Selection, Succession, and Stabilization of Soil Microbial Consortia
ABSTRACT Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbio...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2019-08-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00055-19 |
| _version_ | 1818345256872050688 |
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| author | Elias K. Zegeye Colin J. Brislawn Yuliya Farris Sarah J. Fansler Kirsten S. Hofmockel Janet K. Jansson Aaron T. Wright Emily B. Graham Dan Naylor Ryan S. McClure Hans C. Bernstein |
| author_facet | Elias K. Zegeye Colin J. Brislawn Yuliya Farris Sarah J. Fansler Kirsten S. Hofmockel Janet K. Jansson Aaron T. Wright Emily B. Graham Dan Naylor Ryan S. McClure Hans C. Bernstein |
| author_sort | Elias K. Zegeye |
| collection | DOAJ |
| description | ABSTRACT Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability. Author Video: An author video summary of this article is available. |
| first_indexed | 2024-12-13T16:59:29Z |
| format | Article |
| id | doaj.art-1baa4b3c42bf4c0e87e37baef2c56bb5 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-13T16:59:29Z |
| publishDate | 2019-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-1baa4b3c42bf4c0e87e37baef2c56bb52022-12-21T23:37:50ZengAmerican Society for MicrobiologymSystems2379-50772019-08-014410.1128/mSystems.00055-19Selection, Succession, and Stabilization of Soil Microbial ConsortiaElias K. Zegeye0Colin J. Brislawn1Yuliya Farris2Sarah J. Fansler3Kirsten S. Hofmockel4Janet K. Jansson5Aaron T. Wright6Emily B. Graham7Dan Naylor8Ryan S. McClure9Hans C. Bernstein10Biological 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, USAEnvironmental Molecular Sciences Laboratory, 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, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USABiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USAABSTRACT Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability. Author Video: An author video summary of this article is available.https://journals.asm.org/doi/10.1128/mSystems.00055-19chitinmicrobial consortiamicrobiomemicrobiome stabilitymodel microbiomeN-acetylglucosamine |
| spellingShingle | Elias K. Zegeye Colin J. Brislawn Yuliya Farris Sarah J. Fansler Kirsten S. Hofmockel Janet K. Jansson Aaron T. Wright Emily B. Graham Dan Naylor Ryan S. McClure Hans C. Bernstein Selection, Succession, and Stabilization of Soil Microbial Consortia mSystems chitin microbial consortia microbiome microbiome stability model microbiome N-acetylglucosamine |
| title | Selection, Succession, and Stabilization of Soil Microbial Consortia |
| title_full | Selection, Succession, and Stabilization of Soil Microbial Consortia |
| title_fullStr | Selection, Succession, and Stabilization of Soil Microbial Consortia |
| title_full_unstemmed | Selection, Succession, and Stabilization of Soil Microbial Consortia |
| title_short | Selection, Succession, and Stabilization of Soil Microbial Consortia |
| title_sort | selection succession and stabilization of soil microbial consortia |
| topic | chitin microbial consortia microbiome microbiome stability model microbiome N-acetylglucosamine |
| url | https://journals.asm.org/doi/10.1128/mSystems.00055-19 |
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