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29 results for “carbon assimilation”
Data associated with the publication "Interannual variability in the Australian carbon cycle over 2015-2019, based on assimilation of OCO-2 satellite data".
<p>This dataset refers to the publication "Interannual variability in the Australian carbon cycle over 2015-2019, based on assimilation of OCO-2 satellite data". https://doi.org/10.5194/acp-2022-15.</p> <p> </p>
Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system
<p>Diatoms serve as the major link between the marine carbon (C) and silicon (Si) biogeochemical cycles through their contributions to primary productivity and requirement for Si during cell wall formation. Although several culture-based studies have investigated the molecular response of diatoms to Si and nitrogen (N) starvation and replenishment, diatom silicon metabolism has been understudied in natural populations. A series of deckboard Si-amendment incubations were conducted using surface water collected in the California Upwelling Zone near Monterey Bay. Steep concentration gradients in macronutrients in the surface ocean coupled with substantial N and Si utilization led to communities with distinctly different macronutrient states: replete ('healthy'), low N ('N-stressed'), and low N and Si ('N- and Si-stressed'). Biogeochemical measurements of Si uptake combined with metatranscriptomic analysis of communities incubated with and without added Si were used to explore the underlying molecular response of diatom communities to different macronutrient availability. Metatranscriptomic analysis revealed that N-stressed communities exhibited dynamic shifts in N and C transcriptional patterns suggestive of compromised metabolism. Expression patterns in communities experiencing both N and Si stress imply that the presence of Si stress may partially ameliorate N stress and dampen the impact on organic matter metabolism. This response builds upon previous observations that the regulation of C and N metabolism is decoupled from Si limitation status, where Si stress allows the cell to optimize the metabolic machinery necessary to respond to episodic pulses of nutrients. Several well-characterized Si-metabolism associated genes were found to be poor molecular markers of Si physiological status; however, several uncharacterized Si-responsive genes were revealed to be potential indicators of Si stress or silica production.</p>
Dataset for the paper submitted for peer-review with the title "Quantifying heterotrophic bacteria parameters and dissolved organic carbon biodegradability through oxygen data assimilation in a river water quality model"
<p>The proposed dataset is related to the following article submitted for peer review:</p> <p>Hasanyar, M., Flipo, N., Romary, T., Wang, S. (2023), Quantifying heterotrophic bacteria parameters and dissolved organic carbon biodegradability through oxygen data assimilation in a river water quality model, UNDER PEER-REVIEW</p> <p>It consists of command files for the prose-pa0.74 software available here: https://gitlab.com/prose-pa/prose-pa </p> <p>To run the model :</p> <p>1. Compile prose-pa0.74</p> <p>2. Copy the executable in the current directory</p> <p>3. In a terminal launch</p> <p>> ./prose-pa0.74 simulation.COMM test.log</p> <p>The “simulation.COMM” holds the settings for the ProSe-PA simulation related to the paper mentioned in the front head of the current file. </p> <p>The information on different parameters of “simulation.COMM” are included in “bathymetrie”, “Cmds”, “Inflows”, “layers”, “meteo”, “o2_obs”, “param_bio”, “Reaches” and “Singularities” folders.</p> <p>The “bathymetrie” folder holds the geometric information of several cross-sections along the river. </p> <p>The Cmds folder holds the “simulation.COMM” file. </p> <p>The “Inflows” folder the information about the boundary condition inflows to the river such as discharge, concentration of organic carbon, etc.</p> <p>The layer folder holds data of the initial conditions of the model (Table 2 in the article).</p> <p>The “meteo” folder holds the meteorological information.</p> <p>The “o2_obs” folder holds the observed oxygen data needed to do data assimilation. </p> <p>The “param_bio” folder holds information on the physiology of bacteria, phytoplankton, and other model species.</p> <p>The “Reaches” folder holds information about river reaches and their manning coefficient. </p> <p>The “param_range” file holds the variation range of model parameters considered in data assimilation together with their perturbation percentage.</p> <p>The output files are written in $HOME/Outputs folder. It is possible to change it directly in simulation.COMM, last entry “Output_folder”.</p>
Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system
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Grazing-N addition interactions drive soil carbon priming and balance via bacterial assimilation in a meadow steppe
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Assessing the ocean carbon sink: Assimilation of temperature and salinity into a global ocean biogeochemistry model
<p>Data underlying figures in manuscript draft.</p>
Data for: Drought impairs herbivore-induced volatiles, but not through constraints on newly assimilated carbon
<p>Volatile terpenes serve multiple biological roles including tree resistance against herbivores. The increased frequency and severity of drought stress observed in forests across the globe may hinder trees from producing defense-related volatiles in response to biotic stress. To assess how drought-induced physiological stress alters volatile emissions alone and in combination with a biotic challenge, we monitored pre-dawn water potential, gas exchange, needle terpene concentrations, and terpene volatile emissions of ponderosa pine (<em>Pinus ponderosa</em>) saplings during three periods of drought and in response to simulated herbivory via methyl jasmonate application. Although three-, six-, and seven-week drought treatments reduced net photosynthetic rates by 20%, 89%, and 105%, respectively, the magnitude of volatile fluxes remained generally resistant to drought. Herbivore-induced emissions, however, exhibited threshold-like behavior; saplings were unable to induce emissions above constitutive levels when pre-dawn water potentials were below the approximate zero-assimilation point. By comparing compositional shifts in emissions to needle terpene concentrations, we found evidence that drought effects on constitutive and herbivore-induced volatile flux and composition are primarily via constraints on the <em>de novo</em> fraction, suggesting that reduced photosynthesis during drought limits the carbon substrate available for <em>de novo</em> volatile synthesis. However, results from a subsequent <sup>13</sup>CO<sub>2</sub> pulse-chase labeling experiment then confirmed that both constitutive (<3% labeled) and herbivore-induced (<8% labeled) <em>de novo</em> emissions from ponderosa pine are synthesized predominantly from older carbon sources with little contribution from new photosynthates. Taken together, we provide evidence that in ponderosa pine, drought does not constrain herbivore-induced <em>de novo</em> emissions through substrate limitation via reduced photosynthesis, but rather, through more sophisticated molecular and/or biophysical mechanisms that manifest as saplings reach the zero-assimilation point. These results highlight the importance of considering drought severity when assessing impacts on the herbivore-induced response and suggest that drought-altered volatile metabolism constrains induced emissions once a physiological threshold is surpassed.</p>
Data for: Drought impairs herbivore-induced volatiles, but not through constraints on newly assimilated carbon
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The response of carbon assimilation and storage to long-term drought in tropical trees is dependent on light availability
<p>1) Whether tropical trees acclimate to long-term drought stress remains unclear. This uncertainty is amplified if drought stress is accompanied by changes in other drivers such as the increases in canopy light exposure that might be induced by tree mortality or other disturbances.</p> <p>2) Photosynthetic capacity, leaf respiration, non-structural carbohydrate (NSC) storage and stomatal conductance were measured on 162 trees at the world's longest running (15 yr) tropical forest drought experiment. We test whether surviving trees have altered strategies for carbon storage and carbon use in the drier and elevated light conditions present following drought-related tree mortality.</p> <p>3) Relative to control trees, the surviving trees experiencing the drought treatment showed functional responses including: i) moderately reduced photosynthetic capacity; ii) increased total leaf NSC; and iii) a switch from starch to soluble sugars as the main store of branch NSC. This contrasts with earlier findings at this experiment of no change in photosynthetic capacity or NSC storage. The changes detected here only occurred in the subset of drought-stressed trees with canopies exposed to high radiation and were absent in trees with less-exposed canopies, and also in the community average. In contrast to previous results acquired through less intensive species sampling from this experiment, we also observe no species-average drought-induced change in leaf respiration.</p> <p>4) Our results suggest that long-term responses to drought stress are strongly influenced by a tree's full-canopy light environment and therefore that disturbance-induced changes in stand density and dynamics are likely to substantially impact tropical forest responses to climate change. We also demonstrate that, while challenging, intensive sampling is essential in tropical forests to avoid sampling biases caused by limited taxonomic coverage.</p>
Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis
<p>The upside-down jellyfish <i>Cassiopea</i> engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. In contrast to most other symbiotic cnidarians, algal endosymbionts in <i>Cassiopea</i> are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in <i>Cassiopea</i> remains unknown. By combining isotopic labelling experiments with correlated SEM and NanoSIMS imaging, we quantified the anabolic assimilation of inorganic carbon and nitrogen at the subcellular level in juvenile <i>Cassiopea</i> medusae bell tissue. Amoebocytes were clustered near the sub-umbrella epidermis and facilitated efficient assimilation of inorganic nutrients. Photosynthetically-fixed carbon was efficiently translocated between endosymbionts, amoebocytes and host epidermis at rates similar to or exceeding those observed in corals. The <i>Cassiopea</i> holobionts efficiently assimilated ammonium, while no nitrate assimilation was detected, possibly reflecting adaptation to highly dynamic environmental conditions of their natural habitat. The motile amoebocytes allow <i>Cassiopea</i> medusae to distribute their endosymbiont population to optimize access to light and nutrients, and transport nutrition between tissue areas. Amoebocytes thus play a vital role for assimilation and translocation of nutrients in <i>Cassiopea</i>, providing an interesting new model for studies of metabolic interactions in photosymbiotic marine organisms.</p>
Data from: Novel reverse radioisotope labelling experiment reveals carbon assimilation of marine calcifiers under ocean acidification conditions
<p><span>1. Ocean acidification by anthropogenic carbon dioxide emissions is projected to depress metabolic and physiological activity in marine calcifiers. To evaluate the sensitivity of marine organisms against ocean acidification, the assimilation of nutrients into carbonate shells and soft tissues must be examined.</span></p> <p><span>2. We designed a novel experimental protocol, reverse radioisotope labelling, to trace partitioning of nutrients within a single bivalve species under ocean acidification conditions. Injecting CO<sub>2</sub> gas, free from radiocarbon, can provide a large contrast between carbon dissolved in the water and the one assimilated from atmosphere. By culturing modern aquifer organisms in acidified seawater, we were able to determine differences in the relative contributions of the end members, dissolved inorganic carbon (DIC) in seawater and metabolic CO<sub>2</sub>, to shell carbonate and soft tissues. </span></p> <p><span>3. Under all pCO<sub>2</sub> conditions (463, 653, 872, 1137, and 1337 μatm), radiocarbon (Δ<sup>14</sup>C) values of the bivalve (<i>Scapharca broughtonii</i>) shell were significantly correlated with seawater DIC values; therefore, shell carbonate was derived principally from seawater DIC. The Δ<sup>14</sup>C results together with stable carbon isotope (δ<sup>13</sup>C) data suggest that in <i>S. broughtonii</i> shell δ<sup>13</sup>C may reflect the kinetics of isotopic equilibration as well as end-member contributions; thus, care must be taken when analyzing end-member contributions by a previous method using δ<sup>13</sup>C. The insensitivity of <i>S. broughtonii</i> to perturbations in pCO<sub>2</sub> up to at least 1337 µatm indicates that this species can withstand ocean acidification.</span></p> <p><span>4. Usage of radioisotope to dope for tracer experiments requires strict rules to conduct any operations. Yet, reverse radioisotope labeling proposing in this study has a large advantage and is a powerful tool to understanding physiology of aquifer organisms that can be applicable to various organisms and culture experiments, such as temperature, salinity, and acidification experiments, to improve understanding of the proportions of nutrients taken in by marine organisms under changing environments.</span></p>
Code produced by the study "Advantages of assimilating multi-spectral satellite retrievals of atmospheric composition: A demonstration using MOPITT carbon monoxide products".
<p>This is the code used in the manuscript entitled "Advantages of assimilating multi-spectral satellite retrievals of atmospheric composition: A demonstration using MOPITT carbon monoxide products".</p>
Convergence in simulating global soil organic carbon by structurally different models after data assimilation
<p>This is the data for results shown in the article accepted by Global Change Biology: Convergence in simulating global soil organic carbon by structurally different models after data assimilation</p>
18S/16S raw amplicon data for Martínez Martínez et al. : "Coastal bacteria and protists assimilate viral carbon and nitrogen"
<p>Raw amplicon (18S and 16S rRNA) sequencing data (.fastq.gz) for Martínez Martínez <em>et al.</em> : "Coastal bacteria and protists assimilate viral carbon and nitrogen". Each sample has forward (*_1.fastq.gz) and reverse (*_2.fastq.gz) reads as separate files. </p>
Data from: Carbon assimilation and habitat segregation in resurrection plants: a comparison between desiccation- and non-desiccation-tolerant species of Neotropical Velloziaceae (Pandanales)
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Data from: Novel reverse radioisotope labelling experiment reveals carbon assimilation of marine calcifiers under ocean acidification conditions
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The response of carbon assimilation and storage to long-term drought in tropical trees is dependent on light availability
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Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis
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Pond excavation reduces coastal wetland carbon dioxide assimilation
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MERRA-2 tavgM_2d_chm_Nx: 2d,Monthly mean,Time-Averaged,Single-Level,Assimilation,Carbon Monoxide and Ozone Diagnostics 0.625 x 0.5 degree V5.12.4 (M2TMNXCHM) at GES DISC
M2TMNXCHM (or tavgM_2d_chm_Nx) is a time-averaged 2-dimensional monthly mean data collection in Modern-Era Retrospective analysis for Research and Applications version 2 (MERRA-2). This collection consists of assimilated carbon monoxide and ozone diagnostics, such as properties of carbon monoxide (column burden, emission, chemical production, and surface concentration), and total column ozone. The collection also includes variance of certain parameters. MERRA-2 is the latest version of global atmospheric reanalysis for the satellite era produced by NASA Global Modeling and Assimilation Office (GMAO) using the Goddard Earth Observing System Model (GEOS) version 5.12.4. The dataset covers the period of 1980-present with the latency of ~3 weeks after the end of a month. Data Reprocessing: Please check “Records of MERRA-2 Data Reprocessing and Service Changes” linked from the “Documentation” tab on this page. Note that a reprocessed data filename is different from the original file.MERRA-2 Mailing List: Sign up to receive information on reprocessing of data, changing of tools and services, as well as data announcements from GMAO. Contact the GES DISC Help Desk (gsfc-dl-help-disc@mail.nasa.gov) to be added to the list.Questions: If you have a question, please read "MERRA-2 File Specification Document", “MERRA-2 Data Access – Quick Start Guide”, and FAQs linked from the ”Documentation” tab on this page. If that does not answer your question, you may post your question to the NASA Earthdata Forum (forum.earthdata.nasa.gov) or email the GES DISC Help Desk (gsfc-dl-help-disc@mail.nasa.gov).
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