Search for: All records

Abstract Biogenic volatile organic compounds (VOCs) constitute a significant portion of gas-phase metabolites in modern ecosystems and have unique roles in moderating atmospheric oxidative capacity, solar radiation balance, and aerosol formation. It has been theorized that VOCs may account for observed geological and evolutionary phenomena during the Archaean, but the direct contribution of biology to early non-methane VOC cycling remains unexplored. Here, we provide an assessment of all potential VOCs metabolized by the last universal common ancestor (LUCA). We identify enzyme functions linked to LUCA orthologous protein groups across eight literature sources and estimate the volatility of all associated substrates to identify ancient volatile metabolites. We hone in on volatile metabolites with confirmed modern emissions that exist in conserved metabolic pathways and produce a curated list of the most likely LUCA VOCs. We introduce volatile organic metabolites associated with early life and discuss their potential influence on early carbon cycling and atmospheric chemistry. 

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 specific¹³C-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. 

Abstract Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO₂and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking¹³C from position-specific¹³C-pyruvate into CO₂and VOCs in parallel with multi-omics. During drought, efflux of¹³C-enriched acetate, acetone and C₄H₆O₂(diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,¹³C-CO₂efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO₂decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate. 

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 calledvolcalcthat 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 howvolcalcmight 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. Withvolcalc, 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. Thevolcalcpackage is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems. 

Volatility describes the tendency for a compound to partition into the gas phase and volatile metabolites facilitate unique biological interactions which have an influence on Earth's atmospheric physics and chemistry. Estimating which metabolites may be volatile is difficult, especially for those which do not have measured vapor pressures. Volcalc is a newly developed vapor pressure estimation tool which utilizes the SIMPOL.1 method, allowing users to rapidly identify plausible volatile metabolites within the Kyoto Encyclopedia for Genes and Genomes (KEGG) database. Here, we estimate the volatiles of all KEGG metabolites and associate them with KEGG reactions, enzymes, orthologs (KOs) and whole genomes within the KEGG database. This information may be used to identify which genes or species may be linked to particular forms of volatile metabolism, for the purpose hypothesis generation and integration into additional bioinformatics pipelines. This data is listed as a compliment to the publication "Automating methods for estimating metabolite volatility". The column "Paper" indicates whether the listed species is one from the subset analyzed within the data for Figure 3.For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu 

Use this package to calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method (Prankow and Asher, 2008) or modified SIMPOL.1 method as in Meredith et al. (2023).