Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies.
Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies.
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DOI：
10.1186/s13068-018-1164-2
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发表时间：
2018
影响因子：
6.3
通讯作者：
Bruce NC
中科院分区：
文献类型：
--
作者：
Alessi AM;Bird SM;Oates NC;Li Y;Dowle AA;Novotny EH;deAzevedo ER;Bennett JP;Polikarpov I;Young JPW;McQueen-Mason SJ;Bruce NC
木质纤维素是生物圈中最丰富的固定碳形式之一。目前降解木质纤维素的工业方法采用通常来自单一真菌物种的酶混合物，其仅在生物质预处理后水解多糖中有效。虽然木质纤维素降解的酶促机制已经在单个微生物物种中详细表征，但在自然界中有效分解植物材料的微生物群落是物种丰富的，并且分泌无数的酶来进行木质纤维素的“群落水平”代谢。因此，单一物种的方法可能会错过木质纤维素降解的重要方面，这将是优化商业过程的核心。在这里，我们研究了微生物降解的小麦秸秆在液体培养，接种了小麦秸秆堆肥。在选定的时间点采集的样品进行多组学分析，目的是确定新的微生物机制，木质纤维素降解，可应用于工业预处理的原料。基于细菌和真核生物核糖体基因序列的系统发育组成表明，随着时间的推移，由于微生物富集，复杂性和多样性逐渐降低。细菌种类的分类隶属关系显示拟杆菌门和变形菌门的优势和高相对丰度的属Asticcacaulis，Leadbetterella和Truepera。该社区的真核生物成员丰富的peritrich纤毛虫从Telotrochidium属，蓬勃发展的液体培养物相比，真菌物种，存在于低丰度。一个有针对性的metasecretome的方法结合metatranscriptomics分析，确定了1127蛋白质，并显示了许多碳水化合物活性酶的存在下提取的生物质结合的馏分和培养上清液。这揭示了广泛的水解纤维素酶，半纤维素酶和碳水化合物结合模块参与木质纤维素降解。这些活动的表达相关的FTIR和ssNMR测量观察到的生物质组成的变化。基于质谱的蛋白质组学与元转录组学相结合，已经能够鉴定大量的木质纤维素降解酶，现在可以进一步探索开发用于处理植物基原料的改进的酶鸡尾酒。除了预期的碳水化合物活性酶，我们的研究揭示了大量的未知蛋白质，其中一些可能发挥关键作用，以社区为基础的木质纤维素降解。本文的在线版本（10.1186/s13068-018-1164-2）包含补充材料，可供授权用户使用。
Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform “community-level” metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation. The online version of this article (10.1186/s13068-018-1164-2) contains supplementary material, which is available to authorized users.
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影响因子：
5.2
作者：
De Gannes V;Eudoxie G;Hickey WJ
通讯作者：
Hickey WJ
影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
4.4
作者：
Griffiths, RI;Whiteley, AS;Bailey, MJ
通讯作者：
Bailey, MJ
影响因子：
7
作者：
Ishihama, Y;Oda, Y;Mann, M
通讯作者：
Mann, M
影响因子：
--
作者：
Ivanova N;Rohde C;Munk C;Nolan M;Lucas S;Del Rio TG;Tice H;Deshpande S;Cheng JF;Tapia R;Han C;Goodwin L;Pitluck S;Liolios K;Mavromatis K;Mikhailova N;Pati A;Chen A;Palaniappan K;Land M;Hauser L;Chang YJ;Jeffries CD;Brambilla E;Rohde M;Göker M;Tindall BJ;Woyke T;Bristow J;Eisen JA;Markowitz V;Hugenholtz P;Kyrpides NC;Klenk HP;Lapidus A
通讯作者：
Lapidus A