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492 results for “microbial communities”
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>
Data from: Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance
Because interactions between plants and microbial organisms can influence species diversity and rates of nutrient cycling, how plants shape microbial communities is fundamental to understanding the structure of ecosystems. Despite this, the spatial and temporal scales over which plants influence microbial communities is poorly understood, particularly whether past abiotic or biotic legacies strongly constrain microbial community development. We examined biogeochemical cycling and microbial community structure in a coastal landscape where historical patterns of vegetation transition after a large fire in 1995 are well known, allowing us to account for past abiotic and biotic conditions. We found that alternative states in microbial community structure and ecosystem processes emerged under different plant species, regardless of past conditions. Greenhouse studies further demonstrated that these differences arise from direct plant selection of microbes, with selection stronger in roots compared with soils, especially for bacteria. Correlation of microbial community structure with seedling growth rates was also stronger for fungi compared to bacteria. Despite these effects, minimal overlap between seedling and field microbial communities indicates that the effects of initial plant selection are not stable, rather plant selection initiated alternative successional trajectories after the fire. Using data from a guild where we have abundant natural history information - ectomycorrhizal fungi - we show that greenhouse communities are dominated by ruderal taxa that are also common in the field after the fire, and that these ruderal fungi strongly alter spatial patterns in plant-soil feedback, enabling invasion and transformation of soils previously occupied by heterospecific plants, thus potentially acting as keystone mutualists.
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.
Fertilization can accelerate the pace of soil microbial community response to rest-grazing duration in the Three-river Source Region of China
<div> <div> <p><strong><span>Objectives</span></strong> </p> <p><span>Overgrazing leads to grassland degradation and productivity decline. Rest-grazing during the regreen-up period can quickly restore grassland and fertilization is a common restoration measure. Meanwhile, soil microorganisms are more sensitive indicators. Therefore, the experiment of rest-grazing time and fertilization was carried out to explore the response of soil microorganisms to rest-grazing time and fertilization measures. </span></p> <p><span><strong>Methods</strong> </span></p> <p><span>A field control experiment with rest-grazing time and fertilization as factors was conducted from the time when grass returned to green till the livestock moved to the summer pasture in Dawu Town of Maqin County.</span> <span>The primary treatment we established was the five</span> <span>rest-grazing times, including rest-grazing times of 20 days, 30 days, 40 days, 50 days, and traditional grazing was used as a check group. At the same time, the secondary treatment was nitrogen addition of 300 kg·hm<sup>-2</sup> in each primary treatment. </span></p> <p><span><strong>Results</strong> </span></p> <p><span>The results showed that: the total phospholipid fatty acid (total PLFA), actinomyces (Act) and arbuscular </span><span>mycorrhizal fungi (AMF) showed an ever-increasing biomass with the increase of rest-grazing time and the highest was at 50 days of rest-grazing, and they were all significantly higher than CK. In addition, soil microbial biomass carbon-nitrogen ratio (MBC/MBN)</span> <span>had a great influence on the change of microbial community. Applying nitrogen fertilizer can increase the maximum value of biomass of all PLFA groups and the biomass of all PLFA groups changed in an "inverted V" shape with the increase of rest-grazing time. Besides, </span><span>instead of MBC/MBN, NO<sub>3</sub><sup>-</sup>-N</span><span> was positively affected by the biomass of</span> <span>all PLFA groups, which actively regulated the trend of microbial functions. </span></p> <p><span><strong>Conclusions</strong> </span></p> <p><span>The longer rest-grazing time is more conducive to the biomass of all PLFA groups. However, applying nitrogen fertilizer could break this pattern, namely, the 30d rest-grazing would</span> <span>be beneficial to the biomass of all PLFA groups. These findings provide key information that rest-grazing during the regreen-up period is beneficial to all PLFA groups and </span><span>fertilization could change the response of microorganisms to rest-grazing</span><span>, which provides reference measures for the restoration of degraded alpine meadows.</span></p> </div> </div>
Data for: Effect of seaweed canopy disturbance on understory microbial communities on rocky shores
<p>The collapse of macroalgal habitats is altering the structure of benthic communities on rocky shores globally. Nonetheless, how the loss of canopy-forming macroalgae influences the structure of epilithic microbial communities is yet to be explored. Here, we used experimental field manipulations and 16S-rRNA-gene amplicon sequencing to determine the effects of macroalgal loss on the understorey bacterial communities and their relationship with epiphytic bacteria on macroalgae. Beds of the fucoid <em>Hormosira</em> <em>banksii</em> were exposed to different levels of disturbance resulting in five treatments: (i) 100% removal of <em>Hormosira</em> individuals, (ii) 50% removal, (iii) no removal, (iv) a procedural control that mimicked the removal process, but no <em>Hormosira</em> was removed and (v) adjacent bare rock. Canopy cover, bacterial communities (epilithic and epiphytic) and benthic macroorganisms were monitored for 16 months. Results showed that reductions in canopy cover rapidly altered understory bacterial diversity and composition. <em>Hormosira</em> canopies in 50% and 100% removal plots showed signs of recovery over time, but understory epilithic bacterial communities remained distinct throughout the experiment in plots that experienced full Hormosira removal. Changes in bacterial communities were not related to changes in other benthic macroorganisms. These results demonstrate that understory epilithic bacterial communities respond rapidly to environmental disturbances at small scales and these changes can be long-lasting. A deeper knowledge of the ecological role of understory epilithic microbial communities is needed to better understand potential cascading effects of disturbances on the functioning of macroalgal-dominated systems.</p>
Data from: Uniqueness of tree stand composition and soil microbial communities are related across urban spruce-dominated forests
<p>The dataset contains data obtained from urban spruce-dominated forests in southern Finland where we have measured tree stand composition, forest management history, soil chemical properties, and soil microbial communities. Data files include (1) microbial OTU tables describing microbial community composition (sequence read counts of Operational Taxonomic Units) across the study plots, (2) taxonomic assignments and other metadata related to OTUs, and (3) measured and calculated variables describing the characteristics of sites and their microbial assemblages (site metadata).</p>
Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
<p>Microorganisms colonize the gastrointestinal tract of animals and establish symbiotic host-associated microbial communities that influence vertebrate physiology. More specifically, these gut microbial communities influence neurodevelopment through the microbiota-gut-brain (MGB) axis. We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (<em>Lithobates pipiens</em>) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioral responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains, and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota was associated with tadpole behavioral responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behavior and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behavior should be considered in future wildlife conservation efforts.</p>
Data for: Male, female and mixed-sex poplar plantations support divergent soil microbial communities
<p>Mixed-species forests are often more productive than monocultures because of a lower niche overlap and higher taxonomic and functional diversity of soil microbial communities. Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The potential of using sexual differences in establishing more diverse poplar plantations has not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities and seasonal variation nitrogen content differ among female, male and mixed-sex <em>Populus cathayana</em> plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced δ<sup>15</sup>N of females under inter-sexual competition. In the field, the root length density, root area density and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, module and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher β-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.</p>
Data from: Relationships between rhizosphere microbial communities, soil abiotic properties and root trait variation within a pine species
<p>Rhizosphere microbes play important roles in plant performance and ecosystem functioning. It is becoming increasingly clear that rhizosphere communities vary with soil properties and variation in root traits among plant species. However, less is known about whether and how variation in root traits within plant species influences the rhizosphere microbial communities.</p> <p>We evaluated the intraspecific root traits variation and explored their associations with bacterial and fungal communities in rhizosphere by focusing on an ectomycorrhizal tree<em> </em>species, i.e., <em>Pinus massoniana</em>, in 22 sites in subtropical China.</p> <p>The first dimension of the principal component analysis on root traits revealed evidence for the 'conservation' gradient of the root economics space. Overall, root traits explained more variation in fungal communities than in bacterial communities in the rhizosphere. Functional composition of rhizosphere microbial communities changed significantly along the 'conservation' gradient, with fast-growing copiotrophic bacteria and symbiotic ectomycorrhizal fungi were significantly enriched on the 'acquisition' side, while slow-growing oligotrophic bacteria were significantly enriched on the 'conservation' side of the gradient.</p> <p><strong><em>Synthesis</em></strong>: Our study demonstrates that intraspecific variation in plant roots significantly influence rhizosphere microbial communities, which in turn can influence plant nutrition and therefore plant performance within the community.</p>
Digital appendix: Microbial communities as sentinels of environmental changes in Svalbard (MicroSIOS)
<p>This is supplementary material for chapter 6 (MicroSIOS) in the State of Environmental Science in Svalbard (SESS) report 2024 (<span><span><a href="https://sios-svalbard.org/SESS_Issue7)%E2%80%9D" target="_blank" rel="noopener">https://sios-svalbard.org/SESS_Issue7)”</a></span></span></p>
Data for Impact of Salinity Origin on Microbial Communities in Saline Springs Within the Illinois Basin, U.S.
<p>Original data for Impact of Salinity Origin on Microbial Communities in Saline Springs Within the Illinois Basin, U.S.</p>
Data for A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community
<p>A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community data</p>
Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways
<p>It is well established that dominant plants shape belowground communities, which in turn influence ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with the plants themselves. However, we know little about how grazing moderates effects of dominant plants on belowground organisms. We established a three-year removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to explore how grazing mediates the effects of the dominant shrub, <em>Dosiphora fruticosa</em>, on nematode communities. We applied structural equation modelling to assess how grazing moderates the effects of <em>D. fruticosa</em> on nematode communities both directly and indirectly via changes in soil physicochemical properties<span>, root biomass and microbial communities</span>. We found that 1) grazing changed the direction of the direct effect of shrub on nematode communities as indicated by the shift from a negative to a positive path coefficient; 2) shrub affected nematode richness mainly through microbial richness. Accordingly, nematode community composition was more closely related to microbial community composition in the ungrazed alpine meadow, while edaphic properties were stronger predictors of nematode community composition responses to shrubs in the grazed meadow; and 3) grazing suppressed the indirect effects of shrub on nematode communities via microbial communities. Our study shows that grazing plays an important role in regulating dominant plant's effects on belowground community composition and interactions in alpine meadows.</p>
Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
<p>Generated draft and consensus reconstructions for the manuscript "COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions" (Wendering & Nikoloski).</p>
Direct and indirect effects of fire on microbial communities in a pyrodiverse dry-sclerophyll forest
<p>Fire is one of the predominant drivers of the structural and functional dynamics of forest ecosystems. In recent years, novel fire regimes have posed a major challenge to the management of pyrodiverse forests. While previous research efforts have focused on quantifying the impacts of fire on above-ground forest biodiversity, how microbial communities respond to fire is less understood, despite their functional significance.</p> <p>Here, we describe the effects of time since fire, fire frequency and their interaction on soil and leaf litter fungal and bacterial communities from the pyrodiverse, <em>Eucalyptus pilularis</em> forests of south-eastern Australia. Using structural equation models, we also elucidate how fire can influence these communities both directly and indirectly through biotic-abiotic interactions.</p> <p>Our results demonstrate that fire is a key driver of litter and soil bacterial and fungal communities, with effects most pronounced for soil fungal communities. Notably, recently burnt forest hosted lower abundances of symbiotic ectomycorrhizal fungi and Acidobacteria in the soil, and basidiomycetous fungi and Actinobacteriota in the litter. Compared with low fire frequencies, high fire frequency increased soil fungal plant pathogens, but reduced Actinobacteriota. The majority of fire effects on microbial communities were mediated by fire-induced changes in litter and soil abiotic properties. For instance, recent and more frequent fire was associated with reduced soil sulphur, which led to an increase in soil fungal plant pathogens and saprotrophic fungi in these sites. Pathogenic fungi also increased in recently burnt forests that had a low fire frequency, mediated by a decline in litter carbon and an increase in soil pH in these sites.</p> <p><em>Synthesis</em>. Our findings indicate that predicted increases in the frequency of fire <span>may select for specific microbial communities directly and indirectly through ecological interactions, which may have functional implications</span> for plants (increase in pathogens, decrease in symbionts), decomposition rates (declines in Actinobacteriota and Acidobacteriota) and carbon storage (decrease in ectomycorrhizal fungi). In the face of predicted shifts in wildfire regimes, which may exacerbate fire-induced changes in microbial communities, adaptive fire-management and monitoring is required to address the potential functional implications of fire-altered microbial communities<span>.</span></p>
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities
<p>Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.</p>
Soil microbial diversity and community composition during conversion from conventional to organic agriculture
<p>It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.</p>
Pre-processed data for "Does host plant drive variation in microbial gut communities in a recently shifted pest?"
<p>Pre-processed fastqs files generated by Illumina sequencing associated with the publication by Javal et al. entitled "Does host plant drive variation in microbial gut communities in a recently shifted pest?".</p>
Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project
<p>Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.</p>
Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
<p><span>Biochar can significantly change soil properties and improve soil quality.</span> <span>However, the effects of long-term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure and crop yield are still obscure. We characterized these relationships in a long-term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha<sup>-1</sup> year<sup>-1</sup> (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha<sup>-1</sup> year<sup>-1</sup> (N0 and N).</span><span> The repeated, long-term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon and nitrogen (MBC and MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as the amount of total phospholipid fatty acids. </span><span>The activity of leucine aminopeptidase (LAP) </span><span>decreased significantly in the biochar-amended and N fertilized treatment, but</span><span> the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum <em>Chloroflexi</em> was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α-1,4-xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN and LAP activity. In addition, long-term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield</span> <span>was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long-term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.</span></p>
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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.
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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.