Plant cell walls represent the majority of the terrestrial plants by mass and mainly consist of polysaccharides and lignin. These constituents are considered as an abundant and renewable carbon resource providing great potential for the production of petroleum-displacing biofuels and biochemicals. However, the complex, rigid and heterogeneous plant cell wall structure are difficult deconstruct, and typically a combination of biological and chemical treatments are required in order to break down the cell wall and maximize the yield of the products. Pretreatments are thermal or chemical processes that facilitate the subsequent sugar-releasing enzymatic hydrolysis. Alkaline pretreatments and alkaline-oxidative pretreatments are one of the main categories of pretreatments that function well on monocot grasses, which include the cereal stovers and the energy crops. These pretreatments target ester cross-links between lignin and hemicelluloses within the grass cell walls formed by the hydroxycinnamates, as well as the ester linked side chains such as acetyl groups in hemicelluloses, results in significant removal of lignin and hemicelluloses. The removal of these cell wall constituents significantly increases the accessibility of water and enzymes to the cell walls. Structural characteristics including higher order structures within the cell wall, covalent and non-covalent cross-linking, and porosity may all impact the conversion process. Also, plant cell walls can exhibit substantial heterogeneity between plant cell type and tissue. The goal of this work is to employ novel and conventional characterization tools to identify how properties of diverse cell walls are impacted by pretreatments and how this correlates to reduced cell wall "recalcitrance", which is important for both plant design with properties suited for deconstruction and the design of deconstruction strategies. This work consists of several related studies. The roles that glycans play in the plant cell wall recalcitrance was investigated using taxonomically and structurally diverse biomass feedstocks. Their responses to alkaline oxidative pretreatment and how differing features of the cell wall matrix contribute to its recalcitrance was assessed by a set of studies. Different mechanisms of improving hydrolysis yields following alkaline oxidative pretreatment was discovered for monocots and dicots. In monocot grasses, the "loosening" of the glycans due to alkaline oxidative pretreatment indicating the overall weaker associations between cell wall polymers in grasses than in dicots, which results in significantly improved hydrolysis yields after the pretreatment. It was found that the hydrolysis yields of alkali pretreated corn stovers are not necessarily correlated with the original contents of lignin and hydroxycinamates, but they are highly related with the removal of these compounds. Multivariate models were applied to predict the hydrolysis yields based on cell wall properties quantified or predicted by high-throughput pyrolysis molecular beam mass spectrometry (py-MBMS). It was found that the untreated cell wall composition properties including lignin and xylan content, as well as the hydrophilicity, set the initial recalcitrance of the cell walls. However, for the alkaline pretreated corn stover, hydrolysis yields were only predictable by the release of lignin and hydroxycinnamates. These findings indicate that the final yield of a biomass feedstock is not necessarily correlated with the structural features, but is highly pretreatment-oriented, and the properties contributing to a "reduced recalcitrance" phenotype following a specific pretreatment are not necessarily the same properties that contribute to recalcitrance in untreated cell wall.
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