Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks.
Microbial nitrogen (N) cycling pathways are largely responsible for producing forms of N that are available for plant uptake or lost from the system as gas or leachate. The temporal dynamics of microbial N pathways in tropical agroecosystems are not well defined, even though they are critical to und...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0281442 |
| _version_ | 1797903558632275968 |
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| author | Marie Schaedel Satoshi Ishii Hao Wang Rodney Venterea Birthe Paul Mupenzi Mutimura Julie Grossman |
| author_facet | Marie Schaedel Satoshi Ishii Hao Wang Rodney Venterea Birthe Paul Mupenzi Mutimura Julie Grossman |
| author_sort | Marie Schaedel |
| collection | DOAJ |
| description | Microbial nitrogen (N) cycling pathways are largely responsible for producing forms of N that are available for plant uptake or lost from the system as gas or leachate. The temporal dynamics of microbial N pathways in tropical agroecosystems are not well defined, even though they are critical to understanding the potential impact of soil conservation strategies. We aimed to 1) characterize temporal changes in functional gene associations across a seasonal gradient, 2) identify keystone genes that play a central role in connecting N cycle functions, and 3) detect gene co-occurrences that remained stable over time. Soil samples (n = 335) were collected from two replicated field trials in Rwanda between September 2020 and March 2021. We found high variability among N-cycle gene relationships and network properties that was driven more by sampling timepoint than by location. Two nitrification gene targets, hydroxylamine oxidoreductase and nitrite oxidoreductase, co-occurred across all timepoints, indicating that they may be ideal year-round targets to limit nitrification in rainfed agricultural soils. We also found that gene keystoneness varied across time, suggesting that management practices to enhance N-cycle functions such as the application of nitrification inhibitors could be adapted to seasonal conditions. Our results mark an important first step in employing gene networks to infer function in soil biogeochemical cycles, using a tropical seasonal gradient as a model system. |
| first_indexed | 2024-04-10T09:34:52Z |
| format | Article |
| id | doaj.art-f7d9f175033e4b2fa5be5f7a2d542727 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-10T09:34:52Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f7d9f175033e4b2fa5be5f7a2d5427272023-02-18T05:31:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01182e028144210.1371/journal.pone.0281442Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks.Marie SchaedelSatoshi IshiiHao WangRodney VentereaBirthe PaulMupenzi MutimuraJulie GrossmanMicrobial nitrogen (N) cycling pathways are largely responsible for producing forms of N that are available for plant uptake or lost from the system as gas or leachate. The temporal dynamics of microbial N pathways in tropical agroecosystems are not well defined, even though they are critical to understanding the potential impact of soil conservation strategies. We aimed to 1) characterize temporal changes in functional gene associations across a seasonal gradient, 2) identify keystone genes that play a central role in connecting N cycle functions, and 3) detect gene co-occurrences that remained stable over time. Soil samples (n = 335) were collected from two replicated field trials in Rwanda between September 2020 and March 2021. We found high variability among N-cycle gene relationships and network properties that was driven more by sampling timepoint than by location. Two nitrification gene targets, hydroxylamine oxidoreductase and nitrite oxidoreductase, co-occurred across all timepoints, indicating that they may be ideal year-round targets to limit nitrification in rainfed agricultural soils. We also found that gene keystoneness varied across time, suggesting that management practices to enhance N-cycle functions such as the application of nitrification inhibitors could be adapted to seasonal conditions. Our results mark an important first step in employing gene networks to infer function in soil biogeochemical cycles, using a tropical seasonal gradient as a model system.https://doi.org/10.1371/journal.pone.0281442 |
| spellingShingle | Marie Schaedel Satoshi Ishii Hao Wang Rodney Venterea Birthe Paul Mupenzi Mutimura Julie Grossman Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. PLoS ONE |
| title | Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. |
| title_full | Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. |
| title_fullStr | Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. |
| title_full_unstemmed | Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. |
| title_short | Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. |
| title_sort | temporal assessment of n cycle microbial functions in a tropical agricultural soil using gene co occurrence networks |
| url | https://doi.org/10.1371/journal.pone.0281442 |
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