Publications

3989

AbstractThis study reports the draft genome ofCandidatusPhytoplasma pyri strain P1, isolated from Argentina, marking the first global sequencing of this species. The genome assembly consisted of 16 contigs, with a total length of 575,431 bp, a GC content of 20.35%, and 125X coverage. A total of 536 genes were annotated, including those related to metabolism, genetic information processing, and signaling. Phylogenetic analysis placed ‘CandidatusPhytoplasma pyri’ within the 16SrX group, supporting its classification as a distinct species from ‘CandidatusPhytoplasma mali’ and ‘CandidatusPhytoplasma prunorum’, despite their close evolutionary proximity. The investigation also identified 17 secreted proteins, including homologs of known effectors such as SAP39 and SAP41, as well as conserved proteins associated with virulence mechanisms. A homologue of the Imp immunodominant membrane protein was also characterized, revealing conserved gene organization across related strains. These findings contribute to the understanding of ‘CandidatusPhytoplasma pyri’ pathogenic and provide valuable genomic data for future research. This study highlights the importance of expanding phytoplasma genomics, as it provides a crucial first step in understanding ‘CandidatusPhytoplasma pyri’ and its role in plant pathology

ABSTRACT “Candidatus Dehalogenimonas loeffleri” strain W, isolated from estuarine sediments, can dechlorinate 1,2-dichloroethane under high salinity. Its genome consists of a circular 1,772,240-bp chromosome with a G + C content of 52.5% and encompasses 1,763 protein-coding sequences, including 28 genes encoding reductive dehalogenases.

ABSTRACT The complete genome of “ Candidatus Phytoplasma solani” GOE was obtained from the infected vector Pentastiridius leporinus by single-molecule real-time sequencing. This 16SrXII-P phytoplasma is associated with the economically important sugar beet disease “syndrome basses richesses.” The genome sequence is an essential resource for diagnosis and understanding pathogen–host interaction.

ABSTRACTThis study explores the metabolic implications of dual substrate uptake in“Candidatus Accumulibacter”, focusing on the co-consumption of volatile fatty acids and amino acids under conditions typical of enhanced biological phosphorus removal (EBPR) systems. Combining batch tests from highly enriched “Ca.Accumulibacter” cultures with conditional flux balance analysis (cFBA) predictions, we demonstrated that co-consumption of acetate and aspartate leads to synergistic metabolic interactions, lowering ATP loss compared to individual substrate consumption. The metabolic synergy arises from the complementary roles of acetate and aspartate uptake: acetate uptake provides acetyl-CoA to support aspartate metabolism, while aspartate conversion generates NADH, reducing the need for glycogen degradation during acetate uptake. We termed this type of metabolic interaction as reciprocal synergy. We further expanded our predictions to uncover three types of interactions between catabolic pathways when substrates are co-consumed by “Ca.Accumulibacter”: (i) neutral, (ii) one-way synergistic and (iii) reciprocal synergistic interactions. Our results highlight the importance of network topology in determining metabolic interactions and optimizing resource use. These findings provide new insights into the metabolism “Ca.Accumulibacter” and suggest strategies for improving EBPR performance in wastewater treatment plants, where the influent typically contains a mixture of organic carbon compounds.SynopsisThis research demonstrates how dual substrate uptake by “Ca.Accumulibacter” enhances metabolic efficiency in EBPR by reducing global ATP losses through optimization of storage polymer usage.

An ongoing outbreak of X-Disease, associated with ‘Candidatus Phytoplasma pruni’ has resulted in severe economic losses for cherry and stone fruit growers in the U.S. Pacific Northwest in the last decade. Given that this pathogen is transmitted by polyphagous leafhopper species, primarily Colladonus montanus ssp. reductus and C. geminatus in the PNW, alternative plant hosts present a significant management concern. Here we surveyed phytoplasma incidence in non-Prunus plants found in and around stone fruit orchard borders and compared these results to the leafhopper feeding patterns through gut content analysis. We confirmed ‘Ca. P. pruni’ infection in 21 plant species from 15 families. Of these, 15 species were commonly found in the diets of phytoplasma-carrying leafhoppers. Due to the abundance of common species, including Taraxacum, Malva, and Trifolium spp., alternative hosts were found across all growing seasons, although ‘Ca. P. pruni’ titer was low (<102 cells) in most of these hosts. No geographic patterns were identified, instead phytoplasma incidence and spread at individual orchards was related to the management of annual and biennial host species, thus removing preferred leafhopper feeding hosts. These data suggest alternative host removal, along with removal of infected trees, is an effective means of slowing disease spread.

Following a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes.

Citrus Huanglongbing (HLB) represents a significant threat to the citrus industry, mainly caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas). In this review, we summarize recent advances in understanding the relationship between citrus and CLas, particularly examining the functions of Sec-dependent effectors (SDEs) and non-classically secreted proteins (ncSPs) in virulence, as well as their targeted interactions with citrus. We further investigate the impact of SDEs on various physiological processes, including systemic acquired resistance (SAR), reactive oxygen species (ROS) accumulation, vesicle trafficking, callose deposition, cell death, autophagy, chlorosis and flowering. Additionally, we focus on the functional research on specific disease-resistant genes in citrus and the molecular mechanisms underlying disease resistance. Finally, we discuss the existing gaps and unresolved questions regarding citrus-CLas interactions, proposing potential solutions to facilitate the development of HLB-resistant citrus varieties.

ABSTRACT Korea, being surrounded by the sea, provides a rich habitat for marine sponges, which have been a prolific source of bioactive natural products. Although a diverse array of structurally novel natural products has been isolated from Korean marine sponges, their biosynthetic origins remain largely unknown. To explore the biosynthetic potential of Korean marine sponges, we conducted metagenomic analyses of sponges inhabiting the East Sea of Korea. This analysis revealed a symbiotic association of Candidatus Entotheonella bacteria with Halichondria sponges. Here, we report a new chemically rich Entotheonella variant, which we named Ca . Entotheonella halido. Remarkably, this symbiont makes up 69% of the microbial community in the sponge Halichondira dokdoensis . Genome-resolved metagenomics enabled us to obtain a high-quality Ca . E. halido genome, which represents the largest (12 Mb) and highest quality among previously reported Entotheonella genomes. We also identified the biosynthetic gene cluster (BGC) of the known sponge-derived Halicylindramides from the Ca . E. halido genome, enabling us to determine their biosynthetic origin. This new symbiotic association expands the host diversity and biosynthetic potential of metabolically talented bacterial genus Ca . Entotheonella symbionts. IMPORTANCE Our study reports the discovery of a new bacterial symbiont Ca . Entotheonella halido associated with the Korean marine sponge Halichondria dokdoensis . Using genome-resolved metagenomics, we recovered a high-quality Ca . E. halido MAG (Metagenome-Assembled Genome), which represents the largest and most complete Ca . Entotheonella MAG reported to date. Pangenome and BGC network analyses revealed a remarkably high BGC diversity within the Ca . Entotheonella pangenome, with almost no overlapping BGCs between different MAGs. The cryptic and genetically unique BGCs present in the Ca . Entotheonella pangenome represents a promising source of new bioactive natural products.