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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction

Abstract “Obelisks” are recently discovered ribonucleic acid (RNA) viroid-like elements present in diverse environments with no phylogenetic similarity to any known biological agent. obelisks were first identified in the human gut and in a commensal bacterium acting as a replicative host. They have a circular ∼1 kb RNA genome, rod-like secondary structures, and the encoding of a protein superfamily called “Oblins”. We performed a large-scale search of obelisks in the ocean using the Pebblescout program and the transcriptomic Sequence Archive Read databases, revealing the biogeography and abundance of these viroid-like RNA elements. We detected 55 obelisk genomes resulting in 35 marine clusters at the species level. These obelisks were detected in the prokaryotic fraction and to a lesser extent in the eukaryotic fraction, and distributed across all the oceans from surface to mesopelagic including the Arctic, and even in the coldest seawater of Earth beneath the Antarctic Ross Ice Shelf. The obelisk hallmark protein Oblin-1 confirmed by 3D models was found in various marine samples. Some of the detected marine obelisks harbor hammerhead self-cleaving ribozymes in both polarities. In the prokaryotic, but not the eukaryotic, fraction of the Tara Ocean dataset, relative abundance of obelisks calculated by transcriptomic fragment recruitment indicated that they are abundant in marine samples, reaching or even exceeding the relative abundance of the previously discovered uncultured RNA viruses. In conclusion, obelisks are abundant and widespread viroid-like elements that should be included in ocean biogeochemical models.

Environmental Sciences & Ecology↗
DOE OSTI2025

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗
DOE OSTI2020

Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas Emissions Across a Permafrost Thaw Gradient in Northern Sweden

Warming-induced permafrost thaw could enhance microbial decomposition of previously stored soil organic matter (SOM) to carbon dioxide (CO 2 ) and methane (CH 4 ), one of the most significant potential feedbacks from terrestrial ecosystems to the atmosphere in a changing climate. The environmental parameters regulating microbe-organic matter interactions and greenhouse gas (GHG) emissions in northern permafrost peatlands are however still largely unknown. The objective of this work is to understand controls on SOM degradation and its impact on porewater GHG concentrations across the Stordalen Mire, a thawing peat plateau in Northern Sweden. Here, we applied high-resolution mass spectrometry to characterize SOM molecular composition in peat soil samples from the active layers of a Sphagnum-dominated bog and rich fen sites in the Mire. Microbe-organic matter interactions and porewater GHG concentrations across the thaw gradient were controlled by aboveground vegetation and soil pH. An increasingly high abundance of reduced organic compounds experiencing greater humification rates due to enhanced microbial activity were observed with increasing thaw, in parallel with higher CH 4 and CO 2 porewater concentrations. Bog SOM however contained more Sphagnum-derived phenolics, simple carbohydrates, and organic- acids. The low degradation of bog SOM by microbial communities, the enhanced SOM transformation by potentially abiotic mechanisms, and the accumulation of simple carbohydrates in the bog sites could be attributed in part to the low pH conditions of the system associated with Sphagnum mosses. We show that Gibbs free energy of C half reactions based on C oxidation state for OM can be used as a quantifiable measure for OM decomposability and quality to enhance current biogeochemical models to predict C decomposition rates. We found a direct association between OM chemical diversity and δ 13 C-CH 4 in peat porewater; where higher substrate diversity was positively correlated with enriched δ 13 C-CH 4 in fen sites. Oxidized sulfur-containing compounds, produced by Sphagnum, were further hypothesized to control GHG emissions by acting as electron acceptors for a sulfate-reducing electron transport chain, inhibiting methanogenesis in peat bogs. These results suggest that warming-induced permafrost thaw might increase organic matter lability, in subset of sites that become wetlands, and shift biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH 4 .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A tale of two extremes: Temperature sensitivity of carbon loss from cool and hot soils

Soils represent the largest terrestrial carbon (C) pool, and the flux of carbon dioxide (CO 2 ) from soils to the atmosphere is ~ 6-10 times more than anthropogenic emissions. Understanding responses of soil CO 2 emissions to warming is crucial for evaluating feedback to ongoing environmental changes. The relationship between microbial respiration and temperature is typically modeled using a Q 10 function. Generally, observations of the apparent Q 10 of soil respiration are higher for cold vs. warm ecosystems, reflecting expected biophysical controls of Arrhenius kinetics. However, results from two field warming experiments in the tropics contradict this expectation, both observing extraordinarily high soil respiration responses to in situ warming. Our overall objective for the proposed work is to reduce uncertainty in temperature sensitivity of soil C loss by systematically synthesizing underlying mechanisms related to soil C turnover and stabilization. We are evaluating the temperature sensitivity of soil respiration in ecosystems across temperature extremes (e.g., arctic/boreal and tropical systems) by integrating data collected from field warming experiments with machine learning and biogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The climate change mitigation potential of annual grasslands under future climates

Abstract Composted manure and green waste amendments have been shown to increase net carbon (C) sequestration in rangeland soils and have been proposed as a means to help lower atmospheric CO 2 concentrations. However, the effect of climate change on soil organic C (SOC) stocks and greenhouse gas emissions in rangelands is not well understood, and the viability of climate change mitigation strategies under future conditions is even less certain. We used a process‐based biogeochemical model (DayCent) at a daily time step to explore the long‐term effects of potential future climate changes on C and greenhouse gas dynamics in annual grassland ecosystems. We then used the model to explore how the same ecosystems might respond to climate change following compost amendments to soils and determined the long‐term viability of net SOC sequestration under changing climates. We simulated net primary productivity (NPP), SOC, and greenhouse gas fluxes across seven California annual grasslands with and without compost amendments. We drove the DayCent simulations with field data and with site‐specific daily climate data from two Earth system models (CanESM2 and HadGEM‐ES) and two representative concentration pathways (RCP4.5 and RCP8.5) through 2100. NPP and SOC stocks in unamended and amended ecosystems were surprisingly insensitive to projected climate changes. A one‐time amendment of compost to rangeland acted as a slow‐release organic fertilizer and increased NPP by up to 390–814 kg C ha −1 year −1 across sites. The amendment effect on NPP was not sensitive to Earth system model or emissions scenario and endured through the end of the century. Net SOC sequestration amounted to 1.96 ± 0.02 Mg C ha −1 relative to unamended soils at the maximum amendment effect. Averaged across sites and scenarios, SOC sequestration peaked 22 ± 1 years after amendment and declined but remained positive throughout the century. Though compost stimulated nitrous oxide (N 2 O) emissions, the cumulative net emissions (in CO 2 equivalents) due to compost were far less than the amount of SOC sequestered. Compost amendments resulted in a net climate benefit of 69.6 ± 0.5 Tg CO 2 e 20 ± 1 years after amendment if applied to similar ecosystems across the state, amounting to 39% of California's rangeland. These results suggest that the biogeochemical benefits of a single amendment of compost to rangelands in California are insensitive to climate change and could contribute to decadal‐scale climate change mitigation goals alongside emissions reductions.

Mayer, Allegra↗
DOE OSTI2021

Soybean fallow and nitrification inhibitors: Strategies to reduce N 2 O emission intensities and N losses in Australian sugarcane cropping systems

The Australian sugar industry is facing mounting pressure to reduce the nitrogen (N) losses and nitrous oxide (N 2 O) emissions associated with N fertiliser use. Research has shown that N 2 O emissions from sugarcane (Saccharum officinarum L.) cropping systems can be reduced with the use of fertilisers coated with nitrification inhibitors, or by sowing legume crops in the fallows between sugarcane crop cycles. However, the efficacy of these two N management strategies across different climatic zones is still unclear, as results from field studies have been contradictory. The objectives of this study were therefore to use the DayCent model to assess the long-term effects of the two strategies (separately or in combination) on N 2 O emissions, N losses and yields. The model was parameterised using data from eight field experiments (39 treatments) conducted across four of the five main districts of the Australian sugarcane industry. A series of long-term scenarios embracing a range of N fertiliser rates (0- 160 kg N ha -1 applied as urea), climatic regions (Tropics and Subtropics), soil textures (fine- and coarse-textured soils) and N-loss risk scenarios (crop fertilised well before or close to the on-set of the wet season) were tested for both N management strategies. Simulations identified that the combined use of soybean (Glycine max L.) fallows and N fertiliser coated with the 3,4-dimethylpyrazole phosphate (DMPP) nitrification inhibitor was the most effective strategy to maintain or even increase current yields while significantly reducing N 2 O and cumulative N (mainly due to nitrate) losses. When used alone, the soybean fallow strategy on average reduced N losses over the entire crop cycle by 29 % compared with current industry best practice. However, this strategy showed a limited capacity to reduce N 2 O emissions over the entire cane crop cycle (median: -3% compared with current industry best practice), or even increased them in scenarios at high-risk of N losses in the Tropics. The use of urea coated with DMPP alone allowed current fertiliser N rates to be reduced by 30 % without any substantial yield penalty. In environments prone to high N losses, DMPP urea abated overall N losses and N 2 O emissions by 41 % and 30 %, respectively. This was the first study to use such an extensive dataset to parameterise a biogeochemical model for yields, N 2 O emissions and N losses in sugarcane cropping systems. Finally, the findings will be instrumental in guiding future research and policies designed to improve the profitability and environmental sustainability of this industry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Carbon mitigation payments can reduce the riskiness of bioenergy crop production

Abstract Perennial bioenergy crops provide substantial carbon mitigation benefits but have risky returns. We couple economic analysis with a biogeochemical model (DayCent) to examine the effect of carbon mitigation payments on the spatially varying bioenergy crop returns and risk profiles relative to conventional crops across the rainfed United States. These payments increase the likelihood of positive profit in the Midwest for miscanthus and southern states for switchgrass. At low biomass prices, these payments make bioenergy crops appealing to risk‐averse farmers. At moderate biomass prices, these payments make bioenergy crops appealing to all farmers regardless of risk preference.

09 BIOMASS FUELS↗
DOE OSTI2022

Marine phytoplankton resilience may moderate oligotrophic ecosystem responses and biogeochemical feedbacks to climate change

Are the oceans turning into deserts? Rising temperature, increasing surface stratification, and decreasing vertical inputs of nutrients are expected to cause an expansion of warm, nutrient deplete ecosystems. Such an expansion is predicted to negatively affect a trio of key ocean biogeochemical features: phytoplankton biomass, primary productivity, and carbon export. However, phytoplankton communities are complex adaptive systems with immense diversity that could render them at least partially resilient to global changes. This can be illustrated by the biology of the Prochlorococcus “collective.” Adaptations to counter stress, use of alternative nutrient sources, and frugal resource allocation can allow Prochlorococcus to buffer climate-driven changes in nutrient availability. In contrast, cell physiology is more sensitive to temperature changes. We argue that biogeochemical models need to consider the adaptive potential of diverse phytoplankton communities. However, a full understanding of phytoplankton resilience to future ocean changes is hampered by a lack of global biogeographic observations to test theories. We propose that the resilience may in fact be greater in oligotrophic waters than currently considered with implications for future predictions of phytoplankton biomass, primary productivity, and carbon export.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Trace metal contents of autotrophic flagellates from contrasting open‐ocean ecosystems

Abstract Nano‐ and picophytoplankton are a major component of open‐ocean ecosystems and one of the main plankton functional types in biogeochemical models, yet little is known about their trace metal contents. In cultures of the picoeukaryote Ostreococcus lucimarinus , iron limitation reduced iron quotas by 68%, a fraction of the plasticity known in diatoms. In contrast, a commonly co‐occurring cyanobacterium, Prochlorococcus , showed variable iron contents with iron availability in culture. Synchrotron X‐ray fluorescence was used to measure single‐cell metal (Mn, Fe, Co, Ni, Zn) quotas of autotrophic flagellates (1.4–16.8‐ μ m diameter) collected from four ocean regions. Iron quotas were tightly constrained and showed little response to iron availability, similar to cultured Ostreococcus . Zinc quotas also did not vary with zinc availability but appeared to vary with phosphorus availability. These results suggest that macronutrient and metal availability may be equally important for controlling metal contents of small eukaryotic open‐ocean phytoplankton.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple spatiotemporal scales, from which macrosystem patterns in SOM emerge. Theory on SOM turnover recognizes the resulting spatial and temporal conditionality in the effect sizes of controls that play out across macrosystems, and couples them through evolutionary and community assembly processes. For example, climate history shapes plant functional traits, which in turn interact with contemporary climate to influence SOM dynamics. Selection and assembly also shape the functional traits of soil decomposer communities, but it is less clear how in turn these traits influence temporal macrosystem patterns in SOM turnover. Here, we review evidence that establishes the expectation that selection and assembly should generate decomposer communities across macrosystems that have distinct functional effects on SOM dynamics. Representation of this knowledge in soil biogeochemical models affects the magnitude and direction of projected SOM responses under global change. Yet there is high uncertainty and low confidence in these projections. To address these issues, we make the case that a coordinated set of empirical practices are required which necessitate (1) greater use of statistical approaches in biogeochemistry that are suited to causative inference; (2) long-term, macrosystem-scale, observational and experimental networks to reveal conditionality in effect sizes, and embedded correlation, in controls on SOM turnover; and (3) use of multiple measurement grains to capture local- and macroscale variation in controls and outcomes, to avoid obscuring causative understanding through data aggregation. Here, when employed together, along with process-based models to synthesize knowledge and guide further empirical work, we believe these practices will rapidly advance understanding of microbial controls on SOM and improve carbon cycle projections that guide policies on climate adaptation and mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Assessing the fidelity of shallow-water carbonates as records of the Ni isotope composition of surface seawater

Nickel is a bioessential metal that is used in enzymes important to the C, N, and O cycles, and changes in its marine abundance and bioavailability may have affected the evolutionary trajectory of early life. Changes over time in the Ni isotope composition (δ 60 Ni) of surface seawater, which reflects biological demand for Ni, could allow for the reconstruction of the dynamics of Ni demand over Earth’s history, but this approach would require geologic records of surface seawater. Here, we investigate the fidelity of shallow-water carbonates as a record of the Ni isotope composition of surface seawater by determining how Ni is first partitioned into natural carbonates and then how post-depositional processes influence the Ni signal. Our samples come from the Great Bahama Bank, which is a well-studied, modern carbonate platform often used to study ancient platforms. We found that Ni is fractionated from seawater upon incorporation into carbonates capturing shallow (<18 cm), recent deposition (0.1 ‰–0.4 ‰ lighter than seawater). Variation among these [Ni] and δ 60 Ni values may be controlled by variation in mineral proportions. Meteoric diagenesis shifts δ 60 Ni to lower values, which we attribute to isotopically light meteoric fluids. In contrast, carbonates that experienced sediment-buffered marine diagenesis with respect to Ca isotopes and Sr/Ca ratios do not appear to differ in δ 60 Ni values from sediments generally representative of their initial deposition. The sensitivity of δ 60 Ni to diagenetic reset in these samples appears comparable to the sensitivities of Ca isotopes and Sr/Ca ratios, to first order. Thus, in general, carbonates that experienced sediment-buffered marine diagenesis with respect to these elements may hold the most promise as a record of the δ 60 Ni of coeval surface seawater. Additionally, we use our results to infer that the fraction of Ni removed from seawater into carbonates is less than 10 % of the total Ni output from the global oceans and incorporation of this Ni sink into global biogeochemical models will only have a minor impact on the modeled modern Ni budget.

Great Bahama Bank carbonates↗
DOE OSTI2023

Controls and variability of soil respiration temperature sensitivity across China

Understanding the temperature sensitivity (Q 10 ) of soil respiration is critical for benchmarking the potential intensity of regional and global terrestrial soil carbon fluxes-climate feedbacks. Although field observations have demonstrated the strong spatial heterogeneity of Q 10 , a significant knowledge gap still exists regarding to the factors driving spatial and temporal variabilities of Q 10 at regional scales. Here, therefore, we used a machine learning approach to predict Q 10 from 1994 to 2016 with a spatial resolution of 1 km across China from 515 field observations at 5 cm soil depth using climate, soil and vegetation variables. Predicted Q 10 varied from 1.54 to 4.17, with an area-weighted average of 2.52. There was no significant temporal trend for Q 10 (p = 0.32), but annual vegetation production (indicated by normalized difference vegetation index, NDVI) was positively correlated to it (p < 0.01). Spatially, soil organic carbon (SOC) was the most important driving factor in 62 % of the land area across China, and varied greatly, demonstrating soil controls on the spatial pattern of Q 10 . These findings highlighted different environmental controls on the spatial and temporal pattern of soil respiration Q 10 , which should be considered to improve global biogeochemical models used to predict the spatial and temporal patterns of soil carbon fluxes to ongoing climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism

Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet the processes regulating aerobic respiration in aquatic environments remain poorly understood. Aerobic respiration is typically predicted through kinetic controls such as organic carbon and oxygen concentrations, while assuming thermodynamic regulation has no influence. The role of OM thermodynamics has been mainly explored under anaerobic conditions; however, recent observations have suggested that thermodynamic properties of OM may influence aerobic respiration rates. Here, we explicitly test OM thermodynamics as a key regulator of aerobic respiration. We pair controlled microcosm experiments with ultrahigh-resolution OM characterization to show that aerobic respiration increases with OM thermodynamic favorability under carbon limitation. We also demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen content when carbon is in excess, highlighting a central role for OM thermodynamics particularly in carbon-limited ecosystems. This illuminates a structural gap in aquatic biogeochemical models by demonstrating that both kinetic and thermodynamic constraints can modulate aerobic respiration. Our work therefore proposes a new conceptual model in which thermodynamic and nutrient limitations dually control aerobic respiration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Impacts of Topography‐Driven Water Redistribution on Terrestrial Water Storage Change in California Through Ecosystem Responses

Abstract Lateral subsurface flow plays an essential role in sustaining the terrestrial ecosystem, but it is not explicitly represented in most Earth System Models. In this study, we implemented an explicit lateral saturated flow model into the E3SM land model (ELM). The model explicitly describes lateral flow in the saturated zone by representing, for each model grid, an idealized hillslope consisting of five hydrologically connected soil columns. We conducted three model experiments driven by 0.125° atmospheric forcing data during 1980–2015 over California using models of the default ELM, a modified version of ELM to enhance infiltration, and the model with the lateral saturated flow model. The simulated runoff, evapotranspiration, and terrestrial water storage anomaly (TWSA) from the three simulations were evaluated against available observations, and the model explicitly representing lateral flow performs best. The new model produces greater gridcell‐averaged evapotranspiration especially over the mountainous regions with moderate relief and seasonally dry climates. Most importantly, it improves the modeled seasonal variations, interannual variabilities, and the recent decadal decline of TWSA. Many of these improvements can be attributed to the enhanced ecosystem resilience to droughts as demonstrated by transpiration increases caused by lateral flow. Model sensitivity experiments suggest that subsurface runoff is most sensitive to the ratio between horizontal and vertical saturated hydraulic conductivity, followed by hillslope planforms (convergent, divergent, and uniform), number of columns, and lower boundary conditions. Future work should effectively characterize hillslopes in global models and explore the long‐term influences of lateral water movement on modeled biogeochemical cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Tendencies of Soil Microbial NO Emissions During HI‐SCALE as Predicted by a Nitrification/Denitrification Scheme

Many atmospheric chemical processes, including the formation of secondary organic aerosol (SOA), are strongly modulated by the reactions of NO and NO 2 (NO x ). Though NO x is controlled by anthropogenic emissions near urban areas, in rural areas soil microbes can be a significant contribution to NO emission globally. The relative rates of emissions of different nitrogen-containing species (e.g., NO, N 2 O, HONO, and N 2 ) are strong functions of soil properties such as temperature, moisture content, pH, and soil carbon and nitrogen pools. However, typical large-scale biogeochemical models either express these emissions simplistically, or not at all. Here we investigate the potential impact of soil NO emissions on atmospheric chemistry and SOA formation over regional and monthly time scales, specifically the 2016 spring and summer Intensive Observational Periods (IOPs) of the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) field campaign. We implement the soil NO nitrification/denitrification parameterization of Rasool et al. (2019) into the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem), supplemented by a 1-km soil moisture analysis. We then simulate both IOPs over the U.S. Great Plains, evaluating against ground stations and flight data. We show that soil NO emissions can account for a large fraction of total NO x and locally increase O 3 concentrations by up to 25%, while alleviating negative biases of gases and aerosols toward observations. Soil moisture and temperature changes between IOP1 and IOP2 lead to overall differences in emissions, but with large regional variability due to heterogeneous surface characteristics.

Atmoshpheric Chemistry↗
DOE OSTI2020

Local-scale Arctic tundra heterogeneity affects regional-scale carbon dynamics

In northern Alaska nearly 65% of the terrestrial surface is composed of polygonal ground, where geomorphic tundra landforms disproportionately influence carbon and nutrient cycling over fine spatial scales. Process-based biogeochemical models used for local to Pan-Arctic projections of ecological responses to climate change typically operate at coarse-scales (1km 2 –0.5°) at which fine-scale (<1km 2 ) tundra heterogeneity is often aggregated to the dominant land cover unit. Here, we evaluate the importance of tundra heterogeneity for representing soil carbon dynamics at fine to coarse spatial scales. We leveraged the legacy of data collected near Utqiagvik, Alaska between 1973 and 2016 for model initiation, parameterization, and validation. Simulation uncertainty increased with a reduced representation of tundra heterogeneity and coarsening of spatial scale. Hierarchical cluster analysis of an ensemble of 21 st -century simulations reveals that a minimum of two tundra landforms (dry and wet) and a maximum of 4km 2 spatial scale is necessary for minimizing uncertainties (<10%) in regional to Pan-Arctic modeling applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs

Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year1, more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative 12/13C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Life and death in the soil microbiome: how ecological processes influence biogeochemistry

We report soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.

59 BASIC BIOLOGICAL SCIENCES↗