Jennifer Pett-Ridge

Determining the environmental limits that govern how engineered metabolic traits control whole‐plant carbon (C) allocation is essential for developing climate‐resilient bioenergy systems. Enhancing sorghum biomass oil (lipid) content is a promising strategy to boost aboveground energy density, yet its system‐wide effects on root C investment and soil C delivery, particularly under drought conditions, are largely uncharacterized. Here, we provide the first comprehensive assessment of these interactions using whole‐plant ¹³ CO ₂ continuous labeling, depth‐specific sampling of roots and rhizosphere soil, and coordinated measurements of photosynthesis, stomatal anatomy, tissue nitrogen, and root nonstructural carbohydrates. The oil‐enhanced sorghum line (TZ424‐5‐3a) differed from wild‐type (TX‐430) in several aboveground traits, with the largest numerical differences observed under well‐watered conditions, including slightly longer stomata, lower stomatal density, and significantly higher leaf nitrogen concentration and biomass. Importantly, these aboveground changes did not translate into detectable shifts in the allocation of new photosynthate to belowground pools. In contrast, drought acted as a dominant regulatory factor, reorganizing C flow across both sorghum genotypes, suppressing photosynthesis and leaf water status, and increasing root nitrogen and root nonstructural carbohydrate concentrations. With depth, drought increased ¹³ C enrichment in shallow roots but reduced enrichment in deep roots; however, deep rhizosphere soils had increased ¹³ C enrichment, indicating contrasting depth‐dependent patterns of tracer recovery between roots and soil. Ultimately, soil moisture availability was the overriding determinant of belowground C partitioning and vertical distribution of recovered ¹³ C, superseding the influence of the engineered lipid sink. These findings provide new mechanistic insight into the environmental constraints on C allocation in an engineered bioenergy crop and identify soil moisture as the major regulator of the short‐term recovery and vertical distribution of recently fixed C.

Microbial life strategies are shaped by a fundamental ecological trade-off: specialization enables peak performance in a narrow niche, while generalization allows persistence across diverse environments, but may constrain maximal growth rates. In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere—and at their interface, where co-occurring living roots and decaying residues are hypothesized to generate emergent biogeochemical conditions. Using H₂¹⁸O quantitative stable isotope probing (qSIP), we measured bacterial and fungal growth rates in the rhizosphere, the detritusphere, and in the combined presence of rhizosphere + root detritus. We classified taxa operationally as specialists (defined as microbes actively growing only within a single habitat) or generalists (defined as microbes actively growing in two or more habitats), reflecting realized growth breadth under the conditions tested. Bacterial specialists exhibited faster growth than generalists within the habitats where they grew, a pattern consistent with a trade-off between niche breadth and growth rate. Net relatedness and nearest taxon indices showed that total bacterial communities were phylogenetically clustered, while specialist and generalist communities were phylogenetically random, consistent with functional traits—rather than lineage—predicting realized growth-breadth strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay may inform predictions of soil-carbon trajectories. IMPORTANCE: Soil microbes play a crucial role in cycling carbon and nutrients, but their strategies for surviving and growing in different environments remain poorly understood. This study asks whether soil microbes that grow rapidly in one habitat trade off that speed against the breadth of habitats they can occupy. Using quantitative stable isotope probing of H ₂ ¹⁸ O —an approach that measures active growth rather than mere presence—we tracked bacterial and fungal growth rates across three root-influenced habitats: the rhizosphere, the detritusphere, and the combined rhizosphere + detritusphere. We found that microbes detected growing in only one habitat (“specialists”) tended to grow faster within their habitat than microbes detected growing across multiple habitats (“generalists”), a pattern consistent with a trade-off between niche breadth and growth rate. This pattern was clearer for bacteria than for fungi. Although these classifications describe realized growth breadth under the conditions tested rather than universal organismal traits, understanding where and when specialists or generalists dominate may help inform predictions about the fate of soil carbon under changing plant inputs.

Quantifying soil properties is important for understanding fundamental biogeochemical processes, improving crop production, and climate change mitigation. Diffuse Reflectance Fourier-Transform Mid-Infrared (DRIFT-MIR) spectroscopy is widely used to estimate soil properties, but most studies have used shallow soils (< 60 cm), potentially limiting predictions for deep soils. We collected soils under shallow- and deep-rooted plants across the central and eastern US, quantified physicochemical properties, and developed whole-profile (0–240 cm), shallow- (0–60 cm), and deep (60–240 cm) soil DRIFT-MIR models. Our objectives were (1) to evaluate how DRIFT-MIR spectra vary with soil depth and plant type, (2) determine whether depth-specific calibration improves prediction relative to whole-profile calibration, and (3) identify spectral regions important for organic and inorganic carbon prediction. DRIFT-MIR spectra varied significantly only with depth, not plant type. Shallow-soil models showed accuracy similar to the whole-profile models for shallow-soil properties (e.g., pH, organic carbon), whereas deep-soil calibration significantly improved deep-soil organic carbon and nitrogen prediction compared to the whole-profile model. For organic carbon, important spectral regions differed among model types: 1570–1540 cm-1, associated with amide-, carboxylate-, and aromatic-related vibrations, was important for both the whole-profile and shallow-soil models, whereas 1830–1750 cm-1, associated with quartz, was important for deep-soil models. For inorganic carbon, all models showed key regions at 2630–2500 cm-1 and 1350–1250 cm-1, which were associated with carbonate and quartz minerals. Overall, our results show that bulk soil DRIFT-MIR spectra show little variation with plant type, that depth-specific calibration improved prediction of selected soil properties, particularly organic carbon, and that relevant spectral regions for organic carbon estimation differ between shallow and deep soils.

Dark colored grassland soils, known as Mollisols, are intensively farmed and rich in organic matter, and hence have an important role in the carbon cycle. Organic carbon storage in Mollisols may result from interactions between organic matter and calcium released by carbonate and silicate weathering. Here we test this hypothesis by using a geochemical model to simulate calcium release from weathering in soils across the USA. We find that calcium released by mineral weathering is associated with soil organic carbon storage and that this effect is stronger in Mollisols than in non-Mollisols. Our model also shows that agriculture has increased calcium inputs to cultivated USA Mollisols 4-5 fold, indicating that humans have fundamentally changed the geochemical conditions that sustain organic carbon in these soils. By implication, moderating the quantity of and timing of calcium release may help to preserve and restore carbon in the world’s most intensively farmed landscapes.

There is increasing evidence that carbon dioxide removal (CDR) strategies will play a significant role in global greenhouse gas management. Enhanced weathering (EW) is a CDR strategy with substantial carbon removal potential, which can simultaneously offer agronomic and soil fertility co-benefits to farmers. These co-benefits have been extensively theorized, but few agronomic field trials have quantified yield increases attributable to EW. In this study, we present substantial (>20%) yield benefits from a 2-year conventional corn-soy strip trial of basalt application in the Southeastern United States. Increases in soil pH and losses in total cation concentration in the upper portion of the soil provide evidence of basalt weathering. We also present stochastic economic analysis of net per-hectare revenue shift with subsidization of basalt purchase, hauling, and application. If rock application is subsidized, these results suggest a potential benefit to the grower of >$250 per-hectare for soybean production, and >$750 per-hectare for corn production within the first two years of application. This work provides some of the first direct evidence of 20% yield increases associated with EW in a large-scale strip trial, as well as substantial economic and agronomic benefits of EW on working lands.

Microbial weathering of minerals represents a key biogeochemical process through which microorganisms access essential nutrients locked within rock and ore substrates. In this study, we investigated the metabolic response of a model fungus during growth on lithium (Li) ore to elucidate the mechanisms underpinning biologically mediated mineral weathering and subsequent metal mobilization. Our results revealed a distinct metabolic shift in the fungus when cultivated on Li ore, characterized by altered patterns of organic acid production and energy metabolism. This shift coincided with measurable weathering of the Li ore matrix and the consequent release of soluble Li into the surrounding environment, demonstrating a direct link between fungal metabolic reprogramming and mineral breakdown. Importantly, these observations are consistent with metabolic shifts documented in previous studies of mineral weathering by this fungus, suggesting that such responses constitute a conserved and reproducible strategy employed during the colonization of mineral substrates. Although the present work was conducted using a single model microorganism under controlled conditions, the findings carry broader ecological implications. Natural microbial communities inhabiting mineral-rich environments may undergo analogous metabolic shifts when weathering minerals to acquire limiting nutrients, thereby contributing to large-scale elemental cycling and metal release. Understanding these processes not only advances fundamental knowledge of microbe–mineral interactions but also informs emerging applications in biomining and bio-based recovery of critical metals such as lithium. Collectively, this study highlights the central role of microbial metabolism in driving mineral weathering and offers a framework for predicting and harnessing similar processes within complex microbial communities. IMPORTANCE: The model fungus exhibits a distinct, reproducible shift in metabolism—particularly in organic acid production and energy pathways—when grown on Li ore, directly linking cellular metabolism to mineral breakdown. This metabolic shift promotes weathering of the ore matrix and the release of soluble lithium, demonstrating a biological route for liberating a critical metal from its mineral host. Because similar shifts occur across different minerals, natural microbial communities likely employ comparable strategies to weather minerals and acquire limiting nutrients, contributing to global elemental cycling. These findings provide a foundation for sustainable biomining and bio-based recovery of lithium and other critical metals, offering a lower-impact alternative to conventional extraction methods.

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O ₂ ) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO ₂ ) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O ₂ exposure. The total amount of CO ₂ respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H ₂ ¹⁸ O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant ¹⁸ O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76–5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10 ¹⁰ to 6.59 × 10 ¹⁰ virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota—bacterial groups known to rapidly resuscitate following rewetting—suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. IMPORTANCE: Soil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H ₂ ¹⁸ O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ . Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.

Most bacterial phyla have few or no pure cultures, including Atribacterota, comprised of ubiquitous anaerobes. Here, we report genome-guided enrichment and isolation of two Atribacterota species representing a new family, Caldatribacterium saccharofermentans from a hot spring, and Caldatribacterium inferamans from a deep aquifer. Both were co-enriched with sulfate-reducing bacteria and initially resisted isolation, which we link to inadvertent removal of precipitated folic acid by filter-sterilization of unbuffered Wolin's vitamin solution. We then predict folate auxotrophy across the Atribacterota and ~29% of all bacteria, with extensive auxotrophy in 27% of phyla. Since ≥604 of 791 ( ≥ 76%) media with folic acid additions in the MediaDive database use unbuffered vitamin solutions in which folic acid is likely removed during filter-sterilization, we propose that folate auxotrophy limits culturability in defined media en masse. We also uncover unusual features of Caldatribacterium, including three lipid membrane-like layers (LMLs), with the inner LML surrounding the nucleoid, and a high percentage of secreted proteins, supporting a unique cell biology of Atribacterota.

Atmospheric carbon dioxide removal (CDR) is required to stabilize global temperature. CDR can be achieved via ecosystem-based approaches that are cost-effective but reversible (e.g., soil and forest management) or by more durable but expensive approaches (e.g., direct air capture coupled with geologic storage). Here, we examine trade-offs between these approaches, focusing on timing, climate impacts, and cost. We simulated reversible carbon accrual for a range of CDR contract structures using a general minimalist model of ecosystem carbon cycling, and parameterized it to simulate US agricultural soil management─specifically cover cropping─as a case study. We then quantified the resulting impact on atmospheric carbon and global temperature using a climate model emulator. We find that maintaining a patchwork of reversible CDR projects by replacing lapsed projects with new projects can reduce warming by 22–195 μ°C in 2100 and that the magnitude of this cooling effect depends on how effectively the patchwork is maintained. Long-term maintenance of reversible CDR projects requires institutional stability that cannot be guaranteed over multiple decades. Consequently, effective CDR ultimately requires replacing reversible projects with durable projects. To address this problem, we modeled the cost of replacing reversible agricultural soil CDR with geologic CDR. We found that using reversible CDR as a bridge to durable CDR is potentially more cost-effective as a global cooling strategy (0.20–0.81 billion USD per μ°C avoided) than perpetual maintenance of reversible CDR (0.32–1.31 billion USD per μ°C avoided) or an immediate transition to durable CDR (1.37–2.19 billion USD per μ°C avoided). However, we emphasize that institutional commitments to maintain reversible CDR projects cannot be guaranteed. Reliance on reversible CDR as a bridge to durable CDR therefore carries an unknown amount of risk and will only function if efforts to maintain reversible CDR are robust.