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opencc-zeroFeb 2024View details →

Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system

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.

opencc-by-4.0Nov 2024View details →

Fluxes of particulate organic carbon, nitrogen and mass from the Station M abyssal time series in the northeast Pacific, (1989-2022)

Overview: This dataset provides particulate fluxes to Station M in the NE Pacific, from 1989 to 2022.  Samples were collected with McLane Parflux sequencing sediment traps deployed on moorings. Data are provided for traps 50 m above bottom and 600 m above bottom, with deployment bottom depths ranging from approximately 3900 m to 4500 m.  Gaps reflect lapses in funding, weather disruptions, clogs in sediment traps, or the occasional spilled sample.  Where available, GPS coordinates and ship-recorded bottom depth at deployment location are given. Where these are not available, approximate location and depth are given and noted.   Methods: This program used McLane Parflux sequencing sediment traps. Attempts to avoid sediment trap clogs, which increasingly became an issue, included replacing manufacture-supplied plastic funnels with Teflon-coated fiberglass funnels (October 2014), doubling the size of sediment trap collection cups (from 250 ML to 500 ML starting in October 2014), and adding a function that periodically agitated material in the funnel constriction (starting in June 2015). Before deployment, sediment trap cups were acid-washed and filled with a preservative (mercuric chloride from 1989 to 2009, 3%–5% buffered formalin from 2009 to 2022). Formalin brine recipe followed that recommended by McLane. Following sample recovery, zooplankton that many have swum into the traps were identified visually and manually removed (KLS). Samples were returned to the lab, freeze-dried, and weighed to calculate mass flux. The freeze-dried sample was analyzed for inorganic carbon content using a coulometer (UIC), and total carbon, hydrogen, and nitrogen using an elemental analyzer (Perkin-Elmer or Exeter Analytical, University of California Santa Barbara Marine Science Institute Analytical Laboratory). Dry mass was corrected for salt content using a AgNO3 titration (<a href="https://www.sciencedirect.com/science/article/pii/S0967064519302395#bib99">Strickland and Parsons, 1972</a>). Data [mass flux, particulate organic carbon flux, and total nitrogen flux] from the 600 mab trap were used. Gaps in this data set were infilled using the linear relationship between data from the 600 mab and 50 mab traps. Full details of these methods can be found in Baldwin et al. (<a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2022GL101018#grl65243-bib-0002">1998</a>). Data provided have been quality-controlled, and only usable data are included here.   References: Baldwin, R. J., Glatts, R. C., & Smith Jr, K. L. (1998). Particulate matter fluxes into the benthic boundary layer at a long time-series station in the abyssal NE Pacific: composition and fluxes. Deep Sea Research Part II: Topical Studies in Oceanography, 45(4-5), 643-665. Strickland, J.D.H., Parsons, T.R. (1972) A Practical Handbook of Seawater Analysis. Fisheries Research Board of Canada, Ottawa  Smith, K. L., Huffard, C. L., & Ruhl, H. A. (2020). Thirty-year time series study at a station in the abyssal NE Pacific: An introduction. Deep Sea Research Part II: Topical Studies in Oceanography, 173, 104764.

opencc-zeroApr 2022View details →

Limited legacy effects of extreme multi-year drought on carbon and nitrogen cycling in a mesic grassland

The intensification of drought throughout the US Great Plains has the potential to have large impacts on grassland functioning, as has been shown with dramatic losses of plant productivity annually. Yet, we have a poor understanding of how grassland functioning responds after drought ends. This study examined how belowground nutrient cycling responds after drought and whether legacy effects persist post-drought. We assessed the two-year recovery of nutrient cycling processes following a four-year experimental drought in a mesic grassland by comparing two different growing season drought treatments - chronic (each rainfall event reduced by 66%) and intense (all rain eliminated until 45% of annual rainfall was achieved) – to the control (ambient precipitation) treatment. At the beginning of the first growing season post-drought, we found that in situ soil CO2 efflux and laboratory-based soil microbial respiration were reduced by 42% and 22% respectively in the intense drought treatment compared to the control, but both measures had recovered by mid-season (July) and remained similar to the control treatment in the second post-drought year. We also found that extractable soil ammonium and total inorganic N were elevated throughout the growing season in the first year after drought in the intense treatment. However, these differences in inorganic N pools did not persist during the growing season of the second year post-drought. The remaining measures of C and N cycling in both drought treatments showed no post-drought treatment effects. Thus, although we observed short-term legacy effects following the intense drought, C and N cycling returned to levels comparable to non-droughted grassland within a single growing season regardless of whether the drought was intense or chronic in nature. Overall, these results suggest that key aspects of C and N cycling in mesic tallgrass prairie do not exhibit persistent legacies from four years of experimentally-induced drought.

opencc-by-4.0Oct 2022View details →

Data from: Sedimentary organic carbon and nitrogen sequestration across a vertical gradient on a temperate wetland seascape including salt marshes, seagrass meadows and rhizophytic macroalgae beds

Dataset    Coastal wetlands are key in regulating coastal carbon and nitrogen dynamics and contribute significantly to climate change mitigation and anthropogenic nutrient reduction. We investigated organic carbon (OC) and total nitrogen (TN) stocks and burial rates at four adjacent vegetated coastal habitats across the seascape elevation gradient of Cádiz Bay (South Spain), including one species of salt marsh, two of seagrasses, and a macroalgae. OC and TN stocks in the upper 1 m sediment layer were higher at the subtidal seagrass Cymodocea nodosa (72.3 Mg OC ha-1, 8.6 Mg TN ha-1) followed by the upper intertidal salt marsh Sporobolus maritimus (66.5 Mg OC ha-1, 5.9 Mg TN ha-1), the subtidal rhizophytic macroalgae Caulerpa prolifera (62.2 Mg OC ha-1, 7.2 Mg TN ha-1), and the lower intertidal seagrass Zostera noltei (52.8 Mg OC ha-1, 5.2 Mg TN ha-1). The sedimentation rates increased from lower to higher elevation, from the intertidal salt marsh (0.24 g cm-2 yr-1) to the subtidal macroalgae (0.12 g cm-2 yr-1). The organic carbon burial rate was highest at the intertidal salt marsh (91 ± 31 g OC m-2 yr-1), followed by the intertidal seagrass, (44 ± 15 g OC m-2 yr-1), the subtidal seagrass (39 ± 6 g OC m-2 yr-1), and the subtidal macroalgae (28 ± 4 g OC m-2 yr-1). Total nitrogen burial rates were similar among the three lower vegetation types, ranging from 5 ± 2 to 3 ± 1 g TN m-2 yr-1, and peaked at S. maritimus salt marsh with 7 ± 1 g TN m-2 yr-1. The contribution of allochthonous sources to the sedimentary organic matter also decreased with elevation, from 72% in C. prolifera to 33% at S. maritimus. Our results highlight the need of using habitat-specific OC and TN stocks and burial rates to improve our ability to predict OC and TN sequestration capacity of vegetated coastal habitats at the seascape level. We also demonstrated that the stocks and burial rates in C. prolifera habitats were within the range of well-accepted blue carbon ecosystems such as seagrass meadows and salt marshes.

Fig 1 in Growth performance of shrimp Litopenaeus vannamei under different carbon: Nitrogen (C/N) ratios of Bioflocs system

Fig 1: Growth Performance details – final weight and weight gain recorded in L.vannamei under different C/N ratios

Fig 4 in Growth performance of shrimp Litopenaeus vannamei under different carbon: Nitrogen (C/N) ratios of Bioflocs system

Fig 4: Growth Performance details – productivity rate recorded in L.vannamei under different C/N ratios

Fig 3 in Growth performance of shrimp Litopenaeus vannamei under different carbon: Nitrogen (C/N) ratios of Bioflocs system

Fig 3: Growth Performance details – Gross Feed Conversion Efficiency (GFCE) recorded in L.vannamei under different C/N ratios

Fig 2 in Growth performance of shrimp Litopenaeus vannamei under different carbon: Nitrogen (C/N) ratios of Bioflocs system

Fig 2: Growth Performance details – Specific Growth Rates (SGR) and Feed Conversion Ratio (FCR) recorded in L.vannamei under different C/N ratios

opencc-by-4.0Jul 2019View details →

Systematic screening of DMOF-1 with NH2, NO2, Br and azobenzene functionalities for elucidation of carbon dioxide and nitrogen separation properties

Publication: M. Xie. N. Prasetya and B. P. Ladewig, Systematic screening of DMOF-1 with NH2, NO2, Br and azobenzene functionalities for elucidation of carbon dioxide and nitrogen separation properties, Inorganic Chemistry Communications (2019). Preprint: M. Xie. N. Prasetya and B. P. Ladewig, Systematic screening of DMOF-1 with NH2, NO2, Br and azobenzene functionalities for elucidation of carbon dioxide and nitrogen separation properties, Inorganic Chemistry Communications (2019), <a href="https://doi.org/10.26434/chemrxiv.8862239.v1">https://doi.org/10.26434/chemrxiv.8862239.v1</a> Dataset supporting publication, including SEM images, optical microscope images, NMR spectra, data used in Figures, and full resolution figures as included in the manuscript. Abstract: In this study, dabco MOF-1 (DMOF-1) with four different functional groups (NH2, NO2, Br and azobenzene) has been successfully synthesized through systematic control of the synthesis condition of their parent framework. The functionalised DMOF-1 is characterized using various analytical techniques including PXRD, TGA and N2 sorption. The effect of the various functional groups on the performance of the MOFs for post-combustion CO2 capture is evaluated. DMOF-1s with polar functional groups are found to have better affinity with CO2 compared with the parent framework as indicated by higher CO2 heat of adsorption. However, imparting steric hindrance to the framework as in Azo-DMOF-1 enhances CO2/N2 selectivity, potentially as a result of lower N2 affinity for the framework.

opencc-by-4.0Sep 2024View details →

Data and analyses for Perkowski et al. (2024) manuscript accepted to AoB Plants: "Symbiotic nitrogen fixation reduces belowground biomass carbon costs of nitrogen acquisition under low, but not high, nitrogen availability"

This repository contains data and scripts for analyses and plots in Perkowski et al. (2024), titled "Symbiotic nitrogen fixation reduces belowground biomass carbon costs of nitrogen acquisition under low, but not high, nitrogen availability". v2.0 updates code and scripts per reviewer comments and is the final release prior to manuscript proofing.

opencc-by-4.0Jul 2021View details →

Dataset for "Climatic Variation Drives Loss and Restructuring of Carbon and Nitrogen in Boreal Forest Wildfire"

This dataset is uploaded to support the report 'Climatic Variation Drives Loss and Restructuring of Carbon and Nitrogen in Boreal Forest Wildfire' published in the journal Biogeosciences. See README file for more details.

opencc-by-4.0Oct 2021View details →

Dataset for "Fire in lichen-rich subarctic tundra changes carbon and nitrogen cycling between ecosystem compartments but has minor effects on stocks"

Data that support the findings of the study  "Fire disturbance promotes biodiversity of plants, lichens and birds in the Siberian subarctic tundra".

opencc-by-4.0Jul 2023View details →

Data of soil mineralization rates, carbon and nitrogen pools in a rainfed almond crop and an irrigated mandarin crop derived from Diverfarming project

Data of soil carbon and nitrogen dynamics, auxiliary data and methods metadata from a rainfed almond crop and an irrigated mandarin crop studied in Diverfarming project

opencc-zeroAug 2023View details →

Data from: Long-term changes in soil carbon and nitrogen fractions in switchgrass, native grasses, and no-till corn bioenergy production systems

Cellulosic bioenergy is a primary land-based climate mitigation strategy, with soil carbon (C) storage and nitrogen (N) conservation as important mitigation elements. Here, we present 13 years of soil C and N change under three cellulosic cropping systems: monoculture switchgrass (Panicum virgatum L.), a five native grasses polyculture, and no-till corn (Zea mays L.). Soil C and N fractions were measured four times over 12 years. Bulk soil C in the 0–25 cm depth at the end of the study period ranged from 28.4 (± 1.4 se) Mg C ha−1 in no-till corn, to 30.8 (± 1.4) Mg C ha−1 in switchgrass, and to 34.8 (± 1.4) Mg C ha−1 in native grasses. Mineral-associated organic matter (MAOM) ranged from 60% to 90% and particulate organic matter (POM) from 10% to 40% of total soil C. Over 12 years, total C as well as both C fractions persisted under no-till corn and switchgrass and increased under native grasses. In contrast, POM N stocks decreased 33% to 45% across systems, whereas MAOM N decreased by less than 13% and only in no-till corn. Declining POM N stocks likely reflect pre-establishment land use, which included alfalfa and manure in earlier rotations. Root production and large soil aggregate formation explained 69% (p < 0.001) and 36% (p = 0.024) of total soil C change, respectively, and 60% (p = 0.020) and 41% (p = 0.023) of soil N change, demonstrating the importance of belowground productivity and soil aggregates for producing and protecting soil C and conserving soil N. Differences between switchgrass and native grasses also indicate a dependence on plant diversity. Soil C and N benefits of bioenergy crops depend strongly on root productivity and pre-establishment land use.

opencc-by-4.0Dec 2022View details →

Data for "Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis"

Raw data associated with the publication "Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis". Data associated with individual figures and corresponding analyses are uploaded as separate tabs in the Excel file. Radecker_etal_NanoSIMS.zip contains the individual NanoSIMS images (names according to treatment). Radecker_etal_Chlorophyll_Fluorescence_Images.zip contains exemplary photographs of chlorophyll fluorescence of Aiptasia (names according to treatment).

opencc-by-4.0Oct 2023View details →

Binned dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved organic phosphorus (DOP) concentration observations in the ocean

Here we provided binned dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved organic phosphorus (DOP) concentration observations in the ocean used for manuscript "Global patterns of surface ocean dissolved organic matter stoichiometry " submitted to Global Biogeochemical Cycles. DOC and DON concentrations observations are from a compilation of DOM data obtained from global ocean observations from 1994 to 2021 (Hansell et al., 2021, https://doi.org/10.25921/s4f4-ye35) DOP concentration observations are from the DOPv2021 database (Liang et al., 2022, https://doi.org/10.1038/s41597-022-01873-7) We binned the data into the OCIM2 grid with a resolution of 2˚x2˚ with 24 vertical layers. More info about OCIM2 grid can be found on <a href="https://tdevries.eri.ucsb.edu/models-and-data-products/">https://tdevries.eri.ucsb.edu/models-and-data-products/</a>

publicFeb 2024View details →

Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system

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publicNov 2024View details →

Local controls modify the effects of timber harvesting on surface soil carbon and nitrogen dynamics

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publicFeb 2025View details →

Data from: Long-term changes in soil carbon and nitrogen fractions in switchgrass, native grasses, and no-till corn bioenergy production systems

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