CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the abili...
| Main Authors: | , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2023
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/170117 |
| _version_ | 1811688431338651648 |
|---|---|
| author | Deng, Xuhan Yuan, Jing Chen, Liping Chen, Hang Wei, Chaohai Nielsen, Per Halkjær Wuertz, Stefan Qiu, Guanglei |
| author2 | School of Civil and Environmental Engineering |
| author_facet | School of Civil and Environmental Engineering Deng, Xuhan Yuan, Jing Chen, Liping Chen, Hang Wei, Chaohai Nielsen, Per Halkjær Wuertz, Stefan Qiu, Guanglei |
| author_sort | Deng, Xuhan |
| collection | NTU |
| description | Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems. |
| first_indexed | 2024-10-01T05:32:06Z |
| format | Journal Article |
| id | ntu-10356/170117 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:32:06Z |
| publishDate | 2023 |
| record_format | dspace |
| spelling | ntu-10356/1701172023-08-29T00:45:45Z CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter Deng, Xuhan Yuan, Jing Chen, Liping Chen, Hang Wei, Chaohai Nielsen, Per Halkjær Wuertz, Stefan Qiu, Guanglei School of Civil and Environmental Engineering Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) Engineering::Environmental engineering Candidatus Accumulibacter Enhanced Biological Phosphorus Removal Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems. Ministry of Education (MOE) National Research Foundation (NRF) Public Utilities Board (PUB) This research was partially supported by the National Natural Science Foundation of China (No. 52270035 and No. 51808297), the Natural Science Foundation of Guangdong Province (2021A1515010494), the Guangzhou Science and Technology Planning Program (202002030340), the Pearl River Talent Recruitment Program (2019QN01L125), and the Program for Science and Technology of Guangdong Province, China (No. 2018A050506009). Additional support came from the Singapore National Research Foundation and the Ministry of Education under the Research centre of Excellence Programme, and through a research grant from the National Research Foundation under its Environment and Water Industry Programme (project number 1102–IRIS–10–02), administered by PUB - Singapore’s national water agency. 2023-08-29T00:45:45Z 2023-08-29T00:45:45Z 2023 Journal Article Deng, X., Yuan, J., Chen, L., Chen, H., Wei, C., Nielsen, P. H., Wuertz, S. & Qiu, G. (2023). CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. Water Research, 235, 119906-. https://dx.doi.org/10.1016/j.watres.2023.119906 0043-1354 https://hdl.handle.net/10356/170117 10.1016/j.watres.2023.119906 37004306 2-s2.0-85151296724 235 119906 en 1102-IRIS-10-02 Water Research © 2023 Elsevier Ltd. All rights reserved. |
| spellingShingle | Engineering::Environmental engineering Candidatus Accumulibacter Enhanced Biological Phosphorus Removal Deng, Xuhan Yuan, Jing Chen, Liping Chen, Hang Wei, Chaohai Nielsen, Per Halkjær Wuertz, Stefan Qiu, Guanglei CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title | CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title_full | CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title_fullStr | CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title_full_unstemmed | CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title_short | CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter |
| title_sort | crispr cas phage defense systems and prophages in candidatus accumulibacter |
| topic | Engineering::Environmental engineering Candidatus Accumulibacter Enhanced Biological Phosphorus Removal |
| url | https://hdl.handle.net/10356/170117 |
| work_keys_str_mv | AT dengxuhan crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT yuanjing crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT chenliping crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT chenhang crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT weichaohai crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT nielsenperhalkjær crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT wuertzstefan crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter AT qiuguanglei crisprcasphagedefensesystemsandprophagesincandidatusaccumulibacter |