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Physical and microbial processing of dissolved organic nitrogen (DON) (Photodegradation Experiment) along an oligotrophic marsh/mangrove/estuary ecotone (Taylor Slough and Florida Bay) for August 2003 in Everglades National Park (FCE), South Florida, USA
A better understanding of the biogeochemical cycling of nutrients entering Florida Bay is a key issue regarding the restoration of the Everglades. In addition to precipitation, the other major source of freshwater to Florida Bay is from Taylor Slough and the C-111 Basin in the northeast section of the Bay. While it is known that these areas deliver significant amounts of N to the Bay, a significant portion of this is in the form of dissolved organic N (DON). The sources, environmental fate and bioavailability to microorganisms of this DON are however, not known. Should this DON be readily available, any increased load as a function of restoration changes might have an impact on internal phytoplankton bloom dynamics. No significant flocculation or precipitation of DOM occurred with increase in salinity, meaning that terrestrial DOM does not get trapped in the sediments but stays in the water column where it subjected to photolysis and advective transport. Sunlight has a significant effect on the chemical characteristics of DOM. While the DOC levels did not change significantly during photo-exposure, the optical characteristics of the DOM were modified. The environmental implications of this are conflicting: photo-induced polymerization may stabilize the DOM by reducing its bioavailability while photolysis may make the DOM more labile. Overall, DON bioavailability was relatively low in this region. Even though the amount of DON loaded to the bay may be significant, the fraction of DON available for microbial cycling is much smaller. The amount of N supplied by recycling may be a significant portion of the total DIN pool. All this must be considered in context with the proposed CERP modifications to flows. As of the latest initial Comprehensive Everglades Restoration Project (CERP) update, the flows to Taylor Slough and C-111/Panhandle Basis are not predicted to change very much from base conditions. Therefore we do not expect any great increases in TN loading in this
Characterization of dissloved organic nitrogen in an oligotrophic subtropical coastal ecosystem (Taylor Slough and Shark River Slough) for December 2001 in Everglades National Park (FCE), South Florida, USA
A better understanding of the biogeochemical cycling of nutrients entering Florida Bay is a key issue regarding the restoration of the Everglades. In addition to precipitation, the other major source of freshwater to Florida Bay is from Taylor Slough and the C-111 Basin in the northeast section of the Bay. While it is known that these areas deliver significant amounts of N to the Bay, a significant portion of this is in the form of dissolved organic N (DON). The sources, environmental fate and bioavailability to microorganisms of this DON are however, not known. Should this DON be readily available, any increased load as a function of restoration changes might have an impact on internal phytoplankton bloom dynamics. No significant flocculation or precipitation of DOM occurred with increase in salinity, meaning that terrestrial DOM does not get trapped in the sediments but stays in the water column where it subjected to photolysis and advective transport. Sunlight has a significant effect on the chemical characteristics of DOM. While the DOC levels did not change significantly during photo-exposure, the optical characteristics of the DOM were modified. The environmental implications of this are conflicting: photo-induced polymerization may stabilize the DOM by reducing its bioavailability while photolysis may make the DOM more labile. Overall, DON bioavailability was relatively low in this region. Even though the amount of DON loaded to the bay may be significant, the fraction of DON available for microbial cycling is much smaller. The amount of N supplied by recycling may be a significant portion of the total DIN pool. All this must be considered in context with the proposed CERP modifications to flows. As of the latest initial Comprehensive Everglades Restoration Project (CERP) update, the flows to Taylor Slough and C-111/Panhandle Basis are not predicted to change very much from base conditions. Therefore we do not expect any great increases in TN loading in this
Dissolved Organic Carbon Stable Isotopes and Lignin Phenols from Everglades National Park (FCE LTER), South Florida, USA, January 2019 - ongoing
Estuarine and coastal waters are home to more than half of the world's population and provide many social and economic benefits to society. Additionally, these ecosystems are sites of intense carbon cycling and are under pressure from changing land uses and climate. DOM is functionally defined as the OM passed through a 0.7 µm borosilicate glass fiber filter (GF/F) and is primarily made up of viruses, bacteria, colloids, lignins, humic substances, organic acids, and other small organic compounds (Repeta, 2015). Approximately 50% of DOM is generally considered to be dissolved organic carbon (DOC) (Stedmon and Nelson, 2015). Thus, DOC can be used as a proxy for quantifying DOM. Whole water samples were collected monthly from three different transects representing marl-dominated (Taylor Slough), peat-dominated (Shark River Slough), and seagrass-dominated (Florida Bay) environments. The water was filtered using 0.7 µm porosity glass fiber filters, then acidified to pH 2 and stored at 4°C until processing occurred. DOC concentration and the stable isotope ratio of DOC (δ13C-DOC) was measured on an OI Analytical TOC analyzer coupled to an Agilent Delta V plus Isotope Ratio Mass Spectrometer using high-temperature combustion (Lalonde et al., 2014). Dissolved vanillyl (vanillin, acetovanillone, vanillin acid), syringyl (syringaldehyde, acetosyringone, syringic acid), cinnamyl (p-coumaric acid, ferulic acid), and 3,5-hydroxybenzoic acid lignin phenols were isolated from ~2 liters of 0.7 µm filtered, acidified (pH 2) water by solid phase extraction (SPE) using 1g PPL cartridges that were pre-conditioned using pH 2 water and methanol. SPE cartridges were extracted using methanol, then dried and redissolved in 2N NaOH. Cupric oxide oxidation and liquid-liquid ethyl acetate extraction were used to extract lignin oxidation products (Hedges and Ertel, 1982, modified by Goñi and Hedges, 1995; Louchouarn et al., 2000; Goñi and Montgomery, 2000; Benner and Kaiser, 2011). Briefly, NaO
Stable isotope values of consumers, producers, and organic matter in the Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2019 – ongoing
Wetland food webs have often been characterized as detrital-based ‘brown’ energy pyramids, whereas the relative role of autotrophic (‘green’) vs. microbial (‘brown’) energy sources falls along a continuum set by physical drivers, as well as autochthonous and allochthonous inputs (Moore et al. 2004; Evans-White & Halvorson 2017) that change with ecosystem development (Schmitz et al. 2006). In the Florida Coastal Everglades (FCE), metabolic imbalances, including the collapse of calcareous periphyton mats, begin with a loss of foundation species primary production and legacy organic matter (Gaiser et al. 2006). This process likely enhances heterotrophic microbial productivity (Schulte 2016) and the supply of detrital energy to consumers by changing bioavailable and recalcitrant carbon supplies (Baggett et al. 2013). A shift from complex periphyton communities to transient planktonic communities under elevated P exposure reduces habitat structure and animal refuges but increases ‘green’ energy supplies and edibility (Trexler et al. 2015; Naja et al. 2017). Multiple sites (n=9) within the FCE were selected to document changes in coastal food webs as a result of eutrophication and increasing hydrologic variability. The project began in 2019 and is currently ongoing. References: Baggett, L. P., Heck, K. L., Frankovich, T. A., Armitage, A. R., & Fourqurean, J. W. (2013). Stoichiometry, growth, and fecundity responses to nutrient enrichment by invertebrate grazers in sub-tropical turtle grass (Thalassia testudinum) meadows. Marine biology, 160, 169-180. Evans-White, M. A., and H. M. Halvorson. 2017. Comparing the Ecological Stoichiometry in Green and Brown Food Webs – A Review and Meta-analysis of Freshwater Food Webs. Frontiers in Microbiology 8:1184. Gaiser, E. E., Childers, D. L., Jones, R. D., Richards, J. H., Scinto, L. J., & Trexler, J. C. (2006). Periphyton responses to eutrophication in the Florida Everglades: cross‐system patterns of structural and compositional cha
Dissolved Organic Matter Composition in Doboy Sound and the Altamaha River near Sapelo Island, Georgia in 2012-2013
The composition of dissolved organic matter (DOM) in the Altamaha River estuary and Doboy Sound near Sapelo Island, Georgia, was investigated at the molecular level using ultrahigh-resolution mass spectrometry and stable carbon isotope analyses. DOM samples were collected in November 2012, May 2013, and September 2013 representing different hydrological regimes, including anomalously low-discharge conditions. DOM was also collected from water as it flooded and ebbed from an extensive marsh area at Sapelo Island in May 2013. The untargeted approach used allowed for identifying the DOM molecular signatures associated with different DOM sources in the estuary.
Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter from Doboy Sound, Sapelo Sound and the Altamaha River near Sapelo Island, Georgia in 2012-2013
Dissolved organic matter (DOM) samples were collected from a marsh-dominated estuarine system (Altamaha River estuary, Doboy Sound and Sapelo Sound near Sapelo Island, Georgia), inoculated with native microbiological samples, and incubated in the dark for up to 70 days. Control and incubated DOM samples were then anlyzed using ultrahigh resolution mass spectrometry to investiage microbially-mediated transformations at the molecular level. Samples were collected at high tide in November 2012 and May 2013.
Seasonal Evolution of Terrigenous Dissolved Organic Matter in the South Atlantic Bight off Georgia in 2014
Six surveys of the central South Atlantic Bight (SAB) off of Georgia were conducted in 2014. The primary objective of the research cruises was to characterize estuary-shelf exchange and the dispersal of freshwater into the coastal ocean around Sapelo Island off the Georgia coast. The surveys, in April, May, July, August, September, and November, were intended to sample shelf conditions under different seasons. Most of the sampling stations were located at the mouth of the estu-aries around Sapelo Island and over the inner and mid-shelf (<60 km offshore). Eighty samples from transects extending across the shelf from the mouths of the Altamaha River and of Sapelo Sound were selected for the analyses of molecular composition using ultrahigh resolution mass spectrometry (Fourier transform ion cyclotron reso-nance mass spectrometry [FT-ICR MS]) and stable carbon iso-topic signatures (delta 13C). This data set includes spectral analysis of the DOM, including spectral slope (275-295nm wavelength), terrigenous peaks from mass spectrometry analysis, and a computed terrigenous index indicating fraction of terrigenous DOM in water samples.
Mass and Chemistry of Organic Horizons and Surface Mineral Soils on Watershed 6 at the Hubbard Brook Experimental Forest, 1976 - present
The forest floor of Watershed 6 was first sampled in 1969-70. These data include forest floor thickness, soil mass, organic matter content, and major-element composition for samples collected since 1976. Watershed 6 has been resampled at intervals varying from one to ten years. Sampling at five to ten year intervals is expected to continue. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Mass and Chemistry of Organic Horizons and Surface Mineral Soils on Watershed 1 at the Hubbard Brook Experimental Forest 1996-present
This data set includes chemistry of O-horizons ("forest floor") and the 0-10 cm mineral soil layer in Watershed 1 at Hubbard Book. Calcium in the form of wollastonite (CaSiO3) was added to Watershed 1 in October 1999. The application rate was 1028 kg Ca per ha, and the application was relatively uniform across the watershed. Pre-treatment forest floor surveys were completed in 1996 and 1998. The first post-treatment forest floor survey was completed in 2000. This data set includes mass and thickness data for the sampled layers. Chemical data include concentrations and pools of organic matter, C, N, Ca, Mg, K, P, Mn, Fe, Al, Cu, Pb, and Zn. Soil pH and exchangeable Al, Ca, Mg, K, and H are also included. Sampling is intended to continue at 4 or 5 year intervals. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Soil organic matter content sampled in and around harvester ant nests in three habitats at the Jornada Basin LTER site, 1987
This dataset contains soil organic matter content measurements from harvester ant nests and reference soils in three nesting habitats at the Jornada Basin LTER site in 1987. The purpose of this investigation was to answer three general questions: 1. How does the modification of soil properties and the ratios of resources (e.g., water-N) by ants alter species assemblages of winter annual plants at the edge of the ant nests? 2. How does the "spring cleaning", clipping, predation or herbivory by ants affect success of the winter annual plants at the edge of ant nests? 3. Are there significant differences in the floristic assemblage and belowground standing crop (root biomass) between the edge of ant nest and the surrounding unaffected soils? Five ant nests and paired (non-nest) reference soils were sampled in three study locations. This dataset contains percent (%) organic matter content measured by mass-loss on combustion in a muffle furnace. This study was completed in 1987.
Data for: Climate warming and drought effects on volatile organic compound emissions from Solidago altissima
Volatile organic compounds (VOCs) were collected from Solidago altissima in drought and warming treatments in the KBS-LTER Rain Exclusion Experiment (REX). This sampling took place in July 2022 when the plants had been experiencing warming (via open-top chambers) for 20 months, and drought (via rainout shelters) for 3 weeks. The data presented here are the final data files used for analysis, and contain VOC abundance values per plant across the four climate treatments: ambient, warmed, drought, and warmed + drought. Code is available at: https://github.com/dobsonk2/REX_VOCs (https://doi.org/10.5281/zenodo.15169943)
Dissolved Organic Carbon (DOC) and Dissolved Total Nitrogen (DTN) from Northeast U.S. Shelf Long Term Ecological Research (NES-LTER) Transect cruises, ongoing since 2022
Dissolved organic carbon and dissolved total nitrogen are measured from discrete bottle samples collected during CTD rosette casts on Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) transect cruises (ongoing since 2022). Sampling frequency is approximately seasonal. Sample collection is paired with particulate organic carbon at surface, subsurface chlorophyll max, and sometimes a third depth. Samples are filtered directly from the CTD rosette and acidified in the field, then analyzed using a Shimadzu TOC-LCPH total organic carbon analyzer coupled to a TNM-L analyzer for total nitrogen. Values are reported in micromoles per liter.
Particulate organic carbon (POC) and nitrogen (PON) from Northeast U.S. Shelf Long Term Ecological Research (NES-LTER) Transect cruises, ongoing since 2017
Particulate organic carbon and nitrogen are measured from discrete bottle samples collected during CTD-rosette casts on Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises (ongoing since 2017). Sampling frequency is approximately seasonal. Samples were filtered and collected on combusted glass fiber filters, pelletized using ultra clean tin disks, and combusted using a Flash EA1112 CHN analyzer to calculate concentrations of particulate organic carbon and particulate organic nitrogen in micromoles per liter. Values are also reported as concentrations in micrograms per liter and carbon to nitrogen molar ratio.
Long-term trends and synchrony in dissolved organic matter characteristics in Wisconsin, USA lakes: quality, not quantity, is highly sensitive to climate
Dissolved organic matter (DOM) is a fundamental driver of many lake processes. In the past several decades, many lakes have exhibited a substantial increase in DOM quantity, measured as dissolved organic carbon (DOC) concentration. While increasing DOC is now widely recognized, fewer studies have sought to understand how characteristics of DOM (DOM quality) change over time. Quality can be measured in several ways, including the optical characteristics spectral slope (S275-295), spectral ratio (SR), absorbance at 254 nm (a254), and DOC-specific absorbance (SUVA; a254:DOC). However, long-term measurements of quality are not nearly as common as long-term measurements of DOC concentration. We used 24 years of DOC and absorbance data for seven lakes in the North Temperate Lakes Long Term Ecological Research site in northern Wisconsin, USA to examine temporal trends and synchrony in both DOC concentration and quality. We predicted lower SR and S275-295 and higher a254 and SUVA trends, consistent with increasing DOC and greater allochthony. DOC concentration exhibited both significant positive and negative trends among lakes. In contrast, DOC quality exhibited trends suggesting reduced allochthony or increased degradation, with significant long-term increases in SR in three lakes. Patterns and synchrony of DOM quality parameters suggest they are more responsive to climatic variations than DOC concentration. SUVA in particular tended to increase with greater moisture and decrease with drier conditions. These results demonstrate that DOC quantity and quality can exhibit different complex long-term trends and responses to climate components, with important implications for aquatic ecosystems.
Modeled Organic Carbon, Dissolved Oxygen, and Secchi for six Wisconsin Lakes, 1995-2014
This data package contains model output data, driving data, and supplemental information for a two-layer modeling study that investigated organic carbon and oxygen dynamics within six Wisconsin lakes over a twenty-year period (1995-2014). The six lakes are Lake Mendota, Lake Monona, Trout Lake, Allequash Lake, Big Muskellunge Lake, and Sparkling Lake. The model output includes daily predictions of six state variables: labile particulate organic carbon, recalcitrant particulate organic carbon, labile dissolved organic carbon, recalcitrant dissolved organic carbon, dissolved oxygen, and Secchi depth. The output also includes daily predictions of physical and metabolism fluxes that were used in the prediction of the state variables. This data package also contains model driving data for each lake and other supplemental information that was calculated during the modeling runs.
Dissolved Organic Carbon Concentration, Dissolved Organic Matter Optical Properties, and Water Quality Indicators in the Plum Island Estuary (PIE), Massachusetts, USA (2018-2023)
This is a data set of paired in situ measurements of water quality parameters, total suspended solids concentration, and concentration and optical properties (absorption coefficient spectra and fluorescence indices) of dissolved organic matter (DOM) collected between 2018 and 2023 in the Plum Island Estuary and nearshore waters. In situ water quality measurements (salinity, temperature, optical dissolved oxygen saturation, turbidity, and dissolved organic matter fluorescence) were collected with a water quality sonde from the surface (top 1 m of water column), along with corresponding samples that were processed and analyzed in the lab for dissolved organic carbon (DOC) concentration, chromophoric DOM (CDOM), absorption coefficient spectra, DOM excitation-emission matrix (EEM) fluorescence, and total suspended sediment (TSS) concentration. The data were used in multiple studies (see manuscripts listed below) focusing on the dynamics of DOC and CDOM in the Plum Island Estuary.
SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of sessile organisms, Uniform Point Contact
These data describe the cover of sessile invertebrates, understory macroalgae, and bottom substrate types as determined by a uniform point contact method. The presence of over 150 taxa of sessile invertebrates and macroalgae are recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Multiple species can be recorded at any given point. Percent cover of a given species on a transect can be estimated from UPC observations as the fraction of total points at which that species was present x 100. The total percent cover of all species combined using this method can exceed 100%; however, the percent cover of any single species cannot exceed 100%. These data are part of SBC LTERs kelp forest monitoring program, which began in 2000 and was designed to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset include nine reef sites along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. Data collection began in 2000 and this dataset is updated annually. The time period of data collection varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. See Methods for more information. The two tables in this data package include: 1) The percent cover of sessile invertebrate and understory macroalage; and 2) the percent cover of bottom substrate.
SBC LTER: Reef: Seasonal Kelp Forest Community Dynamics: Cover of sessile organisms, Uniform Point Contact
These data describe the percent cover of sessile invertebrates and understory macroalgae within permanent plots of SBCLTER's seasonal kelp forest monitoring program to track long-term patterns in species abundance and diversity. Percent cover was determined using a uniform point contact method that consists of noting the identity and relative vertical position of all organisms under 80 uniformly placed points located within a 1 m wide band centered on permanent 40 m transects in each sampling plot. Each species may only be recorded once per point. Using this method, the percent cover of all species combined may exceed 100%, however, the maximum percent cover possible for any single species cannot exceed 100%. The experiment was initiated in 2008 at five reef sites along the mainland coast of the Santa Barbara Channel.
SBC LTER: Reef: Long-term experiment: Kelp removal: Cover of sessile organisms, Uniform Point Contact
These data describe the percent cover of sessile invertebrates and understory macroalgae within permanent plots of a long-term experiment designed to examine trajectories of change in the structure and productivity of kelp forest communities in response to changes in the frequency and severity of disturbance to giant kelp. Percent cover was determined using a uniform point contact method that consists of noting the identity and relative vertical position of all organisms under 80 uniformly placed points located within a 1 m wide band centered on permanent 40 m transects in each sampling plot. Each species may only be recorded once per point. Using this method, the percent cover of all species combined may exceed 100%, however, the maximum percent cover possible for any single species cannot exceed 100%. The experiment was initiated in 2008 at five reef sites along the mainland coast of the Santa Barbara Channel and included an annual kelp removal treatment designed to simulate increases in the frequency and severity of winter wave disturbance and a continual kelp removal treatment that allowed the effects of giant kelp on the community to be evaluated. The last experimental removals of giant kelp occurred in winter 2016 or winter 2017, depending on the site. Data collection continued in all plots until spring 2023 to document the recovery trajectory of the reef fish community following the cessation of experimental kelp removal.
Sediment organic matter and infauna at eight sites on the Virginia Coast, 2016 and 2019
To determine how oysters impact the spatial distribution of infauna and sediment composition through ecosystem engineering, we sampled 8 intertidal mud- flats adjacent to oyster reefs in coastal Virginia, USA. This work describes how local site characteristics, including distance to oysters, elevation, and hydrodynamics, influence infaunal community structure and sediment composition.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.