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360 results for “microbes”
Novel plant-microbe interactions: rapid evolution of a legume-rhizobium mutualism in restored prairies
1. When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. 2. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010. Six years later, we compared how populations of the legume Chamaecrista fasciculata from these sites and their original (shared) source population responded to nitrogen-fixing rhizobia from the restoration sites in a greenhouse reciprocal cross-inoculation experiment. 3. We found that the two populations differed both from their original source population and from each other in the benefits they derive from rhizobia, that one population has evolved reduced allocation to rhizobia (i.e., forms fewer rhizobium-housing nodules). 4. Synthesis. Our results suggest that these plant populations have evolved different ways of interacting with rhizobia, potentially in response to differences in rhizobium quality between sites. Our study illustrates how microbial mutualists may shape plant evolution in new environments and highlights how variation in microbial mutualists potentially may select for different evolutionary strategies in plant hosts.
Data from: Dispersal enhances beta diversity in nectar microbes
Dispersal is considered a key driver of beta diversity, the variation in species composition among local communities, but empirical tests remain limited. We manipulated dispersal of nectar-inhabiting bacteria and yeasts via flower-visiting animals to examine how dispersal influenced microbial beta diversity among flowers. Contrary to the prevailing view that dispersal lowers beta diversity, we found beta diversity was highest when dispersal was least limited. Our analysis suggested that this unexpected pattern might have resulted from stronger priority effects under increased dispersal. Dispersal is highly stochastic, generating variability in species arrival history and consequently the potential for community divergence via priority effects, in these and likely many other microbial, plant, and animal communities. Yet most previous experiments eliminated this possibility. We suggest that the positive effects of dispersal on beta diversity, like the one we report here, may have been greatly underappreciated.
Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits
<p>Shade tolerance is a central concept in forest ecology and strongly influences forest community dynamics. However, the plant traits and conditions conferring shade tolerance are yet to be resolved. We propose that shade tolerance is shaped not only by responses to light but also by a species' defense and recovery functional traits, soil microbial communities, and interactions of these factors with light availability. We conducted a greenhouse experiment for three temperate species in the genus <em>Acer </em>that vary in shade tolerance. We grew newly germinated seedlings in two light levels (2% and 30% sun) and controlled additions of microbial filtrates using a wet-sieving technique. Microbial filtrate treatments included: <20 µm, likely dominated by pathogenic microbes; 40-250 µm, containing arbuscular mycorrhizal fungi (AMF); combination, including both filtrate sizes; and sterilized combination. We monitored survival for nine weeks and measured fine root AMF colonization, hypocotyl phenolics, stem lignin, and stem+root nonstructural carbohydrates (NSC) at three-week intervals. We found that differences in seedling survival between low and high light only occurred when microbes were present. AMF colonization, phenolics, and NSC generally increased with light. Phenolics were greater with <20 µm microbial filtrate, suggesting that soil-borne pathogens may induce phenolic production and NSC was greater with 40-250 µm filtrate, suggesting that mycorrhizal fungi may induce NSC production. Across species, microbe treatments, and light availability, survival increased as phenolics and NSC increased. Therefore, shade tolerance can be explained by interactions among soil-borne microbes, seedling traits, and light availability, providing a more mechanistic and trait-based explanation of shade tolerance and thus forest community dynamics.</p>
Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata
<p><strong>Premise of the study</strong></p> <p>Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of <em>Larrea tridentata </em>(creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes.</p> <p><strong>Methods</strong></p> <p>We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants.</p> <p><strong>Key results</strong></p> <p>Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations.</p> <p><strong>Conclusions</strong></p> <p>This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.</p>
Microbe-induced plant resistance against insect pests depends on timing of inoculation, but is consistent across climatic conditions
<ol> <li>To cope with abiotic and biotic stressors, plants have developed mutualistic associations with beneficial soil microbes, but little is known about how extreme abiotic conditions impact microbe-induce resistance to insect herbivores.</li> <li>Extreme temperatures are often accompanied by extremes in plant water availability, which together reduce plant growth and change plant physiology. There are potential consequences for increasing plant susceptibility to biotic stresses, and this poses a real challenge for plant productivity.</li> <li>We evaluated how the effects of beneficial soil bacteria (<em>Acidovorax radicis </em>N35e) on barley plant growth and resultant resistance against aphid infestation (<em>Sitobion</em> <em>avenae</em>) were impacted by a single heatwave event across a plant water availability gradient. We also tested if timing of bacterial inoculation (before or after the temperature treatment) affected bacteria-plant interactions on aphids.</li> <li>We found that heatwaves affected plant biomass allocation from aboveground to belowground tissues. Inoculation with <em>A. radicis</em> led to reduction of aphid numbers, but depended on timing of inoculation, and led to stronger resistance when inoculations occurred closer to aphid infestation. Remarkably, microbe-induced resistance against aphids was consistent across heatwave and water availability treatments.</li> <li>This study provides evidence that beneficial plant-bacteria interactions may represent a potential solution for sustainable agricultural practices to enhance plant growth and response to insect pests under climate change. Future field trials should investigate the consistency of beneficial effects reported here for a better understanding of multispecies interactions in the context of global change.</li> </ol>
Meta-analysis of the effects of abiotic factors on plant microbes
<p>The abiotic environment exerts strong effects on plant-associated microbes, shaping their interactions with plants and resulting ecosystem processes. However, these abiotic effects on plant-microbe interactions are often highly specific and contingent on the abiotic driver or microbial group, requiring synthesis work describing general patterns and from this generate hypotheses and guide mechanistic work. To address this, we conducted a meta-analysis of the effects of climate change-related abiotic factors, namely warming, drought, and eCO<sub>2</sub>, on plant-associated microbes distinguishing by microbial taxonomic or biological group (bacteria, fungi or virus) and the plant part where microbes are found or associated with (phyllosphere or rhizosphere). We found abiotic driver-specific patterns, whereby drought significantly reduced microbial abundance, whereas warming and eCO<sub>2</sub> had no significant effects. In addition, these abiotic effects were contingent on the microbial taxonomic group, with fungi being negatively affected by drought but positively affected by warming (eCO<sub>2</sub> enrichment had no effect), whereas bacteria and viruses were not significantly affected by any factor. Likewise, rhizopheric microbes were negatively affected by drought but positively affected by warming (eCO<sub>2</sub> enrichment had no effect), whereas phyllospheric microbes were not significantly affected by any factor. Collectively, these findings point to important implications for global change research by highlighting contrasting effects of climate change-related abiotic drivers on plant-associated microbes and the contingency of such effects on microbe life histories and the nature of their interactions with plants.</p>
Data from: Infant microbes and metabolites point to childhood neurodevelopmental disorders
<p>This study has followed a birth cohort for over twenty years to find factors associated with neurodevelopmental disorder (ND) diagnosis. Detailed, early-life longitudinal questionnaires captured infection and antibiotic events, stress, prenatal factors, family history, and more. Biomarkers including cord serum metabolome and lipidome, HLA genotype, infant microbiota, and stool metabolome were assessed. Among the 16,440 Swedish children followed across time, 1,197 developed an ND. Significant associations emerged for future ND diagnosis in general and for specific ND subtypes, spanning intellectual disability, speech disorder, attention deficit hyperactivity disorder, and autism. This investigation revealed microbiome connections to future diagnosis, as well as early-emerging mood and gastrointestinal problems. The findings suggest links to immunodysregulation and metabolism, compounded by stress, early-life infection, and antibiotics. The convergence of infant biomarkers and risk factors in this prospective, longitudinal study on a large-scale population establishes a foundation for early-life prediction and intervention in neurodevelopment.</p>
Data and code to reproduce analyses in Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites"
<p>This datasets archives the GitHub version found at https://github.com/ThieleLab/CodeBase to reproduce simulations for the article Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", Cell Systems, in press.</p>
Data from: From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape
<p>Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (α & β diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, <i>Bacteria</i> and <i>Archaea</i> in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the <i>Bacteria</i>, <i>Archaea</i>, and Eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off today's detectable differences in KH biodiversity between land-use types.</p>
Temperature perturbation of cellular host-microbe interactions explains continent-wide endosymbiont prevalence
<p>Endosymbioses influence host physiology, reproduction, and fitness, but these relationships require efficient microbe transmission between host generations to persist. Maternally transmitted <i>Wolbachia</i> are the most common known endosymbionts, but their frequencies vary widely within and among host populations for unknown reasons. Here we integrate genomic, cellular, and phenotypic analyses with mathematical models to provide an unexpectedly simple explanation for global <i>w</i>Mel <i>Wolbachia</i> prevalence in <i>Drosophila melanogaster</i>. Cooling temperatures decrease <i>w</i>Mel cellular abundance at a key stage of host oogenesis, producing temperature-dependent variation in maternal transmission that plausibly explains latitudinal clines of <i>w</i>Mel frequencies on multiple continents. <i>w</i>Mel sampled from a temperate climate targets the germline more efficiently in the cold than a recently differentiated tropical variant (~2,200 years ago), indicative of rapid <i>w</i>Mel adaptation to climate. Genomic analyses identify a very narrow list of <i>w</i>Mel alleles—most notably, a derived stop codon in the major <i>Wolbachia</i> surface protein WspB—that underlie thermal sensitivity of cellular<i>Wolbachia</i> abundance and covary with temperature globally. Decoupling temperate <i>w</i>Mel and host genomes further reduces transmission in the cold, a pattern that is characteristic of host-microbe co-adaptation to a temperate climate. Complex interactions among <i>Wolbachia</i>, hosts, and the environment (GxGxE) mediate <i>w</i>Mel cellular abundance and maternal transmission, implicating temperature as a key determinant of <i>Wolbachia</i> spread and equilibrium frequencies, in conjunction with <i>Wolbachia</i> effects on host fitness and reproduction. Our results motivate strategic use of locally selected <i>w</i>Mel variants for <i>Wolbachia</i>-based biocontrol efforts, which currently protect millions of individuals from arboviruses that cause human disease.</p>
Diversity and predicted function of gut microbes from two species of viviparid snails
<p>Animal gut bacteria are involved in numerous critical functions. In snails, gut bacteria play crucial roles in organic material digestion and nutrient production, and have been implicated in aspects of reproduction. Snail gut microbes are known to differ between species, and between anatomical compartments of the digestive tract; dietary changes are also known to alter snail gut flora. In an effort to better understand their diversity and function, we studied the gut microbial communities from two viviparid snails, <em>Campeloma decisum</em> and <em>Cipangopaludina japonica</em>. We were interested in whether significant differences in bacterial community composition existed between the two species, and whether differences in microbial diversity corresponded to differences in community function. Using next-generation sequencing of the bacterial 16S V4 region, we found no significant differences in alpha and beta diversity between <em>Ca. decisum</em> and <em>Ci. japonica</em>. Firmicutes and Proteobacteria were the most abundant bacterial phyla in both species, while Bacteroidetes had a higher mean abundance in <em>Ci. japonica</em>. Nine taxonomic groups were significantly different between the snail species. Pseudomonads and Enterobacteriaceae were notably more abundant in <em>Ca. decisum</em>, while Proteobacteria and Chitinophagaceae were more abundant in <em>Ci. japonica</em>. Peptidoglycan synthesis, pyruvate fermentation, and aerobic respiration by cytochrome c were the three most abundant microbial pathways represented in the viviparid gut. Fourteen functional pathways differed significantly between <em>Ca. decisum</em> and <em>Ci. japonica</em>, potentially correlated with differences in bacterial community composition and snail life history. Our data fill in data gaps regarding gut microbes in Viviparidae, and highlight future research paths examining the prevalence of Firmicutes and unidentified diversity in both snail species.</p>
Interactions between soil microbes and native species drive a diversity-invasibility relationship
<p>Soil microbes can affect both the invasiveness of exotic plants and the invasibility of native plant communities, but it still remains unclear whether soil microbes can influence the relationship between native plant species diversity and community invasibility. We constructed native plant communities with three levels of species richness (one, three, or six species) in un-sterilized or sterilized soil (i.e., with or without soil microbes) and let them not be invaded by exotic plant species or invaded by one of three exotic species (<em>Solidago canadensis</em>, <em>Erigeron canadensis</em> or <em>Symphyotrichum subulatum</em>) highly invasive in China. The soils conditioned by the native plant communities not invaded by the exotic species were used as soil microbe inocula to test whether richness-induced differences in soil microbes affect the growth of each of the three invasive species. Compared with the presence of soil microbes, the absence of soil microbes weakened the negative species richness-invasibility relationship, indicating that soil microbes can contribute to the higher invasion resistance of more diverse native plant communities. In the presence of soil microbes, the higher invasion resistance of more diverse communities was mainly ascribed to the complementarity effect. However, soil microbes from communities with a higher species richness did not have a stronger negative effect on the growth of any of the three invasive species. We conclude that soil microbes can alter the diversity-invasibility relationship through promoting the complementarity effect on the community invasion resistance. Our results highlight the importance to integrate the role of soil microbes in testing the diversity-invasibility hypothesis.</p>
Soil microbes respond to four-year warming and precipitation alteration
<p><span>The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon (SOC), which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon (C) stock changes under future climate warming is hampered by our limited understanding of below-ground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH<sub>4</sub>) uptake by 93.8% and aerobic respiration (CO<sub>2</sub>) by % in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO<sub>2</sub> exchange (NEE), the warming-stimulated CH<sub>4</sub> uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation didn't alter such warming effects, despite the significant effects of precipitation on NEE and soil CH<sub>4</sub> flux</span><span><span>es</span><span> were observed. Metagenomic sequencing revealed that </span></span><span>warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (<em>R<sup>2</sup> </em>= 0.59, <em>P</em> < 0.001) correlated with warming-enhanced CH<sub>4</sub> uptakes. Furthermore, 212 metagenome-assembled genomes (MAGs) were recovered, including many populations involved in the degradation of various organic matter and a highly-abundant methylotrophic population of the <em>Methyloceanibacter</em> genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH<sub>4 </sub>and CO<sub>2</sub> cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially-enhanced CH<sub>4</sub> uptake.</span></p>
Microbe Directory Data v1.0.0
<p>This upload contains the data from v1.0.0 of The Microbe Directory.</p> <p> </p> <p>The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart (https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.</p>
Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship
<p>Understanding the relationship between plant diversity and invasibility is essential in invasion ecology. Species-rich communities are hypothesized to be more resistant to invasions than species-poor communities. However, while soil microorganisms play a crucial role in regulating this diversity–invasibility relationship, the effects of plant competition mode and soil nutrient status on their role remain unclear. To address this, we conducted a two-stage greenhouse experiment. Soils were first conditioned by growing nine native species separately in them for 1 year, then mixed in various configurations with soils conditioned using one, three, or six species, respectively. Next, we inoculated the mixed soil into sterilized substrate soil and planted the alien species <em>Rhus typhina</em> and native species <em>Ailanthus altissima</em> as test plants. We set up two competition modes (intraspecific and interspecific) and two nutrient levels (fertilization using slow-release fertilizer and non-fertilization). Under intraspecific competition, regardless of fertilization, the biomass of the alien species was higher in soil conditioned by six native species. By contrast, under interspecific competition, the biomass increased without fertilization but remained stable with fertilization in soil conditioned by six native species. Analysis of soil microbes suggests that pathogens and symbiotic fungi in diverse plant communities influenced <em>R. typhina</em> growth, which varied with competition mode and nutrient status. Our findings suggest that the soil microbiome is pivotal in mediating the diversity–invasibility relationship, and this influence varies according to competition mode and nutrient status.</p>
Genetic architecture of heritable leaf microbes
<p><em>Background</em></p> <p>Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown, yet fundamental to the community assembly of host-associated microbiomes, and with implications for the eco-evolutionary dynamics of microbes and hosts. Using <em>Ipomoea hederacea</em>, Ivy-leaved morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome, and how these two sources of genetic variation contributed to microbe heritability.</p> <p><em>Results</em></p> <p>We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation were important in contributing to microbe heritability, and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some microbes in the leaf microbiome.</p> <p><em>Conclusions</em></p> <p>The genetic architecture of plant-associated microbiomes depends on both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. Our results demonstrate the roles of different scales of host genetic variation in the assembly of a natural microbiome. The genetic basis and heritability of a host's microbial phenotype is important for host evolution and ecology because microbes can affect host fitness, and because it can influence reciprocal selection between hosts and microbiomes. Additionally, when host-associated microbiomes have heritability, then this suggests they have the capacity to evolve as other host traits might, with potentially adaptive functions.</p>
Carbon Dioxide and Methane Flux Meta Analysis, Schaerer et al: Permafrost microbes unleashed: thaw reactors provide timely insights into greenhouse gas feedbacks for climate stewardship
<p>Meta-analysis results and workflow: <strong>Meta-Analysis-Report-V1.pdf</strong> </p> <p>raw data tables for input into meta-analysis:</p> <p><strong>co2_flux_by_layer_temp.csv</strong></p> <p><strong>co2_flux_by_layer_time.csv</strong></p> <p><strong>ch4_flux_by_layer_temp.csv</strong></p> <p><strong>ch4_flux_by_layer_time.csv</strong></p> <p><strong>co2_flux_by_headspace_temp.csv</strong></p> <p>(Data included in these tables was digitized using the R package metaDigitize)</p> <p>****</p> <p>We also attempted to summarize the raw data from 12 studies which is summarized in the <strong><em>Flux_Summary_Report </em></strong>document. we converted all units into mg C / g Soil * d (calculations are included in the <strong><em>co2_meta_analysis</em></strong> spreadsheet). For studies not reporting raw data or data tables (7/12 studies), we estimated the values from the figures manually. This typically resulted in an estimate of the mean flux of several replicates (all studies had 3-10 replicates). We filled in metadata as well as we could based on the information available in the papers, although there were many gaps. This information is summarized in the <strong><em>flux_data_compilation</em> </strong>spreadsheet.</p> <p>Studies in the raw data comparison include: Mackelprang 2011, Waldrop 2010 & 2021, Barbato 2022, Dang 2022, Muller 2018, Monteaux 2020, Dutta 2006, Lee 2012, O'Donnell 2009, Roy Chowdhury 2014, Trubl 2021.</p>
ODIS Graph marine microbe related entries
<p>All extracted URIs and dataset descriptions from the ODIS graph mentioning any of the top 100 most frequent words directly associated to marine microbes.</p> <p>See Sallard, G. Extracted microbial terms from Wikipedia - Marine Microbiology related pages (refined), https://doi.org/10.5281/zenodo.12651803 for the index used for the SPARQL query.</p> <p> </p> <p> </p>
Habitat quality drives the species-area relationship of plants and soil microbes in an ocean archipelago
<p>While the positive species-area relationship on islands is frequently observed, the mechanisms underlying this pattern remain poorly studied. By analyzing insular community diversity across spatial scales and the soil properties within the islands, we were able to explore potential mechanisms leading to the island species-area relationship of plants, as well as associated soil bacteria and fungi, from a tropical archipelago.<strong> </strong>We found that both plant and soil microbial communities showed similar positive species-area relationships across scales and the greater taxonomic diversity on larger islands was mainly driven by the higher richness within samples. These patterns arose primarily due to shifting habitat quality with island area, rather than spatial processes generally attributed to species-area relationships. Specifically, for plants, changes in soil total phosphorus content with island area were most explanatory, while changes in soil pH appeared to play the most important role in shaping soil bacteria and fungi patterns. By contrast, we found little evidence for the role of spatial processes (i.e., dispersal limitation or soil heterogeneity) within the island.<strong> </strong>Overall, this study highlights the importance of dissecting potential mechanisms underlying multi-trophic community dynamics to explain patterns of biodiversity and its variation on islands.</p>
Trait Spreadsheet to DwCA: Microbes Ecomorphological Guilds
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Created: 2022-09-29 15:12
ScienceDex guides
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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.