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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 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 (R 2 = .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.

SUBMITTER: Kaplan I

PROVIDER: S-EPMC7463318 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

Kaplan Ian I Bokulich Nicholas A NA Caporaso J Gregory JG Enders Laramy S LS Ghanem Wadih W Ingerslew Kathryn S KS

Evolutionary applications 20200422 8

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 tomat ...[more]

PMID: 32908599

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Project description:BackgroundThe importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil.MethodologyOur organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic.ResultsWe observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and β- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields.ConclusionDifferent organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.

Project description:Plant-soil feedback (PSF) can be a major driver of plant performance in communities, and this concept can be used in selecting crop rotation sequences to maximize agricultural yields. Potential benefits of using PSF in this context include nutrient use optimization, pathogen reduction, and enhancement of mutualisms between crops and microbes. Yet the contributions of these combined mechanisms are poorly understood. Here we investigated the relative contributions of these mechanisms using five major crops commonly cultivated in rotation (alfalfa, canola, maize, soybean, and wheat) under controlled conditions. We trained soil by growing each of the five crops in a "training phase," and then reciprocally planted the five crops in the trained soils in a "feedback phase." To tease out soil biota from nutrient effects, we established three treatments: "control" (trained unsterilized soil used in the feedback phases), "biota" (sterilized soil in the feedback phase inoculated with soil biota from the control treatment after the training phase), and "nutrient" (sterilized soils in both phases). Plant-soil feedback for each crop was calculated by comparing the total biomass of each crop grown in soils trained by each of the four other crops (i.e., in rotation) against total biomass in self-trained soil (i.e., monocropping). We found that PSF values varied among crop combinations in all the treatments, but such variation was the greatest in the nutrient treatment. Overall, soil biota feedback tended to be lower, whereas nutrient feedback tended to be greater compared to the unsterilized control soil, suggesting that effects of antagonistic biota outweighed those of beneficial microbes in the biota treatment, and that plants optimized nutrient uptake when the soil microbiome was absent in the nutrient treatment. Furthermore, soils in the nutrient treatment trained by the legume crops (alfalfa and soybean) tended to provide the greatest positive feedback, emphasizing the important legacy of N2 fixers in crop rotation. Taken together, our data demonstrate how nutrients and soil biota can be integral to PSFs among crops, and that assessing PSFs under controlled conditions can serve as a basis to determine the most productive crop rotation sequences prior to field testing.

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Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

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Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

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