Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?
Open Access
- 22 March 2020
- journal article
- research article
- Published by Wiley in Evolutionary Applications
- Vol. 13 (8), 1984-1999
- https://doi.org/10.1111/eva.12956
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.Keywords
Funding Information
- National Institute of Food and Agriculture (2017‐67013‐26255)
This publication has 75 references indexed in Scilit:
- Experimental evidence that evolutionarily diverse assemblages result in higher productivityProceedings of the National Academy of Sciences of the United States of America, 2013
- Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsThe ISME Journal, 2012
- Phylogenetic relatedness as a tool in restoration ecology: a meta-analysisProceedings. Biological sciences, 2011
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaThe ISME Journal, 2011
- More closely related species are more ecologically similar in an experimental testProceedings of the National Academy of Sciences of the United States of America, 2011
- Global patterns of 16S rRNA diversity at a depth of millions of sequences per sampleProceedings of the National Academy of Sciences of the United States of America, 2010
- Emerging patterns in the comparative analysis of phylogenetic community structureMolecular Ecology, 2009
- A common tendency for phylogenetic overdispersion in mammalian assemblagesProceedings. Biological sciences, 2008
- Phylogenetic signal in plant pathogen–host rangeProceedings of the National Academy of Sciences of the United States of America, 2007
- Conservation evaluation and phylogenetic diversityBiological Conservation, 1992