Non-pathogenic Xanthomonas Research Articles

Xanthomonas sontii, and Not X. sacchari, Is the Predominant Vertically Transmitted Core Rice Seed Endophyte.

Seed endophytes, particularly the abundant, core, and vertically transmitted species, are major areas of focus in host microbiome studies. Apart from being the first members to colonize, they accompany the plant throughout its development stages and to the next generation. Recently published studies have reported the keystone species to be Xanthomonas sacchari, a core endophyte that is vertically transmitted in rice with probiotic properties. Furthermore, the Xanthomonas species was reported to be involved in the assembly of beneficial bacteria after early inoculation in rice seeds. However, the strains discussed in these studies were misclassified as X. sacchari, a well-known pathogen of sugarcane. By including nonpathogenic Xanthomonas species with plant-protective functions reported from rice seeds, we have correctly established the phylogenetic and taxonomic identity of the keystone species as X. sontii. This will enable researchers to use the correct reference or lab strain of X. sontii for further systematic and in-depth studies as a model endophyte in plant-microbe interactions apart from its exploitation in seed health.

Xanthomonas indica sp. nov., a Novel Member of Non-Pathogenic Xanthomonas Community from Healthy Rice Seeds.

Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560T and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.

Development of Designer Transcription Activator-Like Effector-Based Plant Growth Regulator for Higher Yield in Rice.

Recent studies have shown that reprogramming of gene expression in a genome can induce the production of proteins enabling yield increase. The transcription activator-like effectors (TALEs) from several species of bacterial Xanthomonas have been extensively studied, and a series of research tools, such as genome editing tool TALENs and gene expression activators, have been developed based on the specific protein–nucleic acid recognition and binding mechanisms of TALEs. In this proof-of-principle study, we designed and constructed a designer TALE (dTALE), designated as dTALE-NOG1, to specifically target the promoter of OsNOG1 gene in rice, and demonstrated that this dTALE can be used as a new type of plant growth regulator for better crop growth and harvest. In doing so, the dTALE-NOG1 was transferred into the non-pathogenic Xanthomonas oryzae pv. oryzae (Xoo) strain PH to generate a genetically engineered bacteria (GEB) strain called PH-dtNOG1. Functional verification showed that dTALE-NOG1 could significantly induce the expression of OsNOG1. By spraying cell suspension of PH-dtNOG1 on the rice plants during the tillering stage, the transcription level of OsNOG1 was highly enhanced, the grain number of rice plants was increased by more than 11.40%, and the grain yield per plant increased by more than 11.08%, demonstrating that the dTALE-NOG1 was highly effective in enhancing rice yield. This work provided a new strategy for manipulating agronomical traits by reprogramming gene expression in a crop genome.

Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles.

Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.

Host range and molecular typing of Xanthomonas spp. strains isolated from wild rocket (Diplotaxis tenuifolia) in Italy

Black rot of crucifers is one of the most important diseases of wild rocket (Diplotaxis tenuifolia L. (D.C.)) caused by the seedborne pathogen Xanthomonas campestris pv. campestris. From 2005, it frequently affected this cultivation in the south of Italy, leading to heavy crop losses. In the present work, we aimed to describe the physiological and molecular characteristics of twenty X. campestris pv. campestris strains isolated from plants and seeds. Ten Xanthomonas spp. strains contaminating seeds were identified on the basis of molecular characterization and in vivo pathogenicity on a discriminating host range. Some of seed-borne isolates were ascribed to the species Xanthomonas campestris pv. raphani and X. campestris pv. incanae, indicating the occurrence of non-host pathogenic Xanthomonas on wild rocket seeds. As well as the presence of pathogenic bacteria, even non-pathogenic Xanthomonas spp. strains were detected on the seeds, underlying the importance of identifying them to evaluate the suitability of lots intended for sowing. A phylogeny using 69 Gyrase B (gyrB) sequences retrieved from the literature, was also carried out, highlighting species relatedness. Overall, this study provides a comprehensive framework for Xanthomonas species affecting wild rocket in Southern Italy.

Improved control of black rot of broccoli caused by Xanthomonas campestris pv. campestris using a bacteriophage and a nonpathogenic Xanthomonas sp. strain

We examined the potential for biological control of black rot of broccoli, caused by Xanthomonas campestris pv. campestris (Xcc), using nonpathogenic Xanthomonas sp. strain 11-100-01 (npX) mixed with bacteriophage XcpSFC211 (pXS). Inoculation of intact broccoli plants in greenhouse trials with either npX or pXS did not control black rot. After injured plant inoculation, however, npX alone or npX with pXS significantly controlled black rot. When a mixed suspension of npX with pXS was placed on a membrane filter, then washed with distilled water and air-dried, a substantial amount of pXS adsorbed to the surface of npX. In a field trial, broccoli plants were sprayed with a suspension of npX with pXS, then inoculated with Xcc. A meta-analysis of the results from five field trials showed an integrated risk ratio (IRR, the ratio of disease incidence in inoculated broccoli plants to the incidence in control plants) of 0.69 after treatment with only npX and 0.59 with npX with pXS, indicating that black rot incidence was significantly reduced by each treatment. The difference between these two treatments was also significant. IRR was 1.24 when comparing suppression by npX with pXS and that by basic copper sulfate wettable powder; thus, their control was comparable. The combination of npX with pXS improved the preventive effect against black rot. This is the first report describing that a nonpathogenic Xanthomonas sp. strain mixed with a bacteriophage effectively controlled black rot of broccoli in field trials.

Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida.

We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.

Editorial: Genomics and Effectomics of the Crop Killer Xanthomonas.

Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds of host plants, including economically important crops, such as bean, cabbage, cassava, citrus, hemp, pepper, rice, sugarcane, tomato, or wheat. Diseases occurring in nature comprise bacterial blight, canker, necrosis, rot, scald, spot, streak, or wilt. Xanthomonas spp., are distributed worldwide, and pathogenic and non-pathogenic strains are essentially found in association to plants. Some phytopathogenic strains are emergent or re-emergent and, consequently, dramatically impact agriculture, economy, and food safety. During the last decades, massive efforts were undertaken to decipher Xanthomonas biology. So far, more than 100 complete or draft genomes from diverse Xanthomonas species have been sequenced (http://www.xanthomonas.org), thus providing powerful tools to study genetic determinants triggering pathogenicity and adaptation to plant habitats. Xanthomonas spp., employ an arsenal of virulence factors to invade its host, including extracellular polysaccharides, plant cell wall-degrading enzymes, adhesins, and secreted effectors. In most xanthomonads, type III secretion (T3S) system and secreted effectors (T3Es) are essential to bacterial pathogenicity through the inhibition of plant immunity or the induction of plant susceptibility (S) genes, as reported for Transcription Activation-Like (TAL) effectors. Yet, toxins can also be major virulence determinants in some xanthomonads while non-pathogenic Xanthomonas species do live in sympatry with plant without any T3S systems nor T3Es. In a context of ever increasing international commercial exchanges and modifications of the climate, monitoring and regulating pathogens spread is of crucial importance for food security. A deep knowledge of the genomic diversity of Xanthomonas spp., is required for scientists to properly identify strains, to help preventing future disease outbreaks and to achieve knowledge-informed sustainable disease resistance in crops. This research topic published in the “Plant Biotic Interactions” section of Frontiers in Plant Science and Frontiers in Microbiology aims at illustrating several of the recent achievements of the Xanthomonas community. We collected twelve manuscripts dealing with comparative genomics or T3E repertoires, including five focusing on TAL effectors which we hope will contribute to advance research on plant pathogenic bacteria.

Biological control of bacterial spot on peach by nonpathogenic Xanthomonas campestris strains AZ98101 and AZ98106

A suspension of nonpathogenic Xanthomonas campestris (nXc) strain AZ98101 or AZ98106 was sprayed on peach trees in biological control tests against bacterial spot caused by Xanthomonas arboricola pv. pruni. Treatment with each strain reduced the number of leaves with spots. Meta-analysis of the results from seven field trials showed an integrated risk ratio (the ratio of leaf spot incidence on inoculated leaves to incidence on control leaves) of 0.46 by treatment with AZ98101 and 0.54 by AZ98106, indicating that leaf spot incidence was significantly reduced by each strain. Each also significantly reduced the incidence of fruit spot. The risk ratio with AZ98101 was significantly lower than that with AZ98106. The population of AZ98101R-1, a rifampicin-resistant mutant of AZ98101, was 6.3 × 103 CFU/g (fresh mass) on leaves and 8.0 × 103 CFU/g on fruit at 12 days after inoculation, but was undetectable (<102 CFU/g) by 24 days. This is the first report that nXc strains AZ98101 and AZ98106 effectively control bacterial spot on peach.

非病原性&lt;i&gt;Xanthomonas&lt;/i&gt;属細菌を用いたブロッコリー黒腐病の生物防除

非病原性&lt;i&gt;Xanthomonas&lt;/i&gt;属細菌を用いたブロッコリー黒腐病の生物防除

Effect of Treating Pepper with Benzothiadiazole Derivative and Non-pathogenic Xanthomonas campestris Pathovars on the Level of Disease Caused by Sclerotinia sclerotiorum

1 Abstract: This study was carried out to determine the effect of CGA 245704 (a Benzothiadiazole derivative) and two non-pathogenic Xanthomonas campestris strains on white mold disease of pepper caused by Sclerotinia sclerotiorum. Pretreatment of pepper seedlings with the bacterial strains did not reduce the disease severity of white mold. Application of CGA 245704 followed by a subsequent inoculation of the plants with the fungus resulted in significant decrease in disease severity. No inhibition of ascospore germination of Sclerotinia sclerotiorum isolate Ss6 but reduced germ tube length, radial growth of mycelium and number of sclerotia on culture medium amended with CGA 245704 was observed. The decrease in disease severity following treatment with CGA 245704 might be the result of both resistance induction and fungistatic effect.

The Citrus Canker Epidemic in Florida: The Scientific Basis of Regulatory Eradication Policy for an Invasive Species

The Citrus Canker Epidemic in Florida: The Scientific Basis of Regulatory Eradication Policy for an Invasive Species

Identification of Non-Pathogenic Xanthomonas Strains Associated with Plants

Summary A total of 70 presumptive non-pathogenic yellow-pigmented strains from different origins were identified to the genus Xanthomonas with the genus-specific monoclonal antibodies (XI and XII), and fatty acid methyl ester (FAME) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) protein databases. On the basis of FAME profiles and SDS-PAGE protein patterns, these non-pathogenic xanth- omonads formed a heterogeneous population. Fourty-two strains were identified as the same species by both methods, whereas five strains were identified as different species. Only eight strains remained unidentified by both methods, whereas in 15 cases the identification was ambiguous. The identification at pathovar level was usually ambiguous and not concordant, which indicated that the non-pathogenic xanthomonads cannot be classified in the described pathovars. None of the non-pathogenic xanth- omonads was identified as belonging to the pathovars of the plant from which they were isolated.