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Data from: Fungal communities are important determinants of bacterial community composition in deadwood
<p>Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns and little is known about the directionality of such interactions. Here we apply joint species distribution modelling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e. dead wood's properties), or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we test the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e. some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment, as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood.</p> <p><b>Importance</b></p> <p>Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modelling to high throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that non-random fungal-bacterial associations derive from shared habitat use, as well as (potentially) biotic interactions. Importantly,<i> </i>the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modelling approach may help gaining insight into the directionality of interactions between different components of the microbiome in other environments.</p>
RAW DATA - The role of aborescent octocorals in shaping the diversity and composition of benthic communities
<p>Spreadsheets with the raw data from the Mediterranean and Antarctic remotely operated vehicle dives used for the Spearman rank correlation analyses, linear regression models, Principal coordinates analyses and PERMANOVA.</p> <p>R code use to carry out all these analyses is also included.</p>
Plant community compositional stability over 40 years in a Fraser River Estuary tidal freshwater marsh
<p class="MsoNormal"><span>Long-term data sets documenting temporal changes in vegetation communities are uncommon, yet imperative for understanding trends and triggering potential conservation management interventions. For example, decreasing species diversity and increasing non-native species abundance may be indicative of decreasing community stability. We explored long-term plant community change over a 40-year period through the contribution of data collected in 2019 to two historical datasets collected in 1979 and 1999 to evaluate decadal changes in plant community biodiversity in a tidal freshwater marsh in the Fraser River Estuary in British Columbia, Canada. We found that plant assemblages were characterized by similar indicator species, but most other indicator species changed, and that overall </span><span>α-diversity</span><span> decreased while </span><span>β</span><span>-diversity increased. Further, we found evidence for plant assemblage homogenization through the increased abundance of invasive species such as yellow flag iris (<em>Iris pseudacorus</em>), and reed canary grass (<em>Phalaris arundinacea</em>). These observations may inform concepts of habitat stability in the absence of direct anthropogenic disturbance and corroborate globally observed trends of native species loss and non-native species encroachment. Our results indicate that within the Fraser River Estuary, active threat management may be necessary in areas of conservation concern in order to prevent further native species biodiversity loss. </span></p>
Fig. 1 in The Composition, Diversity And Community Dynamics Of Limnetic Zooplankton In A Tropical Caldera Lake (Lake Taal, Philippines)
Fig. 1. Map of Lake Taal with the six sampling sites (NB – North Basin, SB – South Basin). The insert shows the location of Lake Taal and the other lakes mentioned in the text (P – Lake Paoay, Lb – Lake Laguna de Bay, N – Lake Naujan and Ln – Lake Lanao).
Fig. 4 in The Composition, Diversity And Community Dynamics Of Limnetic Zooplankton In A Tropical Caldera Lake (Lake Taal, Philippines)
Fig. 4. Monthly variations in Shannon-Wiener Diversity (H') Index values of rotifers and cladocerans in the north and south basins of Lake Taal.
Fig. 3 in The Composition, Diversity And Community Dynamics Of Limnetic Zooplankton In A Tropical Caldera Lake (Lake Taal, Philippines)
Fig. 3. Mean monthly biomass (μg / l) of common zooplankton species from the north and south basins of Lake Taal for the year 2008.
Drivers of plant diversity, community composition, functional traits and soil processes along an alpine gradient in the central Chilean Andes
<p>The datasets in this repository include plant community surveys, hyperspectral reflectance data at the leaf and canopy level, leaf trait data, and soil chemistry data collected at five sites along an elevation gradient of 2400m-3500m in the Chilean Andes (33°S, 70°W). The purpose of this study was to evaluate the environmental drivers of community assembly processes along the elevation gradient.</p>
Figure 5 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 5. Principal components analysis of the relative abundance (mol %, logit- transformed) of individual NLFAs of Trochosa ruricola using body size (small, large), flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.
Figure 4 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 4. Variations in δ15N signatures of Trochosa ruricola as affected by flooding index (P = 0.04, R2 = 0.12) and body size (small, large; P <0.01).
Figure 1 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 1. Variations in δ15N and δ13C signatures of Harpalus rufipes (black) and Trochosa ruricola (pink) across the study site of the Jena Experiment.
Figure 3 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 3. Principal components analysis of the relative abundance (mol %, logit-transformed) of individual NLFAs of Harpalus rufipes using flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.
Figure 6 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 6. Principal components analysis of the relative abundance (mol%, logit- transformed) of individual PLFAs of soil microorganisms using flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.
Figure 2 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids
Figure 2. Variations in δ15N signatures of Harpalus rufipes (P <0.01, R2 = 0.11) as affected by plant species richness (log-transformed).
Supplementary Datasets for "Oceanic enrichment of ammonium and its impacts on phytoplankton community composition under a high-emissions scenario"
<p>These are the four supplementary datasets used in the analysis and work presented in the publication </p> <p><strong><span>Oceanic enrichment of ammonium and its impacts on phytoplankton community composition under a high-emissions scenario</span></strong></p> <p> </p>
Plankton community composition and productivity near the Subantarctic Prince Edward Islands archipelago in autumn
<p>This data set, shows hydrographic (CTD) and biogeochemical (Chl-a, nitrate+nitrite, nitrite, ammonium and silicic acid concentrations) parameters, nitrate uptake rates and net primary production, egg production rates (<em>Calanus simillimus)</em>, Pheophytin-a concentrations in zooplankton guts, and phytoplankton and zooplankton abundances and biomass from the Prince Edward Islands archipelago in the Indian Sector of the Subantarctic Ocean, during April-May 2017.</p> <p> </p>
Fig. 3 in Impact Of Coastal Wetland Restoration Strategies In The Chongming Dongtan Wetlands, China: Waterbird Community Composition As An Indicator
Fig. 3. Densities of Charadriidae (a), Anatidae (b), Ardeidae (c), and Laridae (d) among autumn, winter and spring in four sites. Error bars represent ±1 SE.
Figure 89 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 89: Reconstruction of the maximum glacial extent during the high point of the last ice-age (26 – 20 thousand years ago). Figure adapted from the publication Geologische Bundesanstalt (Hrsg.) (2013): Der Alpenraum zum Höhepunkt der letzten Eiszeit – Posterkarte. Geologische Bundesanstalt, Wien.
Figure 90 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 90: Representation of the seasonal cycle of stratification and mixing in a dimictic lake throughout a year.
Figure 88 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 88: Water temperature in lakes of the Po river catchment (orange) were generally warmer than in lakes of the Rhone (green) and Rhine (red) catchments. The lakes on the northern edge of the Alps remain cooler in summer and the lakes in the south remain warmer in winter. Upper panel shows 95 % quartile and lower panel shows 5% quartile of monthly mean lake surface water temperatures based on remote sensing (Advanced Very High Resolution Radiometer; 1989 – 2014 [214]). Quar- tiles were used rather than true minimum/maximum to avoid the effects of outliers.
Figure 85 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 85: Histograms showing variation in lake surface area (left column), lake maximum depth (middle column) and height above sea level (altitude; right column) among the major catchments.
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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.