Publications

3979

‘Candidatus Phytoplasma ulmi’ (16SrV-A) is the causal agent of elm yellows (EY), a lethal and/or decline disease of several Ulmus (elm) species and hybrids in North America and Europe. In this study, field observations and PCR assays were used to detect phytoplasma infections in diseased U. minor, U. pumila and U. glabra trees in southern Italy. Also, a multigene sequence analysis employing various less conserved genes was carried out to explore the genetic variation in detected strains. All the symptomatic elm trees tested were infected with ‘Ca. Phytoplasma ulmi’. No other phytoplasmas or variants could be detected. Although ‘Ca. Phytoplasma ulmi’ was already known to occur in southern Italy on European field elm, the current work expands the information on the presence, disease incidence and severity, plant host range and molecular aspects of EY phytoplasma strains occurring in southern Italy. In addition, this is the first report from Italy on the molecular characterization of EY phytoplasma strains through map, imp and groEL gene sequence and phylogenetic analyses. Among the newly detected EY phytoplasma strains, some proved distantly related to each other and to other previously characterized EY phytoplasma strains within the genes examined. This implies the presence of distinct taxonomic entities within the material examined. The occurrence of different strains was not linked to the biological traits and geographical distribution. However, the data obtained may provide a basis for further studies aimed at elucidating several other unknown aspects of the EY agent, knowledge of which is essential for effective disease management and control strategies. The results of the current work also show that the EY phytoplasma is particularly widespread in southern Italy and is of considerable economic and ecological relevance.

Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.

Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs) and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the species Patescibacterium danicumTS gen. Nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicumTS in the class ABY1 within Ca. Patescibacteria. Based on these results, we propose Patescibacterium gen. Nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. Nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (< 1Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, this effort, focused on the fourth-largest phylum in the bacterial domain, aims to provide nomenclatural stability in the scientific literature.

AbstractThe poinsettia (Euphorbia pulcherrimaWilld. ex Klotzsch.) is one of Turkey’s most important potted ornamental crops. Potted poinsettia plants exhibiting smaller-sized brilliant red bracts against the green leaves with free-branching were collected from commercial florists in three provinces of Turkey. In iPhyClassifier analysis, the query 16SrDNA sequences of our isolates shared 99.58% identity with that of theCandidatusPhytoplasma pruni. Our leaf samples consistently yielded a product of 0.7 kb by PCR with primers (KFD4F/KFD4R), which was newly designed based on X-Disease group (16SrIII) of phytoplasma secY sequences available in GenBank. The partial 16S rRNA sequences were used for phylogenetic analyses covering 41 taxa from the group of 16SrIII’Candidatus Phytoplasma’ strains, including 14 strains causing disease on poinsettia worldwide. The sequences that caused the same disease in poinsettia plants in Finland, the USA, Mexico, Taiwan, Japan, Korea, and Canada, including three strains from Turkey, formed a mono-phylogenetic group with a support value of 87%.

AbstractThe endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.

The global citrus industry faces a great threat from Huanglongbing (HLB), a destructive disease caused by ‘Candidatus Liberibacter asiaticus’ (CLas) that induces significant economic losses without any known cure. Understanding how citrus plants defend against HLB, particularly at the early stages of infection, is crucial for developing long-term solutions. This study investigated the earliest metabolic responses of fresh citrus leaves to CLas infection using untargeted metabolomics and machine learning models. HLB-tolerant and HLB-sensitive cultivars were compared to analyze their biochemical reactions within 48 hours post-infection. HESI/Q-Orbitrap MS analysis identified temporal differential metabolites, revealing distinct metabolic pathways activated in response to CLas infection. Both cultivars responded by increasing specific metabolite concentrations, such as flavonoids, within 2 hours post-infection, but the HLB-tolerant cultivar maintained higher levels throughout the 48-hour period. This early metabolic activity could influence long-term plant health by enhancing disease resistance and reducing pathogen impact. These findings provide potential biomarkers for breeding HLB-resistant cultivars and offer valuable insights for developing sustainable management strategies to mitigate the impact of HLB on the citrus industry, ensuring its long-term productivity and economic viability.

AbstractBACKGROUNDHuanglongbing (HLB) is the primary and most destructive disease affecting citrus, caused by a pathogen transmitted by an insect vector, Diaphorina citri. There are no curative methods for the disease, and rapid and accurate methods are needed for early detection in the field, even before symptoms appear. These will facilitate the faster removal of infected trees, preventing the spread of the bacteria through commercial citrus orchards.RESULTSIt was possible to determine ranges of hyperspectral bands that demonstrated significant differences in relative reflectance between treatments consisting of healthy and infected plants from the first days of evaluation, when plants infected with ‘Candidatus Liberibacter asiaticus’ (CLas) were still in the asymptomatic stage of the disease. From the Week 2 of evaluation [58 days after infection (DAI) of plants] until the last week, spectral differences were detected in the red edge region (660–750 nm). From the Week 6 onwards (86 DAI), spectral differences between healthy and symptomatic plants were observed in bands close to the visible region (520–680 nm).CONCLUSIONSpectral differences were detected in the leaves of C. sinensis infected by CLas before the appearance of symptoms, making it feasible to use the hyperspectral sensor to monitor the disease. Our results indicate the need for future studies to validate the use of hyperspectral sensors for managing and detecting HLB in commercial citrus orchards, contributing to the integrated management of the disease. © 2024 Society of Chemical Industry.