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At least 415 records · Page 23

Electron transport across the cell envelope via multiheme c -type cytochromes in Geobacter sulfurreducens

Extracellular electron transfer (EET) enables certain microorganisms to respire using soluble and insoluble extracellular electron acceptors by transporting electrons across the cell envelope. Among these, G. sulfurreducens serves as a model organism for understanding direct EET pathways, where multiheme c-type cytochromes mediate electron transport from intracellular redox carriers to extracellular acceptors such as Fe(III) oxides and electrodes. This review focuses on heme-dependent electron transfer in Geobacter sulfurreducens, detailing the roles of inner membrane cytochromes, periplasmic carriers, outer membrane conduits, and recently characterized extracellular nanowires formed by polymerized multiheme c-type cytochromes, including OmcS, OmcE, and OmcZ. We examine the state of understanding of their physiological function, their structural features, expression patterns, and essentiality under various respiratory conditions. These insights advance our understanding of microbial anaerobic respiration and have implications for biogeochemical cycling, bioenergy generation, and bioremediation. The molecular architecture, assembly mechanisms, and secretion pathways of multiheme c-type cytochrome nanowires remain active areas of investigation, offering promising directions for future research and biotechnological innovation in engineered microbial systems.

Chemistry↗

The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest

Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.

54 ENVIRONMENTAL SCIENCES↗

Extracellular electron uptake from a cathode by the lactic acid bacterium Lactiplantibacillus plantarum

A subset of microorganisms that perform respiration can endogenously utilize insoluble electron donors, such as Fe(II) or a cathode, in a process called extracellular electron transfer (EET). However, it is unknown whether similar endogenous EET can be performed by primarily fermentative species like lactic acid bacteria. We report for the first time electron uptake from a cathode by Lactiplantibacillus plantarum, a primarily fermentative bacteria found in the gut of mammals and in fermented foods. L. plantarum consumed electrons from a cathode and coupled this oxidation to the reduction of both an endogenous organic (pyruvate) and an exogenous inorganic electron acceptor (nitrate). This electron uptake from a cathode reroutes glucose fermentation toward lactate degradation and provides cells with a higher viability upon sugar exhaustion. Moreover, the associated genes and cofactors indicate that this activity is mechanistically different from that one employed by lactic acid bacteria to reduce an anode and to perform respiration. Our results expand our knowledge of the diversity of electroactive species and of the metabolic and bioenergetic strategies used by lactic acid bacteria.

biocathode↗

Coupled Biotic-Abiotic Processes Control Biogeochemical Cycling of Dissolved Organic Matter in the Columbia River Hyporheic Zone

A critical component of assessing the impacts of climate change on watershed ecosystems involves understanding the role that dissolved organic matter (DOM) plays in driving whole ecosystem metabolism. The hyporheic zone—a biogeochemical control point where ground water and river water mix—is characterized by high DOM turnover and microbial activity and is responsible for a large fraction of lotic respiration. Yet, the dynamic nature of this ecotone provides a challenging but important environment to parse out different DOM influences on watershed function and net carbon and nutrient fluxes. We used high-resolution Fourier-transform ion cyclotron resonance mass spectrometry to provide a detailed molecular characterization of DOM and its transformation pathways in the Columbia river watershed. Samples were collected from ground water (adjacent unconfined aquifer underlying the Hanford 300 Area), Columbia river water, and its hyporheic zone. The hyporheic zone was sampled at five locations to capture spatial heterogeneity within the hyporheic zone. Our results revealed that abiotic transformation pathways (e.g., carboxylation), potentially driven by abiotic factors such as sunlight, in both the ground water and river water are likely influencing DOM availability to the hyporheic zone, which could then be coupled with biotic processes for enhanced microbial activity. The ground water profile revealed high rates of N and S transformations via abiotic reactions. The river profile showed enhanced abiotic photodegradation of lignin-like molecules that subsequently entered the hyporheic zone as low molecular weight, more degraded compounds. While the compounds in river water were in part bio-unavailable, some were further shown to increase rates of microbial respiration. Together, river water and ground water enhance microbial activity within the hyporheic zone, regardless of river stage, as shown by elevated putative amino-acid transformations and the abundance of amino-sugar and protein-like compounds. This enhanced microbial activity is further dependent on the composition of ground water and river water inputs. Our results further suggest that abiotic controls on DOM should be incorporated into predictive modeling for understanding watershed dynamics, especially as climate variability and land use could affect light exposure and changes to ground water essential elements, both shown to impact the Columbia river hyporheic zone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Effect of Rapid Development on Soil CO2 Efflux in a Cellulosic Biofuel Stand

As awareness of climate change increases, the need for carbon neutral fuel sources is growing. Lignocellulosic biofuel derived from pine trees has been suggested as one potential energy source; however, it requires more research before its efficacy for climate change mitigation can be determined. Due to the large share of forest carbon held in soils and the extensive area of pine plantations in the southeast U.S., a better understanding of plantation soil carbon dynamics is critical for biofuel carbon accounting. This study evaluated the effects of canopy development and productivity on soil CO2 efflux, a proxy for soil respiration (Rs), in an intensively managed loblolly pine (Pinus taeda) stand over a period from May 2015 to December 2019. We found that leaf area index (LAI) and gross ecosystem production (GEP), as well as meteorological variables, had significant effects on Rs, but that both overall Rs and soil carbon pools did not increase over the course of the study. We thus hypothesize that GEP and LAI had intra-annual effects on Rs, and that the lack of change in Rs is the result of an increase in autotrophic respiration (Ra) that offset a decrease in decomposition of the previous stand’s organic matter.

09 BIOMASS FUELS↗

Filtration Performance of Layering Masks and Face Coverings and the Reusability of Cotton Masks after Repeated Washing and Drying

In this study, filtration efficiency of different respirators, face masks, and a 2-ply cotton handkerchief bandana was compared for particles in the size range of 60 nm-4 um under a "perfect fit" condition. The filtration efficiency at the most penetrating particle size of 0.3 um on average ranged from 83-99% for N95 and KN95 respirators, 42-88% for surgical masks, 16-23% for cloth masks, and 9% for bandana. We also investigated the effects of using double surgical masks or layering a cloth mask over various surgical masks in terms of their filtration characteristics. In most of these combinations, the filtration efficiency improved by ~25% for particles 0.3-1 um in diameter without any substantial change in the filter quality factor when compared to the highest of the individual mask results. To investigate the reusability of cotton cloth masks, 2-layer cotton fabric sample coupons were machine washed and dried for 52 cycles leading to an increase in inhalation resistance (~20 Pa) without affecting size-resolved filtration efficiency. Scanning electron microscopy revealed that washing and drying led to the gradual deconstruction of cotton fibers at the scale of several micrometers to hundreds of nanometers in the form of delamination of the fiber wall and fibrillation of the nanofiber constituents. Results indicate that cloth masks may be layered over surgical masks for additional benefits, and that cloth masks made out of cotton fabric can be washed and reused numerous times without a significant loss in filtration efficiency.

99 GENERAL AND MISCELLANEOUS↗

Disturbance triggers non-linear microbe–environment feedbacks

Abstract. Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting–drying transitions. Our refined framework includes relationships between cumulative properties of a microbial community (e.g., microbial membership, community assembly properties, and biogeochemical rates), environmental features (e.g., organic matter thermodynamics), and emergent ecosystem function. Our primary aim was to evaluate the hypothesized relationships that comprise the conceptual framework and contrast outcomes from the whole and putatively active bacterial and archaeal communities. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community – but not the whole bacterial and archaeal community – responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter (OM) became less favorable for oxidation (an environmental component), and respiration decreased (a microbial process). While these responses were step functions of desiccation, we found that in deterministically assembled active communities, respiration was lower and thermodynamic properties of OM were less favorable. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance and mediated by thermodynamics and that cause the impacts of disturbance to be dependent on the history of disturbance.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a plant carbon–nitrogen interface coupling framework in a coupled biophysical-ecosystem–biogeochemical model (SSiB5/TRIFFID/DayCent-SOM v1.0)

Plant and microbial nitrogen (N) dynamics and N availability regulate the photosynthetic capacity and capture, allocation, and turnover of carbon (C) in terrestrial ecosystems. Studies have shown that a wide divergence in representations of N dynamics in land surface models leads to large uncertainties in the biogeochemical cycle of terrestrial ecosystems and then in climate simulations as well as the projections of future trajectories. In this study, a plant C–N interface coupling framework is developed and implemented in a coupled biophysical-ecosystem–biogeochemical model (SSiB5/TRIFFID/DayCent-SOM v1.0). The main concept and structure of this plant C–N framework and its coupling strategy are presented in this study. This framework takes more plant N-related processes into account. The dynamic ratio (CNR) for each plant functional type (PFT) is introduced to consider plant resistance and adaptation to N availability to better evaluate the plant response to N limitation. Furthermore, when available N is less than plant N demand, plant growth is restricted by a lower maximum carboxylation capacity of RuBisCO (V c,max ), reducing gross primary productivity (GPP). In addition, a module for plant respiration rates is introduced by adjusting the respiration with different rates for different plant components at the same N concentration. Since insufficient N can potentially give rise to lags in plant phenology, the phenological scheme is also adjusted in response to N availability. All these considerations ensure a more comprehensive incorporation of N regulations to plant growth and C cycling. This new approach has been tested systematically to assess the effects of this coupling framework and N limitation on the terrestrial carbon cycle. Long-term measurements from flux tower sites with different PFTs and global satellite-derived products are employed as references to assess these effects. The results show a general improvement with the new plant C–N coupling framework, with more consistent emergent properties, such as GPP and leaf area index (LAI), compared to the observations. The main improvements occur in tropical Africa and boreal regions, accompanied by a decrease in the bias in global GPP and LAI by 16.3 % and 27.1 %, respectively.

54 ENVIRONMENTAL SCIENCES↗

Rapidly changing high-latitude seasonality: Implications for the 21st century carbon cycle in Alaska: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "Rapidly changing high-latitude seasonality: Implications for the 21st century carbon cycle in Alaska" DOI: 10.1088/1748-9326/ac4362.The dataset contains "ecosys" model outputs reported in Shirley et al. (2022) that explored how climate warming will shift carbon cycle seasonality in Alaska. The study used analysis of seasonal dynamics to support the prediction that high-latitude ecosystems are carbon sinks and will continue to accumulate carbon throughout the century. The study predicts surprisingly large increases in spring net carbon uptake that result in larger net carbon uptake in spring than in summer by year 2100. Included as *.nc files are modeled daily net ecosystem exchange (NEE), net primary productivity (NPP), heterotrophic respiration (Rh), autotrophic respiration (Ra), gross primary productivity (GPP), and plant nitrogen uptake. The output is provided (1) at 25 km resolution across Alaska; (2) for years 2010 through 2100. Scripts to generate publication figures included as text files (*.m) from MATLAB. A user guide included as *.pdf.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Panama Rainforest Changes with Experimental Drought (PaRChED): Initial Effects of Partial Throughfall Exclusion on Soil Dynamics in Lowland Forests Across Variation in Rainfall and Soil Fertility

Changes in rainfall are predicted across tropical regions, with effects on nutrient, water, and carbon cycling. This chapter summarizes results from the first two years of a throughfall exclusion experiment in four lowland Panamanian forests that span a 1,000-mm change in rainfall and variation in soil fertility. Soil respiration (i.e., soil carbon dioxide [CO2 ] flux) declined with throughfall exclusion, with a site*season interaction, and the radiocarbon age of respired carbon was older in exclusion versus control plots. The decline in soil CO2 flux could be related to reduced fine root production and soil microbial biomass. Microbial community composition also changed with throughfall exclusion in infertile soils, and soil nutrients accumulated more in exclusion versus control plots during the dry season. The net effects on soil carbon storage will depend on the relative strengths of these effects over time. Continued research could improve predictions of tropical forest-climate feedbacks with changes in precipitation.

54 ENVIRONMENTAL SCIENCES↗

BSEC VPRM 10m Hourly Biogenic Fluxes in Baltimore (2021)

Model outputs from the Vegetation Photosynthesis and Respiration Model (VPRM: version from Horne et al. in prep). Model remote sensing inputs come from Sential 2-derived EVI and LSWI. Model meteorological inputs for two-meter air temperature and shortwave incoming come from the BSEC WRF 2021 Control Run (Foust, W. 2023). Plant functional Types (PFTs) are spatially classified using the Chesapeake Bay Program 2018 land use land cover product. The final biogenic flux (µmol CO2 m^-2 s^-1) outputs of NEE, RESP, and GEE are a weighted average based on the portion of PFTs within the cell. Individual PFT outputs are saved inside PFT directories (e.g., Crops, Grass, etc.) inside the specific month directory. Model outputs are denoted as a negative flux into the land system (i.e., photosynthesis) and a positive flux as a net release into the overlying atmosphere. Respiration (RESP) fluxes are positive and combine heterotrophic (only soil) and autotrophic sources. Gross ecosystem exchange (GEE) is a negative flux driven by only photosynthetic activity from vegetation, and the Net ecosystem exchange (NEE) is the sum of the two (i.e., NEE=RESP+GEE). Data Characteristics Spatial Resolution: 10m Temporal Resolution: Hourly File Format: VPRM_ _BSEC. .tif (Hour is in UTC) For more information on the model results, please email Jason Horne (jph6488@psu.edu). References: Foust, W. (2023). BSEC WRF 2021 Control Run Output (v0.1.0) [Data set]. MSD-LIVE Data Repository. https://data.msdlive.org/records/m0e6m-vvq17

Baltimore↗

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism

Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD + /NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Data for "Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding"

This dataset contains data used for the paper "Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding". The Related References field will be updated with a full citation when available.Climate change is intensifying the global water cycle, with increased frequency of drought and flood. Water is an important driver of soil carbon dynamics, and it is crucial to understand how moisture disturbances will affect carbon availability and fluxes in soils. Here we investigate the role of water in substrate-microbe connectivity and soil carbon cycling under extreme moisture conditions. We collected soils from Alaska, Florida, and Washington USA, and incubated them under Drought and Flood conditions. Drought had a stronger effect on soil respiration, pore-water carbon, and microbial community composition than flooding. Soil response was not consistent across sites, and was influenced by site-level pedological and environmental factors. Soil texture and porosity can influence microbial access to substrates through the pore network, driving the chemical response. Further, the microbial communities are adapted to the historic stress conditions at their sites and therefore show site-specific responses to drought and flood.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv and .txt format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/kaizadp/TES_3Soils_2021 (DOI: 10.5281/zenodo.4792655).

54 ENVIRONMENTAL SCIENCES↗

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗

Large emissions of CO2 and CH4 due to active-layer warming in Arctic tundra: Supporting Data

Climate warming may accelerate decomposition of Arctic soil carbon, but few controlled experiments have manipulated the entire active layer. To determine surface-atmosphere fluxes of carbon dioxide and methane under anticipated end-of-century warming, we used heating rods to warm soil (by 3.8 °C) to the depth of permafrost in polygonal tundra over two growing seasons at the Barrow Environmental Observatory in Utqiaġvik (formerly Barrow), Alaska. This data product includes supporting data for the companion paper entitled "Large emissions of CO2 and CH4 due to active-layer warming in Arctic tundra", published in Nature Communications by Torn et al. This data package contains seven data files in csv format with corresponding data dictionaries and file-level metadata, describing vegetation biomass dry weight ("Utqiagvik_Vegetation_Biomass_2014.csv"), radiocarbon measurements of respired carbon dioxide ("Utqiagvik_Radiocarbon_2015_2016.csv"), surface-atmosphere fluxes of carbon dioxide and methane and associated soil temperature ("Utqiagvik_Fluxes_Temperature_2015_2016.csv"), and soil temperature measurements averaged every 15-min and 1-hr for 2015 and 2016 ("Utqiagvik_Temperature_15min_2015.csv", "Utqiagvik_Temperature_15min_2016.csv", "Utqiagvik_Temperature_1hr_2015.csv", "Utqiagvik_Temperature_1hr_2016.csv"). There are no specific software requirements to use these data. UIC Science Native Corporation facilitated our scientific research on the Barrow Environmental Observatory, which is Iñupiat land.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

How initial conditions-, structural-, and parameter-based model uncertainty interact and influence predictions in permafrost ecosystems: Modeling Archive

This dataset contains model output and input data, as well as source code examples for the Terrestrial Ecosystem Model with the Dynamic Vegetation Model and Dynamic Organic Soil (DVM-DOS-TEM) for the field sites Imnavait creek and the Bonanza creek Long Term Ecological Research Network (LTER). The data covers simulations from the last glacial maximum (LGM) until 2100 for a selection of paleo scenarios, setting the mean temperature of the LGM up to 10°C lower than pre-industrial conditions. The model structure was modulated to represent various model versions, and this dataset contains the relevant changes in the source code. The raw output data, the processed statistical data, the setup and processing scripts as well as parameter value distribution files from a parameter sensitivity analysis are included as well. Model outputs include active layer depth, organic soil carbon, soil layer depths, gross primary productivity (GPP) with and without nitrogen limitation, net primary productivity (NPP), soil liquid water content, heterotrophic, maintenance, and growth respiration, soil temperature, and vegetation carbon (*.nc files). The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research.Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

54 ENVIRONMENTAL SCIENCES↗

Responses of Drying-rewetting (Transient Soil Moisture) and Steady State Soil Moisture Incubation on Soil Organic Carbon Dynamics in Three US Soils, 2017

This data set contains measurements of soil characteristics (aggregate size distribution and mean size, total aggregate associated carbon, extractable organic C, and microbial biomass C), microbial respiration, and soil metabolite concentrations from a transient and steady soil moisture incubation experiment using soils of different textures (sandy, loamy, and clayey). The study investigated mechanisms driving the Birch effect (increased carbon mineralization pulses with wetting following a drying period) in differing soil textures. Three different soils of distinctly different textures were collected from 0-15cm depth in Georgia (sandy, 2017-05-01), Missouri (loamy, 2017-06-14), and Texas (clayey, December 2017). Soils were incubated for 140 days with destructive harvests done on days 1, 29, 33, 56, 112, 116, and 140 in transient soil moisture incubation and on days 1, 33, 116, and 140 in steady state soil moisture incubation. This dataset contains six data files in comma separate (.csv) format. Additional metadata are provided: six data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

1-Methyladenosine concentration↗

A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

59 BASIC BIOLOGICAL SCIENCES↗