Preferred name: Xanthomonas oryzae pv. oryzae
Authority: (Ishiyama) Swings, van den Mooter, Vauterin, Hoste, Gillis, Mew & Kersters
Taxonomic position: Bacteria: Proteobacteria: Gammaproteobacteria: Lysobacterales: Lysobacteraceae
Other scientific names: Bacillus oryzae Hori & Bokura, Bacterium oryzae (Uyeda & Ishiyama) Nakata, Phytomonas oryzae (Ishiyama) Magrou, Pseudomonas oryzae Uyeda & Ishiyama, Xanthomonas campestris pv. oryzae (Ishiyama) Dye, Xanthomonas kresek Schure
Common names in English: BLB, bacterial blight of rice, bacterial leaf blight of rice, kresek disease of rice, leaf blight of rice
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Notes on taxonomy and nomenclature EPPO Categorization: A1 list
EU Categorization: A1 Quarantine pest (Annex II A)
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EPPO Code: XANTOR

The principal host of X. oryzae pv. oryzae is cultivated rice, Oryza sativa. Other hosts also belong to the Poaceae family, including wild Oryza species such as O. australiensis (Australian wild rice), O. longistaminata (African wild rice, long stamen rice or red rice), O. rufipogon (brownbeard wild rice), as well as annual and perennial grasses such as Cenchrus ciliaris (buffelgrass), Cynodon dactylon (Bermuda grass), Echinochloa crus-galli (cockspur or barnyard millet), Leersia hexandra (southern cutgrass or swamp rice grass), L. japonica, L. oryzoides (common rice cutgrass), L. sayanuka, Leptochloa chinensis (red sprangletop), L. mucronata (mucronate sprangletop), Megathyrsus maximus (Guinea grass or green panic grass), Paspalum scrobiculatum (Kodo millet), Urochloa (Brachiaria) mutica (para grass), Zizania aquatica (southern wild rice), Z. latifolia (Manchurian wild rice), Zizania palustris (northern wild rice), Zoysia japonica (Korean or Japanese lawn grass or zoysia grass) Aldrick et al., 1973; Reddy & Nayak, 1974; Li et al., 1985; Ou, 1985; Gonzalez et al., 1991; Mew et al., 1993; Noda & Yamamoto, 2008; Lang et al., 2019; EFSA, 2018; CABI, 2022a). In particular, Leersia spp. may be latently infected and form reservoirs of X. oryzae. pv. oryzae that are pathogenic and cause symptoms in rice upon artificial inoculation (Gonzalez et al., 1991; Lang et al., 2019).

Within the grass-like family of Cyperaceae, there is a single record mentioning Cyperus difformis and C. rotundus as hosts (Chattopadhyay and Mukherjee, 1968).

Host list: Cenchrus ciliaris, Cynodon dactylon, Cyperus difformis, Cyperus rotundus, Echinochloa crus-galli, Leersia hexandra, Leersia japonica, Leersia oryzoides, Leersia sayanuka, Leptochloa chinensis, Leptochloa mucronata, Megathyrsus maximus, Oryza australiensis, Oryza glaberrima, Oryza longistaminata, Oryza rufipogon, Oryza sativa, Paspalum distichum, Paspalum scrobiculatum, Urochloa mutica, Zizania aquatica, Zizania latifolia, Zizania palustris, Zoysia japonica

Both X. oryzae pv. oryzae and X. oryzae pv. oryzicola are present in the main rice-producing areas of the world. X. oryzae ‘USA’ has only been reported from the USA in two states, Louisiana and Texas, X. oryzae pv. leersiae has been reported from China, Burkina Faso, India, Mali, and Uganda (Lang et al., 2019).

As stated before, bacterial leaf blight was first reported from the Fukuoka Prefecture, Japan, in 1884. This disease subsequently was observed in other continents. Since the early 1960s, bacterial leaf blight has been reported from virtually all South East Asian countries where it is widespread, and affects rice crops in its severe form (Ou, 1985; Goto, 1992). It has also been reported from several (mainly West-) African countries, from Australia and North America (Louisiana and Texas, USA), and from Central and South America (CABI, 2022a).

There are only several dated (and poorly substantiated) reports on the occurrence of X. oryzae pv. oryzae in Mexico and parts of Central and South America, indicating that bacterial leaf blight is not of importance in those areas. It cannot be excluded, however, that in those countries strains similar to the X. oryzae ‘USA ‘occur, since infestations reported were low to moderate. In whatever cases, climate could also play a role in moderation of the infection (Lozano, 1977; Ou, 1985; Bradbury, 1986; Guevara & Maselli, 1999; USDA, 2013.

At present bacterial leaf blight is not known to be present in the EPPO region. Iran, where bacterial leaf blight spread rapidly since 2004, is the nearest country to Europe where X. oryzae pv. oryzae has been reported (Ghasemie et al., 2008; Khoshkdaman et al., 2009 and 2012).

Africa: Benin, Burkina Faso, Burundi, Cameroon, Gabon, Kenya, Madagascar, Mali, Niger, Senegal, Togo, Uganda
Asia: Bangladesh, Cambodia, China (Anhui, Fujian, Guangdong, Guangxi, Hainan, Hebei, Henan, Hubei, Hunan, Jiangsu, Jiangxi, Jilin, Liaoning, Shandong, Sichuan, Yunnan, Zhejiang), India (Andaman and Nicobar Islands, Andhra Pradesh, Assam, Bihar, Chhattisgarh, Delhi, Goa, Gujarat, Haryana, Himachal Pradesh, Jammu & Kashmir, Jharkand, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Meghalaya, Nagaland, Odisha, Punjab, Rajasthan, Tamil Nadu, Tripura, Uttarakhand, Uttar Pradesh, West Bengal), Indonesia (Java, Sulawesi, Sumatra), Iran, Japan (Honshu, Kyushu), Korea Dem. People's Republic, Korea, Republic, Laos, Malaysia (Sabah, Sarawak, West), Myanmar, Nepal, Pakistan, Philippines, Sri Lanka, Taiwan, Thailand, Vietnam
North America: Mexico, United States of America (Louisiana, Texas)
Central America and Caribbean: Costa Rica, El Salvador, Honduras, Panama
South America: Bolivia, Ecuador, Venezuela
Oceania: Australia (Northern Territory, Queensland)

X. oryzae pv. oryzae is a vascular pathogen, colonizing mainly vascular tissues and causing a leaf blight disease, as opposed to X. oryzae pv. oryzicola which invades mainly the mesophilic parenchymal tissues, causing a leaf streak disease. Bacterial leaf blight occurs in both temperate and tropical rice-growing climate zones, with temperatures between 25°- 34°C and over 70% relative humidity. Conditions of strong wind and frequent, heavy rains (e.g., typhoons) are conducive for disease development (Mew et al., 1993). Spread is principally via flood and irrigation water (Dath & Devadath, 1983; Ou, 1985; Niño-Liu et al., 2006).

The bacterium enters mainly via water pores (hydathodes) at the leaf tip and margin, and also via stomata and wounds on leaves, stems or roots. When a hydathode is infected, subsequently bacterial multiplication takes place in the epithem (parenchymatic cells without chlorophyll, lining the cavity under the hydathode), and then the bacteria move to the xylem vessels causing the typical bacterial blight symptoms on the rice leaves (Tabei, 1977; Mew et al., 1984; Guo & Leach, 1989; Mew et al., 1993). After multiplication bacteria may exude in slime droplets and re-enter the plant through hydathodes. Inside the vascular system, bacteria multiply and move in both directions (Ou, 1985; Huang & De Cleene, 1989; Leach et al., 1989; Noda & Kaku, 1999).

Inoculum sources include infected planting material (including seed), volunteer rice plants, contaminated water, infected straw, stubble or chaff, and infected weed hosts (with or without symptoms), although the exact role of these sources in nature is still poorly understood and dependent on the crop system. In rice monoculture areas, for example, most if not all infected material such as stubble, straw, and other plant material are drastically diminished when the land is prepared for the next crop and therefore there is less risk of maintaining the pathogen in the environment (Reddy & Nayak, 1974; Durgapal, 1985; Ou, 1985; Devadath & Dath, 1985; Reddy & Yin, 1989; Vera Cruz et al., 2017).

In temperate regions, X. oryzae pv. oryzae survives the winter in the rhizosphere of weeds of the genera Leersia and Zizania and in roots and stem bases of rice stubble (Mizukami and Wakimoto, 1969, Hsieh & Buddenhagen, 1974; Reddy and Nayak, 1974; Reddy & Yin, 1989).

The disease occurrence and development are favoured in areas with insufficient weed and stubble control in both tropical and temperate climates. High levels of nitrogen fertilization can induce severe outbreaks of bacterial leaf blight (Noda & Kaku, 1999; Yu et al., 2015; IRRI, 2021).

The data on seed transmission show that it is possible, though probably infrequent under most natural conditions (e.g., Mew et al., 1989; Reddy & Yin, 1989; Sakthivel et al., 2001; Vera Cruz et al., 2017). X. oryzae pv. oryzae has been isolated from the glumes (leaf-like structures below the spikelet) and a few times from within the endosperm of seeds originating from heavily infected fields (Fang et al., 1956; Srivastava & Rao, 1964; Hsieh & Buddenhagen, 1974). Murty & Devadath (1984) found that the bacterium could survive for 120-180 days in rice seeds, but had difficulty in demonstrating that this seed infection gave rise to infected plants in the field. Singh (1971) found that the bacterium cannot survive in unsterilized soil, but survived 15-38 days in field and pond water and >12 months in tap and distilled water. Hsieh & Buddenhagen (1974) found that in wet, warm (flooded) soil or in leaves the pathogen survived up to 40 days, and under colder dryer conditions up to almost a year. Reddy (1972) stated that X. oryzae pv. oryzae survives for 7-8 months in rice seed, but for only 3-4 months in straw and stubble; Kauffman & Reddy (1975) reported that, although glumes were readily infected, viable bacteria could not be detected on seed stored for 2 months. Sakthivel et al. (2001) using bio-PCR could recover X. oryzae pv. oryzae from naturally infected seeds after storage at 4°C for up to 9 months. The bacterium was also detected in seedlings, mature plants and seeds from plants raised from naturally infected seeds. Singh et al. (2015) could detect X. oryzae pv. oryzae on seed, obtained after artificial inoculation of rice plants at the flowering stage for up to 8 months using bio-PCR. Hassankiadeh et al. (2011) using bio-PCR could detect the bacterium in seed washes from naturally infected seeds and found up to 10 months survival in seeds. They also obtained infected seedlings from naturally infected seeds. 

Leaf clipping in young plants, when transplanting rice, is an effective means of spread and can lead to the severe so-called ‘kresek’ form of the disease in these transplants. These young plants show pale yellow leaves, severe wilting, and frequent plant death. 

Isolates of X. oryzae pv. oryzae from different regions of the world show a high genetic diversity, which is to some extent geographically determined, generally necessitating tailored breeding programmes to obtain resistance against local pathotypes (also called races), see e.g., Leach et al. (1992). For example, Chen et al. (2012) detected that pathotype (race) variation can be altitude dependent. Low virulence strains have been reported from the United States and India (Jones et al., 1989; Gnanamanickam et al., 1993). 

Moreover, geographically distinct lineages occurring in Asia and Africa, and the USA have been characterized, where South American strains were congruent with the Asian lineage (Gonzalez et al., 2007; Hajri et al., 2012; Poulin et al., 2015). Three new races were recently characterized in African strains of X. oryzae pv. oryzae, although these strains are generally less variable than the Asian ones (Verdier et al., 2012; Poulin et al., 2015; Djedatin et al., 2016; Tran et al., 2018).

The pathogenicity of X. oryzae pv. oryzae is based on a type-3 secretion system, that injects a range of type-3 effectors into rice cells (Niño-Liu et al., 2006; Jiang et al., 2020). This includes members of the Transcription Activator-like Effector family (TALEs), major virulence factors, activating susceptibility genes of the host (Hutin et al., 2015).

For further information also see Ezuka, 2000; EFSA 2018, IRRI (2021).

Symptoms

Bacterial leaf blight appears on leaves of young plants, after planting, as pale-green to grey-green water-soaked streaks near the leaf tip and margins. In the early morning bacterial ooze may be observed on these water-soaked streaks.  On panicles grey to light brown lesions may be observed on glumes, which may result in infertility or impaired quality of the grains. In later stages of the disease development lesions coalesce and become yellowish-white with wavy edges. Eventually, the whole leaf is affected and, becomes whitish or greyish and then dies. Leaf sheaths and culms of the more susceptible cultivars may be attacked. Systemic infection, known as ‘kresek’ (Reitsma & Schure, 1950; Mizukami & Wakimoto, 1969, Reddy, 1984), on young plants or during the tillering stage of older plants of very susceptible cultivars results in desiccation and wilting of leaves and death, particularly of young, transplanted plants. In older plants, the leaves become yellow, wither and may die. Surviving plants appear yellowish and stunted. In later stages, the disease may be difficult to distinguish from bacterial leaf streak (BLS) caused by X. oryzae pv. oryzicola. Bacterial leaf blight in temperate regions is usually observed in the later part of the seed bed stage (Ou, 1985). For more information see Ou, 1985; Goto 1992; Mew et al., 1993; Niño-Liu et al., 2006; EPPO, 2007; EFSA, 2018. 

A rapid, preliminary test on symptomatic or asymptomatic plants can be performed using classical (bio-) PCR according to Sakthivel et al. (2001), see also EPPO (2007).

Morphology

X. oryzae pv. oryzae is an aerobic, motile, Gram-negative, non-spore-forming, capsulated rod, occurring singly or in pairs, 1.1-2.0 x 0.4-0.6 µm in size, with one polar flagellum.

Isolation of Xanthomonas from symptomatic material is preferably performed using Peptone sucrose agar (PSA), Nutrient Broth Yeast Extract agar medium (NBY), Growth Factor (GF) agar or otherwise using semi- selective media (Agarwal et al., 1989; Sakthivel et al.,2001; EPPO, 2007). On nutrient agar (NA), after 3-7 days of growth, colonies of X. oryzae pv. oryzae are circular, entire, smooth, convex, opaque, and pale to straw yellow,1-2 mm in size. Optimum growth temperature is between 25 and 30°C. Survival of X. oryzae pv. oryzae on solid media is short. For growth on other media, see EPPO (2007).

Detection and identification methods

Like the genus as a whole, X. oryzae is catalase-positive, unable to reduce nitrate and a weak producer of acids from carbohydrates. Pathovars oryzae and oryzicola can be differentiated by (a) acetoin production (X. oryzae pv. oryzae–, X. oryzae pv. oryzicola+), (b) growth on l-alanine as sole carbon source (X. oryzae pv. oryzae–, X. oryzae pv. oryzicola+), (c) growth on 0.2% vitamin-free casamino acids (X. oryzae pv. oryzae–, X. oryzae pv. oryzicola+) and (d) resistance to 0.001% Cu (NO₃)₂ (X. oryzae pv. oryzae+, X. oryzae pv. oryzicola–) (Dye & Lelliott, 1974; Reddy & Ou, 1976; Gossele et al., 1985; Mew & Misra, 1994; Niño-Liu et al., 2006; EPPO, 2007).

Direct isolation from seeds or plants, seedling tests, detection via use of bacteriophages, (semi-selective) media, immuno-fluorescence (IF), the enzyme-linked immuno-sorbent assay (ELISA), where both polyclonal and monoclonal antibodies can be used (Zhu et al., 1988; Benedict et al., 1989; Cottyn et al., 1994; Wu et al., 2015; EPPO, 2007) and (real-time) PCR are available for screening of symptomatic or asymptomatic plant samples and seed extracts. For detection in seeds a bio-PCR, which includes an enrichment step in semi-selective medium, can also be used. Moreover, diagnostic kits for ELISA and PCR are available on the (European) commercial market (Mew & Misra, 1994; Alvarez et al., 1997; EPPO, 2007; Vera Cruz et al., 2017). 

A specific TaqMan probe for detection in seed was developed by Zhao et al. (2007). A specific TaqMan-based multiplex PCR for detection and discrimination of X. oryzae pv. oryzae and X. oryzae pv. oryzicola was developed and validated by Lang et al. (2010), Noh et al. (2012) and Lee & Vera Cruz (2014). A SYBR green-based multiplex PCR for this purpose and also including Burkholderia glumae (causing bacterial grain rot of rice), was developed by Lu et al. (2014). Another, SYBR-green based test is the bio-PCR for X. oryzae pv. oryzae of Cho et al. (2011). Song et al. (2012 and 2014) developed a race-specific PCR (for a new race K3a emerging in Korea), based on an AFLP-derived marker. A padlock probe (PLP)-based PCR with dot blot hybridisation was developed for simultaneous detection of X. oryzae pv. oryzae and X. oryzae pv. oryzicola by Tian et al., 2014. Lang et al. (2014) developed a sensitive and rapid loop-mediated isothermal amplification (LAMP) test, using primer sets to distinguish not only between X. oryzae pv. oryzae and X. oryzae pv. oryzicola, but also between Asian and African lines within the species X. oryzae pv. oryzae.

Kang et al. (2016) developed a multiplex PCR for the detection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola and Burkholderia glumae, the causal agent of rice grain rot. Cui et al. (2016) developed a multiplex conventional and real-time PCR for the simultaneous detection of six bacterial pathogens of rice, X. oryzae pv. oryzae, X. oryzae. pv. oryzicola, Pseudomonas fuscovaginae causing rice sheath brown rot, Burkholderia glumae, B. gladioli causing bacterial panicle blight of rice and Acidovorax avenae subsp. avenae causing bacterial brown stripe of rice. A validated multiplex PCR to detect P. fuscovaginae, X. oryzae pv. oryzae and X. oryzae pv. oryzicola, Burkholderia (both B. glumae and B. gladioli) as well as Sphingomonas and Pantoea spp. was published by Bangratz et al. (2020).

Apart from recent molecular tests mentioned above, there are seed testing methods based on seedlings grow out tests (Cottyn et al., 1994) or seed soaking followed by plating on semi-selective media (Gnanamanickam et al., 1994) or serological detection (Benedict et al., 1989). The seedling and plating methods have the advantage over serology and PCR methods that they are selective for live cells of the pathogen. 

Pathogenicity tests include needle-pricking, spraying and leaf clipping, or dipping of non-leaf parts of rice in a bacterial suspension (Akhtar et al., 2008; EPPO, 2007). The leaf clipping method was originally developed by Kauffman et al. (1973), where crosscut veins are exposed to a suspension of X. oryzae pv. oryzae by cutting off leaf tips with X. oryzae pv. oryzae suspension contaminated scissors. The latter method has been perfected, detailed and validated by Ke et al. (2017).

Details about presumptive diagnosis with rapid tests, detection and identification methods (including methods for extraction of bacterial cells and DNA), biochemical, serological and molecular and pathogenicity tests for latent and symptomatic infected material, including seeds, flow chart, culture media, chemicals and reference material) are provided in Vera Cruz et al. (2017) and EPPO Standard PM 7 on Xanthomonas oryzae pv. oryzae and pv. oryzicola (EPPO, 2007).

X. oryzae pv. oryzae can only move short distances in infected crops, mainly via contaminated (flood and irrigation) water and wind-driven rain (Devadath & Dath, 1970; Dath & Devadath, 1983). The only means of long-distance dispersal is via infected rice (or other hosts) seeds. The bacteria are usually found in the glumes, but may also penetrate the endosperm. Seed material used in breeding programmes is therefore a possible means of spreading the pathogen. For example, using a genetically hereditable sequence, clustered regularly interspaced short palindromic repeats (CRISPR) and genomic (SNP) sequencing showed that some strains in Taiwan were related to Japanese strains of X. oryzae pv. oryzae and others to those from the Philippines, which could be related to earlier imports of rice breeding material from those countries (Chien et al., 2019).

Only limited investigations into dispersal via machinery, humans and animals and water have been carried out and this is poorly understood. In particular, there are no substantiated data on spread or transmission via insects or other animal (Ou, 1985; Niño-Liu et al., 2006; EFSA, 2018).

Persistence and continuation of infection in the field can be due to colonization (epiphytic and endophytic) of symptomless-host plants, especially Leersia and Zizania spp. (Dath & Devadath, 1983; Gonzalez et al., 1991). Therefore contaminated/infected seeds are the most probable, although poorly proven, way to spread the pathogen to other areas in the world. Symptomless weed and cultivated hosts and surface water play a local role.

Economic impact

Bacterial leaf blight is the most serious disease of rice in South-East Asia, particularly since the widespread cultivation of dwarf high-yielding cultivars in the 1960s (Reddy et al., 1979; Ou, 1985; Mew, 1987) In Japan over the years up to 400 000 ha have been reported to be infested annually with losses of 20-50% and when kresek form occurs, even 70% and more (Mizukami and Wakimoto, 1969; Reddy et al., 1979; Ou, 1985). In Africa, losses of 2.7-41% in grain yield were reported (Awoderv et al., 1991). Severe infection leads to degradation of seed quality, i.e., nutritional composition and broken and less developed, sterile grains (Reddy, 1979; Ou, 1985; Adhikari et al., 1994a and b). The disease was first reported in India in 1951, but it was not until 1963 that a major outbreak occurred. In the Philippines, in the 1970s losses were in the order of 22% during the wet season and 7% during the dry season in susceptible crops and 9 and 2%, respectively, in resistant crops (Exconde, 1973). In China epidemics were recorded in the 1970s. Then, after a quiet period of approximately 20 years (starting in 1980), disease incidence and yield losses increased since the 2000s (Zhang, 2009), although very little information on exact damage and losses are known from this country. In the Republic of Korea, from 2002 to 2005 the infested acreage increased more than 10-fold to reach approximately 27 000 ha (Noh et al., 2007). In this country, the disease spread especially in rice-cultivating areas of the southwestern coastal plain, and the epidemic in 2003 caused substantial yield loss with the emergence of a new race (K3a) of X. oryzae pv. oryzae (Jeung et al., 2006). Rajarajeswari & Muralidharan (2006) in an extensive survey in India recorded 17-44% crop losses. In Pakistan, Ahsan et al., 2021 reported losses of 30-100% and year after year increasing incidence and severity of bacterial leaf blight. Losses are generally lower in the less fertile soils and in summer-grown crops (December-April). However, crops that are transplanted in autumn (May-September) and winter (July-December) suffer considerable losses. Epidemics that start before panicle initiation are especially vulnerable to substantial damage and losses (Reddy et al., 1979) due to significantly reduced, panicle fertility, kernel weight and ultimately grain yield.

Control

The most effective measures to prevent the entry, establishment and spread of X. oryzae pv. oryzae are the use of resistant varieties, the application of appropriate cultural control measures and the use of healthy seeds. Seed transmission is not common for X. oryzae pv. oryzae, (compared to X. oryzae pv. oryzicola) so this is a measure is not as important as for X. oryzae pv. oryzicola. 

Chemical control

Chemical treatments, including sodium hypochlorite (NaOCl), mercury and copper compounds and chemical compounds such as probenazole, L-chloramphenicol, nickel-dimethyldithiocarbamate, dithianon, fentiazon, tecloftalam, phenazine oxide, nickel dimethyldithiocarbamate and antibiotics, either applied to seeds or sprayed on plants have not been found very effective against X. oryzae pv. oryzae and their use in many cases has led to severe phytotoxicity (Mizukami & Wakimoto, 1969; Ou, 1985; Chand et al., 1979; Devadath, 1989; Niño-Liu et al., 2006; Shekhar et al., 2020). The use of mercury compounds has been practically banned worldwide, and use of antibiotics against plant pathogens is not permitted in many EPPO countries, although in Asia their use is still ongoing and resistance of X. oryzae pv oryzae has already been established (Xu et al., 2010; Xu et al., 2013; Niño-Liu et al., 2006). Fubianezuofeng (FBEZF), a sulfone bactericide with an oxadiazole moiety, viz 2-(4-fluorobenzyl)-5-(methyl sulfonyl)-1,3,4-oxadiazole, applied in China, has a good control effect on bacterial leaf blight, but resistance against the compound by strains of the pathogen was recently reported (Yi et al., 2020). Bacterial leaf blight is effectively controlled by niclosamide, an oral anthelminthic drug and molluscicide. This compound also has a direct control effect on X. oryzae pv. oryzae (cell membrane disruption, interfering with biofilm regulating genes/proteins and some enhancement of systemic resistance by inducing some defence-related genes. This compound is plant- and environmentally friendly (Kim et al., 2016; Sahu et al., 2018)

Heat treatment

Hot water treatment of rice seeds at 52-54°C for 30 min, preceded by 8-10 hour of pre-soaking at room temperature in water, has been recommended and successfully used to treat seeds against X. oryzae pv. oryzae (Jain, 1970; Reddy, 1983). However, it never became a general practice, probably due to the fact that seed contamination and transmission for this bacterium, unlike X. oryzae pv. oryzae is not common.

Biological control

Biological control has been tried, but has only been applied in a limited manner (Niño-Liu et al., 2006). Fluorescent pseudomonads (Anuratha & Gnanamanickam, 1987), bacteriocinogenic strains of X. oryzae pv. oryzae (Sakthivel & Mew, 1991) and plant extracts (Wonni et al., 2016) were tried. 

Native strains of the rice-associated rhizobacteria, occurring also as endophytes, such as Pseudomonas fluorescens and P. putida strain V14i (the latter also used in biocontrol of the rice sheath blight pathogen Rhizoctonia solani) significantly reduced bacterial leaf blight severity when they were sprayed on leaves. (Sivamani et al., 1987; Gnanamanickam et al., 1999; Johri et al., 2003). Bacillus spp. have been used as seed treatment before sowing, as a root dip before transplanting and also as foliar sprays. Vasudevan et al. (2002), using Bacillus spp. reported 60% disease reduction and two-fold increase in plant height and grain yield. These authors suspected a systemic resistance response to be involved in this successful application. Pantoea spp. were also found to be potential biocontrol candidates in a rice microbiome environment infested with X. oryzae pv. oryzae (Yang et al., 2020). Also see Niño-Liu et al. (2006) and Gnanamanickam (2009). 

A mixture of Myoviridae bacteriophages reduced disease severity by approximately 50%, in a two-year experiment under field conditions, which was, however, still substantially less effective than the treatment with the standard control chemical tecloftalam (1 g/L), which was used as a control (Chae et al., 2014). Also see Shekhar et al. (2020).

Plant resistance

To date breeding for resistance has been the most effective way to control bacterial leaf blight. It must be noted, however, that it can also become a bottleneck when resistance, which is based on one gene only, is widely used and the pathogen breaks this resistance. A clear example is the general use over millions of hectares in South East Asia of the IRRI variety IR20 carrying the Xa4 resistance gene, located at chromosome 11 that occurred during the green revolution of the 1960-2000s. This massive use of this variety (> 80% of the acreage) created a strong selection pressure towards a Xa4 breaking bacterial strain adaptation and subsequent epidemics and yield reduction (Quibod et al., 2020).

To date, more than 50 resistance (R) genes have been identified, originating primarily from O. sativa subsp. indica cultivars, a few from subsp. japonica and wild rice species such as O. longistaminata, O. minuta, O. officinalis and O. rufipogon (Brar and Khush, 1997; Lee et al., 2003; Chukwu et al., 2019; Oryzabase, 2022). Some resistance genes or alleles were obtained by mutation, using N-methyl-N-nitrosourea, thermal neutron irradiation, or somaclonal mutagenesis (Gao et al., 2001; Lee et al., 2003; Nakai et al., 1988, Taura et al., 1991; Busungu et al., 2016; Niño-Liu et al., 2006)

Most resistance genes have been introgressed into the susceptible indica cultivar IR24 in order to obtain near isogenic lines (NILs), and several of those genes have been combined in a single new line. To this end classical breeding and (mainly DNA based) marker-assisted selection, but also genetic engineering has been applied (Narayanan et al., 2002; Singh et al., 2012, Chukwu et al., 2019, Kesh & Kaushik (2020). Pyramid lines have the advantage of a higher level and/or wider spectrum of resistance than the parental NILs with single resistance genes, implying that there is synergism and complementation among resistance genes (Huang et al., 1997; Adhikari et al., 1999; Narayanan et al., 2002). The pyramid lines now available, yielding a broader resistance (as it is based on more than one gene) provide a more durable form of resistance (Hsu et al., 2020).

However, recently a broad-spectrum resistance gene (Xa23) obtained from wild rice (Oryza rufipogon) was described by Wang et al. (2015). Furthermore Chen et al. (2021), after a decade of research, reported the isolation and characterisation of a new executor resistance gene, Xa7, that confers extremely durable, broad-spectrum, and heat-tolerant resistance to X. oryzae pv. oryzae. This gene may become important in durable resistance breeding in the (near) future. Highly resistant (often, but not always, immune) populations of the wild rice species Oryza meyeriana were discovered in Yunnan province, China. Their resistance genes were characterized, and they are evaluated to be further used in breeding programs (A et al., 2021)

Recent genome-editing methodology, via zinc-finger nucleases (ZFNs), TAL effector nucleases (TALEs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein-9 nuclease), has also been applied to obtain targeted modifications, leading to improved and broad-spectrum resistance in the varieties modified (Ji et al., 2018; Li et al., 2019; Kim et al., 2019; Jiang et al., 2020; Zeng et al., 2020; Tao et al., 2021). A curated TALE database (daTALbase - http://bioinfo-web.mpl.ird.fr/cgi-bin2/datalbase/index.cgi) has been created and include TALE-related data for rice bacteria (Pérez-Quintero et al., 2018). Reviews on the availability of resistance genes/varieties and their interaction with X. oryzae pv. oryzae and X. oryzae pv. oryzicola are available (e.g., Vikal & Bathia, 2017; Jiang et al., 2020). 

An excellent infrastructure and body of resources is available for rice, including for example an expanding, well-characterized germplasm collection, completed genome sequence, whole genome microarrays and a growing collection of mutant libraries. Large collections of documented geographically distinct isolates and pathotypes are also available for X. oryzae pv. oryzae (see Quibod et al., 2020 - https://mhn1.shinyapps.io/PathoTracer/).

Cultural control

Prophylactic measures (such as use of healthy seeds, adequate fertilization and irrigation, destruction or ploughing under of crop residues, disinfection of machinery and equipment, production of seedlings in boxes and removal of diseased plants and weed hosts from fields and along canals) have all been found useful in the control of bacterial leaf blight. Regular monitoring for disease symptoms in rice fields, including in weed hosts is advised.

Forecasting of bacterial leaf blight and bacterial leaf streak has been practised, but appeared to be difficult, due to variations in climatic regions, cultivars and cultural practices and the limited possibilities for chemical or biological control. Methods used were scouting for early disease development, including in weed hosts (since they may show the disease earlier) and correlation to weather conditions (Mizukami & Wakimoto, 1969; Devadath, 1989). Presence of X. oryzae pv. oryzae-specific bacteriophages in flood/irrigation water has also been used to forecast bacterial leaf blight in temperate regions (Murty & Devadath, 1982; Wakimoto & Mew, 1979).

For further information see also Goto (1992); Mizukami & Wakimoto (1969); Ou (1985); Niño-Liu et al. (2006); USDA (2013), COSAVE (2018) and CABI Plantwise Knowledge Bank (2022).

Phytosanitary risk

Bacterial leaf blight is a severe disease, causing extensive crop losses in the Far East, but is not known to occur in the European rice-growing areas. Its existing distribution suggests that it could survive in Mediterranean countries, and it clearly presents a serious risk for the EPPO region (EFSA, 2018). 

Rice cultivation (mainly O. sativa subsp. japonica) in the EPPO region occurs in Bulgaria, France, Greece, Hungary, Italy Portugal, Romania, the Russian Federation, Spain, Turkey and Ukraine. In the EU, about 80% of the rice production takes place in Italy (>220 000 ha) and Spain (>115 000 ha), another 12% in Greece and Portugal (some 20-25 000 ha each). The remainder is cultivated in Bulgaria, France, Hungary and Romania, (10-20 000 ha each). Outside the EU, rice is also grown in the Russian Federation (120 000 ha in the Krasnodar region) as well as in Ukraine (25 000 ha). In those countries, all rice fields are under irrigation, planted in spring and harvested in autumn (Ferrero & Nguyen, 2004; https://ricepedia.org/rice-around-the-world/europe). Resistance of European rice varieties against X. oryzae pv. oryzae is unknown. Non-European varieties are only introduced, in small quantities, for breeding (Cai et al., 2013; Kraehmer et al., 2017).

The main weeds in European rice cultivation are Cyperus, Echinochloa and Heteranthera spp., some of which have been reported as hosts of X. oryzae pv. oryzae (Kraehmer et al., 2017). Other Oryza species reported as hosts may become or are already invasive weed hosts and may introduce X. oryzae pv. oryzae to the EPPO region. These are O. barthii, O. longistaminata, O. rufipogon and O. australiensis (Aldrick et al., 1973). Some related weed species which have also already become unwanted invasive species (e.g., Leersia spp. in the USA) or occur in the EPPO region (e.g., Leersia hexandra in the southern Mediterranean basin) may also introduce the disease and potentially contribute to its establishment. 

Climatic conditions for X. oryzae pv. oryzae in the southern parts of Europe could allow establishment of X. oryzae pv. oryzae when compared with the temperate climatic conditions of Iran, Japan and parts of China and the Republic of Korea where bacterial leaf blight is widespread and from time to time a major problem in rice cultivation. This is contradictory to the outcome of a study using a NAPFAST prediction model for X. oryzae pv. oryzae (Magarey et al., 2011) where the model only used temperature over 30°C and high humidity growing conditions. Europe seemed not to be vulnerable, however the model predicted the same for Japan, where the disease is widespread and where climatic conditions are very similar to those in Southern Europe. Also see EFSA (2018).

No interceptions of X. oryzae pv. oryzae were reported in the EU from 1995 to May 2022 https://ec.europa.eu/food/plants/plant-health-and-biosecurity/european-union-notification-system-plant-health-interceptions-europhyt/interceptions_en. The main risk of introduction is via imported rice seed used for breeding purposes (germplasm) and therefore direct sowing. Milled rice poses negligible risk, because hulls are removed, and endosperm infection is very rare. Moreover, milled rice has its main destination outside rice-growing areas.

Phytosanitary (quarantine) measures can be implemented to reduce the risk of long-distance dissemination of the pathogen. It can be recommended that consignments of rice seeds should have been produced from pest-free areas, or from pest-free places of production.

General inspection and sampling procedures for imported rice, which include X. oryzae pv. oryzae are described in EPPO Standard PM 3/78(2) ‘Consignment inspection of seed and grain of cereals’. Seed inspections of rice intended for breeding purposes in international trade may assist in preventing spread of the pathogen to areas with no history of the disease. However, visual inspection of imported seeds is not very reliable due to the occurrence of latent infections and therefore, when material is imported from areas where the disease is known to occur, certification for disease freedom via field inspections and laboratory testing are necessary. For diagnostic testing methods see EPPO (2007).

In other parts of the world, COSAVE (2019), via the Inter-American Institute for Cooperation on Agriculture developed a surveillance program for the detection of bacterial leaf blight and X. oryzae pv. oryzae in rice and weed hosts in South America. In the USA a contingency plan, to prepare for possible introductions of X. oryzae pv. oryzae, was developed by the USDA (USDA, 2013).

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This datasheet was extensively revised in 2022 by Dr Jaap D. Janse, independent consultant, bacteriologist. His valuable contribution is gratefully acknowledged.

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EPPO (1980) Data sheets on quarantine organisms No. 2, Xanthomonas oryzae. EPPO Bulletin 10(1), 4 pp. https://doi.org/10.1111/j.1365-2338.1980.tb02685.x