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Meredith LK, Ledford SM, Riemer K, Geffre P, Graves K, Honeker LK, LeBauer D, Tfaily MM, Krechmer J. Automating methods for estimating metabolite volatility. Front Microbiol 2023; 14:1267234. [PMID: 38163064 PMCID: PMC10755872 DOI: 10.3389/fmicb.2023.1267234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called volcalc that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how volcalc might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With volcalc, we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The volcalc package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.
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Affiliation(s)
- Laura K. Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - S. Marshall Ledford
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States
| | - Kristina Riemer
- Arizona Experiment Station, University of Arizona, Tucson, AZ, United States
| | - Parker Geffre
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Kelsey Graves
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Linnea K. Honeker
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - David LeBauer
- Arizona Experiment Station, University of Arizona, Tucson, AZ, United States
| | - Malak M. Tfaily
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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Pugliese G, Ingrisch J, Meredith LK, Pfannerstill EY, Klüpfel T, Meeran K, Byron J, Purser G, Gil-Loaiza J, van Haren J, Dontsova K, Kreuzwieser J, Ladd SN, Werner C, Williams J. Effects of drought and recovery on soil volatile organic compound fluxes in an experimental rainforest. Nat Commun 2023; 14:5064. [PMID: 37604817 PMCID: PMC10442410 DOI: 10.1038/s41467-023-40661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
Drought can affect the capacity of soils to emit and consume biogenic volatile organic compounds (VOCs). Here we show the impact of prolonged drought followed by rewetting and recovery on soil VOC fluxes in an experimental rainforest. Under wet conditions the rainforest soil acts as a net VOC sink, in particular for isoprenoids, carbonyls and alcohols. The sink capacity progressively decreases during drought, and at soil moistures below ~19%, the soil becomes a source of several VOCs. Position specific 13C-pyruvate labeling experiments reveal that soil microbes are responsible for the emissions and that the VOC production is higher during drought. Soil rewetting induces a rapid and short abiotic emission peak of carbonyl compounds, and a slow and long biotic emission peak of sulfur-containing compounds. Results show that, the extended drought periods predicted for tropical rainforest regions will strongly affect soil VOC fluxes thereby impacting atmospheric chemistry and climate.
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Affiliation(s)
- Giovanni Pugliese
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany.
- Atmospheric Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany.
| | - Johannes Ingrisch
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Universität Innsbruck, Department of Ecology, Innsbruck, Austria
| | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
- Biosphere 2, University of Arizona, Oracle, AZ, USA
| | - Eva Y Pfannerstill
- Atmospheric Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, USA
| | - Thomas Klüpfel
- Atmospheric Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | - Joseph Byron
- Atmospheric Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Gemma Purser
- UK Centre for Ecology & Hydrology, Penicuik, Edinburgh, UK
- School of Chemistry, The University of Edinburgh, Edinburgh, UK
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Joost van Haren
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
- Biosphere 2, University of Arizona, Oracle, AZ, USA
| | - Katerina Dontsova
- Biosphere 2, University of Arizona, Oracle, AZ, USA
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Jürgen Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - S Nemiah Ladd
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Christiane Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Jonathan Williams
- Atmospheric Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- Climate and Atmosphere Research Center, The Cyprus Institute, Nicosia, Cyprus
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