Publications

4481

A Microviridae phage, CLasMV1, was recently identified in ‘ Candidatus Liberibacter asiaticus’ (CLas), the bacterium associated with citrus Huanglongbing (HLB). The CLasMV1 strain GDHZ11D (CP045566) exhibited a circular genome of 8,869 bp containing eight open reading frames (ORFs). Phages of CLas play crucial roles in regulating bacterial population diversity that have potential use for HLB control. However, knowledge of CLasMV1 population diversity is currently limited. In this study, 1,520 CLas samples were collected from 10 citrus-growing provinces in China. PCR screening revealed that 1,042 samples (69%) harbored CLasMV1. Complete genome sequences of 43 CLasMV1 strains were obtained through Illumina HiSeq sequencing with genome sizes ranging from 8,696 to 8,881 bp. Variations were mostly related to single-nucleotide polymorphisms and sequence insertions/deletions. Notably, two hypervariable regions (HVRs) were identified. Two new ORFs were detected, ORF-A (144 bp) in HVR-1 and ORF-B (342 bp) in HVR-2. Whole-genome phylogenetic analysis using 43 strains from this study, 9 previously reported Chinese strains, and 2 Florida strains (CP040636 and MZ382797) delineated five genomic groups. Chinese strains dominated Groups 1 to 4, and Group 5 contained the Florida strains. Further analyses of HVR-1 across all 1,042 CLasMV1 samples detected a 173-bp sequence with suspected mobile activity. Analysis of a PacBio long-read assembly published previously detected a concatemer of the CLasMV1 sequence, suggesting that the phage used the rolling circle mechanism for its replication. These findings significantly enhance our understanding of CLasMV1 genomic diversity and will facilitate future research on CLasMV1 classification and HLB biology.

Abstract Huanglongbing (HLB), a devastating citrus disease caused by Candidatus Liberibacter asiaticus (CLas), triggers persistent immune activation marked by excessive callose deposition and reactive oxygen species (ROS) accumulation, which impairs phloem function. This maladaptive response has led to HLB being described as a “pathogen-triggered immune disease”. Overexpression of the Arabidopsis (Arabidopsis thaliana) NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (AtNPR1) gene, a master regulator of systemic acquired resistance (SAR), confers robust HLB tolerance in susceptible citrus varieties, with transgenic lines exhibiting minimal or no disease symptoms following CLas infection. However, the mechanism underlying this tolerance remains unclear. In this study, we demonstrate that AtNPR1 restores immune homeostasis in CLas-infected trees by suppressing callose and ROS hyperaccumulation, thereby alleviating HLB symptom development. Similarly, silencing the Citrus sinensis homolog of NPR3 (CsNPR3), a negative regulator of SAR, mitigates CLas-induced immune overactivation and enhances HLB tolerance. Notably, salicylic acid (SA) levels are lower in AtNPR1-overexpressing citrus plants than wild-type controls after CLas infection, consistent with NPR1's role in negative feedback regulation of pathogen-induced SA accumulation. In Arabidopsis, overexpression of AtNPR1 or disruption of AtNPR3/AtNPR4 also attenuates pathogen-induced callose and ROS responses. Together, these findings reveal conserved roles for NPR1/NPR3/NPR4 in immune regulation across species and suggest that HLB susceptibility in commercial citrus varieties stems from a diminished capacity to maintain immune balance.

Polyphosphate-accumulating organisms (PAOs) play a crucial role in enhanced biological phosphorus removal (EBPR) processes. In addition to biosynthesis, they rely on phosphate for energy generation. However, Candidatus Accumulibacter, a model PAO, has been shown to adapt to low phosphate conditions by switching to a glycogen-accumulating metabolism (GAM), with variable success across genus members and experiments. This study aimed to explore the metabolic shift of several Accumulibacter species subjected to low-phosphate concentration in different operating conditions using metatranscriptomics analysis. Furthermore, the study enabled a comparison of the transcriptomic profiles of Accumulibacter with those of Propionivibrio , a glycogen-accumulating organism typically found in EBPR plants. Two sequencing batch reactors were operated with different carbon sources to enrich for different populations of Accumulibacter . After decreasing the influent phosphate concentration, carbon removal performance was maintained while anaerobic phosphate release dropped dramatically, suggesting a shift from a phosphate-accumulating to a glycogen-accumulating metabolism. Analysis of metatranscriptomics data indicated that Accumulibacter regalis (type I) and Propionivibrio aalborgensis remained the most abundant species after the phosphate decrease in the reactor with acetate-propionate and allylthiourea, while Accumulibacter delftensis (type I) and Accumulibacter phosphatis (type II) remained active in the reactor with acetate-glucose and no allylthiourea. Transcription of the genes from the ethylmalonyl-CoA pathway involved in the production of propionyl-CoA and regulation of the anaerobic redox balance was enhanced under low-phosphate conditions, especially for type I Accumulibacter . Conversely, the transcription of the methylmalonyl-CoA pathway was enhanced under low-phosphate conditions in Propionivibrio and type II Accumulibacter .

Abstract Background Phytoplasma research encounters limitations due to the lack of availability of pure cultures of these microorganisms. In this study a culture-independent approach was employed to investigate the genome and pathogenic mechanisms of phytoplasma responsible for witches’ broom disease in Trema levigata (Yunnan province, China). The phytoplasma genome was assembled using Illumina sequencing data and the Phytoassembly pipeline based on mixed samples. Results Nested PCR analysis identified a 16Sr group I, ‘ Candidatus Phytoplasma asteris’ strain in Trema levigate showing witches’ broom disease. Comparative study between infected and healthy plants resulted in an 849.7 kb draft genome with 94.1% coverage, 27.6% GC content, encoding 1356 predicted genes, of which 587 were functionally annotated. Multilocus phylogenetic analysis showed that this phytoplasma is closely related to ‘ Ca. P. asteris’. The genome possesses complete pathways for glycolysis and pyruvate metabolism pathways and harbors specific transporters (spermidine/putrescine, lysine), indicating dependency on host metabolites. Thirty-one putative secreted proteins, including TENGU and SAP05/54-like effectors were identified along with three potential mobile units carrying replication/recombination genes. Conclusions This approach demonstrates the effectiveness of pathogen purification-free analysis for phytoplasma studies in naturally infected host species, thereby enhancing the understanding of phytoplasma-host interactions.

Huanglongbing (HLB), or citrus greening, remains one of the most destructive diseases affecting citrus production globally. Associated with the phloem-limited bacterium Candidatus Liberibacter asiaticus ( C Las) and vectored by Diaphorina citri , HLB leads to canopy decline, fibrous root loss, and reductions in fruit yield and quality. Recently, the systemic delivery of oxytetracycline (OTC) via trunk injection was approved in Florida as a targeted therapy to reduce C Las titers and improve tree health. In parallel, Individual Protective Covers (IPCs) have been adopted to delay C Las infection in newly planted citrus trees by vector exclusion. This study investigates the combined use of IPCs and trunk injection of OTC for post-IPC therapy. ‘Valencia’ sweet orange trees grafted on US-812 and US-942 rootstocks were planted in December 2020 under HLB-endemic conditions in southwest Florida. IPCs were installed at planting and removed after 18 months. The first OTC injection was performed in May 2023, 10 months after IPC removal. A second injection was performed in May 2024. A 2 × 2 × 2 factorial experimental design evaluated the effects of infection history (early-infected and late-infected), rootstock cultivar (US-812 and US-942), and injection treatment (OTC-injected and non-injected) on tree responses over two consecutive production seasons. In year 1, infection history significantly influenced tree size, fruit yield, total soluble solids (TSS), TSS/titratable acidity ratio, and peel color. Late-infected trees outperformed early-infected trees, regardless of injection treatment and rootstock cultivar. In year 2, OTC-injected trees exhibited significantly higher yields, improved juice quality, and enhanced canopy health regardless of infection history and rootstock cultivar. Fibrous root microbiome analyses based on 16S rRNA sequencing revealed no significant effects of OTC injection on bacterial alpha or beta diversity, with stable community structure observed across treatments and time points. This suggests that targeted vascular delivery of OTC may not cause any major disruption to the root endorhizosphere microbiome. Together, the results from this study demonstrate the efficacy of integrating preventative (use of IPCs) and therapeutic (OTC vascular delivery) strategies for sustainable HLB management while preserving microbial integrity and offering a model for citrus production in parts of the world where HLB is prevalent.

ABSTRACT Methanol, the simplest alcohol, has long been known to be a key energy and carbon source for soil and plant-associated bacteria and fungi and is increasingly recognized as an important substrate for marine bacteria. Lanthanide-dependent methanol dehydrogenases (encoded by the gene xoxF ) have been shown to be key catalysts for methylotrophy in many environments, yet the identity of the most transcriptionally active methylotrophs in open ocean waters (“Clade X”) has remained elusive. Here, we show that “Clade X” methylotrophs belong to the deep-branching alphaproteobacterial order TMED127, which we propose be renamed “Methylaequorales”: “methyl” for “methylotrophic metabolism” and “aequor” for “ocean surface,” as these bacteria are most transcriptionally active near the sea surface. TMED127/Methylaequorales are present in surface waters of tropical and subtropical oceans throughout the global ocean. They have small, streamlined genomes (~1.5 Mb) and appear to be obligate methylotrophs that use the serine cycle for carbon assimilation. They display a diel pattern of xoxF5 and glucose dehydrogenase ( gdh ) transcription, peaking in the late afternoon, in oligotrophic surface water of the Sargasso Sea. Several other highly transcribed genes of unknown function had no homologs outside of TMED127/Methylaequorales genomes. Our findings illuminate an overlooked marine methylotrophic bacterium and predict a diel cycle of methanol production in surface seawater by an unknown pathway. IMPORTANCE Methanol metabolism is increasingly recognized as an important process in the marine carbon cycle, yet the identity and metabolism of the microorganisms mediating methylotrophy in the open ocean have remained unknown. This study reveals that bacteria in the TMED127 order of Alphaproteobacteria, renamed here as “Methylaequorales,” abundantly transcribe the key gene for lanthanide-dependent methylotrophy in oligotrophic surface waters of the world’s oceans. TMED127/Methylaequorales likely require methanol as a carbon and energy source and display a diel pattern of transcription of key genes for methylotrophy that peaks in the late afternoon. These findings motivate future studies on the mechanisms of methanol production in surface seawater.