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. 2020 Feb 29;10(3):86.
doi: 10.3390/metabo10030086.

Local Phenomena Shape Backyard Soil Metabolite Composition

Free PMC article

Local Phenomena Shape Backyard Soil Metabolite Composition

Tra D Nguyen et al. Metabolites. .
Free PMC article


Soil covers most of Earth's continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography-tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.

Keywords: LC-MS/MS; human activity; metabolomics; molecular networking; natural products; soil.

Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.


Figure 1
Figure 1
Impact of collection city, state and National Oceanic and Atmospheric Administration (NOAA) region on the overall soil metabolite profile. (a) Sampling sites. (b) Principal coordinate analysis (PCoA), Bray–Curtis–Faith distance metric, with samples colored by NOAA climate region. (c) PCoA analysis, Bray–Curtis–Faith distance metric, with samples colored by state. (d,e) PCoA analysis, Bray–Curtis–Faith distance metric, with samples colored by city. (d) All samples. (e) Analysis restricted to the cities with 5 or more samples (Binger, McLoud, Norman and Oklahoma City, OK; Blue Springs, MO; Ladera Ranch, CA; Oak Ridge, TN; Wilmington, NC).
Figure 2
Figure 2
Limited between-sample overlap of detected metabolite features. (a) Venn diagram of the detected metabolite features’ distribution across the five sampled regions. (b) Venn diagrams of the metabolite features, common or unique, between states. (c) Venn diagrams of the metabolite features, common or unique, between cities with ten or more samples: Oklahoma City, Binger and Norman, OK; Ladera Ranch, CA; Blue Springs, MO. (d) Rarefaction curve showing that most detected metabolite features only occur in a single sample.
Figure 3
Figure 3
Chemical family analysis of backyard soil metabolites. (a) Feature-based molecular networking grouped metabolite features into 171 chemical families. Each node in the network represents one metabolite feature. Nodes connected to each other are structurally-related (cosine MS2 similarity score ≥0.7). Nodes are colored by the relative abundance of this metabolite feature between states. (b) Molecular network of soil samples colored by 13 selected chemical super classes as indicated in the legend. Node size based on the chemical classification scores for the ClassyFire super class. (c) Geographic heterogeneity in diterpenoid and triterpenoid family members. Nodes are colored by the relative abundance of this metabolite feature between states (colors as in panel (a)). Five structures of Global Natural Products Social Molecular Networking (GNPS) annotations for this subnetwork are displayed (level 2 annotation confidence [24]; ppm error <1; mass difference <0.001), with arrows pointing to the corresponding node.

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