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In this peer-reviewed Commentary, we argue that ultra-slow-growing microbes should be referred to as "aeonophiles". 

Participation in authentic scientific research has been shown to greatly benefit undergraduate students, both in terms of perception of science and knowledge of scientific concepts. We define authentic scientific research as projects in which results are unknown prior to performing experiments and are appropriate for presentation in peer-reviewed scientific journals and/or scientific conferences. Kindergarten through grade 12 (K–12) students have less frequent opportunities to participate in authentic research than university students, and the effects of research participation on such students are less well understood. From 2013 to the present, we organized two collaborations with different groups of K–12 students and teachers, each aimed at engaging K–12 students in authentic geoscience research, with a focus on K–12 students from excluded backgrounds who may have had restricted access to resources. First, the Malcolm X Shabazz Aquatic Geochemistry Team was an initiative to involve high school students at Malcolm X Shabazz High School in Newark, New Jersey, USA, in research focused on the activities of microbial communities inhabiting streams and rivers in New Jersey and eastern Pennsylvania. Second, the Integrating Continuous Experiential Activities for Geoscience Education (ICE-AGE) project is a Pathways into the Earth, Ocean, Polar and Atmospheric & Geospace Sciences (GEOPAths) project funded by the National Science Foundation that involves K–12 students in experiential learning through diverse means, including involving middle school students taking part in a summer program pseudonymously referred to as the Liberation Literacy Program (LLP) in geoscience research on a number of topics. Here, we report qualitative observations of the successes and challenges of these programs, as well as lessons learned, which may be useful for other researchers seeking to involve groups of K–12 students in authentic geoscience research education. 

We present geochemical data from gas samples from ~1200 km of arc in the Central Volcanic Zone of the Andes (CVZA), the volcanic arc with the thickest (~70 km) continental crust globally. The primary goals of this study are to characterize and understand how magmatic gases interact with hydrothermal systems, assess the origins of the major gas species, and constrain gas emission rates. To this end, we use gas chemistry, isotope compositions of H, O, He, C, and S, and SO2 fluxes from the CVZA. Gas and isotope ratios (CO2/ST, CO2/CH4, H2O/ST, δ13C, δ34S, 3He/4He) vary dramatically as magmatic gases are progressively affected by hydrothermal processes, reflecting removal and crustal sequestration of reactive species (e.g., S) and addition of less reactive meteoric and crustal components (e.g., He). The observed variations are similar in magnitude to those expected during the magmatic reactivation of volcanoes with hydrothermal systems. Carbon and sulfur isotope compositions of the highest temperature emissions (97–408 ◦C) are typical of arc magmatic gases. Helium isotope compositions reach values similar to upper mantle in some volcanic gases indicating that transcustal magma systems are effective conduits for volatiles, even through very thick continental crust. However, He isotopes are highly sensitive to even low degrees of hydrothermal interaction and radiogenic overprinting. Previous work has significantly underestimated volatile fluxes from the CVZA; however, emission rates from this study also appear to be lower than typical arcs, which may be related to crustal thickness. 

Molecular hydrogen is produced by the fermentation of organic matter and consumed by organisms including hydrogenotrophic methanogens and sulfate reducers in anoxic marine sediment. The thermodynamic feasibility of these metabolisms depends strongly on organic matter reactivity and hydrogen concentrations; low organic matter reactivity and high hydrogen concentrations can inhibit fermentation so when organic matter is poor, fermenters might form syntrophies with methanogens and/or sulfate reducers who alleviate thermodynamic stress by keeping hydrogen concentrations low and tightly controlled. However, it is unclear how these metabolisms effect porewater hydrogen concentrations in natural marine sediments of different organic matter reactivities. MethodsWe measured aqueous concentrations of hydrogen, sulfate, methane, dissolved inorganic carbon, and sulfide with high-depth-resolution and 16S rRNA gene assays in sediment cores with low carbon reactivity in White Oak River (WOR) estuary, North Carolina, and those with high carbon reactivity in Cape Lookout Bight (CLB), North Carolina. We calculated the Gibbs energies of sulfate reduction and hydrogenotrophic methanogenesis. ResultsHydrogen concentrations were significantly higher in the sulfate reduction zone at CLB than WOR (mean: 0.716 vs. 0.437 nM H₂) with highly contrasting hydrogen profiles. At WOR, hydrogen was extremely low and invariant (range: 0.41–0.52 nM H₂) in the upper 15 cm. Deeper than 15 cm, hydrogen became more variable (range: 0.312–2.56 nM H₂) and increased until methane production began at ~30 cm. At CLB, hydrogen was highly variable in the upper 15 cm (range: 0.08–2.18 nM H₂). Ratios of inorganic carbon production to sulfate consumption show AOM drives sulfate reduction in WOR while degradation of organics drive sulfate reduction in CLB. DiscussionWe conclude more reactive organic matter increases hydrogen concentrations and their variability in anoxic marine sediments. In our AOM-dominated site, WOR, sulfate reducers have tight control on hydrogen via consortia with fermenters which leads to the lower observed variance due to interspecies hydrogen transfer. After sulfate depletion, hydrogen accumulates and becomes variable, supporting methanogenesis. This suggests that CLB’s more reactive organic matter allows fermentation to occur without tight metabolic coupling of fermenters to sulfate reducers, resulting in high and variable porewater hydrogen concentrations that prevent AOM from occurring through reverse hydrogenotrophic methanogenesis. 

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions. 

Abstract Microbial aerobic methane oxidation is an important sink for aquatic methane worldwide. Despite its importance to global methane fluxes, few aerobic methane oxidation rates have been obtained in freshwater or marine environments without imposing changes to the microbial community through use of ex situ methods. A novel in situ incubation method for continuous time‐series measurements was used in Jordan Lake, North Carolina, during 2020–2021, to determine reaction kinetics for aerobic methane oxidation rates across a wide range of naturally varying methane (55–1833 nM) and dissolved oxygen (DO; 28–366 μM) concentrations and temperatures (17–30°C). Methane oxidation began immediately at the start of each of 21 incubations and methane oxidation rates were 1^storder with respect to methane. The data density allowed for accurate calculation of 1^st‐order rate constants,k, that ranged from 0.018 to 0.462 h⁻¹(R² > 0.967). Addition of ammonium (20–45 μM) to natural concentrations ranging from 0.057 to 2.4 μM did not change aerobic methane oxidation rate kinetics, suggesting that the natural population of aerobic methane oxidizers in this eutrophic lake was not nitrogen limited. Values ofkinversely correlated most strongly with initial DO concentrations (R² = 0.82) rather than temperature. Values forkincreased with Julian day throughout our sampling period, suggesting seasonal influences on methane oxidation via responses to geochemical changes or shifts in microbial community abundance and composition. These experiments demonstrate a high variability in the enzymatic capacity for 1^st‐order methane oxidation rates in this eutrophic lake that is tightly and inversely coupled to oxygen concentrations. Measurements of in situ aerobic methane oxidation rate constants allow for the direct quantification and modeling of the microbial community's capacity for methane oxidation over a wide range of natural methane concentrations. 

Subduction of the Cocos and Nazca oceanic plates beneath the Caribbean plate drives the upward movement of deep fluids enriched in carbon, nitrogen, sulfur, and iron along the Central American Volcanic Arc (CAVA). These compounds fuel diverse subsurface microbial communities that in turn alter the distribution, redox state, and isotopic composition of these compounds. Microbial community structure and functions vary according to deep fluid delivery across the arc, but less is known about how microbial communities differ along the axis of a convergent margin as geological features (e.g., extent of volcanism and subduction geometry) shift. Here, we investigate changes in bacterial 16S rRNA gene amplicons and geochemical analysis of deeply-sourced seeps along the southern CAVA, where subduction of the Cocos Ridge alters the geological setting. We find shifts in community composition along the convergent margin, with communities in similar geological settings clustering together independently of the proximity of sample sites. Microbial community composition correlates with geological variables such as host rock type, maturity of hydrothermal fluid and slab depth along different segments of the CAVA. This reveals tight coupling between deep Earth processes and subsurface microbial activity, controlling community distribution, structure and composition along a convergent margin.