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At least 145 records · Page 8

Microbial extracellular enzyme activity with simulated climate change

It is critical to understand the consequences of environmental change for the microbial regulation of carbon and nutrient cycling. Specifically, understanding microbial community traits, such as extracellular enzyme activity, can help inform nutrient cycling models and address knowledge gaps. We analyzed data on extracellular enzyme activities and litter decomposition from an 18-month experiment in which microbial communities were reciprocally transplanted along a climate gradient in Southern California. Communities were from desert, scrubland, grassland, pine–oak, and subalpine ecosystems. We aimed to test how enzyme activities responded to climate change following transplantation and how those responses related to decomposition rates. We hypothesized that microbial communities would specialize on their native climate conditions, resulting in higher enzyme activities when transplanted back into their native climate. We investigated the relationship between extracellular enzyme Vmax values, substrate mass loss, and microbial biomass as well as variation in these variables across the climate gradient. We found little evidence for climate specialization, and there was rarely a reduction in enzyme functioning after microbial communities were transplanted into new climate conditions. Moreover, observed differences in decomposition were not related to changes in extracellular enzyme potential, although there were significant differences in enzyme activities and decomposition rates across sites. These results suggest that direct, physiological impacts of climate are likely to be important for enzyme-mediated decomposition, but climate specialization will not constrain the microbial response to climate change in our system.

54 ENVIRONMENTAL SCIENCES↗

Experimental Soil Warming Impacts Soil Moisture and Plant Water Stress and Thereby Ecosystem Carbon Dynamics

Experimental soil heating experiments have found a consistent increase in soil-surface CO 2 emissions ( F s ), but inconsistent soil organic carbon (SOC) responses. Interpretation of heating effects is complicated by spatial heterogeneity and soil moisture, nitrogen availability, and microbial and plant responses. Here we applied a mechanistic ecosystem model to interpret heating impacts on a California forest subjected to 1 m deep, 4°C heating. The model accurately simulated control-plot CO 2 fluxes, SOC stocks, fine root biomass, soil moisture, and soil temperature, and the observed increases in F s and decreases in fine root biomass. We show that a complex suite of interactions can lead to a consistent increase in F s (~17%) over the 5-year study period, with very small changes in SOC stocks (<1%). Modeled increases in leaf water stress from soil drying reduced GPP and NPP. The resulting reduction in leaf and fine root allocation increased fine root litter inputs to the soil and reduced root exudation. Soil heating led to about a 50% larger increase in root autotrophic respiration than in heterotrophic respiration, with the heating effect on both these fluxes decreasing over the simulation period. Increased heterotrophic respiration led to increased soil N availability and plant N uptake. These heating responses are mechanistically linked, of magnitudes that can affect ecosystem dynamics, and long-term observations of them are rarely made. Therefore, we conclude that a coupled observational and mechanistic modeling framework is needed to interpret manipulation experiments, and to improve projections of climate change impacts on terrestrial ecosystem carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant–microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Soil organic carbon cycling in response to simulated soil moisture variation under field conditions

The combination of extended dry periods and high intensity rainfall, common in the southeastern US, leads to greater variability in soil moisture and consequently increases uncertainty to microbial processes pertinent to soil carbon (C) mineralization. However, field-based findings on soil moisture sensitivity to soil C cycling are very limited. Therefore, a field experiment was conducted in 2018 and 2019 on a soybean (Glycine max L.) cropland in the southeastern US with three soil moisture treatments: drought (simulated using rainout-shelter from June to October in each year), rainfed (natural precipitation), and irrigated (irrigation and precipitation). Soil respiration was measured weekly from May to November in both years. Soil samples were collected multiple times each year from 0–5, 5–15, and 15–30 cm depths to determine microbial biomass C (MBC), extractable organic C (EOC), hydrolytic enzyme activities, and fungal abundance. The cumulative respiration under drought compared to other treatments was lower by 32% to 33% in 2018 and 38% to 45% in 2019. Increased MBC, EOC, and fungal abundance were observed under drought than other treatments. Specific enzyme activity indicated fewer metabolically active microbes under drought treatment compared to rainfed and irrigated treatments. Also, maintenance of enzyme pool was observed under drought condition. These results provide critical insights on microbial metabolism in response to soil moisture variation and how that influences different pools of soil C under field conditions.

54 ENVIRONMENTAL SCIENCES↗

Ecological strategies of microbes: Thinking outside the triangle

Abstract I asked whether Grime's triangle of competitive, stress tolerance and ruderal ecological strategies—which was originally developed for plants—applies to microbes. I conducted a synthesis of empirical studies that tested relationships among microbial traits presumed to define the competitive, stress tolerance and ruderal, and other ecological strategies. There was broad support for Grime's triangle. However, the ecological strategies were inconsistently linked to shifts in microbial communities under environmental changes like nitrogen and phosphorus addition, warming, drought, etc. We may be missing important ecological strategies that more closely influence microbial community composition under shifting environmental conditions. We may need to start by documenting changes in microbial communities in response to environmental conditions at fine spatiotemporal scales relevant for microbes. We can then develop empirically based ecological strategies, rather than modifying those based on plant ecology. Synthesis . Microbes appear to sort into similar ecological strategies as plants. However, these microbial ecological strategies do not consistently predict how community composition will shift under environmental change. By starting ‘from the ground up’, we may be able to delineate ecological strategies more relevant for microbes.

54 ENVIRONMENTAL SCIENCES↗

Microbial inoculants for soil restoration: A Risk-Proportional Stewardship Framework Integrating Strain-Resolved Genomics and Adaptive Governance

Global soil degradation and increasing reliance on chemical inputs threaten agricultural sustainability, driving interest in microbial inoculants as tools for soil restoration. These biological products have the potential to enhance nutrient cycling, improve soil structure, and support plant resilience, but their environmental release raises important safety and stewardship considerations. Here, we propose a risk-proportional framework for the responsible deployment of microbial inoculants grounded in release-based stewardship. The framework integrates genome-resolved strain identification, exclusionary hazard screening, bioassay-based risk triage, ecological testing under realistic conditions, and monitored field deployment. Drawing on evidence from microbial ecology and invasion biology, we highlight how inoculants can alter resident microbial communities, influence ecosystem function, and, in some cases, facilitate gene flow, underscoring the need for risk assessment. We further outline a federated, genome-informed data infrastructure to support traceability, cross-jurisdiction learning, and adaptive management. Together, this approach provides a scalable and scientifically grounded pathway to balance innovation and safety, enabling microbial technologies to contribute to soil restoration and climate-resilient agriculture.

Edlund, Anna [OATH Inc]↗

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO 2 in northern peatlands

Warming and elevated CO 2 (eCO 2 ) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO 2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO 2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO 2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

59 BASIC BIOLOGICAL SCIENCES↗

The Influence of Microbial Priming Effects on the Hydro-bio-geochemistry of Large River Reservoirs

River-tributary confluences, where diverse organic matter (OM) sources mix, are considered aquatic critical zones for biogeochemical cycling. Here we evaluate dissolved OM composition and bioavailability in the mainstem of the Columbia River and three of its tributaries (Snake, Yakima, and Walla Walla rivers) along a hydrologic gradient in the Columbia River drainage basin using a variety of bulk and molecular level measurements. Field replicates and mixtures representing river-tributary confluences were incubated in the dark for 15 days to investigate the response of the microbial community to varying OM quantity/composition. The Columbia, Snake, and Yakima rivers did not differ in dissolved organic carbon (DOC), fluorescent dissolved OM (fDOM), or Chlorophyll-a (Chl-a) concentrations. However, the Walla Walla River had significantly greater DOC, fDOM, and Chl-a concentrations, indicative of greater contributions from algal DOM. FT-ICR-MS spectra for Walla Walla had significantly more peaks corresponding to amino sugars, carbohydrates and proteins while the Columbia River had more peaks for lignin, unsaturated hydrocarbons, and condensed aromatics. When incubated for 15 days in the dark, total DOC did not decrease for any of the river samples. DOC did decrease, however, in a mix representing the confluence of the Columbia and Walla Walla rivers, suggesting the microbial consortia of the Columbia River were primed by the Walla Walla River OM. OM composition was significantly different for several compound classes (e.g., lignin, protein, and tannin) following the incubations of unmixed river and tributary samples. However, the microbial community in the Walla Walla-Columbia mixture appeared to be indiscriminate of the molecular structure of the DOM as the compound class distribution did not change significantly. This provides preliminary evidence that the heterotrophs in river-tributary critical zones remineralize diverse OM structures.

54 ENVIRONMENTAL SCIENCES↗

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum -dominated bog

Abstract Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Song, Tianze (ORCID:0000000282060247)↗

Electrochemically recovered struvite matches conventional fertilizers in soil nutrient supply

Phosphorus (P) is an essential macronutrient for agriculture, yet global reliance on finite phosphorite reserves raises concerns about long-term food and nutrient security. Struvite (MgNH 4 PO 4 ·6H 2 O), a mineral recovered from municipal wastewater, represents a sustainable and circular source of P, but uncertainty remains regarding its nutrient availability relative to conventional fertilizers. This study evaluated the fertilizer value and environmental safety of electrochemically recovered struvite (RecoP) in comparison with diammonium phosphate (DAP), triple superphosphate (TSP), and rock phosphate (RockP). Nutrient availability, potential contaminant concentrations, and soil P and nitrogen (N) dynamics were assessed using standardized chemical analyses and an 8-week incubation experiment across three soils with contrasting soil types. RecoP contained 14.7% citrate-soluble P, significantly greater than RockP and comparable to DAP and TSP. Across all soils, RecoP increased both readily available and moderately labile P pools (p < 0.01), matching the performance of conventional fast-release fertilizers. Despite containing approximately half the total of DAP, RecoP stimulated nitrification rates that were 2.2 times greater than the control and exceeded those of TSP, suggesting that fertilizer-derived N bioavailability, rather than total N loading, governed microbial N transformation responses. Concentrations of potentially toxic elements in RecoP were consistently well below US Environmental Protection Agency regulatory limits thresholds. Collectively, these results indicate that RecoP functions as a readily available source of both P and N, comparable to widely used conventional fertilizers, while meeting environmental safety standards. RecoP therefore represents a viable component of sustainable nutrient management strategies that support P recycling and agricultural productivity.

Kharal, Sudarshan [Ohio Univ., Athens, OH (United ↗

Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential

Chemicals involved in plutonium uranium reduction extraction (PUREX) can be released from nuclear reprocessing facilities and accumulate in the environment. We exposed chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. The responses of soil microbial communities are dependent on soil type, and tributyl phosphate exposure generates the most reproducible changes in microbial communities. We reconstructed the genomes of key bacteria and find several phosphotriesterase genes found only in Rhizobiaceae. The abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. In conclusion, these phosphotriesterase genes may be involved in breakdown of tributyl phosphate, and a means of accessing phosphate for these bacteria.

Bioremediation↗

Oxidation of soil organic carbon during an anoxic-oxic transition

Redox reactions of iron (Fe) can play an important role in controlling the stability and transformation of organic carbon (OC) in soils. However, there is limited knowledge about the dynamics of Fe and OC in soils during anoxic-oxic transitions, which are common in temperate and tropical biomes. In this study, we investigated the fate and transformation of Fe and OC during a 5-day oxic incubation of four pre-reduced (8 days anoxic) forest soils. Up to 3.7% of total OC in the pre-reduced soils was oxidized to CO 2 , in conjunction with the oxidation of 31 –84% of the extractable Fe(II). OC oxidation in pre-reduced soils was lower than non-reducedcontrol soils, indicating that recently anoxically-incubated soils support lower OC metabolism upon re-oxidation than consistently oxic soils. Oxic OC oxidation was negatively correlated with the fraction of Fe-bound OC and also the fraction of short-range-ordered (SRO) Fe oxides. These results suggest that association with Fe oxides—especially SRO Fe oxides—can inhibit the availability of OC for oxidation. However, the difference between the oxidation of OC in pre40 reduced soils and consistently oxic controls could not be linked to the moderate changes in the Fe mineral composition during the anoxic-oxic transition, indicating the importance of longer term OC association with Fe oxides, as well as other processes, in regulating the oxidation of OC during the redox fluctuations. OC association with Fe oxides should be considered during simulations of biogeochemical cycling of OC in soils during the redox fluctuations, for which other processes such as the anoxic transformation of OC and response of the microbial community also need to be incorporated.

58 GEOSCIENCES↗

Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N)

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018–2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5°C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2–4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Further, genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ~6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.

54 ENVIRONMENTAL SCIENCES↗

Robust Rapid Cellular Metabolite Sensing Using Benchtop NMR and SABRE-Hyperpolarized [1- 13 C]Pyruvate

Hyperpolarized NMR has emerged as a powerful analytical technique to significantly enhance targeted NMR signals, improving the sensitivity for investigations of unique chemical and biological dynamics. Here, we demonstrate the use of a hyperpolarization strategy based on Signal Amplification By Reversible Exchange (SABRE) to generate highly reproducible doses of a hyperpolarized [1- 13 C]pyruvate probe for benchtop characterization of yeast metabolism. This method allows rapid, scalable, and benchtop preparation of biocompatible hyperpolarized solutions suitable for live-cell experiments. We show that this production can be dove-tailed into a modular, compact workflow to characterize real-time metabolism in cell cultures, using Saccharomyces cerevisiae (Baker’s yeast) as a model organism. With high temporal resolution, we show that this method can resolve the conversion of hyperpolarized [1- 13 C]pyruvate into oxidative decarboxylation products CO 2 and bicarbonate. This conversion exhibits sustained and detectable metabolic activity for over 300 s after introduction of the agent to the cells. We model the metabolite kinetics to show decarboxylation activity and derive estimates of the pH over time from the CO 2 and bicarbonate (carbonic acid buffer system) equilibrium to probe changes in the cellular environment during active metabolism. These results highlight the utility of benchtop SABRE-hyperpolarized [1- 13 C]pyruvate as a scalable, specific probe for metabolic phenotyping of living cells using compact, low-cost instrumentation well-suited for future high-throughput applications across microbial engineering, drug response profiling, and dynamic metabolic screening.

fungi↗

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming

Abstract Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration ( Q 10 ) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5–19%, and reduces model parametric uncertainty by 55–71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

54 ENVIRONMENTAL SCIENCES↗

Thermal responses of dissolved organic matter under global change

The diversity of intrinsic traits of different organic matter molecules makes it challenging to predict how they, and therefore the global carbon cycle, will respond to climate change. Here we develop an indicator of compositional-level environmental response for dissolved organic matter to quantify the aggregated response of individual molecules that positively and negatively associate with warming. We apply the indicator to assess the thermal response of sediment dissolved organic matter in 480 aquatic microcosms along nutrient gradients on three Eurasian mountainsides. Organic molecules consistently respond to temperature change within and across contrasting climate zones. At a compositional level, dissolved organic matter in warmer sites has a stronger thermal response and shows functional reorganization towards molecules with lower thermodynamic favorability for microbial decomposition. The thermal response is more sensitive to warming at higher nutrients, with increased sensitivity of up to 22% for each additional 1 mg L -1 of nitrogen loading. The utility of the thermal response indicator is further confirmed by laboratory experiments and reveals its positive links to greenhouse gas emissions.

54 ENVIRONMENTAL SCIENCES↗

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil

The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.

59 BASIC BIOLOGICAL SCIENCES↗