Publications

3996

In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864T (JF-1T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108T (=JCM 39522T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.

Abstract Citrus Huanglongbing and Citrus tristeza are two diseases that affect the citrus industry worldwide. The pathogens causing these diseases are the phloem-limited bacteria ‘Candidatus Liberibacter spp.’ (mainly Ca. L. asiaticus, CLas) and citrus tristeza virus (CTV). We recently found that both CLas and CTV could be acquired and retained by the Asian citrus psyllid Diaphorina citri. However, the mechanism through which CLas and CTV interact with the insect vectors and plant hosts has not been defined. In this study, an electrical penetration graph was used to study the feeding behavior of D. citri adults on four groups of Citrus reticulata Blanco cv. Hongjü plants: healthy, CLas-infected, CTV-infected, and CTV-CLas coinfected plants. Liquid chromatography with tandem mass spectrometry (LC–MS/MS) was applied to analyze the metabolites of the four groups of plants. The combined results are as follows: (1) The lowest number of metabolites were enriched in CTV-infected plants, which hardly influenced the feeding behavior of D. citri, suggesting that mild CTV strain (CT31) infection caused limited disorders in citrus plants compared with CLas infection; (2) Increased levels of L-arabinose and kaempferol in CTV-infected and CLas-CTV coinfected plants were suggested to contribute to increased penetration time during feeding of D. citri. CLas-infection increases the difficulty of finding appropriate feeding sites by the vector and results in xylem feeding for certain duration; (3) A significant reduction in α-linolenic acid metabolism in CLas-infected plants was found to be related to methyl jasmonate signaling, which induced resistance to D. citri and increased the duration of salivation. This effect was reversed by coinfection with CTV and was consistent with the phloem structure and carbohydrate accumulation alteration; (4) Stress response-associated 2'-hydroxygenistein and sakuranetin were highly upregulated flavonoid in CTV-CLas coinfected plants. This combinged with the anatomical alterations might interfere with D. citri feeding in the citrus phloem, as reflected by the time reduction of sap-sucking there. These findings will provide new insights into the interactions between CTV and CLas in citrus and the insect vector D. citri that transmiting these pathogens.

Citrus HLB, caused by Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease worldwide. Usually 10% of total genes in bacteria are regulatory genes, but only 2% of CLas genes encode transcriptional factors. Here, 20 transcriptional regulators were predicted including eight genes (lsrB, ldtR, rem, visR, visN, ctrA, mucR, pelD, and atoC) directly or indirectly involved in regulating motility, and five genes (i.e., rpoH, prbP, phrR, rirA, and lsrB) involved in oxidative stress response. We demonstrated that rem, lsrB, and visNR of CLas can complement the corresponding mutants of S. meliloti in their reduced motility. We further investigated traits controlled by Rem in S. meliloti and CLas using RNA-seq analyses of rem mutant vs. complementation strains with remSmc or remLas. Transcriptomic analysis showed RemLas significantly regulates the expression of genes in S. meliloti, which was used to infer its regulation of CLas genes by identification of homologous genes. We found Rem is involved in regulating motility, chemotaxis, transporters, and oxidative phosphorylation in S. meliloti and regulating flagellar and transporter genes in CLas. Among the 39 putative RemLas-regulated genes in CLas, 16 contain Rem binding motif, including 10 genes involved in flagellar assembly. Taken together, this study offers valuable insights regarding regulatory genes of CLas with many of them involved in regulating motility and oxidative stress response. The regulation of flagellar genes by Rem in CLas unravels critical information regarding motility in CLas infection of hosts.

ABSTRACTCitrus huanglongbing (HLB), caused by “Candidatus Liberibacter” spp., is one of the most disastrous citrus diseases worldwide. HLB‐affected citrus fruits are significantly more acidic than healthy fruits. However, the molecular mechanism behind this phenomenon remains to be elucidated. Here, we report that HLB‐affected fruits have higher levels of citric acid (CA) than healthy fruits. Moreover, Citrus PH4 (CitPH4), which encodes a MYB transcription factor that functions as a key regulator of CA accumulation, was upregulated in HLB‐affected fruits relative to healthy fruits. Heterologous overexpression of CitPH4 in tobacco (Nicotiana tabacum) plants enhanced tolerance to HLB. Subsequently, overexpression and gene‐editing experiments indicated that CitPH4 can affect the salicylic acid (SA) pathway, which directly binds to and activates the promoter of CsPBS3, a key gene of SA biosynthesis. HLB‐affected fruits had higher SA levels than healthy fruits. Furthermore, application of SA activated CA biosynthesis and application of CA activated SA biosynthesis and signalling in citrus fruits and decreased “Candidatus Liberibacter asiaticus” (CLas) titres in infected leaves. This work suggests that CitPH4 is a key node between CA and SA, thus revealing crosstalk between defence responses and fruit quality in citrus.

ABSTRACTRaccoons (Procyon lotor) are reservoirs for pathogens of other wildlife species, domestic animals, and humans, including several tick‐borne pathogens. A relatively understudied organism in raccoons is Candidatus Neoehrlichia procyonis which has been detected in raccoons from the southeastern United States. A related species in Europe and Asia, Neoehrlichia mikurensis, uses rodents as reservoirs and Ixodes spp. as vectors; however, studies on rodents suggest they are not susceptible to Ca. N. procyonis. N. mikurensis has been associated with cases of neoehrlichiosis in people and dogs, which emphasizes the need to better understand the natural history of Ca. N. procyonis. We conducted a molecular survey of raccoons from selected regions of the United States and Canada. Of 394 raccoons tested, 167 (42.4%) were confirmed to be positive for Ca. N. procyonis based on sequence analysis. There was spatial variation in prevalence with significantly higher prevalence (68%, 268/394) being detected in the Southeast region of the United States compared with all other regions, although a high prevalence (55.1%, 217/394) was detected in California. Lower prevalence was detected in the Midwest (3.8%, 15/394) and none of the raccoons from Canada were positive. These data suggest that Ca. N. procyonis is widespread in raccoon populations in the United States but there is spatial variation which may be related to vector distribution or some other factor. Although not known to infect hosts other than raccoons, neoehrlichiosis should be considered in cases of suspected ehrlichiosis in immunocompromised dogs or people that have no known etiologic agent.

AbstractThis study reports the draft genome ofCandidatusPhytoplasma pyri strain P1, isolated from Argentina, marking the first global sequencing of this species. The genome assembly consisted of 16 contigs, with a total length of 575,431 bp, a GC content of 20.35%, and 125X coverage. A total of 536 genes were annotated, including those related to metabolism, genetic information processing, and signaling. Phylogenetic analysis placed ‘CandidatusPhytoplasma pyri’ within the 16SrX group, supporting its classification as a distinct species from ‘CandidatusPhytoplasma mali’ and ‘CandidatusPhytoplasma prunorum’, despite their close evolutionary proximity. The investigation also identified 17 secreted proteins, including homologs of known effectors such as SAP39 and SAP41, as well as conserved proteins associated with virulence mechanisms. A homologue of the Imp immunodominant membrane protein was also characterized, revealing conserved gene organization across related strains. These findings contribute to the understanding of ‘CandidatusPhytoplasma pyri’ pathogenic and provide valuable genomic data for future research. This study highlights the importance of expanding phytoplasma genomics, as it provides a crucial first step in understanding ‘CandidatusPhytoplasma pyri’ and its role in plant pathology

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.