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Scientific Reports Volume 12 ,Issue 1 ,2022-10-21
Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks
Article
Min-Zhi Jiang 1 Hai-Zhen Zhu 2 Nan Zhou 2 Chang Liu 2 Cheng-Ying Jiang 2 Yulin Wang 1 Shuang-Jiang Liu 1 , 2 , 3
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DOI:10.1038/s41598-022-23000-7
Received 2022-5-26, accepted for publication 2022-10-21, Published 2022-10-21
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摘要

Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.

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© The Author(s) 2022
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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通讯作者

1. Yulin Wang.State Key Laboratory of Microbial Technology, Shandong University, 266000, Qingdao, People’s Republic of China.wangyulin@sdu.edu.cn
2. Shuang-Jiang Liu.State Key Laboratory of Microbial Technology, Shandong University, 266000, Qingdao, People’s Republic of China;State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, People’s Republic of China;University of Chinese Academy of Sciences, 100049, Beijing, People’s Republic of China.liusj@sdu.edu.cn

推荐引用方式

Min-Zhi Jiang,Hai-Zhen Zhu,Nan Zhou,Chang Liu,Cheng-Ying Jiang,Yulin Wang,Shuang-Jiang Liu. Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks. Scientific Reports ,Vol.12, Issue 1(2022)

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