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Environmental, community and trait data of small water bodies in Zijin Mountain, Nanjing, Jiangsu, China, 2022
Small water bodies (SWBs) are vulnerable to drought and play a vital role in the conservation of aquatic biodiversity. Currently climate change is intensifying the seasonal drought of SWBs in monsoonal east Asia. However, little is known about the response of benthic macroinvertebrates of small ponds and streams that simultaneously suffer from climate-induced extreme drought. This study aimed to explore the taxonomic and functional response of macroinvertebrates in ponds and streams, either respectively or jointly, to extreme summer drought. We calculated taxonomic and functional diversity indices of communities in 11 streams and 12 ponds across three seasons: spring, summer and winter in 2022. We performed a permutational multivariate analysis of variance, Moran’s eigenvector maps, Moran Spectral Randomization based variation partitioning and convex hull analysis of trait space to examine temporal compositional and functional, as well as trait changes, and the contributions of environmental and spatial factors in shaping communities. The responses of taxonomic and functional diversity in ponds and streams were contrasting during the summer drought. Ponds showed increased taxonomic richness (TR), functional richness (FRic), functional richness (FRed) and trait space volume, while streams experienced decreased TR, FRic and trait space volume but increased FRed. The taxonomic and functional increases of ponds were driven by an influx of generalist taxa from streams, while the increase of FRed in streams resulted from the loss of species with strong dispersal and lentic adaptation traits. Dispersal played a more significant role than environmental filtering in shaping community structure during the drought, especially for streams lacking hydrological connectivity. This study provides the first insights into the complex response of macroinvertebrates to summer drought of SWBs in east Asia monsoonal region. Our results underscore the refuge effect of ponds during summer
Benthic community response to different disturbance type events across six islands between two timepoints in the Central Pacific
A coral reef's response to disturbance can be driven by various factors including community composition. This dataset highlights benthic cover and its changes between two timepoints at six islands across the central Pacific. The survey islands include Ant Atoll, Pakin Atoll, and Pohnpei located within the Federated States of Micronesia (FSM) as well as Upon and Savai'i in Samoa and Rarotonga in the Cook Islands. Survey years differed between sites but all sites had an estimated two-year time-difference between resampling. To extract benthic cover, photos were annotated using randomized points and labeled to their highest taxonomic resolution, down to genus-level for hard corals. Both abiotic and biotic substrate were identified and major functional groups included: hard corals, soft corals, invertebrates, turf algae, Halimeda spp., crustose coralline algae, and other (sand/debris/etc.). Disturbance type and community composition at the initial survey period drove changes in percent cover for major functional groups. Data was collected by annotating photos from transect surveys on a coral reef. This effort was completed by the 2020 SIO 'Pop-up' SURF REU that was formed in rapid response due to COVID-19 research limitations.
Long-term studies of secondary succession and community assembly in the prairie-forest ecotone of eastern Kansas, Hay meadow restoration experiment
Local and regional-scale processes interact to govern the assembly, diversity and functioning of ecological communities. Evaluating the interplay of these differently-scaled processes in the regulation of ecological systems is a challenging problem, but is crucial towards understanding and predicting the potential effects of accelerated human activity on biological diversity and ecosystem sustainability. Since 2000, two long-term field experiments have been underway in grasslands of eastern Kansas to investigate the interplay of soil resource availability, species interactions and regional processes governing plant secondary succession, community assembly, biodiversity, and ecosystem functioning. Both experiments involve manipulations of soil nutrients in permanent grassland study plots and employ multi-species seed addition treatments to evaluate the contribution of dispersal limitation and regional constraints on local species pools to the regulation of plant community dynamics. Hay meadow restoration experiment, previously funded by USDA, was established in 2000 in a section of the field that was left unplowed at the start of the experiment. Thus Experiment 2 was initiated in the context of secondary succession on recently abandoned cool-season hayfield where hay grass species were dominant at the start of the study. In this experiment we have been monitoring plant community change annually since 2001 in response to two aspects of hay management important in our area: annual fertilization and annual haying. The experimental design involves factorial manipulations of nutrient supply (two levels of NPK fertilization), annual haying (two levels: hayed; not hayed) and propagule input achieved by adding seeds of 41 native prairie species to half of the plots. Experiment 2 parallels Experiment 1 with manipulations of soil resources and species pools, but does so in the contexts of hay management and native prairie hay meadow restoration.
American Residential Macrosystems - Bird community data within parks and residential yards in six major metropolitan areas in the United States, 2017-2018
"This dataset includes abundance of breeding bird species recorded in residential yards and nearby natural and interstitial areas (i.e.unmanaged vegetation areas in the residential/wildland interface) in six cities across the U.S. Baltimore, MD, Boston, MA, Los Angeles, CA, Miami, FL, Minneapolis-St. Paul, MN, and Phoenix, AZ. Yards were grouped in 4 categories based on fertilizer input frequency, landscaping style and their impact on hydrology: high-input lawns, low-input lawns, wildlife-certified yards and yards with low impact on hydrology (or rain gardens). Bird data was collected via standardized 10-min point counts during the breeding season in 2017 or 2018. "
Forest Invasibility in Communities in Southeastern New York
While biological invasions have been the subject of considerable attention both historically and recently the factors controlling the susceptibility of communities to plant invasions remain controversial. In order to examine relationships between plant community characteristics, soil characteristics, and nonnative plant invasion, we surveyed 44 sites in southeastern New York State, USA in the summer of 1998. We examined both plant community characteristics (diversity and species membership) and soil characteristics (litter depth, pH, nitrogen, calcium, magnesium, cation exchange capacity, phosphorus, and soil texture). The data collected was then used to study patterns of invasion both within and among broad forest community types, in order to determine what factors were most closely associated with the success of invasive plants
SBC LTER: Reef: Kelp Forest Community Dynamics: Fish abundance (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/189/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/17/35. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located 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. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The two tables in this data package include: 1) The annual benthic fish community survey which was conducted on 11 reefs once a year around late July or early August; and 2) The monthly fish survey which was conducted once a month at a subset of the sites (3 of the annual sites) The time period of data collection for the annual benthic fish community survey 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. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE
Crossing Treeline: Bacterioplankton community composition in alpine and subalpine lakes of the Rocky Mountain southern ecoregion and associated physical and chemical characteristics
This dataset includes lake water samples collected in the summer of 2016 from 16 different mountain lakes in the Rocky mountains in both Rocky Mountain National Park and the Snowy Range of southern Wyoming. Each lake was sampled twice: once in the early summer when hydrologic connections with the surrounding terrestrial environment were high and again in the late summer when hydrologic connections were low. The main goal of the study was to compare communities of bacterioplankton in alpine and subalpine lakes to determine if communities differed across treeline as soil microbes in the surrounding terrestrial environment were. To do so, we collected water samples from the deepest point of each lake, mixed it with a surface water sample and characterized bacterioplankton communities with 16S sequencing technology. Additionally, we wanted to identify abiotic factors that may correlate with community dissimilarity and characterized a suite of chemical attributes for each lake. Lake characteristics reported included surface temperature, soluble reactive phosphorous (SRP), ammonia (NH3+), pH, total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and total dissolved organic carbon (DOC), and chlorophyll a (chl-a).
Ground Arthropod Community Survey in Grassland, Shrubland, and Woodland at the Sevilleta National Wildlife Refuge, New Mexico (1992-2004) (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/333/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sev/29/175390. The abstract below was extracted from the Level 0 data package and is included for context: This data set contains records for the numbers of selected groups of ground-dwelling arthropod species and individuals collected from pitfall traps at 4 sites on the Sevilleta NWR, including creotostebush shrubland, both black and blue grama grasslands, and a pinyon/juniper woodland. Data collections begin in May of 1989, and are represented by subsequent sample collections every 2 months. One site (Goat Draw/Cerro Montosa) was discontinued in 2001, and a new site (Blue Grama) was initiated . Only three sites, creosotebush, black grama, and blue grama were continued between 2001-2004.
Post-logging community structure and biomass accumulation in Watershed 10, Andrews Experimental Forest , 1974 to present
Old-growth and mature Douglas-fir forest were clearcut logged in 1975. Large slash was removed from the site rather than burned. Douglas-fir seedlings were planted in 1976 and 1977, but due to poor survival 4.9 ha were replanted in 1978. Despite planting, most tree stems originated naturally, either as sprouts from cut stumps (hardwoods) or as natural regeneration (conifers and hardwoods). Study plots were established and sampled for cover and frequency of understory vegetation and counts of seedlings and saplings prior to harvest (1973) and resampled annually for cover and biomass of understory vegetation and tree growth from 1976-1981, then in 1983, 1985, and then in 4-6 year intervals. WS10 was intensively studied in the 1970’s and 80’s. The entire watershed was surveyed into a 25 x 25-m grid and then 36 15 by 10 meter plots were established for long-term sampling.
Catalog of GenBank sequence read archive (SRA) entries of 16S and 18S rRNA genes from bacterial and protistan planktonic communities along the Eastern Beaufort Sea coast, North Slope, Alaska, 2011-2013
Microbial communities in the coastal Arctic Ocean experience extreme variability in organic matter and inorganic nutrients driven by seasonal shifts in sea ice extent and freshwater inputs. Lagoons border more than half of the Beaufort Sea coast and provide important habitats for migratory fish and seabirds; yet, little is known about the planktonic food webs supporting these higher trophic levels. To investigate seasonal changes in bacterial and protistan planktonic communities, amplicon sequences of 16S and 18S rRNA genes were generated from samples collected during periods of ice-cover (April), ice break-up (June), and open water (August) from shallow lagoons along the eastern Alaska Beaufort Sea coast from 2011 through 2013. This data package catalogs sequence read archive (SRA) entries available through GenBank BioProject PRJNA530074 at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA530074. This data package is associated with the following publication: Kellogg CTE, McClelland JW, Dunton KH and Crump BC (2019) Strong Seasonality in Arctic Estuarine Microbial Food Webs. Front. Microbiol. 10:2628. doi: 10.3389/fmicb.2019.02628 Environmental variables (physiochemical data from YSI and HOBO data loggers, as well as organic matter analysis and stable isotope data from discrete water samples) associated with this genomic dataset are available from the Arctic Data Center: Kenneth Dunton, Byron Crump, and James McClelland. Physical, chemical, and biological data from lagoons and open coastal waters in the nearshore environment of the eastern Alaska Beaufort Sea, 2011-2013. Arctic Data Center. doi:10.18739/A2DG13. To join the two datasets together, please use the provided site codes (column "site_name" here) and collection dates (column "collection_date" here) in each dataset. Note that the site codes in this package are without hyphens (e.g. JAA) while site codes in the above environmental data package have hyphens (e.g. JA-A). Instead of citing this package which is jus
Catalog of GenBank sequence read archive (SRA) entries of metagenomic DNA sequence analyses of bacterial and archaeal water column communities along the Eastern Beaufort Sea coast, North Slope, Alaska, 2012
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. This study characterizes the metabolic capabilities of microbial communities across three seasons in two lagoons and one open coastal site along the eastern Alaska Beaufort Sea coast. We used metagenomic DNA sequence data of bacterial and archaeal water column communities to identify genes of relevant biogeochemical pathways. This data package catalogs sequence read archive (SRA) entries available through GenBank BioProject PRJNA642637 at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA642637. This data package is associated with the following publication: Baker, Kristina D., Colleen T. E. Kellogg, James W. McClelland, Kenneth H. Dunton, and Byron C. Crump. “The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons.” Frontiers in Microbiology 12 (2021). https://doi.org/10.3389/fmicb.2021.601901. Environmental variables (physiochemical data from YSI and HOBO data loggers, as well as organic matter analysis and stable isotope data from discrete water samples) associated with this genomic dataset are available from the Arctic Data Center: Kenneth Dunton, Byron Crump, and James McClelland. Physical, chemical, and biological data from lagoons and open coastal waters in the nearshore environment of the eastern Alaska Beaufort Sea, 2011-2013. Arctic Data Center. doi:10.18739/A2DG13. To join the two datasets together, please use the provi
Artificial Communities Experiment: Seedling growth
This study considers the relative role of competition and facilitation in primary succession of the boreal forest floodplain of Bonanza Creek Experimental Forest. Alder (Alnus tenuifolia Nutt.) is an early colonist of young floodplain sites, where it contributes greatly to soil development through the addition of nitrogen to the soil. White spruce (Picea glauca (Moench.) Voss) typically colonizes such sites later; it becomes established beneath a canopy of alder and willow (Salix spp.) which is sometimes overtopped by young balsam poplar (Populus balsamifera L.). The alder may potentially influence white spruce both positively and negatively. Possible facilitative effects include protection of small seedlings from excess heat or heavy siltation accompanying flooding and addition of soil nitrogen, an effect that may extend for many years. Competition for light (and other resources) before the white spruce has overtopped the alder canopy may prove to be a major negative effects. This study seeks to determine the net balance of these effects on the floodplain successional sequence.
Artificial Communities Experiment: Predictor Variables
This study considers the relative role of competition and facilitation in primary succession of the boreal forest floodplain of Bonanza Creek Experimental Forest. Alder (Alnus tenuifolia Nutt.) is an early colonist of young floodplain sites, where it contributes greatly to soil development through the addition of nitrogen to the soil. White spruce (Picea glauca (Moench.) Voss) typically colonizes such sites later; it becomes established beneath a canopy of alder and willow (Salix spp.) which is sometimes overtopped by young balsam poplar (Populus balsamifera L.). The alder may potentially influence white spruce both positively and negatively. Possible facilitative effects include protection of small seedlings from excess heat or heavy siltation accompanying flooding and addition of soil nitrogen, an effect that may extend for many years. Competition for light (and other resources) before the white spruce has overtopped the alder canopy may prove to be a major negative effects. This study seeks to determine the net balance of these effects on the floodplain successional sequence.
Artificial Communities Experiment: Alder Seedlings
This study considers the relative role of competition and facilitation in primary succession of the boreal forest floodplain of Bonanza Creek Experimental Forest. Alder (Alnus tenuifolia Nutt.) is an early colonist of young floodplain sites, where it contributes greatly to soil development through the addition of nitrogen to the soil. White spruce (Picea glauca (Moench.) Voss) typically colonizes such sites later; it becomes established beneath a canopy of alder and willow (Salix spp.) which is sometimes overtopped by young balsam poplar (Populus balsamifera L.). The alder may potentially influence white spruce both positively and negatively. Possible facilitative effects include protection of small seedlings from excess heat or heavy siltation accompanying flooding and addition of soil nitrogen, an effect that may extend for many years. Competition for light (and other resources) before the white spruce has overtopped the alder canopy may prove to be a major negative effects. This study seeks to determine the net balance of these effects on the floodplain successional sequence.
Artificial Communities Experiment: Species Data for Ordination
This study considers the relative role of competition and facilitation in primary succession of the boreal forest floodplain of Bonanza Creek Experimental Forest. Alder (Alnus tenuifolia Nutt.) is an early colonist of young floodplain sites, where it contributes greatly to soil development through the addition of nitrogen to the soil. White spruce (Picea glauca (Moench.) Voss) typically colonizes such sites later; it becomes established beneath a canopy of alder and willow (Salix spp.) which is sometimes overtopped by young balsam poplar (Populus balsamifera L.). The alder may potentially influence white spruce both positively and negatively. Possible facilitative effects include protection of small seedlings from excess heat or heavy siltation accompanying flooding and addition of soil nitrogen, an effect that may extend for many years. Competition for light (and other resources) before the white spruce has overtopped the alder canopy may prove to be a major negative effects. This study seeks to determine the net balance of these effects on the floodplain successional sequence.
Tree survey:Effects of Long Term Fertilization and Oak Canopy Cover on Plant Communities and Ecosystem Processes
In 1996 E142 was established in field D on top of the E004 macroplots. E004 was conducted in fields A, B, C and D by Dave Tilman. The purpose of E004 was to see what effect NH4NO3 addition has on large areas over a longer period of time with exposure to naturally-occurring levels of herbivory. The nutrient addition treatments in E004, E142 plots have been applied annually since 1982. These experiments, along with others at Cedar Creek, examine the community and ecosystem consequences of chronic nutrient loading.
Canopy litter biomass:Effects of Long Term Fertilization and Oak Canopy Cover on Plant Communities and Ecosystem Processes
In 1996 E142 was established in field D on top of the E004 macroplots. E004 was conducted in fields A, B, C and D by Dave Tilman. The purpose of E004 was to see what effect NH4NO3 addition has on large areas over a longer period of time with exposure to naturally-occurring levels of herbivory. The nutrient addition treatments in E004, E142 plots have been applied annually since 1982. These experiments, along with others at Cedar Creek, examine the community and ecosystem consequences of chronic nutrient loading.
Herbaceous Vegetation Survey:Effects of Long Term Fertilization and Oak Canopy Cover on Plant Communities and Ecosystem Processes
In 1996 E142 was established in field D on top of the E004 macroplots. E004 was conducted in fields A, B, C and D by Dave Tilman. The purpose of E004 was to see what effect NH4NO3 addition has on large areas over a longer period of time with exposure to naturally-occurring levels of herbivory. The nutrient addition treatments in E004, E142 plots have been applied annually since 1982. These experiments, along with others at Cedar Creek, examine the community and ecosystem consequences of chronic nutrient loading.
Consequences of non-random tree species loss on litter mass loss, nutrient dynamics, carbon cycling, and decomposer communities across a terrestrial-aquatic interface at Coweeta Hydrologic Lab, Otto, NC
Although litter decomposition is a fundamental ecological process, most of our understanding comes from studies of single-species decay. Recently, litter-mixing studies have tested whether monoculture data can be applied to mixed-litter systems. These studies have mainly attempted to detect non-additive effects of litter mixing, which address potential consequences of random species loss. The focus is not on which species are lost, but the decline in diversity per se. Under global change, species loss is likely to be non-random, with some species more vulnerable to extinction than others. Under such scenarios, the effects of individual species (additivity) as well as of species interactions (non-additivity) on decomposition rates are of interest. To examine potential impacts of non-random species loss on ecosystems, we studied additive and non-additive effects of litter mixing on decomposition. A full-factorial litterbag experiment was conducted using four deciduous leaf species, from which mass loss and nitrogen content were measured. Data were analysed using a statistical approach that first looks for additive identity effects based on the presence or absence of species and then significant species interactions occurring beyond those. It partitions non-additive effects into those caused by richness and or composition.
Percent cover, species richness, and canopy height data of seagrass communities in Shark Bay, Western Australia, with accompanying abiotic data, from October 2012 to July 2013
This dataset provides cover, canopy height, and species richness estimates for seagrass communities throughout Shark Bay, as well as ancilliary physical data. These data will be used to determine spatial patterns of seagrass loss and recovery, as well as recovery rates and succisional changes in community composition, if present.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.