Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature
Abstract Due to the challenges in detecting in situ activity and cultivating the not-yet-cultured, functional assessment and mining of living microbes from nature has typically followed a ‘culture-first’ paradigm. Here, employing phosphate-solubilizing microbes (PSM) as model, we introduce a ‘screen...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2022-10-01
|
| Series: | ISME Communications |
| Online Access: | https://doi.org/10.1038/s43705-022-00188-3 |
| _version_ | 1797230741144207360 |
|---|---|
| author | Xiaoyan Jing Yanhai Gong Huihui Pan Yu Meng Yishang Ren Zhidian Diao Runzhi Mu Teng Xu Jia Zhang Yuetong Ji Yuandong Li Chen Wang Lingyun Qu Li Cui Bo Ma Jian Xu |
| author_facet | Xiaoyan Jing Yanhai Gong Huihui Pan Yu Meng Yishang Ren Zhidian Diao Runzhi Mu Teng Xu Jia Zhang Yuetong Ji Yuandong Li Chen Wang Lingyun Qu Li Cui Bo Ma Jian Xu |
| author_sort | Xiaoyan Jing |
| collection | DOAJ |
| description | Abstract Due to the challenges in detecting in situ activity and cultivating the not-yet-cultured, functional assessment and mining of living microbes from nature has typically followed a ‘culture-first’ paradigm. Here, employing phosphate-solubilizing microbes (PSM) as model, we introduce a ‘screen-first’ strategy that is underpinned by a precisely one-cell-resolution, complete workflow of single-cell Raman-activated Sorting and Cultivation (scRACS-Culture). Directly from domestic sewage, individual cells were screened for in-situ organic-phosphate-solubilizing activity via D2O intake rate, sorted by the function via Raman-activated Gravity-driven Encapsulation (RAGE), and then cultivated from precisely one cell. By scRACS-Culture, pure cultures of strong organic PSM including Comamonas spp., Acinetobacter spp., Enterobacter spp. and Citrobacter spp., were derived, whose phosphate-solubilizing activities in situ are 90–200% higher than in pure culture, underscoring the importance of ‘screen-first’ strategy. Moreover, employing scRACS-Seq for post-RACS cells that remain uncultured, we discovered a previously unknown, low-abundance, strong organic-PSM of Cutibacterium spp. that employs secretary metallophosphoesterase (MPP), cell-wall-anchored 5′-nucleotidase (encoded by ushA) and periplasmic-membrane located PstSCAB-PhoU transporter system for efficient solubilization and scavenging of extracellular phosphate in sewage. Therefore, scRACS-Culture and scRACS-Seq provide an in situ function-based, ‘screen-first’ approach for assessing and mining microbes directly from the environment. |
| first_indexed | 2024-04-24T15:33:18Z |
| format | Article |
| id | doaj.art-9dc56589eaa7420480198edfce7a5367 |
| institution | Directory Open Access Journal |
| issn | 2730-6151 |
| language | English |
| last_indexed | 2024-04-24T15:33:18Z |
| publishDate | 2022-10-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | ISME Communications |
| spelling | doaj.art-9dc56589eaa7420480198edfce7a53672024-04-02T03:11:20ZengOxford University PressISME Communications2730-61512022-10-012111410.1038/s43705-022-00188-3Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from natureXiaoyan Jing0Yanhai Gong1Huihui Pan2Yu Meng3Yishang Ren4Zhidian Diao5Runzhi Mu6Teng Xu7Jia Zhang8Yuetong Ji9Yuandong Li10Chen Wang11Lingyun Qu12Li Cui13Bo Ma14Jian Xu15Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesQingdao Zhang Cun River Water Co., LtdSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesThe First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesSingle-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesAbstract Due to the challenges in detecting in situ activity and cultivating the not-yet-cultured, functional assessment and mining of living microbes from nature has typically followed a ‘culture-first’ paradigm. Here, employing phosphate-solubilizing microbes (PSM) as model, we introduce a ‘screen-first’ strategy that is underpinned by a precisely one-cell-resolution, complete workflow of single-cell Raman-activated Sorting and Cultivation (scRACS-Culture). Directly from domestic sewage, individual cells were screened for in-situ organic-phosphate-solubilizing activity via D2O intake rate, sorted by the function via Raman-activated Gravity-driven Encapsulation (RAGE), and then cultivated from precisely one cell. By scRACS-Culture, pure cultures of strong organic PSM including Comamonas spp., Acinetobacter spp., Enterobacter spp. and Citrobacter spp., were derived, whose phosphate-solubilizing activities in situ are 90–200% higher than in pure culture, underscoring the importance of ‘screen-first’ strategy. Moreover, employing scRACS-Seq for post-RACS cells that remain uncultured, we discovered a previously unknown, low-abundance, strong organic-PSM of Cutibacterium spp. that employs secretary metallophosphoesterase (MPP), cell-wall-anchored 5′-nucleotidase (encoded by ushA) and periplasmic-membrane located PstSCAB-PhoU transporter system for efficient solubilization and scavenging of extracellular phosphate in sewage. Therefore, scRACS-Culture and scRACS-Seq provide an in situ function-based, ‘screen-first’ approach for assessing and mining microbes directly from the environment.https://doi.org/10.1038/s43705-022-00188-3 |
| spellingShingle | Xiaoyan Jing Yanhai Gong Huihui Pan Yu Meng Yishang Ren Zhidian Diao Runzhi Mu Teng Xu Jia Zhang Yuetong Ji Yuandong Li Chen Wang Lingyun Qu Li Cui Bo Ma Jian Xu Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature ISME Communications |
| title | Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature |
| title_full | Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature |
| title_fullStr | Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature |
| title_full_unstemmed | Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature |
| title_short | Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature |
| title_sort | single cell raman activated sorting and cultivation scracs culture for assessing and mining in situ phosphate solubilizing microbes from nature |
| url | https://doi.org/10.1038/s43705-022-00188-3 |
| work_keys_str_mv | AT xiaoyanjing singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT yanhaigong singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT huihuipan singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT yumeng singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT yishangren singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT zhidiandiao singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT runzhimu singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT tengxu singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT jiazhang singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT yuetongji singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT yuandongli singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT chenwang singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT lingyunqu singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT licui singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT boma singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature AT jianxu singlecellramanactivatedsortingandcultivationscracscultureforassessingandmininginsituphosphatesolubilizingmicrobesfromnature |