological, serological, and molecular methods, as well as new approaches—metagenomics, CRISPR diagnostics, and remote sensing (Venbrux et al., 2023; Yang et al., 2025).

6.2. General Scheme of the Diagnostic Process

Diagnosis of bacterioses includes several stages:

1. Sampling — selection of typical affected organs, fresh symptoms, exudate, seeds, tubers, and planting material.

2. Sample preparation — maceration, extraction in buffer, enrichment (if necessary).

3. Detection — isolation on nutrient media, serological or molecular tests.

4. Identification — determination of species, subspecies, pathovar, and race.

5. Confirmation of pathogenicity — inoculation of healthy plants, fulfillment of Koch’s postulates (for culturable pathogens).

6. Documentation — preservation of isolates, recording of results, and, if necessary, deposition in collections.

Koch’s postulates remain the basis for proving pathogenicity for many bacteria: the pathogen must be present in all diseased plants, be isolated in pure culture, cause the same symptoms when inoculated into a healthy host, and be reisolated from the infected plant (Sigee, 1993; Agrios, 2005). However, for unculturable and facultative pathogens (e.g., Candidatus Liberibacter, phytoplasmas, some Xylella), Koch’s postulates are impossible to fulfill, and diagnosis is based on molecular and serological data, as well as on correlation of symptoms with the presence of the pathogen (Charkowski et al., 2020; Venbrux et al., 2023).

6.3. Classical Methods

Sampling and Sample Preparation

The success of diagnosis largely depends on proper sampling. For bacterioses, it is recommended to take tissue at the border of healthy and affected zones, fresh exudate, young leaves with symptoms, vascular tissue, seeds, and tubers. Samples should be transported cooled and processed as quickly as possible (Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023).

Extraction is carried out in sterile water, phosphate-buffered saline (PBS), or special maceration buffers with antioxidants (e.g., DIECA) to protect bacteria from oxidative stress. To increase sensitivity, enrichment in selective liquid media (PEB, PGEM, LEM366, etc.) is used (Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023).

Isolation on nutrient media

Isolation of pure cultures is a classical and still important stage. Both non-selective and selective and semi-selective media are used:

King’s B — for fluorescent pseudomonads;
NSA, CCT — for Erwinia amylovora;
CVP (crystal violet pectate) — for Pectobacterium and Dickeya, which form characteristic cavities;
YDC (yeast extract dextrose agar) — for Clavibacter;
NGM — for differentiation of Dickeya by blue pigment;
PD3, SC, PW — for Xylella fastidiosa;
media for Xanthomonas — usually yellow colonies (Sigee, 1993; Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023; Charkowski et al., 2020).

Selective media contain inhibitors of the growth of contaminating microflora (crystal violet, cycloheximide, polymyxin, etc.) and nutrient sources available to the target pathogens. However, even semi-selective media do not always suppress all saprophytes, so additional tests are necessary for reliable identification (Czajkowski et al., 2015; EPPO, 2023).

Morphological and biochemical tests

After isolation, colonies are studied macro- and microscopically: shape, size, color, consistency, motility, presence of flagella, capsules, and spores. Gram staining divides bacteria into gram-positive and gram-negative; this is an important taxonomic character (Sigee, 1993).

Biochemical tests include:

oxidase test (LOPAT scheme for fluorescent pseudomonads);
catalase test;
OF test (oxidative/fermentative use of glucose);
utilization of carbohydrates, alcohols, organic acids (API 20E, API 50CH, Biolog GEN III);
hydrolysis of esculin, gelatin, starch;
production of indole, hydrogen sulfide, acetoin;
nitrate reaction;
fatty acid profile (FAME) — used for identification to species and subspecies (Sigee, 1993; Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023).

For many genera, standardized schemes have been developed: LOPAT for Pseudomonas syringae, API for Erwinia, Pectobacterium, Dickeya, Clavibacter; Biolog for a broad spectrum (Sigee, 1993; Czajkowski et al., 2015; Charkowski et al., 2020).

Pathogenicity tests

Confirmation of pathogenicity is carried out by inoculating healthy host plants or test plants:

Hypersensitive reaction (HR) on tobacco or other non-hosts — a rapid test for general pathogenicity;
Inoculation of susceptible varieties — appearance of typical symptoms;
Inoculation of fruits, tuber slices, leaves — for assessing virulence;
Race determination — inoculation of a set of differential varieties (Sigee, 1993; Agrios, 2005; EPPO, 2022; EPPO, 2023; Akhatov et al., 2013).

Pathogenicity tests are labor-intensive, require greenhouses and time, but they are necessary for final confirmation of the diagnosis and for characterization of strains (Czajkowski et al., 2015; EPPO, 2022).

6.4. Serological methods

Serological methods are based on the interaction of bacterial antigens with antibodies. They make it possible to rapidly detect the pathogen in plant tissues, seeds, soil, and water. Main formats:

ELISA — enzyme-linked immunosorbent assay; used in the DASI-ELISA format for detection of Erwinia amylovora, Clavibacter, Ralstonia, Pectobacterium, Dickeya (EPPO, 2022; EPPO, 2023; Czajkowski et al., 2015).
Immunofluorescence (IF) — direct or indirect; allows visualization of bacteria in tissues; sensitivity about 10⁴–10⁶ cells/ml (EPPO, 2022; Sigee, 1993).
Immunofluorescence colony staining (IFC) — a more sensitive variant, allows detection of single colonies (Czajkowski et al., 2015).
Latex agglutination — a rapid slide test; used for Clavibacter, Erwinia, Xanthomonas (Sigee, 1993; Akhatov et al., 2013).
Lateral flow — rapid field tests; used for Erwinia amylovora, Ralstonia, Xanthomonas (EPPO, 2022; Venbrux et al., 2023).

Advantages of serology — speed, simplicity, possibility of mass screening. Disadvantages — low sensitivity in latent infections, cross-reactions with related species, inability to distinguish living cells from dead ones (EPPO, 2022; Czajkowski et al., 2015; Sigee, 1993).

6.5. Molecular methods

PCR and its variants

PCR is the main method of molecular diagnostics of bacterioses. The following are used:

conventional PCR with electrophoretic detection;
multiplex PCR — simultaneous detection of several pathogens;
PCR with primers for species- and pathovar-specific sequences (16S rRNA, ITS, housekeeping genes, pathogenicity genes);
real-time qPCR — quantitative detection with fluorescent probes (TaqMan, SYBR Green);
droplet digital PCR (ddPCR) — absolute quantitative detection (Czajkowski et al., 2015; EPPO, 2023; Yang et al., 2025; Venbrux et al., 2023).

Targets for PCR: pel genes (pectate lyases) for Pectobacterium and Dickeya; amsC and ITS for Erwinia amylovora; hrpB, egl, mutS for Ralstonia; avrBs2, avrBsT for Xanthomonas; txtAB for Streptomyces; celA, chp-7 for Clavibacter (EPPO, 2022; EPPO, 2023; Czajkowski et al., 2015; Charkowski et al., 2020; Chuang et al., 2025).

Isothermal amplifications

Isothermal methods include:

LAMP (loop-mediated isothermal amplification) — rapid, sensitive, does not require a thermocycler; widely used for Erwinia amylovora, Pectobacterium, Dickeya, Ralstonia, Xanthomonas, Clavibacter, viruses, and viroids (Yang et al., 2025; EPPO, 2022; EPPO, 2023).
RPA (recombinase polymerase amplification) — rapid, possible in the field;
RCA (rolling circle amplification) — for circular DNA (plasmids, viroids);
NASBA — for RNA targets (Venbrux et al., 2023; Yang et al., 2025).

LAMP detection can be colorimetric (hydroxynaphthol blue, calcein, neutral red), turbidimetric, or fluorescent. LAMP is combined with lateral flow and CRISPR-Cas12a to increase specificity (Yang et al., 2025; Venbrux et al., 2023).

Sequencing and DNA barcoding

Sequencing is used for:

identification to species and pathovar (MLSA based on atpD, dnaK, gyrB, recA, rpoB);
phylogenetic analysis;
detection of new pathogens;
metagenomics and metabarcoding (16S rRNA, ITS, gyrB);
whole-genome sequencing for taxonomy and epidemiology (Mousavi and Young, 2023; Bansal et al., 2023; Chuang et al., 2025; Venbrux et al., 2023).

DNA barcoding using standardized markers makes it possible to identify pathogens even without cultivation (EPPO, 2025; Venbrux et al., 2023).

Hybridization and DNA probes

DNA probes (radioactive or chromogenic) are used to detect pathogens in tissues, seeds, and soil. The hybridization method is less sensitive than PCR but allows working with large volumes of samples and detecting latent infections. It is used for Xanthomonas, Clavibacter, Ralstonia, Erwinia (Sigee, 1993; Czajkowski et al., 2015).

6.6. Problems of diagnostics and ways to solve them

1. Latent infections. The pathogen is present in tissues without symptoms. Solution: enrichment, highly sensitive qPCR and LAMP, metagenomics (Czajkowski et al., 2015; EPPO, 2022; Venbrux et al., 2023).

2. Low titer. The pathogen is present in small amounts. Solution: enrichment in selective media, concentration, immunomagnetic separation (IMS), qPCR, ddPCR (Czajkowski et al., 2015; Venbrux et al., 2023).

3. VBNC state. Bacteria are viable but do not grow on media. Solution: PCR, LAMP, RT-PCR, metabarcoding; for Erwinia amylovora — enrichment and PCR (EPPO, 2022; Czajkowski et al., 2015).

4. Mixed infections. Several pathogens on one plant. Solution: multiplex PCR, metagenomics, sequencing (Venbrux et al., 2023; Yang et al., 2025).

5. PCR inhibitors. Phenolic compounds, polysaccharides, humic acids. Solution: dilution, DNA purification, internal controls, use of BSA, PVP (Czajkowski et al., 2015; EPPO, 2023).

6. False positive and false negative results. Solution: internal controls (IPC), positive and negative controls, confirmation by a second method, sequencing of amplicons (EPPO, 2022; EPPO, 2023; Yang et al., 2025).

7. Distinguishing living and dead cells. Solution: PMA/EMA treatment before PCR (viability PCR), RT-PCR for mRNA, LAMP with preliminary enrichment (Venbrux et al., 2023; Yang et al., 2025).

6.7. Modern and promising approaches

Metagenomics and metabarcoding — simultaneous detection of all microorganisms in a sample, including unculturable ones; allows detection of new pathogens and study of the microbiome (Venbrux et al., 2023).
CRISPR diagnostics — high specificity and sensitivity, possible in the field; combined with LAMP and RPA (Yang et al., 2025; Venbrux et al., 2023).
Biosensors and nanotechnologies — portable devices for rapid detection (Venbrux et al., 2023).
Remote sensing — hyperspectral and thermal imaging, machine learning for detecting presymptomatic changes over large areas; supplements laboratory diagnostics (Venbrux et al., 2023).
Artificial intelligence and machine learning — analysis of spectra, images, genomic data for prediction and identification (Venbrux et al., 2023).

6.8. Examples of diagnostic protocols for major pathogens

Erwinia amylovora. Diagnostics according to EPPO PM 7/20: collection of symptomatic and asymptomatic samples, isolation on King’s B, NSA, CCT; serology (IF, DASI-ELISA, lateral flow); PCR (Taylor et al., 2001; Gottsberger, 2010); LAMP (Shin et al., 2018); pathogenicity on immature pear fruits or shoots (EPPO, 2022; Pedroncelli and Puopolo, 2024).

Pectobacterium and Dickeya. EPPO PM 7/155: collection of tubers, stems, enrichment in PGEM or LEM366; isolation on CVP; PCR (Darrasse et al., 1994 for Pectobacterium; Nassar et al., 1996 for Dickeya); qPCR (van der Wolf et al., 2017; Muzhinji et al., 2020; Pritchard et al., 2013); LAMP (Yasuhara-Bell et al., 2017); pathogenicity on potato slices, tomato, Chinese cabbage (EPPO, 2023; Czajkowski et al., 2015; Arif et al., 2022).

Ralstonia solanacearum species complex. EPPO PM 7/21: isolation on TZC medium, serology (IF, ELISA), PCR (phylotype-specific), qPCR, LAMP; identification to species, phylotype, sequevar; pathogenicity on tomato, potato, banana (Charkowski et al., 2020; Vailleau and Genin, 2023; EPPO, 2025).

Xanthomonas citri pv. citri. EPPO PM 7/...: isolation on selective media, serology, PCR, qPCR, LAMP; pathovar identification; quarantine measures (Chuang et al., 2025; EPPO, 2025).

Clavibacter michiganensis subsp. michiganensis. Isolation on YDC, ELISA, PCR, LAMP, pathogenicity on tomato; subspecies identification (Akhatov et al., 2013; EPPO, 2025).

Candidatus Liberibacter. Unculturable; diagnostics only molecular: PCR, qPCR, LAMP, sequencing; detection in plants and vectors (Charkowski et al., 2020; Venbrux et al., 2023; Yang et al., 2025).

6.9. Conclusion

Diagnostics of phytopathogenic bacteria is a complex, multi-stage process requiring a combination of classical microbiological, serological, and molecular methods. Accurate identification is impossible without understanding modern systematics, taxonomic rearrangements, and infraspecific categories (pathovars, pathotypes, races, biovars). Errors in diagnostics lead to ineffective treatments, unjustified quarantine measures, loss of variety resistance, and economic losses (Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023; Charkowski et al., 2020).

Modern diagnostics is developing in the direction of greater sensitivity, specificity, speed, and portability. Metagenomics, CRISPR diagnostics, biosensors, remote sensing, and artificial intelligence open new possibilities for early detection and monitoring of bacterioses (Venbrux et al., 2023; Yang et al., 2025). However, classical methods — isolation on media, biochemical tests, serology, pathogenicity — remain important for confirming the diagnosis, characterizing strains, and fulfilling Koch’s postulates (Sigee, 1993; Agrios, 2005; EPPO, 2022).

For plant protection specialists, it is important to master the entire arsenal of methods, be able to interpret results, and constantly monitor taxonomic changes. Only in this way can accurate identification of pathogens and effective plant protection be ensured in a changing world.

7. Conclusion

7.1. Systematics of phytopathogenic bacteria: a dynamic basis for plant protection

We have covered a long path — from a general understanding of bacterioses as an underestimated threat to specific diagnostic methods and taxonomic rearrangements. Concluding the course, it is important to formulate key conclusions and outline prospects.

Phytopathogenic bacteria are not a single taxonomic group but a broad spectrum of organisms distributed among several major branches of the domain Bacteria: from gram-negative proteobacteria (Pseudomonas, Xanthomonas, Ralstonia, Erwinia, Pectobacterium, Dickeya, Agrobacterium, Xylella, Candidatus Liberibacter) to gram-positive actinobacteria (Clavibacter, Streptomyces, Curtobacterium) (Agrios, 2005; Sigee, 1993; Charkowski et al., 2020). Each genus is characterized by certain symptoms, mechanisms of pathogenicity, ecology, and diagnostic methods.

Modern systematics of these organisms is undergoing profound changes. Molecular methods — 16S rRNA sequencing, MLSA, DDH, ANI, AAI, phylogenomics — have shown that many traditional species and genera are not monophyletic groups, and some names are synonyms (Mousavi and Young, 2023; Bansal et al., 2023; Chuang et al., 2025). As a consequence, major taxonomic rearrangements have occurred and continue:

Erwinia was divided into Pectobacterium, Dickeya, Brenneria, Pantoea, Samsonia, Lonsdalea (Arif et al., 2022; Czajkowski et al., 2015; EPPO, 2023).
Agrobacterium was partly transferred to Rhizobium and Allorhizobium (Mousavi and Young, 2023).
Pseudomonas was divided into Ralstonia, Burkholderia, Acidovorax, and other genera (Safni et al., 2014; Charkowski et al., 2020).
Ralstonia solanacearum species complex was divided into three species: R. solanacearum, R. pseudosolanacearum, R. syzygii (Safni et al., 2014; Prior et al., 2016; Charkowski et al., 2020).
Xanthomonas underwent splitting and reclassification of many pathovars into separate species (Chuang et al., 2025; Bansal et al., 2023).

These changes are not an end in themselves — they reflect the accumulation of new knowledge about genomes, phylogeny, and ecology of pathogens. But they create serious practical problems: synonyms in literature, diagnostic kits, databases, and quarantine lists; the need to update protocols and regulatory frameworks; and the risk of identification errors (Czajkowski et al., 2015; EPPO, 2025; Mousavi and Young, 2023).

7.2. Pathovars and pathotypes: the key to understanding infraspecific diversity

For practical phytopathology, it is not enough to know only the species or subspecies of the pathogen. Within one species, there may be groups of strains differing in the range of affected plants (pathovars) or in virulence to certain varieties (pathotypes, races) (Sigee, 1993; Agrios, 2005).

Pathovar is an infraspecific category uniting strains by a common host range and similar symptoms. Pathovars have been described in the genera Xanthomonas, Pseudomonas, Erwinia, Curtobacterium, and others (Sigee, 1993; Chuang et al., 2025; Akhatov et al., 2013).

Pathotype (race) is a narrower category uniting strains by virulence to a set of differential varieties. Classic examples: races of Pseudomonas syringae pv. phaseolicola (1–9), races of Xanthomonas euvesicatoria pv. euvesicatoria (1–11), races of Ralstonia solanacearum (1–3) (Sigee, 1993; Akhatov et al., 2013; Charkowski et al., 2020).

Pathovars and pathotypes do not have official taxonomic status in the ICNP, but they are widely used in breeding, quarantine, diagnostics, and epidemiology. They make it possible to:

predict disease development and select resistant varieties;
determine quarantine measures and restrictions on the movement of plant material;
choose diagnostic methods and interpret results;
understand the evolution of pathogens and their adaptation to hosts (Agrios, 2005; Vailleau and Genin, 2023; Chuang et al., 2025).

However, the pathovar system has limitations: pathovars may be polyphyletic, unstable, and difficult to identify (Arif et al., 2022; Chuang et al., 2025). Modern genomic taxonomy is gradually replacing traditional pathovars with monophyletic species and subspecies, but the full transition will take time (Bansal et al., 2023; Mousavi and Young, 2023).

7.3. The role of systematics in plant protection: from identification to strategy

Systematics of phytopathogenic bacteria is not an abstract science but a practical tool. Accurate identification of the pathogen to species, subspecies, pathovar, or race determines:

the choice of strategy and control methods — different species and pathovars differ in biology, ecology, and sensitivity to control agents (Czajkowski et al., 2015; EPPO, 2023);
the effectiveness of chemical and biological preparations — resistance to copper, antibiotics, and bacteriophages is species-specific (Agrios, 2005; EPPO, 2022; Pedroncelli and Puopolo, 2024);
quarantine measures and restrictions — quarantine lists operate with specific species, subspecies, and pathovars (EPPO, 2025);
breeding of resistant varieties — knowledge of races and pathovars is necessary for selecting resistance genes and pyramiding (Agrios, 2005; Akhatov et al., 2013; Vailleau and Genin, 2023);
prediction of epiphytotics — disease models take into account the biology and race composition of the pathogen (Agrios, 2005; EPPO, 2022; Venbrux et al., 2023);
integrated pest management (IPM) — accurate diagnostics and monitoring are the basis of IPM (Charkowski et al., 2020; Czajkowski et al., 2015).

Errors in identification lead to ineffective treatments, unjustified quarantine measures, loss of variety resistance, and economic losses (Czajkowski et al., 2015; Chuang et al., 2025; EPPO, 2025). The cost of accurate diagnostics and taxonomic research is many times repaid by prevented losses and effective control measures.

7.4. Diagnostics: a synthesis of classics and modern technologies

Diagnostics of phytopathogenic bacteria is a complex, multi-stage process. It includes sample collection, isolation on nutrient media, biochemical tests, serology (ELISA, lateral flow, immunofluorescence), molecular methods (PCR, qPCR, LAMP, sequencing, metagenomics), and confirmation of pathogenicity (Sigee, 1993; Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023; Yang et al., 2025).

Classical methods — isolation on media, Gram staining, biochemical tests, pathogenicity — remain important for confirming the diagnosis, characterizing strains, and fulfilling Koch’s postulates (Sigee, 1993; Agrios, 2005). However, they are labor-intensive, time-consuming, and not always applicable to unculturable pathogens (Candidatus Liberibacter, phytoplasmas, some Xylella) (Charkowski et al., 2020; Venbrux et al., 2023).

Molecular methods — PCR, qPCR, LAMP, ddPCR, metagenomics, CRISPR diagnostics — provide high sensitivity, specificity, and speed. They make it possible to detect pathogens at low titer, in latent form, in mixed infections, and in the VBNC state (Czajkowski et al., 2015; Yang et al., 2025; Venbrux et al., 2023). LAMP is especially convenient for field conditions due to its simplicity and the absence of a thermocycler (Yang et al., 2025). Metagenomics and metabarcoding open possibilities for simultaneous detection of all microorganisms in a sample, including unculturable and new pathogens (Venbrux et al., 2023).

Modern approaches — biosensors, nanotechnologies, remote sensing, artificial intelligence — supplement laboratory diagnostics and make it possible to detect presymptomatic changes over large areas (Venbrux et al., 2023). However, their introduction into routine practice requires training, equipment, and harmonization of methods.

Problems of diagnostics — latent infections, low titer, VBNC, mixed infections, PCR inhibitors, false positive and false negative results, distinguishing living and dead cells — are solved by combining methods, internal controls, enrichment, PMA/EMA treatment, RT-PCR, and confirmation by a second method (Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023; Venbrux et al., 2023).

7.5. Practical conclusions for plant protection specialists

For effective work with bacterioses, a plant protection specialist must:

1. Master modern nomenclature — monitor taxonomic changes, check synonyms, use current names in diagnostics, quarantine, and scientific communication (Mousavi and Young, 2023; EPPO, 2025; Bansal et al., 2023).

2. Understand infraspecific diversity — know pathovars, pathotypes, races, biovars, serovars of major pathogens and their significance for breeding, quarantine, and diagnostics (Sigee, 1993; Agrios, 2005; Akhatov et al., 2013).

3. Combine classical and modern methods — use isolation on media, biochemical tests, serology, PCR, qPCR, LAMP, sequencing, metagenomics depending on the task and available resources (Czajkowski et al., 2015; EPPO, 2022; EPPO, 2023; Yang et al., 2025).

4. Take into account the biology of the pathogen — temperature optima, development cycles, ecology, modes of spread, resistance to control agents (Charkowski et al., 2020; Czajkowski et al., 2015; EPPO, 2023).

5. Integrate control methods — combine cultural, biological, chemical, and genetic measures within IPM (Agrios, 2005; Charkowski et al., 2020; Pedroncelli and Puopolo, 2024).

6. Comply with quarantine requirements — know quarantine lists, diagnostic protocols, and measures when quarantine pathogens are detected (EPPO, 2025; Czajkowski et al., 2015).

7. Predict and monitor — use epiphytotic models, remote sensing, and decision support systems (Venbrux et al., 2023; Agrios, 2005; EPPO, 2022).

7.6. Prospects and challenges

Systematics and diagnostics of phytopathogenic bacteria continue to develop. Main prospects and challenges:

Whole-genome sequencing and phylogenomics — refinement of species, genus, and pathovar boundaries; detection of new pathogens; understanding evolution and horizontal gene transfer (Bansal et al., 2023; Mousavi and Young, 2023; Chuang et al., 2025).
Metagenomics and microbiome studies — study of plant microbial communities, detection of pathogens in the context of the microbiome, development of microbiome-based biocontrol (Venbrux et al., 2023; Charkowski et al., 2020).
CRISPR diagnostics and biosensors — portable, rapid, highly specific tests for field and laboratory (Yang et al., 2025; Venbrux et al., 2023).
Remote sensing and artificial intelligence — early detection and monitoring of diseases over large areas, discrimination of biotic and abiotic stresses (Venbrux et al., 2023).
Breeding for resistance — gene pyramiding, genome editing, use of wild relatives, resistance to multiple pathovars and races (Vailleau and Genin, 2023; Charkowski et al., 2020; Akhatov et al., 2013).
Biological control — new antagonists, bacteriophages, endophytes, resistance inducers (Pedroncelli and Puopolo, 2024; Charkowski et al., 2020; Sigee, 1993).
Harmonization of nomenclature and quarantine — international cooperation, updating lists and protocols, training specialists (EPPO, 2025; Czajkowski et al., 2015; Mousavi and Young, 2023).
Climate change — expansion of pathogen ranges, emergence of new diseases, need to adapt protection strategies (Charkowski et al., 2020; Vailleau and Genin, 2023; Venbrux et al., 2023).

7.7. Final summary

Phytopathogenic bacteria are a diverse and dynamic group of organisms causing serious diseases of agricultural crops. They cause direct and indirect damage, are difficult to diagnose, respond poorly to chemical control, and require integrated strategies including quarantine, certification, breeding, and accurate diagnostics.

Systematics of phytopathogenic bacteria is the basis of effective plant protection. It provides the language for describing pathogens, tools for their identification, and understanding of their evolution and diversity. Taxonomic rearrangements occurring in recent decades reflect the accumulation of new knowledge and require specialists to constantly monitor changes, update methods, and harmonize nomenclature.

Accurate identification of the pathogen to species, subspecies, pathovar, or race determines the choice of strategy and control methods, the effectiveness of preparations, quarantine measures, breeding of resistant varieties, and prediction of epiphytotics. Errors in identification lead to economic losses and environmental risks.

Modern diagnostics combines classical microbiological, serological, and molecular methods with new approaches — metagenomics, CRISPR diagnostics, biosensors, remote sensing, and artificial intelligence. This makes it possible to detect pathogens at low titer, in latent form, in mixed infections, and in the VBNC state.

For plant protection specialists, it is important to master the entire arsenal of methods, understand the biology and ecology of pathogens, integrate control methods within IPM, and constantly monitor taxonomic changes. Only in this way can food security, sustainable agriculture, and environmental conservation be ensured in a changing world.

References

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