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PubMed2026

Addressing lignin composition and content via Arabidopsis arogenate dehydratase knockout and over-expression genotypes.

Following the down-selection of 14 Arabidopsis thaliana arogenate dehydratase (ADT) knockout and over-expression (OE) genotypes, the most highly contrasting quadruple knockout adt3/4/5/6 and ADT OE genotypes were subjected to proteomics, metabolomics, and scanning electron microscopy (SEM) analyses as needed, with results compared to Columbia wild-type (WT). The basal adt3/4/5/6 stem cross-sections, ∼70% lignin content reduced, exhibited buckled vessel cell walls and partially detached xylary fibers, in contrast to WT and ADT4m/5 m OE genotypes that did not. Anatomical defects primarily resulted from guaiacyl lignin level reductions in vessels with concomitant increased stem syringyl:guaiacyl (S/G) ratios. Phenylpropanoid and various upstream shikimate-chorismate pathway enzyme abundances, as well as specific monolignol oxidases (laccases/peroxidases), generally increased in adt3/4/5/6 at different stem and rosette leaf growth/development stages, relative to WT. Opposite effects were largely observed with the ADT5m OE genotype. By contrast, flavonoid and glucosinolate pathway enzyme amounts varied. Such enzyme abundance increases were overall unproductive as adt3/4/5/6 was unable to restore WT, ADT4 OE, ADT5 OE, ADT5m OE, and ADT4m/5 m OE secondary metabolite (lignin, phenylpropanoid, lignan, flavonoid, phenolic acid, and glucosinolate) levels. Conversely, ADT OE genotypes did not significantly increase programmed lignin levels or alter S/G compositions. In sum, proteomics analyses of adt3/4/5/6 and adt5 'perceived' that lignin and low molecular weight secondary metabolite amounts were not at 'programmed' levels as for WT and ADT OE genotypes but observed increases in relevant pathway protein abundances were futile. Notably though, proteomics analyses did not lead to predicting that lignin and associated biochemical pathways would have reduced metabolite levels, relative to WT and ADT OE genotypes. Genotype adt3/4/5/6, possibly the highest lignin level reduced genotype reported, did not utilize other phenolics to compensate. By contrast, the differential temporal and spatial deposition of cell wall oxidases again indicate the exquisite control over lignin deposition, and our lack of knowledge of precise lignin structure and assembly in subcellular regions of the lignified cell walls.

Lignin↗

PubMed2025

Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants.

The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.

Populus↗

PubMed1977

Dietary fiber components: relationship to the rate and extent of ruminal digestion.

A mathematical model can serve as a useful reference for describing the mechanisms involved in digestion and for discussing the factors that influence the rate and extent of ruminal digestion. Ruminal digestion can be divided into four components: digestion rate, digestion lag, potential extent of digestion, and passage rate. Each component affects the apparent extent of digestion in a distinct manner and is influenced by separate factors. Digestion rate is directly related to apparent extent of digestion. It is not influenced by chemical entities presently being measured, but may be related to the morphological, crystalline, or physical nature of fiber. It may also be influenced by factors that inhibit or stimulate ruman microbial growth and their fiber-degrading enzymes. Digestion lag is inversely related to apparent extent of digestion; however, factors influencing it are poorly defined. The may include factors affecting microbial populations and their attachment to fiber prior to digestion; or the digestion lag may be related to the chemical or physical alteration of fiber that must occur before digestion can begin. The potential extent of digestion is directly related to apparent extent of digestion and is influenced by plant fiber composition, primarily. Lignin, and possibly silica, functions to limit the potential extent of digestion. Rate of passage essentially competes with rate of digestion for fiber particles as they pass through the rumen; therefore it is inversely related to the apparent extent of digestion. Passage rate is associated with feed intake level and particle size, although other factors such as type of diet and animal physiology may be important.

Animals↗

PubMed2026

Selection of GhTT2-A07 promoter enhances fiber quality in improved cotton varieties.

Modern cultivated cotton fibers are predominantly white with enhanced quality compared to their wild ancestors. However, the molecular mechanisms and evolutionary drivers linking fiber color to quality remain least focused. In this study, we identified FQC1 (Fiber Quality and Color 1), a major quantitative trait locus (QTL) on chromosome A07 that concurrently regulates both fiber quality and pigmentation. Through map-based cloning, we revealed that Gossypium hirsutum TRANSPARENT TESTA2-A07 (GhTT2-A07), an R2R3-MYB transcription factor, resides within this locus. GhTT2-A07 modulates fiber development by directly activating genes in the general phenylpropanoid pathway, thereby promoting the metabolic flux toward downstream secondary metabolites. Variations in the GhTT2-A07 promoter led to its reduced expression in modern white cotton cultivars. This down-regulation suppresses the accumulation of S/G/H-type lignin monomers and proanthocyanidins, resulting in altered secondary cell wall composition and ultimately enhancing the quality of mature white fibers. Population genetic analyses further indicate that the white-fiber allele GhTT2-A07W has been fixed in modern breeding genotypes, underscoring the impact of artificial selection during cotton domestication. Overall, our study elucidates the biochemical and molecular mechanisms underlying fiber quality and pigmentation in cotton, clarifies the selection criteria for high-quality white fibers in modern cultivars, and provides a theoretical basis for future targeted genetic improvement of cotton fibers.

Alleles↗

PubMed1979

Evaluation of Myrothecium verrucaria as a nutrient source for ruminants.

The soil saprophytic fungus Myrothecium verrucaria was cultivated from glucose, starch, or xylan as the carbon source, and the biomass was compared with three selected feedstuffs. Fungal biomass was analyzed for nitrogen, protein, lipid, water soluble fraction, hemicellulose, cellulose, lignin, and residual ash, and the in vitro dry matter disappearance was determined. The chemical composition of M. verrucaria varied with substrate. In nitrogen content, the fungal biomass was more similar to alfalfa hay than to milo stalks or wheat straw. Content of water soluble fraction of fungal biomass was between those of alfalfa hay and milo stalks; content of hemicellulose was between those of milo stalks and wheat straw. The fungal fractions identified as cellulose and lignin varied widely with substrate. The fungal biomass was less digestible than alfalfa hay but more digestible than milo stalks or wheat straw. There may be potential uses of this organism in upgrading nutritive value of low-quality forages.

Animal Feed↗

PubMed2026

High-Density Genome-Wide Association Mapping Identifies Candidate Loci Associated with Maize Stalk Cell Wall Composition.

Maize (Zea mays L.) stalk cell wall composition is a key determinant of forage digestibility, lodging resistance, and biomass utilization efficiency. Although previous genome-wide association studies (GWAS) have identified loci associated with lignin (LIG), cellulose (CEL), and hemicellulose (HC), advances in genomic resources provide an opportunity to revisit existing phenotypic datasets at substantially higher resolution. Here, we re-analyzed a maize association panel consisting of 341 diverse inbred lines using an expanded genotype dataset containing 10.77 million SNPs, two derived compositional indices (CEL/HC and [LIG/(CEL + HC)], and six complementary GWAS models. Across all traits and models, we identified 855 unique significant SNPs associated with 579 candidate genes. Among the traits examined, LIG/(CEL + HC) yielded the greatest number of associations, suggesting that indices representing the relative balance among cell wall components may better capture the genetic architecture of cell wall composition than individual component measurements alone. Integration of multiple GWAS models with functional enrichment, haplotype, and selective sweep analyses prioritized three biologically relevant candidate genes encoding a MYB58 transcription factor, the glycosyltransferase Xt9, and a putative xyloglucan 6-xylosyltransferase. Haplotype analysis revealed significant effects of Xt9 and the xyloglucan 6-xylosyltransferase on cell wall composition, while selective sweep analysis identified Xt9 as a target of repeated selection during maize domestication, ecological adaptation, and modern breeding. Although these candidate genes provide promising targets for future investigation, the associations identified here are based on a single association panel and require functional and independent population validation. Collectively, our results demonstrate how high-density genotyping combined with complementary GWAS models can refine candidate associations and generate testable hypotheses from existing phenotypic datasets.

cell wall composition↗

PubMed1976

Comparison of the binding of various bile acids and bile salts in vitro by several types of fiber.

The binding in vitro of the sodium salts of cholic acid, chenodeoxycholic acid, deoxycholic acid, taurocholic acid, taurochenodeoxycholic acid, taurodeoxycholic acid, glycocholic acid, glycochenodeoxycholic acid, and glycodeoxycholic acid by alfalfa, bran, cellulose, lignin, and cholestyramine was measured. Cholestyramine bound an average of 81.3% of all the bile acids and salts tested whereas cellulose bound only negligible amounts (1.4%). Of the other substances tested, lignin bound 29.2%, alfalfa, 15.9% and bran, 9.0%. No distinct pattern of binding was discerned. It is therefore apparent that the validity of statements concerning the effect of fiber on bile salf metabolism rests upon the specificity of the composition of the fiber involved and the bile acids or salts tested.

Bile Acids and Salts↗

PubMed1978

[Nutrient composition of some newly bred high protein and/or high lysine grains and their digestibility determined on growing pigs].

With the view to complementing the feedstuff data store and, consequently, to further improving the GDR Feed Evaluation System, some newly bred high-protein and/or high-lysine cereal varieties and strains (spring barley, winter wheat, maize) were studied for their nutrient composition and digestibility. Apart from from WEENDER's feed analysis technique, more recent methods were applied to determine total fat (after HCl treatment), carbohydrates (enzymatic method), lignin and amino acids. The digestibility of the nutrients was determined using growing pigs of different live weight, the test rations being made up of the cereals under and supplementations of limiting amino acids as well as vitamins and minerals. In comparison with the values from currently applied tables, the newly bred strains and varieties proved to have markedly higher contents of crude protein, digestible crude protein, lysine and energetic feed equivalents. Compared to crude fat, the total fat values proved markedly higher in the barley and wheat samples. The readily soluble and easily hydrolizable carbohydrates found with the new analysis procedure suggested, were 100% digestible in all cereal samples used. Lignin proved the constituent most difficult to digest and must be regarded as virtually undigestible in the case of pigs.

Animal Nutritional Physiological Phenomena↗

PubMed1979

Dietary fibre and colonic neoplasia.

Dietary plant fibre, or plantix, is thought to play a significant role in the pathogenesis of colon cancer in humans. It is a complex polymeric substance that has several distinct components resistant to hydrolysis by the digestive enzymes of humans. These components include cellulose, hemicelluloses, pectins, lignin, gums, mucilages and, in certain instances, algal polysaccharides. These polymers have different physicochemical properties, and recent evidence from experimental studies in animals treated with carcinogens suggests that some may exert protective effects in the intestine and others may enhance colon carcinogenesis. This review synthesizes information on the chemical composition, methods of analysis and physicochemical properties of dietary plant fibre and reviews available studies examining the role of fibre in colonic neoplasia in animals and humans.

Animals↗

PubMed1976

Fertilizer calcium as a factor affecting the voluntary intake, digestibility and retention time of pangola grass (Digitaria decumbens) by sheep.

1. Pangola grass (Digitaria decumbens) grown with and without calcium fertilizer was cut at three stages of regrowth to measure voluntary intake of dry matter (DM) and digestibility of various components of the dried-grass diet by sheep kept in metabolism crates. To determine the extent of a simple Ca deficiency half the sheep on each diet was supplemented with 1-4 g Ca/d. Retention times of the various dietary components in the reticulo-rumen were also determined. 2. Feeding a Ca supplement had no effect on voluntary intake or digestibility. 3. Ca fertilizer increased the Ca content of the grass from 2-2 to 3-8 g/kg DM and DM digestibility from 0-455 to 0-476 (P less than 0-01) due to an increase in the digestibility of the hemicellulose. 4. Voluntary intake was increased from 38-8 to 43-2 g/kg body-weight0.75 per d by Ca fertilizer due to an 18% reduction in the period of time the DM was retained in the reticulorumen. 5. Regressions relating voluntary intake to DM digestibility for the Ca-fertilized and control grass were significantly different (P less than 0-01). When compared at the same DM digestibility the voluntary intake of the Ca-fertilized grass was 2-6 g/kg body-weight0.75 per d higher than that of the control. 6. It was concluded that Ca fertilizer increased both DM digestibility and voluntary intake as a result of changes in the structural composition of the grass and not by a simple increase in the Ca content of the diet.

Animal Feed↗

PubMed2026

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.

BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.

Soil Microbiology↗

PubMed2026

Isoquinoline alkaloids enhance growth performance through multifaceted modulation of the bacterial-fungal microbiome, CAZyme profiles, gut health, and neuroendocrine function in broilers.

The bacterial-fungal microbiome and its carbohydrate-active enzyme (CAZyme) capacity play critical roles in regulating gut health and growth performance in broiler chickens. This study evaluated the effects of dietary isoquinoline alkaloids (IQ) on growth performance, gut microbiome composition, CAZyme profiles, and the microbiome-gut-neuroendocrine axis in broilers. A total of 400 Ross 308 (1-day-old) chicks were randomly assigned to either a Basal diet (CON) or IQ supplemented diet (IQ). Dietary IQ supplementation significantly increased final body weight and cumulative body weight gain (P < 0.0001) and improved feed conversion ratio (P < 0.05). Intestinal permeability was reduced (lower FITC-dextran; P < 0.05), accompanied by increased serotonin and serotonin-to-corticosterone ratio and decreased corticosterone (P < 0.05). Expression of inflammatory genes (TNF-α, NF-κB, IL-4, and TLR-1) was downregulated (P < 0.05). Microbiome analysis showed increased α-diversity (P < 0.05) and clear β-diversity separation (PERMANOVA, P < 0.001), with enrichment of beneficial bacteria (Akkermansia muciniphila, Lactobacillus salivarius, Turicibacter sanguinis, Bacillus subtilis) and suppression of fungal taxa (Aspergillus, Penicillium). CAZyme-related pathways involved in lignin and carbohydrate degradation were increased (P < 0.05). Microbial diversity was negatively correlated with inflammation and gut permeability, whereas network analysis identified 164 significant associations (|ρ| ≥ 0.50), revealing strong negative correlations between beneficial bacteria and inflammatory markers (ρ = -0.65 to -0.78) and positive associations for fungal taxa (ρ = 0.62-0.81). Serotonin was positively associated with microbial diversity (ρ = 0.63-0.70). In conclusion, IQ supplementation promotes a bacteria-dominant and metabolically active microbiome, reduces inflammation and intestinal permeability, and improves neuroendocrine balance, collectively enhancing gut health and growth performance in broiler chickens.

Bacteriome↗

PubMed2026

Trimming galactose side chains of arabinogalactan proteins alters pectin and hemicellulose deposition in secondary cell walls of Arabidopsis thaliana floral stem internodes.

Shaping the cell wall composition and structure to meet the requirements of different tissues and developmental stages relies on multiple actors, including arabinogalactan proteins (AGPs). Although the specific role of these proteins in cell wall dynamics is still under debate, especially in events involving significant remodeling of the cell wall, their carbohydrate motif, type II arabinogalactan (AGII), seems to be crucial for their function. This study aims to investigate the function of AGII, specifically the galactose residues of its side chains, in the structural organization of the cell wall during the cessation of elongation and the transition to secondary growth. To achieve this, we characterized floral stem internodes of Arabidopsis thaliana plants overproducing the chickpea βV-galactosidase protein (35S::βV-Gal plants), an enzyme that specifically hydrolyzes the β-(1,3)- and β-(1,6)-galactosyl residues of AGII. Changes induced in the cell wall by trimming galactose residues of AGII resulted in a noticeable increase in homogalacturonan methyl esterification. Additionally, these neutral galactose side chains may regulate hemicellulose-cellulose interactions and influence xylan distribution through the cellulose network, which in turn affects the deposition of lignin and determines its recalcitrance to enzymatic degradation.

Arabidopsis↗

PubMed2026

Degradation of a graphene-reinforced polyamide by fungi: When culture conditions matter.

The large-scale production, marketing and disposal of polymer-based graphene products can lead to the dispersal of graphene-enriched plastic particles into terrestrial ecosystems, where they might accumulate if not degraded by organisms. The objective of this work is to test the degradability and compatibility of one polyamide-6 polymer reinforced with reduced graphene-oxide (PA6-rGO) and its base constituents (polyamide-6, PA6; reduced graphene oxide, rGO) using mono- and co-cultures of two lignin-degrading fungi (Bjerkandera adusta and Morchella esculenta) grown under different nutrient conditions. Fungal (co-)cultures were exposed to pure rGO or abraded powders of PA6 and PA6-rGO in two different liquid media, and monitored over time for biomass growth, H2O2 production, and activity of two lignolytic enzymes (i.e., Laccase, Lac, and Lignin peroxidase, LiP). The changes in polyamide structure were evaluated by proton nuclear magnetic resonance and mass spectrometry, and changes in rGO were evaluated by Raman spectroscopy. The materials had no effect on fungal growth. PA6 increased Lac secretion only in low nutrient medium, while PA6-rGO slightly suppressed LiP activity. Only M. esculenta promoted polyamides oxidation when cultured in a low nutrient medium, as evidenced by a change in mass distribution values (m/z: 400-420) and the appearance of a new resonance peak (at 5.37 ppm). Lignolytic exudates in co-cultures low in nutrients caused a greater change in rGO, as shown by the increase in the ID/IG ratio. The degradation of rGO, PA6 and PA6-rGO depended on culture conditions.

Graphite↗

PubMed2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC-MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner-Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.IMPORTANCEBiomass pretreatment processes release fermentable sugars from lignocellulosic biomass, but they also generate inhibitors that can impact microbial metabolism. This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses. While some stress responses overlap with those induced by ethanol and isobutanol toxicity, both valuable biofuels, hydrolysate exposure elicits unique metabolic shifts. These findings offer valuable insights for engineering Z. mobilis strains with improved tolerance and performance for efficient bioconversion of lignocellulosic hydrolysates into biofuels and bioproducts.

Zymomonas↗