Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Bacterial Community Weighted rrn Operon Copy Numbers and Enzyme Activity in Costa Rica and Alaska Soils.

Datasets of bacterial community weighted rrn operon copy number and enzyme activity in Alaska and Costa Rica soils. The Alaska soils were collected from across four elevational terraces in a tidal wetland on the western coast. The Costa Rica soils were collected from plots subjected to precipitation manipulation treatments in La Selva Biological Research Station.  The variable descriptions for the Alaska dataset are as follows: simple_id: an identifier variable. id: an identifier variable that includes terrace identity. transect_id: a variable that identifies collection transect location. BG_umol_g_h: the activity rate of beta-glucosiadase in micromoles per gram soil per hour. NAG_umol_g_h: the activity rate of N-acetyl-glucosaminidase in micromoles per gram soil per hour. LAP_umol_g_h: activity rate of leucine-aminopeptidase in micromoles per grams soil per hour. AP_umol_g_h: the activity rate of acid phosphatase in micromoles per gram soil per hour. BG_g_C: the activity rate of beta-glucosiadase in micromoles per gram soil carbon per hour. NAG-g_N: activity rate of N-acetyl-glucosaminidase in micromoles per gram soil nitrogen per hour. LAP_g_N: activity rate of leucine-aminopeptidase in micromoles per gram soil nitrogen per hour. AP_mg_P: activity rate of acid-phosphatase in micromoles per gram soil phosphorus per hour. P_mg_kg: soil phosphorus concentration in milligrams phosphorus per kilogram soil. K_mg_kg: soil potassium concentration in milligrams potassium per kilogram soil. C_pct: soil carbon concentration in percent. N_pct: soil nitrogen concentration in percent. pH: soil pH. cn_ratio: the carbon-to-nitrogen ratio of soil. cp_ratio: the carbon-to-phosphorus ratio of soil. np_ratio: the nitrogen to phosphorus ratio of soil. weighted_copy_number: the bacterial community weighted rrn operon copy number. The variable descriptions for the Costa Rica dataset are as follows: ID: a variable that identifies the soil core collected. Plot: a variable that identifies the experimental plot from which soils were collected. Precip: a variable that describes the precipitation manipulation treatment applied. Core: a variable that identifies whether soil cores were enclosed in mesh or not. Moisture: the soil moisture of the collected core in grams water per grams dry soil. weighted copy_number: the bacterial community weighted rrn operon copy number. AP: activity rate of acid-phosphatase in micromoles per gram soil  per hour. BG: the activity rate of beta-glucosiadase in micromoles per gram soil per hour. Also included are files of the code used to analyze the data in the R Statistical Computing Environment.

opencc-by-4.0Nov 2023View details →

Data and scripts for: Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities

These files include the data, the scripts, and the pipeline for bioinformatic analyses for reproducing the results presented in the manuscript "Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities". Description of the files can be found from the README.docx file.

Climate warming shifts riverine macroinvertebrate communities to be more sensitive to chemical pollutants

Freshwaters are highly threatened ecosystems that are vulnerable to chemical pollution and climate change. Freshwater taxa vary in their sensitivity to chemicals and changes in species composition can potentially affect the sensitivity of assemblages to chemical exposure. Here we explore the potential consequences of future climate change on the composition and sensitivity of freshwater macroinvertebrate assemblages to chemical stressors using the UK as a case study. Macroinvertebrate assemblages under end of century (2080-2100) and baseline (1980-2000) climate conditions were predicted for 608 UK sites for four climate scenarios corresponding to mean temperature changes of 1.28°C to 3.78°C. Freshwater macroinvertebrate toxicity data were collated for 19 chemicals and the hierarchical Species Sensitivity Distribution (hSSD) model was used to predict the sensitivity of untested taxa using relatedness within a Bayesian approach. All four future climate scenarios resulted in shifts in assemblage composition, with increases in the prevalence of molluscan, crustacean and annelid species, and towards increasing insect taxa of Odonata, Chironomidae, and Baetidae species. In contrast decreases in were projected for Plecoptera, Ephemeroptera (except for Baetidae) and Coleoptera species. Shifts in taxonomic composition were associated with changes in the percentage of species at risk from chemical exposure. For the 3.78°C climate scenario, 76% of all assemblages became more sensitive to chemicals and for 18 of the 19 chemicals, the percentage of species at risk increased. Climate warming-induced increases in sensitivity were greatest for assemblages exposed to metals and were dependent on baseline assemblage composition, which varied spatially. Climate warming is predicted to result in changes in the use, environmental exposure and toxicity of chemicals. Here we show that, even in the absence of these climate-chemical interactions, shifts in species composition due to climate warming will increase chemical risk and that the impact of chemical pollution on freshwater macroinvertebrate biodiversity may double or quadruple by the end of the 21st century.

Data from: Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition

Antibiotic resistance genes (ARGs) benefit host bacteria in environments containing corresponding antibiotics, but it is less clear how they are maintained in environments where antibiotic selection is weak or sporadic. In particular, few studies have measured the effect of ARGs on host fitness in the absence of direct selection or determined if any costs are fixed or depend on the host strain, perhaps marking some ARG-host combinations as reservoirs that can maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in 11 diverse Escherichia spp. strains. Three ARGs (blaTEM-116, cat, and dfrA5, encoding resistance to β-lactams, chloramphenicol, and trimethoprim, respectively) imposed an overall cost but all ARGs had an effect in at least one host strain, reflecting a significant strain interaction effect. A simulation predicts these interactions cause the success of ARGs to depend on available host strains, and, to a lesser extent, for successful host strains to depend on the ARGs present in a community. These results indicate the importance of considering ARG effects over different host strains, especially the potential of reservoir strains that allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.

openmit-licenseMay 2024View details →

Source Data for main text and supplemental figures for manuscript "Community assessment of methods to deconvolve cellular composition from bulk gene expression"

Source Data for main text and supplemental figures for manuscript "Community assessment of methods to deconvolve cellular composition from bulk gene expression"

Data from: Migratory singers dynamically overlap the signal space of a breeding warbler community

Migratory species inhabit many communities along their migratory routes. Across taxa, these species repeatedly move into and out of communities, interacting with each other and locally breeding species and competing for resources and niche space. However, their influence is rarely considered in analyses of ecological processes within the communities they temporarily occupy. Here, we explore the impact of migratory species on a breeding community using the framework of acoustic signal space, a limited resource in which sounds of species within communities co-exist. Migrating New World warblers (Parulidae, hereafter referred to as migrant species) often sing during refueling stops in areas and at times during which locally breeding warbler species (hereafter breeding species) are singing to establish territories and attract mates. We used eBird data to determine co-occurrence of 19 migrant and 11 breeding warbler species across spring migration in SW Michigan, generated a signal space from song recordings of these species, and examined patterns of signaling overlap experienced by breeding species as migrants moved through the community. Migrant species were present for two-thirds of the breeding season of local species, including periods when breeding species established territories and attracted mates. Signaling niche overlap experienced by individual breeding species was idiosyncratic and varied over time, yet niche overlap between migrant and breeding species occurred more commonly than between breeding species or between migrant species. Nevertheless, the proportion of niche overlap between migrant and breeding warblers was similar to overlap among breeding species. Our findings showed that singing by migrant species overlapped the signals of many breeding species, suggesting that migrants could have unexplored impacts on communication in breeding species, potentially affecting song detection and song evolution. Our study contributes to a growing body of research documenting impacts of migratory species on communities and ecosystems.

Data from: Climatic disequilibrium of recruit communities across a drought-induced die-off gradient in Mediterranean shrubland

Positive plant–plant interactions (facilitation) may enhance the recruitment and establishment of species less adapted to local macroclimatic conditions. A major cause of this effect is climatic buffering, which implies an increased mismatch between the macroclimatic conditions and the climatic requirements of the existing community – climatic disequilibrium – of plants living under canopies. Here we explore the effect of drought-induced defoliation of Mediterranean shrubland canopy on the recruitment of woody species. We analyzed the differences in the climatic disequilibrium across different categories of canopy defoliation and plant–plant interactions: facilitation, neutral and inhibition. Climatic disequilibrium was estimated as the Euclidean distance in the multivariate environmental space between observed macroclimate and community inferred climate. The inferred climate was calculated by averaging the coordinates of the species' climatic niche centroids, obtained from species distribution, weighted by the species' relative abundances in each community. We found that the recruiting community growing under canopy showed higher climatic disequilibrium than the community growing in the gaps. The facilitated recruiting community growing under dead and living canopy showed the highest disequilibrium, followed by the community growing under mid-affected canopy. The climatic disequilibrium of the recruiting communities experiencing neutral and inhibited interaction was not affected by canopy defoliation. These findings indicate that the climatic disequilibrium of the recruiting community is determined by the facilitation–competition balance. Living canopy provides climatic buffering, but it also implies competition, while dead canopy may provide some structural climatic buffering, without implying competition for resources. These results highlight the relevance of incorporating plant–plant interactions, particularly facilitation, to better forecast plant community responses to extreme climate events and climate change.

opencc-by-4.0May 2024View details →

Tara Pacific 16S rRNA ASV table for bacterial communities of crustose coralline algae from the Tuamotu archipelago (French Polynesia)

This data is the result of the primary analysis of the 16S rRNA gene sequencing data collected from the CCA samples collected  during the Tara Pacific expedition. The analysis was conducted using cutadapt/snakemake/dada2 and usearch. A full README is contained within the parent data upload (<a href="https://doi.org/10.5281/zenodo.4451892">https://doi.org/10.5281/zenodo.4451892</a>).

Data from: Species richness and evenness of European bird communities show differentiated responses to measures of productivity

Understanding patterns of species diversity is crucial for ecological research and conservation, and this understanding may be improved by studying patterns in the two components of species diversity, species richness and evenness of abundance of species. Variation in species richness and evenness has previously been linked to variation in total abundance of communities as well as productivity gradients. Exploring both components of species diversity is essential because these components could be unrelated or driven by different mechanisms. The aim of this study was to investigate the relationship between species richness and evenness in European bird communities along an extensive latitudinal gradient. We examined their relationships with latitude and Net Primary Productivity, which determines energy and matter availability for heterotrophs, as well as their responses to territory densities (i.e., the number of territories per area) and community biomass (i.e., the bird biomass per area). We applied a multivariate Poisson log-normal distribution to unique long-term, high-quality time-series data, allowing us to estimate species richness of the community as well as the variance of this distribution, which acts as an inverse measure of evenness. Evenness in the distribution of abundance of species in the community was independent of species richness. Species richness increased with increasing community biomass, as well as with increasing density. Since both measures of abundance were explained by NPP, species richness was partially explained by energy-diversity theory (i.e., the more energy, the more species sustained by the ecosystem). However, species richness did not increase linearly with NPP but rather showed a unimodal relationship. Evenness was not explained either by productivity nor by any of the aspects of community abundance. This study highlights the importance of considering both richness and evenness to gain a better understanding of variation in species diversity. We encourage the study of both components of species diversity in future studies, as well as use of simulation studies to verify observed patterns between richness and evenness.

opencc-by-4.0May 2024View details →

Species-specific differences in bumblebee worker body size between elevations: Implications for pollinator community structure under climate change

Code and dataset for manuscript titled "Species-specific differences in bumblebee worker body size between elevations: Implications for pollinator community structure under climate change". Authors: Caterina Massa, Janneke Hille Ris Lambers, Sarah K. Richman. Manuscript accepted to Journal of Pollination Ecology in May 2024. All data collected and analyzed by the authors.

opencc-zeroJun 2024View details →

Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly

The intricate mechanisms shaping plant diversity and community composition are the cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis, the fundamental partnership between fungi and plant roots, in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1,315 terrestrial ecosystem sites to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and its implications for community assembly processes. Our findings demonstrate that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Furthermore, we unveil a distinct dichotomy in the assembly processes governed by mycorrhizal status. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the complex mechanisms shaping ecological communities and the way for more informed conservation and management practices that acknowledge the complex interplay between symbiosis and ecological community dynamics.

opencc-zeroJun 2024View details →

Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes

Unraveling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. To understand the response of individual animals to environmental change, physiology and individual metabolism are often studied. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behavior in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.

Figure 3 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil

Figure 3. Locations and copy numbers for human- and ruminant-indicative Bacteroides spp. DNA extracted from the material retained from filtration of 500 ml was used for qPCR determination of rDNA copy number. The size of the indicated shapes in the figure is proportional to the copy number/ml at that point as indicated in the legend. Inset shows points 12 and 13 at the same scale as the main figure.

Figure 2 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil

Figure 2. Locations and concentrations of coliforms and E. coli at water collection points. A volume of water (100 µl – 1 ml) collected mid-stream was plated using the Coliscan culture system. Colonies were identified and counted at 48h. The size of the indicated shapes in the figure is proportional to the number of colonies/ml cultured as indicated in the legend. Inset shows points 12 and 13 at the same scale as the main figure.

Figure 1 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil

Figure 1. Study area, rivers and water collection sites. The collection points on the Jiquiriçá River are P1-5; collection points on the Brejões P6-8. P3 is at the junction of the 2 rivers, and P9 and P10 are from the water treatment plant and an outside faucet, respectively. Left inset – Location of Bahia state, Salvador and Jenipapo within Brazil based on Wikimedia Commons (2011). Right inset – relationship of P12 and P13 to Jenipapo. These 2 points represent the source of piped water for the community and the furthest point upstream for collection on the Brejões River, respectively. Inset modified from Wikimedia Commons (2011).

opencc-by-4.0Jun 2024View details →

Survey of herbaceous communities in St Martin de Londres basin

The repository documents the composition of mediterranean herbaceous communities obtained from a survey of 12 sites in St Martin de Londres basin, south of France. It also provides measures of sites environmental condition. Plant sampling took place in 2010 and is described in Ehlers et al. (<a href="https://doi.org/10.1111/1365-2745.12171">10.1111/1365-2745.12171</a>). The design involves quadrats with and without wild thyme in each site. The 12 csv files with four-letter names provides species-per-quadrat presence (1) -absence (0) data derived from this sampling. For some plant species, the percentage of cover in quadrats is available (numbers above 1). The envData.csv file contains environmental data independently obtained in a set of sites of St Martin de Londres basin in 2013, some of them matching the plant survey sites.

Figure 4 in Community structure of benthic invertebrates in the Allipén River basin, North Patagonia, Araucania region (38º S, Chile)

Figure 4. Mean abundance (individuals/m2) the families more representative of benthic macroinvertebrates at site 3 Las Hortensias in the Allipen river.

Figure 3 in Community structure of benthic invertebrates in the Allipén River basin, North Patagonia, Araucania region (38º S, Chile)

Figure 3. Mean abundance (individuals/m2) the families more representative of benthic macroinvertebrates at site 2 Huereré in the Allipen river.

Figure 1 in Community structure of benthic invertebrates in the Allipén River basin, North Patagonia, Araucania region (38º S, Chile)

Figure 1. Map of Allipen river, Tolten river basin, La Araucania Region Chile.Where S1 "Melipeuco" (265639 S, 5694829 W), S2: "Huerere" (758774 S- 5681448 W) and S3: "Las Hortensias" (746454 S; 5684086 W) represent the specific sampling stations, respectively.

Figure 2 in Community structure of benthic invertebrates in the Allipén River basin, North Patagonia, Araucania region (38º S, Chile)

Figure 2. Mean abundance (individuals/m2) the families more representative of benthic macroinvertebrates at site 1 Melipeuco in the Allipen river.