Institute of Marine Science and Technology, Shandong University, Qingdao, China.
Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.
Environ Microbiol. 2021 Jan;23(1):160-173. doi: 10.1111/1462-2920.15289. Epub 2020 Nov 3.
A major conundrum in the isolation of prokaryotes from open environments is stochasticity. It is especially difficult to study low abundance groups where very little biological information exists, although single-cell genomics and metagenomics have alleviated some of this bottleneck. Here, we report an approach to capture lignin-utilizing bacteria by linking a physical model to actual organisms. Extracellular enzymes, lignin degradation and cell growth are crucial phenotypes of lignin-utilizing bacteria, but their interrelationships remain poorly understood. In this study, the phenotypes of bacteria isolated from in situ lignocellulose enrichment samples in coastal waters were traced and statistically analysed. It suggested cell growth, dye-decolorizing peroxidase (DyP) and reactive oxygen species (ROS) were significantly correlated with lignin degradation, exhibiting a genus-specific property. The established models enabled us to efficiently capture lignin-utilizing bacteria and rapidly evaluate lignin degradation for Bacillus and Vibrio strains. Through the model, we identified several previously unrecognized marine bacterial lignin degraders. Moreover, it demonstrated that the isolated marine lignin-utilizing bacteria employ a DyP-based system and ROS for lignin depolymerization, providing insights into the mechanism of marine bacterial lignin degradation. Our findings should have implications beyond the capture of lignin-utilizing bacteria, in the isolation of other microorganisms with as-yet-unknown molecular biomarkers.
从开放环境中分离原核生物的一个主要难题是随机性。研究丰度较低的群体尤其困难，因为这些群体的生物信息很少，尽管单细胞基因组学和宏基因组学已经缓解了一些这种瓶颈。在这里，我们报告了一种通过将物理模型与实际生物体联系起来来捕获木质素利用细菌的方法。胞外酶、木质素降解和细胞生长是木质素利用细菌的关键表型，但它们之间的相互关系仍知之甚少。在这项研究中，追踪并统计分析了从沿海水域原位木质纤维素富集样品中分离出的细菌的表型。结果表明，细胞生长、染料脱色过氧化物酶（DyP）和活性氧（ROS）与木质素降解显著相关，表现出属特异性。所建立的模型使我们能够有效地捕获木质素利用细菌，并快速评估 Bacillus 和 Vibrio 菌株的木质素降解。通过该模型，我们鉴定出了几种以前未被识别的海洋细菌木质素降解菌。此外，它表明，分离出的海洋木质素利用细菌采用 DyP 为基础的系统和 ROS 进行木质素解聚，为海洋细菌木质素降解的机制提供了新的见解。我们的研究结果应该不仅限于木质素利用细菌的捕获，对于其他具有未知分子生物标志物的微生物的分离也具有重要意义。
