Advances in environmental metal and nutrient 'omics'

Advances in environmental metal and nutrient 'omics'

Overview:

Rapid advances in mass spectrometry for the analysis of organic molecules (Orbitrap and FT-ICR MS) is driving a revolution in geochemistry because these instruments are able to resolve the complex mixture of organic molecules and isotopologues present in marine, river, and soil environments. This ability to detect rare isotopic forms of organic molecules gives us a new tool to investigate the components of organic matter that incorporate specific elements (nutrients,  metals, contaminants) . These approaches are still nascent, and often require the development of new experimental designs and data processing algorithms that enable us to answer specific geochemical questions. We often leverage tools from the cutting edge of 'metabolomics', which seeks to quantitatively study the complete suite of small molecule metabolites that provide a functional readout of the physiological status of an organism. 

Identification of organic nutrient and metal species in environmental samples by ultrahigh resolution mass spectrometry

Molecular formula assignments of ultrahigh resolution mass spectra (HRMS) hold promise for elucidating the molecular composition of organic nutrients and organically complexed metals in the environment. However, the need to account for an assortment of heteroatoms increases the uncertainty associated with individual assignments - and ultimately the ecological, biological, and biogeochemical insights gleaned from the assignments. To address this challenge, we developed corems-tools, an open source data processing pipeline designed to annotate LCMS data with confident molecular formula assignments, filter false assignments, and mitigate bias in assignment routines. The strategy first identifies the highest confidence assignment for a recurring ion in a data set by assessing the mass accuracy and isotopologue similarity of all assignments to the ion across the data set. The second component of the strategy examines the consistency of mass errors for an assigned ion throughout a data set and flags formulas with statistically unlikely deviations in mass error. Because the efficacy of our strategy improves with data set size, it is particularly useful for enhancing assignment confidence in large HRMS data sets common in studies of environmental systems. Many of our projects leverage CoreMS-tools to efficiently and confidently identify organic molecules containing specific nutrients and trace elements from biological cultures and environmental samples. One example is the identification of the organic molecules in the ocean that control the cycling of trace elements such as Fe, Cu, Ni, and Zn.

https://pypi.org/project/coremstools/ 

Measurement of metal-binding properties of environmental organic ligands

Thermodynamic and kinetic models of organic-metal speciation in sediments and natural waters are essential tools for assessing metal transport, reactivity, bioavailability and toxicity. These models rely on measurements of the binding strength and kinetics of organic ligands with various metals, but often the relevant parameters are poorly constrained due to the challenge of measuring these properties under the complex and often low abundance conditions that are relevant in the environment. We are developing new analytical approaches that address this issue by measuring metal binding properties and rates using sensitive chromatography mass spectrometry methods that can quantitatively monitor many chemical species at the same time. Our ultimate aim is to develop next-generation speciation models that provide more accurate assessments of metal bioavailability, pollution transport, and water quality.