Biology subjects

Potnis, N.

Publications and source records attributed to Potnis, N..

11 recordsLinked to original sources

bioRxiv2026

Drought-tolerant phenotypes associated with patterns of deterministic microbiome assembly across peanut genotypes

Plant-associated microbiomes contribute to plant health and resilience, yet the extent to which host traits shape microbiome assembly remains poorly understood despite increasing interest in leveraging them for crop performance. Here, we investigated whether drought-response phenotypes are associated with reproducible patterns of microbiome assembly across peanut genotypes under field conditions. The cultivars represented three drought-response categories: water-savers with tighter stomatal regulation, water-spenders with deeper root systems, and drought-sensitive genotypes. Bacterial and fungal communities were characterized from bulk soil, rhizosphere, and root endosphere compartments of six non-stressed peanut cultivars. Both host genotype and drought-response phenotype were associated with microbiome composition, with phenotype-associated patterns remaining detectable across multiple genetic backgrounds. Unexpectedly, the strongest phenotype-associated differences occurred in bulk soil communities, suggesting plant-mediated effects extending beyond the immediate root zone. Community differences were driven primarily by shifts in the relative abundance of existing taxa rather than turnover of distinct microbial lineages. Fungal communities responded more strongly to host phenotype than bacterial communities, with water-spender genotypes supporting greater fungal diversity and uniquely enriched taxa in the rhizosphere and endosphere. Neutral community modeling indicated stronger deterministic filtering of fungi than bacteria. Together, these findings demonstrate that drought-response phenotypes shape reproducible microbiome variation before stress exposure. HighlightThis study investigates the potential for host phenotype-associated drivers of microbiome assembly in drought-tolerant peanut cultivars that represented different physiological mechanisms for drought tolerance.

microbiology↗

bioRxiv2026

Spatio-temporal coordination of virulence, metabolism, and stress responses shapes infection dynamics of Xanthomonas perforans

Plants provide distinct ecological niches for diverse microbial communities, with each member adopting strategies tailored to the specific ecological niche it inhabits. Two foliar niches, the leaf surface (epiphytic environment) and the apoplast, impose distinct physiological constraints on microbial fitness, particularly for hemibiotrophic pathogens. In this study, we investigated how these environments shape the transcriptional responses of Xanthomonas perforans (Xp), a tomato pathogen, and how its virulence factors, metabolic pathways, and regulatory networks are spatially and temporally coordinated during disease progression. Transcriptome profiling of a pathogen recovered from the leaf surface and apoplast revealed pronounced niche-specific and colonization stage-specific gene expression patterns. Early epiphytic colonization was characterized by activation of chemosensing, and motility pathways that facilitate pathogen relocation and acquisition of limiting nutrients such as iron and phosphate. This stage also featured induction of DNA and protein repair systems, quorum sensing pathways, phenylalanine degradation and tyrosine conversion to counter phenylpropanoid defenses, genes involved in mitigating osmotic and oxidative stress, active DNA exchange machinery, and type VI secretion system-mediated microbial competition. Upon entry into the apoplast, Xp shifted toward active metabolism and replication, accompanied by investment in type II and III secreted virulence factor expression. Genes involved in evasion of plant immunity and overcoming of host-mediated nutrient sequestration were also upregulated, including those involved in quinone detoxification, phosphate and sulfur uptake, and fatty acid, xanthan, and LPS biosynthesis. During late apoplastic colonization, the pathogen transitioned again towards strong stress response activation, followed by renewed expression of flagellar motility and chemotaxis genes, suggesting preparation for dissemination. Notably, genes associated with oxidative and nutrient stress were enriched across both niches, although specific components differed. Type IV pili, conjugation genes, and plasmid-borne type III effectors were induced early in both niches, suggesting their niche-independent role in initial establishment. Together, these findings reveal a coordinated spatio-temporal regulatory strategy during the transition from the leaf surface to the apoplast. Author SummaryXanthomonas perforans is a foliar bacterial pathogen that infects tomato plants and leads to severe yield losses. To establish a successful infection, the pathogen must overcome a series of environmental and host-imposed challenges. This study characterizes the traits activated at distinct stages of infection, during both early and late pathogenesis, and across different niches, including the leaf surface and its interior (apoplastic) space. On the leaf surface Xanthomonas mainly focuses on movement, communication, and survival against stress and starvation with the major functions related to motility, nutrient uptake, and DNA transfer during early stages. Once inside the leaf, the bacteria switches tactics to focus primarily on reproduction, defense against the plant immune response, production of factors that weaken the plants defenses and gaining access to nutrients the plant normally restricts. Understanding the different stages of infection may inform how the crosstalk among host and pathogen unfolds during pathogenesis allowing us to understand the host environment. These findings can help us discover pathogen weaknesses that could be targeted for disease management.

microbiology↗

bioRxiv2024

Climatic fluctuations modulate eco-evolutionary processes associated with pathogen dynamics and continue to fuel bacterial spot epidemics in tomato

Recurring outbreaks caused by endemic pathogens continue to pose problems in managing plant, wildlife, livestock and human health. Understanding how these outbreaks unfold and what drives the variability in disease epidemics across space and time is less understood, especially in the agricultural settings. In this study, we investigated the contribution of pathogen genetic diversity, climatic variation and their interaction towards disease dynamics, with an integrative approach grounded on multitype, high resolution sequencing data and analysis techniques. This investigation was carried out for bacterial spot disease epidemic by surveying tomato fields for bacterial pathogen (Xanthomonas perforans) across southeastern US over a span of three years. The strength of epidemic severity varied across space and time in the agricultural fields. Disease severity was positively associated with strain diversity, and was linked to environmental fluctuations, specifically, large variation and extreme changes in certain climatic factors. Strain-resolved metagenomics approach revealed that co-existence of multiple pathogen lineages was common in the individual fields, although accompanied by differential lineage dynamics. The co-occurring lineages displayed environmentally dependent fitness contributions. By tracing allelic frequencies in pathogen populations across temporal scales, we find evidence for asynchronous allele cycling across seasons, hinting at the presence of adaptive single-nucleotide polymorphisms (SNPs) being polymorphic in space in response to seasonality. Despite this pathogen heterogeneity, we identified positively selected loci under parallel evolution, which may explain the nature of selection pressures experienced by the pathogen. While single pathogen lineage is assumed to dominate the host in the agricultural settings, our findings challenge this notion by demonstrating genetic diversity in the pathogen population observed within a single field and linking it to the disease dynamics. Our results explain the role of pathogen genetic diversity, climate-dependent compositional dynamics, and differential fitness contributions in dictating the variability of disease epidemics in the agricultural settings. Such findings will be invaluable for building predictive models in disease epidemiology. Our high-resolution combinatorial approach exploiting high- resolution sequence data, metadata types and analysis tools, is general enough to finely investigate disease epidemics at large scales in diverse case-studies concerning plant, animal and human health.

microbiology↗

bioRxiv2024

Within-host adaptation of a foliar pathogen, Xanthomonas, on pepper in presence of quantitative resistance and ozone stress

O_LIThe evolving threat of new pathogen variants in the face of global environmental changes poses a risk to the plant health and can impact the efficacy of resistance-based disease management. C_LIO_LIHere, we studied short-term eco-evolutionary response of the pathogen, Xanthomonas perforans, on quantitative resistant and susceptible pepper during a single growing season in open-top chambers under the influence of elevated Ozone (O3). C_LIO_LIWe observed increased disease severity, accompanied by higher variation on resistant cultivar under elevated O3, with no apparent change on the susceptible cultivar. This altered resistance response under elevated O3 is linked to altered eco-evolutionary dynamics of pathogen. While a single pathogen genotype remained prevalent on susceptible cultivar, resistant cultivar supported heterogenous pathogen population, with the evidence of short- term evolutionary modifications seeded by de novo parallel mutations. Altered O3 levels led to strain turnover on resistant cultivar with higher within-host polymorphism containing higher proportion of random de novo mutations lacking parallelism. C_LIO_LIPopulation heterogeneity is a mechanism of pathogen adaptation in response to the stressors. While parallel mutations in response to quantitative resistance may provide clues to predicting long-term pathogen evolution, high proportion of transient mutations suggest less predictable pathogen evolution under climatic alterations. C_LI

evolutionary biology↗

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↗

bioRxiv2023

Influence of co-occurring weakly pathogenic bacterial species on bacterial spot disease dynamics on tomato

Mixed infections caused by multiple pathogenic and/ weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of co-infection on disease dynamics on tomato using bacterial spot pathogen, Xanthomonas perforans (Xp) and two co-occurring weakly pathogenic strains of X. arboricola (Xa) and Pseudomonas capsici (Pc). Time-series greenhouse co-infection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in co-infection by three species compared to infection by Xp alone. However, co-infection by dual species, Xp and Pc or Xa resulted in lower disease severity compared to Xp alone. Thus, co-infection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in co-infection. However, Xp population dynamics was dependent on co-infecting partner. While resource competition might be a possible explanation for lower Xp population in dual co-infection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in presence of three-species interaction compared to Xp and Xa co-infection, suggesting potential modulation of co-operative interactions among Xp and Xa in three-species co-infection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted importance of co-infection dynamics in studying plant disease outbreaks.

ecology↗

bioRxiv2022

Complete functional analysis of type IV pilus components of a reemergent plant pathogen reveals neofunctionalization of paralog genes

Type IV pilus (TFP) is a multifunctional bacterial structure involved in twitching motility, adhesion, biofilm formation, as well as natural competence. Here, by mutagenesis and functional analysis, we dissected the roles of all genes required for TFP biosynthesis and regulation in the reemergent plant pathogenic fastidious prokaryote Xylella fastidiosa. This xylem-limited, insect-transmitted pathogen lives constantly under flow conditions and therefore is highly dependent on TFP for host colonization. In addition, TFP-mediated natural transformation is a process that impacts genomic diversity and environmental fitness. Ten out of the thirty-eight genes analyzed were essential for movement and natural competence. Interestingly, seven sets of paralogs exist, and mutations showed opposing phenotypes, indicating evolutionary neofunctionalization of subunits within TFP. The minor pilin FimT3 was the only protein exclusively required for natural competence. We determined that FimT3 (but not the other two FimT paralogs) is a DNA receptor that is conserved among X. fastidiosa strains and binds DNA non-specifically via an electropositive surface. Among plant pathogens, this gene was also found in the genome of strains of the plant associated Xanthomonadaceae family. Overall, we highlight here the complex regulation of TFP in X. fastidiosa, providing a blueprint to understand TFP in other bacteria living under flow conditions.

microbiology↗

bioRxiv2022

Biotic and abiotic stress distinctly drive the phyllosphere microbial community structure

While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance to these stresses. We evaluated the impact of one such abiotic stress, elevated tropospheric ozone (O3), under open-top chamber field conditions on host susceptibility and phyllosphere microbiome associated with pepper cultivars resistant and susceptible to Xanthomonas. Pathogen challenge resulted in distinct microbial community structures in both cultivars under an ambient environment. Elevated O3 alone affected microbial community structure associated with resistant cultivar but not the susceptible cultivar, indicating the role of host genotypic background in response to abiotic stress. Elevated O3 did not influence overall host susceptibility but did increase disease severity on the resistant cultivar, indicating a possible compromise in the resistance. Interestingly, combined stress resulted in a shift in microbial composition and structure like that observed with pathogen challenge alone. It indicates the possible prioritization of community response towards the most significant stress and pathogen being most influential regardless of the cultivar. Despite community composition differences, overall functional redundancy was observed in the phyllosphere community. To gain insights into community-level interactions, network topology assessment indicated a stable network with enhanced taxon connectedness upon pathogen challenge. However, an observation of destabilized random network with a shift in hub taxa in the presence of combined stress warrants future studies on the consequences of such unstable microbial communities on host response to pathogens in the face of climate change.

ecology↗

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↗

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↗