Publications

3996

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.

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.

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.

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.

Phytoplasma, a potentially hazardous pathogen associated with witches’ broom, is an economically harmful disease-producing bacteria that damages chilli cultivation. Phytoplasma-infected plants display various symptoms that indicate significant disruptions in normal plant physiology and behaviour. Diseases caused by phytoplasma are widespread and have a major economic impact on crop quality and yield. This work focuses on identifying and examining chilli microRNAs (miRNAs) as potential targets against the 16S rRNA and secA gene of “Candidatus Phytoplasma trifolii” (“Ca. P. trifolii”) through plant miRNA prediction algorithms. Mature chilli miRNAs (CA-miRNAs) were collected and used to hybridise the 16S rRNA and secA genes. A total of four common CA-miRNAs were picked according to genetic consensus. Three algorithms applied in the present study suggested that the physiologically relevant, top-ranked miR169b_2 has a possibly specific site at nucleotide position 1,006 for targeting the ‘Ca. P. trifolii’ 16S rRNA gene. The circos algorithm was then utilised to create the miRNA-mRNA regulatory network. The free energy between the miRNA:mRNA duplex was also computed, and the best value of −17.46 kcal/mol was obtained for CA-miR166c_2. Currently, there are no suitable commercial ‘Ca. P. trifolii’-resistant chilli crops. As a result, the expected biological data provide useful evidence for developing ‘Ca. P. trifolii’-resistant chilli plants.

Citrus Huanglongbing (HLB) is caused by the phloem-limited α-proteobacterium ‘Candidatus Liberibacter spp.’, among which ‘Ca. L. africanus’ (CLaf) has posed a significant threat to citrus production in Africa for nearly a century. CLaf is closely related to the globally prevalent ‘Ca. L. asiaticus’ (CLas), whereas little is known about the virulence of CLaf, primarily because of limited genome resources. In this study, we completed the whole-genome assembly and annotation of the CLaf strain Zim (from Zimbabwe). Compared with CLas, a total of 102 CLaf unique genes were identified, including 14 potential Sec-dependent effector (SDE) genes, 29 phage-associated genes, and 59 genes with hypothetical function. Among 14 SDEs, V9J15_03810 was able to induce a significant hypersensitive response in Nicotiana benthamiana, indicating its potential as a virulence factor for CLaf. Genome analysis showed that the CLaf strain Zim genome harbored a complete prophage region (named P-Zim-1, 42,208 bp). P-Zim-1 retained two immunosuppressive peroxidase genes (V9J15_02125 and V9J15_02130) homologous to CLas prophage SC1/SC2, whereas the lysogen-associated genes encoding integrase (V9J15_01970) and repressor (V9J15_02080) were homologous to the prophage of ‘Ca. L. solanacearum’, the causal agent of potato zebra chip disease. In addition, P-Zim-1 carried a novel CRISPR/Cas system, including a CRISPR array (located within V9J15_02040, ranging from 443,643 to 443,897) and five CRISPR-related Cas proteins (V9J15_02005, V9J15_02010, V9J15_02015, V9J15_02025, and V9J15_02035). This study first characterized the unique genomic feature of CLaf related to virulence and prophage, which will facilitate future research on CLaf biology and African HLB management.

El maíz (Zea mays L.) se ha constituido como el cultivo de mayor importancia económica a nivel mundial; esté cereal perteneciente a la familia Poaceae, es originario de México y utilizado tanto para consumo humano como ganadero. En México, su importancia va mucho mas allá de lo económico, su influencia a nivel social y cultural se ha visto plasmada en los vestigios de civilizaciones antiguas como la establecida por los mayas, para quienes el maíz tenía un significado religioso; sin embargo, algunos factores bióticos como bacterias, virus, hongos y fitoplasmas pueden limitar la producción de las diversas variedades de maíz cultivadas en territorio mexicano. Durante el ciclo de cultivo 2021, se colectaron plantas de maíz presentes en parcelas comerciales en el municipio de Valparaiso, Zacatecas, México las cuales presentaban una sintomatología relacionada con la presencia de fitoplasmas (enanismo, cambios de color en hojas de verde a blanco, declive general y muerte); además, se muestrearon plantas de maiz asintomáticas como testigos e insectos de la especie Dalbulus maidis. Las muestras se analizaron mediante la reacción en cadena de la polimerasa (PCR) anidada utilizando la combinación de oligonucleótidos universales P1/Tint, seguida por el par de oligonucleótidos R16F2n/R16R2 con lo que se logró obtener secuencias del gen 16S rDNA de fitoplasmas. Los análisis filogenético y RFLP virtual de las secuencias de 16S rDNA obtenidas a partir de las muestras analizadas mostraron una identidad de secuencia del 100% entre sí y una identidad de secuencia del 99.7 % con el gen homólogo de Candidatus Phytoplasma asteris (accesión del GenBank M30790). La incidencia de esta nueva enfermedad fue del 15 % en los cultivos muestreados. Estos resultados relacionan a Dalbulus maidis y a Candidatus Phytoplasma asteris como pobible vector y agente causal de una nueva sintomatología en maiz.