Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management
ABSTRACT Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions....
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-12-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00571-22 |
| _version_ | 1827150134354378752 |
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| author | Ning Duan Mark Radosevich Jie Zhuang Jennifer M. DeBruyn Margaret Staton Sean M. Schaeffer |
| author_facet | Ning Duan Mark Radosevich Jie Zhuang Jennifer M. DeBruyn Margaret Staton Sean M. Schaeffer |
| author_sort | Ning Duan |
| collection | DOAJ |
| description | ABSTRACT Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes. |
| first_indexed | 2024-04-11T12:26:10Z |
| format | Article |
| id | doaj.art-caf0115b9d374bedab37aeae9fa62734 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2025-03-20T21:29:15Z |
| publishDate | 2022-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-caf0115b9d374bedab37aeae9fa627342024-08-11T18:59:20ZengAmerican Society for MicrobiologymSystems2379-50772022-12-017610.1128/msystems.00571-22Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping ManagementNing Duan0Mark Radosevich1Jie Zhuang2Jennifer M. DeBruyn3Margaret Staton4Sean M. Schaeffer5Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USADepartment of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USADepartment of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USADepartment of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USADepartment of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USADepartment of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USAABSTRACT Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes.https://journals.asm.org/doi/10.1128/msystems.00571-22soilvirusesphagebacteriaarchaeametagenomics |
| spellingShingle | Ning Duan Mark Radosevich Jie Zhuang Jennifer M. DeBruyn Margaret Staton Sean M. Schaeffer Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management mSystems soil viruses phage bacteria archaea metagenomics |
| title | Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management |
| title_full | Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management |
| title_fullStr | Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management |
| title_full_unstemmed | Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management |
| title_short | Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management |
| title_sort | identification of novel viruses and their microbial hosts from soils with long term nitrogen fertilization and cover cropping management |
| topic | soil viruses phage bacteria archaea metagenomics |
| url | https://journals.asm.org/doi/10.1128/msystems.00571-22 |
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