Functional metagenomic analysis of quorum sensing signaling in a nitrifying community
Abstract Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS product...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-10-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-021-00250-3 |
| _version_ | 1818732606021173248 |
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| author | Chuan Hao Tan Yee Phan Yeo Muhammad Hafiz Noele Kai Jing Ng Sujatha Subramoni Shireen Taj Martin Tay Xie Chao Staffan Kjelleberg Scott A. Rice |
| author_facet | Chuan Hao Tan Yee Phan Yeo Muhammad Hafiz Noele Kai Jing Ng Sujatha Subramoni Shireen Taj Martin Tay Xie Chao Staffan Kjelleberg Scott A. Rice |
| author_sort | Chuan Hao Tan |
| collection | DOAJ |
| description | Abstract Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community. |
| first_indexed | 2024-12-17T23:36:14Z |
| format | Article |
| id | doaj.art-c58990a866c84ad180846d1eeac274b5 |
| institution | Directory Open Access Journal |
| issn | 2055-5008 |
| language | English |
| last_indexed | 2024-12-17T23:36:14Z |
| publishDate | 2021-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj.art-c58990a866c84ad180846d1eeac274b52022-12-21T21:28:33ZengNature Portfolionpj Biofilms and Microbiomes2055-50082021-10-017111010.1038/s41522-021-00250-3Functional metagenomic analysis of quorum sensing signaling in a nitrifying communityChuan Hao Tan0Yee Phan Yeo1Muhammad Hafiz2Noele Kai Jing Ng3Sujatha Subramoni4Shireen Taj5Martin Tay6Xie Chao7Staffan Kjelleberg8Scott A. Rice9Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological UniversityAbstract Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.https://doi.org/10.1038/s41522-021-00250-3 |
| spellingShingle | Chuan Hao Tan Yee Phan Yeo Muhammad Hafiz Noele Kai Jing Ng Sujatha Subramoni Shireen Taj Martin Tay Xie Chao Staffan Kjelleberg Scott A. Rice Functional metagenomic analysis of quorum sensing signaling in a nitrifying community npj Biofilms and Microbiomes |
| title | Functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| title_full | Functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| title_fullStr | Functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| title_full_unstemmed | Functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| title_short | Functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| title_sort | functional metagenomic analysis of quorum sensing signaling in a nitrifying community |
| url | https://doi.org/10.1038/s41522-021-00250-3 |
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