Publications

4467

Abstract The candidate phylum Cloacimonadota is frequently detected in anaerobic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood due to the lack of cultured representatives. Metagenomic evidence suggests capacities for amino acid fermentation, cellulose degradation, and production of carbohydrate-active enzymes, with particular interest in their presumed role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from a lab-scale anaerobic baffled reactor fed with sugar beet pulp, where a sharp increase in an uncultured Cloacimonadota OTU coincided with recovery of methanogenesis and enhanced methane production. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of this OTU, complemented by a curated database of 47 genome-resolved Cloacimonadota species. Comparative genomics revealed conserved protein clusters indicative of an alternative mmc pathway, suggesting that this variant of the SPO pathway is a widespread, phylum-specific trait potentially linked to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a primary syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

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, while 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 two potential mobile units. Analyses of published peanut and sweet potato phytoplasma genomes revealed the 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 pan-genome analysis has 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 (GEMs) of the genome. This study provides valuable genomic insights into this phytoplasma, characterising 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.

Insecticide applications are commonly recommended for managing Diaphorina citri, the vector of huanglongbing (HLB), but their effectiveness in reducing transmission of ‘Candidatus Liberibacter asiaticus’ (CLas), especially during continuous psyllid influx and shoot growth, remains unclear. This study evaluated the efficacy of foliar application of thiamethoxam and spinetoram in reducing CLas transmission in sweet orange seedlings. Two experiments were conducted up to 13th days after first spray. In experiment #1, CLas-positive psyllids were confined in seedlings every two days. Treatments were: control; S14 — one spray at day 0; and S7 — sprays at days 0 and 7. In experiment #2, psyllids were released for free choice within a screenhouse every two days. Treatments were: control; S14; S7; and S3 — sprays at day 0 and every 3 days. Sprays on day 0 were over unfolded leaves (V2 stage). Psyllid mortality was assessed in experiment #1. Psyllid occupancy (percentage of seedlings with at least one psyllid) and abundance (number of psyllids per seedling) were assessed in experiment #2. After 6 months, seedlings were tested for CLas by qPCR. In experiment #1, cumulative psyllid mortality was higher in sprayed treatments than control for both insecticides, but HLB incidence was similar. In experiment #2, both psyllid occupancy and abundance decreased with shorter spray intervals, with the lowest HLB incidence in S3. These findings suggest that reducing spray intervals can limit CLas transmission during periods of shoot growth and continuous vector pressure. However, CLas transmission was not entirely prevented, highlighting the need for integrated, area-wide management strategies.

Brinjal little leaf (BLL) disease, caused by phytoplasmas, leads to significant yield losses, but its pathogenic mechanisms remain poorly understood. This study characterizes SAP54LP/S54LP (SAP54-like protein of BLL), an effector protein associated with the 16SrVI-D phytoplasma strain linked to BLL in Tamil Nadu, India. Molecular analyses, including nested PCR and virtual RFLP, confirmed the phytoplasma's classification within the 16SrVI group. The S54LP effector gene was amplified from infected brinjal, confirming its presence. Sequence comparisons showed that S54LP was 100 % identical to homologs in the 16SrVI-A group and 98 % identical to those in the 16SrIB group (phyl1 and S54LP), indicating group-specific divergence. Comparative analysis identified 13 single nucleotide polymorphisms (SNPs), 69 % of which led to nonsynonymous substitutions in the mature protein, potentially affecting host interactions. Haplotype network analysis revealed a globally distributed Hap_6 lineage and region-specific haplotypes, suggesting localized evolutionary dynamics. Evolutionary analysis indicated strong purifying selection on the coding sequence (Ka/Ks ≈ 0.3), reflecting the conservation of functional domains essential for pathogenicity. Conversely, positive selection was detected in the signal peptide region, implying adaptive evolution related to secretion and host targeting. Additionally, AT-rich codon usage at specific sites highlights multiple layers of evolutionary constraints shaping S54LP. Overall, these findings establish S54LP as a model for studying host-phytoplasma coevolution, providing insights into effector biology and informing strategies to manage phytoplasma diseases in crops.

Background New tick-borne pathogens are being discovered worldwide, and recognized tick-borne diseases are becoming increasingly diverse. Candidatus R. jingxinensis is endemic in Asia, but its potential to cause clinical infection in humans remains unclear. This study was designed to elucidate the prevalence and delineate the clinical profile of Candidatus Rickettsia jingxinensis infection in Liaoning Province, China. Methods The subjects of this study were suspected cases of tick-borne infectious diseases admitted to the First Affiliated Hospital of China Medical University or reported to the Liaoning Provincial Center for Disease Control and Prevention in 2018–2022. Epidemiological and clinical data were collected. Tick-borne pathogens were detected with a microfluidic chip detection system, and specific gene fragments of the screened pathogens were amplified, sequenced, and compared. Evolutionary and phylogenetic trees were constructed and analyzed. Results In total, 398 infected subjects from 14 cities were included in the study, and 255 tick-borne pathogens were detected. Among these, 11 subjects were found to be infected with Candidatus Rickettsia jingxinensis. This is the first time this strain has been shown to cause infection and illness in humans. The main clinical features of subjects infected with Candidatus R. jingxinensis included fever, fatigue, dizziness, headache, nausea, diarrhea, general pain or muscle and joint pain, reduced leukocytes and platelets, abnormal coagulation function and liver function. Conclusions This study documents the first human infections with Candidatus R. jingxinensis, confirms its prevalence in Liaoning Province, and delineates the primary clinical manifestations of the disease.

Abstract Cable bacteria are filamentous microorganisms capable of centimeter‐scale electron transport, which have great impacts on sediment biogeochemistry, especially oxygen consumption and sulfide depletion. While 16S rRNA sequences related to known cable bacteria have been identified in saline lakes, their genomic diversity, metabolic potentials, and evolution remain unknown. Eight cable bacteria genomes were retrieved from 23 sediment metagenomes across four saline lakes, representing five novel species adapted to different salinity niches. A deep‐branching Electronema species, named Electronema qinghaiense , was found preferentially in brackish to saline environments, implying an ecological and evolutionary link between marine and freshwater lineages. Based on genome analysis, the three newly named cable bacteria species are likely mixotrophic diazotrophs capable of degrading diverse complex carbohydrates, while also participating in hydrogen metabolism via various groups 3 and 4 [NiFe]‐hydrogenases. Genome streamlining and horizontal gene transfer likely drove ecophysiological differentiation among these Electrothrix and Electronema species, including an interphylum horizontal transfer of glycine/sarcosine N‐methyltransferase ( gsmt ) and sarcosine/dimethylglycine N‐methyltransferase ( sdmt ) genes into their common ancestor. Subsequent loss of these genes in some descendants led to adaptation to different salinity niches. Given the inferred ancestral physiological properties, phylogenomic analysis and the evidence that “freshwater” Electronema species experienced stronger purification selection than “saline” Electronema and “hypersaline” Electrothrix species, the evolutionary progression of cable bacteria occurred most likely in the saline‐to‐freshwater direction. Additionally, cable bacteria ecotypes adapted to specific salinity niches likely formed from selective sweeps with low homologous recombination. Collectively, these findings deepen our understanding of the ecophysiology and evolution of cable bacteria.