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188 results for “Microbial diversity”
Data from: Long-term balanced fertilization improves the soil microbial functional diversity in a phosphorus-limited paddy soil
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Data from: Plant diversity improves resistance of plant biomass and soil microbial communities to drought
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Data from: Interactive effects of soil moisture, air temperature and litter nutrient diversity on soil microbial communities and Folsomia candida population
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Soil microbial respiration rate:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Figure 2 from: Heintz-Buschart A, Guerra C, Djukic I, Cesarz S, Chatzinotas A, Patoine G, Sikorski J, Buscot F, Küsel K, Wegner C-E, Eisenhauer N (2020) Microbial diversity-ecosystem function relationships across environmental gradients. Research Ideas and Outcomes 6: e52217. https://doi.org/10.3897/rio.6.e52217
Figure 2 Overview of the sample collection. Decomposition, as a central soil function, and the biodiversity of involved microbial communities will be studied in a large, international monitoring network (sampling locations indicated in a) to assess the generality of microbial biodiversity-function relationships across climates (mean annual air temperature and annual precipitation in b) and land use and cover types (c).
Figure 1 from: Heintz-Buschart A, Guerra C, Djukic I, Cesarz S, Chatzinotas A, Patoine G, Sikorski J, Buscot F, Küsel K, Wegner C-E, Eisenhauer N (2020) Microbial diversity-ecosystem function relationships across environmental gradients. Research Ideas and Outcomes 6: e52217. https://doi.org/10.3897/rio.6.e52217
Figure 1 A Environmental change and heterogeneity determine the biodiversity and the functioning of ecosystems (modified after Eisenhauer et al. 2016). In addition, changes in biodiversity can have significant effects on ecosystem functioning, which can be masked by strong environmental gradients. Only by accounting for environmental heterogeneity can the role of biodiversity for ecosystem functioning be wholly realized (Grace et al. 2016). B Hypothesized positive relationship between microbial diversity and decomposition (overall positive relationship with confidence intervals; no real data was used to create this figure). The diversity gradient in soil microbes is supposed to be caused by different environmental conditions. The different grey lines indicate BEF relationships across different experimental and environmental gradients.
Soil microbial legacy drives crop diversity advantage: linking ecological plant-soil feedback with agricultural intercropping
<ol> <li>Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant-soil feedback (PSF) theory and method, we quantified how much soil microbes contributed to intercropping overyielding and detected which microbial groups mediated this effect.</li> <li>Soils were collected as inocula and sequenced from a unique 10-year field experiment, consisting of monoculture, intercropping and rotation planted with wheat (<i>Triticum aestivum</i>), maize (<i>Zea mays</i>) or faba bean (<i>Vicia faba</i>). A PSF study was conducted to test microbial effects on three crops' growth in monoculture or intercropping.</li> <li>In wheat & faba bean (W&F) and maize & faba bean (M&F) systems, soil microbes drove intercropping overyielding compared to monoculture, with 28-51% of the overyielding contributed by microbial legacies. The overyielding effects resulted from negative PSFs in both systems, as crops, in particular faba bean grew better in soils conditioned by other crops than itself. Moreover, faba bean grew better in soils from intercropping or rotation than from the average of monocultures, indicating a strong positive legacy effect of multispecies cropping systems. However, with positive PSF and negative legacy benefit effect of intercropping/rotation, we did not observe significant overyielding in the W&M system.</li> <li>With more bacterial and fungal dissimilarities by metabarcoding in heterospecific than its own soil, the better it improved faba bean growth. More detailed analysis showed faba bean monoculture soil accumulated more putative pathogens with higher <i>Fusarium</i> relative abundance and more <i>Fusarium oxysporum</i> gene copies by qPCR, while in heterspecific soils, there was less pathogenetic effects when cereals were engaged. Further analysis in maize/faba bean intercropping also showed an increase of rhizobia relative abundance.</li> <li> <i>Synthesis and applications</i>. Our results demonstrate a soil microbiome-mediated advantage in intercropping through suppression of the negative PSF of pathogens and increasing beneficial microbes. As microbial mediation of overyielding is context-dependent, we conclude that the dynamics of both beneficial and pathogenic microbes should be considered in designing cropping systems for sustainable agriculture, particularly including combinations of legumes and cereals.</li> </ol>
Data from: Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits
Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43) for fungi. Using variance partitioning, we showed that the effect of aboveground vegetation was the most significant descriptor for both bacterial and fungal communities. The floristic significant predictors explained 43% of the variation for both the bacterial and fungal community structures, while the edaphic significant predictors explained only 32% and 31% of these variations, respectively. These results confirm the previous hypothesis that the distribution of microorganisms was more structured by the vegetation cover rather than the edaphic characteristics and that microbial diversity is not limited in ultramafic ecosystems.
Data from: Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long-term fertilization management
1.An increasing number of studies indicate that microbial diversity plays a crucial role in the mediation of ecosystem multifunctionality (EMF) in natural ecosystems. However, this point remains mostly overlooked in managed ecosystems, especially in agriculture. 2.Here, we compiled promising strategies for the targeted exploitation of the associations between microbial diversity and EMF of agricultural soils using samples from two long-term (more than 30 years) experimental field sites in southern China. The two sites experienced a similar subtropical monsoon climate and fertilization management practices. We used high-throughput amplicon sequencing, structural equation modeling (SEM), and random forest analysis, to analyze our data and validate our hypotheses. 3.We found that soil physiochemical properties and the C-, N-, P- and S-cycle enzyme activities were increased with the increase of microbial diversity. Specifically, a positive linear relationship was observed between microbial diversity and EMF, which was mediated by long-term fertilization management via changes in soil microbial communities and physiochemical properties. Random forest analysis and SEM showed that the important role of microbial diversity on EMF was maintained even when simultaneously taking multiple multifunctionality drivers (soil physiochemical properties, soil aggregation and enzymatic patterns) into account. In addition, microbial diversity, C-cycle enzyme activity and pH value are feasible predictors of EMF; these factors were shown to be the main drivers of EMF of arable soils. 4. Our findings suggest that there may be a limited degree of multifunctional redundancy in arable soils. The relationship we observed between microbial diversity and EMF suggests that management practices that foster more diverse soil microbial communities may have the potential to improve the functioning of agroecosystems.
Data from: Plant, soil and microbial controls on grassland diversity restoration: a long-term, multi-site mesocosm experiment
The success of grassland biodiversity restoration schemes is determined by many factors; as such their outcomes can be unpredictable. There is a need for improved understanding of the relative importance of belowground factors to restoration success, such as contrasting soil type and management intensities, as well as plant community composition and order of assembly. We carried out an eight-year mesocosm experiment across three locations in the UK to explore the relative and interactive roles of various aboveground and belowground factors in the establishment of target species, to determine general constraints on grassland restoration. Each location had a series of mesocosms with contrasting soil types and management status, which were initially sown with six grasses typical of species-poor grasslands targeted for restoration. Over five years, sets of plant species were added, to test how different vegetation treatments, including early-coloniser species and the hemiparasite Rhinanthus minor, and soil type and management, influenced the establishment of target plant species and community diversity. The addition of early-coloniser species to model grasslands suppressed the establishment of target species, indicating a strong priority effect. Soil type was also an important factor, but effects varied considerably across locations. In the absence of early-coloniser species, low soil nutrient availability improved establishment of target species across locations, although R. minor had no beneficial effect. Synthesis and applications. Our long-term, multi-site study indicates that successful restoration of species rich grassland is dependent primarily on priority effects, especially in the form of early-coloniser species that suppress establishment of slow-growing target species. We also show that priority effects vary with soil conditions, being stronger in clay than sandy soils, and on soils of high nutrient availability. As such, our work emphasises the importance of considering priority effects and local soil conditions in developing management strategies for restoring plant species diversity in grassland.
Supplementary Data of microbial diversity in the eastern Atlantic Ocean
<p>Supplementary Data of microbial diversity in the eastern Atlantic Ocean</p>
Microbial diversity of sub-bottom sediment cores from a tropical reef system
<p>R code for analysing 16S of microbial communities from sub-bottom sediment cores</p>
Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - raw data
<p>environmental data, plant community data, CLPP profiles, microbial activity data</p>
Microbial diversity regulates ecosystem multifunctionality during natural secondary succession
<p>Natural forest succession after disturbances is one of the most important restoration strategies. However, the responses of ecosystem multifunctionality during natural forest succession remains poorly understood in forest ecosystem.</p> <p>Here we evaluated how the ecosystem multifunctionality including nutrient cycling, carbon stocks, water regulation, decomposition, wood production and symbiosis develops using a chronosequence, and identified the key factors contributing to the variations in the ecosystem multifunctionality during natural forest succession.</p> <p>We provide evidence that the ecosystem multifunctionality gradually increased along with succession stages. The individual functions of carbon stocks and water regulation also exhibited increasing patterns with stand development. The microbial diversity were more principal factors than plant diversity and soil properties for the explanation of changes in the ecosystem multifunctionality. <span>The regression analysis showed that </span>the diversity of <span>bacteria, general fungi, actinomycetes, nematodes, </span>G<sup>+</sup><span> bacteria and </span>G<sup>-</sup><span> bacteria significantly and positively associated with ecosystem multifunctionality. Soil nematodes exhibited significantly positive correlation with most of the individual functions. </span></p> <p>Synthesis and Applications: Taken together, our results demonstrate that natural forest restoration plays a key role in promoting ecosystem multifunctionality, and emphasize the importance of soil microbial diversity for the maintenance of ecosystem functions and health.</p>
Supplementary material 4 from: Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R (2019) Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 441-475. https://doi.org/10.3897/natureconservation.34.30631
: Data type: statistical data
Supplementary material 5 from: Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R (2019) Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 441-475. https://doi.org/10.3897/natureconservation.34.30631
: Data type: measurement
Supplementary material 3 from: Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R (2019) Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 441-475. https://doi.org/10.3897/natureconservation.34.30631
: Data type: measurements
Supplementary material 2 from: Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R (2019) Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 441-475. https://doi.org/10.3897/natureconservation.34.30631
: Data type: parameters data
Supplementary material 1 from: Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R (2019) Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 441-475. https://doi.org/10.3897/natureconservation.34.30631
: Data type: measurement
Plant and soil microbial diversity and related spatial and environmental factors in the grasslands of northern China
<p>Plant and soil microbial diversity and related spatial and environmental factors in the grasslands of northern China from 2018 and 2019. The data included 54 and 27 sites in 2018 and 2019 respectively. The data table contains two sheets, one for 2018 and the other for 2019. Spatial factors include longitude and latitude; climatic factors include mean annual temperature, mean annual precipitation, temperature seasonality, precipitation seasonality, potential evapotranspiration, and aridity index; soil factors include soil bulk density, soil moisture, soil pH, soil organic carbon, soil clay content, soil silt content, soil sand content, soil total carbon, soil total nitrogen, and soil C:N ratio; plant functional diversity include functional richness (FRic), functional evenness (FEve), functional divergence (FDiv), functional dispersion (FDis), Rao's quadratic entropy (RaoQ); community-weighted mean (CWM) traits include specific leaf area (SLA), leaf dry matter content (LDMC), leaf nitrogen content (leafN),ratio of leaf carbon to nitrogen (leaf C:N), and stem density; soil microbial diversity include bacterial diversity and fungal diversity; fungal functional guilds include pathotrophic fungi, saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi; bacterial functional guilds include aerobic chemoheterotrophy, predatory or exoparasitic, cellulolysis, aerobic nitrite oxidation, sulfur respiration, nitrate reduction, ureolysis, aromatic compound degradation, intracellular parasites, fermentation, and methanotrophy in the data sheet of 2018. </p> <p><br> Soil microbial diversity include bacterial diversity and fungal diversity; fungal functional guilds include pathotrophic fungi, saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi; bacterial functional guilds include aerobic chemoheterotrophy, predatory or exoparasitic, cellulolysis, aerobic nitrite oxidation, sulfur respiration, nitrate reduction, ureolysis, aromatic compound degradation, intracellular parasites, fermentation, and methanotrophy in the data sheet of 2019.</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)
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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.