An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community
[1];
- Peking Univ., Beijing (China); Univ. of Hong Kong (Hong Kong); Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States)
- Univ. of Hong Kong (Hong Kong); Tsinghua Univ., Beijing (China)
- Univ. of Hong Kong (Hong Kong); Xiamen Univ. (China)
- Univ. of Hong Kong (Hong Kong); Sun Yat-Sen Univ., Guangzhou (China)
- Univ. of Hong Kong (Hong Kong); Shanghai Jiao Tong Univ. (China)
- Peking Univ., Beijing (China)
- Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Hong Kong (Hong Kong)
BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. RESULTS:The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. CONCLUSION:The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC)
- Grant/Contract Number:
- AC02-05CH11231
- OSTI ID:
- 1605230
- Journal Information:
- Microbiome, Vol. 7, Issue 1; Conference: Microbiome; ISSN 2049-2618
- Publisher:
- BioMed CentralCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges
|
journal | July 2019 |
Biodegradation of endocrine disruptor Bisphenol A by Pseudomonas putida strain YC-AE1 isolated from polluted soil, Guangdong, China
|
journal | January 2020 |
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