Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing
ABSTRACT Assembling a functional consortium and identifying novel degraders from contaminated environments are still challenging due to the large diversity of microorganisms and the difficulty in isolating pure cultures. Here, we constructed a relatively simple functional consortium by enriching 1,4...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-12-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01787-23 |
| _version_ | 1797393627857551360 |
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| author | Kun Tian Yue Zhang Ruihuan Chen Ding Tan Ming Zhong Dandan Yao Yuanhua Dong Yun Liu |
| author_facet | Kun Tian Yue Zhang Ruihuan Chen Ding Tan Ming Zhong Dandan Yao Yuanhua Dong Yun Liu |
| author_sort | Kun Tian |
| collection | DOAJ |
| description | ABSTRACT Assembling a functional consortium and identifying novel degraders from contaminated environments are still challenging due to the large diversity of microorganisms and the difficulty in isolating pure cultures. Here, we constructed a relatively simple functional consortium by enriching 1,4-dioxane-degrading-consortia using a culture-dependent dilution-to-extinction (DTE) method and reported a new key dioxane-degrader Shinella sp. Our results showed that serial dilution and reculture led to a divergence in the degradation ability of each consortium. Next-generation sequencing data revealed that the divergence in degradation performance was due to the reassembly of microbiota in the DTE process, which occurred most notably in 10−8 and 10−9 dilutions. The shift in community structure at 10−9 prevented the recovery of 1,4-dioxane degradation capacity, and the newly dominant taxa, Xanthobacter and Acinetobacter, struggled to replace the original dominant genus Shinella for 1,4-dioxane biodegradation. Combining differential analysis of community structure and metabolic function, we confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, we verified our findings using our isolated dioxane-degrading bacteria, Shinella yambaruensis, resulting in the rapid recovery of degradation performance of a 10−9 dilution consortium with Xanthobacter and Acinetobacter as the dominant microbiota. Taken together, this study provides a strategy for self-assembling functional consortiums and identifying the key degraders to explore the underlying biological mechanisms of enriched contaminant-degrading consortia. IMPORTANCE Assembling a functional microbial consortium and identifying key degraders involved in the degradation of 1,4-dioxane are crucial for the design of synergistic consortia used in enhancing the bioremediation of 1,4-dioxane-contaminated sites. However, due to the vast diversity of microbes, assembling a functional consortium and identifying novel degraders through a simple method remain a challenge. In this study, we reassembled 1,4-dioxane-degrading microbial consortia using a simple and easy-to-operate method by combining dilution-to-extinction and reculture techniques. We combined differential analysis of community structure and metabolic function and confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, a new dioxane-degrading bacterium was isolated, Shinella yambaruensis, which verified our findings. These results demonstrate that DTE and reculture techniques can be used beyond diversity reduction to assemble functional microbial communities, particularly to identify key degraders in contaminant-degrading consortia. |
| first_indexed | 2024-03-09T00:06:37Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-09T00:06:37Z |
| publishDate | 2023-12-01 |
| publisher | American Society for Microbiology |
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| series | Microbiology Spectrum |
| spelling | doaj.art-c03599dacc664052b1df4065edd29ba32023-12-12T13:17:19ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-12-0111610.1128/spectrum.01787-23Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturingKun Tian0Yue Zhang1Ruihuan Chen2Ding Tan3Ming Zhong4Dandan Yao5Yuanhua Dong6Yun Liu7Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaCollege of Life and Environmental Science, Wenzhou University , Wenzhou, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaKey Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, ChinaABSTRACT Assembling a functional consortium and identifying novel degraders from contaminated environments are still challenging due to the large diversity of microorganisms and the difficulty in isolating pure cultures. Here, we constructed a relatively simple functional consortium by enriching 1,4-dioxane-degrading-consortia using a culture-dependent dilution-to-extinction (DTE) method and reported a new key dioxane-degrader Shinella sp. Our results showed that serial dilution and reculture led to a divergence in the degradation ability of each consortium. Next-generation sequencing data revealed that the divergence in degradation performance was due to the reassembly of microbiota in the DTE process, which occurred most notably in 10−8 and 10−9 dilutions. The shift in community structure at 10−9 prevented the recovery of 1,4-dioxane degradation capacity, and the newly dominant taxa, Xanthobacter and Acinetobacter, struggled to replace the original dominant genus Shinella for 1,4-dioxane biodegradation. Combining differential analysis of community structure and metabolic function, we confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, we verified our findings using our isolated dioxane-degrading bacteria, Shinella yambaruensis, resulting in the rapid recovery of degradation performance of a 10−9 dilution consortium with Xanthobacter and Acinetobacter as the dominant microbiota. Taken together, this study provides a strategy for self-assembling functional consortiums and identifying the key degraders to explore the underlying biological mechanisms of enriched contaminant-degrading consortia. IMPORTANCE Assembling a functional microbial consortium and identifying key degraders involved in the degradation of 1,4-dioxane are crucial for the design of synergistic consortia used in enhancing the bioremediation of 1,4-dioxane-contaminated sites. However, due to the vast diversity of microbes, assembling a functional consortium and identifying novel degraders through a simple method remain a challenge. In this study, we reassembled 1,4-dioxane-degrading microbial consortia using a simple and easy-to-operate method by combining dilution-to-extinction and reculture techniques. We combined differential analysis of community structure and metabolic function and confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, a new dioxane-degrading bacterium was isolated, Shinella yambaruensis, which verified our findings. These results demonstrate that DTE and reculture techniques can be used beyond diversity reduction to assemble functional microbial communities, particularly to identify key degraders in contaminant-degrading consortia.https://journals.asm.org/doi/10.1128/spectrum.01787-23dilution-to-extinctionnext-generation sequencingconsortium1,4-dioxanekey degraders |
| spellingShingle | Kun Tian Yue Zhang Ruihuan Chen Ding Tan Ming Zhong Dandan Yao Yuanhua Dong Yun Liu Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing Microbiology Spectrum dilution-to-extinction next-generation sequencing consortium 1,4-dioxane key degraders |
| title | Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing |
| title_full | Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing |
| title_fullStr | Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing |
| title_full_unstemmed | Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing |
| title_short | Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing |
| title_sort | self assembling a 1 4 dioxane degrading consortium and identifying the key role of shinella sp through dilution to extinction and reculturing |
| topic | dilution-to-extinction next-generation sequencing consortium 1,4-dioxane key degraders |
| url | https://journals.asm.org/doi/10.1128/spectrum.01787-23 |
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