Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome
Camelina (Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations...
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The American Phytopathological Society
2025-06-01
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| Series: | Phytobiomes Journal |
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| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-08-24-0080-R |
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| author | Elle M. Barnes Chuntao Yin Daniel Schlatter Hao Peng Cody Willmore Chaofu Lu Susannah G. Tringe Timothy C. Paulitz |
| author_facet | Elle M. Barnes Chuntao Yin Daniel Schlatter Hao Peng Cody Willmore Chaofu Lu Susannah G. Tringe Timothy C. Paulitz |
| author_sort | Elle M. Barnes |
| collection | DOAJ |
| description | Camelina (Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations, we grew camelina in the greenhouse using soil transplanted from 33 locations in the dryland wheat production area of eastern Washington. Bacterial, archaeal, and fungal communities from bulk soil, rhizosphere, and endosphere were characterized with 16S rRNA and internal transcribed spacer amplicon sequencing and were analyzed alongside site-specific climatic and edaphic data. We found that soil from the highest precipitation zone had higher alpha diversity than soil from the driest zone, but this effect was not seen in the greenhouse rhizosphere or endosphere. Plant compartment, cropping system zone, and soil origin all significantly influenced microbial composition, with soil pH and organic matter, as well as precipitation at origin, as major predictors. Analysis of abundance–occupancy distributions showed that the Actinobacteriota Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus in the rhizosphere were plant-selected, while the endosphere was characterized by a number of Actinobacteriota, Rhizobium, and Clostridium. Sphingomonas amplicon sequence variants were also consistently enriched in the rhizosphere, suggesting that they are present in soils collected throughout eastern Washington and may represent good candidate biostimulants. Several lignin decomposing fungi had site-specific rhizospheric distributions, suggesting that they may be dispersal-limited or result from the legacy effect of long-term wheat cropping. Overall, this study contributes to our understanding of microbiome assembly in and on camelina roots while also highlighting the potential impact of cropping history on soil- and plant-associated microbiomes. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025. |
| format | Article |
| id | doaj-art-510aa42d6e494e579ab60f2fdfbf2de3 |
| institution | OA Journals |
| issn | 2471-2906 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | The American Phytopathological Society |
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| series | Phytobiomes Journal |
| spelling | doaj-art-510aa42d6e494e579ab60f2fdfbf2de32025-08-20T02:34:50ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062025-06-019232733910.1094/PBIOMES-08-24-0080-RLegacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa MicrobiomeElle M. Barnes0Chuntao Yin1Daniel Schlatter2Hao Peng3Cody Willmore4Chaofu Lu5Susannah G. Tringe6Timothy C. Paulitz7US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.USDA-ARS, North Central Agricultural Research Laboratory, USDA-ARS, Brookings, SD, U.S.A.USDA-ARS, Plant Science Research Unit, St. Paul, MN, U.S.A.USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, U.S.A.USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, U.S.A.Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, U.S.A.US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, U.S.A.Camelina (Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations, we grew camelina in the greenhouse using soil transplanted from 33 locations in the dryland wheat production area of eastern Washington. Bacterial, archaeal, and fungal communities from bulk soil, rhizosphere, and endosphere were characterized with 16S rRNA and internal transcribed spacer amplicon sequencing and were analyzed alongside site-specific climatic and edaphic data. We found that soil from the highest precipitation zone had higher alpha diversity than soil from the driest zone, but this effect was not seen in the greenhouse rhizosphere or endosphere. Plant compartment, cropping system zone, and soil origin all significantly influenced microbial composition, with soil pH and organic matter, as well as precipitation at origin, as major predictors. Analysis of abundance–occupancy distributions showed that the Actinobacteriota Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus in the rhizosphere were plant-selected, while the endosphere was characterized by a number of Actinobacteriota, Rhizobium, and Clostridium. Sphingomonas amplicon sequence variants were also consistently enriched in the rhizosphere, suggesting that they are present in soils collected throughout eastern Washington and may represent good candidate biostimulants. Several lignin decomposing fungi had site-specific rhizospheric distributions, suggesting that they may be dispersal-limited or result from the legacy effect of long-term wheat cropping. Overall, this study contributes to our understanding of microbiome assembly in and on camelina roots while also highlighting the potential impact of cropping history on soil- and plant-associated microbiomes. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-08-24-0080-Rcamelinacropping systemmicrobiomeplant compartmentprecipitation |
| spellingShingle | Elle M. Barnes Chuntao Yin Daniel Schlatter Hao Peng Cody Willmore Chaofu Lu Susannah G. Tringe Timothy C. Paulitz Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome Phytobiomes Journal camelina cropping system microbiome plant compartment precipitation |
| title | Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome |
| title_full | Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome |
| title_fullStr | Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome |
| title_full_unstemmed | Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome |
| title_short | Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome |
| title_sort | legacy effects of cropping system and precipitation influence the core camelina sativa microbiome |
| topic | camelina cropping system microbiome plant compartment precipitation |
| url | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-08-24-0080-R |
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