Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?
Abstract Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on‐farm “rule of thumb” has never been rigorously tested in a scientific f...
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Online Access: | https://doi.org/10.1111/eva.12956 |
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doaj-b53011a7d17740d1b40fc0ef9d415fc82020-11-25T02:44:05ZengWileyEvolutionary Applications1752-45712020-09-011381984199910.1111/eva.12956Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?Ian Kaplan0Nicholas A. Bokulich1J. Gregory Caporaso2Laramy S. Enders3Wadih Ghanem4Kathryn S. Ingerslew5Department of Entomology Purdue University West Lafayette IN USACenter for Applied Microbiome Science The Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USACenter for Applied Microbiome Science The Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USADepartment of Entomology Purdue University West Lafayette IN USADepartment of Entomology Purdue University West Lafayette IN USADepartment of Entomology Purdue University West Lafayette IN USAAbstract Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on‐farm “rule of thumb” has never been rigorously tested in a scientific framework. To experimentally evaluate the relationship between phylogenetic distance and crop performance, we used a plant–soil feedback approach whereby 35 crops and weeds varying in their relatedness to tomato (Solanum lycopersicum) were tested in a two‐year field experiment. We used community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth. Overall, tomato yield was ca. 15% lower in soil previously cultivated with tomato; yet, past the species level there was no effect of phylogenetic distance on crop performance. Soil microbial communities, on the other hand, were compositionally more similar between close plant relatives. Random forest regression predicted log10 phylogenetic distance to tomato with moderate accuracy (R2 = .52), primarily driven by bacteria in the genus Sphingobium. These data indicate that, beyond avoiding conspecifics, evolutionary history contributes little to understanding plant–soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness.https://doi.org/10.1111/eva.12956crop rotationphylogenyplant–soil feedbackspecies relatednesstomato |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ian Kaplan Nicholas A. Bokulich J. Gregory Caporaso Laramy S. Enders Wadih Ghanem Kathryn S. Ingerslew |
spellingShingle |
Ian Kaplan Nicholas A. Bokulich J. Gregory Caporaso Laramy S. Enders Wadih Ghanem Kathryn S. Ingerslew Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evolutionary Applications crop rotation phylogeny plant–soil feedback species relatedness tomato |
author_facet |
Ian Kaplan Nicholas A. Bokulich J. Gregory Caporaso Laramy S. Enders Wadih Ghanem Kathryn S. Ingerslew |
author_sort |
Ian Kaplan |
title |
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? |
title_short |
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? |
title_full |
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? |
title_fullStr |
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? |
title_full_unstemmed |
Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? |
title_sort |
phylogenetic farming: can evolutionary history predict crop rotation via the soil microbiome? |
publisher |
Wiley |
series |
Evolutionary Applications |
issn |
1752-4571 |
publishDate |
2020-09-01 |
description |
Abstract Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on‐farm “rule of thumb” has never been rigorously tested in a scientific framework. To experimentally evaluate the relationship between phylogenetic distance and crop performance, we used a plant–soil feedback approach whereby 35 crops and weeds varying in their relatedness to tomato (Solanum lycopersicum) were tested in a two‐year field experiment. We used community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth. Overall, tomato yield was ca. 15% lower in soil previously cultivated with tomato; yet, past the species level there was no effect of phylogenetic distance on crop performance. Soil microbial communities, on the other hand, were compositionally more similar between close plant relatives. Random forest regression predicted log10 phylogenetic distance to tomato with moderate accuracy (R2 = .52), primarily driven by bacteria in the genus Sphingobium. These data indicate that, beyond avoiding conspecifics, evolutionary history contributes little to understanding plant–soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness. |
topic |
crop rotation phylogeny plant–soil feedback species relatedness tomato |
url |
https://doi.org/10.1111/eva.12956 |
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