Author: slquinlan

Fungal Genet Biol. 2025 Sep 23:104038. doi: 10.1016/j.fgb.2025.104038. Online ahead of print.

ABSTRACT

Nitrous oxide (N₂O) derived from agricultural activity is a major contributor to Earth’s greenhouse effect. Synthetic nitrogen fertilizer applied at high levels, particularly combined with heavy rainfall events, generates hot spots of N₂O emissions in agricultural fields due to the process of microbial denitrification. Here, a key conserved fungal denitrification enzyme necessary for N₂O emissions was identified. Phylogenetic analysis revealed that fungal NOR1-like genes, with rare exceptions, are highly conserved and confined to the phylum Ascomycota. Plant pathogenic Fusarium species that possess NOR1 exhibited drastic differences in N₂O production based on denitrification potential. Functional characterization of the p450nor nitric oxide reductase encoding gene, NOR1, in the soil-borne denitrifying maize pathogen, Fusarium verticillioides, showed that this enzyme is critical for fungal N₂O production. Deletion of the single copy NOR1 gene in F. verticillioides eliminated N₂O emissions. Complementation of deletion mutants via the NOR1 gene add-back restored wild type N₂O emission levels and segregation analysis further corroborated the pivotal role of NOR1 for N₂O emissions. We suggest targeting of the NOR1 enzyme as an effective strategy to reduce fungal-based N₂O emissions.

PMID:40998212 | DOI:10.1016/j.fgb.2025.104038

Plant J. 2025 Sep;123(6):e70498. doi: 10.1111/tpj.70498.

ABSTRACT

The apoplast is a critical interface in plant-pathogen interactions, particularly in the context of pattern-triggered immunity (PTI), which is initiated by recognition of microbe-associated molecular patterns. Our study characterizes the proteomic profile of the Arabidopsis apoplast during PTI induced by flg22, a 22-amino-acid bacterial flagellin epitope, to elucidate the output of PTI. Apoplastic washing fluid was extracted with minimal cytoplasmic contamination for liquid chromatography-tandem mass spectrometry analysis. By comparing our data to publicly available transcriptome profiles of flg22 treatment from 1 to 18 h, we observed that several highly abundant proteins exhibit relatively unchanged gene expression across all time points. We also observed topological bias in peptide recovery of 19 enriched receptor-like kinases with peptides predominantly recovered from their ectodomains. Notably, tetraspanin 8, an exosome marker, was enriched in PTI samples. We additionally confirmed increased concentrations of exosomes during PTI. This study enhances our understanding of the proteomic changes in the apoplast during plant immune responses and lays the groundwork for future investigations into the molecular mechanisms of plant defense under recognition of pathogen molecular patterns.

PMID:40991770 | DOI:10.1111/tpj.70498

Phytopathology. 2025 Sep 23. doi: 10.1094/PHYTO-05-25-0178-R. Online ahead of print.

ABSTRACT

Pantoea stewartii subspecies indologenes (Psi) isolates can cause disease in several Poaceae hosts, including millets and rice and were recently known to cause foliar and bulb symptoms characteristic of center rot in onions. Cover crops such as millet and cash crops like corn are commonly grown in the summer after onion harvest in Vidalia, Georgia, USA. However, the risk of pathogen transmission to onions in the cropping systems where summer crops precede onion planting is largely understudied. We evaluated the survivability of Psi in corn and pearl millet residues and assessed its ability to colonize onions transplanted into the infested soil. Our microplot study showed that millet and corn residues support the transient survival of Psi. The presence of the pathogen in the soil also overlapped with the presence of onion transplants. However, despite planting onion seedlings in Psi-infested soil, no bacterial colonization was observed in their rhizosphere and foliar surfaces. We further investigated genetic determinants for bacterial survival in millet residue and bare soil by creating deletion mutants of the genes responsible for exopolysaccharides, flagellar motility, quorum sensing and pathogenicity in a Psi pathovar cepacicola strain PNA 14-12. All mutant strains persisted for at least 24 days in millet residue at high population levels and colonies of all the strains remained detectable in bare soil until 44 days. Overall, our findings suggest that the risk of Psi transmission from millet or corn residue to onions appears is considerably low.

PMID:40986336 | DOI:10.1094/PHYTO-05-25-0178-R

Carbohydr Polym. 2025 Nov 15;368(Pt 2):124161. doi: 10.1016/j.carbpol.2025.124161. Epub 2025 Aug 2.

ABSTRACT

Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I) and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model species Arabidopsis thaliana. Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and nuclear magnetic resonance analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical α-1,5-arabinan, β-1,4-galactan, β-1,6-galactan and arabinogalactan RG-I side chains of varying lengths, we show that a large portion of the β-1,6-galactan is terminated by either 4-O-methyl β-glucuronic acid (GlcA) residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification while 10 % of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha is additionally branched with β-galactose substituents. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.

PMID:40947194 | DOI:10.1016/j.carbpol.2025.124161

Microbiol Resour Announc. 2025 Sep 12:e0008325. doi: 10.1128/mra.00083-25. Online ahead of print.

ABSTRACT

Aspergillus parasiticus is a fungus recognized for producing highly carcinogenic mycotoxins. In this study, we collected 38 isolates of A. parasiticus from fields in South Georgia. We performed whole genome re-sequencing and developed 38 draft genome assemblies of A. parasiticus. The average genome size was 38.7 Mb, with larger genomes (~40 Mb) found in peanut fields in Turner County. Scaffold N50 was recorded highest for isolates collected from the corn fields of Tifton. The average BUSCO completeness score for these assemblies was 99.1%. The genome sequences generated for these 38 isolates will serve as a valuable genomic resource for the community working on aflatoxin mitigation strategies in crops.

PMID:40938094 | DOI:10.1128/mra.00083-25

Front Genet. 2025 Aug 25;16:1626083. doi: 10.3389/fgene.2025.1626083. eCollection 2025.

ABSTRACT

This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019-2022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.

PMID:40927363 | PMC:PMC12414770 | DOI:10.3389/fgene.2025.1626083

Appl Environ Microbiol. 2025 Sep 4:e0108325. doi: 10.1128/aem.01083-25. Online ahead of print.

ABSTRACT

Seeds can serve as a vehicle for the dissemination of pests and pathogens around the world. We recently demonstrated the association of pathogenic Alternaria brassicicola isolates with reduced sensitivity to azoxystrobin (quinone-outside inhibitor [QoI]) in naturally infested commercial broccoli seeds. In this study, we further demonstrate that these isolates were also resistant to two succinate dehydrogenase inhibitor (SDHI) fungicides. Sensitivity of representative A. brassicicola isolates (n = 58) from naturally infested broccoli seedlots to QoI and SDHI fungicides was evaluated under in vitro conditions. Interestingly, 15% (n = 9/58) of the A. brassicicola isolates with reduced sensitivity to azoxystrobin also displayed reduced sensitivity to two commonly used SDHI fungicides (boscalid and penthiopyrad) in broccoli, indicating a potential case of cross-resistance to SDHI fungicides. Ninety-three percent of the isolates (n = 54/58) were resistant to both boscalid and penthiopyrad, while 100% isolates displayed sensitivity to fluopyram. Sequence analysis of sdh genes revealed the presence of only one point mutation (H134R) in the sdhC gene in isolates that displayed resistance to boscalid and penthiopyrad. We also developed and validated allele-specific primers targeting the H134R mutation for rapid screening of SDHI resistance in A. brassicicola. We also found that boscalid-resistant isolates exhibited significantly reduced mycelial growth. However, spore germination rates among different resistant isolates were not different, suggesting that resistant isolates remain competitive in natural populations. Overall, this study provides the first evidence of fungicide resistance to SDHI fungicides in A. brassicicola isolated from naturally infested broccoli seeds and underscores the importance of seeds as a potential source for introducing fungicide resistance across geographical locations.

IMPORTANCE: Alternaria brassicicola is a fungal seed-borne pathogen that can be disseminated via commercial seeds across transplant houses and commercial broccoli fields. Our study provides the first evidence that commercial broccoli seeds can harbor pathogenic A. brassicicola isolates with cross-resistance to two succinate dehydrogenase inhibitor (SDHI) fungicides. We observed that 93% of the A. brassicicola isolates from naturally infested commercial broccoli seeds contained a point mutation that conferred resistance to two SDHI fungicides (boscalid and penthiopyrad). Furthermore, we developed a PCR-based allele-specific assay for the rapid detection and monitoring of fungicide resistance. Our study highlights the importance of seed health testing and potential dissemination of fungicide-resistant isolates locally and globally, thus impacting disease management strategies.

PMID:40905662 | DOI:10.1128/aem.01083-25

Sci Adv. 2025 Sep 5;11(36):eadw7764. doi: 10.1126/sciadv.adw7764. Epub 2025 Sep 3.

ABSTRACT

Respiratory tract infections pose considerable global health challenges. Upper airway colonization is pivotal to these infections, including those caused by Bordetella species. We identified an oligosaccharide, bordetellae colonization oligosaccharide (b-Cool), crucial for early nasal colonization of Bordetella bronchiseptica. We characterized the structure of b-Cool by LC-MS and NMR and found that it is prevalent across a diverse range of bordetellae, including Bordetella pertussis, which causes whooping cough in humans. A B. bronchiseptica mutant lacking b-Cool (Δb-Cool) showed significantly delayed and decreased colonization in mouse nasopharynx and nasal epithelia, resulting in decreased transmission. The colonization defect of Δb-Cool was rescued in mucin deficient mice, suggesting that b-Cool may facilitate colonization in the presence of airway mucins.

PMID:40901963 | DOI:10.1126/sciadv.adw7764

Plant Physiol. 2025 Sep 1:kiaf375. doi: 10.1093/plphys/kiaf375. Online ahead of print.

ABSTRACT

Plant specialized metabolism is intricately regulated and often compartmentalized at the cell-type level. Understanding where and when metabolites accumulate is essential for uncovering their function, biosynthesis, and regulation. Historically, studies have inferred metabolite localization based on the expression patterns of genes encoding biosynthetic enzymes, but these approaches fall short due to the complexity of metabolite transport and the discrepancy between transcript, protein, and metabolite abundance. Recent advances in mass spectrometry imaging, single-cell transcriptomics, and multi-omics have enabled the direct visualization and quantification of metabolites and gene expression at cellular resolution. These technologies have revealed striking cell type- and organ-specific patterns of metabolite accumulation, as well as the underlying transcriptional and chromatin regulatory networks. In this review, we describe case studies in several model and medicinal plant species that highlight the roles of rare or specialized cell types in specialized metabolite biosynthesis and the importance of spatiotemporal regulation. In addition, we discuss why it is becoming increasingly important to transition from single- to multi-omics approaches. As new tools continue to evolve, the regulation of plant metabolism will be uncovered at higher resolution, enabling precise pathway discovery and metabolic engineering for agriculture, biotechnology, and medicine.

PMID:40889291 | DOI:10.1093/plphys/kiaf375

Plant Dis. 2025 Aug 26. doi: 10.1094/PDIS-03-25-0469-RE. Online ahead of print.

ABSTRACT

The severity of tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) in commercially grown tomato cultivars has been increasingly exacerbated in recent years in the southeastern United States. Four research trials were conducted over two consecutive fall seasons in the years 2022 and 2023 to assess the performance of tomato (Solanum lycopersicum L.) cultivars introgressed with single (Ty-1) or combinations of (Ty-3 and Ty-6) resistance gene(s) in Georgia, USA. In 2022, studies were conducted on a commercial farm in Colquitt County and a research farm in Tift County. In 2023, experiments were performed on a commercial farm in Grady County and a Tift County research farm. Tomato cultivars (cv.) with an intermediate resistance to tomato yellow leaf curl virus (TYLCV-IR), including Camaro, Grand Marshall, Jolene, Red Snapper, STM 2255, and Varsity, were compared to the TYLCV-susceptible (TYLCV-s) cv. Myrtle. This study evaluates the total produced yield of tomato cv. under natural disease incidence, severity, relative maturity and marketable yield. Our findings suggest TYLCV-IR cv. STM 2255, Jolene and Grand Marshall, except Red Snapper, had a lower virus incidence compared to cv. Myrtle. Moreover, cv. Red Snapper, Varsity and Camaro exhibited moderate disease progression in our research plots. The cultivars Grand Marshall and Jolene had significantly lower TYLCD severity than Myrtle. Furthermore, fruit yields per plant were highest for Camaro, Grand Marshall, Jolene, and STM 2255. Overall, Camaro, Grand Marshall, Jolene, and STM 2255 performed the best based on moderate-to-low TYLCD incidence and severity, and superior yield among the evaluated tomato cultivars. Therefore, identifying the most resistant/tolerant and environmentally suitable cultivars is needed to mitigate the viral disease in tomatoes.

PMID:40857747 | DOI:10.1094/PDIS-03-25-0469-RE