Publications

4482

We present a genome assembly from a specimen of Ctena decussata (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1,658.05 megabases. Most of the assembly (97.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 53.28 kilobases in length. The genome of Candidatus Thiodiazotropha sp. CDECU1, a bacterium associated with C. decussata was also assembled,

Most micro-organisms remain unculturable under standard laboratory conditions, limiting our understanding of microbial diversity and ecological interactions. One major cause of this uncultivability is the loss of access to essential cross-fed metabolites when bacteria are removed from their natural communities. During a bioprospecting campaign targeting actinomycetes of an Apis mellifera beehive, we identified five isolates (DT32, DT45T, DT55, DT59 and DT194) that required co-cultivation for growth recovery, suggesting a dependence on microbial interactions in their native habitat. Whole-genome sequencing and phylogenetic analysis positioned these isolates within a distinct lineage of Micromonosporaceae, separate from the five officially recognized clades of the Micromonospora genus. A combination of microscopic, chemotaxonomic and physiological characterizations further supported their uniqueness. Notably, they exhibited high auxotrophy, being unable to use all carbon sources tested, likely due to genome reduction (4.6 Mbp) compared to other Micromonosporaceae. Pangenomic comparisons with their closest Micromonospora relatives revealed gene losses in key metabolic pathways, including the glyoxylate bypass and the Entner–Doudoroff pathway, which may explain their metabolic reliance. These findings reveal a highly specialized, ecologically adapted lineage with deep evolutionary divergence and further support microbial interdependence isolation strategies to explore the microbial dark matter. We propose Melissospora conviva as a novel genus and species within the Actinomycetota phylum, with isolate DT45T as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.

Abstract ‘Candidatus Liberibacter asiaticus’ (CLas), the prevalent agent associated with Huanglongbing (HLB), poses a severe threat to global citrus production. This study aimed to investigate the occurrence of psyllid species (other than Diaphorina citri) landing on citrus trees, evaluate their survival on citrus over optimal acquisition access periods (AAP), assess their ability to acquire CLas, and infer their potential role in pathogen transmission. Field surveys were conducted in Citrus sinensis plants located in backyards and poorly managed groves in two locations of São Paulo State, Brazil. Psyllids from twelve genera were identified, with Isogonoceraia divergipennis and Heteropsylla cubana being among the most constant species, showing greater abundance particularly in late winter and early spring. Controlled acquisition assays demonstrated that I. divergipennis, H. cubana, and Triozoida limbata could acquire CLas following a 72-h AAP, post-acquisition latency of 14 days and a subsequent 72-h post-latency period, with acquisition rates of 8.1%, 3.2%, and 2.4%, respectively, compared to 85.7% in D. citri. Notably, CLas was detected in the 'head-mesothorax' region only in T. limbata and D. citri, suggesting potential bacterial presence in the salivary glands and possible transmission competence. CLas titers were consistently higher in the 'metathorax-abdomen' than in the 'head-mesothorax'. While the data indicate occasional CLas acquisition by psyllids other than D. citri, there is currently no evidence supporting their role as natural vectors. Nonetheless, these species may serve as valuable models for elucidating transmission barriers in non-competent psyllids and highlight the need for further investigation into their epidemiological relevance.

ABSTRACT Psyllids (Psylloidea) are host-specific, phloem-feeding insects that are associated with the transmission of destructive plant diseases caused by the bacterial genus “ Candidatus Liberibacter”. While psyllid-liberibacter interactions have been studied in great detail, most research mainly focused on species associated with important crop diseases. Therefore, a more general understanding of the associations between these two groups of organisms remains limited. The present study investigated the occurrence of infection by “ Ca . Liberibacter” across undercharacterized psyllid lineages in Taiwan. Samples of 46 psyllid species, representing six of the seven known Psylloidea families from host plants spanning 22 families, were obtained. The presence of “ Ca . Liberibacter” in adult psyllid DNA samples was determined by PCRs targeting 16S rDNA of “ Ca . Liberibacter”. PCR tests amplifying mitochondrial 16S DNA of the psyllids were also carried out for quality confirmation. The assays detected “ Ca . Liberibacter” in five of the psyllid species tested, namely Calophya nigridorsalis , Homotoma radiata , Cacopsylla tobirae , Epipsylla albolineata , and Trioza quadrimaculata . BLASTn searches and phylogenetic analysis on near-full-length 16S rDNA sequences identified the strain detected in C. tobirae as “ Ca . Liberibacter europaeus” and showed that E. albolineata carried a strain closely related to a “ Ca . Liberibacter” strain found in Bhutan, while the remaining detected strains could potentially be novel “ Ca . Liberibacter” species. The findings from this study showed that a large diversity of “ Ca . Liberibacter” could exist among underexplored psyllid and plant species, opening new avenues for investigating the ecology of “ Ca . Liberibacter”. IMPORTANCE Bacteria of the genus “ Candidatus Liberibacter” can cause some of the most devastating plant diseases. Gaining a broader perspective on the diversity of associations between these bacteria and their psyllid vectors is crucial for both fundamental and applicative purposes. By taking advantage of the biological diversity in Taiwan, the present study conducted one of the broadest surveys on the presence of “ Ca . Liberibacter” in psyllids, in terms of the diversities of the psyllids examined. The data from this work indicated that previously unknown “ Ca . Liberibacter” genotypes and perhaps even novel species may be more prevalent among psyllid species than previously known. These findings highlight the potential importance of exploring psyllid-liberibacter associations from a broader ecological perspective.

A Gram-stain-negative, anaerobic and rod-shaped bacterium was isolated from gut of rainbow trout in Japan. The temperature range for the growth of 9N8T was 10–30 °C with an optimum at 20 °C. The organism produced acetate and butyrate when grown on AccuDia™ Gifu Anaerobic Medium broth, Modified. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 9N8T was related to the genus Fusobacterium (<92.9% similarity) and formed a distinct phylogenetic lineage from existing genera within the family Fusobacteriaceae. Strain 9N8T has a genome size of 2.60 Mb. The genomic DNA G+C content was 29.4 mol%. Average amino acid identity values between strain 9N8T and strains in the family Fusobacteriaceae ranged from 39.2 to 57.5%. The major fatty acids of strain 9N8T were C14 : 0, C16 : 1 ω7c and C16 : 0. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Piscibacter tructae, is proposed, with 9N8T (=NBRC 116745T=DSM 118263T) as the type strain.

Areca palm yellow leaf phytoplasma (AYLP) and Areca palm velarivirus 1 (APV1) are two critical pathogens associated with yellow leaf in areca palm, resulting in devastating damage to areca production. However, evidence of their co-infection remains unclear. Areca palms showing yellow leaf symptoms (suspected to be caused by phytoplasma and velarivirus 1) were surveyed and sampled around Hainan Island of China and the pathogens were identified and analyzed in the study. The results showed that infectious leaf yellowing symptoms of areca palms primarily occurred in eastern and southern cities and counties of Hainan Island. Molecular identification revealed co-infection of 'Candidatus Phytoplasma asteris' (16SrI-B subgroup) and APV1 in individual areca palm samples. Among 520 samples tested by qPCR, AYLP was detected in 23.46% (n=122), APV1 in 53.46% (n=278), and a co-infection with both AYLP and APV1 in 10.96% (n=57). A statistically significant difference in APV1 detection rate was observed between asymptomatic and symptomatic plantations (P < 0.0001), suggesting APV1 infection likely represents an important risk factor for yellowing development in cultivated areca palm populations. These results confirm the co-infection of AYLP and APV1 on Hainan Island, offering epidemiological evidence for targeted disease management.

A strictly aerobic, Gram-stain-negative, ovoid-shaped and non-motile bacterium, designated as strain MJ-SS7T, was isolated from tidal mudflat sediment collected at a macro-tidal clam farm in Gochang, Republic of Korea. Strain MJ-SS7T exhibited oxidase- and catalase-positive activities. Growth occurred at 20–37 °C (optimum: 30 °C), pH 6–8 (optimum: pH 7) and in the presence of 0–9% (w/v) NaCl (optimum: 3%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that MJ-SS7T belonged to the family Roseobacteraceae. Its closest relatives, based on sequence similarity, were Rhodophyticola porphyridii KACC 18805T (95.9%), Kangsaoukella pontilimi KCTC 72224T (95.8%) and Actibacterium pelagium JN33T (95.5%). The major fatty acids included summed feature 8 (C18:1  ω7c/C18:1  ω6c), C16:0, C16:0 2OH and C18:0. The major polar lipids consisted of phosphatidylglycerol, five unidentified phospholipids, four unidentified aminolipids, two unidentified aminophospholipids and four unidentified lipids. The major respiratory quinone was ubiquinone-10. The genome size was 5.20 Mb, with a DNA G+C content of 63.4 mol%, encoding 5,031 protein-coding genes, 3 rRNA genes and 46 tRNA genes. Comparative genomic analyses confirmed its novelty, with average nucleotide identity (<73%) and average amino acid identity (<70%) values below the species delineation thresholds. Based on polyphasic taxonomic data, strain MJ-SS7T represents a novel species of a new genus within the family Roseobacteraceae, for which the name Ovoidimarina sediminis gen. nov., sp. nov. is proposed. The type strain is MJ-SS7T (=KEMB 21436T=KCTC 8329T=JCM 36750T).

Genomic information can yield new insights into the molecular and physiological mechanisms that underpin pathogen virulence and transmission. We decode the genome of Spirobacillus cienkowskii Metchnikoff 1889, a gram-negative bacterium and one of the first described parasites of Daphnia. We use long-read sequencing and extensive annotation to assemble the complete circular genome of 2.81 Mbp with 2,486 protein-coding genes. In addition to antiviral systems, including CRISPR-Cas and restriction-modification systems, we describe the likely molecular basis of the unusual red phenotype of S. cienkowskii, which results from carotenoid production. We further describe genetic modules that may mediate this bacterium’s interactions with its host and environment. Our study provides insight into the metabolic and functional capacities of a parasite through the assessment of its genome. More generally, it demonstrates what can be learnt by applying recent advances in high-throughput sequencing to the study of parasites.