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Sherbo et al. 2023 Data Package. Data associated with study assessing effects of dissolved organic matter on phytoplankton productivity in boreal lakes. The majority of data was collected in 2018 at the IISD Experimental Lakes Area in Northwestern Ontario
Allochthonous dissolved organic matter (DOM) structures many physical, chemical, and biological properties of lakes, including key variables that control productivity at the base of freshwater food webs. We examined phytoplankton biomass and productivity and their drivers, across eight pristine boreal lakes with DOM ranging from 3.5 to 9.5 mg DOC L-1. Increases in DOM were associated with significant increases in epilimnetic nitrogen, phosphorus and chlorophyll a (Chl a) concentrations suggesting that nutrients associated with DOM stimulate phytoplankton biomass and productivity. Such results were misleading; there was no significant relationship between Chl a and phytoplankton biomass measured via microscopy, and results did not incorporate the effects of DOM on thermocline and euphotic depth. Chl a:biomass and Chl a: carbon ratios indicated that increases in Chl a with DOM were driven by photo-acclimation to declining light availability. Increases. Further, increases in DOM led to large declines in thermocline (~50 %) and euphotic (~75 %) depths, and depth-integrated phytoplankton biomass and primary production (~70 %).
Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy
Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
The interactive effects of predator stress, predation, and the herbicide Roundup®
These data are from a mesocosm experiment examined how lethal predators and cues from caged predators potentially interacted with four concentrations of the herbicide Roundup® in its effects on three species of tadpoles (gray tree frogs, green frogs, bulfrogs).
Predator effects on metamorphosis: The effects of scaring versus thinning at high prey densities.
Organisms with complex life cycles face the challenge of when to switch between habitats and foraging strategies over ontogeny in ways that improve their fitness. Metamorphosis is a well-studied life history event in animals and ecologists have spent decades trying to understand how the size at and time to metamorphosis are altered by natural stressors such as competition and predation. The challenges in interpreting the effects of predators on metamorphic decisions include the need to compare predator species that pose different levels of risk, compare the roles of predators inducing fear versus thinning of the density of prey, and examine prey life history traits and behavior over ontogeny. We addressed these challenges in a mesocosm experiment in which we introduced a high initial density of hatchling Northern Leopard Frogs (Rana pipiens) and exposed them to three different species of caged predators (to induce three different levels of fear), three rates of hand-thinning (to mimic the thinning effect of each predator), or three species of lethal predators (to cause induction and thinning). Under these initial high densities, we found that caged predators had no effects on tadpole activity, growth, and development. This outcome was likely due to the high density of tadpoles causing high competition, which can inhibit anti-predator responses. High rates of hand thinning caused decreased tadpole activity, greater mass, and faster development. Interestingly, lethal predators caused phenotypic changes that were largely in line with the hand thinning effects alone. These results suggest that at high initial prey densities, the thinning process of predation appears plays a much more important role in prey metamorphosis than induction from predatory chemical cues.
Ecological memory effects on plants and soils in early post-fire steppe, Barton Ecological Research Area, Pocatello, Idaho, 2021
In many regions of the world, wildfires are becoming more frequent due to the invasion of exotic grasses that are highly flammable and often replace native plants as burned landscapes regrow. To prevent invasive species from dominating post-burn landscapes, land managers are increasingly applying seeds of native plants to suppress invasive plants and encourage ecosystem recovery. However, there is still much to learn about the ability of seeded species to establish and suppress flammable invaders. It is also unclear how previous human-caused landscape changes, such as nitrogen pollution or the removal of shrubs (a common practice in western USA rangelands), affect the success of native seed additions and plant recovery from fire. This study addresses these issues by building on a long-term experiment investigating the legacy effects of past nitrogen pollution and shrub removal in a highly invaded sagebrush steppe ecosystem at Idaho State University’s Barton Ecological Research Area in Pocatello, ID. This experiment burned in a wildfire in August, 2020, providing a unique opportunity to evaluate how a history of nitrogen pollution and shrub removal influences plant recovery from wildfire. We developed three native seed mixes intended to suppress invasive plants, particularly flammable annual grasses, and in April, 2021, we sowed the experimental mixes into research plots within the original experiment. To measure the initial effects of the experimental seed additions and the legacy effects of previous nitrogen pollution and shrub removal, we collected the data provided here during the summer of 2021, the first growing season following the wildfire. We established 240 monitoring quadrats (1 m²) within the original experiment, dividing the quadrats between areas where shrubs had formerly been (evidenced by stumps) and intershrub areas. At a microhabitat scale, the presence of shrubs alters soil properties and can create legacy effects after shrub death, and we were int
Effect of Restoration on Physical and Chemical Peat Properties in Previously Drained Boreal Peatlands, latitude 57-63, Sweden, 2021
The major objective behind peatland restoration is to improve ecosystem services, such as increased biodiversity, increased carbon sequestration, increased groundwater storage, and improved surface water quality. However, a century or more of drained conditions has drastically changed the soil properties in relation to natural wetlands and this is likely to profoundly influence the potential for various biogeochemical peat processes. Thus, peatland restoration may result in undesired impacts and potential environmental threats. Two such undesired effects are increased methane production and increased mercury methylation. In this study, we investigated how nine boreal peatlands across a latitudinal gradient in Sweden have been affected by rewetting after up to a century of drained conditions. Each peatland was sampled for three 50 cm deep peat cores that were analyzed for carbon, nitrogen, δ13C, δ15N, bulk density, and organic matter proportion. Adjacent to each restored peatland, we sampled a corresponding pristine (natural) peatland to facilitate a comparison of how the peat properties have been affected by drainage and subsequent rewetting of the peatlands. Groundwater depth was monitored at all peatland locations to confirm restored conditions at the rewetted peatlands. The results indicate that a long period of drained conditions and subsequent rewetting have changed the peat properties, with differences shown in C/N ratio, dry bulk density, and organic matter content. Rewetting will thus not regenerate a pristine environment. Instead, it creates new conditions to which various biogeochemical processes will respond and these do not necessarily represent conditions prior to disturbance. Our study will provide background information to understand the biogeochemical dynamics in peatlands after restoration, especially since the study covers a large span of nutrient conditions and catchment settings. This understanding will be fundamental for the development of strat
Influence of cockle bioturbation on microphytobenthic primary producers: habitat and density-dependent effect
The purpose of this study was to better understand the non-trophic interactions of benthic macrofauna, especially through their bioturbation activity, on microphytobenthos (MPB), which remain poorly studied and understood. For this purpose, a mesocosm experiment was performed, using the common cockles Cerastoderma edule. This species plays a key role in coastal ecosystem, especially impacting sediment characteristics and biogeochemistry through their bioturbation, including sediment reworking and bioirrigation. For the first time, bioturbation rates, biogeochemical fluxes at the sediment-water interface and MPB biomass and photosynthetic variables were measured at the same time. The effect of cockles density and sediment type were also investigated. This mesocosm experiment took place at the marine station of Arcachon. Experimental units consisted of PVC tubes filled with 2 types of sediment (medium sand or fine sand; samples in Arachon Bay and Baie des Veys in France). Then, 4 density of cockles were added in triplicate (0, 288, 720 and 1,297 ind. m-2), for each sediment type. The whole design was repeated twice, because in one of them luminophores were added at the top to measure sediment reworking, and could interfere with fluorescence measurement of MPB variables. All experimental units were incubated 6 days into a big tank, with artificial tide and light. Dissolved tracers were added into the natural seawater (close system) to measure bioirrigation rates of cockles. After 6 days, regarding experimental units with luminophores, they were slices and porewater was extracted to quantify bioturbation rates. Regarding units without luminophores, surface biomass and photosynthetic parameters of MPB were first measured in all unit with an IMAGING PAM. Then, oxygen and nutrient fluxes at the sediment water interface were measured using incubations. And finally, the first centimeter was sliced to measure total MPB biomass. This study demonstrated that bioturbation intens
Land use and management effects on soil carbon in the Lake States, Northern United States - Nave, et al 2022
There is growing need to quantify and communicate how land use and management activities influence soil organic carbon (SOC) at scales relevant to, and in the tangible control of landowners and forest managers. The continued proliferation of publications and growth of datasets, data synthesis and meta-analysis approaches allows the application of powerful tools to such questions at ever finer scales. In this analysis, we combined a literature review and effect-size meta-analysis with two large, independent, observational databases to assess how land use and management impact SOC stocks, primarily with regards to forest land uses. We performed this work for the (Great Lakes) Lake States, which comprise 6% of the land area, but 7% of the forest and 9% of the forest SOC in the U.S., as the second in a series of ecoregional SOC assessments. Most importantly, our analysis indicates that natural factors, such as soil texture and parent material, exert more control over SOC stocks than land use or management. With that for context, our analysis also indicates which natural factors most influence management impacts on SOC storage. We report an overall trend of significantly diminished topsoil SOC stocks with harvesting, consistent across all three datasets, while also demonstrating how certain sites and soils diverge from this pattern, including some that show opposite trends. Impacts of fire grossly mirror those of harvesting, with declines near the top of the profile, but potential gains at depth and no net change when considering the whole profile. Land use changes showing significant SOC impacts are limited to reforestation on barren mining substrates (large and variable gains) and conversion of native forest to cultivation (losses). We describe patterns within the observational data that reveal the physical basis for preferential land use, e.g., cultivation of soils with the most favorable physical properties, and forest plantation establishment on the most marginal so
Comparing effects of auditory and visual disturbances on smallmouth bass parental care behaviors during the summer of 2025 at Douglas Lake, Michigan, USA
A prevalent source of sensory pollution within aquatic systems is recreational motorboats that can impact aquatic organisms through several exposure mechanisms. Auditory and visual sensory disturbances are particularly important as fish may utilize these cues during critical reproductive behaviors such as parental care. Here, we conducted a field study in Douglas Lake, Michigan, and located wild smallouth bass nests actively guarded by males. We exposed smallmouth bass to two sequential treatments of playback auditory noise and visual disturbances. Using an underwater drone, parental care behaviors of smallmouth bass were monitored before, during, and after both auditory and visual disturbances. The results show that auditory and visual disturbances may alter smallmouth bass parental care behaviors differently.
Effects of chronic nutrient enrichment on plant diversity and ecosystem productivity, 2008-2019
Human activities are enriching many of Earth's ecosystems with biologically limiting mineral nutrients such as nitrogen (N) and phosphorus (P). In grasslands, this enrichment generally reduces plant diversity and increases productivity. The widely demonstrated positive effect of diversity on productivity suggests a potential negative feedback, whereby nutrient induced declines in diversity reduce the initial gains in productivity arising from nutrient enrichment. In addition, plant productivity and diversity can be inhibited by accumulations of dead biomass, which may be altered by nutrient enrichment. Over longer timeframes, nutrient addition may increase soil fertility by increasing soil organic matter and nutrient pools. We examined the effects of 5-11 years of nutrient addition at 47 grasslands in twelve countries. Nutrient enrichment increased aboveground live biomass and reduced plant diversity at nearly all sites, and these effects became stronger over time. We did not find evidence that nutrient induced losses of diversity reduced the positive effects of nutrients on biomass, however nutrient effects on live biomass increased more slowly at sites where litter was also increasing, regardless of plant diversity. This work suggests that short-term experiments may underestimate the long term nutrient enrichment effects on global, grassland ecosystems.
Salmonid habitat use monitoring used to determine effectiveness of habitat improvement projects in the Sacramento River, CA
Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains five datasets. Enclosure Study – Growth Data This dataset covers enclosure studies that examined salmonid growth rates in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Data was collected in July and August 2019 from project sites, constructed habitat project sites, and control sites where no treatment is planned. Six enclosures with juvenile Fall Run Chinook salmon from Coleman National Fish Hatchery were placed in each habitat type. Fish growth was tracked for approximately 6.5 weeks. Annual reports summarize the survey findings. Enclosure Study – Gut Contents Data This dataset covers enclosure studies that examined salmonid growth rates in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Data was collected in July and August 2019 from project sites, constructed habitat project sites, and control sites where no treatment is planned. Six enclosures with juvenile Fall Run Chinook salmon from Coleman National Fish Hatchery were placed in each habitat type. Enclosures remained in the river for approximately 6.5 weeks. At the end of the study, fish were euthanized, and we dissected their guts and enumerated the taxa found. Annual reports summarize the survey findings. Microhabitat Use Data This dataset covers salmonid microhabitat use conducted in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Surveys are conducted roughly monthly and include pre-project sites, constructed habitat project sites, and control sites where no treatment is planned. Based upon habitat inventory data, annually identify which habitat units within each side channel will be selected for the collectio
Effect of mangroves on transplanted marsh plants, Port Aransas, Texas: 2013
We transplanted three common species of salt marsh plants (Spartina alterniflora, Batis maritima, Sarcocornia sp.) into eight experimental plots (24 x 42 m) varying in plot-level mangrove cover in Port Aransas, Texas in 2013. We transplanted marsh plants into 3 x 3 m “cells” with one of 3 different vegetation treatments (cleared, mangrove, pneumatophores) in each of the eight plots. Marsh plants were harvested to measure final size.
Effects of topography on soil characteristics in the Andrews Experimental Forest, 1998
This is the third and final data set in a series of basin-scale summer forest soil surveys. We conducted soil survey in 1998 designed to provide an accurate assessment of soil properties over the entire H.J. Andrews Experimental Forest. This dataset represents the results of that effort. Since the 1994 survey, we changed the way we measured soil field respiration rates. Initially we used the 24 hr soda-lime CO2 adsorption method in chambers with only one measurement per site. In 1998 we converted to using the Li-Cor portable respirometer with 5 measurements made per site. Since 1994, it was also discovered that there were significant edge effects to 30 meters from an edge. For this reason, all sample locations were moved at least 40 meters from the road. While conducting autocorrelation analyses, we found that for the variables studied, samples collected at 5 m intervals were not autocorrelated and could thus be considered independent for statistical analysis. Our subsequent work also allowed us to chose those variables that would most likely be influenced by topography. The previous two surveys were conducted in the late summer when the forests are dry and microbial activity at a minimum. The current study was conduced from mid June to the first of July while the soils were still moist and when microbial activity was more typical of wet months. In the other two studies, only one measurement was made per site. In the current survey, replicate samples were collected and pooled or multiple measurements were made in the field. As a result of experimental design modifications, it is thought that this represents the best and most definitive dataset of basin-scale soil properties on the HJA. In the first survey, forest floor respiration rates were measured at 130 sites covering a large portion of the HJA. The sample sites were located at 0.5 km intervals along most of the main roads. In addition to field respiration rates measured by the soda-lime method, soil and air tem
Factorial experiment to test effects of food availability and temperature on slimy sculpin (Cottus cognatus) at Toolik Field Station, 2018
We used a fully factorial experiment to test effects of food availability and temperature (7.6, 12.7 and 17.4 degrees C; 50 days) on growth, consumption, respiration, and excretion of slimy sculpin (Cottus cognatus).
Tree regeneration after fire: Effects of burn severity, CPCRW soil analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains more detailed data on organic soil measurements for the site at CPCRW. Data are included from 3 measurement dates: 4 August 2000 (org. depth and pH) 23 July 2001 (org. depth, soil wet and dry weights, pH) 16 July 2002 (org. depth, sample volume, soil wet and dry weights) Dry weights were obtained following drying in an oven for 48 hourse at 40-60 degrees C.
Tree regeneration after fire: Effects of burn severity, Delta soil analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains more detailed data from organic and mineral soil measurements made in the Delta 99 burn. Note that the file format differs from the CPCRW soil datafile. Information on warming manipulation plots at the Delta site are included here. Measurements of soil organic layer depth, wet weight, dry weight, %moisture, and pH are included for 4 sample dates. Some data are available only for one or two sample dates. Samples were taken with a 5-cm hand corer, except in 2001, where a 2-cm diameter corer was used. The sample dates are: 1 August 2000 17 July 2001 11 July 2002 17 July 2002
Tree regeneration after fire: Effects of burn severity, CPCRW vegetative cover analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains visual cover estimates, by species, for 2000-2002 at the CPCRW site. Sample dates are: 4 August 2000 25 July 2001 16 July 2002. Values are percent cover in a 1x1m quadrat, where T=trace (less than 0.5%), out=outside quadrat but inside experimental plot. An additional line is included which give the full species names associated with the 6-letter codes used as column headers.
Tree regeneration after fire: Effects of burn severity, Delta vegetative cover analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains visual cover estimates, by species, for 2000-2002 at the Delta site. Data for severity and warming treatments are included. Sample dates are: 31 July 2000 18 July 2001 13 July 2002. Values are percent cover in a 1x1m quadrat, where T=trace (less than 0.5%), out=outside quadrat but inside experimental plot. An additional line is included which give the full species names associated with the 6-letter codes used as column headers.
Tree regeneration after fire: Effects of burn severity, seedling germination analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains data on seedlings that germinated in the severity plots, for seeded and un-seeded (control) subplots. Data from the control subplots has been standardized by area (seedlings/subplot, where the subplot area=0.28 m2), and could be used to estimate natural rates of seedling establishment. Control values are the same for black and white spruce, as these species could not be distinguished.
Tree regeneration after fire: Effects of burn severity, germinated seedlings analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains data on total aboveground dry biomass of germinated seedlings harvested in late August, 2002. Seedlings are separated into those found in seeded subplots (target), non-seeded control plots (ctl), or partially-seeded control plots (seed-ctl, where plots were seeded in Sept 2000 but not June 2000). Cohorts indicate the year in which the seedlings were first observed. All seedlings of a species*cohort within a subplot were weighed together, and the average weight/seedling calculated. Note that a plot entry is included in the file only where a seedling was present.
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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.