The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common “-omics”-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

中文翻译：

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结合全细胞壁分析和简化的硅碳水化合物活性酶发现，以提高农作物残留物的生物催化转化

由于不断增长的能源需求和减少温室气体排放的监管激励措施，生物燃料作为一种有效的可再生能源的生产受到了相当多的关注。第二代生物燃料原料，包括每年收获期间农场产生的农作物残留物，丰富、廉价且可持续。与富含易发酵碳水化合物的第一代原料不同，作物残渣细胞壁对糖化、发酵和增值具有高度抵抗力。作物残渣含有顽固多糖，包括纤维素、半纤维素、果胶、木质素和木质素-碳水化合物复合物。此外，它们的细胞壁在植物来源之间的连接结构和单糖组成可能有所不同。总细胞壁结构的表征，包括使用基于色谱的方法、核磁共振、组学和抗体糖组分析对糖组成、连接和复杂结构进行高分辨率分析，为原料细胞壁的精细化学提供了重要的见解。此外，提高生物消化反应器中微生物群落的催化潜力和生物乙醇生产中使用的预处理效率可能会提高生物转化率和产量。为此，参与动态生物质解构的碳水化合物活性酶（CAZymes）的知识和表征至关重要。在这里，我们概述了使用常见的基于“组学”的方法来研究木质纤维素代谢群落和微生物，以及注释和发现 CAZymes 的方法，以及准确预测 CAZyme 功能的方法。还讨论了分析大型数据集（包括宏基因组组装基因组）的新兴方法。使用互补的糖组学和元组学方法来表征农业残留物和消化它们的微生物群落，为最大限度地提高作物废物流中的价值和能源提取提供了有前途的研究流。