Biomass Enzymatic Saccharification Is Determined by the Non-KOH-Extractable Wall Polymer Features That Predominately Affect Cellulose Crystallinity in Corn

Corn is a major food crop with enormous biomass residues for biofuel production. Due to cell wall recalcitrance, it becomes essential to identify the key factors of lignocellulose on biomass saccharification. In this study, we examined total 40 corn accessions that displayed a diverse cell wall composition. Correlation analysis showed that cellulose and lignin levels negatively affected biomass digestibility after NaOH pretreatments at p<0.05 & 0.01, but hemicelluloses did not show any significant impact on hexoses yields. Comparative analysis of five standard pairs of corn samples indicated that cellulose and lignin should not be the major factors on biomass saccharification after pretreatments with NaOH and H₂SO₄ at three concentrations. Notably, despite that the non-KOH-extractable residues covered 12%–23% hemicelluloses and lignin of total biomass, their wall polymer features exhibited the predominant effects on biomass enzymatic hydrolysis including Ara substitution degree of xylan (reverse Xyl/Ara) and S/G ratio of lignin. Furthermore, the non-KOH-extractable polymer features could significantly affect lignocellulose crystallinity at p<0.05, leading to a high biomass digestibility. Hence, this study could suggest an optimal approach for genetic modification of plant cell walls in bioenergy corn.     

Structural Insights into the Affinity of Cel7A Carbohydrate-binding Module for Lignin

The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs.     

Understanding biomass recalcitrance in grasses for their efficient utilization as biorefinery feedstock

One of the main challenges for the deployment of lignocellulosic biorefineries in future years is to find renewable and secured biomass sources in order to obtain bio-sourced products, as an alternative to petroleum-based commodities. Grass biomass, considering its characteristics (availability, composition, productivity, possibility of being harvested from both arable (post-harvest residues) and non-agricultural lands), can be considered as a biomass source for the future. Nevertheless, because of its complex structure and composition, which need deconstructive pre-treatments to render possible further biological conversions, grasses utilisation in biorefinery is today not widespread. Indeed, recalcitrance to polymers degradation in grasses concerns structural and compositional characteristics and can result in costly and complicated biorefinery processes. Grass recalcitrance is due to various natural factors strongly related and difficult to dissociate: rind and vascular structures; composition (lignin content is a key factor for cellulose hydrolysis acting like a physical barrier while hemicelluloses seem to play a more significant role in woody biomass than in grass plants); physical structures (crystalline nature and insoluble surface of cellulose, specific surface area, particle size), etc. Physico-chemical pretreatments are efficient solutions to overcome recalcitrance, while phenotypic selections are interesting but not efficient enough to obtain an optimal enzymatic hydrolysis. In some cases, the structural elements of grass biomass can be negatively affected by physico-chemical pretreatments, causing pre-treatment-induced recalcitrance, like cellulose hornification (irreversible alteration of cellulose microfibers), vascular structure collapsed and reduced cellulose bioaccesibility to enzymes due to cellulose covering by lignin, following lignin solubilisation.     

Pretreatment of Populus tomentosa with Trametes velutina supplemented with inorganic salts enhances enzymatic hydrolysis for ethanol production

Different nutrients were added into the solid fermentation of woody biomass, Populus tomentosa, to improve pretreatment by a white rot fungus, Trametes velutina. Fungal pretreatment supplemented with trace elements resulted in large amount of lignin loss but low degradation of carbohydrate. Only 12.6?% of Klason lignin was left in the residues pretreated by T. velutina for 8?weeks supplemented with 1?% trace elements (TE group). When fungal-pretreated residues were subjected to enzymatic hydrolysis for 96?h, a maximum reducing sugar yield of 44?% was obtained from the TE group at the 8th week, 2.3 times higher than that of untreated samples. In addition, the highest ethanol yield of 22?% was observed by the fermentation of 8-week pretreated residues from the basic medium plus trace element group, which was five times more than that of untreated samples.     

Decomposition of soybean grown under elevated concentrations of CO2 and O3

A critical global climate change issue is how increasing concentrations of atmospheric CO₂ and ground‐level O₃ will affect agricultural productivity. This includes effects on decomposition of residues left in the field and availability of mineral nutrients to subsequent crops. To address questions about decomposition processes, a 2‐year experiment was conducted to determine the chemistry and decomposition rate of aboveground residues of soybean (Glycine max (L.) Merr.) grown under reciprocal combinations of low and high concentrations of CO₂ and O₃ in open‐top field chambers. The CO₂ treatments were ambient (370 μmol mol^?1) and elevated (714 μmol mol^?1) levels (daytime 12 h averages). Ozone treatments were charcoal‐filtered air (21 nmol mol^?1) and nonfiltered air plus 1.5 times ambient O₃ (74 nmol mol^?1) 12 h day^?1. Elevated CO₂ increased aboveground postharvest residue production by 28–56% while elevated O₃ suppressed it by 15–46%. In combination, inhibitory effects of added O₃ on biomass production were largely negated by elevated CO₂. Plant residue chemistry was generally unaffected by elevated CO₂, except for an increase in leaf residue lignin concentration. Leaf residues from the elevated O₃ treatments had lower concentrations of nonstructural carbohydrates, but higher N, fiber, and lignin levels. Chemical composition of petiole, stem, and pod husk residues was only marginally affected by the elevated gas treatments. Treatment effects on plant biomass production, however, influenced the content of chemical constituents on an areal basis. Elevated CO₂ increased the mass per square meter of nonstructural carbohydrates, phenolics, N, cellulose, and lignin by 24–46%. Elevated O₃ decreased the mass per square meter of these constituents by 30–48%, while elevated CO₂ largely ameliorated the added O₃ effect. Carbon mineralization rates of component residues from the elevated gas treatments were not significantly different from the control. However, N immobilization increased in soils containing petiole and stem residues from the elevated CO₂, O₃, and combined gas treatments. Mass loss of decomposing leaf residue from the added O₃ and combined gas treatments was 48% less than the control treatment after 20 weeks, while differences in decomposition of petiole, stem, and husk residues among treatments were minor. Decreased decomposition of leaf residues was correlated with lower starch and higher lignin levels. However, leaf residues only comprised about 20% of the total residue biomass assayed so treatment effects on mass loss of total aboveground residues were relatively small. The primary influence of elevated atmospheric CO₂ and O₃ concentrations on decomposition processes is apt to arise from effects on residue mass input, which is increased by elevated CO₂ and suppressed by O₃.     

Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass

Lignocellulosic biomass from agricultural crop residues and forest waste represents an abundant renewable resource for bioenergy and future biofuel. The current bottleneck of lignocellulosic biofuel production is the hydrolysis of biomass to sugar. To understand the enzymatic hydrolysis of complex biomasses, in this report, lignocellulolytic enzymes secretion by Phanerochaete chrysosporium cultivated in different natural lignocellulosic biomass such as corn stover, hay, sawdust, sugarcane baggase, wheat bran and wood chips were quantitatively analyzed with the iTRAQ technique using LC-MS/MS. A diverse groups of enzymes, including cellulases, glycoside hydrolases, hemicellulases, lignin degrading enzymes, peroxidases, esterases, lipases, chitinases, peptidases, protein translocating transporter and hypothetical proteins were quantified, of which several were novel lignocellulosic biomass hydrolyzing enzymes. The quantitative expression and regulation of lignocellulolytic enzymes by P. chrysosporium were dependent on the nature and complexity of lignocellulosic biomass as well as physical size of the biomass. The iTRAQ data revealed oxidative and hydrolytic lignin degrading mechanism of P. chrysosporium. Numerous proteins presumed to be involved in natural lignocellulosic biomass transformation and degradation were expressed and produced in variable quantities in response to different agricultural and forest wastes.     

Fiber fractionation to understand the effect of mechanical refining on fiber structure and resulting enzymatic digestibility of biomass

Mechanical refining results in fiber deconstruction and modifications that enhance enzyme accessibility to carbohydrates. Further understanding of the morphological changes occurring to biomass during mechanical refining and the impacts of these changes on enzymatic digestibility is necessary to maximize yields and reduce energy consumption. Although the degree of fiber length reduction relative to fibrillation/delamination can be impacted by manipulating refining variables, mechanical refining of any type (PFI, disk, and valley beater) typically results in both phenomena. Separating the two is not straightforward. In this study, fiber fractionation based on particle size performed after mechanical refining of high-lignin pulp was utilized to successfully elucidate the relative impact of fibrillation/delamination and fiber cutting phenomena during mechanical refining. Compositional analysis showed that fines contain significantly more lignin than larger size fractions. Enzymatic hydrolysis results indicated that within fractions of uniform fiber length, fibrillation/delamination due to mechanical refining increased enzymatic conversion by 20–30 percentage points. Changes in fiber length had little effect on digestibility for fibers longer than ~0.5 mm. However, the digestibility of the fines fractions was high for all levels of refining even with the high-lignin content.     

Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane

Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5?% along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52–76?% improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.     

Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) ¹H-¹³ C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45–0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = –0.95 to –0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.     

Quality and decomposition in soil of rhizome, root and senescent leaf from Miscanthus x giganteus, as affected by harvest date and N fertilization

To predict the environmental benefits of energy crop production and use, the nature and fate of biomass residues in the soil need to be quantified. Our objective was to quantify Miscanthus x giganteus biomass recycling to soil and to assess how harvesting time and N fertilization affect their characteristics and subsequent biodegradability. The quantification of aerial and belowground biomass and their sampling were performed on 2- and 3-year-old Miscanthus stands, either fertilized with 120 kg N ha^?1 year^?1 or not fertilized, in autumn (maximal biomass production) and winter (maturity). Plant biomass was chemically characterized (total sugars, Klason lignin, C/N) and incubated in optimum decomposition conditions (15°C, ?80 kPa) for 263 days, for C and N mineralization. Accumulation of carbon in rhizomes and roots was 7.5 to 10 t C ha^?1 and represented about 50% of total plant biomass C. Senescent leaves represented about 1.5 t C ha^?1 year^?1. All residues, especially the roots, had high lignin contents, while the rhizomes also had a high soluble content due to their nutrient storage function. The C mineralization rates were closely related to the chemical characteristics of the residue, higher sugar and lower lignin contents leading to faster decomposition, as observed for rhizomes.     

The Minor Wall-Networks between Monolignols and Interlinked-Phenolics Predominantly Affect Biomass Enzymatic Digestibility in Miscanthus

Plant lignin is one of the major wall components that greatly contribute to biomass recalcitrance for biofuel production. In this study, total 79 representative Miscanthus germplasms were determined with wide biomass digestibility and diverse monolignol composition. Integrative analyses indicated that three major monolignols (S, G, H) and S/G ratio could account for lignin negative influence on biomass digestibility upon NaOH and H₂SO₄ pretreatments. Notably, the biomass enzymatic digestions were predominately affected by the non-KOH-extractable lignin and interlinked-phenolics, other than the KOH-extractable ones that cover 80% of total lignin. Furthermore, a positive correlation was found between the monolignols and phenolics at p<0.05 level in the non-KOH-extractable only, suggesting their tight association to form the minor wall-networks against cellulases accessibility. The results indicated that the non-KOH-extractable lignin-complex should be the target either for cost-effective biomass pretreatments or for relatively simply genetic modification of plant cell walls in Miscanthus.     

Interactions between Litter Lignin and Nitrogenitter Lignin and Soil Nitrogen Availability during Leaf Litter Decomposition in a Hawaiian Montane Forest

Previous work in a young Hawaiian forest has shown that nitrogen (N) limits aboveground net primary production (ANPP) more strongly than it does decomposition, despite low soil N availability. In this study, I determined whether (a) poor litter C quality (that is, high litter lignin) poses an overriding constraint on decomposition, preventing decomposers from responding to added N, or (b) high N levels inhibit lignin degradation, lessening the effects of added N on decomposition overall. I obtained leaf litter from one species, Metrosideros polymorpha, which dominates a range of sites in the Hawaiian Islands and whose litter lignin concentration declines with decreasing precipitation. Litter from three dry sites had lignin concentrations of 12% or less, whereas litter from two wet sites, including the study site, had lignin concentrations of more than 18%. This litter was deployed 2.5 years in a common site in control plots (receiving no added nutrients) and in N-fertilized plots. Nitrogen fertilization stimulated decomposition of the low-lignin litter types more than that of the high-lignin litter types. However, in contrast to results from temperate forests, N did not inhibit lignin decomposition. Rather, lignin decay increased with added N, suggesting that the small effect of N on decomposition at this site results from limitation of decomposition by poor C quality rather than from N inhibition of lignin decay. Even though ANPP is limited by N, decomposers are strongly limited by C quality. My results suggest that anthropogenic N deposition may increase leaf litter decomposition more in ecosystems characterized by low-lignin litter than in those characterized by high-lignin litter. Received 26 October 1999; accepted 2 June 2000.     

Mechanism of lignin inhibition of enzymatic biomass deconstruction

Background

The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process.

Results

By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493).

Conclusions

Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.

     

Improved Sugar Conversion and Ethanol Yield for Forage Sorghum (Sorghum bicolor L. Moench) Lines with Reduced Lignin Contents

Lignin is known to impede conversion of lignocellulose into ethanol. In this study, forage sorghum plants carrying brown midrib (bmr) mutations, which reduce lignin contents, were evaluated as bioenergy feedstocks. The near-isogenic lines evaluated were: wild type, bmr-6, bmr-12, and bmr-6 bmr-12 double mutant. The bmr-6 and bmr-12 mutations were equally efficient at reducing lignin contents (by 13% and 15%, respectively), and the effects were additive (27%) for the double mutant. Reducing lignin content was highly beneficial for improving biomass conversion yields. Sorghum biomass samples were pretreated with dilute acid and recovered solids washed and hydrolyzed with cellulase to liberate glucose. Glucose yields for the sorghum biomass were improved by 27%, 23%, and 34% for bmr-6, bmr-12, and the double mutant, respectively, compared to wild type. Sorghum biomass was also pretreated with dilute acid followed by co-treatment with cellulases and Saccharomyces cerevisiae for simultaneous saccharification and fermentation (SSF) into ethanol. Conversion of cellulose to ethanol for dilute-acid pretreated sorghum biomass was improved by 22%, 21%, and 43% for bmr-6, bmr-12, and the double mutant compared to wild type, respectively. Electron microscopy of dilute-acid treated samples showed an increased number of lignin globules in double-mutant tissues as compared to the wild-type, suggesting the lignin had become more pliable. The mutations were also effective for improving ethanol yields when the (degrained) sorghum was pretreated with dilute alkali instead of dilute acid. Following pretreatment with dilute ammonium hydroxide and SSF, ethanol conversion yields were 116 and 130 mg ethanol/g dry biomass for the double-mutant samples and 98 and 113 mg/g for the wild-type samples.     

Unveiling the Structural Heterogeneity of Bamboo Lignin by In Situ HSQC NMR Technique

One of the primary challenges for efficient utilization of lignocellulosic biomass is to clarify the complicated structure of lignin. In this study, in situ heteronuclear single quantum coherence nuclear magnetic resonance (NMR) characterization of the structural heterogeneity of lignin polymers during successively treated bamboo was emphatically performed without componential separation. Specially, the NMR spectra were successfully obtained by dissolving the acetylated and non-acetylated bamboo samples in appropriate deuterated solvent (CDCl₃ and DMSO-d ₆). The heterogeneous lignin polymers in bamboo samples were demonstrated to be HGS-type and partially acylated at the ??-carbon of the side chain by p-coumarate and acetate groups. The major lignin linkages (?¨CO?C4, ?¨C??, and ?¨C5, etc.) and various lignin?Ccarbohydrate complex linkages (benzyl ether and phenyl glycoside linkages) can be assigned, and the frequencies of the major lignin linkages were quantitatively obtained. In particular, the residual enzyme lignin (REL) contained a higher amount of syringyl units and less condensed units as compared to other samples. Inspiringly, the method gives us a vision to track the structural changes of plant cell wall (e.g., lignin polymers) during the different pretreatments.     

Evaluation of pretreatment methods on mixed inoculum for both batch and continuous thermophilic biohydrogen production from cassava stillage

Anaerobic sludges, pretreated by chloroform, base, acid, heat and loading-shock, as well as untreated sludge were evaluated for their thermophilic fermentative hydrogen-producing characters from cassava stillage in both batch and continuous experiments. Results showed that the highest hydrogen production was obtained by untreated sludge and there were significant differences (p < 0.05) in hydrogen yields (varied from 32.9 to 65.3 mlH₂/gVS) among the tested pretreatment methods in batch experiments. However, the differences in hydrogen yields disappeared in continuous experiments, which indicated the pretreatment methods had only short-term effects on the hydrogen production. Further study showed that alkalinity was a crucial parameter influencing the fermentation process. When the influent was adjusted to pH 6 by NaHCO₃ instead of NaOH, the hydrogen yield increased from about 40 to 52 mlH₂/gVS in all the experiments. Therefore, pretreatment of anaerobic sludge is unnecessary for practical thermophilic fermentative hydrogen production from cassava stillage.     

Optimization of culturing conditions for production of somatic embryos and lignins of <Emphasis Type="Italic">Schisandra chinensis</Emphasis> (Turcz.) Baill

Schisandra chinensis (Turcz.) Baill. is a valuable medicinal plant species increasingly used in phytotherapy worldwide. This study systematically detected the lignin content and production during somatic embryogenesis of S. chinensis. The effect of various culture parameters on biomass accumulation and lignin production were also examined to optimize the accumulation of lignins in SEs in bioreactors, including the culture method, inoculum density, aeration volume and photoperiod. An inoculum density of 20 g L^??1 embryogenic calli enhanced production of lignin, while 30 g L^??1 embryogenic calli increased the biomass of somatic embryos. During somatic embryo induction, an aeration volume of 0.2 vvm and photoperiod of 16 h day^??1 were found to be optimal for biomass accumulation and lignin production. An approximately threefold increase in the biomass production rate and a fourfold increase in the total lignin production rate in SEs were achieved in bioreactors than on solid medium. The present study indicated, therefore, that the culturing of S. chinensis somatic embryos in bioreactors is an effective method for the industrialized production of lignin in vitro.     

Study of the antioxidant capacity of Miscanthus sinensis lignins

The present work studied the antioxidant capacity of the lignin obtained from Miscanthus sinensis. As the lignin structure is very complex, extraction and separation processes highly influence obtained lignin structure and its properties, including the antioxidant activity. Lignin fractions were obtained from black liquor resulting from different fractionating and autohydrolysis processes of M. sinensis. Different lignin fractions with specific molecular weight were separated by ultrafiltration using different cut-off ceramic membranes (10 and 15 kDa). The physico-chemical properties, phenolic groups content and the antioxidant capacity of each lignin sample were studied. It was found that antiradical activity of the analyzed lignin samples was closely related with the used fractionating process (soda, organosolv and autohydrolysis treatments). The ultrafiltration process allows obtaining lignins with different antioxidant capacity, improving this property as the used cut-off was greater.     

Developmental Control of Lignification in Stems of Lowland Switchgrass Variety Alamo and the Effects on Saccharification Efficiency

The switchgrass variety Alamo has been chosen for genome sequencing, genetic breeding, and genetic engineering by the US Department of Energy Joint Genome Institute (JGI) and the US Department of Energy BioEnergy Science Center. Lignin has been considered as a major obstacle for cellulosic biofuel production from switchgrass biomass. The purpose of this study was to provide baseline information on cell wall development in different parts of developing internodes of tillers of switchgrass cultivar Alamo and evaluate the effect of cell wall properties on biomass saccharification. Cell wall structure, soluble and wall-bound phenolics, and lignin content were analyzed from the top, middle, and bottom parts of internodes at different developmental stages using ultraviolet autofluorescence microscopy, histological staining methods, and high-performance liquid chromatography (HPLC). The examination of different parts of the developing internodes revealed differences in the stem structure during development, in the levels of free and well-bound phenolic compounds and lignin content, and in lignin pathway-related gene expression, indicating that the monolignol biosynthetic pathway in switchgrass is under complex spatial and temporal control. Our data clearly show that there was a strong negative correlation between overall lignin content and biomass saccharification efficiency. The ester-linked p-CA/FA ratio showed a positive correlation with lignin content and a negative correlation with sugar release. Our data provide baseline information to facilitate genetic modification of switchgrass recalcitrance traits for biofuel production.