Dual Transcriptional Profiling of Carrot and 'Candidatus Liberibacter solanacearum' at Different Stages of Infection Suggests Complex Host-Pathogen Interaction

Challenges and Opportunities in the Sustainable Improvement of Carrot Production

From an agricultural perspective, carrots are a significant tap root vegetable crop in the Apiaceae family because of their nutritional value, health advantages, and economic importance. The edible part of a carrot, known as the storage root, contains various beneficial compounds, such as carotenoids, anthocyanins, dietary fiber, vitamins, and other nutrients. It has a crucial role in human nutrition as a significant vegetable and raw material in the nutraceutical, food, and pharmaceutical industries. The cultivation of carrot fields is susceptible to a wide range of biotic and abiotic hazards, which can significantly damage the plants' health and decrease yield and quality. Scientific research mostly focuses on important biotic stressors, including pests, such as nematodes and carrot flies, as well as diseases, such as cavity spots, crown or cottony rot, black rot, and leaf blight, caused by bacteria, fungi, and oomycetes. The emerging challenges in the field include gaining a comprehensive understanding of the interaction between hosts and pathogens in the carrot-pathogen system, identifying the elements that contribute to disease development, expanding knowledge of systemic treatments, exploring host resistance mechanisms, developing integrated control programs, and enhancing resistance through breeding approaches. In fact, the primary carrot-growing regions in tropical and subtropical climates are experiencing abiotic pressures, such as drought, salinity, and heat stress, which limit carrot production. This review provides an extensive, up-to-date overview of the literature on biotic and abiotic factors for enhanced and sustainable carrot production, considering the use of different technologies for the shelf-life extension of carrots. Therefore, it addresses the current issues in the carrot production chain, opening new perspectives for the exploration of carrots both as a food commodity and as a source of natural compounds.

Differential expression of "Candidatus Liberibacter solanacearum" genes and prophage loci in different life stages of potato psyllid

Psyllid species, including the potato psyllid (PoP) Bactericera cockerelli (Sulc) (Triozidae) serve as host and vector of "Candidatus Liberibacter spp." ("Ca. Liberibacter"), which also infects diverse plant hosts, including citrus and tomato. Psyllid transmission of "Ca. Liberibacter" is circulative and propagative. The time of "Ca. Liberibacter" acquisition and therefore vector life stage most competent for bacterial transmission varies by pathosystems. Here, the potato psyllid-"Ca. Liberibacter solanacearum" (CLso) pathosystem was investigated to dissect CLso-prophage interactions in the tomato plant and PoP-psyllid host by real-time quantitative reverse transcriptase amplification of CLso genes/loci with predicted involvement in host infection and psyllid-CLso transmission. Genes/loci analyzed were associated with (1) CLso-adhesion, -invasion, -pathogenicity, and -motility, (2) prophage-adhesion and pathogenicity, and (3) CLso-lysogenic cycle. Relative gene expression was quantified by qRT-PCR amplification from total RNA isolated from CLso-infected 1st-2nd and 4th-5th nymphs and teneral adults and CLso-infected tomato plants in which CLso infection is thought to occur without SC1-SC2 replication. Gene/loci expression was host-dependent and varied with the psyllid developmental stage. Loci previously associated with repressor-anti-repressor regulation in the "Ca Liberibacter asiaticus"-prophage pathosystem, which maintains the lysogenic cycle in Asian citrus psyllid Diaphorina citri, were expressed in CLso-infected psyllids but not in CLso-infected tomato plants.

The type IVc pilus: just a Tad different

Bacteria utilize type IV pili (T4P) to interact with their environment, where they facilitate processes including motility, adherence, and DNA uptake. T4P require multisubunit, membrane-spanning nanomachines for assembly. The tight adherence (Tad) pili are an Archaea-derived T4P subgroup whose machinery exhibits significant mechanistic and architectural differences from bacterial type IVa and IVb pili. Most Tad biosynthetic genes are encoded in a single locus that is widespread in bacteria due to facile acquisition via horizontal gene transfer. These loci experience extensive structural rearrangements, including the acquisition of novel regulatory or biosynthetic genes, which fine-tune their function. This has permitted their integration into many different bacterial lifestyles, including the Caulobacter crescentus cell cycle, Myxococcus xanthus predation, and numerous plant and mammalian pathogens and symbionts.

The functional decline of tomato plants infected by Candidatus Liberbacter solanacearum: an RNA-seq transcriptomic analysis

Introduction

Candidatus Liberibacter solanacearum (CLso) is a regulated plant pathogen in European and some Asian countries, associated with severe diseases in economically important Apiaceous and Solanaceous crops, including potato, tomato, and carrot. Eleven haplotypes of CLso have been identified based on the difference in rRNA and conserved genes and host and pathogenicity. Although it is pathogenic to a wide range of plants, the mechanisms of plant response and functional decline of host plants are not well defined. This study aims to describe the underlying mechanism of the functional decline of tomato plants infected by CLso by analyzing the transcriptomic response of tomato plants to CLso haplotypes A and B.

Methods

Next-generation sequencing (NGS) data were generated from total RNA of tomato plants infected by CLso haplotypes A and B, and uninfected tomato plants, while qPCR analysis was used to validate the in-silico expression analysis. Gene Ontology and KEGG pathways were enriched using differentially expressed genes.

Results

Plants infected with CLso haplotype B saw 229 genes upregulated when compared to uninfected plants, while 1,135 were downregulated. Healthy tomato plants and plants infected by haplotype A had similar expression levels, which is consistent with the fact that CLso haplotype A does not show apparent symptoms in tomato plants. Photosynthesis and starch biosynthesis were impaired while starch amylolysis was promoted in plants infected by CLso haplotype B compared with uninfected plants. The changes in pathway gene expression suggest that carbohydrate consumption in infected plants was more extensive than accumulation. In addition, cell-wall-related genes, including steroid biosynthesis pathways, were downregulated in plants infected with CLso haplotype B suggesting a reduction in membrane fluidity, cell signaling, and defense against bacteria. In addition, genes in phenylpropanoid metabolism and DNA replication were generally suppressed by CLso infection, affecting plant growth and defense.

Discussion

This study provides insights into plants' defense and functional decline due to pathogenic CLso using whole transcriptome sequencing and qPCR validation. Our results show how tomato plants react in metabolic pathways during the deterioration caused by pathogenic CLso. Understanding the underlying mechanisms can enhance disease control and create opportunities for breeding resistant or tolerant varieties.