Detection of Ralstonia solanacearum in Irrigation Ponds and Aquatic Weeds Associated with the Ponds in North Florida

Comparative genomics and host range analysis of four Ralstonia pseudosolanacearum strains isolated from sunflower reveals genomic and phenotypic differences

BACKGROUND

Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is one of the devastating diseases in crop production, seriously reducing the yield of crops. R. pseudosolanacearum, is known for its broad infrasubspecific diversity and comprises 36 sequevars that are currently known. Previous studies found that R. pseudosolanacearum contained four sequevars (13, 14, 17 and 54) isolated from sunflowers sown in the same field.

RESULTS

Here, we provided the complete genomes and the results of genome comparison of the four sequevars strains (RS639, RS642, RS647, and RS650). Four strains showed different pathogenicities to the same cultivars and different host ranges. Their genome sizes were about 5.84 ~ 5.94 Mb, encoding 5002 ~ 5079 genes and the average G + C content of 66.85% ~ 67%. Among the coding genes, 146 ~ 159 specific gene families (contained 150 ~ 160 genes) were found in the chromosomes and 34 ~ 77 specific gene families (contained 34 ~ 78 genes) in the megaplasmids from four strains. The average nucleotide identify (ANI) values between any two strains ranged from 99.05% ~ 99.71%, and the proportion of the total base length of collinear blocks accounts for the total gene length of corresponding genome was all more than 93.82%. Then, we performed a search for genomic islands, prophage sequences, the gene clusters macromolecular secretion systems, type III secreted effectors and other virulence factors in these strains, which provided detailed comparison results of their presence and distinctive features compared to the reference strain GMI1000. Among them, the number and types of T2SS gene clusters were different in the four strains, among which RS650 included all five types. T4SS gene cluster of RS639 and RS647 were missed. In the T6SS gene cluster, several genes were inserted in the RS639, RS647, and RS650, and gene deletion was also detected in the RS642. A total of 78 kinds of type III secreted effectors were found, which included 52 core and 9 specific effectors in four strains.

CONCLUSION

This study not only provided the complete genomes of multiple R. pseudosolanacearum strains isolated from a new host, but also revealed the differences in their genomic levels through comparative genomics. Furthermore, these findings expand human knowledge about the range of hosts that Ralstonia can infect, and potentially contribute to exploring rules and factors of the genetic evolution and analyzing its pathogenic mechanism.

Ralstonia solanacearum pandemic lineage strain UW551 overcomes inhibitory xylem chemistry to break tomato bacterial wilt resistance

Plant-pathogenic Ralstonia strains cause bacterial wilt disease by colonizing xylem vessels of many crops, including tomato. Host resistance is the best control for bacterial wilt, but resistance mechanisms of the widely used Hawaii 7996 tomato breeding line (H7996) are unknown. Using growth in ex vivo xylem sap as a proxy for host xylem, we found that Ralstonia strain GMI1000 grows in sap from both healthy plants and Ralstonia-infected susceptible plants. However, sap from Ralstonia-infected H7996 plants inhibited Ralstonia growth, suggesting that in response to Ralstonia infection, resistant plants increase inhibitors in their xylem sap. Consistent with this, reciprocal grafting and defence gene expression experiments indicated that H7996 wilt resistance acts in both above- and belowground plant parts. Concerningly, H7996 resistance is broken by Ralstonia strain UW551 of the pandemic lineage that threatens highland tropical agriculture. Unlike other Ralstonia, UW551 grew well in sap from Ralstonia-infected H7996 plants. Moreover, other Ralstonia strains could grow in sap from H7996 plants previously infected by UW551. Thus, UW551 overcomes H7996 resistance in part by detoxifying inhibitors in xylem sap. Testing a panel of xylem sap compounds identified by metabolomics revealed that no single chemical differentially inhibits Ralstonia strains that cannot infect H7996. However, sap from Ralstonia-infected H7996 contained more phenolic compounds, which are known to be involved in plant antimicrobial defence. Culturing UW551 in this sap reduced total phenolic levels, indicating that the resistance-breaking Ralstonia strain degrades these chemical defences. Together, these results suggest that H7996 tomato wilt resistance depends in part on inducible phenolic compounds in xylem sap.

Future of Bacterial Disease Management in Crop Production

Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.

Genetic Structure of Ralstonia solanacearum and Ralstonia pseudosolanacearum in Brazil

Bacterial wilt-causing Ralstonia threaten numerous crops throughout the world. We studied the population structure of 196 isolates of Ralstonia solanacearum and 39 isolates of Ralstonia pseudosolanacearum, which were collected from potato- and tomato-growing areas in 19 states of Brazil. Regardless of the species, three groups of isolates were identified. One group encompassed R. pseudosolanacearum isolates. The other two groups comprise isolates of R. solanacearum (phylotype II) split according to geographic regions, one made of isolates from the North and Northeast and the other made of isolates from the Central, Southeast, and South regions (CSS). Among the isolates collected in CSS, those from tomato were genetically distinct from the potato isolates. The genetic variability in the population of R. pseudosolanacearum was lower than that of R. solanacearum, suggesting that the former was introduced in Brazil. Conversely, the high genetic variability of R. solanacearum in all regions, hosts, and times supports the hypothesis that this species is autochthonous in South America, more precisely in Brazil and Peru. For R. solanacearum, higher variability and lower migration rates were observed when tomato isolates were analyzed, indicating that the variability is caused mainly by the differences of the local, native soil population. The North subpopulation was distinct from all others, possibly because of differences in environmental features of this region. The proximity of some geographic regions and the movement of potato tubers could have facilitated migration and therefore low genetic differentiation between geographic regions. Finally, geography, which also influences host distribution, affects the structure of the population of R. solanacearum in Brazil. Despite quarantine procedures in Brazil, increasing levels of trade are a threat to biosecurity, and these results emphasize the need for improving our regional efforts to prevent the dispersal of pathogens.

Biocontrol of the Major Plant Pathogen Ralstonia solanacearum in Irrigation Water and Host Plants by Novel Waterborne Lytic Bacteriophages

Three new lytic bacteriophages were found to effectively control the pathogen Ralstonia solanacearum, a quarantine bacterium in many countries, and causative agent of bacterial wilt, one of the most important vascular plant diseases. Bacterial wilt management has been carried out with fluctuating effects, suggesting the need to find alternative treatments. In this work, three lytic phages were isolated from environmental water from geographically distant regions in Spain. They proved to specifically infect a collection of R. solanacearum strains, and some of the closely related pathogenic species Ralstonia pseudosolanacearum, without affecting non-target environmental bacteria, and were able to lyze the pathogen populations within a wide range of conditions comprising environmental values of water temperatures, pH, salinity, and lack of aeration found in storage tanks. The three bacteriophages displayed high efficiency in controlling R. solanacearum, with reductions of the bacterial populations of several orders of magnitude in just a few hours, and proved to be able to survive in freshwater for months at environmental temperatures keeping activity on R. solanacearum, pointing out their suitability for field application through irrigation. Concerning their biocontrol potential, they were effective in reducing high populations of the pathogen in environmental water, and bacterial wilt incidence in planta by watering with either one phage or their combinations in assays with more than 300 plants. This is the first report on effective R. solanacearum biocontrol by applying single or combined bacteriophages through irrigation water in conditions mimicking those of the natural settings. The three phages belong to the Podoviridae family and are members of the T7likevirus genus. They are the first isolated phages from river water with activity against R. solanacearum, showing the longest persistence in natural water reported until now for phages with biocontrol potential, and consistently being able to control the disease in the host plant under environmental conditions. Consequently, the use of these bacteriophages for the prevention and/or biocontrol of the bacterial wilt disease caused by R. solanacearum has been patented. Evidence provided reveals the suitability of these waterborne phages to be effectively considered as a valuable strategy within the frame of sustainable integrated management programs.

Pest categorisation of the Ralstonia solanacearum species complex

Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of the Ralstonia solanacearum species complex (RSSC), a distinguishable cosmopolitan group of bacterial plant pathogens (including R. solanacearum, Ralstonia pseudosolanacearum and two subspecies of Ralstonia syzygii) of the family Burkholderiaceae. The RSSC causes bacterial wilt in solanaceous crops, such as potato, tomato and pepper, but can also cause wilts in other important food crops such as fruit banana, plantain banana and cassava. The pest survives in the soil, and a number of weed species can also be infected by the pest, often asymptomatically. The RSSC is regulated in Council Directive 2000/29/EC (Annex IAII) (indicated by its former name R. solanacearum, as delimited by Yabuuchi et al.) as a harmful organism whose introduction into the EU is banned. In addition, Council Directive 1998/57/EC (amended by Commission Directive 2006/63/CE) concerns the measures to be taken within EU Member States (MS) against the RSSC to (a) detect it and determine its distribution, (b) prevent its occurrence and spread, and (c) control it with the aim of eradication. The pest is present in several EU MS, but in all cases with a restricted distribution and under official control. New phylotypes of the RSSC could enter the EU primarily via host plants for planting (including seed tubers). The pest could establish in the EU, as climatic conditions are favourable, hosts are common and the pathogen has high adaptability. Spread is mainly via plants for planting. Substantial crop losses in the EU would occur in the presence of RSSC epidemics. The RSSC is regarded as one of the world's most important phytopathogenic bacteria due to its broad geographical distribution, large host range, aggressiveness, genetic diversity and long persistence in soil and water. The list of hosts and commodities for which the pest is regulated is incomplete due to the high diversity of hosts and the lack of knowledge of the complete host range. Moreover, the comparative epidemiology of the different pathogen species has not yet been studied. The criteria assessed by the Panel for consideration of the RSSC as potential quarantine pest are met, while, for regulated non-quarantine pests, the criterion on the widespread presence in the EU is not met.

Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551

Ralstonia solanacearum is a globally distributed plant pathogen that causes bacterial wilt diseases of many crop hosts, threatening both sustenance farming and industrial agriculture. Here, we present closed genome sequences for the R. solanacearum type strain, K60, and the cool-tolerant potato brown rot strain R. solanacearum UW551, a highly regulated U.S. select agent pathogen.

Foliar Applications of Acibenzolar-S-Methyl Negatively Affect the Yield of Grafted Tomatoes in Fields Infested with Ralstonia solanacearum

Three field experiments were conducted in Florida from 2012-2014 to assess the impact of acibenzolar-S-methyl (ASM), a systemic acquired-resistance inducer, applied as foliar spray or through drip-irrigation lines, on bacterial wilt incidence and yield of grafted tomatoes. The experiments were conducted in a field with race 1, biovar 1 strain of Ralstonia solanacearum, causal agent of tomato bacterial wilt. In all three experiments, the susceptible tomato variety BHN 602, grafted onto a resistant rootstock BHN 998, was compared with nongrafted BHN 602, treated with or without foliar applications of ASM and with grafted plants treated with foliar applications of ASM. In two experiments, an additional treatment of drip applications of ASM on grafted and nongrafted plants was evaluated. Grafting alone or in combination with drip applications of ASM (178.6 μM) significantly reduced disease incidence and increased total marketable yield relative to nongrafted treatments. There were no significant differences between grafted plants with or without drip ASM applications in terms of bacterial wilt incidence or total marketable yield. However, we demonstrate for the first time that foliar ASM applications on grafted plants negatively affects the total marketable yield compared with drip ASM applications on grafted plants or nontreated grafted control.

Sensitive, Secure Detection of Race 3 Biovar 2 and Native U.S. Strains of Ralstonia solanacearum

Detecting and correctly identifying Ralstonia solanacearum in infected plants is important because the race 3 biovar 2 (R3bv2) subgroup is a high-concern quarantine pathogen, while the related sequevar 7 group is endemic to the southeastern United States. Preventing accidental import of R3bv2 in geranium cuttings demands sensitive detection methods that are suitable for large-volume use both onshore and offshore. However, detection is complicated by frequent asymptomatic latent infections, uneven pathogen distribution within infected plants, pathogen viable-but-not-culturable state, and biosecurity laws that restrict transport of R3bv2 strains for diagnosis. There are many methods to detect R3bv2 strains but their relative utility is unknown, particularly in the realistic context of infected plant hosts. Therefore, we compared the sensitivity, cost, and technical complexity of several assays to detect and distinguish R3bv2 and sequevar 7 strains of R. solanacearum in geranium, tomato, and potato tissue in the laboratory and in naturally infected tomato plants from the field. The sensitivity of polymerase chain reaction (PCR)-based methods in infected geranium tissues was significantly improved by use of Kapa3G Plant, a polymerase with enhanced performance in the presence of plant inhibitors. R3bv2 cells were killed within 60 min of application to Whatman FTA(R) nucleic acid-binding cards, suggesting that samples on FTA cards can be safely transported for diagnosis. Overall, culture enrichment followed by dilution plating was the most sensitive detection method (10¹ CFU/ml) but it was also most laborious. Conducting PCR from FTA cards was faster, easier, and sensitive enough to detect approximately 10⁴ CFU/ml, levels similar to those found in latently infected geranium plants.

Tropical strains of Ralstonia solanacearum Outcompete race 3 biovar 2 strains at lowland tropical temperatures

Bacterial wilt, caused by members of the heterogenous Ralstonia solanacearum species complex, is an economically important vascular disease affecting many crops. Human activity has widely disseminated R. solanacearum strains, increasing their global agricultural impact. However, tropical highland race 3 biovar 2 (R3bv2) strains do not cause disease in tropical lowlands, even though they are virulent at warm temperatures. We tested the hypothesis that differences in temperature adaptation and competitive fitness explain the uneven geographic distribution of R. solanacearum strains. Using three phylogenetically and ecologically distinct strains, we measured competitive fitness at two temperatures following paired-strain inoculations of their shared host, tomato. Lowland tropical strain GMI1000 was only weakly virulent on tomato under temperate conditions (24°C for day and 19°C for night [24/19°C]), but highland tropical R3bv2 strain UW551 and U.S. warm temperate strain K60 were highly virulent at both 24/19°C and 28°C. Strain K60 was significantly more competitive than both GMI1000 and UW551 in tomato rhizospheres and stems at 28°C, and GMI1000 also outcompeted UW551 at 28°C. The results were reversed at cooler temperatures, at which highland strain UW551 generally outcompeted GMI1000 and K60 in planta. The superior competitive index of UW551 at 24/19°C suggests that adaptation to cool temperatures could explain why only R3bv2 strains threaten highland agriculture. Strains K60 and GMI1000 each produced different bacteriocins that inhibited growth of UW551 in culture. Such interstrain inhibition could explain why R3bv2 strains do not cause disease in tropical lowlands.

Whole-Genome Sequence of Ralstonia solanacearum P673, a Strain Capable of Infecting Tomato Plants at Low Temperatures

Ralstonia solanacearum is the causal agent of bacterial wilt, one of the most destructive bacterial plant diseases. We present the whole-genome sequence of the strain P673 (phylotype IIB, sequevar 4). This strain is capable of producing disease in tomato plants at low temperatures. P673 has 311 unique genes.

Effects of pesticides on the reduction of plant and human pathogenic bacteria in application water

Overhead spray applications of in-field tomato treatments dissolved in aqueous solutions have specific pest targets (fungal, bacterial, insect, or other). Any organism present in the solution or on treated plant surfaces that is not a specific target of the application is unlikely inactivated and can instead be spread through the phyllosphere. In this laboratory study, commercially labeled pesticides (including Actigard 50WG, Bravo Weather Stik 6F, Cabrio 20EG, Kasumin, Kocide 3000 46WG, Oxidate 27L, Penncozeb 75DF, ProPhyt 54.5L, Stimplex 100L, Firewall, 22.4WP, and Tanos 50DF) in common use in commercial tomato production fields of the Eastern Shore of Virginia were investigated for activity against in vitro bacterial contamination of pesticide application waters. Pesticides of interest were tank mixed individually with one of the plant pathogens Ralstonia solanacearum, Xanthomonas campestris pv. vesicatoria, Pseudomonas syringae pv. tomato, Erwinia carotovora subsp. carotovora, or one of two serovars (Newport and Montevideo) of the human pathogen Salmonella enterica to assess reduction values during the average time between mixing and initial application. Observations suggested that while some treatments had a noticeable effect on population levels, only the oxidizer, peroxyacetic acid, showed significant and consistent levels of suppression against all bacteria investigated, at levels that could have practical implications.

Diversity among Ralstonia solanacearum strains isolated from the southeastern United States

This is the first comprehensive study of a collection of Ralstonia solanacearum strains from the southeastern United States to be characterized based on biovar, pathogenicity, hypersensitive reaction on tobacco, and phylogenetic analyses of the egl sequence. Rigorous phylogenetic analysis of the commonly used egl gene produced robust phylogenies that differed significantly from a neighbor-joining tree differed from and previously published phylogenies for R. solanacearum strains. These robust trees placed phylotype IV within the phylotype I clade, which may suggest that phylogenies based solely on egl may be misleading. As a result of phylogenetic analyses in this study, we determined that U.S. strains from Georgia, North Carolina, South Carolina, and older Florida strains isolated from solanaceous crops all belong to phylotype II sequevar 7. However, many strains recently isolated in Florida from tomato and other crops were more diverse than the southeastern United States population. These unique Florida strains grouped with strains mostly originating from the Caribbean and Central America. One of the exotic strains, which in a previous study was determined to be established in northern Florida, was characterized more extensively. Upon using Musa-specific multiplex polymerase chain reaction, this strain produced a unique banding pattern, which has not previously been reported. Inoculation of this strain into Musa spp. did not result in wilt symptoms; however, the plants were stunted and root masses were significantly reduced. Furthermore, following root inoculation, the bacterium, unlike a typical Florida race 1 biovar 1 strain, was recovered from the roots and stems, indicating systemic movement. This is the first report of an R. solanacearum strain isolated in the United States that is deleterious to the growth of Musa plants.

A Rapid, Sensitive Assay for Ralstonia solanacearum Race 3 Biovar 2 in Plant and Soil Samples Using Magnetic Beads and Real-Time PCR

The Ralstonia solanacearum species complex causes economically significant diseases in many plant families worldwide. Although generally limited to the tropics and subtropics, strains designated race 3 biovar 2 (R3Bv2) cause disease in cooler tropical highlands and temperate regions. R3Bv2 has not become established in North America but, due to concerns that it could devastate the U.S. potato industry, it has been designated a Select Agent, and is subject to strict quarantine regulations. Quarantine screening for R3Bv2 requires rapid and robust assays applicable to small populations present in plant tissues or soil, and must distinguish R3Bv2 from the multiple other R. solanacearum subgroups. We developed a 100%-accurate real-time polymerase chain reaction (RT-PCR) assay that can detect R3Bv2 populations >1,000 cells ml^-1. However, detection by RT-PCR was inhibited by compounds present in some plant and soil samples. Therefore, we developed simple immunomagnetic separation (IMS) and magnetic capture hybridization (MCH) methods to purify R. solanacearum cells or DNA from PCR inhibitors. When coupled with RT-PCR, these tools permitted detection of R3Bv2 at levels >500 cells ml^-1 in stem, tuber, and soil samples when direct RT-PCR failed, and reduced detection time from days to hours. IMS-RT-PCR was usually more sensitive than MCH-RT-PCR, especially at lower population levels.