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6,175 results for “Composite”
Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition
<ol> <li>Microbial communities are increasingly recognised as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison to other factors such as host characteristics or spatial proximity of hosts.</li> </ol> <p> </p> <ol> <li>Here we ask how gut microbial communities are structured in a population of North American moose (<i>Alces alces</i>). We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition.</li> </ol> <p> </p> <ol> <li>We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information.</li> </ol> <p> </p> <ol> <li>We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure, or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy.</li> </ol> <p> </p> <ol> <li>Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.</li> </ol>
Effects of three-dimensional soil heterogeneity and species composition on plant biomass and biomass allocation of grass-mixtures
<p>Soil heterogeneity significantly affects plant dynamics such as plant growth and biomass. Most studies developed soil heterogeneity in two dimensions, i.e. either horizontally or vertically. However, soil heterogeneity in natural ecosystems varies both horizontally and vertically i.e. in three dimensions. Previous studies on plant biomass and biomass allocation rarely considered the joint effects of soil heterogeneity and species composition. Thus, to investigate such joint effects on plant biomass and biomass allocation, a controlled experiment was conducted, where three levels of soil heterogeneity and seven types of species compositions were applied. Such soil heterogeneity was developed by filling nutrient-rich and nutrient-poor substrates in an alternative pattern in pots with different patch sizes (small, medium or large), and species compositions was achieved by applying three plant species (i.e. Festuca elata, Bromus inermis, Elymus breviaristatus) in all possible combinations (growing either in monoculture or in mixtures). Results showed that patch size significantly impacted plant biomass and biomass allocation, which differed among plant species. Specially, at the pot scale, with increasing patch size, shoot biomass decreased, while root biomass and R: S ratio increased, and total biomass tended to show a unimodal pattern, where the medium patch supported higher total biomass. Moreover, at the substrate scale, more shoot biomass and total biomass were found in nutrient-rich substrate. Furthermore, at the community scale, two of the three target plant species growing in monoculture had more shoot biomass than those growing together with other species. Thus, our results indicate soil heterogeneity significantly affected plant biomass and biomass allocation, which differ among plant species, though more research is needed on the generalization on biomass allocation. We propose that soil heterogeneity should be considered more explicitly in studies with more species in long-term experiments.</p>
Figure 5 in Distribution and composition of Dragonfly and Damselfly species (Odonata) of the upper Rio das Velhas, Ouro Preto, Minas Gerais State, Brazil
Figure 5. Dorsolateral view of live individual of Heteragrion cauei Ávila-Júnior et al., 2017 in life. Photo: W.F. Ávila-Júnior.
Figure 4 in Distribution and composition of Dragonfly and Damselfly species (Odonata) of the upper Rio das Velhas, Ouro Preto, Minas Gerais State, Brazil
Figure 4. Odonata species accumulation curves: (A) collector method; (B) rarefaction curve. (vertical bars represent ± 2 standard deviations).
Figure 2 in Distribution and composition of Dragonfly and Damselfly species (Odonata) of the upper Rio das Velhas, Ouro Preto, Minas Gerais State, Brazil
Figure 2. Some species of the suborder Anisoptera collected in the upper Rio das Velhas, Parque Natural Municipal Cachoeira das Andorinhas, Ouro Preto Municipality, Minas Gerais State, Brazil: (a) Erythrodiplax acantha, (b) Elasmothemis alcebiadesi, (c) Zonophora campanulata machadoi, (d) Castoraeschna colorata, (e) Coryphaeschna perrensi and (f) Macrothemis heteronycha.
Figure 1 in Distribution and composition of Dragonfly and Damselfly species (Odonata) of the upper Rio das Velhas, Ouro Preto, Minas Gerais State, Brazil
Figure 1. Map showing the sampled sites in the, Parque Natural Municipal Cachoeira das Andorinhas (green line), Ouro Preto Municipality, Minas Gerais State, Brazil.
Figure 3 in Distribution and composition of Dragonfly and Damselfly species (Odonata) of the upper Rio das Velhas, Ouro Preto, Minas Gerais State, Brazil
Figure 3. Some species of the suborder Zygoptera collected in the upper Rio das Velhas, Parque Natural Municipal Cachoeira das Andorinhas, Ouro Preto Municipality, Minas Gerais State, Brazil: (a) Heteragrion cauei, (b) Heteragrion rogertaylori, (c) Telebasis carmesina, (d) Heteragrion gracile, (e) Oxyagrion basale, (f) Hetaerina longipes, (g) Minagrion waltheri and (h) Mnesarete guttifera.
Data from: Landscape composition, configuration, and trophic interactions shape arthropod communities in rice agroecosystems
<p>1. Increasing landscape heterogeneity of agroecosystems can enhance natural enemy populations and promote biological control. However, little is known about the multi-scale effects of landscape heterogeneity on arthropod communities in rice agroecosystems, especially in combination with trophic interactions. 2. We examined for the first time how landscape heterogeneity, measured by four independent metrics of landscape composition and configuration at three spatial scales, affected species abundance and species richness of rice arthropods within four functional groups and the abundance of the most common species at 28 sites in the Philippines. We additionally examined the influence of trophic interactions among these functional groups. 3. We found that both the compositional and configurational landscape heterogeneity in combination with trophic interactions determine the structure of rice-arthropod communities. Herbivore abundance decreased with increasing landscape diversity. The abundance of parasitoids and species richness of both parasitoids and predators increased with the structural connectivity of rice bunds. Fragmentation of the rice landscape had a clear negative effect on most arthropod groups, with the exception of highly mobile predatory arthropods. Abundance of common predators and detritivore species decreased with increasing complexity in the shape of rice patches. 4. Trophic interactions, measured as the abundance of prey, outweighed the importance of landscape heterogeneity for predators. In contrast, parasitoids responded positively to configurational landscape heterogeneity but were unaffected by prey abundance. 5. Synthesis and applications. Landscape heterogeneity and trophic interactions had different effects on different functional groups. While predator abundance was solely driven by the availability of prey, all other functional groups in the rice-arthropod community were significantly affected by the composition and configuration of surrounding landscape features. Landscape management aiming to improve biodiversity and biological pest control in rice agroecosystems should promote a diversity of land uses and habitat types within 100–300 m radii to reduce the presence of pests. Management practices should also focus on maintaining smaller rice patches and the structural connectivity of rice bunds to enhance populations of the natural enemies of rice pests. Future research should focus on the temporal and spatial manipulation of rice fields to maximize the effects of biological control.</p>
Diet composition and social environment determine food consumption, phenotype and fitness in an omnivorous insect
Nutrition is the single most important factor for individual's growth and reproduction. Consequently, the inability to reach the nutritional optimum imposes severe consequences for animal fitness. Yet, under natural conditions organisms may face a mixture of stressors that can modulate the effects of nutritional asymmetry. For instance, stressful environments caused by intense interaction with conspecifics. Here, we subjected the house-cricket Acheta domesticus to i) either of two types of diet that have proven to affect cricket performance and ii) simultaneously manipulated their social environment throughout their complete lifecycle. We aimed to track sex-specific consequences for multiple traits during insect development throughout all life stages. Both factors affected critical life-history traits with potential population-level consequences: Diet composition induced strong effects on insect development time, lifespan and fitness, whilst the social environment affected the number of nymphs that completed development, food consumption and whole-body lipid content. Additionally, both factors interactively determined female body mass. Our results highlight that insects may acquire and invest resources in a different manner when subjected to an intense interaction with conspecifics or when isolated. Furthermore, while only diet composition affected individual reproductive output, the social environment would determine the number of reproductive females, thus indirectly influencing population performance.
Data from: Between-year changes in community composition shape species' roles in an Arctic plant-pollinator network
Inter-annual turnover in community composition can affect the richness and functioning of ecological communities. If incoming and outgoing species do not interact with the same partners, ecological functions such as pollination may be disrupted. Here, we explore the extent to which turnover affects species' roles --as defined based on their participation in different motifs positions-- in a series of temporally replicated plant-pollinator networks from high-Arctic Zackenberg, Greenland. We observed substantial turnover in the plant and pollinator assemblages, combined with significant variation in species' roles between networks. Variation in the roles of plants and pollinators tended to increase with the amount of community turnover, although a negative interaction between turnover in the plant and pollinator assemblages complicated this trend for the roles of pollinators. This suggests that increasing turnover in the future will result in changes to the roles of plants and likely those of pollinators. These changing roles may in turn affect the functioning or stability of this pollination network.
Data from: Influences of species interactions with aggressive ants and habitat filtering on nest colonization and community composition of arboreal twig-nesting ants
Ant community assembly is driven by many factors including species interactions (e.g. competition, predation, parasitism), habitat filtering (e.g. vegetation differences, food and nesting resources), and dispersal. Canopy ant communities, including dominant and twig-nesting ants, are structured by all these different factors, but we know less about the impacts of species interactions and habitat filters acting at the colonization or recruitment stage. We examined occupation of artificial twig nests placed in shade trees in coffee agroecosystems. We asked whether species interactions -- aggression from the dominant canopy ant, Azteca sericeasur (Hymenoptera: Formicidae) -- or habitat filtering -- species of tree where nests were placed, tree size, or surrounding vegetation -- influence colonization, species richness, and community composition of twig-nesting ants. We found 20 species of ants occupying artificial nests. Nest occupation was lower on trees with A. sericeasur, but did not differ depending on tree species or surrounding vegetation. Yet, there were species-specific differences in occupation depending on A. sericeasur presence and tree species. Ant species richness did not vary with A. sericeasur presence or tree species. Community composition varied with A. sericeasur presence, tree height, and surrounding vegetation. Our results suggest that species interactions with dominant ants are important determinants of colonization and community composition of twig-nesting ants. Habitat filtering by tree species did not affect twig-nesting ants, but changes in tree size or coffee management may contribute to differences in community composition with important implications for ant conservation in agricultural landscapes, as well as biological control of coffee pests.
Liana communities exhibit different species composition, diversity and community structure across forest types in the Congo Basin
<p>Lianas are poorly characterized for central African forests. We quantify variation in liana composition, diversity and community structure in different forest types in the Yangambi Man and Biosphere Reserve, Democratic Republic of Congo. These attributes of liana assemblages were examined in 12 1-ha plots, randomly demarcated within regrowth forest, old-growth monodominant forest, old-growth mixed forest and old-growth edge forest. Using a combination of multivariate and univariate community analyses, we visualize the patterns of these liana assemblage attributes and/or test for their significant differences across forest types. The combined 12 1-ha area contains 2,638 lianas (≥ 2 cm diameter) representing 105 species, 49 genera and 22 families. Liana species composition differed significantly across forest types. Taxonomic diversity was higher in old-growth mixed forests compared to old-growth monodominant and regrowth forests. Trait diversity was higher than expected in the regrowth forest as opposed to the rest of forest types. Similarly, the regrowth forest differed from the rest of forest types in the pattern of liana species ecological traits and diameter frequency distribution. The regrowth forest was also less densely populated in lianas, and had lower liana total basal area than the rest of forest types. We speculate that the mechanism of liana competitive exclusion by dominant tree species is mainly responsible for the lower liana species diversity in monodominant compared to mixed forests. We attribute variation in liana community structure between regrowth and old-growth forests mostly to short development time of size hierarchies.</p>
Data from: Characterization of gut microbiota composition in hemodialysis patients with normal weight obesity
<p><b>Background:</b> Normal weight obesity (NWO), defined by a normal body mass index (BMI) but increased body fat percentage (BF%), is associated with an increased risk of cardiovascular disease and mortality. NWO is characterized by inflammation and muscle wasting in chronic kidney disease (CKD), but the underlying mechanisms remain largely unknown. Gut microbiota has been implicated in the regulation of host metabolism and may play important roles in the development of NWO in CKD.</p> <p><b>Methods:</b> In this case-control study, we examined the gut microbial diversity and taxonomy in 96 hemodialysis patients with normal weight (BMI <25 kg/m<sup>2</sup> and BF% ≤25% for men or ≤35% for women, n = 32), NWO (BMI <25 kg/m<sup>2</sup> and BF% >25% for men or >35% for women, n = 32), and overweight/obesity (BMI ≥25 kg/m<sup>2</sup>, n = 32), matched for age, gender, and diabetes. BF% was measured using bioimpedance spectroscopy device. Gut microbiota was determined by 16S rRNA sequencing.</p> <p><b>Results:</b> We found that α-diversity was significantly different among the 3 adiposity phenotypes, with NWO being the least diverse. α-diversity was positively correlated with BMI, subjective global assessment score, and physical activity, but negatively correlated with interleukin-6 and tumor necrosis factor-α. Patients with or without NWO were distinguished with respect to principal coordinate analysis of β-diversity. Notably, the relative abundance of butyrate-producing bacteria, such as <i>Faecalibacterium </i><i>prausnitzii</i> and<i> Coprococcus</i>, was markedly reduced in patients with NWO.</p> <p><b>Conclusion:</b> Our findings support associations between gut dysbiosis and a proinflammatory and catabolic state in hemodialysis patients with NWO.</p>
Data from: Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre
Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. OTU richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100m, 300m, and 500m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions, and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.
Community composition and photosynthetic physiology of phytoplankton in the western subarctic Pacific near the Kuril Islands with special reference to iron availability
<p class="Abstract">The western subarctic Pacific (WSP) is known as one of the most productive regions among the world's oceans in spring. However, its oceanic waters are also known as a High Nutrient, Low Chlorophyll (HNLC) region during summer due to low iron (Fe) availability in seawater. Indeed, recent studies have demonstrated that the distribution of Fe in the WSP is complex and heterogeneous. This study thus investigated the effects of Fe availability on the community composition and photophysiology of surface phytoplankton from coastal to offshore waters in the WSP in the summer of 2014. Although relatively high concentrations (>2 mg m<sup>–3</sup>) of chlorophyll (chl) <i>a</i> were found in the Sea of Okhotsk and some coastal waters, low chl <i>a</i> concentrations (<1 mg m<sup>–3</sup>) were commonly observed. Based on dissolved Fe and macronutrient concentrations, we deduced that low Fe availability limited phytoplankton growth in offshore waters, whereas low silicate and/or nitrate levels limited growth in the shelf areas. Scanning electron microscopy also revealed that the centric diatom <i>Chaetoceros</i> exclusively dominated the diatom assemblages in the shelf<i> </i>and coexisted with pennate diatoms in offshore waters, respectively<i>.</i> Primary productivity in surface waters was negatively correlated with the bottom of the euphotic layer or the light saturation index of the photosynthesis–irradiance curve, which indicates that the phytoplankton assemblages were well acclimated to <i>in situ</i> light conditions regardless of the water masses.</p>
Data from: Oyster aquaculture impacts Zostera marina epibiont community composition in Akkeshi-ko estuary, Japan
Coastal fisheries are in decline worldwide, and aquaculture has become an increasingly popular way to meet seafood demand. While finfish aquaculture can have substantial adverse effects on coastal ecosystems due mostly to necessary feed inputs, bivalves graze on natural phytoplankton and are often considered for their positive ecosystem services. We conducted two independent studies to investigate the effects of long-line Crassostrea gigas oyster aquaculture on Zostera marina seagrass beds and associated epibiont communities in Akkeshi-ko estuary, Japan. Results from both studies yielded no evidence of an effect of oyster aquaculture on the morphology, density, or biomass of Z. marina, but significant differences were apparent in the epibiont community. Reference seagrass beds located away from aquaculture had higher seagrass epiphyte loads and higher abundances of amphipods. Conversely, seagrass beds below aquaculture lines had higher sessile polychaete biomass and higher isopod abundances. Our results suggest that the presence of oyster aquaculture may have indirect effects on seagrass by changing epibiont community composition and relative abundances of species. One proposed mechanism is that cultured oysters feed on epiphytic diatoms and epiphyte propagules before they can settle on the seagrass, which reduces epiphyte loads and influences subsequent faunal settlement. If carefully implemented and monitored, long-line oyster aquaculture may be a sustainable option to consider as bivalve aquaculture expands to meet global seafood demand, but further work is needed to fully assess and generalize the community-level effects on seagrass epibionts.
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.
Figure 1 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 1. Location of the Paulo Cesar Vinha State Park – PEPCV within Brazil, State of Espírito Santo and Guarapari. Latter A and B are the Sampled point one (P1) and two (P2), letter C and D are Feia and Vermelha lagoon, respectively.
Figure 4 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 4. Principal Component Analyses of the bat composition in the Paulo CesarVinha State Park – PEPCV,Espírito Santo,Brazil.Ordination was performed by species abundance and the matrix was transformed by Hellinger procedure.
Figure 3 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 3. Observed and estimated bat species richness in the tree lagoons sampled in the Paulo Cesar Vinha State Park – PEPCV, Espírito Santo, Brazil. (A) 'Caraís' lagoon, (B) 'Feia' lagoon, (C) 'Vermelha' lagoon, and (D) Final observed and estimated species richness. Vertical bars represent 95% confidence intervals.
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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.