Molecular and Pathogenic Diversity Among Brazilian Isolates of Xanthomonas albilineans Assessed with SSR Marker Loci

Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease

Leaf scald caused by the bacteria Xanthomonas albilineans is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against X. albilineans using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5 to 144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of X. albilineans and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi). The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.

Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness

An integrative approach combining genomics, transcriptomics, and cell biology is presented to address leaf scald disease, a major problem for the sugarcane industry. To gain insight into the biology of the causal agent, the complete genome sequences of four Brazilian Xanthomonas albilineans strains with differing virulence capabilities are presented and compared to the GPEPC73 reference strain and FJ1. Based on the aggressiveness index, different strains were compared: Xa04 and Xa11 are highly aggressive, Xa26 is intermediate, and Xa21 is the least, while, based on genome structure, Xa04 shares most of its genomic features with Xa26, and Xa11 share most of its genomic features with Xa21. In addition to presenting more clustered regularly interspaced short palindromic repeats (CRISPR) clusters, four more novel prophage insertions are present than the previously sequenced GPEPC73 and FJ1 strains. Incorporating the aggressiveness index and in vitro cell biology into these genome features indicates that disease establishment is not a result of a single determinant factor, as in most other Xanthomonas species. The Brazilian strains lack the previously described plasmids but present more prophage regions. In pairs, the most virulent and the least virulent share unique prophages. In vitro transcriptomics shed light on the 54 most highly expressed genes among the 4 strains compared to ribosomal proteins (RPs), of these, 3 outer membrane proteins. Finally, comparative albicidin inhibition rings and in vitro growth curves of the four strains also do not correlate with pathogenicity. In conclusion, the results disclose that leaf scald disease is not associated with a single shared characteristic between the most or the least pathogenic strains. IMPORTANCE An integrative approach is presented which combines genomics, transcriptomics, and cell biology to address leaf scald disease. The results presented here disclose that the disease is not associated with a single shared characteristic between the most pathogenic strains or a unique genomic pattern. Sequence data from four Brazilian strains are presented that differ in pathogenicity index: Xa04 and Xa11 are highly virulent, Xa26 is intermediate, and Xa21 is the least pathogenic strain, while, based on genome structure, Xa04 shares with Xa26, and Xa11 shares with X21 most of the genome features. Other than presenting more CRISPR clusters and prophages than the previously sequenced strains, the integration of aggressiveness and cell biology points out that disease establishment is not a result of a single determinant factor as in other xanthomonads.

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum

Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.

Sugarcane responses to two strains of Xanthomonas albilineans differing in pathogenicity through a differential modulation of salicylic acid and reactive oxygen species

Leaf scald caused by Xanthomonas albilineans is one of the major bacterial diseases of sugarcane that threaten the sugar industry worldwide. Pathogenic divergence among strains of X. albilineans and interactions with the sugarcane host remain largely unexplored. In this study, 40 strains of X. albilineans from China were distributed into three distinct evolutionary groups based on multilocus sequence analysis and simple sequence repeats loci markers. In pathogenicity assays, the 40 strains of X. albilineans from China were divided into three pathogenicity groups (low, medium, and high). Twenty-four hours post inoculation (hpi) of leaf scald susceptible variety GT58, leaf populations of X. albilineans strain XaCN51 (high pathogenicity group) determined by qPCR were 3-fold higher than those of strain XaCN24 (low pathogenicity group). Inoculated sugarcane plants modulated the reactive oxygen species (ROS) homoeostasis by enhancing respiratory burst oxidase homolog (ScRBOH) expression and superoxide dismutase (SOD) activity and by decreasing catalase (CAT) activity, especially after infection by X. albilineans XaCN51. Furthermore, at 24 hpi, plants infected with XaCN51 maintained a lower content of endogenous salicylic acid (SA) and a lower expression level of SA-mediated genes (ScNPR3, ScTGA4, ScPR1, and ScPR5) as compared to plants infected with XaCN24. Altogether, these data revealed that the ROS production-scavenging system and activation of the SA pathway were involved in the sugarcane defense response to an attack by X. albilineans.

Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate

This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodis pv. punicae strains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xap genomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xap isolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xap isolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xap isolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03209-z.

Genetic Diversity and Streptomycin Sensitivity in Xanthomonas axonopodis pv. punicae Causing Oily Spot Disease in Pomegranates

Xanthomonas axonopodis pv. punicae (Xap) causes bacterial blight disease in pomegranates, often leading to 60–80% economic loss. In absence of a suitable Xap-resistant variety, the near-monoculture of the susceptible variety, Bhagwa, has aggravated the problem further. In recent times, Xap has spread to different geographical regions, indicating the wide adaptability of the pathogen. Moreover, lower sensitivity of Xap towards streptocycline containing streptomycin sulphate and tetracycline sulphate (9:1) under field conditions is frequently reported. Therefore, the current study was undertaken to assess the genetic variability of Xap isolates using SSR markers, their in vitro sensitivity towards streptomycin was evaluated, and the probable molecular basis of acquired resistance was studied. Two highly diverse isolates showed extreme differences in their pathogenicity, indicating the highly evolving nature of the pathogen. Moreover, all the isolates showed less than 50% growth inhibition on media containing 1500 µg/mL streptomycin, indicating a lower level of antibiotic sensitivity. On the molecular level, 90% of the isolates showed the presence of strA-strB genes involved in streptomycin metabolism. Additionally, G to A transitions were observed in the rpsL gene in some of the isolates. The molecular data suggest that horizontal gene transfer (strAB) and/or spontaneous gene mutation (in rpsL) could be responsible for the observed lower sensitivity of Xap towards streptomycin.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.