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553 results for “soil communities”
Figure 5 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 5 Fungal guild assignment of the soil fungal community in gallery forest and woodlands. Abundance measured as fraction of reads (A) and richness measured as fraction of species hypotheses (SH) (B) Guilds representing less than 2% of both abundance and richness are grouped together in "other".
Figure 2 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 2 NMDS ordination of tree communities based on Bray-Curtis dissimilarities between sites, based on total basal areas of each ECM trees species separately and all non-ECM trees combined. The nine sites were classified into two distinct woodland types, woodlands in red and gallery forests in blue. Site abbreviations: Bissandougou Forest Reserve (BISS-W), Moussaya Forest Reserve (MOUS-W), Kota Waterfall (KOTA-G and KOTA-W), Kouadianikro Forest Reserve (KDNK-W), Kou Forest Reserve (KOUF-G), Niangoloko Forest Reserve (NIAN-W) and Farako Forest Reserve (FA01-W and FA15-W). ECM tree species abbreviations: Afzelia africana (Aa), Ac: Anthonotha crassifolia (Ac), Bg: Berlinia grandiflora (Bg), Id: Isoberlinia doka (Id), I. tomentosa (It), Monotes kerstingii (Mk), Uapacaguineensis (Ug) and Uapaca togoensis (Ut).
Figure 1 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 1 Sampling sites of the West African Centre for Tropical Mycology's 2018 National Geographic Explorer Grant expedition. Shapes and colors separate the different woodland types with blue circles for gallery forests and red triangles for woodlands. With site names (abbreviations): Bissandougou (BISS-W), Moussaya (MOUS-W), Kota (KOTA-G and KOTA-W), Kouadianikro (KDNK-W), Kou (KOUF-G), Niangoloko (NIAN-W) and Farako (FA01-W and FA15-W). The dotted line represents the route taken on the sampling trip, beginning on the coast of Benin and concluding in Ivory Coast. Ecoregions are from White (1983), digitized in Olson et al. (2001).
Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning
1.Plant-soil feedback (PSF) has been identified as a key driver of local plant diversity and evenness in competitive communities. However, while it has been shown that spatial PSF heterogeneity can alter plant performance and competitive interactions, there is no proof of principle that spatial PSF heterogeneity enhances community diversity. 2.Using a grassland model system we separated two aspects of spatial heterogeneity: the number of species conditioning the soil and spatial distribution of the PSFs. 3.Our data show that PSFs promoted a higher plant evenness when the soil was conditioned by multiple species (mixed-conditioned), then when the soil was conditioned by a single species (mono-conditioned). On mono-conditioned soils, heterospecifics typically outperformed the focal species. In addition, there was a trend for increasing community evenness from uniform, via fine-grained to coarse-grained mixed-conditioned soils, but this was not significant. 4.On mixed-conditioned soils, performance of all competing species was intermediate to the best and the worst mono-conditioned soils, leading to higher community evenness. 5.Our data demonstrate that PSFs play a role in promoting plant evenness. Across mono-conditioned soils, PSF led to altered competitive hierarchies. However, on soils conditioned by multiple species, competitive ability among species was more similar and this led to higher plant evenness. The spatial distribution of the heterogeneity, on the other hand, did not significantly affect plant evenness. Our data therefore show that community evenness was more strongly related to the number of plant species that conditioned the soil than the spatial distribution of the PSF heterogeneity. Future studies need to investigate the importance of PSFs in the field across plant life-stages and multiple generations.
Data from: Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties.
The encroachment of shrubs into grasslands is common in terrestrial ecosystems dominated by grass. Land abandonment and favourable climatic trends in recent decades have favoured the expansion of shrubs into subalpine grasslands in many mountainous regions across Europe. The advance of the succession from grassland to shrubland is expected to have a major impact on ecosystem functioning. We used DNA metabarcoding to assess whether the structure of soil fungal communities varied along the succession from subalpine grassland to shrubland in the Pyrenees, and investigated whether shrub encroachment was associated with changes in soil properties. The expansion of shrubs increased the soil C:N ratio and/or reduced the N, P, or K contents. Plant-driven changes in soil properties were strongly associated with the compositional turnover of fungi, including arbuscular mycorrhizal, ectomycorrhizal, ericoid, root endophytic, saprotrophic, lichenised, and pathogenic fungi. Total richness and the richness of most functional groups were correlated with soil P, N, and the C:N or N:P ratios. We show that the interplay between abiotic factors (changes in soil properties) and biotic factors (occurrence and identity of shrubs) played a key role in the structure and uniqueness of soil fungal communities along the succession.
Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities
Horizontal gene transfer (HGT) between bacterial lineages is a fundamental evolutionary process that accelerates adaptation. Sequence analyses show that conjugative plasmids are principal agents of HGT in natural communities. However, we lack understanding of how the ecology of bacterial communities and their environments affect the dynamics of plasmid-mediated gene mobilization and transfer. Here we show, in simple experimental soil bacterial communities containing a conjugative mercury resistance plasmid, the repeated, independent mobilization of transposon-borne genes from chromosome to plasmid, plasmid to chromosome and, in the absence of mercury selection, interspecific gene transfers from the chromosome of one species to the other via the plasmid. By reducing conjugation, positive selection for plasmid-encoded traits, like mercury resistance, can consequently inhibit HGT. Our results suggest that interspecific plasmid-mediated gene mobilization is most likely to occur in environments where plasmids are infectious, parasitic elements rather than those where plasmids are positively selected, beneficial elements.
Data from: Relationships between plant traits, soil properties and carbon fluxes differ between monocultures and mixed communities in temperate grassland
1. The use of plant traits to predict ecosystem functions has been gaining growing attention. Aboveground plant traits, such as leaf nitrogen (N) content and specific leaf area (SLA), have been shown to strongly relate to ecosystem productivity, respiration, and nutrient cycling. Further, increasing plant functional trait diversity has been suggested as a possible mechanism to increase ecosystem carbon (C) storage. However, it is uncertain whether belowground plant traits can be predicted by aboveground traits, and if both above- and belowground traits can be used to predict soil properties and ecosystem-level functions. 2. Here, we used two adjacent field experiments in temperate grassland to investigate if above- and belowground plant traits are related, and whether relationships between plant traits, soil properties and ecosystem C fluxes (i.e., ecosystem respiration and net ecosystem exchange) measured in potted monocultures could be detected in mixed field communities. 3. We found that certain shoot traits (e.g., shoot N and C, and leaf dry matter content) were related to root traits (e.g., root N, root C:N, and root dry matter content) in monocultures, but such relationships were either weak or not detected in mixed communities. Some relationships between plant traits (i.e., shoot N, root N and/or shoot C:N) and soil properties (i.e., inorganic N availability and microbial community structure) were similar in monocultures and mixed communities, but they were more strongly linked to shoot traits in monocultures and root traits in mixed communities. Structural equation modelling showed that above- and belowground traits and soil properties improved predictions of ecosystem C fluxes in monocultures, but not in mixed communities on the basis of community-weighted mean traits. 4. Synthesis: Our results from a single grassland habitat detected relationships in monocultures between above- and belowground plant traits, and between plant traits, soil properties and ecosystem C fluxes. However, these relationships were generally weaker or different in mixed communities. Our results demonstrate that while plant traits can be used to predict certain soil properties and ecosystem functions in monocultures, they are less effective for predicting how changes in plant species composition influence ecosystem functions in mixed communities.
Data from: Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modeling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection, and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection, and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.
Data from: Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion
1. Belowground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR-based nematode identification techniques are well available, but high throughput sequencing (HTS) might be more suitable for non-targeted nematode community analysis. 2. We compared effectiveness of qPCR and HTS-based approaches with morphological nematode identification while examining how climate warming-induced plant range expansion may influence belowground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach. 3. HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances. 4. Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost-effective, in-depths methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.
Data from: Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales
The extent to which the distribution of soil bacteria is controlled by local environment versus spatial factors (e.g., dispersal, colonisation limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here we constrained environmental factors (soil chemistry, climate, above-ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 102 km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilisation) was also shown to be highly correlated to community structure, but not to abiotic factors, suggesting non-stochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance, and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio-temporal patterns of microbial diversity, as well as life-history of the groups being investigated, much as is the case for macro-organisms.
Data from: Effects of between-site variation in soil microbial communities and plant-soil feedbacks on the productivity and composition of plant communities
A critical challenge in the science and practice of restoration ecology is to understand the drivers of variation in restoration outcomes. Soil microbial communities may have a role in explaining this variation due to both site-to-site variation in the composition of soil microbial communities and due to variation that can arise due to plant-soil feedbacks. We tested the relative importance of between-site variation in soil microbial community composition and plant-soil feedbacks in shaping plant community composition and ecosystem function. We used a standard two-phase plant-soil feedback design. Soil inoculum was collected from four tallgrass prairie sites. Then, soils were conditioned separately with nine plant species, and conditioned soils were used to inoculate prairie community mesocosms. In a separate experiment using soil from an additional site we tested conditioned soil samples for the abundance of arbuscular mycorrhizal fungi (AMF) and rhizobia. Site of soil origin and plant-soil feedbacks both had effects on the composition and productivity of our plant communities, and the magnitudes of these effects were similar. We also found changes in the abundance of AMF and rhizobia due to plant-soil feedbacks and that AMF abundance were associated with differences in plant community composition. These results indicate that the composition of soil communities due to site-to-site variation and plant-soil feedbacks are both important determinants of plant community composition and productivity. Our results also suggest that AMF and rhizobia are key microbial functional groups underlying plant-soil feedback effects. Synthesis and applications. Site-to-site variation in soil communities can explain some variation in restoration of plant communities. Since plant-soil feedback effects of restored plant species do not overcome this variation, knowledge of soil microbial communities present at a site prior to initiation of restoration efforts may improve predictability of restoration outcomes, and reintroduction of some components of the soil community may be necessary to achieve restoration goals. Additionally, by understanding variation due to plant-soil feedbacks, restoration practitioners can choose plant species for reintroduction that will create favourable soil conditions, including promoting microbial mutualists. Plant-soil feedbacks should also make it possible to increase heterogeneity in soil microbial communities, leading to increases in beta diversity in plant communities.
Data from: Effects of two grass species on the composition of soil fungal communities
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake.
Data from: Cyanobacteria drive community composition and functionality in rock-soil interface communities
Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa, are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules) and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.
Data from: Plant community composition but not plant traits determine the outcome of soil legacy effects on plants and insects
1.Plants leave species-specific legacies in the soil they grow in that can represent changes in abiotic or biotic soil properties. It has been shown that such legacies can affect future plants that grow in the same soil (plant-soil feedback, PSF). Such processes have been studied in detail, but mostly on individual plants. Here we study PSF effects at the community level and use a trait-based approach both in the conditioning phase and in the feedback phase to study how twelve individual soil legacies influence six plant communities that differ in root size. 2.We tested if (I) grassland perennial species with large root systems would leave a stronger legacy than those with small root systems, (II) grass species would leave a more positive soil legacy than forbs and (III) communities with large root systems would be more responsive than small-rooted communities. We also tested (IV) whether a leaf chewing herbivore and a phloem feeder were affected by soil legacy effects in a community framework. 3.Our study shows that the six different plant communities that we used respond differently to soil legacies of twelve different plant species and their functional groups. Species with large root systems did not leave stronger legacies than species with small root systems, nor were communities with large root systems more responsive than communities with root systems. 4.Moreover, we show that when communities are affected by soil legacies, these effects carry over to the chewing herbivore Mamestra brassicae (Lepidoptera: Noctuidae) through induced behavioral changes resulting in better performance of a chewing herbivore on forb-conditioned soils than on grass-conditioned soils, whereas performance of the phloem feeder Rhopalosiphum padi (Hemiptera: Aphididae) remained unaffected. 5.Synthesis: The results of this study shed light on the variability of soil effects found in previous work on feedbacks in communities. Our study suggests that the composition of plant communities determines to a large part the response to soil legacies. Furthermore, the responses to soil legacies of herbivores feeding on the plant communities that we observed, suggests that in natural ecosystems, the vegetation history may also have an influence on contemporary herbivore assemblages. This opens up exciting new areas in plant-insect research and can have important implications for insect pest management.
Effects of transformation of inefficient Camellia oleifera plantation on soil quality and fungal community(supplementary)
Open the record for dataset details and reuse information.
Soil trenching – are microbial communities alike in experimental peatland plots measuring total and heterotrophic respiration?
<p> </p> <table> <tbody> <tr> <td>Data obtained within a project financed by LIFE Programme of the European Union ‘Demonstration of climate change mitigation potential of nutrients rich organic soils in Baltic States and Finland (LIFE OrgBalt, LIFE18 CCM/LV/001158)</td> </tr> <tr></tr> </tbody> </table>
Copiotrophic taxa in pig manure mitigate nitrogen limitation of soil microbial communities
<p>Dataset for soil properties, enzyme activities and stoichiometric parameters.</p>
Data from: Impact of local forest composition on soil fungal communities in a mixed boreal forest
[No abstract entered]
Influence of soil type and vertical zonation on soil fungal communities associated with natural jack pine forests
<p>Natural jack pine forests established on sandy eskers and clayey soils represent a unique habitat in the boreal forest in northeastern Canada and are generally associated with well-differentiated soil horizons, but little is known regarding their soil fungal diversity and how soil type and vertical zonation would shape their communities. To address this question, we characterized soil fungal communities from litter, organic and mineral horizons in 18 natural jack pine forests in esker and clayey soils using ITS2 rDNA metabarcoding. Ectomycorrhizal fungi dominated the organic and mineral horizons in esker soils, while saprotrophic fungi were dominant in clayey soils. The dominance of ectomycorrhizal fungi coincided with higher C accumulation within the organic horizon in esker soils. The nutrient-poor and more acidic esker sites harbored less diverse ectomycorrhizal and saprotrophic communities than clayey soils. Several stress-tolerant and melanin-rich fungal taxa were indicators of esker soils. However, fungal communities were more distinct between horizons than soil types and soil type effects differed along the soil profile. Our findings highlight the need to fill knowledge gaps in soil fungal diversity associated with jack pine forests and pave the way for adapted and multi-resource forest management in esker forest ecosystems considering their underground fungal specificities.</p>
Figs. 1. A-E in Macrophytes communities associated to soil bioengineering techniques for erosion control in riverbanks
Figs. 1. A-E. Collection sites of aquatic microphytes at Amparo de São Francisco. A. Vegetated Slope; B. Vegetated Riprap; C. Eroded Slope; D. Cribwall; E. Vetiver Grass Contour Line.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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