Local Phenomena Shape Backyard Soil Metabolite Composition

Abstract

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.

Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

“…Studies of the metabolites produced by plant-associated microbiomes in situ are still limited and complex owing to the dynamics and heterogeneity of the soil environment. Soil metabolites are composed of both plant and microbial secreted molecules and their production is influenced by the soil properties and by the interactions of soil microorganisms with host plants (Pétriacq et al, 2017;Mhlongo et al, 2018;Hayden et al, 2019;Jacoby and Kopriva, 2019;Nguyen et al, 2020). Moreover, recent studies have also been using new approaches to study soil metabolites.…”

An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures

“…The soil extract contained >1000 potential chemical features as determined by LC-MS that occurred in a wide range of concentrations (data not shown). 41 Two DNA intercalators, 1 and 2, were spiked into the soil extract in low concentrations [1:1:600 (w/w/w), respectively] to test the robustness of the assay. Analysis revealed that even under those challenging conditions both compounds were readily detected (Figure 5), affording confidence that LLAMAS could be expected to function even in cases presenting extreme levels of chemical complexity.…”

“…We employed a potential “worst-case” scenario that consisted of an organic extract prepared from soil (the top ∼7 cm of material collected from a low-lying hardwood forest plot that supported lush herbaceous plant growth). The soil extract contained >1000 potential chemical features as determined by LC-MS that occurred in a wide range of concentrations (data not shown) . Two DNA intercalators, 1 and 2 , were spiked into the soil extract in low concentrations [1:1:600 (w/w/w), respectively] to test the robustness of the assay.…”

Assessing soil organic matter features under drought and normal conditions using direct infusion high resolution mass spectrometry and LC-MS/MS feature based molecular networking

“…Assessing soil organic matter features under drought and normal conditions using direct infusion high resolution mass spectrometry and LC-MS/MS feature based molecular networking NICOLE DIDONATO 1 , ALBERT RIVAS UBACH 1 , CHAEVIEN CLENDINEN 1 , NOAH SOKOL 2 , NIKOLA TOLIC 1 , DINESH ADHIKARI 2 , CARMEN ENID MARTINEZ 3 , JENNIFER PETT-RIDGE 2 AND LJILJANA PASA TOLIC 1 1 Pacific Northwest National Laboratory 2 Lawrence Livermore National Laboratory 3 Cornell University Presenting Author: nicole.didonato@pnnl.gov Knowledge of the type of carbon that escapes mineralization and persists in soils is important for predicting carbon fluxes in a warming climate. Direct infusion FTICRMS enables observations of broad differences in compositions of soil organic matter molecular formulas among treatments 1 .…”

“…Although complete separation of soil organic matter is not yet achievable, LC-MS/MS compliments direct infusion by reducing charge competition, improving feature detection and allowing for molecular identification 2 . However, only a fraction of soil organic matter features can be identified due to the lack of comprehensive libraries 3 . Molecular networking can further improve identifcation of unknown compounds by matching their fragmentation spectra with similar spectra of known compounds.…”