Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level
The soil microbiome is dynamically structured at the local soil aggregate level by a combination of bottom-up and top-down processes. The soil microbiome is structured at the local soil aggregate scale by a dynamic interplay of bottom-up and top-down processes, yet less attention has been given to t...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-11-01
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| Series: | Geoderma |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S001670612300335X |
| _version_ | 1797634030246559744 |
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| author | Yuji Jiang Shuzhen Li Andrew D. Barnes Jia Liu Guofan Zhu Lu Luan Francisco Dini-Andreote Stefan Geisen Bo Sun |
| author_facet | Yuji Jiang Shuzhen Li Andrew D. Barnes Jia Liu Guofan Zhu Lu Luan Francisco Dini-Andreote Stefan Geisen Bo Sun |
| author_sort | Yuji Jiang |
| collection | DOAJ |
| description | The soil microbiome is dynamically structured at the local soil aggregate level by a combination of bottom-up and top-down processes. The soil microbiome is structured at the local soil aggregate scale by a dynamic interplay of bottom-up and top-down processes, yet less attention has been given to the latter (e.g., predation). We aimed to identify distinct groups of predators (protists and nematodes) and prey (bacteria) to determine the effect of predation on microbial gene abundances associated with carbon and nitrogen metabolisms. We partitioned soil aggregate size at three distinct levels to distinguish potential differences in predator–prey microbe interactions that take place at the soil micro-structure level. Our results revealed that the bacterial diversity and the abundance of protists were significantly higher in microaggregates than in macroaggregates. Correlation analysis, structural equation modeling, and co-occurrence networks suggested that predation by protists and nematodes impacted the diversity (Shannon index) and stability (average variation degree) of soil bacterial community, with a more pronounced effect on the bacterial community in soil macroaggregates than in smaller microaggregates. Compared to microaggregates, the higher frequency of predation within macroaggregates was found to promote faster microbiome turnover with direct implications for the abundance of genes involved in carbon and nitrogen metabolisms. Lastly, we also studied the importance of predation as a mechanism promoting bacterial diversity using field and microcosm studies, with a specific focus on the dominant bacterivorous nematode Protorhabditis. We addressed the influence of top-down processes on soil microbiome diversity and modulation of the genetic potential of genes involved in carbon and nitrogen metabolisms. Our study provides evidence for the importance of predation impacting the diversity and stability of soil bacterial communities. In addition, it shows that predation alters the abundance of microbial genes associated with carbon and nitrogen metabolisms at the soil aggregate level. |
| first_indexed | 2024-03-11T12:02:03Z |
| format | Article |
| id | doaj.art-cb71f46eafe24608b816231a0a964942 |
| institution | Directory Open Access Journal |
| issn | 1872-6259 |
| language | English |
| last_indexed | 2024-03-11T12:02:03Z |
| publishDate | 2023-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Geoderma |
| spelling | doaj.art-cb71f46eafe24608b816231a0a9649422023-11-08T04:08:40ZengElsevierGeoderma1872-62592023-11-01439116658Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate levelYuji Jiang0Shuzhen Li1Andrew D. Barnes2Jia Liu3Guofan Zhu4Lu Luan5Francisco Dini-Andreote6Stefan Geisen7Bo Sun8State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Corresponding author.Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, ChinaTe Aka Mātuatua - School of Science, University of Waikato, Private Bag 3105, Hamilton 3204, New ZealandSoil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, ChinaState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, ChinaState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, ChinaDepartment of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USALaboratory of Nematology, Wageningen University, 6700 ES Wageningen, NetherlandsState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, ChinaThe soil microbiome is dynamically structured at the local soil aggregate level by a combination of bottom-up and top-down processes. The soil microbiome is structured at the local soil aggregate scale by a dynamic interplay of bottom-up and top-down processes, yet less attention has been given to the latter (e.g., predation). We aimed to identify distinct groups of predators (protists and nematodes) and prey (bacteria) to determine the effect of predation on microbial gene abundances associated with carbon and nitrogen metabolisms. We partitioned soil aggregate size at three distinct levels to distinguish potential differences in predator–prey microbe interactions that take place at the soil micro-structure level. Our results revealed that the bacterial diversity and the abundance of protists were significantly higher in microaggregates than in macroaggregates. Correlation analysis, structural equation modeling, and co-occurrence networks suggested that predation by protists and nematodes impacted the diversity (Shannon index) and stability (average variation degree) of soil bacterial community, with a more pronounced effect on the bacterial community in soil macroaggregates than in smaller microaggregates. Compared to microaggregates, the higher frequency of predation within macroaggregates was found to promote faster microbiome turnover with direct implications for the abundance of genes involved in carbon and nitrogen metabolisms. Lastly, we also studied the importance of predation as a mechanism promoting bacterial diversity using field and microcosm studies, with a specific focus on the dominant bacterivorous nematode Protorhabditis. We addressed the influence of top-down processes on soil microbiome diversity and modulation of the genetic potential of genes involved in carbon and nitrogen metabolisms. Our study provides evidence for the importance of predation impacting the diversity and stability of soil bacterial communities. In addition, it shows that predation alters the abundance of microbial genes associated with carbon and nitrogen metabolisms at the soil aggregate level.http://www.sciencedirect.com/science/article/pii/S001670612300335XMicrobiome diversityNematodesProtistsSoil aggregatesSoil functioningTrophic interactions |
| spellingShingle | Yuji Jiang Shuzhen Li Andrew D. Barnes Jia Liu Guofan Zhu Lu Luan Francisco Dini-Andreote Stefan Geisen Bo Sun Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level Geoderma Microbiome diversity Nematodes Protists Soil aggregates Soil functioning Trophic interactions |
| title | Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level |
| title_full | Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level |
| title_fullStr | Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level |
| title_full_unstemmed | Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level |
| title_short | Unraveling the importance of top-down predation on bacterial diversity at the soil aggregate level |
| title_sort | unraveling the importance of top down predation on bacterial diversity at the soil aggregate level |
| topic | Microbiome diversity Nematodes Protists Soil aggregates Soil functioning Trophic interactions |
| url | http://www.sciencedirect.com/science/article/pii/S001670612300335X |
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