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To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.

Hemicelluloses account for 15–30 % of the lignocellulosic biomass and are considered as abundant renewable biopolymers. They are the major byproducts from pulping and other biorefinery industries, but are highly underutilized and usually burned as low value fuel. In this study, glucuronoxylan recovered from dissolving pulp mill were used to produce a high-quality bio-based emulsifier. Octylamine, dodecylamine and hexadecylamine were used to modify oxidized glucuronoxylan in order to improve the amphipathic properties of glucuronoxylan. Alkyl aminated glucuronoxylan emulsions showed smaller droplet size, higher emulsion activity and lower zeta potential compared to that of unmodified glucuronoxylan emulsions. With the increasing of alkyl contents, the emulsifying properties were improved. However, when the contents of alkyl groups increased beyond a certain value, the emulsifying properties were not changed significantly. Furthermore, the alkyl chain length also had a positive impact on emulsifying properties of alkylamine aminated glucuronoxylans. These results suggest that alkyl aminated glucuronoxylans have the potential to substitute for petroleum-based emulsifiers in many applications.

Aimed at decreasing the environmental pollution caused by petroleum-derived packing materials, many efforts have been directed towards fabricating biodegradable substitutes, especially of cellulose-based film with functional properties. In this paper, a totally plant-derived antibacterial film was successfully prepared. Regenerated cellulose films were used as substrate and poacic acid, a decarboxylated product from 8–5-diferulic acid, as fungicides. The physical properties and thermal stability of the prepared plant-derived antibacterial films were characterized, and the antibacterial activity was also assessed as the function poacic acid contents. The morphology showed that the cellulose/poacic acid films exhibited a homogeneous and smooth surface and poacic acid was successfully incorporated into cellulose films as revealed by Fourier-transform infrared (FT-IR) spectroscopy and fluorescent microscopy. It was noted that both the tensile strength and thermal stability of the antibacterial films decreased due to the incorporation of the poacic acid. Remarkably, the prepared cellulose/poacic acid films exhibited superior antibacterial activity against Staphylococcus aureus. The notable properties of the cellulose/poacic acid films are promising for applications in food and medical packaging to enhance their safety.

Glucuronoxylans, a low-value byproduct from pulping, biomass pretreatment and other biomass processing industries, have been considered to be potentially used as emulsifiers. However, the poor amphipathic property of glucuronoxylans limits their application as emulsifiers. To improve the amphipathic property of glucuronoxylans and develop high quality natural-based/green emulsifiers, glucuronoxylans were chemically modified by alkenyl succinic anhydrides to produce a novel emulsifer. The effects of degree of substitution (DS) and alkenyl chain length on the emulsifying properties of long-chain succinic anhydride modified glucuronoxylans were investigated. Dodecenyl succinic anhydride–glucuronoxylans (DDSA–glucuronoxylans) emulsions showed much smaller droplet size, lower zeta potential, higher emulsifying activity and better emulsion stability compared to that of glucuronoxylans emulsion. When DS increased from 0.014 to 0.09, the emulsifying properties of DDSA–glucuronoxylans were improved. However, when DS increased beyond 0.09, the emulsifying properties were not changed significantly. Furthermore, the alkenyl chain length also has a positive impact on emulsifying properties of long-chain succinic anhydride modified glucuronoxylans. These results suggested that long-chain succinic anhydride modified glucuronoxylans had a potential to be used as emulsifiers, while the DS and chain length should be kept at a proper value.

To protect forest resources and increase the value of agro-industrial residues, it would be helpful to produce paper-based materials from non-woody or recycled fiber resources. This study investigated the reinforcement mechanism of bacterial cellulose (BC) on paper sheets made from different sources including softwood, hardwood, sugarcane bagasse, bamboo, wheat straw, and recycled fiber, which represent a selection of high quality, medium quality, and low quality fibers. The results showed that by maintaining BC addition at a low level of 0.5–1.5% (total paper dry weight), the paper sheets made from high and medium quality fibers have the maximum tensile index improvement, with 5–25%. The tensile index of low quality fiber including wheat straw pulp and recycled fiber pulp increased slightly and gradually with the level of BC addition; at 5% BC addition, the tensile indexes increased by 9 and 40%, respectively. To investigate the BC reinforcement mechanism, different fiber characteristics, SEM images of BC reinforced paper, BC retention rate on paper, and the effects of dispersant addition were evaluated. It was found that high BC addition or retention rate in paper sheets do not necessarily result in good BC reinforcement effects but that proper dispersion of BC is important.

Bacterial cellulose (BC) was used to reinforce paper sheets made from non-woody fibers, e.g. sugarcane bagasse. BC produced from static and agitated fermentation methods was mixed with bleached sugarcane bagasse pulp (BSBP) to produce composite paper sheets. BC from static culture had a higher degree of polymerization, crystallinity, and crystallite width. Adding BC at a low ratio (

Catalytic oxidation via the application of molecular oxygen and copper complexes is a useful pathway toward valuable low molecular mass compounds from in situ or waste stream lignins. In this study, two dimeric β-ether model compounds, one β-ether oligomer, and a milled wood lignin sample from Loblolly pine were catalytically oxidized. Yields and stability of the aromatic aldehyde and acid products were measured. Nuclear magnetic resonance spectroscopy and gel permeation chromatography were used to monitor structure/composition and molecular mass changes of the lignin before and after catalytic oxidation to study the degree of depolymerization and structure of the residual lignin. Oxidized units appear to be derived from β-aryl ether, phenylcoumaran, and biphenyl ether components. To date, this method breaks down the lignin polymeric structure reasonably effectively, producing low molecular mass products; this work also highlights some of the issues that need to be overcome to optimize this approach.

Recent advances in nuclear magnetic resonance (NMR) technology have made it possible to rapidly screen plant material and discern whole cell wall information without the need to deconstruct and fractionate the plant cell wall. This approach can be used to improve our understanding of the biology of cell wall structure and biosynthesis, and as a tool to select plant material for the most appropriate industrial applications. This is particularly true in an era when renewable materials are vital to the emerging bio-based economies. This protocol describes procedures for (i) the preparation and extraction of a biological plant tissue, (ii) solubilization strategies for plant material of varying composition and (iii) 2D NMR acquisition (for typically 15 min-5 h) and integration methods used to elucidate lignin subunit composition and lignin interunit linkage distribution, as well as cell wall polysaccharide profiling. Furthermore, we present data that demonstrate the utility of this new NMR whole cell wall characterization procedure with a variety of degradative methods traditionally used for cell wall compositional analysis.

Grasses are a predominant source of nutritional energy for livestock systems around the world. Grasses with high lignin content have lower energy conversion efficiencies for production of bioenergy either in the form of ethanol or to milk and meat through ruminants. Grass lignins are uniquely acylated with p-coumarates (pCA), resulting from the incorporation of monolignol p-coumarate conjugates into the growing lignin polymer within the cell wall matrix. The required acyl-transferase is a soluble enzyme (p-coumaroyl transferase, pCAT) that utilizes p-coumaroyl-CoenzymeA (pCA-CoA) as the activated donor molecule and sinapyl alcohol as the preferred acceptor molecule. Grasses (C3and C4) were evaluated for cell wall characteristics; pCA, lignin, pCAT activity, and neutral sugar composition. All C3 and C4 grasses had measurable pCAT activity, however the pCAT activities did not follow the same pattern as the pCA incorporation into lignin as expected.

Grass cell walls are atypical because their xylans are acylated with ferulate and lignins are acylated with p-coumarate. To probe the role and interactions of these p-hydroxycinnamates during lignification, feruloylated primary cell walls isolated from maize cell suspensions were lignified with coniferyl and sinapyl alcohols and with varying levels of p-coumarate esters. Ferulate xylan esters enhanced the formation of wall-bound syringyl lignin more than methyl p-coumarate, however, maximal concentrations of syringyl lignin were only one-third that of guaiacyl lignin. Including sinapyl p-coumarate, the presumed precursor of p-coumaroylated lignins, with monolignols unexpectedly accelerated peroxidase inactivation, interfered with ferulate copolymerization into lignin, and had minimal or adverse effects on cell wall lignification. Free phenolic groups of p-coumarate esters in isolated maize lignin and pith cell walls did not undergo oxidative coupling with each other or with added monolignols. Thus, the extensive formation of syringyl-rich lignins and the functional role of extensive lignin acylation by p-coumarate in grasses remains a mystery.

Peroxidases are heavily implicated in plant cell wall cross-linking reactions, altering the properties of the wall and impacting its utilization. Polysaccharide-polysaccharide cross-linking in grasses is achieved by dehydrodimerization of hydroxycinnamate-polysaccharide esters; a complex array of hydroxycinnamic acid dehydrodimers are released by saponification. Ferulates are the major cross-linking agents, but sinapate-ferulate cross-products have been discovered implicating sinapates in a similar role. New dehydrodimers have been authenticated, expanding our knowledge of the chemistry, role, and extent of cross-linking reactions. Ferulate dehydrotrimers have been discovered; whether these trimers truly cross-link three independent polysaccharide chains or only two remains to be determined. Hydroxycinnamates and their dehydrodimers also undergo radical coupling reactions with lignin monomers and possibly oligomers, resulting in lignin-polysaccharide cross-linking in the wall. Both polysaccharide-polysaccharide and lignin-polysaccharide cross-links inhibit the enzymatic hydrolysis of cell walls. The cross-linking process has particular relevance to plant physiology, human and animal nutrition and health, and food technology.

Lignins are complex natural polymers resulting from oxidative coupling of, primarily, 4-hydroxyphenylpropanoids. An understanding of their nature is evolving as a result of detailed structural studies, recently aided by the availability of lignin-biosynthetic-pathway mutants and transgenics. The currently accepted theory is that the lignin polymer is formed by combinatorial-like phenolic coupling reactions, via radicals generated by peroxidase-H2O2, under simple chemical control where monolignols react endwise with the growing polymer. As a result, the actual structure of the lignin macromolecule is not absolutely defined or determined. The ``randomness'' of linkage generation (which is not truly statistically random but governed, as is any chemical reaction, by the supply of reactants, the matrix, etc.) and the astronomical number of possible isomers of even a simple polymer structure, suggest a low probability of two lignin macromolecules being identical. A recent challenge to the currently accepted theory of chemically controlled lignification, attempting to bring lignin into line with more organized biopolymers such as proteins, is logically inconsistent with the most basic details of lignin structure. Lignins may derive in part from monomers and conjugates other than the three primary monolignols (p-coumaryl, coniferyl, and sinapyl alcohols). The plasticity of the combinatorial polymerization reactions allows monomer substitution and significant variations in final structure which, in many cases, the plant appears to tolerate. As such, lignification is seen as a marvelously evolved process allowing plants considerable flexibility in dealing with various environmental stresses, and conferring on them a striking ability to remain viable even when humans or nature alter ``required'' lignin-biosynthetic-pathway genes/enzymes. The malleability offers significant opportunities to engineer the structures of lignins beyond the limits explored to date.

A promoter-trap screen allowed us to identify an Arabidopsis line expressing GUS in the root vascular tissues. T-DNA border sequencing showed that the line was mutated in the caffeic acid O-methyltransferase 1 gene (AtOMT1) and therefore deficient in OMT1 activity. Atomt1 is a knockout mutant and the expression profile of the AtOMT1 gene has been determined as well as the consequences of the mutation on lignins, on soluble phenolics, on cell wall digestibility, and on the expression of the genes involved in monolignol biosynthesis. In this mutant and relative to the wild type, lignins lack syringyl (S) units and contain more 5-hydroxyguaiacyl units (5-OH-G), the precursors of S-units. The sinapoyl ester pool is modified with a two-fold reduction of sinapoyl-malate in the leaves and stems of mature plants as well as in seedlings. In addition, LC-MS analysis of the soluble phenolics extracted from the seedlings reveals the occurrence of unusual derivatives assigned to 5-OH-feruloyl malate and to 5-OH-feruloyl glucose. Therefore, AtOMT1 enzymatic activity appears to be involved not only in lignin formation but also in the biosynthesis of sinapate esters. In addition, a deregulation of other monolignol biosynthetic gene expression can be observed in the Atomt1 mutant. A poplar cDNA encoding a caffeic acid OMT (PtOMT1) was successfully used to complement the Atomt1 mutant and restored both the level of S units and of sinapate esters to the control level. However, the over-expression of PtOMT1 in wild-type Arabidopsis did not increase the S-lignin content, suggesting that OMT is not a limiting enzyme for S-unit biosynthesis.