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DOE OSTI2021

Extending a land-surface model with <i>Sphagnum</i> moss to simulate responses of a northern temperate bog to whole ecosystem warming and elevated CO<sub>2</sub>

Abstract. Mosses need to be incorporated into Earth system models to better simulate peatland functional dynamics under the changing environment. Sphagnum mosses are strong determinants of nutrient, carbon, and water cycling in peatland ecosystems. However, most land-surface models do not include Sphagnum or other mosses as represented plant functional types (PFTs), thereby limiting predictive assessment of peatland responses to environmental change. In this study, we introduce a moss PFT into the land model component (ELM) of the Energy Exascale Earth System Model (E3SM) by developing water content dynamics and nonvascular photosynthetic processes for moss. The model was parameterized and independently evaluated against observations from an ombrotrophic forested bog as part of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) project. The inclusion of a Sphagnum PFT with some Sphagnum-specific processes in ELM allows it to capture the observed seasonal dynamics of Sphagnum gross primary production (GPP) albeit with an underestimate of peak GPP. The model simulated a reasonable annual net primary production (NPP) for moss but with less interannual variation than observed, and it reproduced aboveground biomass for tree PFTs and stem biomass for shrubs. Different species showed highly variable warming responses under both ambient and elevated atmospheric CO2 concentrations, and elevated CO2 altered the warming response direction for the peatland ecosystem. Microtopography is critical: Sphagnum mosses on hummocks and hollows were simulated to show opposite warming responses (NPP decreasing with warming on hummocks but increasing in hollows), and hummock Sphagnum was modeled to have a strong dependence on water table height. The inclusion of this new moss PFT in global ELM simulations may provide a useful foundation for the investigation of northern peatland carbon exchange, enhancing the predictive capacity of carbon dynamics across the regional and global scales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Aneuploidy induces premature aging in yeast due to defects in Ribosome Quality Control [RNASeqData]

Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21; but the reason is unclear and difficult to study in humans. We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes. We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). Aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest. Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects. Our results raise major implications for other aneuploidy disorders including Down syndrome.

aneuploidy↗

DOE OSTI2024

Aneuploidy induces premature aging in yeast due to defects in Ribosome Quality Control [MoBYSeqData]

aneuploidy↗

DOE OSTI2024

Premature aging in aneuploid yeast is influenced by aneuploidy-induced defects in Ribosome Quality Control [RiboSeq]

aneuploidy↗

NASA NTRS1990

Preparatory space experiments for development of a CELSS

The goal of Closed Ecological Life Support System (CELSS) studies is to examine the effects of microgravity on yield and quality of plant products and on the interactions between irradiance and crop area. Measuring yield and quality of crops as a function of irradiance in microgravity is virtually unique to the CELSS program, as is the emphasis on canopies rather than individual plants. The first step for space experiments is to develop a relatively stress free environment for plant growth, something that has so far never been achieved. High light levels are essential, and there must be time enough to complete a significant portion of the life cycle. Optimal atmosphere and nutrients must be provided. Such responses as germination, orientation of roots and shoots, photosynthesis and respiration, floral initiation and development, and seed maturation and viability will be studied.

Salisbury, Frank B.↗

DOE OSTI2020

Terrestrial Ecosystem Science (Flyer 2020)

A significant fraction of the carbon dioxide (CO 2 ) released to the atmosphere during energy production is taken up by terrestrial ecosystems. This carbon “sink” represents an important but poorly characterized buffer for offsetting the greenhouse gas effects of anthropogenic CO 2 emissions. Also unclear are the effects of related processes such as nutrient, water, and energy cycling—in addition to climate variability and change— on that uptake. Resolving the terrestrial biosphere’s role in the global carbon cycle is consequently a high priority for the Terrestrial Ecosystem Science (TES) program within the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER). Understanding the mechanisms and dynamics of ecosystem processes in the face of a changing climate is also essential for improving the representation of terrestrial ecosystems and climate feedbacks in Earth system models (ESMs). TES supports research to advance fundamental understanding of terrestrial ecosystems and their roles in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Root Characteristics Vary with Depth Across Four Lowland Seasonal Tropical Forests

Fine roots are key to ecosystem-scale nutrient, carbon (C), and water cycling, yet our understanding of fine root trait variation within and among tropical forests, one of Earth’s most C-rich ecosystems, is limited. We characterized root biomass, morphology, nutrient content, and arbuscular mycorrhizal fungal (AMF) colonization to 1.2 m depths across four distinct lowland Panamanian forests, and related root characteristics to soil C stocks. We hypothesized that: (H1) Fine root characteristics vary consistently with depth across seasonal tropical forests, with deeper roots exhibiting more exploratory traits, such as for deep water acquisition; (H2) fine root characteristics vary among tropical forests mainly in surface soils, where resource availability also varies. Here we found consistent variation with depth across the four forests, including decreased root biomass, root tissue density, and AMF, and increased specific root length. Among the forests, there was variation in some fine root characteristics, including greater surface root biomass and lower SRL in the wettest forest, and smaller fine root diameter in the driest forest. We also found that root characteristics were related to total soil C stocks, which were positively related to root biomass and negatively related to specific root length. These results indicate emergent properties of root variation with depth across tropical forests, and show site-scale variation in surface root characteristics. Future work could explore the flexibility in root characteristics under changing conditions such as drought.

13C NMR↗

DOE OSTI2024

Root biomass and traits across four lowland Panamanian forests from 0 - 1.2 m soil depths

Fine roots are key to ecosystem-scale nutrient, carbon (C), and water cycling, yet our understanding of fine root traits variation within and among tropical forests, one of Earth’s most C-rich ecosystems, is limited. We characterized root biomass, morphology, nutrient content, and arbuscular mycorrhizal fungal (AMF) colonization in 10 cm increments to 1.2 m depth across four distinct lowland Panamanian forests. The datasets provided include a .xlsx file for fine root characteristics across 10 cm increment depths to 1.2 m collected from late 2017 to 2018 across four different forests. Root characteristics include live fine root biomass, dead fine root biomass, coarse root biomass, specific root length, root diameter, root tissue density, specific root area, arbuscular mycorrhizal fungi colonization, root chemistry (e.g., organic chemistry), root %N, root %C, root C/N ratio, and root radiocarbon content. This .xlsx file contain four tabs with 1) Dataset; 2) Metadata with information about each column in the dataset; 3) The sampling methods summarized; 4) Sites information. We also provided csv files for each of these tabs. Additionally, a .kml file is provided with coordinates for all 32 plots included in the study across four forests (n = 8 plots per site/forest). This dataset serves as baseline data before a throughfall exclusion experiment, Panama Rainforest Changes with Experimental Drying (PARCHED), was implemented. No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

The circular nutrient economy of terrestrial ecosystems and the consequences for rock weathering

Earth’s biosphere is thought to exert a substantial influence on regolith evolution and chemical weathering rates. However, ecosystems are also highly efficient at retaining and recycling nutrients. Thus, when the ecological demand for rock-derived nutrients (e.g., P, Ca, K) exceeds the rates of regolith supply, ecological retention and recycling strategies can minimize nutrient limitations. To evaluate the balance between nutrient recycling and new nutrient input, we combined a plant model that drives growth according to foliar P levels with a weathering model that includes regolith rejuvenation via erosion and export via chemical weathering according to water flow, regolith thickness, mineral dissolution rates, secondary minerals, and nutrient storage in organic and mineral phases. We find that plant growth is strongly dependent on the total regolith nutrient inventory, resulting in a strong correlation between plant productivity and erosion. Increased water export or decreased regolith thickness diminish the total inventory of nutrient corresponding to lower rates of recycling and lower plant growth. In contrast, purported biogenic drivers of weathering, such as enhanced mineral dissolution, only support higher growth rates at high erosion rates. At erosion rates typical of the global land surface, more rapid mineral dissolution combined with enhanced formation of secondary minerals, depletes the inventory of mineral P, resulting in no benefit for plant growth. We also find that the increased chemical weathering export does not scale directly with plant growth. For example, accelerated mineral weathering does increase chemical weathering export but not potential plant growth. Conversely, thicker regolith is associated with a small increase in weathering export, but a large increase in potential plant growth. Collectively, when plant growth is coupled to regolith weathering our calculations suggest that plant productivity is not directly correlated with silicate weathering fluxes, and that biotic drivers of silicate weathering may only be effective at high erosion rates not typical at the Earth’s surface.

58 GEOSCIENCES↗

NASA NTRSDate not supplied

Merging Analytic Collaborative Frameworks with New Observing Strategies Toward a Digital Twin: Earth – Episodic Pulse Event Impacts on Ocean Carbon Cycle as an Example

Virtual representations of the Earth will allow us to address some of the most critical environmental issues of our time. Here, we show the first steps toward representation of riverine, estuarine, and coastal carbon processes to enable scenario driven “what-if” analyses of the carbon system and human footprint. Excess sediment and nutrient runoff from land-based human activities impact water quality and can pose serious threats to coastal and marine ecosystems. Episodic pulse events, such as extreme precipitation events, can increase the amount of nutrients entering estuaries and coastal regions, potentially leading to large phytoplankton blooms followed by anoxic conditions. Consequences of coastal runoff are predicted to increase with the higher intensity and frequency of extreme events. Beyond the threat to coastal ecosystems, recent findings suggest these episodic pulses might play a significant role for biological production influencing regional and global carbon fluxes and budgets. An improved understanding of these events through optimal, dynamic observing strategies will increase our knowledge of the land-ocean continuum and how regional events and nutrient fluxes affect the carbon cycle and ocean ecosystem. This conceptual framework enables focused science investigations by pairing data analytics and artificial intelligence tools (otherwise termed an Analytic Center Framework, ACF) with targeted measurement acquisition through distributed sensing and intelligent asset tasking (or New Observing Strategies, NOS). This NOS and ACF iterative approach acquires and integrates complementary and coincident satellite, in-situ and model data to build a more complete and in-depth picture of science phenomena. Specifically, Apache Science Data Analytic Platform (SDAP) is extended to incorporate relevant datasets for data access, harmonized analysis, and anomaly detection. When conditions are met for a likely pulse event, NASA’s D-SHIELD (Distributed Spacecraft with Heuristic Intelligence to Enable Logistical Decisions) tool is triggered to optimize asset overpass frequency and schedule observations for persistent monitoring. Targeted data is ingested by SDAP for enhanced investigation via iterative analysis until the trigger criteria is no longer met - steps toward a digital twin.

Laura Rogers↗

NASA NTRS1998

Automated pH Control of Nutrient Solution in a Hydroponic Plant Growth System

Over, the years, NASA has played an important role in providing to and the development of automated nutrient delivery and monitoring, systems for growing crops hydroponically for long term space missions. One example are the systems used in the Biomass Production Chamber (BPC) at Kennedy Space Center (KSC). The current KSC monitoring system is based on an engineering workstation using standard analog/digital input/output hardware and custom written software. The monitoring system uses completely separate sensors to provide a check of control sensor accuracy and has the ability to graphically display and store data form past experiment so that they are available for data analysis [Fortson, 1992]. In many cases, growing systems have not been fitted with the kind of automated control systems as used at KSC. The Center for Food and Environmental Systems for Human Exploration of Space (CFESH) located on the campus of Tuskegee University, has effectively grown sweetpotatoes and peanuts hydroponically for the past five years. However they have adjusted the pH electrical conductivity and volume of the hydroponic nutrient solution only manually at times when the solution was to be replenished or changed out according to its protocol (e.g. one-week, two-week, or two-day cycle). But the pH of the nutrient solution flowing through the channel is neither known nor controlled between the update, change out, or replenishment period. Thus, the pH of the nutrient solution is not held at an optimum level over the span of the plant's growth cycle. To solve this dilemma, an automated system for the control and data logging of pH data relative to sweetpotato production using the nutrient film technique (NFT) has been developed, This paper discusses a microprocessor-based system, which was designed to monitor, control, and record the pH of a nutrient solution used for growing sweetpotatoes using NFT.

Smith, B.↗

DOE OSTI2022

Simulation of anoxic lenses as exporters of reactivity in alluvial aquifer sediments

Sedimentary interfaces between contrasting hydrogeological facies in alluvial aquifers drive the development of biogeochemical interfaces that influence subsurface and surface water quality. Here, we calibrate a reactive transport model on a series of dual-domain column experiments, where centimeter-scale, low-permeability, organic-rich anoxic lenses are embedded in coarser-grained aquifer material. Simulations explicitly account for C, Fe, and S cycling at the interface between the lenses and the aquifer in water-saturated conditions. Our results highlight the role of fine-grained, organic-rich inclusions not only as sources or sinks for redox-sensitive species, but also as exporters of nutrients that stimulate downgradient biogeochemical cycling. By releasing large amounts of organic carbon into the surrounding aquifer, such lenses drive the development of proximal secondary reduction zones ("halos"), characterized by high microbial activity (e.g., sulfate reduction) and accumulation of reduced reaction products (e.g., iron sulfide). If similar secondary reduction zones develop within the hydraulically conductive domain of an aquifer, they would be highly susceptible to changes in hydrologic conditions, for instance oxygen pulses associated with seasonal snowmelt. Furthermore, our results also emphasize the limitations of relying solely on aqueous species measurements to inform reactivity in systems where fast redox cycling and/or sizeable particulate transport may limit the signature of reactivity in the dissolved phase.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change

Aims Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA. Methods N and P within plants, soils, and water are quantified based on field measurements. The resulting empirical dataset are then compared to modern-day, site-level simulations from the peatland land surface version of the Energy Exascale Earth System Model (ELM-SPRUCE).

Salmon, Verity G.↗

DOE OSTI2022

Modeling Global Carbon Costs of Plant Nitrogen and Phosphorus Acquisition

Abstract Most Earth system models (ESMs) do not explicitly represent the carbon (C) costs of plant nutrient acquisition, which leads to uncertainty in predictions of the current and future constraints to the land C sink. We integrate a plant productivity‐optimizing nitrogen (N) and phosphorus (P) acquisition model (fixation & uptake of nutrients, FUN) into the energy exascale Earth system (E3SM) land model (ELM). Global plant N and P uptake are dynamically simulated by ELM‐FUN based on the C costs of nutrient acquisition from mycorrhizae, direct root uptake, retranslocation from senescing leaves, and biological N fixation. We benchmarked ELM‐FUN with three classes of products: ILAMB, a remotely sensed nutrient limitation product, and CMIP6 models; we found significant improvements in C cycle variables, although the lack of more observed nutrient data prevents a comprehensive level of benchmarking. Overall, we found N and P co‐limitation for 80% of land area, with the remaining 20% being either predominantly N or P limited. Globally, the new model predicts that plants invested 4.1 Pg C yr −1 to acquire 841.8 Tg N yr −1 and 48.1 Tg P yr −1 (1994–2005), leading to significant downregulation of global net primary production (NPP). Global NPP is reduced by 20% with C costs of N and 50% with C costs of NP. Modeled and observed nutrient limitation agreement increases when N and P are considered together ( r 2 from 0.73 to 0.83).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Activity-based protein profiling of chitin catabolism

Microbial catabolism of chitin, a highly abundant component of polymeric organic matter worldwide, is a fundamental cog in the carbon and nitrogen cycles that govern CO2 emissions, nutrient dynamics in aquatic systems, and soil vitality. Despite this critical biogeochemical function, we have a poor understanding of the synergy between various microbial chitinases and key accessory enzymes involved in chitin catabolism. We designed and synthesized activity-based probes (ABPs) for profiling active chitinolytic enzymes by modifying the chitin derivatives N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. This approach allowed us to demonstrate the utility of these ABPs in determining the intricate synergy between chitinases and other glycoside hydrolases that microbes employ to catabolize chitin. The strategy can be used to gain molecular level insights that can be used to better understand microbial roles in soil C and N cycling in the face of a changing climate.

Zegeye, Elias↗

NASA NTRS2014

Far-Reaching Impacts of African Dust- A Calipso Perspective

African dust can transport across the tropical Atlantic and reach the Amazon basin, exerting far-reaching impacts on climate in downwind regions. The transported dust influences the surface-atmosphere interactions and cloud and precipitation processes through perturbing the surface radiative budget and atmospheric radiative heating and acting as cloud condensation nuclei and ice nuclei. Dust also influences biogeochemical cycle and climate through providing nutrients vital to the productivity of ocean biomass and Amazon forests. Assessing these climate impacts relies on an accurate quantification of dust transport and deposition. Currently model simulations show extremely large diversity, which calls for a need of observational constraints. Kaufman et al. (2005) estimated from MODIS aerosol measurements that about 144 Tg of dust is deposited into the tropical Atlantic and 50 Tg of dust into the Amazon in 2001. This estimated dust import to Amazon is a factor of 3-4 higher than other observations and models. However, several studies have argued that the oversimplified characterization of dust vertical profile in the study would have introduced large uncertainty and very likely a high bias. In this study we quantify the trans-Atlantic dust transport and deposition by using 7 years (2007-2013) observations from CALIPSO lidar. CALIPSO acquires high-resolution aerosol extinction and depolarization profiles in both cloud-free and above-cloud conditions. The unique CALIPSO capability of profiling aerosols above clouds offers an unprecedented opportunity of examining uncertainties associated with the use of MODIS clear-sky data. Dust is separated from other types of aerosols using the depolarization measurements. We estimated that on the basis of 7-year average, 118142 Tg of dust is deposited into the tropical Atlantic and 3860 Tg of dust into the Amazon basin. Substantial interannual variations are observed during the period, with the maximum to minimum ratio of about 1.6 and 2.5 for the deposition to the tropical Atlantic and Amazon, respectively. The MODIS-based estimates appear to fall within the range of CALIPSO-based estimates; and the difference between MODIS and CALIPSO estimates can be largely attributed to the interannual variability, which is corroborated by long-term surface dust concentration observations in the tropical Atlantic. Considering that CALIPSO generally tends to underestimate the aerosol loading, our estimate is likely to represent a low bound for the dust transport and deposition estimate. The finding suggests that models have substantial biases and considerable effort is needed to improve model simulations of dust cycle.

dust↗

DOE OSTI2025

Host Species–Microbiome Interactions Contribute to Sphagnum Moss Growth Acclimation to Warming

Sphagnum moss is the dominant plant genus in northern peatlands responsible for long-term carbon accumulation. Sphagnum hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome + environment) plays a key role in nutrient acquisition along with carbon cycling. Climate change can modify the Sphagnum -associated microbiome, resulting in enhanced host growth and thermal acclimation as previously shown in warming experiments. However, the extent of microbiome benefits to the host and the influence of host–microbe specificity on Sphagnum thermal acclimation remain unclear. Here, we extracted Sphagnum microbiomes from five donor species of four peatland warming experiments across a latitudinal gradient and applied those microbiomes to three germ-free Sphagnum species grown across a range of temperatures in the laboratory. Using this experimental system, we test if Sphagnum 's growth response to warming depends on the donor and/or recipient host species, and we determine how the microbiome's growth conditions in the field affect Sphagnum host growth across a range of temperatures in the laboratory. After 4 weeks, we found that the highest growth rate of recipient Sphagnum was observed in treatments of matched host–microbiome pairs, with rates approximately 50% and 250% higher in comparison to maximum growth rates of non-matched host–microbiome pairs and germ-free Sphagnum , respectively. We also found that the maximum growth rate of host–microbiome pairs was reached when treatment temperatures were close to the microbiome's native temperatures. Our study shows that Sphagnum's growth acclimation to temperature is partially controlled by its constituent microbiome. Strong Sphagnum host–microbiome species specificity indicates the existence of underlying, unknown physiological mechanisms that may drive Sphagnum 's ability to acclimatize to elevated temperatures. Together with rapid acclimation of the microbiome to warming, these specific microbiome–plant associations have the potential to enhance peatland resilience in the face of climate change.

acclimation↗