Biology subjects

Lowe-Power, T.

Publications and source records attributed to Lowe-Power, T..

9 recordsLinked to original sources

bioRxiv2026

Phylogenomic Taxonomic Analysis of Ralstonia solanacearum Strains causing Bacterial Wilt Disease in Northeastern Argentina.

Ralstonia solanacearum species complex (RSSC) is a genetically diverse group of plant pathogens, yet genomic data from South America remain limited. Here, we characterize 13 RSSC strains isolated from tomato, pepper, and eggplant in northeastern Argentina. Phylogenetic analysis of the egl marker gene assigned these strains to phylotype IIA and suggested two closely related lineages. Complete genomes (5.63-5.76 Mb) were generated for four representative strains, yielding high-quality (99.94% completeness with f_Burkholderiaceae CheckM markers), closed assemblies with canonical bipartite architecture. Phylogenetic analysis of the egl marker, 49 conserved bacterial genes, and average nucleotide identity (ANI) analyses, consistently assigned one lineage to sequevar IIA-50, forming a coherent and monophyletic group. In contrast, although egl analysis suggested the second lineage was related to one sequevar IIA-38 reference strain, genomic analysis did not support this assignment. Further, the genomic analysis revealed significant genomic distance between the genomes for two sequevar 38 representative strains, supporting a conclusion that sequevar 38 itself was not monophyletic and instead appears paraphyletic. These findings highlight limitations of single-locus classification and support genome-informed refinement of RSSC sub-phylotype taxonomy. Outcome statementReports of bacterial wilt disease in Argentina had not yet been published in the international literature although the disease has been long-standing. This study provides complete genome sequences for four Ralstonia solanacearum strains from Northern Argentina and places them within a global phylogenomic framework. The Argentine strains cluster into two closely related phylotype IIA lineages, indicating that bacterial wilt in this regional dataset is associated with genetically similar populations. For clear communication of which strains are present in Northern Argentina, we attempted to classify the lineages to the long-standing sequence variant (sequevar) system for naming R. solanacearum species complex (RSSC) strains. One lineage was confidently assigned to IIA-50 with genomic support that confirmed phylogenetic analysis of the classical genetic marker egl. However, newly available genomes for sequevar reference strains revealed an issue where two distantly related strains are currently recognized as references for sequevars. Overall, these results provide evidence supporting the need for genome-informed refinement of sub-phylotype classification and expand genomic representation of South American RSSC populations. Data summaryComplete genome assemblies and raw reads for INTABV18, INTABV29, INTABV624 and INTABV2657 are deposited to NCBI under the project number PRJNA1407867. The curated dataset of public RSSC genomes is available to users who register a free account on KBase via a KBase narrative (https://narrative.kbase.us/narrative/189849). The narrative described in a living BioRxiv pre-print [1]. Supplemental files such as Figure S1, rectangular versions of all trees (Figure 2 and 3 and S1) and supplementary table S1, S2, S3 and S4 are available on Zenodo at doi.org/10.5281/zenodo.19502890 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/721750v1_figS1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1ac3168org.highwire.dtl.DTLVardef@1dfd0d6org.highwire.dtl.DTLVardef@107ae42org.highwire.dtl.DTLVardef@141937c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO Maximum-likelihood phylogenetic tree inferred from 471 bp of endoglucanase (egl) gene sequences assigned Argentine strains as phylotype II sequevar 38 and sequevar 50. The tree was constructed using PhyML v3.0 under the GTR nucleotide substitution model with gamma-distributed rate heterogeneity ( = 0.33), as selected by the SMART model selection procedure implemented in PhyML (Lefort et al., 2017). The egl sequences from Argentine strains are highlighted in blue, and their corresponding GenBank accession numbers for both the egl nucleotide sequence and the whole-genome assembly are shown in parentheses. Reference egl sequences representing sequevars IIA-38 (CFBP6801 and CIP120) and IIA-50 (T1-UY and ACH1076) are also shown in bold and marked with yellow circles. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/721750v1_fig2.gif" ALT="Figure 2"> View larger version (53K): org.highwire.dtl.DTLVardef@39d776org.highwire.dtl.DTLVardef@170bd89org.highwire.dtl.DTLVardef@aba166org.highwire.dtl.DTLVardef@1f156dd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Maximum-likelihood phylogenetic tree inferred from 710 bp of endoglucanase (egl) gene sequences assigned Argentine strains as phylotype II sequevar 38 and sequevar 50. The phylogenetic tree was constructed using PhyML v3.0 under the GTR+R nucleotide substitution model, as selected by the SMART model selection procedure (Lefort et al., 2017). egl sequences from four Argentine strains (INTABV18, INTABV29, INTABV624, and INTABV2657) are shown in bold and highlighted in blue. Reference egl sequences representing sequevars IIA-38 (CFBP6801 and CIP120) and IIA-50 (T1-UY and ACH1076) are also shown in bold and marked with yellow circles. Two USA strains identified as IIA-38 (UCD576 and RS124) are shown in bold. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/721750v1_fig3.gif" ALT="Figure 3"> View larger version (37K): org.highwire.dtl.DTLVardef@17dd372org.highwire.dtl.DTLVardef@1c5156corg.highwire.dtl.DTLVardef@179d9org.highwire.dtl.DTLVardef@e6d529_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Approximate maximum-likelihood phylogeny based on a concatenated alignment of 49 conserved genes places four Argentine genomes (INTABV18, INTABV29, INTABV624 and INTABV2657) within the phylotype IIA clade. The tree was constructed using the SpeciesTreeBuilder v0.1.4 application on the KBase platform, incorporating the four Argentine genomes into a reference dataset of 825 genomes representing the known global diversity of the RSSC. The tree was visualized and annotated using iTOL v7.4.2. Argentine genomes are shown in bold and highlighted in blue, and egl reference strains for the sequevar IIA-38 (CIP120 and CFBP6801) and IIA-50 (T1-UY) are shown in bold and marked with yellow circles. Branches with approximate likelihood-ratio support values higher than >70% are colored in blue. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG

microbiology↗

bioRxiv2026

GIRAF 1.0: A unified global framework to anticipate plant pest invasions

Plant pests threaten 10-40% of global food production, resulting in $55-220 billion in annual economic losses. Despite these escalating risks, biosecurity remains largely reactive, lacking anticipatory frameworks that integrate pest-specific drivers governing transboundary spread. We present GIRAF 1.0 (Global Invasion Risk Assessment Framework), the first quantitative, data-driven system that unifies pest-specific multi-host landscapes, abiotic suitability, and global trade networks with international phytosanitary policies. We applied GIRAF to four globally devastating pests - ranging from viral to insect taxa - to reconstruct a century of transcontinental spread and generate the first multiscale atlases of future invasion potential. GIRAF reveals that 22-37% of Earths land surface can contain host communities that largely overlap with environmentally suitable hotspots. Over 115 countries are highly vulnerable to trade-mediated pest introductions despite adopted phytosanitary policies. GIRAF provides a foundation for proactive surveillance and pandemic preparedness, offering a scalable path for transnational biosecurity agencies and global food industries.

ecology↗

bioRxiv2026

Evolutionary and functional genomics reveal that Ralstonia wilt pathogens actively deploy antimicrobial warfare while leveraging physiological adaptations during plant infection

The xylem pathogens in the Ralstonia solanacearum species complex (RSSC) cause wilt diseases that threaten global food security. These diverse pathogens are highly adapted to the in planta environment where they proliferate and cause rapid, aggressive diseases. To understand the genetic underpinnings of these pathogens in planta fitness, we performed forward genetic screens in three RSSC species, using high-throughput random barcode transposon sequencing (RB-TnSeq). We quantified the competitive fitness of hundreds of thousands of mutants during stem colonization of susceptible tomato plants. We compared this in planta forward genetic screen with a prior forward genetic screen performed in a reductionist, plant-like environment: ex vivo xylem sap harvest from healthy tomato plants. The comparative genetic screens revealed both conserved and lineage-specific orthologs that enable RSSCs pathogenic success. Consistently, these diverse pathogens navigated the opportunities and stressors in planta by maintaining a resilient cell envelope barrier, complementing the nutritional availability in xylem sap, fine-tuning their utilization of the host-manipulating type III secretion system, and dynamically regulating their gene expression through a suite of environment sensing and transcriptional regulatory proteins. Surprisingly, the strain-specific fitness factors shed light on ecological interactions beyond pathogen dominance of their susceptible host, even during the single-strain infections, the pathogens wielded arsenals of anti-microbial weapons. Specifically during growth in planta, each RSSC strain required a unique repertoire of type VI secretion system immunity proteins that provide self-protection to their own toxins. We contextualized the in planta fitness factors through evolutionary genomic comparisons of the RSSC wilt pathogens to their non-pathogenic neighbors. Together, these analyses reveal how conserved and lineage-specific fitness determinants have evolved to support pathogenic success in the plant vascular niche.

genetics↗

bioRxiv2024

Gene editing of the E3 ligase PIRE1 fine-tunes ROS production for enhanced bacterial disease resistance in tomato

Reactive oxygen species (ROS) accumulation is required for effective plant defense. Accumulation of the Arabidopsis NADPH oxidase RBOHD is regulated by phosphorylation of a conserved C-terminal residue (T912) leading to ubiquitination by the RING E3 ligase PIRE. Arabidopsis PIRE knockouts exhibit enhanced ROS production and resistance to the foliar pathogen Pseudomonas syringae. Here, we identified 170 PIRE homologs, which emerged in Tracheophytes and expanded in Angiosperms. We investigated the role of Solanum lycopersicum (tomato) PIRE homologs in regulating ROS production, RBOH stability, and disease resistance. Mutational analyses of residues corresponding to T912 in the tomato RBOHD ortholog, SlRBOHB, affected protein accumulation and ROS production in a PIRE-dependent manner. Using CRISPR-cas9, we generated mutants in two S. lycopersicum PIRE homologs (SlPIRE). SlPIRE1 edited lines (Slpire1) in the tomato cultivar M82 displayed enhanced ROS production upon treatment with flg22, an immunogenic epitope of flagellin. Furthermore, Slpire1 exhibited decreased disease symptoms and bacterial accumulation when inoculated with foliar bacterial pathogens Pseudomonas syringae and Xanthomonas campestris. However, Slpire1 exhibited similar levels of colonization as wild type upon inoculation with diverse soilborne pathogens. These results indicate that phosphorylation and ubiquitination crosstalk regulate RBOHs in multiple plant species, and PIRE is a promising target for foliar disease control. This study also highlights the pathogen-specific role of PIRE, indicating its potential for targeted manipulation to enhance foliar disease resistance without affecting root-associated interactions, positioning PIRE as a promising target for improving overall plant health.

plant biology↗

bioRxiv2024

Lectins and polysaccharide EPS I have flow-responsive roles in the attachment and biofilm mechanics of plant pathogenic Ralstonia

Bacterial biofilm formation and attachment to hosts are mediated by carbohydrate- binding lectins, exopolysaccharides, and their interactions in the extracellular matrix (ECM). During tomato infection Ralstonia pseudosolanacearum (Rps) GMI1000 highly expresses three lectins: LecM, LecF, and LecX. The latter two are uncharacterized. We evaluated the roles in bacterial wilt disease of LecF, a fucose-binding lectin, LecX, a xylose-binding lectin, and the Rps exopolysaccharide EPS I. Interestingly, single and double lectin mutants attached to tomato roots better and formed more biofilm under static conditions in vitro. Consistent with this finding, static bacterial aggregation was suppressed by heterologous expression of lecFGMI1000 and lecXGMI1000 in other Ralstonia strains that naturally lack these lectins. Crude ECM from a {Delta}lecF/X double mutant was more adhesive than the wild-type ECM, and LecF and LecX increased Rps attachment to ECM. The enhanced adhesiveness of the {Delta}lecF/X ECM could explain the double mutants hyper-attachment in static conditions. Unexpectedly, mutating lectins decreased Rps attachment and biofilm viscosity under shear stress, which this pathogen experiences in plant xylem. LecF, LecX, and EPS I were all essential for biofilm development in xylem fluid flowing through cellulose-coated microfluidic channels. These results suggest that under shear stress, LecF and LecX increase Rps attachment by interacting with the ECM and plant cell wall components like cellulose. In static conditions such as on root surfaces and in clogged xylem vessels, the same lectins suppress attachment to facilitate pathogen dispersal. Thus, Rps lectins have a dual biological function that depends on the physical environment. Author SummaryBacterial wilt diseases caused by Ralstonia species inflict significant losses on diverse, globally important agricultural plants. The pathogen first colonizes roots and ultimately the water-transporting xylem. There it attaches to host cell walls and other bacterial cells to form biofilms that eventually block xylem vessels and disrupt sap flow. It is not well known how Ralstonia spp. modulate attachment, but precise control of both attachment and dispersal is critical for successful host colonization over the disease cycle. Excessive adhesion could trap bacteria in a toxic or nutrient-depleted environment. Conversely, insufficient adhesion in a flowing environment could displace bacteria from an optimal niche. We provide evidence of dual, environment-specific roles of carbohydrate-binding lectins and exopolysaccharide EPS I in Ralstonia pseudosolanacearum (Rps) attachment. In static conditions, which Rps experiences on a host root, two lectins suppress bacterial aggregation and adhesion to roots. However, in flowing conditions, which Rps experiences in healthy xylem vessels, the same two lectins and EPS I are essential for biofilm development. The lectins increase the biofilm viscosity and support colony structural integrity, likely by interacting with polysaccharides in the biofilm matrix. This novel multifunctionality of bacterial lectins reveals how pathogens adapt to a physically dynamic host environment.

microbiology↗

bioRxiv2024

Genotypic and Phenotypic Analyses Show Ralstonia solanacearum Cool Virulence is a Quantitative Trait Not Restricted to 'Race 3 biovar 2'

Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as Race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of ten Ralstonia strains on tomato and potato at both 22{degrees}C and 28{degrees}C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, while other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as R3bv2 group. To aid detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.

microbiology↗

bioRxiv2023

A pangenomic atlas reveals that eco-evolutionary dynamics shape plant pathogen type VI secretion systems

Soil-borne Ralstonia solanacearum species complex (RSSC) bacteria disrupt rhizosphere and endophytic microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped pathogen T6SS biology, we analyzed the T6SS gene content and architecture across the RSSC pangenome and their evolutionarily relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem pathogenic RSSC bacteria and Acidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,069 auxiliary ("aux") T6SS toxin clusters across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Secondary replicons like megaplasmids often evolve more rapidly than the more evolutionarily stable chromosome. Although the single ancestral T6SS was broadly conserved in the RSSC, the T6SS was convergently lost in atypical lineages with vectored transmission. Overall, our data suggest dynamic interplay between the lifestyle of soil-transmitted RSSC lineages and the evolution of T6SSs with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.

evolutionary biology↗

bioRxiv2021

Meta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures, and physiological traits. To increase our understanding of the evolution, diversity, and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4,940 genes on average, and a pangenome analysis found that there are 3,262 genes in the core genome ([~]60% of the mean RSSC genome) with 13,128 genes in the extensive flexible genome. Although a core genome phylogenetic tree and a genome similarity matrix aligned with the previously named species (R. solanacearum, R. pseudosolanacearum, R. syzygii) and phylotypes (I-IV), these analyses also highlighted an unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. Additionally, we also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced Ralstonia strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service. IMPACT STATEMENTThe Ralstonia solanacearum species complex (RSSC) includes dozens of economically important pathogens of many cultivated and wild plants. The extensive genetic and phenotypic diversity that exists within the RSSC has made it challenging to subdivide this group into meaningful subgroups with relevance to plant disease control and plant biosecurity. This study provides a solid genome-based framework for improved classification and identification of the RSSC by analyzing one hundred representative RSSC genome sequences with a suite of comparative evolutionary genomic tools. The results also lay the foundation for additional in-depth studies to gain further insights into evolution and biology of this heterogeneous complex of destructive plant pathogens. DATA SUMMARYThe authors confirm that all raw data and code and protocols have been provided within the manuscript. All publicly available sequencing data used for analysis have been supplemented with accession numbers to access the data. The assembled genome of strain 19-3PR_UW348 was submitted to NCBI under Bioproject PRJNA775652 Biosample SAMN22612291. This Whole Genome Shotgun project has been deposited at GenBank under the accession JAJMMU000000000. The version described in this paper is version JAJMMU010000000.

genomics↗

bioRxiv2020

A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex

The Ralstonia species complex is a group of genetically diverse plant wilt pathogens. Our goal is to create a database that contains the reported global distribution and host range of Ralstonia clades (e.g. phylotypes and sequevars). In this fifth release, we have cataloged information from 304 sources that report one or more Ralstonia strains isolated from 107 geographic regions. Metadata for nearly 10,000 strains are available as a supplemental table. The aggregated data suggest that the pandemic brown rot lineage (IIB-1) is the most widely dispersed lineage, and the phylotype I and IIB-4 lineages have the broadest natural host range. Although phylotype III is largely restricted to Africa, one strain collection reports a phylotype III strain isolated from Jamaica in the mid-1900s. In the previous release, we included reported presence of phylotype III strains in Brazil, but closer inspection of those results reveals that the strains were actually phylotype I strains that were mis-identified. Similarly, although phylotype IV is mostly found in East and Southeast Asia, phylotype IV strains are reported to be present in Kenya. Additionally, we have created an open science resource for phylogenomics of the RSSC. We associated strain metadata (host of isolation, location of isolation, and clade) with almost 700 genomes in a public KBase narrative. Our colleagues can use this narrative to identify the phylogenetic position of newly sequenced strains. We further curate a set of 601 high quality genomes based on low contamination and high completeness by CheckM. Our colleagues can use the curated dataset for comparative genomics studies.

microbiology↗