Publications

4861

Date palm is a staple food crop and crucial export agricultural commodity in Arab countries. Date palm diseases caused by phytoplasmas are devastating diseases that severely constrain the sustainable development of date palm cultivation and industry. The phytoplasmas associated with date palm diseases mainly consist of three taxa: ‘Candidatus Phytoplasma asteris’ of the 16SrI group, ‘Ca. Phytoplasma citri’ of the 16SrII group, and ‘Ca. Phytoplasma fraxini’ of the 16SrVII group. Based on the 16S rRNA gene sequences of the three groups of phytoplasmas, two sets of primer pairs (Da-1 and Da-5) enabling simultaneous visual detection of date palm phytoplasmas were designed and screened. Universal simultaneous visual detection methods were successfully established for different groups and candidate species of date palm pathogenic phytoplasmas. The whole detection procedure of this optimized method can be accomplished via isothermal amplification at 64 °C within 30–50 min, and the detection results can be directly and intuitively judged by the color variation of the reaction system. Sensitivity verification showed that for the three groups of phytoplasmas, the minimum detection limit of the Da-1 primer set for simultaneous visual detection ranged from 1 fg/μL to 10 fg/μL, while that of the Da-5 primer set ranged from 1 fg/μL to 100 pg/μL. The established LAMP assay demonstrated high sensitivity and specificity using synthetic DNA templates. This method provides a promising laboratory tool for the simultaneous visual detection of three major date palm phytoplasma groups. Further validation on naturally infected field samples is required before practical application in field diagnosis, epidemic monitoring, and port quarantine.

Abstract The demand for D-amino acids is increasing as their unique physiological role continues to be elucidated. meso-Diaminopimelate dehydrogenase catalyzes the reversible NADP+-dependent oxidative deamination of meso-diaminopimelate to produce L-2-amino-6-oxopimelate. Moreover, a few enzymes show a broad range of reductive amination activity toward 2-oxo acids, synthesizing D-amino acids. Here, we report the identification and characterization of a novel NADP+-dependent meso-diaminopimelate dehydrogenase from Candidatus Syntrophocurvum alkaliphilum (CSaDAPDH). The purified enzyme exhibited oxidative deamination activity toward meso-diaminopimelate, as well as reductive amination activity toward several 2-oxo acids to produce the corresponding D-amino acids. The optimum pH and temperature for oxidative deamination of meso-diaminopimelate were 9.0 and 45°C, respectively. The optimum pH for reductive amination of pyruvate was 6.5, which was the lowest optimum pH among known enzymes, and thus, may lead to the development of new enzymatic methods for D-amino acid production. CSaDAPDH retained more than 60% of its activity after incubation for 30 min at 50°C (pH 7.0) or at pHs ranging from 5.5 to 7.0 (50°C). Moreover, using known enzymes as comparisons, the coenzyme and substrate recognition mechanisms of CSaDAPDH were elucidated based on a multiple sequence alignment and the homology model.

Abstract The critically endangered Caribbean staghorn coral Acropora cervicornis hosts microbiomes frequently dominated by the putatively parasitic intracellular bacterium Candidatus Aquirickettsia rohweri, which is associated with reduced coral growth and heightened disease susceptibility. Whether this dominance can be disrupted through antibiotic treatment and a sequential disturbance of thermal stress, remains unknown. In this study, we exposed disease-susceptible A. cervicornis fragments to broad-spectrum antibiotics, sub-bleaching thermal stress, or the combination of an antibiotic pre-treatment followed by thermal stress, and tracked changes in microbiome composition and diversity across all experimental phases using 16S rRNA amplicon sequencing and quantitative PCR (qPCR). We find that while the minor microbial fraction exhibits sustained compositional shifts in response to treatment, Ca. Aquirickettsia rohweri is resilient to antibiotic and thermal perturbation and may in fact increase in abundance following antibiotic exposure, suggesting that its dominance is actively maintained and not readily displaced by current disease mitigation strategies.These results indicate that antibiotic intervention is unlikely to be a viable strategy for disrupting Ca. A. rohweri dominance in disease-susceptible A. cervicornis , underscoring the urgency of understanding its transmission routes to inform microbiome rescue efforts.

Mungbean yellow mosaic India virus (MYMIV, Begomovirus vignaradiataindiaense, Genus Begomovirus) is well understood to incite chlorosis on mung bean (Vigna radiata) and yard long bean (V. unguiculata ssp. sesquipedalis). However, presence of the virus in mung bean in Indonesia has not been studied. Furthermore, leaf deformation symptoms, typical of phytoplasma disease, are also observed occasionally on both horticultural species. On February 2025, two yard long bean and two mung bean samples showing chlorosis, mosaic, and small leaf as well as non-symptomatic yard long bean and mung bean, one sample respectively, were collected in Nganjuk Regency, East Java Province. The samples were tested by PCR using Krusty/Homer and SPG1/SPG2 universal primers for begomoviruses, and the nested R16mF2/R16mR2 and R16F2n/R16R2 universal primers for phytoplasmas detection. One mung bean (no. 119) and one yard long bean (no. 419) were shown to be mixed-infected by begomovirus and phytoplasma. One mung bean (no. 219) was positive for phytoplasma only. One yard long bean (no. 519) and both non-symptomatic samples (no. 319 and 619) were negative for both pathogens. BLAST and phylogenetic analyses demonstrated that both begomovirus isolates are MYMIV, and the three phytoplasma strains are associated with the ‘Candidatus Phytoplasma aurantifolia’ (16SrII-A group, peanut witches'-broom). This research reported the first occurrences of MYMIV in mung bean and mixed infection of MYMIV and phytoplasma in mung bean and yard long bean in Indonesia, to the best of our knowledge. Further surveys are necessary to study both pathogens distribution among legumes in the country.

Abstract Anammox bacteria require large amounts of iron for hydrazine synthase (HZS) and hydrazine oxidoreductase (HZO). By analyzing 8 anammox genomes across four genera, we found that only Candidatus Brocadia sinica harbors a compact genomic island (<10 kb) where hzs co-localizes with iron uptake ( TonB , FeoAB ) and Fe-S cluster assembly ( NifU / NifS ) genes. All other species show dispersed architectures (>100 kb separation). In the dispersed species Ca. Kuenenia stuttgartiensis , transcriptomic data revealed a 300- to 1500-fold excess of hzs over iron genes, indicating severe expression uncoupling. Thus, physical co-localization of iron support genes with anammox core enzymes is rare but exists in one Brocadia lineage, potentially enabling better co-regulation. These findings provide a genomic basis for predicting iron responsiveness across anammox species in engineered systems.