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Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.

Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.

Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and aSphagnumleachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

 

Soils harbor complex biological processes intertwined with metabolic inputs from microbes and plants. Measuring the soil metabolome can reveal active metabolic pathways, providing insight into the presence of specific organisms and ecological interactions. A subset of the metabolome is volatile; however, current soil studies rarely consider volatile organic compounds (VOCs), contributing to biases in sample processing and metabolomic analytical techniques. Therefore, we hypothesize that overall, the volatility of detected compounds measured using current metabolomic analytical techniques will be lower than undetected compounds, a reflection of missed VOCs. To illustrate this, we examined a peatland metabolomic dataset collected using three common metabolomic analytical techniques: nuclear magnetic resonance (NMR), gas chromatography-mass spectroscopy (GC-MS), and fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). We mapped the compounds to three metabolic pathways (monoterpenoid biosynthesis, diterpenoid biosynthesis, and polycyclic aromatic hydrocarbon degradation), chosen for their activity in peatland ecosystems and involvement of VOCs. We estimated the volatility of the compounds by calculating relative volatility indices (RVIs), and as hypothesized, the average RVI of undetected compounds within each of our focal pathways was higher than detected compounds ( p < 0.001). Moreover, higher RVI compounds were absent even in sub-pathways where lower RVI compounds were observed. Our findings suggest that typical soil metabolomic analytical techniques may overlook VOCs and leave missing links in metabolic pathways. To more completely represent the volatile fraction of the soil metabolome, we suggest that environmental scientists take into consideration these biases when designing and interpreting their data and/or add direct online measurement methods that capture the integral role of VOCs in soil systems. 

Engineered nanoparticle (NP) size and natural organic matter (NOM) composition play important roles in determining NP environmental behaviors. The aim of this work was to investigate how NP size and NOM composition influence the colloidal stability of polyvinylpyrrolidone coated platinum engineered nanoparticles (PVP-PtNPs). We evaluated PVP-PtNP aggregation as a function of the NP size (20, 30, 50, 75, and 95 nm, denoted as PVP-PtNP 20–95 ) in moderately hard water (MHW). Further, we quantified the effect of the hydrophobic organic acid (HPOA) fraction of NOM on the aggregation of PVP-PtNP 20 and PVP-PtNP 95 using 6 NOM samples from various surface waters, representing a range of NOM compositions and properties. NOM samples were characterized for bulk elemental composition ( e.g. , C, H, O, N, and S), specific ultraviolet absorbance at 254 nm (SUVA 254 ), and molecular level composition ( e.g. , compound classes) using ultrahigh resolution mass spectrometry. Single particle-inductively coupled plasma-mass spectrometry (sp-ICP-MS) was employed to monitor the aggregation of PVP-PtNPs at 1 μg PVP-PtNP per L and 1 mg NOM per L concentrations. PVP-PtNP aggregate size increased with decreasing primary PVP-PtNP size, likely due to the lower zeta potential, the higher number concentration, and the higher specific surface area of smaller NPs compared to larger NPs at the same mass concentration. No aggregation was observed for PVP-PtNP 95 in MHW in the presence and absence of the different NOM samples. PVP-PtNP 20 formed aggregates in MHW in the presence and absence of the six NOM samples, and aggregate size increased in the presence of NOM likely due to interparticle bridging of NOM-coated PVP-PtNPs by divalent counterions. PVP-PtNP 20 aggregate size increased with the increase in NOM elemental ratio of H to C and the relative abundance of lignin-like/carboxyl rich-alicyclic molecules (CRAM)-like compounds. However, the aggregate size of PVP-PtNP 20 decreased with the increase in NOM molecular weight, NOM SUVA 254 , elemental ratio of O to C, and the relative abundance of condensed hydrocarbons and tannin-like compounds. Overall, the results of this study suggest that the composition and sources of NOM are key factors that contribute to the stability of PVP-PtNPs in the aquatic environment.