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93 results for “nematodes diversity”
Fig. 4 in Gastric nematode diversity between estuarine and inland freshwater populations of the American alligator (Alligator mississippiensis, daudin 1802), and the prediction of intermediate hosts
Fig. 4. Prey stomach contents categorized to taxonomic class levels.
Data from: Contrasting impacts of nitrogen enrichment on soil nematode diversity in natural and managed ecosystems
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Spatial patterns and ecological drivers of soil nematode β-diversity in natural grasslands vary among vegetation types and trophic position
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Contrasting latitudinal clines of nematode diversity in Spartina alterniflora saltmarshes between native and introduced ranges
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Drivers of nematode diversity in forest soils across climatic zones
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Long-term nitrogen addition alters the community and energy channel but not diversity of soil nematodes in a subtropical forest
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Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK, and adopt a metagenetics approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one fifth contain a mix of mitotypes, and less than 3 % contain all three mitotypes. Within mixed fields we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying "pathoscape". Finally, we assess mitotype distribution at the level of the individual cyst, and provide evidence of "hybrids". This study provides a method for accurate, quantitative and high throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant-parasite.
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: Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life-history groups are used for calculating food web indices, i.e. maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high-throughput amplicon sequencing to investigate the effects of tillage (conventional vs reduced) and organic matter addition (low vs high) on nematode communities and food web indices in ten European long-term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.
Supplementary material 3 from: Ahmed M, Slos D, Holovachov O (2024) Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding. Metabarcoding and Metagenomics 8: e111307. https://doi.org/10.3897/mbmg.8.111307
Proportions of total ASVs assigned to various nematode families including those unassigned at the family level across all samples
The functional role and diversity of soil nematodes are stronger at high elevation in the lesser Himalayan mountain ranges
<p>Soil nematodes are a foremost component of terrestrial biodiversity, they display the whole gamut of trophic guilds and life strategies, and by their activity, affect major ecosystem process, such as organic matter degradation and carbon cycling. Based on nematodes' functional types, nematode community indices have been developed, and can be used to link variation in nematodes community composition and ecosystem processes. Yet, the use of these indices has been mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes' derived ecological indices in order to link soil and climate properties with soil food webs, and ecosystem processes that all vary along steep elevation gradients. For this purpose, we explored how elevation affects the trophic and functional diversity of nematode communities sampled every 300 m, from about 1000 m to 3700 m above sea level, across four transects in the lesser Himalayan range of Jammu and Kashmir. We found that (1) the trophic and functional diversity of nematodes increases with elevation; (2) differences in nematodes communities generate habitat-specific functional diversity; (3) the maturity index (MI), increases with elevation, while the enrichment index decreases, indicating less mature and less productive ecosystems, enhanced fungal-based energy flow, and a predominant role of nematodes in generating carbon influxes at high elevation sites. We thus confirm that the functional contribution of soil nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. Overall, this study highlights the central importance of nematodes in sustaining soil ecosystems and brings insights into their functional role, particularly in alpine and arctic soils.</p>
FIGURE 11 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 11. Light microscope images of female Lobocriconema sp. specimens from clade D. A, F, K (group 9), Nine-Mile Prairie, Nebraska, A) NID 1155, entire, 400X, F) NID 1156, head, 1000X, K) NID 1156, tail, 1000X. B, G, L) (group 11), Big Thicket National Preserve, Texas, B) NID 5647, entire, 400X, G) NID 5647, head, 1000X, L) NID 5653, tail, 1000X. C, H, M) (group 12), Tunica Hills, Louisiana, C) NID 3057, entire, 400X, H) NID 3057, head, 1000X, M) NID 3090, tail, 1000X. D, I, N) NID 3403 (group 13), Gregory Bald, Great Smoky Mountains National Park, North Carolina, D) entire, 400X, I) head, 1000X, N) tail, 1000X. E, J, O) NID 3297 (group 14), Torreya State Park, Florida, E) entire, 400X, J) head, 1000X, O) tail, 1000X.
FIGURE 10. Neighbor-joining ITS1 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 10. Neighbor-joining ITS1 tree (Internal Transcribed Spacer 1). Terminal branches identified by NID numbers, taxon, location information and COI group. GenBank Accession sequences are highlighted in green, NID numbers from Criconema arkaense collection sites in Cordero et al. (2012) are highlighted in orange. Clade designation follows the COI tree structure. Red bootstrap values of 5,000 replications.
FIGURE 9 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 9. Light microscope images of female specimens from Criconema arkaense topotype and paratype localities. A, E, I) NID 3229 (clade C, singleton), host maple, Ozark National Forest, Arkansas, A) entire, 400X, E) head, 1000X, I) tail, 1000X. B, F, J) (clade A, group 1) host wild cherry, Ozark National Forest, Arkansas, B) NID 3267, entire, 400X, F) NID 3265, head, 1000X, J) NID 3267, tail, 1000X. C, G, K) (clade D, group 10), host hackberry, Ozark National Forest, Arkansas, C) NID 3259, entire, 400X, G) NID 3259, head, 1000X, K) NID 3257, tail, 1000X. D, H, L) NID 3256 (clade D, group 11), host hackberry, Ozark National Forest, Arkansas D) entire, 400X, H) head, 1000X, L) tail, 1000X.
FIGURE 8 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 8. Light microscope images of female specimens in clade A (group 1) provisionally identified as Lobocriconema crassiannulatum. A, E, I) NID 1149, Lobocriconema sp., Avoca Prairie, Wisconsin, A) entire, 400X, E) head, 1000X, I) tail, 1000X. B, F, J) NID 3267, Lobocriconema sp., Ozark National Forest, Arkansas. B) entire, 400X, F) head, 1000X, J) tail, 1000X. C, G, K) NID 1462, Lobocriconema sp., Roth Prairie, Arkansas. C) entire, 400X, G) head, 1000X, K) tail, 1000X. D, H, L) NID 1214, Lobocriconema sp., Fairfax County, Virginia. D) entire, 400X, H) head, 1000X, L) tail, 1000X.
FIGURE 13 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 13. Images of juveniles and males. A) NID 3121 (group 12), Lobocriconema sp., juvenile, entire, 1000X, Tunica Hills, Louisiana. B) NID 2527 (group 5), Lobocriconema thornei, moulting juvenile, head, 1000X, Ingham County, Michigan - type locality. C) NID 3301 (group 11), Lobocriconema sp., juvenile, head, 1000X, Torreya State Park, Florida. D) NID 938 (group 9), Lobocriconema sp., juvenile, cuticle with scales and fine projections, 1000X, Spring Creek Prairie, Nebraska. E–H) NID 589 (group 7), male, Ichetucknee River, Florida, hardwood forest, E) entire, 400X, F) head, 1000X, G) tail region with spicule and subterminal bursa, 1000X, H) midbody cuticle with lateral lines, 1000X.
FIGURE 15 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 15. Discriminant function analysis of the 18 haplotype groups. A) Stepwise selection of morphological variables and estimated ability to separate haplotype groups. B) Mapping of classifications into discriminant space.
FIGURE 6 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 6. Light microscope images of female specimens in group 2, provisionally identified as Criconema lamellatum. A, E, I) NID 1465, Lobocriconema sp., Purchase Knob, GSMNP, A) entire, 400X, E) head, 400X, I) tail, 400X. B, F, J) NID 2582, Lobocriconema sp., Purchase Knob, GRSM, B) entire, 400X, F) head, 1000X, J) tail, 1000X. C, G, K) NID 3001, Lobocriconema sp., Goshen Prong, GRSM. C) entire, 400X, G) head, 1000X, K) tail, 1000X. D, H, L) NID 899, Lobocriconema sp., Chimney Creek, GRSM D) entire, 400X, H) head, 1000X, L) tail, 1000X.
FIGURE 5 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 5. Light microscope images of Criconema lamellatum paratype, a single female collected from Florence, South Carolina in October 17, 1957. Hosts were recorded as fern, grass and trees. A, B) entire 400X, C) head 1000X, D) tail 1000X.
FIGURE 2 in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
FIGURE 2. Light microscope images of female L. incrassatum and L. thornei specimens from clade C (groups 3, 5, and 16). A, D, G) NID 5563 (group 3), Lobocriconema incrassatum, Emigration Canyon, Utah, A) entire, 400X, D) head, 1000X, G) tail, 1000X. B, E, H) NID 5575 (group 16), Lobocriconema incrassatum. Providence Canyon, Utah, B) entire, 400X, E) head, 1000X, H) tail, 1000X. C, F, I) NID 2525 (group 5), Lobocriconema thornei, Ingham County, Michigan, C) entire, 400X, F) head, 1000X, I) tail, 1000X.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.