Publications

4861

Sweet potato witches’ broom disease caused by phytoplasmas threatens crop productivity in Fujian, China. Here, we report a complete phytoplasma genome consisting of a single circular chromosome (680,179 bp with a G + C content of 29.44%) via the next-generation sequencing of sweet potato witches’ broom-infected samples. A total of 730 genes were predicted, and two 16S rRNAs were revealed to be identical to sequences in ‘ Candidatus Phytoplasma australasiaticum’. Following the latest guidelines for the description of phytoplasma species, we have named the strain ‘ Candidatus Phytoplasma australasiaticum’ SPWBPT2024. The genome contained 33 transporters, 35 putative effectors (including SAP11 and SAP54 with multiple copies), and 2 potential mobile units. Analyses of published peanut and sweet potato phytoplasma genomes revealed similarities between their effectors and the effectors in this phytoplasma genome. A motif analysis was performed to clarify the difference between the two SAP54 copies in the obtained phytoplasma genome, as well as the trends in conserved motifs in other strains. In addition, metabolic pathway-related genes in three genomes were examined, revealing deficiencies in the glycolysis and pyrimidine synthesis pathways. A pangenome analysis revealed that the phytoplasma genome is an open genome. To gain further insights into whole-cell metabolic processes, we reconstructed draft genome-scale metabolic models of the genome. This study provides valuable genomic insights into this phytoplasma, characterizing conserved and strain-specific SAP effectors, as well as distinct metabolic deficiencies that may help advance research to combat phytoplasma infections, including accurate diagnostics, vector transmission control, and antimicrobial interventions.

ABSTRACT Ubiquitin‐proteasome is a conserved mechanism that regulates cellular responses and disease resistance in plants. However, the regulatory role of ubiquitin‐proteasome in the pathogenicity of “ Candidatus Liberibacter asiaticus” ( C Las), the causal agent of citrus huanglongbing (HLB), one of the most serious citrus diseases, remains poorly defined. In this study, we demonstrated that CLIBASIA_04250 (SDE4250) suppresses 26S proteasome activity in citrus, leading to a reduction in salicylic acid (SA) levels and downregulation of SA‐responsive genes. Further investigation revealed that SDE4250 specifically targets the citrus 26S proteasome non‐ATPase regulatory subunit 4 homologue (CsRPN10) and enhances its degradation via the 26S proteasome pathway. Moreover, overexpression of CsRPN10 inhibited C Las proliferation in citrus hairy roots, which was accompanied by a significant accumulation of SA content and upregulation of related defence genes. Collectively, our findings indicate that SDE4250 targets the citrus 26S proteasome to disrupt SA‐mediated citrus immunity.

Abstract Environmental genomics has led to the discovery of many new lineages of archaea, including “DPANN” (or Nanobdellati), comprising organisms with small genomes, reduced gene content, and potentially symbiotic or parasitic lifestyles. DPANN live in various environments, and several lineages have been identified that are adapted to extremely high-salt concentrations, including the Nanohaloarchaeota. Since it was long thought that the Haloarchaea (within “Euryarchaeota”) were the only high salt-adapted archaea, the origins of these genome-reduced halophiles have been debated. Here, we used phylogenetic, comparative genomic, and gene tree-species tree reconciliation approaches to resolve the evolution of halophily within DPANN, making use of recently published genomes that help to inform the phylogenetic placement and genome evolution of salt-adapted lineages. Phylogenetic analysis placed Nanohaloarchaeota sister to a previously uncharacterized lineage, which we here refer to as Terrarchaeota. Terrarchaeota appear to be predominantly anaerobic thermophiles that are not adapted to high-salt concentrations, indicating that adaptation to high salt evolved after their divergence from Nanohaloarchaeota. Furthermore, our analyses identified genomic hallmarks of salt adaptation in another recently discovered halophilic DPANN lineage within Aenigmatarchaeota, the Haloaenigmatarchaeaceae. We found that the Nanohaloarchaeota and Haloaenigmatarchaeaceae have distinct sets of proteins that enable life at high salt concentrations but share a common mechanism of evolutionary adaptation, in which niche-relevant genes were acquired horizontally from their halophilic hosts. This work provides the first detailed investigation into the enigmatic Terrarchaeota, and new insights into the convergent evolution of high salt adaptation within symbiotic clades of Archaea.

Citrus huanglongbing (HLB), caused by ‘Candidatus Liberibacter asiaticus’ (CLas), is a destructive disease threatening global citrus industry. Although citrus cultivars differ in HLB sensitivity, how infection alters endophytic bacterial communities in cultivars with contrasting susceptibility remains unclear. Here, we compared endophytic microbiome shifts in leaf and root tissues of HLB-susceptible Shatangju mandarin (Citrus reticulata cv. Shatangju) and HLB-tolerant Shatian pomelo (C. maxima cv. Shatian) at 10 months postgrafting with CLas-infected buds. Infected Shatangju mandarin showed severe symptoms and higher CLas levels in leaves than in roots, while infected Shatian pomelo remained asymptomatic with higher CLas in roots than in leaves. High-throughput 16S rRNA gene sequencing revealed that CLas infection restructured the endophytic microbial community in a tissue-specific manner. CLas-infected Shatian pomelo leaves displayed increased microbial diversity and network complexity, while CLas-infected Shatangju mandarin roots harbored more disease-suppressive taxa like Streptomyces. Across both cultivars, network complexity correlated inversely with CLas abundance. Key genera (e.g., Pseudomonas, Streptomyces, and Prevotella) correlated positively with CLas, suggesting roles in mitigating pathogen effects. Predicted functional profiling indicated activated pathways (amino acid metabolism, terpenoid/polyketide biosynthesis, and xenobiotic biodegradation) potentially supporting host defense in infected tissues. The HLB tolerance of Shatian pomelo appeared linked to tissue-specific bacterial restructuring, particularly recruitment of antibiotic-producing bacteria and enhanced metabolic resilience. These findings elucidated cultivar-specific microbial strategies against CLas, offering insights for microbiome-mediated HLB management.

ABSTRACT Insect‐vectored pathogens pose a significant threat to global agriculture. The colonization efficiency of pathogens in vectors plays a central role in these pathosystems, yet studies of the factors that affect this aspect are limited. This study investigates the genetic and microbial symbiont factors influencing the susceptibility of Diaphorina citri to Candidatus Liberibacter asiaticus ( C Las), the pathogen causing citrus greening disease (huanglongbing). Through a microbiome Genome Wide Association Study (mGWAS) based on 16S amplicon sequencing and genomic resequencing of 120 D. citri individuals from six populations, we identified 79 SNPs significantly associated with the relative abundance of C Las within insects. Additionally, some of these SNPs were also associated with the relative abundance of Candidatus Profftella armature, a key endosymbiont of D. citri . SNPs in the regulatory region of gene Dcitr04g11610.1 led to its overexpression in C Las‐susceptible D. citri , and C Las infection further elevated its expression. Conversely, RNAi knockdown of Dcitr04g11610.1 reduced C Las infection rates and abundance, accompanied by increased abundance of Profftella . Phylogenetic analysis revealed Dcitr04g11610.1 ’s high homology to Major Facilitator Superfamily‐type transporter SLC18B1 proteins, suggesting a role in C Las polyamine utilization. These findings highlight the importance and potential interplay of insect genetics and symbiotic microbiota in insect‐vectored plant pathogen systems.

'Candidatus Phytoplasma solani' is a distinct species of the class Mollicutes (16SrXII group), characterized by phloem-limited localization and strong host dependence. It is widely distributed, mainly in Europe, and affects over 100 plant species, including economically important crops for Moldova. The name reflects its significant impact on plants of the Solanaceae family, causing stolbur disease. It also infects grapevine, pepper, maize, lavender, and other crops. Climate change has favored the spread of the pathogen and its insect vectors into new regions and host plants. Therefore, monitoring and controlling its dissemination in economically important crops is essential. Accurate diagnosis can be achieved by molecular methods, with PCR-based techniques offering a reliable and cost-effective approach. The aim of the study was to determine the presence or absence of infection in some agricultural crops: tomato, maize, potato, pepper, eggplant, wheat, plum and apple growing in experimental fields of Institute of Genetics, Physiology and Plant Protection, MSU. Materials and methods: Various DNA extraction methods were used depending on plant culture: boiling in alkaline solution, DNAzol, SDS, CTAB. Nested PCR analysis was carried out using specific to 'Ca. P. solani' primers designed on the base of chaperonine or 16S rRNA gene sequences. Amplification results were recorded using gel agarose electrophoresis (1.5% agarose, 0.5 x TBE buffer) stained with ethidium bromide and visualized in UV. Results: A comprehensive study of tomato conducted during 2016-2025 showed the continuous presence of the pathogen, with infection rates reaching up to 72% depending on annual conditions, confirming the high susceptibility of tomato to 'Ca. P. solani'. In potato, 14.6% of plants were infected, while sweet pepper showed a much lower incidence of 4%. Overall, the results indicate the predominant distribution of the pathogen within the Solanaceae family, further supported by its detection in the ruderal species Solanum nigrum. The phytoplasma was not detected only in eggplant among the analyzed Solanaceae species. In contrast, molecular diagnostics gave negative results in crops from other families, including maize and wheat (cereals), as well as apple and plum (fruit crops). The pathogen was not detected in orchard trees during either the dormant or fruit-bearing stages. Conclusions: Thus, obtained results demonstrate an ecological and epidemiological specificity of 'Ca. P. solani' for certain host species, characterized by a high incidence in Solanaceae, particularly tomato. Additionally, the study confirms the potential role of ruderal species within the same family as natural reservoirs of the pathogen. These data contribute to a deeper understanding of the spread of the phytoplasma providing a base for effective monitoring and phytosanitary management strategies.

Abstract Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately one hundred cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.