Publications

4857

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 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.

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.

Plant-pathogenic bacteria threaten crop productivity and quality, yet chemical options remain limited compared with those for fungal and oomycete diseases. Current management relies mainly on copper bactericides, limited antibiotics, induced-resistance agents, biocontrol and resistant cultivars. However, copper and streptomycin resistance, efflux-mediated multidrug tolerance and rapid pathogen adaptation have weakened these strategies. Target-oriented research provides a framework for exploring agricultural antibacterials, anti-virulence agents, anti-colonization strategies, resistance sensitizers and host-resistance interventions, but many of these approaches remain conceptual, model-system, greenhouse or medical-bacteriology-derived rather than proven field solutions. This review classifies bacterial control targets into two interconnected groups: growth-essential targets, including peptidoglycan biosynthesis, membrane/envelope systems, nucleic-acid processes, protein synthesis, metabolism, nutrient transport and cell division; and anti-virulence/anti-adaptation targets, including secretion systems, quorum sensing, biofilms, motility, adhesion, cell-wall-degrading enzymes, tolerance systems, oxidative-stress responses and host susceptibility factors. Using “Candidatus Liberibacter asiaticus” (CLas) as a case study, genome annotation and infection-stage transcript-abundance data prioritized Sec-dependent secretion, outer-membrane/surface proteins, Bam assembly, nutrient transporters, Clp proteostasis, redox adaptation and core cellular processes as candidate target classes. Envelope-associated, secretion/anti-virulence, nutrient-acquisition and stress-sensitization modules may represent potential directions for downstream validation, but CLas candidates remain hypothesis-generating priorities requiring validation for essentiality, conservation, druggability, delivery feasibility, crop safety and field performance.

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. Significance Statement Only Candidatus Brocadia sinica harbors a compact <10 kb iron-nitrogen genomic island. All other anammox species show dispersed iron-nitrogen architectures (>100 kb separation). Dispersed species exhibit 300⁓1500-fold expression mismatch between hzs and iron genes. Physical co-localization may enable co-regulation of iron supply with anammox metabolism. Genomic architecture predicts lineage-specific iron responsiveness in anammox engineering.

Abstract Krum.hol.zi.bac.te.ri.o'ta. N.L. neut. n. Krumholzibacterium , type genus of the type class of the phylum; L. neut. pl. n. suff. ‐ota , ending to denote a phylum; N.L. neut. pl. n. Krumholzibacteriota , the phylum of the class Krumholzibacteria. The phylum Candidatus Krumholzibacteriota was proposed to accommodate genomic assemblies of yet‐uncultured microorganisms. The type species, of the genus, Candidatus Krumholzibacterium zodletonense Zgenome0171 T was recovered from an anaerobic, sulfide‐ and sulfur‐rich spring in Southwestern Oklahoma, USA. The phylum comprises one described class, order, family, genus, and species. However, currently available genomes ( n  = 90) in GTDB (release 08‐RS214) are accommodated in 1 class, 6 orders, 8 families, 30 genera, and 58 species. Phylogenetically, the phylum is closely related to Gemmatimonadota and multiple phyla with no cultured representatives ( Ca . Edwardsbacteria, Ca . Eisenbacteria, Ca . Latescibacterota, Ca . Zixibacteria, 4572‐55, ARS69, GCA‐2686955, JAAXHH01, JABDJQ01, JAGLTZ01, JAGLYR01, TA06, TA06_A, and VGIX01); all of which are part of the FCB ( Fibrobacteres , Chlorobia , Bacteroidetes ) superphylum in the Gracilicutes clade. Candidatus Krumholzibacteriota genomes have mainly been recovered from marine, freshwater, engineered, and host‐associated ecosystems. The prevailing in‐situ conditions in sampled habitats, gene content analysis, and the use of predictive machine learning‐based approaches suggest a phylum‐wide preference for anaerobic conditions, mesophilic temperatures, circumneutral pH, and low salinities. Metabolically, the type species of the type genus of the phylum is predicted to be a fermentative anaerobe with preference for amino acids over sugars as substrates. Later studies indicate that some members of the phylum harbor respiratory capacities (dissimilatory sulfate reduction, dissimilatory sulfite reduction, iron‐reduction, and high‐affinity oxygen respiration with a few members possessing the potential for low‐affinity oxygen respiration), while others possess the machinery for anaerobic degradation of aromatic hydrocarbons. Finally, although all members of Candidatus Krumholzibacteriota remain uncultured, a representative of the phylum was enriched in a methane‐ and iron‐fed bioreactor inoculated with Bothnian Sea sediments. Type genus : Candidatus Krumholzibacterium Youssef et al. 2019, CL2.