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Abstract Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications. 

Abstract The degradation of isoprene – a prevalent volatile organic compound (VOC) – in soil has primarily been attributed as a microbial process, but chemical degradation may also play a role. Separating simultaneous abiotic and biotic degradation pathways under representative conditions has been a technical challenge, leaving the fate of surface and subsurface isoprene inputs from the atmosphere, litter roots, and microbes to the soil uncertain. Here, we investigated the real-time dynamics of belowground isoprene degradation by introducing isoprene into the subsurface through an artificial root and tracking its fate along with primary gas-phase oxidation products viain situsoil gas probes and online high-resolution proton transfer reaction time-of-flight mass spectrometry. Isoprene additions generated oxidation products from known NO- and •OH-initiated pathways, revealing chemical degradation as an active loss pathway for isoprene in soil. Over time, isoprene concentrations plummeted relative to an inert tracer despite continuous and repeated isoprene addition, revealing a lasting up-regulation of microbial isoprene degradation that ultimately outcompeted the chemical sink. We verified the presence of putative bacterial isoprene-degrading genes in the soil by quantitative PCR ofisoAand identified microbial groups that increased in abundance in response to isoprene availability using 16S amplicon sequencing. Overall, our results show for the first time the relevance of chemical degradation pathways to isoprene in soil and the capacity and dynamics of the soil microbiome to respond using community memory to increased isoprene availability. Soil is a dynamic oxidative and adaptive environment beneath our feet that may play additional roles in the biosphere–atmosphere exchange of isoprene, and by extension other VOCs, beyond what was previously expected. 

ABSTRACT Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soilArthrobacter. While drying reduced cultivability relative to hydrated controls, water vapor rehydration fully restored it. Ribosomal RNA proportions remained constant throughout all treatments, and mRNA profiles showed stable composition during desiccation—changing only during transitions into and out of desiccation-induced dormancy. Six transcriptional modules displayed distinct expression patterns in desiccated-rehydrated samples relative to hydrated controls, including desiccation-rehydration responsive and rehydration-specific profiles. Targeted intracellular metabolomics revealed similarly static profiles during desiccation, with a cluster of ribonucleosides and nucleobases increasing in response to desiccation and returning to baseline levels upon rehydration with water vapor. These findings demonstrate that both mRNA and metabolite profiles remain essentially frozen in desiccatedArthrobacter, with dynamic changes occurring only during state transitions. These results have important implications for environments with frequent drying cycles where stable mRNA in dormant cells combined with intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity. Our results suggest that RNA-based activity assessments in periodically dry environments require careful consideration of dormancy-associated molecular preservation.IMPORTANCEMetabolic activity quickly ceases in drying bacteria as they enter desiccation-induced dormancy. We show that mRNA and metabolite profiles were variable during drying and rewetting but did not change while desiccated. Additionally, water vapor stimulated the shift from the static to active state when exiting desiccation-induced dormancy. These shifts coincided with increased cultivability, indicating water vapor resuscitated dry cells. Because RNAs are transient, labile molecules that are turned over rapidly in growing bacteria, the presence of RNA in the environment is used as a marker for microbial activity. Our research shows this assumption may not hold for desiccated cells, indicating reliance on RNA as a marker of activity in environments that experience drying may obscure estimates ofin situmicrobial activity. 

Microbial metabolic functions are increasingly conceptualized as fitness-regulating traits. However, volatile compounds (the volatilome), despite their key roles in metabolism and ecology, are often overlooked in trait-based frameworks. We propose that volatile traits not only reflect ecological strategies but also shape them by mediating responses to selection pressures. Their volatility affects diffusion, substrate access, and interactions across space, conferring selective advantages as resources or waste products. We outline approaches to incorporate volatile traits into predictive models to improve understanding of microbial selection and community dynamics. This integration enables a more holistic view of microbial life by accounting for the ecological and evolutionary consequences of volatile-mediated processes. 

ABSTRACT In boreal and tundra ecosystems, mosses are abundant and ecologically important members of the vegetation due to their ability to insulate permafrost and maintain soil moisture. Mosses also harbour diverse bacterial and fungal symbionts that can provide nutrients and protection against environmental stressors.Sphagnummosses are particularly important due to their significant role in carbon sequestration, which has been attributed in part to the production of antimicrobial metabolites that slow decomposition. AlthoughSphagnumleachate has been shown to inhibit bacteria, howSphagnumchemical traits impact fungal communities remains understudied. Here, we used culture‐free and culture‐based methods to examine the relationship between moss fungal communities and metabolomes in living and senescing tissues ofSphagnumand two co‐occurring moss genera across four Alaskan boreal/tundra sites. Although their richness was similar among moss genera, fungal and metabolite composition differed significantly among moss genera, regardless of tissue age. Importantly, mosses with more similar metabolome composition harboured more similar fungal communities, particularly in living tissues. Numerous OTU‐metabolite correlations suggest direct interactions whereby fungi may consume, degrade, and/or be inhibited by metabolites; however, in vitro growth of moss‐associated fungi showed inhibition in only 25% of replicates with two phenolic metabolites. Overall, our data suggest that metabolites may be a key factor structuring fungal communities inSphagnumand other mosses, although not solely via inhibitory effects. Given the significance of mosses to ecosystem function and carbon sequestration in northern regions, it is critical to better understand factors that shape fungal communities potentially involved in stress adaptation and decomposition. 

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. 

Leaf litter emits volatile organic compounds (VOCs) that can impact atmospheric and soil processes, particularly in ecosystems with episodic litterfall and decomposition such as dry‐wet transitions in tropical forests. Litter VOCs may originate from both plant and microbial sources that are challenging to disentangle but may be reflected in the temporal patterns of litter VOC fluxes to wetting. Here, we collectedClitoria fairchildianalitter after an ecosystem‐scale experimental drought in the Biosphere 2 Tropical Rainforest and measured litter VOC fluxes over a 10‐day incubation to: (a) identify and quantify litter VOC fluxes; (b) examine the impacts of moisture; and (c) distinguish plant from microbial VOCs. In total, we observed 121 masses exhibiting either significant emission (88%) or uptake (12%) fluxes. Emissions of methanol, acetaldehyde, and acetone were the dominant fluxes. Wetting dry litter altered the flux of 47% of VOCs: 66 decreased to pre‐wetting levels within 24 hr although 25 sustained higher emission rates. We categorized VOCs during wetting as plant derived (55%), microbial‐derived production (21%), microbial uptake (12%), and unknown (13%) by visual inspection of the flux time series. Automated classification of the wetting pulses with fitted model parameters was consistent with the visual categorization approximately 80% of the time. Our results provide measurements of litter VOC fluxes for a widespread tropical plant. Moreover, we illustrate an automated data‐model approach to efficiently characterize and categorize trace gas pulses for litter VOC fluxes that is translatable to other types of trace gases, forcings, and ecosystem components including soil. 

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. 

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).