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Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945). This data package is associated with the following publication: Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215 Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
Vegetation and invertebrate communities in 500 plots in the Duplin and Dean Creek watersheds: ground truth data for matching hyperspectral imagery
We measured characteristics of vegetation (Aster tenuifolius, Batis maritima, Borrichia frutescens, Distichlis spicata, Iva frutescens, Juncus roemerianus, Limonium carolinianum, Salicornia biglovii, Salicornia virginica, Spartina alterniflora, Spartina patens, Sporobolus virginicus), soil (salinity, proportion organic and proportion water) and densities of common gastropods and bivalves in 500 plots in the Duplin and Dean Creek watersheds on Sapelo Island on June 20-26, 2006. Plot locations were determined using a high precision hand-held GPS. These data were used to help ground-truth hyperspectral aerial images collected at the same time by Dr. John Schalles.
Plant community surveys along transects at multiple sites on Sapelo Island and St. Simons Island in Georgia during June and July 2005
I sampled 59 sites around Sapelo Island and St. Simons Island, Georgia, in June-July 2005. Sites were chosen to include a range of mainland, barrier island, and back-barrier hammock island locations. All sites were dominated by salt marsh plant species, primarily Spartina alterniflora. To provide a general indication of the salinity conditions prevailing at each site, I measured salinity of the nearest body of water with a refractometer on the date that the site was sampled. Plant richness was documented along a single 5.0m wide transect at each site. Each transect began at the lower elevational limit of vegetation and continued perpendicular to the water’s edge to the shrub community at the upper marsh border. Plant presence was noted in a series of nested subplots within a 1.0m x 5.0m plot at each meter along the transect. The results posted here are sites, position, salinity, and the composition of the plant community in 0.5 x 0.5 m quadrats located at 1 m intervals along the transect. This data set is a companion to PLT-GCET-0608, which provides pooled data for sites in Georgia.
Disturbance and recovery of salt marsh arthropod communities in Louisiana and Mississippi following the 2010 BP Deepwater Horizon oil spill in the Gulf of Mexico
Oil spills represent a major environmental threat to coastal wetlands, which provide a variety of critical ecosystem services to humanity. The U.S. Gulf of Mexico is a hub of oil and gas exploration and production with recognized consequences on intertidal habitats, such as the salt marsh. Following the BP Deepwater Horizon oil spill, we sampled the marine invertebrate and the terrestrial arthropod community found in stands of Spartina alterniflora, the most abundant plant in coastal salt marshes, in 2010 as oil was washing ashore and a year later in 2011. In 2010, intertidal crabs and terrestrial arthropods (insects and spiders) were suppressed by oil exposure even in seemingly unaffected stands of plants; however, Littoraria snails appeared unaffected. One year later, crab and arthropods appeared to have largely recovered. Our work is the first attempt that we know of assessing vulnerability of the salt marsh arthropod community to oil exposure, and it suggests that arthropods are both quite vulnerable to oil exposure, and quite resilient, able to recover from exposure within a year if host plants remain healthy. BP's Deepwater Horizon spill in the Gulf Coast presented an opportunity to understand how stress from an oil spill might affect variables that we were measuring in the area. The study was conducted at sites in Louisiana and Mississippi. At each site, a 100m transect was sampled within 5m of the dead zone boundary. Sampling was conducted in August 2010 and August 2011. The number of sites and location of sites differed slightly among years.
Effects of fallen Spanish moss (Tillandsia usneoides) on understory plant, invertebrate, and fungi communities
For nearly two years, natural deposition of Spanish moss was excluded from 2m x 2m plots positioned in the understory of a single live oak at each of two field sites. After 29 months, we measured the effects of fallen Spanish moss, relative to unmanipulated control plots that intercepted natural levels of fallen Spanish moss, on understory grass, invertebrate, and fungi communities as well as on litter layer depth, and litter decomposition rates using litter bags. This research was conducted in two fields on Sapelo Island, GA: Long Tabby (LT) and King's Field (KF). Experimental exclusions were maintained by manually removing Spanish moss from experimental plots monthly over the duration of the experiment.
Effects of ribbed mussel aggregation size on marsh invertebrate community structure and multiple eocsystem functions
Ribbed mussels (Geukensia demissa) were added in aggregations containing 0, 1, 3, 5, 10, 20, 40 or 80 mussels (N=3 replicates per aggregation size) in Spring of 2012 in a high marsh platform at the Airport Marsh on Sapelo Island, GA. In summer of 2013, we measured the response of invertebrate communities and six ecosystem functions. Specifically, we counted the number of Littoraria irrorata, Sesarma reticulatum burrows, Uca pugnax burrows (those > and <5mm in diameter were counted separately), and mud crab (Eurythium limosum and Panopeus herbstii) in 50cm x 50cm sampling frames. And, we measured aboveground cordgrass biomass, benthic algae biomass, invertebrate biomass, decomposition rate, infiltration rate, and soil accretion in the same size sampling frames in August of 2013.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2018
A quadrat survey was conducted in October 2018 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2019
A quadrat survey was conducted in October 2019 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
Gridded 1-hectare estimates of shrub community structure at the Jornada Basin LTER site derived from NAIP (2011) and LiDAR (2019) data
This dataset contains four raster maps of shrub community structure at the Jornada Basin LTER site in southern New Mexico U.S.A. These shrub structure estimates were created by combining an existing categorical shrub map (Ji et al. 2019) with USGS LiDAR shrub height estimates from 2019. The resulting raster dataset includes four bands of spatially aligned shrub volume, cover, height, and density estimates at one hectare resolution. Data are also included in tabular format, extracted from the 1 hectare grid upon which estimates were created. These shrub structure estimates are intended to facilitate analyses of habitat structure and community dynamics within the northern Chihuahuan Desert.
GFE01 Ghost Fire: an experimental manipulation of fire effects on multi-trophic community dynamics in the ungrazed uplands of unburned and annually burned watersheds of Konza Prairie
Frequent burning is a common land practice in many grasslands worldwide, and this land use strategy has large impacts on a wide variety of ecosystem functions and services. Fire in tallgrass prairie, in the absence of grazing, alters plant community composition, decreases richness, and increases plant production. Proposed mechanisms for the changes in community composition and function are that fire decreases N availability (through volatilization) and removes litter (thereby increasing light availability and decreasing soil moisture). However, few experiments explicitly test these mechanisms, and those that do monitor short-term effects.Yet, the strength of these mechanisms likely differ over longer time scales, as other ecosystem attributes (e.g., plant community composition) change through time. Ghost Fire aims to determine the mechanisms behind community and ecosystem differences between annually burned grassland and 20-year burned grassland (hereafter called unburned) by experimentally manipulating N availability and litter. We impose litter and N conditions found in unburned grassland onto annually burned grassland, and litter and N conditions typically found in annually burned grassland onto unburned grassland. Importantly, Ghost Fire monitors both below-and above-ground plant community and ecosystem dynamics as well other dimensions of the ecosystem including microbial and mycorrhizal communities and insect community composition and biomass.
CFC01 Kings Creek long-term fish and crayfish community sampling at Konza Prairie
Prairie stream fish communities have been monitored seasonally at multiple sites within the Kings Creek watershed since 1995. The objective of this sampling is to evaluate how these communities respond to seasonal and annual variation in environmental conditions. Specifically, we are interesting in testing the resistance and resilience of stream communities in response to flood and drought disturbances. One site in a downstream perennial reach of the watershed has been sampled since 1995. Five sites have been sampled in smaller tributaries in the watershed, two were discontinued due to often lack of flow, two have been sampled since 1995 and one was added in 2008. Sampling is conducted with backpack electrofishing with at least one person dip netting. At each site, multiple habitats (pools and riffles) are sampled. Length of all fish and crayfish are measured.
SMB01 Variation in soil respiration and bacterial community due to species-specific plant-soil history at konza prairie
We conducted a “home vs. away” plant-soil feedback greenhouse experiment using two C3 grass species (Bromus inermis and Pascopyrum smithii) grown in soil collected from Konza Prairie. We used a closed-circuit CO2 trapping method and isotopic analysis to differentiate between root-derived and SOM-derived CO2 production. We investigated how soil chemistry and soil bacterial communities differed in soils with a history of B. inermis vs soils with a history of P. smithii.
CMY01 Mycorrhizal colonization and plant community responses to long-term suppression of Mycorrhizal Fungi
Twenty replicate permanent 2x2 m plots were established in early 1991 along a randomly located transect, with a 2m space between each plot, on the following watersheds: 1B, 1D, annually burned HQB, 10B, 20D and infrequently burned HQB. Ten of the plots were randomly assigned as long-term mycorrhizal suppression plots. In each of these plots, AM fungi were suppressed by the application of the fungicide benomyl as a soil drench (7.5 liters per plot) at the rate of 1.25 g/m2 (active ingredient). The mycorrhizal suppression plots were treated biweekly throughout each growing season (April through October) beginning in 1991. The control plots each received no fungicide, but an equivalent volume of water (7.5 liters) was applied biweekly. To evaluate the effectiveness of the fungicide, three soil cores (2.5 cm diameter x 14 cm deep) were removed from both fungicide-treated and control plots each October throughout the study. Roots were extracted from the soil, washed free of soil, stained in trypan blue (Phillips and Hayman, 1970), and examined microscopically to assess percentage root colonization by mycorrhizal fungi using a Petri dish scored in 1-cm squares (Daniels et al.1981).
VIR01 Effects of invertebate and vertebrate herbivory on tallgrass prairie plant community composition and biomass, Konza Prairie LTER
The effects of herbivores and their interactions with nutrient availability on primary production and plant community composition in grassland systems is expected to vary with herbivore type. Although nutrient additions are known to affect plant species diversity and primary productivity, the role of herbivores in mediating the strength of these effects also remains unclear. Herbivores may alter plant responses to nutrient additions in several ways. First, herbivores can alter the plant community response to nutrient additions by either selectively feeding on particular groups of species (e.g. grasses versus forbs) or by generally opening up space, allowing for species turnover and immigration. Second, feeding by herbivores may reduce the production response to nutrient additions if the plants cannot compensate for tissue lost to herbivory. As the functional effects of vertebrate and invertebrate herbivores on plant community composition and production may vary, the interactive effects of vertebrate versus invertebrate herbivores with nutrient additions may also vary. Here we are experimentally assessing the independent and interactive effects of removing vertebrate and invertebrate herbivores on aboveground biomass and plant community composition in native tallgrass prairie. Further, we are examining whether the removal of vertebrate and invertebrate herbivores interacts with nutrient availability. By doing this, we address three related questions: 1) what is the relative strength of the effects of invertebrate versus vertebrate herbivory in a grassland system; 2) how does herbivory (invertebrate and/or vertebrate) affect the relative abundances of grasses and forbs, the two dominant plant functional types within the ecosystem; and 3) what are the consequences of these changes in composition for aboveground net primary productivity, an important ecosystem function?
Litter invertebrate communities at different elevations in the LEF
Identification and number of invertebrates recovered from each litter sample. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
MCR LTER: Coral Reef: Community Dynamics: Juvenile Coral Density from 2005, ongoing
These data describe the density (colonies per quadrat of 0.5 x 0.5 m size) of juvenile corals on the fringing reefs and outer reef (10 m depth) of Moorea. Beginning in 2005, surveys are completed annually at LTER 1 and 2 in the austral autumn (April-May). Addition event-motivated sampling began in 2011 with additional sites from the other two shores of Moorea surveyed and surveys at LTER 1 and 2 repeated in August; these surveys will likely continue for 1-2 years but will not become a maintained component of the annual sampling. The focus is on juvenile corals defined as individuals less than or equal to 40 mm diameter. These data include juvenile scleractinian corals and juvenile Millepora spp. (Class: Hydrozoa; Order Hydroida, Sub Order Anthomedusae, Family Milleporidae). These transects are co-located with annual photographic surveys and, therefore, broad community descriptors are also available.
MCR LTER: Coral Reef: Long-Term Coral Population and Community Dynamics: Annual Island Wide Coral Demography Survey 2011 ongoing
Demographic performance (recruitment, growth, and survival) are quantified annually for multiple individual colonies of the three most common genera (Acropora, Pocillopora, Porites) at both backreef and forereef sites. Each coral was tagged in 2011 and subsequently sampled again in 2012 to track colony growth and mortality dynamics. However, since 2013, investigators have transitioned to identifying coral through detailed mapping methodology and will continue to identify corals using this method in the subsequent years. The mapping system developed in 2013 provides data appropriate for detailed demographic study of coral on varying spatial scales around the island. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2022). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
MCR LTER: Coral Reef: Priority effects in coral-macroalgae interactions can drive alternate community paths in the absence of top-down control, data for Adam 2022 Ecology
These data were generated in support of the manuscript: Adam TC, Holbrook SJ, Burkepile DE, Speare KE, Brooks AJ, Ladd MC, Shantz AA, Thurber RLV, and Schmitt RJ, Ecology The outcomes of species interactions can vary greatly in time and space with the outcomes of some interactions determined by priority effects. On coral reefs, benthic algae rapidly colonize the disturbed substrate. In the absence of top-down control from herbivorous fishes, these algae can inhibit the recruitment of reef-building corals, leading to a persistent phase shift to a macroalgae-dominated state. Yet, corals may also inhibit colonization by macroalgae, and thus the effects of herbivores on algal communities may be strongest following disturbances that reduce coral cover. Here, we report results from experiments conducted on the fore reef of Moorea, French Polynesia, where we: 1) tested the ability of macroalgae to invade coral-dominated and coral-depauperate communities under different levels of herbivory, 2) explored the ability of juvenile corals (Pocillopora spp.) to suppress macroalgae, and 3) quantified the direct and indirect effects of fish herbivores and corallivores on juvenile corals. We found that macroalgae proliferated when herbivory was low but only in recently disturbed communities where coral cover was also low. When coral cover was < 10%, macroalgae increased 20-fold within one year under reduced herbivory conditions relative to high herbivory controls. Yet, when coral cover was high (50%), macroalgae were suppressed irrespective of the level of herbivory despite ample space for algal colonization. Once established in communities with low herbivory and low coral cover, macroalgae suppressed recruitment of coral larvae, reducing the capacity for coral replenishment. However, when we experimentally established small juvenile corals (2 cm diameter) following a disturbance, juvenile corals inhibited macroalgae from invading local neighborhoods, even in the absence of herbivore
Analysis of the planning process for a new park in Minneapolis, Minnesota, at the Upper Harbor Terminal site with planners and community members focusing on redevelopment that addresses green gentrification concerns, 2019 to 2021
This dataset is from a study focuses on the Minneapolis Park and Recreation Board’s planning process for a new park at the Upper Harbor Terminal (UHT) site - a defunct barge-to-rail terminal on the Mississippi River being redeveloped with a mix of housing, commercial uses, and park space (see "UHT_location_map in Other Entities). While the redevelopment affords an opportunity to remediate pollution and provide new greenspace, a high portion of nearby residents are low-income and housing-cost burdened, raising concerns among community members about gentrification. As a counter to green gentrification, the concept of “Just Green Enough” (JGE) became a common theme around the UHT development process. JGE aims to center community-centered greening efforts with broader community development goals in mind (i.e. living-wage jobs and affordable housing). Amidst growing community pressure, the Minneapolis Park and Recreation Board (MPRB) appointed a Community Advisory Committee (CAC). The CAC was tasked with meeting monthly for in-depth deliberations (facilitated by planning staff and external consultants) with the goal of making final park design and programming recommendations, which planning staff would present to the MPRB Board of Commissioners. The Upper Harbor Terminal CAC consisted of 16 members, mostly residents of North Minneapolis and Northeast, and many with a background in nonprofit, environmental, or community organizing work. Meetings began in July 2019 and lasted nearly two years until in May 2021. This dataset includes the qualitative codebooks for the CAC meetings, accompanied by the meeting minutes and other documents related to the UHT planning process. The transcripts of semi-structured interviews with stakeholders in the UHT planning process were also analyzed and coded, but specific quotations are omitted from this dataset to protect the privacy the participants.
Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2020
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter, spring, and summer Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2020. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
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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.