Biology subjects

Jones, J. B.

Publications and source records attributed to Jones, J. B..

16 recordsLinked to original sources

bioRxiv2026

Allelic Diversity and Core Conservation of Type III Effectors Across Xanthomonads Causing Bacterial Spot of Pepper and Tomato

Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria (Xe), X. euvesicatoria pv. perforans (Xp), X. hortorum pv. gardneri (Xg), and X. vesicatoria (Xv). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp, 350 Xe, 69 Xg, and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in [≥]95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

genomics↗

bioRxiv2026

Cryo-EM structure analysis of phage {Phi}Xacm4-11 that infects the phytopathogen Xanthomonas citri

Very few bacteriophages that infect Xanthomonas species have been characterized genetically and only one 3D structure, the capsid of a siphovirus that infects the phytopathogen Xanthomonas citri, has been determined at high resolution. This study presents the annotated DNA sequence and detailed structural analysis of {Phi}Xacm4-11, a podovirus that infects Xanthomonas citri, shedding light on its unique architecture and functional attributes, providing insights into the molecular mechanisms underlying host recognition and infection. Annotation of the genome revealed conserved features among related phages, but also distinct genetic elements that may contribute to {Phi}Xacm4-11s specificity toward X. citri. Genes associated with host recognition and infection were identified, including the genes potentially coding for the receptor-binding proteins (RBPs) at the tail fibre tip, offering insights into their role in bacterial attachment. Using high-resolution cryo-electron microscopy, we resolved the architecture of the mature, pre-released virion, revealing a T7-like head-tail assembly with a well-defined portal-tail complex embedded at a unique fivefold vertex. Our findings provide a detailed view of the structural and functional components of {Phi}Xacm4-11, furthering our understanding of its molecular interactions with X. citri and its potential application in phage therapy against phytopathogens. SIGNIFICANCE STATEMENTBacteriophages are increasingly recognized as powerful tools to control bacterial pathogens in medicine and agriculture, yet the structural basis of host recognition and genome delivery remains poorly understood for most phages. Here, we present a comprehensive structural and functional analysis of {Phi}Xacm4-11, a podovirus that infects the plant pathogen Xanthomonas citri. By combining genome annotation, proteomics, and high-resolution cryo-electron microscopy, we reveal the complete architecture of the mature virion and its specialized portal-tail machinery. Our results show how this short-tailed phage deploys an internal injection device to penetrate the bacterial cell envelope and highlight structural features linked to type IV pilus-dependent infection. These findings provide insights into phage entry mechanisms and establish {Phi}Xacm4-11 as a model for engineering biocontrol strategies.

biochemistry↗

bioRxiv2025

Rapid population flux in bacterial spot xanthomonads during a transition in dominance between two genotypes in consecutive tomato production seasons and identification of a new species Xanthomonas oklahomensis sp. nov.

In the bacterial spot of tomato disease complex, Xanthomonas euvesicatoria pv. perforans (Xep) is known to outcompete X. euvesicatoria pv. euvesicatoria (Xee). The result, over time in tomato production systems where both pathogens are present, is the anticipated displacement of Xee by Xep. In this study, we characterized the population of recovered strains from grower fields in response to a bacterial spot of tomato outbreak in east and central Oklahoma in 2018 and 2019. Tomato and pepper strains sampled in earlier years were included to provide additional context. Phenotypic and genome-based analyses showed marked differences in race and species composition in recovered strains. All pre-2018 (2001-2014) tomato bacterial spot strains were Xep race T3, except one T4 strain. Tomato bacterial spot strains in 2018 consisted of Xee race T1 and Xep T3, while strains recovered in 2019 from the same locations were exclusively Xep T4 strains. The 2019 Xep T4 strains form the same cluster with the 2014 Xep T4 strain on the phylogenetic tree, suggesting the same population. Only the Xep race T4 strains showed an expanded host range to pepper. The recovered strains were also variable in copper sensitivity and effector content. We additionally recovered non-bacterial spot xanthomonads, one of which belongs to the new species, Xanthomonas oklahomensis sp. nov. These results contributes to novel insights in understanding genomic heterogeneity and seasonal population flux between competing bacterial genotypes during disease outbreaks and can be considered when developing disease management strategies.

plant biology↗

bioRxiv2024

Intercontinental dissemination and diversification of Xanthomonas perforans in tomato production

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of Xop effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

microbiology↗

bioRxiv2023

Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism

Type VI secretion system (T6SS) is a versatile, contact dependent contractile nano-weapon in Gram-negative bacteria that fires proteinaceous effector molecules directly into prokaryotic and eukaryotic cells aiding in manipulation of the host and killing of competitors in complex niches. In plant pathogenic xanthomonads, T6SS has been demonstrated to play these diverse roles in individual pathosystems. However, the regulatory circuit involved in mediating biological functions carried out by T6SS are still elusive in Xanthomonas sp. To bridge this knowledge gap, we conducted an in vitro transcriptome screen using plant apoplast mimicking minimal medium, XVM2 medium, to decipher the effect of tssM deletion, a core gene belonging to T6SS-cluster i3*, on the regulation of gene expression in Xanthomonas perforans strain AL65. Transcriptomic data revealed that a total of 277 and 525 genes were upregulated, while 307 and 392 genes were downregulated in the mutant strain post 8 and 16 hours of growth in XVM2 medium. The transcript abundance of several genes associated with flagellum and pilus biogenesis as well as type III secretion system were downregulated in the mutant strain. Deletion of tssM of cluster-i3* resulted in upregulation of several T6SS genes belonging to cluster-i3*** and genes involved in biofilm and cell wall biogenesis. Similarly, transcription regulators like rpoN, Pho regulon, rpoE and csrA were identified to be upregulated in the mutant strain. Our results suggest that T6SS modulates the expression of global regulators like csrA, rpoN and pho regulons triggering a signaling cascade and co-ordinates the expression of suite of virulence factors, stress response genes and metabolic genes. ImportanceType VI secretion system (T6SS) has received attention due to its significance in mediating inter-organismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies targeting core genes of T6SS have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including Xanthomonas studied here. However, it is not clear whether such effect on virulence is merely because of a shift in the microbiome-mediated protection or if T6SS is involved in a complex regulatory network governing virulence in plant pathogens involving type III secretion system or c-di-GMP signaling pathways. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in Xanthomonas perforans strain AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.

microbiology↗

bioRxiv2023

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their co-occurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life-history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically, the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We gathered evidence for gene flow among co-occurring pathogenic and nonpathogenic strains, suggesting the potential of nonpathogenic strains to act as a reservoir of adaptive traits for pathogenic strains and vice versa. We further identified traits enriched in nonpathogens that suggest a strategy of stress tolerance, rather than avoidance, during their association with a broad range of host plants.

ecology↗

bioRxiv2022

Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri

Xanthomonas citri subspecies citri (XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. Other X. citri subsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread of X. citri disease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes. In this study we developed a core genome multilocus typing scheme (cgMLST) for X. citri based upon 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A* and Aw, X. citri subsp. malvacearum and X. citri pathovars aurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicola and single isolates of X. citri pathovars dieffenbachiae and punicae. This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes and X. citri subsp. and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates at PubMLST.org to allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.

microbiology↗

bioRxiv2022

Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregant populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6 of pepper. We also identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. Mapping of bs5 and bs6 will facilitate their use in breeding programs through marker-assisted selection and is also a crucial step towards understanding the mechanisms of resistance. Key messageTwo recessive bacterial spot resistance genes were mapped in the pepper genome, which will facilitate their advancement in commercial pepper for management of all races of Xanthomonas euvesicatoria.

plant biology↗

bioRxiv2022

Identification of functional Spo0A residues critical for sporulation in Clostridioides difficile

Clostridioides difficile is an anaerobic, Gram-positive pathogen that is responsible for C. difficile infection (CDI). To survive in the environment and spread to new hosts, C. difficile must form metabolically-dormant spores. The formation of spores requires activation of the transcription factor Spo0A, which is the master regulator of sporulation in all endospore-forming bacteria. Though the sporulation initiation pathway has been delineated in the Bacilli, including the model spore-former Bacillus subtilis, the direct regulators of Spo0A in C. difficile remain undefined. C. difficile Spo0A shares highly conserved protein interaction regions with the B. subtilis sporulation proteins Spo0F and Spo0A, although many of the interacting factors present in B. subtilis are not encoded in C. difficile. To determine if comparable Spo0A residues are important for C. difficile sporulation initiation, site-directed mutagenesis was performed at conserved receiver domain residues and the effects on sporulation were examined. Mutation of residues important for homodimerization and interaction with both positive and negative regulators of B. subtilis Spo0A and Spo0F impacted C. difficile Spo0A function. The data also demonstrated that mutation of many additional conserved residues altered C. difficile Spo0A activity, even when the corresponding Bacillus interacting proteins are not apparent in the C. difficile genome. Finally, the conserved aspartate residue at position 56 of C. difficile Spo0A was determined to be the phosphorylation site that is necessary for Spo0A activation. The finding that Spo0A interacting motifs maintain functionality suggests that C. difficile Spo0A interacts with yet unidentified proteins that regulate its activity and control spore formation.

microbiology↗

bioRxiv2019

Potential soil transmission of a novel Candidatus Liberibacter strain detected in citrus seedlings grown in soil from a huanglongbing infested citrus grove

Candidatus Liberibacter spp. are Alphaproteobacteria associated with plants and psyllid vectors. Most cause plant diseases, including Ca Liberibacter asiaticus (Las) associated with citrus huanglongbing (HLB). Replacing HLB-infected by Las-free citrus trees results in fast re-infection despite psyllid control. To check if HLB could be soil-borne, we performed an insect-free greenhouse-experiment with 130 mandarin seedlings in two citrus-grove soils (A and B), non-autoclaved or autoclaved. Liberibacter-specific 16S-rDNA PCR primers to detect Las were used to search for Ca. Liberibacter spp. in mandarin leaves. Seven plants grown in non-autoclaved soil B showed HLB-like symptoms and tested positive after 2.5 and 8.5 months using three different primer systems: two based on the 16S-rDNA gene (primers HLBas/HLBr and OI2c/OI1) and one based on the rplA/rplJ gene (primers LAA2/LAJ5). DNA segments from these plants amplified by primers OI2c/OI1 were cloned and sequenced; they were 95.9 % similar to Las and 94.8% to Ca. Liberibacter africanus (Laf). The DNA product from Liberibacter-group specific PCR primers for the rplA/rplJ gene was 87.6% similar to that of Las and 78.2% of Laf. As the strain obtained originated from soil and was different from existing Ca. Liberibacter species, this strain may be a new species.

ecology↗

bioRxiv2019

Gene Transfer Agents in Plant Pathogenic Bacteria: Comparative Mobilomics, Genomic Survey and Recombinogenic Impacts

BackgroundGene transfer agents (GTAs) are phage-like mediators of gene transfer in bacterial species. Typically, strains of a bacteria species which have GTA shows more recombination than strains without GTAs. GTA-mediated gene transfer activity has been shown for few bacteria, with Rhodobacter capsulatus being the prototypical GTA. GTA have not been previously studied in plant pathogenic bacteria. A recent study inferring recombination in strains of the bacterial spot xanthomonads identified a Nigerian lineage which showed unusual recombination background. We initially set out to understand genomic drivers of recombination in this genome by focusing on mobile genetic elements.\n\nResultsWe identified a unique cluster which was present in the Nigerian strain but absent in other sequenced strains of bacterial spot xanthomonads. The protein sequence of a gene within this cluster contained the GTA_TIM domain that is present in bacteria with GTA. We identified GTA clusters in other Xanthomonas species as well as species of Agrobacterium and Pantoea. Recombination analyses showed that generally, strains of Xanthomonas with GTA have more inferred recombination events than strains without GTA, which could lead to genome divergence.\n\nConclusionThis study identified GTA clusters in species of the plant pathogen genera Xanthomonas, Agrobacterium and Pantoea which we have named XpGTA, AgGTA and PaGTA respectively. Our recombination analyses suggest that Xanthomonas strains with GTA generally have more inferred recombination events than strains without GTA. The study is important in understanding the drivers of evolution of bacterial plant pathogens.

genomics↗

bioRxiv2019

Phase variation of a signal transduction system controls Clostridioides difficile colony morphology, motility, and virulence

Recent work has revealed that Clostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. Many C. difficile strains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show that C. difficile reversibly differentiates into rough and smooth colony morphologies, and that bacteria derived from the isolates display opposing surface and swimming motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein CmrRST, which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of Type IV pili, suggesting a novel mechanism of surface expansion in C. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration. In a hamster model of acute C. difficile disease, colony morphology correlates with virulence, and the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressing C. difficile. Our findings indicate that C. difficile employs phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis.\n\nSignificance StatementPhenotypic heterogeneity within a genetically clonal population allows many mucosal pathogens to survive within their hosts, balancing the need to produce factors that promote colonization and persistence with the need to avoid the recognition of those factors by the host immune system. Recent work suggests that the human intestinal pathogen Clostridium difficile employs phase variation during infection to generate a heterogeneous population differing in swimming motility, toxin production, and more. This study identifies a signal transduction system that broadly impacts C. difficile physiology and behavior in vitro and in an animal model. Phase variation of this system is therefore poised to modulate the coordinated expression of multiple mechanisms influencing C. difficile disease development.

microbiology↗

bioRxiv2019

Recently emerged and diverse lineages of Xanthomonas perforans have independently evolved through plasmid acquisition and homologous recombination originating from multiple Xanthomonas species

Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of two decades including a shift in race, diversification into three genetic groups, and host range expansion to pepper. Recombination originating from X. euvesicatoria was identified as the primary factor driving the diversification of X. perforans in Florida. The aim of this study was to genetically characterize X. perforans strains that were isolated from tomato and pepper plants grown in Alabama and compare them to the previously published genomes available from GenBank. Surprisingly, a maximum likelihood phylogeny coupled with a Bayesian analysis of population structure revealed the presence of two novel genetic groups in Alabama, which each harbored a different transcription activation-like effector (TALE). While one TALE, avrHah1, was associated with adaptation of X. perforans to pepper, the other was identified as a new class within the avrBs3 family, designated here as pthXp1. Examination of patterns of homologous recombination between X. perforans and other closely related Xanthomonas spp. indicated that the lineages identified here emerged in part through recent recombination events originating from xanthomonads associated with diverse hosts of isolation. Our results also suggest that the evolution of pathogenicity to pepper has likely emerged independently within X. perforans and in one lineage, was associated with the recombination-mediated remodeling of the Xps type II secretion and TonB transduction systems.\n\nImportanceThe emergence of novel pathogen lineages has important implications in the sustainability of genetic resistance as a disease management tool in agricultural ecosystems. In this study, we identified two novel lineages of X. perforans in Alabama. While one lineage was isolated from symptomatic pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, pthXp1. Unlike AvrBs4, PthXp1overcomes Bs4-mediated resistance in tomato, indicating the evolution of this novel lineage towards fitness on this host. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts which results in the emergence of novel pathogen lineages and associated phenotypes, including host range expansion.

genomics↗

bioRxiv2019

Transfer of Xanthomonas campestris pv. arecae, and Xanthomonas campestris pv. musacearum to Xanthomonas vasicola (Vauterin) as Xanthomonas vasicola pv. arecae comb. nov., and Xanthomonas vasicola pv. musacearum comb. nov. and description of Xanthomonas vasicola pv. vasculorum pv. nov.

LETTER TO THE EDITOR LETTER TO THE EDITOR EMENDED DESCRIPTION OF... REFERENCES Members of the genus Xanthomonas, within the gamma-Proteobacteria, collectively cause disease on more than 400 plant species (Hayward 1993), though some members are apparently non-pathogenic (Vauterin et al. 1996) and some have been isolated from clinical samples such as skin microbiota (Seite, Zelenkova, and Martin 2017). Historically, taxonomy of Xanthomonas was tied to the host of isolation (Starr 1981; Wernham 1948), with the genus being split into large numbers of species, each defined by this single phenotypic feature (Dye 1962). Subsequently, most of the species were transferred (lumped) into a single species, X. campestris, and designated as nomenspec ...

microbiology↗

bioRxiv2018

Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding

With the growing importance of aquaculture worldwide, characterisation of the microbial flora of high-value aquaculture species and identification of gut flora shifts induced by changes in fish physiology or nutrition is of special interest.\n\nHere we report the first metabarcoding survey of the intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and intestinal samples, and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles.\n\nOver 1,000 operational taxonomic units (OTUs) were identified within the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae.\n\nThis survey was performed amid a summer heat wave, during which the fish exhibited reduced feeding. Although the sampled fish appeared healthy, they had minimal intestinal content, and the observed intestinal flora may represent the microbiota of fasting and stressed fish. Limited comparison between Mycoplasma and Vibrio sequences from the Chinook salmon gut and published microbial sequences from the intestines of a variety of fish species (including Atlantic salmon) indicated that despite the starvation and temperature variations, the replacement of Vibrio with Mycoplasma is occurring within expected ecological parameters and does not necessarily reflect colonisation by atypical microbes.\n\nDATA SUMMARYRaw sequences from Chinook salmon intestinal microbiome 16S survey generated on the Illumina platform are publically available through NCBI Sequence Read Archive (SRA) database:\n\nBioproject PRJNA421844\n\nSRA study SRP134829\n\nhttps://www.ncbi.nlm.nih.gov/bioproject/PRJNA421844\n\nIMPACT STATEMENTAlthough 16S metabarcoding surveys are becoming routine, little is still known about the microbiota of fish. This is the first survey of the intestinal microbiota of Chinook salmon, a species native to the Pacific Northwest which is farmed in New Zealand and Chile. While most intestinal microbiota studies are performed on faecal material, we directly sampled the intestine epithelium and content.\n\nDuring the time of sampling, the farmed fish population was experiencing stress from a summer heat wave and had little intestinal content. Over 1,000 operational taxonomic units (OTUs) were identified within the intestines of the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon.\n\nWe believe this survey will be of interest not only to those interested in fish biology and aquaculture, but also as an addition to the ongoing debate in the literature on sampling and DNA extraction methods for challenging samples.

microbiology↗

bioRxiv2017

Genome shuffling in a globalized bacterial plant pathogen: Recombination-mediated evolution in Xanthomonas euvesicatoria and X. perforans

Bacterial recombination and clonality underly the evolution and epidemiology of pathogenic lineages as well as their cosmopolitan spread. While the spread of stable clonal bacterial pathotypes drives disease epidemics, recombination leads to the evolution of new bacterial lineages. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages has generated new recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria (Xe) and X. perforans (Xp) are two closely related monophyletic species causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of strains representing populations on tomato in Nigeria and found shuffling of secretion systems and effectors such that these strains contain genes from both Xe and Xp. Multiple strains, from populations in Nigeria, Italy, and Florida, USA, exhibited extensive genomewide homologous recombination and both species exhibited dynamic open pangenomes. Our results show that recombination is generating new lineages of bacterial spot pathogens on tomato with consequences for disease management strategies.\n\nImportanceThe Xanthomonas pathogens that cause bacterial spot of tomato and pepper have been model systems for plant-microbe interactions. Two of these pathogens, X. euvesicatoria and X. perforans, are very closely related. Genome sequences of bacterial spot field strains from Nigeria, Italy, and the United States showed varying levels of homologous recombination that changed the amino sequence of effectors, secretion systems, and other proteins. This shuffling of genome content occurred between X. euvesicatoria and X. perforans, while a Nigerian lineage also contained the lipopolysaccharide cluster of a distantly related Xanthomonas species. Gene content varied among strains and the affected genes are important in the establishment of disease, therefore our findings point to global variation in the host-pathogen interaction driven by gene exchange among evolutionarily distinct lineages.

evolutionary biology↗