Complete Genome Sequence of Xylella taiwanensis and Comparative Analysis of Virulence Gene Content With Xylella fastidiosa

Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon

BACKGROUND

Cyanobacteria have diversified through their long evolutionary history and occupy a wide range of environments on Earth. To advance our understanding of their adaptation mechanisms in extreme environments, we performed stress tolerance characterizations, whole genome sequencing, and comparative genomic analyses of a novel heat-tolerant and euryhaline strain of the unicellular cyanobacterium Cyanobacterium sp. Dongsha4 (DS4). This strain was isolated from a lagoon on Dongsha Island in the South China Sea, a habitat with fluctuations in temperature, salinity, light intensity, and nutrient supply.

RESULTS

DS4 cells can tolerate long-term high-temperature up to 50 ℃ and salinity from 0 to 6.6%, which is similar to the results previously obtained for Cyanobacterium aponinum. In contrast, most mesophilic cyanobacteria cannot survive under these extreme conditions. Based on the 16S rRNA gene phylogeny, DS4 is most closely related to Cyanobacterium sp. NBRC102756 isolated from Iwojima Island, Japan, and Cyanobacterium sp. MCCB114 isolated from Vypeen Island, India. For comparison with strains that have genomic information available, DS4 is most similar to Cyanobacterium aponinum strain PCC10605 (PCC10605), sharing 81.7% of the genomic segments and 92.9% average nucleotide identity (ANI). Gene content comparisons identified multiple distinct features of DS4. Unlike related strains, DS4 possesses the genes necessary for nitrogen fixation. Other notable genes include those involved in photosynthesis, central metabolisms, cyanobacterial starch metabolisms, stress tolerances, and biosynthesis of novel secondary metabolites.

CONCLUSIONS

These findings promote our understanding of the physiology, ecology, evolution, and stress tolerance mechanisms of cyanobacteria. The information is valuable for future functional studies and biotechnology applications of heat-tolerant and euryhaline marine cyanobacteria.

Diffusible Signal Factors and Xylella fastidiosa: A Crucial Mechanism Yet to Be Revealed

Xylella fastidiosa (Xf) is a xylem-limited Gram-negative phytopathogen responsible for severe plant diseases globally. Colonization and dissemination on host plants are regulated primarily by diffusible signal factors (DSFs) and quorum sensing (QS) molecules regulating biofilm formation, motility, and virulence factor synthesis. DSFs play a critical role in the transition of bacteria from adhesion to dispersal phases, influencing plant infection and transmission by vector. Because of Xf's host range (over 550 plant species), effective containment strategies are highly demanded. In this review, we discuss the molecular mechanism of DSF-mediated signalling in Xf, especially concerning its role in pathogenicity and adaptation. Moreover, we shed light on innovative approaches to manage Xf, including quorum-quenching (QQ) strategies and transgenic plants targeted to disrupt QS pathways. Improved knowledge of DSF interactions with host plants and bacterial communities could provide an entry point for novel, sustainable disease control strategies to decrease Xf's agricultural and ecological impact.

Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes

Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, the percentage of conserved proteins and genome-wide average amino acid identity are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae and Spiroplasma-Entomoplasmataceae-Mycoides. However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and Entomoplasmataceae into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of misclassification were identified. These findings demonstrated the utility of this approach and its potential application to other bacteria.

The perception and evolution of flagellin, cold shock protein and elongation factor Tu from vector-borne bacterial plant pathogens

Vector-borne bacterial pathogens cause devastating plant diseases that cost billions of dollars in crop losses worldwide. These pathogens have evolved to be host- and vector-dependent, resulting in a reduced genome size compared to their free-living relatives. All known vector-borne bacterial plant pathogens belong to four different genera: 'Candidatus Liberibacter', 'Candidatus Phytoplasma', Spiroplasma and Xylella. To protect themselves against pathogens, plants have evolved pattern recognition receptors that can detect conserved pathogen features as non-self and mount an immune response. To gain an understanding of how vector-borne pathogen features are perceived in plants, we investigated three proteinaceous features derived from cold shock protein (csp22), flagellin (flg22) and elongation factor Tu (elf18) from vector-borne bacterial pathogens as well as their closest free-living relatives. In general, vector-borne pathogens have fewer copies of genes encoding flagellin and cold shock protein compared to their closest free-living relatives. Furthermore, epitopes from vector-borne pathogens were less likely to be immunogenic compared to their free-living counterparts. Most Liberibacter csp22 and elf18 epitopes do not trigger plant immune responses in tomato or Arabidopsis. Interestingly, csp22 from the citrus pathogen 'Candidatus Liberibacter asiaticus' triggers immune responses in solanaceous plants, while csp22 from the solanaceous pathogen 'Candidatus Liberibacter solanacearum' does not. Our findings suggest that vector-borne plant pathogenic bacteria evolved to evade host recognition.

Detection and Characterization of Xylella fastidiosa subsp. fastidiosa in Rabbiteye Blueberry in South Carolina

Xylella fastidiosa causes bacterial leaf scorch in southern highbush (Vaccinium corymbosum interspecific hybrids) and is also associated with a distinct disease phenotype in rabbiteye blueberry (V. virgatum) cultivars in the southeastern United States. Both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex have been reported to cause problems in southern highbush blueberry, but so far only X. fastidiosa subsp. multiplex has been reported in rabbiteye cultivars in Louisiana. In this study, we report detection of X. fastidiosa in rabbiteye blueberry plants in association with symptoms of foliar reddening and shoot dieback. High throughput sequencing of an X. fastidiosa-positive plant sample and comparative analyses identified the strain in one of these plants as being X. fastidiosa subsp. fastidiosa. We briefly discuss the implications of these findings, which may spur research into blueberry as a potential inoculum source that could enable spread to other susceptible fruit crops in South Carolina.

TaqMan Quantitative PCR Detection of Xylella taiwanensis in Taiwan

Xylella taiwanensis (Xt) is a nutritionally fastidious bacterial pathogen causing pear leaf scorch disease (PLSD) in Taiwan. The disease causes early defoliation, loss of tree vigor, and reduction in fruit yield and quality. No cure for PLSD is available. The only option for growers to control the disease is to use pathogen-free propagation material, which requires early and accurate detection of Xt. Currently, only one simplex PCR method is available for the diagnosis of PLSD. We developed five Xt-specific TaqMan quantitative PCR (TaqMan qPCR) systems (primers-probe sets) for the detection of Xt. The PCR systems target three conserved genomic loci commonly used in bacterial pathogen detection: the 16S rRNA gene (rrs), the 16S-23S rRNA intergenic transcribed sequence (16S-23S rRNA ITS), and the DNA gyrase gene (gyrB). BLAST analysis using the GenBank nr sequence database, including whole genome sequences of 88 Xanthomonas campestris pv. campestris (Xcc) strains, 147 X. fastidiosa (Xf) strains, and 32 Xt strains, showed that all primer and probe sequences were specific only to Xt. Single nucleotide polymorphisms (SNPs) provided the primer/probe specificity to Xt. The PCR systems were evaluated by using DNA samples from pure cultures of two Xt strains, one Xf strain, one Xcc strain, and 140 plant samples collected from 23 pear orchards in four counties in Taiwan. The two-copy rrs and 16S-23S rRNA ITS-based PCR systems (Xt803-F/R, Xt731-F/R, and Xt16S-F/R) showed higher detection sensitivity than the two single-copy gyrB-based systems (XtgB1-F/R and XtgB2-F/R). A metagenomic analysis of a representative PLSD leaf sample detected the presence of non-Xt proteobacteria and fungal pathogens that should be taken into consideration in PLSD, as they might interfere with diagnosis.

EFSA Panel on Plant Health (PLH), Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Chen J, Migheli Q, Vloutoglou I, Streissl F, Reignault PL. Pest categorisation of Xylella taiwanensis

The EFSA Plant Health Panel performed a pest categorisation of Xylella taiwanensis, a Gram-negative bacterium belonging to the Xanthomonadaceae. The pathogen is a well-defined taxonomic entity, and it is the causal agent of the pear leaf scorch. X. taiwanensis is present in subtropical and temperate areas of the island of Taiwan, where it affects low chilling pear cultivars of the species Pyrus pyrifolia (Asian pear). No other plant species are reported to be affected by the pathogen. The pathogen is not known to be present in the EU territory and it is not included in the Commission Implementing Regulation (EU) 2019/2072. The main pathway for the entry of the pathogen into the EU territory is host plants for planting (except seeds); another possible pathway might be represented by putative insect vectors, though their identity remains unknown. The cultivated area of P. pyrifolia in the EU territory is very limited. Conversely, the genetically related P. communis is widely cultivated in most EU Member States and there is no information so far on the susceptibility of its several cultivars. Should the pest establish in the EU, economic impact is expected, provided that suitable insect vectors are present and P. communis is as susceptible to infection as P. pyrifolia. Phytosanitary measures are available to prevent the introduction and spread of the pathogen into the EU, since plants for planting from Taiwan is a closed pathway; nonetheless, putative vectors, if confirmed and identified, may represent an additional risk of the pathogen's introduction and spread. The lack of knowledge on whether X. taiwanensis can infect P. communis, the identity and presence of suitable vectors in the EU lead to key uncertainties on entry, establishment, spread and impact. X. taiwanensis satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest.

Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1

Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that dominates microbial mats in Asian non-acidic hot springs. These cyanobacteria are the major primary producers in their ecological niches and are promising sources of thermostable enzymes for biotechnology applications. To improve our understanding of these organisms, we conducted whole-genome sequencing of a novel strain for comparative analysis with other representatives in the same genus. This newly characterized strain, Thermosynechococcus sp. TA-1, was isolated from the Taian hot springs in Taiwan. Analyses based on average nucleotide identity (ANI) and genome-scale phylogeny suggested that TA-1 and another Taiwanese strain CL-1 belong to a novel species-level taxon. Two metagenome-assembled genomes (MAGs) originated from India represent the sister group, and Thermosynechococcus elongatus PKUAC-SCTE542 from China is the next closest lineage. All cultivated strains and MAGs from Japan form a separate monophyletic clade and could be classified into two species-level taxa. Intriguingly, although TA-1 and CL-1 share 97.0% ANI, the genome alignment identified at least 16 synteny breakpoints that are mostly associated with transposase genes, which illustrates the dynamic nature of their chromosomal evolution. Gene content comparisons identified multiple features distinct at species- or strain-level among these Thermosynechococcus representatives. Examples include genes involved in bicarbonate transportation, nitric oxide protection, urea utilization, kanamycin resistance, restriction-modification system, and chemotaxis. Moreover, we observed the insertion of type II inteins in multiple genes of the two Taiwanese strains and inferred putative horizontal transfer of an asparagine synthase gene (asnB) associated with exopolysaccharides gene cluster. Taken together, while previous work suggested that strains in this genus share a highly conserved genomic core and no clear genetic differentiation could be linked to environmental factors, we found that the overall pattern of gene content divergence is largely congruent with core genome phylogeny. However, it is difficult to distinguish between the roles of phylogenetic relatedness and geographic proximity in shaping the genetic differentiation. In conclusion, knowledge of the genomic differentiation among these strains provides valuable resources for future functional characterization.

Xylella fastidiosa's relationships: the bacterium, the host plants, and the plant microbiome

Xylella fastidiosa is the causal agent of important crop diseases and is transmitted by xylem-sap-feeding insects. The bacterium colonizes xylem vessels and can persist with a commensal or pathogen lifestyle in more than 500 plant species. In the past decade, reports of X. fastidiosa across the globe have dramatically increased its known occurrence. This raises important questions: How does X. fastidiosa interact with the different host plants? How does the bacterium interact with the plant immune system? How does it influence the host's microbiome? We discuss recent strain genetic typing and plant transcriptome and microbiome analyses, which have advanced our understanding of factors that are important for X. fastidiosa plant infection.

Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure

Metagenomics has become a prominent technology to study the functional potential of all organisms in a microbial community. Most studies focus on the bacterial content of these communities, while ignoring eukaryotic microbes. Indeed, many metagenomics analysis pipelines silently assume that all contigs in a metagenome are prokaryotic, likely resulting in less accurate annotation of eukaryotes in metagenomes. Early detection of eukaryotic contigs allows for eukaryote-specific gene prediction and functional annotation. Here, we developed a classifier that distinguishes eukaryotic from prokaryotic contigs based on foundational differences between these taxa in terms of gene structure. We first developed Whokaryote, a random forest classifier that uses intergenic distance, gene density and gene length as the most important features. We show that, with an estimated recall, precision and accuracy of 94, 96 and 95 %, respectively, this classifier with features grounded in biology can perform almost as well as the classifiers EukRep and Tiara, which use k-mer frequencies as features. By retraining our classifier with Tiara predictions as an additional feature, the weaknesses of both types of classifiers are compensated; the result is Whokaryote+Tiara, an enhanced classifier that outperforms all individual classifiers, with an F1 score of 0.99 for both eukaryotes and prokaryotes, while still being fast. In a reanalysis of metagenome data from a disease-suppressive plant endospheric microbial community, we show how using Whokaryote+Tiara to select contigs for eukaryotic gene prediction facilitates the discovery of several biosynthetic gene clusters that were missed in the original study. Whokaryote (+Tiara) is wrapped in an easily installable package and is freely available from https://github.com/LottePronk/whokaryote.

Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce's disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.