Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil
ABSTRACT Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such interactions. Here, we sought to address this challen...
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| Language: | English |
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American Society for Microbiology
2025-07-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.00404-25 |
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| author | Ryan McClure Albert Rivas-Ubach Kim K. Hixson Yuliya Farris Marci Garcia Robert Danczak Michelle Davison Vanessa L. Paurus Janet K. Jansson |
| author_facet | Ryan McClure Albert Rivas-Ubach Kim K. Hixson Yuliya Farris Marci Garcia Robert Danczak Michelle Davison Vanessa L. Paurus Janet K. Jansson |
| author_sort | Ryan McClure |
| collection | DOAJ |
| description | ABSTRACT Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such interactions. Here, we sought to address this challenge by analysis of a model soil consortium (MSC-2) consisting of eight soil bacterial species. Our aim was to elucidate the specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over 3 months. Multi-omics was used to understand how the community composition, transcripts, proteins, and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles the interactions between soil microorganisms.IMPORTANCEAlthough soil microorganisms carry out decomposition of organic matter in soil, the details are unclear due to the complexity of the soil microbiome and the heterogeneity of the soil habitat. Understanding carbon decomposition is of vital importance to determine how the soil carbon cycle functions. This is especially important with regard to understanding the fertility of soils and their ability to support plant growth. To overcome these challenges, we investigated in considerable detail a model soil community during its decomposition of a typical soil organic molecule—chitin. By using a multi-omics approach, we were able to decipher community interactions during chitin breakdown. This information provides a basis for understanding how more complex soil microbial communities interact in nature. |
| format | Article |
| id | doaj-art-c7390b77fe004d7b87d0d79a7bfce785 |
| institution | Kabale University |
| issn | 2150-7511 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj-art-c7390b77fe004d7b87d0d79a7bfce7852025-08-20T03:28:41ZengAmerican Society for MicrobiologymBio2150-75112025-07-0116710.1128/mbio.00404-25Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soilRyan McClure0Albert Rivas-Ubach1Kim K. Hixson2Yuliya Farris3Marci Garcia4Robert Danczak5Michelle Davison6Vanessa L. Paurus7Janet K. Jansson8Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USAEnvironmental and Molecular Sciences Division (EMSL), Pacific Northwest National Laboratory, Richland, Washington, USAEnvironmental and Molecular Sciences Division (EMSL), Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USAPhysical and computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USAABSTRACT Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such interactions. Here, we sought to address this challenge by analysis of a model soil consortium (MSC-2) consisting of eight soil bacterial species. Our aim was to elucidate the specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over 3 months. Multi-omics was used to understand how the community composition, transcripts, proteins, and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles the interactions between soil microorganisms.IMPORTANCEAlthough soil microorganisms carry out decomposition of organic matter in soil, the details are unclear due to the complexity of the soil microbiome and the heterogeneity of the soil habitat. Understanding carbon decomposition is of vital importance to determine how the soil carbon cycle functions. This is especially important with regard to understanding the fertility of soils and their ability to support plant growth. To overcome these challenges, we investigated in considerable detail a model soil community during its decomposition of a typical soil organic molecule—chitin. By using a multi-omics approach, we were able to decipher community interactions during chitin breakdown. This information provides a basis for understanding how more complex soil microbial communities interact in nature.https://journals.asm.org/doi/10.1128/mbio.00404-25soil microbiomemodel soil consortium-2chitinchitin decompositionmulti-omicsmetabolomics |
| spellingShingle | Ryan McClure Albert Rivas-Ubach Kim K. Hixson Yuliya Farris Marci Garcia Robert Danczak Michelle Davison Vanessa L. Paurus Janet K. Jansson Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil mBio soil microbiome model soil consortium-2 chitin chitin decomposition multi-omics metabolomics |
| title | Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| title_full | Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| title_fullStr | Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| title_full_unstemmed | Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| title_short | Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| title_sort | multi omics of a model bacterial consortium deciphers details of chitin decomposition in soil |
| topic | soil microbiome model soil consortium-2 chitin chitin decomposition multi-omics metabolomics |
| url | https://journals.asm.org/doi/10.1128/mbio.00404-25 |
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