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61 results for “nematode community”
Data from: Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages
Annelids (Lumbricidae and Enchytraeidae) and nematodes are common soil organisms and play important roles in organic matter decomposition, nutrient cycling and creation of soil structure and porosity. However, these three groups have rarely been studied together and only few studies exist for urban soils. We studied the diversity and community composition of annelids and nematodes in soils spanning more than two centuries of urban soil development in Neuchâtel (Switzerland) and assessed the relationships 1) among these three groups and 2) between each group and environmental (physical, chemical and functional) characteristics of soils and soil age. While the groups of environmental variables were correlated (Mantel tests) no correlation was found between pairs of soil fauna groups and between each soil fauna group and environmental variables. More specifically, redundancy analyses showed that earthworm assemblages were best correlated with soil bulk density and with soil depth, the latter being positively correlated with soil age. Enchytraeid assemblages and the proportion of enchytraeid r-strategists were respectively best correlated with soil carbonate content and negatively correlated with soil age. Nematodes assemblages were best correlated with soil water content. Moreover, relationships between pairs of soil biota groups, and between each group and environmental (physical, chemical and functional) variables, varied along the soil age gradient (moving window analysis). This study provides new knowledge on urban soil biodiversity and how environmental conditions can influence soil diversity and community patterns in the urban context. The contrasted community patterns of earthworms, enchytraeids and nematodes in urban soils of different ages and their different ecological roles suggest that they represent potential complementary indicators of soil quality and functioning such as soil formation and organic matter dynamics.
Data from: A combined parasitological-molecular approach for non-invasive characterization of parasitic nematode communities in wild hosts
Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity of lethal sampling severely restricts the host species that can be studied, the adequacy of sample sizes to assess diversity, the geographic scope of collections and the research questions that can be addressed. Focusing on gastrointestinal nematodes of wild African buffalo, we evaluated whether accurate characterization of nematode communities could be made using a noninvasive technique that combined conventional parasitological approaches with molecular barcoding. To establish the reliability of this new method, we compared estimates of gastrointestinal nematode abundance, prevalence, richness and community composition derived from lethal sampling with estimates derived from our noninvasive approach. Our noninvasive technique accurately estimated total and species-specific worm abundances, as well as worm prevalence and community composition when compared to the lethal sampling method. Importantly, the rate of parasite species discovery was similar for both methods, and only a modest number of barcoded larvae (n = 10) were needed to capture key aspects of parasite community composition. Overall, this new noninvasive strategy offers numerous advantages over lethal sampling methods for studying nematode–host interactions in wildlife and can readily be applied to a range of study systems.
Agriculture causes homogenization of plant-feeding nematode communities at the regional scale
<p>1. An emerging research line in conservation ecology addresses how environmental change drivers may cause the biotic homogenization of ecological communities by shifts in species diversity and community composition. While the drivers have been explored in unmanaged ecosystems and managed agricultural systems, this issue has received limited attention in regards to a key soil bioindicator organisms, soil nematodes.<br> <br> 2. In this study, we evaluated the effect of land-use change and intensification on the diversity of plant-feeding nematodes (PFN) thought taxonomic and functional measures of alpha and beta diversity. We selected olive tree farms in southern Spain as the study system, given the wide distribution of wild forms in unmanaged systems and cultivated forms in agricultural systems, thus providing the opportunity to assess the effects of land use intensity.<br> <br> 3. Notably, our study revealed that the conversion from natural to agricultural systems and even moderate increases in land-use intensity caused a significant biotic homogenization by enhancing the functional similarities of PFN communities. Our study emphasizes the key role of body size in structuring nematode communities in response to land-use type and intensity. <br> <br> 4. Synthesis and applications. The importance of soil nematodes in soil processes is well known. We show that land use intensification reduces soil nematode diversity. Our study has important implications for the development of management strategies that foster soil biodiversity conservation such as no or minimal tillage and logging, vegetative covers and the maintenance of natural habitat.</p>
Data from: High-throughput sequencing of nematode communities from total soil DNA extractions
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Data from: Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host
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Data from: Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages
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Agriculture causes homogenization of plant-feeding nematode communities at the regional scale
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Data from: A combined parasitological-molecular approach for non-invasive characterization of parasitic nematode communities in wild hosts
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Data from: Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest
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Data from: Nematode community responses to range-expanding and native plant communities in original and new range soils
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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Nematode community dynamics in Johnson Su compost
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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.
Fig. 3 in Taxonomic Structure Of Nematode Communities Of Epiphytic Mosses In Green Plantations Of Chernihiv, Ukraine
Fig. 3. Structure of nematode communities of epiphytic mosses in green plantations of Chernihiv according to the dominance criterion.
Fig. 6 in Nematode morphometry and biomass patterns in relation to community characteristics and environmental variables in the Mekong Delta, Vietnam
Fig. 6. Variation in the morphology of nematodes in the Mekong Delta, Vietnam. mean (± SD) nematode length in the Mekong Delta (a); mean (± SD) nematode length along the Co Chien estuary (b); mean (± SD) nematode width in the Mekong Delta (c); mean (± SD) nematode width along the Co Chien estuary (d); ratio L/W (the mouth stations [e], along estuary ECC [f]), individual biomass (μg) (the mouth stations [g], along estuary ECC [h]) and total biomass (μg 10 cm−2) (the mouth stations [i], along estuary ECC [k]).
Nematodes community composition and environmental parameters, Eastern Antarctic Peninsula
<p>This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel and Duse Bay. We compared five stations sampled at different water depths along the shelf and investigated their meiobenthic community structure. We approached nematode biodiversity comparing traditional taxonomic identification and high throughput sequencing (HTS), with the use of Amplicon Sequence Variants (ASVs). Additionally, we characterized the environment by primary production proxies, grain size and seasonal ice conditions. Our results suggest that the availability of organic matter and its freshness are responsible for the high densities found at all depths. However, potential factors influencing the high local and regional variability of meiofauna density and biodiversity are less clear. A bathymetric transect consisting of three stations in Duse Bay (200 m, 500 m and 1000 m depth) showed increasing pigment concentrations in the first centimeters of the sediment vertical profile with increasing water depth, whereas the meiofauna densities showed the opposite trend. The deepest station of Duse Bay seems to function as a sink for fine material as supported by the higher silt fraction and higher organic matter concentrations. When comparing the two basins in the Prince Gustav Channel (1000 m and 1250 m) and the one in Duse Bay (1000 m), differences in terms of environmental variables, meiofaunal densities and composition were observed. The deepest basin in Prince Gustav Channel is located further South (closer to the highly unstable Larsen area), and marked differences with the other basins suggest that it might be experiencing different conditions as a result of its presence near the summer ice margin and its more elongated topography. Both, the shallowest and the deepest stations showed the highest number of unique sequences, suggesting a more biodiverse nematode assemblage. The morphological identification did not show significant differences in the biodiversity of all stations which suggests that molecular approaches can be more efficient for biodiversity studies. However the lack of reference sequences in online databases is still an important issue to consider as it potentially leads to underestimations of biodiversity and functional traits.</p>
Supplementary material 1 from: van Nouhuys S, Harris DC, Hajek AE (2023) Population level interactions between an invasive woodwasp, an invasive nematode and a community of native parasitoids. NeoBiota 82: 67-88. https://doi.org/10.3897/neobiota.82.96599
The number of Sirex, nematodes, and parasitoids collected from each site, each year.
Data from: Nitrogen deposition cancels out exotic earthworm effects on plant-feeding nematode communities
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Data from: Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion
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Nematodes community composition and environmental parameters, Eastern Antarctic Peninsula
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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.