Author: slquinlan

Biotechnol Biofuels Bioprod. 2025 Oct 27;18(1):109. doi: 10.1186/s13068-025-02703-9.

ABSTRACT

BACKGROUND: Liquid fuels from lignocellulosic feedstocks are required for transition to a sustainable bioeconomy. However, the recalcitrance of carbon-containing feedstock cell walls to deconstruction poses a barrier to cost effective biological conversion of plant biomass to biofuels. One-step consolidated bioprocessing (CBP) in which anaerobic thermophilic bacteria convert lignocellulosic biomass into liquid fuels is a platform for overcoming the recalcitrance of plant biomass.

RESULTS: The amounts of hemicellulosic and pectic polysaccharides, two complex cell wall glycans that contribute to plant biomass recalcitrance and that are partially solubilized during CBP of switchgrass aerial biomass by Clostridium thermocellum were evaluated in the liquor, solid residues and residue washate recovered during a 120-h CBP process. After 120 h, 24% of milled switchgrass was solubilized in the C. thermocellum CBP platform. Higher concentrations of arabinose, xylose, galactose, and glucose accumulated in the CBP-fermentation liquor and washate compared to fermentation controls without C. thermocellum, indicating that C. thermocellum solubilized hemicelluloses, but did not fully metabolize them. After five days of fermentation, the relative amount of rhamnose in the solid residues increased by 16% compared to controls, and CBP solid residues had more than 23% increased reactivity against RG-I reactive monoclonal antibodies, indicating that the pectic polymer rhamnogalacturonan I (RG-I) was not effectively solubilized from switchgrass biomass by C. thermocellum CBP. Similarly, the amount of mannose (Man) in the CBP solid residues increased by 7% and reactivity against galactomannan reactive antibodies increased by greater than 14%, indicating that the hemicellulosic polymer galactomannan was also resistant to degradation by C. thermocellum during CBP fermentation.

CONCLUSIONS: These findings show that C. thermocellum is unable to effectively degrade RG-I pectic and galactomannan hemicellulosic components in switchgrass biomass. Targeting these polymers for improved solubilization could enhance the efficiency of conversion of grass biomass to biofuels.

PMID:41146239 | DOI:10.1186/s13068-025-02703-9

G3 (Bethesda). 2025 Oct 23:jkaf253. doi: 10.1093/g3journal/jkaf253. Online ahead of print.

ABSTRACT

Solanum microdontum Bitter is a diploid wild Andean relative of potato that has shaped the domestication and adaptation of modern cultivated potato to diverse environments. Solanum microdontum has the potential to provide a wealth of untapped genetic material for use in addressing current challenges in potato breeding. Here, we report a high-quality 772 Mb reference genome sequence for S. microdontum that is anchored to 12 chromosomes. The resulting genome assembly has 99.0% complete Benchmarking Universal Single Copy Orthologs and an N50 scaffold length of over 57 Mb, indicating a high level of completeness. Annotation of the assembly resulted in the identification of 37,324 protein coding genes and 65% repetitive sequence. A total of 1,187 nucleotide-binding leucine-rich repeat genes were predicted from the assembly, of which 93.1% overlapped an annotated high-confidence gene model. A k-mer based kinship matrix derived from a 107-member S. microdontum diversity panel revealed an underlying population structure that corresponds to geographic proximity. The S. microdontum dataset enhances publicly available potato genome resources by providing breeders with genetic, molecular, and germplasm resources for newly developed diploid potato breeding programs.

PMID:41128648 | DOI:10.1093/g3journal/jkaf253

Biotechnol Biofuels Bioprod. 2025 Oct 22;18(1):108. doi: 10.1186/s13068-025-02704-8.

ABSTRACT

BACKGROUND: Plant-based materials have the potential to replace some petroleum-based products, offering compostability and biodegradability as critical advantages. Xylan-rich biomass sources are gaining recognition due to their abundance and underutilization in current industrial applications. Research of potential xylan applications has been complicated by the complex and heterogeneous structure that varies for different xylan feedstocks. Acylation is a broadly used reaction in functionalization of polysaccharides at an industrial scale. However, the efficiency of this reaction varies with the xylan source. To optimize xylan valorization, a systematic understanding of structure-reactivity relationships is essential.

RESULTS: This study explores, characterizes, and compares various xylan feedstocks in the acylation process. Xylan feedstocks were analyzed for their chemical composition, degree of polymerization, branching, solubility, and presence of impurities. These features were correlated with xylan glycotypes’ reactivity toward functionalization with succinic anhydride in an optimized DMSO/KOH condition, achieving carboxyl contents of up to 1.46. We used principal component analysis and hierarchical clustering to identify key structural features of xylan that promote its reactivity. Our findings reveal that xylans with higher xylose content and lower degrees of branching exhibit enhanced reactivity, achieving higher carboxyl content and yields. Structural analyses confirmed successful modification, and light scattering analyses showed dramatic changes in the solution properties. Succinylation improves the solubility and film-forming properties of native xylans.

CONCLUSIONS: This study shows key structure-reactivity relationships in xylan succinylation, establishing that low branching, high xylose content, and reduced lignin impurity enhance chemical functionalization. The results offer a framework for selecting optimal biomass feedstocks and support future efforts in genetic and synthetic biology to design plants with tunable xylan architectures. These findings advance the hemicellulose valorization for applications in coatings and packaging.

PMID:41126303 | DOI:10.1186/s13068-025-02704-8

Plant Dis. 2025 Oct 21. doi: 10.1094/PDIS-05-25-1023-RE. Online ahead of print.

ABSTRACT

Maize, a globally important staple crop, faces significant yield losses due to corn smut disease, caused by the fungal pathogen Ustilago maydis. Most cultivated maize lines lack genetic resistance, necessitating the identification of new resistance sources. This study evaluated resistance to U. maydis across diverse maize germplasm, including four maize inbred lines (B73, H95, Mo17, and Golden Bantam), three teosinte accessions (Zea mays ssp. parviglumis, Z. mays ssp. luxurians, and Z. mays ssp. diploperennis), and two maize-teosinte near-isogenic lines (NILs). Phenotypic resistance was assessed at the seedling and reproductive growth stages (ear and tassel) 7-, 10-, 14-, and 21-days post-inoculation with U. maydis at four inoculum concentrations. At the seedling stage, teosinte accessions demonstrated resistance to U. maydis, while maize inbreds showed varying levels of susceptibility. The maize-teosinte NILs had better resistance than maize genotypes at the seedling and reproductive stages, with up to 75% fewer ear/tassel galls and 65% less area under the disease progress curve. This enhanced resistance likely stems from introgressed teosinte genomic segments, particularly a 3.9 Mbp region on chromosome 9. Resistance differed across developmental stages and exhibited dose-dependent responses to inoculum concentration. These results suggest that resistance to U. maydis is based on genotype, developmental stage, and dose-dependent genetic resistance. The maize-teosinte NILs have genes associated with resistance to U. maydis that were derived from the teosinte parent, suggesting maize-teosinte NILs and teosinte are valuable genetic resources for enhancing U. maydis resistance in cultivated maize.

PMID:41117632 | DOI:10.1094/PDIS-05-25-1023-RE

Ecol Appl. 2025 Oct;35(7):e70125. doi: 10.1002/eap.70125.

ABSTRACT

The misalignment of species adaptations with current environmental conditions can cause ecosystems to lose resilience, accumulate resilience debt, and transition to another state. Such a state change is evident in eastern North American broadleaf forests where dominant tree species are shifting from oaks (Quercus spp.) to mesophytic species such as maples (Acer spp.). The replacement of oaks is widespread and threatens the ecosystem services these forests provide, generating interest in using forest management to halt or reverse this change. The national Fire and Fire Surrogate (FFS) study was a large-scale study of forest management practices, and the Green River FFS site in western North Carolina (initiated in 2001) offers the opportunity to understand how management actions affect oak forest resilience. The Green River FFS site implemented three experimental treatments replicated across three spatial blocks: mechanical felling of saplings and ericaceous shrubs (Mech), prescribed fire (Fire), and a combination (Mech + Fire), which were compared to untreated controls (Control). Here, we used this long-running experiment to evaluate oak forest resilience by examining changes in overstory basal area and forest composition among overstory trees, saplings, and seedlings. We found that basal area increased in the Control and Mech treatments, was unchanged in the Fire treatment, and decreased in the Mech + Fire treatment as a result of mortality. Oak sapling abundances increased with reduced basal area, a pattern not found with the major mesophytic representative, maples. This suggests that oaks are well positioned to recruit to the overstory where basal area has decreased due to overstory mortality, and at the Green River FFS site, this was best achieved in the Mech + Fire treatment. Creating conditions where oak saplings have an advantage over maples requires the mortality of some overstory trees, including desirable oaks. Taken together, our findings suggest that the misalignment of oak traits and current environmental conditions has led to resilience debt, which may be reduced when management actions mimic a severe disturbance that results in the opening of the canopy. Thus, management actions that combine mechanical felling and repeated prescribed fires may promote sustained oak dominance in the future.

PMID:41111267 | DOI:10.1002/eap.70125

Theor Appl Genet. 2025 Oct 19;138(11):278. doi: 10.1007/s00122-025-05062-z.

ABSTRACT

We identified QTLs and candidate genes associated with resistance to Heterodera sojae and then designed KASP markers from candidate genes on chromosomes 1 and 18 for marker-assisted selection. Heterodera sojae is a recently discovered cyst nematode species that parasitizes soybean roots, reducing soybean growth and yield. However, genes associated with resistance to H. sojae in soybean remain unknown. A genome-wide association study of genes related to resistance to H. sojae was performed with a panel of 385 soybean accessions using an Axiom 180 K SoyaSNP array and whole-genome sequencing data. Thirteen significant single-nucleotide polymorphisms (SNPs) were identified; among them, four SNPs located on chromosomes 1 and 18 were selected to identify candidate resistance genes and develop kompetitive allele-specific PCR (KASP) markers for efficient genotyping. Haplotype analysis revealed 16 candidate genes within two haplotype blocks adjacent to the SNPs that were significantly associated with resistance to H. sojae. The functions of these candidate genes were predicted based on the JGI Plant Gene Atlas, which showed that they were specifically expressed in soybean roots. The KASP markers developed based on these SNPs can be used to perform marker-assisted selection in soybean breeding programs to develop soybean cultivars resistant to H. sojae.

PMID:41110016 | DOI:10.1007/s00122-025-05062-z

Phytopathology. 2025 Oct 17. doi: 10.1094/PHYTO-04-25-0142-R. Online ahead of print.

ABSTRACT

Globally, tomato spotted wilt virus (TSWV) is a serious pest causing tomato spotted wilt disease (TSWD) on a wide range of plant hosts. Integrated pest management (IPM) strategies are crucial for mitigating TSWD incidence in horticultural and row crops. To assess the impact of various IPM approaches on TSWV, we studied four different TSWV isolates collected from peanut (TSWV peanut), tobacco (TSWV tobacco), and tomato (TSWV tomato-1 and tomato-2) crops commonly grown in southeast Georgia, USA. All four isolates were phenotypically assessed based on disease incidence (DI), disease severity (DS), and serially passaged in Nicotiana tabacum cv NC196. In addition, viral genomic molecules were measured in the newly emerged leaves of the inoculated tobacco plants. Nucleocapsid (NP), non-structural movement (NSm), and non-structural silencing suppressor (NSs) gene sequences were analyzed from passages zero, two, and four. Our findings suggested 80-100% of DI in mechanically inoculated plants by all the isolates at 21 days post inoculation (DPI). Based on the expression of symptoms in inoculated plants, high DS was observed in plants inoculated with the TSWV peanut isolate. The difference between viral titer at 7, 14, and 21 DPI was not observed for any of the isolates. On successive passages, virulence decreased for all the isolates (except TSWV tomato-2 isolate). Our study indicated the difference in virulence between TSWV isolates from peanut, tobacco, and tomato crops on N. tabacum.

PMID:41105392 | DOI:10.1094/PHYTO-04-25-0142-R

BMC Genomics. 2025 Oct 16;26(1):925. doi: 10.1186/s12864-025-11945-8.

ABSTRACT

BACKGROUND: Photoperiodic changes in diel cycles of gene expression are pervasive in plants. The timing of circadian regulators, together with light signals, regulate multiple photoperiod-dependent responses such as growth, flowering or tuber formation. However, for most genes, the importance of cyclic mRNA levels is less clear. We analyzed the diel transcriptome of modern cultivated potato, a highly heterozygous autotetraploid. Clonal propagation and limited meiosis have led to the accumulation of deleterious alleles, making tetraploid potato an ideal model system to investigate the conservation of cyclic expression and cyclic genes during artificial selection and clonal propagation.

RESULTS: Our results indicate that rhythmic alleles of cultivated potato are more highly expressed than non-rhythmic genes and are highly co-expressed not only under diel cycles but also across tissues, developmental stages, and stress conditions. Moreover, the smaller ratio of non-synonymous to synonymous differences within rhythmic versus non-rhythmic allelic groups indicates that cyclic genes, in general, have more conserved core functions than non-cyclic genes. In accordance with this observation, fully rhythmic allelic groups are highly enriched in photosynthesis and ribosome biogenesis genes, which have core functions in plants. Furthermore, we investigated differences in cyclic expression patterns between photoperiods identifying potential regulators for the strong changes in phase of expression of ribosome biogenesis and pathogen response genes. Finally, analyses of genes involved in tuber formation suggests that the regulation of CO gene transcription is not the only factor enabling tuberization under long days in modern cultivated potato.

CONCLUSIONS: This study not only provides high quality diel transcriptomic datasets of cultivated potato but also provides important insight on the role of allelic diversity in rhythmic expression in plants.

PMID:41102621 | DOI:10.1186/s12864-025-11945-8

Animals (Basel). 2025 Sep 26;15(19):2813. doi: 10.3390/ani15192813.

ABSTRACT

Natural areas near farmland can provide refuge for birds that contribute to natural pest control. However, birds can endanger food safety by defecating on or near produce. Work in the western US suggests that Campylobacter spp. are the potential foodborne pathogens most commonly associated with wild birds and that pathogen prevalence is higher in landscapes dominated by animal agriculture. However, relatively little is known about other fresh-market-produce growing regions. Working on produce farms in the Southeastern US, we characterized bird communities, tested bird feces deposited on crop foliage for Campylobacter and Salmonella, and searched for landscape features associated with heightened bird-associated food safety risks. We found that bird communities on farms were generally similar across ecoregions. Campylobacter was never detected from bird feces deposited on crop foliage, but Salmonella was detected in 8.6% of fecal samples. Salmonella prevalence in crop-surface-collected bird feces was highest when farms also produced livestock and when wetland cover was prevalent in the landscape. Overall, our results suggest that on-farm livestock production may be an indicator of bird-associated food safety risks in the Southeast, as in the West. We suggest there may be some similarities, but important differences, in food safety risks posed by birds in different US produce growing regions.

PMID:41096407 | DOI:10.3390/ani15192813

J Hered. 2025 Oct 15:esaf081. doi: 10.1093/jhered/esaf081. Online ahead of print.

ABSTRACT

A central goal of evolutionary biology is to understand the mechanisms conferring adaptation. Gene expression is sensitive to environmental variability; thus, investigating gene expression differentiation among populations may reveal signatures of selection from predictable environmental conditions. Environmental pressures that covary with elevation gain (e.g., temperature) result in stark environmental differences along short distances. The phenological and life history traits of plants inhabiting elevational gradients might track these variables, providing an opportunity for testing hypotheses. Boechera stricta occupies a steep elevation gradient in the Rocky Mountains. Here, we grew F3 seeds from at least two genotypes each from five populations of B. stricta in a greenhouse. Analysis of leaf RNAseq data permitted tests of these hypotheses: 1) populations exhibit significant among population genetic variation in gene expression; 2) differentiation in gene expression (QST) exceeds neutral expectations (FST); and 3) the putative functions of differentially expressed genes are predicable based on a priori knowledge of environmental pressures that vary with elevation. Differentiation in gene expression (average QST = 0.53) significantly exceeded neutral differentiation (average FST = 0.17), implicating selection as a potential cause of genetically divergent patterns of gene expression. The putative functions of differentially expressed genes covarying with elevation were enriched for biological processes related to conditions that vary with elevation (circadian rhythm, response to light, chloroplast organization, and vegetative to reproductive meristem transitions). This study reveals considerable differentiation in gene expression, which may provide a mechanism for rapid adaptation to local environmental conditions in this and other species.

PMID:41092278 | DOI:10.1093/jhered/esaf081