Flavor-cyber-agriculture: Optimization of plant metabolites in an open-source control environment through surrogate modeling.

Arielle J Johnson,John De La Parra,Timothy L Savas,Risto Miikkulainen,Elliiot Meyerson,Elliot Meyerson,Caleb B Harper,Jie Zhang

doi:10.1371/journal.pone.0213918

Abstract

Food production in conventional agriculture faces numerous challenges such as reducing waste, meeting demand, maintaining flavor, and providing nutrition. Contained environments under artificial climate control, or cyber-agriculture, could in principle be used to meet many of these challenges. Through such environments, phenotypic expression of the plant—mass, edible yield, flavor, and nutrients—can be actuated through a “climate recipe,” where light, water, nutrients, temperature, and other climate and ecological variables are optimized to achieve a desired result. This paper describes a method for doing this optimization for the desired result of flavor by combining cyber-agriculture, metabolomic phenotype (chemotype) measurements, and machine learning. In a pilot experiment, (1) environmental conditions, i.e. photoperiod and ultraviolet (UV) light (known to affect production of flavor-active molecules in edible plants) were applied under different regimes to basil plants (Ocimum basilicum) growing inside a hydroponic farm with an open-source design; (2) flavor-active volatile molecules were measured in each plant using gas chromatography-mass spectrometry (GC-MS); and (3) symbolic regression was used to construct a surrogate model of this chemistry from the input environmental variables, and this model was used to discover new combinations of photoperiod and UV light to increase this chemistry. These new combinations, or climate recipes, were then implemented in the hydroponic farm, and several of them resulted in a marked increase in volatiles over control. The process also led to two important insights: it demonstrated a “dilution effect”, i.e. a negative correlation between weight and desirable chemical species, and it discovered the surprising effect that a 24-hour photoperiod of photosynthetic-active radiation, the equivalent of all-day light, induces the most flavor molecule production in basil. In this manner, surrogate optimization through machine learning can be used to discover effective recipes for cyber-agriculture that would be difficult and time-consuming to find using hand-designed experiments.

Highlights

The so-called “dilution effect,” noted since the 1940’s and systematically reviewed since the early 1980’s [1], describes an inverse relationship between yield and nutrient concentration in food: For many nutritionally-important chemical constituents of food plants, such as minerals, protein, and vitamins, an increase in biomass is accompanied by a decrease in nutrient concentration
The basil plant, O. basilicum, is typical of herbaceous plants in that it produces many aromatic molecules, the terpenoids 1,8-cineole, linalool, camphor, borneol, bergamotene, and farnesene, and the phenylpropenes eugenol, methyleugenol, and estragole [24]. These molecules are thought to play varying roles in stress adaptation and defense, and the production by the basil plant of aromatic molecules has been shown to increase upon exposure to these stresses, including water stress [25], ultraviolet (UV) and photosynthetic-active radiation (PAR) light [26,27,28], heat [29], bacteria [30], chitosan, and sodium and other minerals [32]
Note in particular that the R-Scores are negatively correlated with weight: Optimizing for flavor results in smaller plants, and larger plants have less flavor, illustrating the “Dilution effect.”

Summary

Introduction

The so-called “dilution effect,” noted since the 1940’s and systematically reviewed since the early 1980’s [1], describes an inverse relationship between yield and nutrient concentration in food: For many nutritionally-important chemical constituents of food plants, such as minerals, protein, and vitamins, an increase in biomass is accompanied by a decrease in nutrient concentration This effect has been systematically demonstrated in historical nutrient content studies over the last 50–70 years [2,3], as well as in controlled side-by-side trials that have shown a relationship between nutrient dilution and genetics [4], artificial fertilization [5], and elevated carbon dioxide levels related to climate change [6,7].

Methods

Results

Discussion

Conclusion