Author: slquinlan

Microbiol Spectr. 2026 Jun 22:e0412425. doi: 10.1128/spectrum.04124-25. Online ahead of print.

ABSTRACT

Pattern-triggered immunity (PTI) provides broad-spectrum protection in plants by activating defense responses upon perception of conserved microbial signatures such as bacterial flagellin. In vitro transcriptome profiling revealed that the Pseudomonas syringae pv. tomato DC3000 two-component regulator CvsR mirrors some of the broader regulatory patterns observed under the exposure to PTI in planta. Our analyses indicated that during infection in planta, CvsR primarily governs a small core regulon centered on carbonic anhydrase and its associated transporter. Comparative RNA-seq analyses between the ΔcvsR and wild-type strain further confirm this narrow regulatory scope. Moreover, the majority of bacterial transcriptional shifts appear to reflect indirect consequences of response to the host immune environment rather than direct CvsR-dependent regulation, including responses associated with sulfate starvation. Together, these findings suggest that PTI-driven bacterial transcriptional reprogramming is shaped predominantly by host immune status, with CvsR exerting modest, targeted control restricted to a limited set of genes.

IMPORTANCE: Pattern-triggered immunity (PTI) provides broad-spectrum disease resistance in plants by recognizing conserved microbial patterns such as bacterial flagellin. Activation of PTI alters the environment that pathogens encounter during infection, yet how bacteria respond to these immune-imposed conditions at the molecular level remains poorly understood. In this study, we profile the bacterial transcriptome directly in planta during infection with RNA-seq, providing a detailed view of pathogen responses under immune pressure. We focus on the previously identified two-component regulator CvsR and show that, despite widespread transcriptional changes induced by PTI, CvsR directly controls only a small core set of genes in planta. Instead, most bacterial transcriptional shifts reflect indirect responses to the immune-modified host environment. By capturing pathogen gene expression during infection, this work clarifies how plant immunity constrains bacterial physiology and provides insight that can inform sustainable strategies for crop protection.

PMID:42390087 | DOI:10.1128/spectrum.04124-25

Microbiol Resour Announc. 2026 Jun 29:e0040126. doi: 10.1128/mra.00401-26. Online ahead of print.

ABSTRACT

Areolate mildew is a foliar disease of cotton, with two fungal species reported as causal pathogens. We announce the first genome of Ramulariopsis gossypii. The genome size is 33.34 Mbp, with an N50 of 2.116 Mb and Benchmarking Universal Single-Copy Orthologs completeness of 98.8%, providing a resource for comparative genomics and disease management.

PMID:42378326 | DOI:10.1128/mra.00401-26

J Food Prot. 2026 Jun 29:100848. doi: 10.1016/j.jfp.2026.100848. Online ahead of print.

ABSTRACT

Food safety at neighborhood stores may differ for communities of distinct socioeconomic strata, but such differences are underexplored. We aimed to characterize microbial contamination (MC) on fresh produce available to Athens, GA communities (k = 2) of diverse socioeconomic composition. MC was assessed as a function of the main effects of season, store type, and community, and their 2- and 3-way interactions. Cucumbers, lettuce, and tomatoes (144 each) from groceries, supermarkets, and superstores – collected over winter and summer from each community – were tested for generic Escherichia coli, coliforms, and Salmonella enterica using culture-based methods. Presumptive S. enterica colonies (n = 338) were identified with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. No S. enterica was detected, and predominant off-target genera showed trends per the isolation media used. Generic E. coli load was below countable range for all samples. Mean coliform load (MCL) variation on cucumbers was driven by the interaction of community and store type (P<0.01) and that of season and store type (P<0.01). Higher resource community (HR) grocery cucumbers had greater MCL, 4.00 log CFU/g, than superstore cucumbers, 3.07 log CFU/g. Lower resource community superstore cucumbers had greater MCL, 3.04 log CFU/g, than grocery cucumbers, 2.05 log CFU/g. Superstore cucumbers had greater MCL, 3.46 log CFU/g, than grocery cucumbers, 2.45 log CFU/g in summer. In winter superstore cucumbers had lower MCL, 2.66 log CFU/g, than grocery cucumbers, 3.60 log CFU/g. MCL variation on lettuce was driven by the interaction of community and store type (P<0.01). MCL on lettuce from HR groceries and superstores, 1.86 log CFU/g and 1.42 log CFU/g, respectively, was greater relative to supermarkets, 0.96 log CFU/g. These findings show that season, the built food environment, and community context interact to drive coliform load differences on retail produce available to Athens communities.

PMID:42373078 | DOI:10.1016/j.jfp.2026.100848

Plant Dis. 2026 Jun 26. doi: 10.1094/PDIS-04-26-0730-RE. Online ahead of print.

ABSTRACT

Silverleaf whitefly (Bemisia tabaci), silverleaf disorder (SLD), and whitefly-transmitted viruses (WTVs) are major constraints to cucurbit production in the southeastern United States. Two field trials were conducted in Tifton, Georgia, USA, during the fall of 2023 and 2024 to evaluate yellow squash and zucchini (Cucurbita pepo L.) cultivars for tolerance to SLD and WTVs. In one experiment, 10 yellow squash cultivars (8 straight neck: ‘Cougar,’ ‘Lioness,’ ‘Multipik,’ ‘Lazor,’ ‘Grand Prize,’ ‘Gold Prize,’ ‘Enterprise,’ and ‘Fortune’; and 2 semi-crook neck: ‘Gentry’ and ‘Gold Star’) were evaluated. In another experiment, 10 zucchini cultivars: three spineless (‘Spineless Perfection,’ ‘Spineless King,’ and ‘Spineless Supreme’), 2 gray types (‘Hurakan,’ and ‘Rocio’), and 5 green types (‘MGO477, ‘Everglade,’ ‘Cardea,’ ‘Fortress,’ and ‘Renegade’) were evaluated. ‘Gold Star’ and ‘Spineless Perfection’ served as susceptible controls. In yellow squash, ‘Lioness’ and ‘Cougar’ displayed the lowest SLD progression. Area under symptom progress curve (AUSPC) values for SLD were 203 in 2023 and 202 in 2024 for ‘Lioness,’ and 446 in 2023 and 490 in 2024 for ‘Cougar.’ Virus incidence was also lowest in ‘Lioness’ (area under disease progress curve (AUDPC) values 315 in 2023 and 403 in 2024) and ‘Cougar’ (AUDPC values of 548 in 2023 and 516 in 2024). Aligned rank transformed (ART) values for virus severity were smallest in ‘Lioness’ (7), followed by ‘Enterprise’ and ‘Grand Prize’ (27), and ‘Cougar’ (31). ‘Cougar’ and ‘Lioness’ cultivars produced the highest marketable yields (25,986 and 24,565 kg ha⁻¹ respectively in 2023). In zucchini, ‘Rocio’ and ‘Hurakan’ had the lowest AUSPC values (204 in 2023 and 197 in 2024 for ‘Rocio’ and 497 in 2023 and 427 in 2024 for ‘Hurakan). ‘Rocio,’ ‘Hurakan’, and ‘Renegade’ recorded the lowest AUDPC values and virus severity (ART = 13). Marketable yields were highest in ‘Renegade’ (40,421 kg ha⁻¹), followed by ‘Hurakan’ and ‘Rocio.’ Across crops and years, cucurbit chlorotic yellows virus (CCYV) predominated over cucurbit yellow stunting disorder virus (CYSDV) and cucurbit leaf crumple virus (CuLCrV). Overall, ‘Lioness’, ‘Cougar’, ‘Renegade’, ‘Hurakan’, and ‘Rocio’ demonstrated superior performance with tolerance to SLD and WTVs while maintaining high yield.

PMID:42360824 | DOI:10.1094/PDIS-04-26-0730-RE

Front Plant Sci. 2026 Jun 10;17:1838203. doi: 10.3389/fpls.2026.1838203. eCollection 2026.

ABSTRACT

Peanut (Arachis hypogaea L.) is an important crop in the world, serving as a key source of edible oil and protein. Comprehensive genomic and phenotypic analyses were conducted on 87 accessions from the U.S. peanut mini-core collection using 217 Gb of high-quality resequencing data to identify the candidate genes and markers that underlie the leaf spot resistance and seed dormancy in peanuts. A total of 87,726 SNPs were identified and mapped across 20 chromosomes, revealing a higher SNP density in the B subgenome (35.55 SNPs/Mb) compared to the A subgenome (33.26 SNPs/Mb). Phylogenetic, population structure, and principal component analyses consistently partitioned the accessions into three distinct gene pools designated as Group 1, 2, and 3. Group 1, comprising primarily Arachis hypogaea, included 28 genotypes; Group 2, mainly fastigiata types, comprised 18 accessions; while Group 3, displaying the highest diversity, contained mixed genotypes from the other groups. Linkage disequilibrium analysis indicated an LD decay distance of approximately 63.1 kb, confirming that the marker density was sufficient for GWAS. Significant SNP associations at a suggestive threshold of p< 1.14 × 10^-1 were identified for leaf spot, seed germination and dormancy agronomic traits. As a result, three candidate genes were identified: Ah11g381400, homologous to Arabidopsis ATE1, was associated with early leaf spot resistance; Ah16g445600, a homolog of ERF34, was linked to late leaf spot resistance; and Ah19g214100, homologous to ICE1, emerged as a central regulator affecting both germination and dormancy. These findings provide actionable targets for marker-assisted selection to enhance disease resilience and seed quality in breeding programs.

PMID:42359412 | PMC:PMC13290452 | DOI:10.3389/fpls.2026.1838203

Struct Dyn. 2026 Jun 15;13(3):034302. doi: 10.1063/4.0001213. eCollection 2026 May.

ABSTRACT

Polysaccharide structural assignment via nuclear magnetic resonance (NMR) spectroscopy remains an analytical challenge due to spectral overlap because of limited chemical shift dispersion. This challenge is exacerbated by the wide-spread use of proton (¹H) detection. Progress has also been hindered by the dispersed nature of carbohydrate databases and the restricted applicability of most prediction tools, which provide limited atom-specific residue discrimination in larger polymers. These limitations hamper the efficient characterization of glycosyltransferase (GT) activity, which depends on defining donor-acceptor substrate pairs and accurately identifying corresponding products. Here, we demonstrate the utility of high field ¹³C-detected NMR for the assignment of two homohexamers. Laminarihexaose and xylohexaose were analyzed using 2D heteronuclear correlation and correlation via long-range coupling (COLOC) experiments to evaluate whether complete residue level assignments could be achieved. The COLOC experiment revealed long range correlations that were not resolved using heteronuclear multiple bond correlation, and the 1D ¹³C spectra provided exceptional resolution, including distinct shoulders corresponding to residue specific chemical shift differences previously assumed to be indistinguishable. These findings suggest that high field ¹³C NMR can provide the nuanced atom level information required to train machine learning models for predicting chemical shift assignments of large, complex, and highly degenerate polysaccharides. Such models offer a promising framework for rapid structural identification of GT reaction products, enabling progress of high throughput characterization of plant derived polysaccharides central to renewable biomaterial development.

PMID:42358500 | PMC:PMC13293230 | DOI:10.1063/4.0001213

Theor Appl Genet. 2026 Jun 24;139(7):189. doi: 10.1007/s00122-026-05302-w.

ABSTRACT

The combination of four variant fatty acid desaturate alleles achieves the desired high oleic and low linolenic acid fatty acid profile in soybean seed oil across U.S. production environments. Soybean is a global crop that represents over half of current world oilseed production. Soybean oil has been utilized in the food system based on the functional and health properties of the fatty acid profile; there is an urgent need to adjust the fatty acids in soybean oil to meet current market demands. The soybean high oleic acid seed oil trait (> 75%) in conjunction with a low linolenic acid trait (< 3%) has emerged as an avenue to improve the oil. The objective of this research was to identify a soybean genotypic group comprised of variant alleles of fatty acid desaturase genes that could meet the target stable seed oil fatty acid thresholds across the U.S. soybean production environments. New soybean genotypes were created with different gene combinations for seed oil fatty acid profile and maturity groups, seeds were produced in their target environments, and fatty acid profiles of the seeds were determined. The results demonstrated that a four-gene combination in soybean genotypes using either of two variant versions of one of the genes achieved both the target thresholds in environments across the U.S. soybean production regions. There were significant differences in individual fatty acid levels in the seed oil when comparing the two four-gene genotypic groups. The impact of this work is the new knowledge to design soybean varieties for U.S. production environments with seed oil fatty acid profiles targeted to meet current market thresholds; the fatty acid profiles obtained can serve as the basis for improved products.

PMID:42342884 | DOI:10.1007/s00122-026-05302-w

Proc Natl Acad Sci U S A. 2026 Jun 30;123(26):e2536339123. doi: 10.1073/pnas.2536339123. Epub 2026 Jun 24.

ABSTRACT

Meiosis is a hallmark of sexual reproduction. Although the core meiotic machinery is evolutionarily conserved from unicellular yeasts to Metazoan, the key regulators responsible for initiating meiosis vary across species and remain largely unidentified in major eukaryotic lineages, including the major phylum Basidiomycota in the Kingdom Fungi. The basidiomycete fungus Cryptococcus neoformans is a critical pathogen listed by the World Health Organization that causes life-threatening meningoencephalitis worldwide. Meiosis not only indirectly facilitates cryptococcal pathogenicity through generating genetically diverse spores but also directly contributes to host adaptation and disease progression. Here, we identified a novel transcription factor Msd1 that is responsible for activating meiosis in C. neoformans. Deletion of MSD1 impaired multiple sexual development events and strikingly abolished meiosis and subsequent sporogenesis (gametogenesis). Conversely, overexpression of MSD1 alone is sufficient to drive meiosis and the formation of meiotic spores, even in the absence of the external mating-inducing cues or when the mating pathway is genetically inactivated. Mechanistically, we demonstrated that Msd1 initiates meiotic entry by targeting two interconnected pathways. First, Msd1 activates the transcription of multiple evolutionarily conserved core meiosis-specific genes such as meiotic recombinase Dmc1. Second, Msd1 activates two RNA-binding proteins, Csa1 and Csa2, which ensure spatiotemporal expression of the aforementioned meiosis-specific genes to drive meiosis and sporogenesis. Collectively, our findings demonstrate that meiosis and the sequential sexual development events are spatiotemporally orchestrated by the master regulator Msd1, and is the first reported regulator initiating meiotic entry in a basidiomycete fungus.

PMID:42341051 | DOI:10.1073/pnas.2536339123

PLoS One. 2026 Jun 24;21(6):e0351929. doi: 10.1371/journal.pone.0351929. eCollection 2026.

ABSTRACT

The introduction of novel generalist predators to new ecosystems can dramatically alter species interactions and established food webs. Invasive predators may contribute to pest control services; however, a net loss of biodiversity can occur if invasives displace natives through intraguild predation or resource competition. Joro spiders (Trichonephila clavata) are an introduced, orb-weaving spider that show rapid range expansion in the United States. Trophic patterns of orb-weaving spiders are largely unknown, and as such, the impact of Joro spiders on established food webs is unclear. We explored patterns of diet composition and prey overlap between Joro spiders and three co-occurring, native orb-weaving species with molecular gut content analysis. In addition, we asked whether the composition of focal native spider diets differed at sites co-inhabited by Joro spiders. We collected female spiders from 52 sites within the Joro spider’s introduced range and analyzed gut content via DNA metabarcoding and high-throughput Illumina sequencing. Despite overlap in many prey taxa consumed, overall diet composition was dissimilar between Joro and native spiders. Joro spider diets were distinct, with at least 26 unique prey taxa not detected in native spider diets. Moreover, native spider diets were similar regardless of whether Joro spiders were present at collection sites. Thus, our initial analysis suggests that while Joro spider diets do overlap with native spiders, their use of many unique food resources does not suggest strong competition. Additional research into web placement and spatial overlap as mechanisms underlying Joro spider invasion success should help clarify the potential for exclusion of native predator populations.

PMID:42340952 | PMC:PMC13293469 | DOI:10.1371/journal.pone.0351929

Phytopathology. 2026 Jun 17. doi: 10.1094/PHYTO-04-26-0136-SC. Online ahead of print.

ABSTRACT

Pantoea ananatis is a widely distributed bacterium and is one of the causal agents of onion center rot, a disease responsible for significant global yield losses. While the environmental isolate P. ananatis SK-1, recovered from the Shirakawa River, Japan, is known to induce tissue necrosis in onion, the genetic basis of its pathogenicity remained uncharacterized. In this study, we generated a high-quality hybrid genome assembly of SK-1 using Oxford Nanopore and Illumina sequencing, yielding a 5.0 Mb genome across three contigs with 100% completeness as determined by CheckM. Genomic analysis identified a highly conserved HiVir (high virulence) cluster, a known pathogenicity gene cluster in onion-pathogenic Pantoea spp. However, the alt (allicin tolerance) cluster, which is responsible for imparting tolerance to thiosulfinates in onion tissue, was absent. Functional assays demonstrated that deletion of pepM, a key gene in the HiVir cluster, abolished necrosis in onion tissues, while complementation restored pathogenesis. In contrast, SK-1 exhibited reduced growth in onion juice, consistent with increased sensitivity to thiosulfinates that supports the lack of alt cluster in the bacterium. These findings indicate that although SK-1 possesses onion-pathogenic potential, it lacked the ability to proliferate in onion tissue, suggesting a limited capacity to rot onion.

PMID:42308459 | DOI:10.1094/PHYTO-04-26-0136-SC