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61 results for “nematode community”
A novel metabarcoding strategy for studying nematode communities
<p>Nematodes are most abundant soil metazoa. How, the ecology of this group of organism remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5, SSU_04F/SSU_22R, Nemf/18Sr2b from earlier studies; and MMSF/MMSR, a newly developed primer set from this study. In order to test these primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 mock communities in soil, and 4 root/rhizosphere soil samples. We successfully amplified the target regions (COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were very efficient in detecting soil nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets could be used to study nematode communities in agricultural environments.</p>
Long-term nitrogen addition alters the community and energy channel but not diversity of soil nematodes in a subtropical forest
Summary <ol> <li>Research has indicated that increases in nitrogen (N) deposition can greatly affect ecosystem processes and functions. There is limited information about the effects of long-term N addition on soil nematodes and their functional composition, although nematodes are the most abundant multicellular animals on Earth.</li> <li>We conducted a field experiment in 2004 with four levels of N addition (0, 60, 120, and 240 kg N ha<sup>-1 </sup>yr<sup>-1</sup>) in a subtropical <i>Cunninghamia lanceolata</i> forest. Soil samples with three depths (0-20, 20-40 and 40-60 cm) were collected and the community structure, diversity and trophic groups of soil nematodes were determined in 2014.</li> <li>N addition significantly increased the abundance of bacterial- and fungal-feeding nematodes, but decreased the abundance of plant-feeding nematodes at the 0-20 cm soil layer. Accordingly, the plant parasite index and enrichment index decreased but the basal index and channel index increased, which weaken the importance of the plant-based energy channel, but enhance the importance of the fungal-based energy channel. N addition had no effects on the diversity of soil nematodes in three soil depths. Structural equation modeling analysis indicated that N loading directly changed plant-feeding (total <i>r<sup>2</sup></i>=0.42) nematodes, or indirectly affected bacterial- (<i>r<sup>2</sup></i>=0.43), fungal- (<i>r<sup>2</sup></i>=0.31) and plant-feeding nematodes via change soil nutrients, soil water content and pH.</li> <li>These findings suggest that N addition can change the community structure and energy channels soil nematodes, which would affect soil processes and food web functions in forest soils under future environmental change scenarios.</li> </ol>
Centaurea population effects on nematode communities
<p>Data set belonging to the study 'Plant population and soil origin effects on nematode community composition in the rhizosphere of a range-expanding plant species and a native congener'. In this study, we experimentally compared the development of nematode communities originating from northern and southern European soils in the rhizospheres of different populations of the range-expanding plant species <i>Centaurea stoebe</i> and the native plant species <em>Centaurea jacea</em>. The experiment was carried out in a greenhouse of the Netherlands Institute of Ecology (NIOO-KNAW; Wageningen, The Netherlands). </p>
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
<p>Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (<i>Peromyscus spp.</i>). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived up to four times longer than uninfected or singly-infected mice. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.</p>
Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community
Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral res-ponses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematode Caenorhabditis elegans and the predatory social bacterium Myxococcus xanthus when cultured together with two basal prey bacteria that both predators can eat—Escherichia coli and Flavobacterium johnsoniae. We found that >90% of C. elegans worms failed to interact with M. xanthus even when it was the only potential prey species available, whereas most worms were attracted to pure patches of E. coli and F. johnsoniae. In addition, M. xanthus altered nematode predatory behavior on basal prey, repelling C. elegans from two-species patches that would be attractive without M. xanthus, an effect similar to that of C. elegans pathogens. The nematode also influenced the behavior of the bacterial predator: M. xanthus increased its predatory swarming rate in response to C. elegans in a manner dependent both on basal-prey identity and on worm density. Our results suggest that M. xanthus is an unattractive prey for some soil nematodes and is actively avoided when other prey are available. Most broadly, we found that nematode and bacterial predators mutually influence one another's predatory behavior, with likely consequences for coevolution within complex microbial food webs.
Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways
<p>It is well established that dominant plants shape belowground communities, which in turn influence ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with the plants themselves. However, we know little about how grazing moderates effects of dominant plants on belowground organisms. We established a three-year removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to explore how grazing mediates the effects of the dominant shrub, <em>Dosiphora fruticosa</em>, on nematode communities. We applied structural equation modelling to assess how grazing moderates the effects of <em>D. fruticosa</em> on nematode communities both directly and indirectly via changes in soil physicochemical properties<span>, root biomass and microbial communities</span>. We found that 1) grazing changed the direction of the direct effect of shrub on nematode communities as indicated by the shift from a negative to a positive path coefficient; 2) shrub affected nematode richness mainly through microbial richness. Accordingly, nematode community composition was more closely related to microbial community composition in the ungrazed alpine meadow, while edaphic properties were stronger predictors of nematode community composition responses to shrubs in the grazed meadow; and 3) grazing suppressed the indirect effects of shrub on nematode communities via microbial communities. Our study shows that grazing plays an important role in regulating dominant plant's effects on belowground community composition and interactions in alpine meadows.</p>
Agriculture erases climate constraints on soil nematode communities across large spatial scales
<p>Data supporting "Agriculture erases climate constraints on soil nematode communities across large spatial scales".</p>
Figure 2 in Community analysis of soil-inhabiting nematodes in natural vegetations of Singalila National Park, West Bengal (India)
Figure 2. Taxonomic diversity (abundance and genera) of nematode orders in Singalila National Park.
Data from: Non-linear responses of soil nematode community composition to increasing aridity
Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have poor understanding of how belowground communities respond. In order to understand the longer-term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3200-km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from 0.43 to 0.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used Generalized Additive (Mixed) Models to analyze the abundance, richness and community similarity patterns of soil nematodes. We used Structural Equation Modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined non-linearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred under arid conditions (aridity > 0.80). However, the shape of response to aridity differed among nematode feeding groups. Under arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but rather were directly affected by aridity. Main conclusions: Our results show that in mesic grasslands increasing aridity primarily caused decline in nematode abundance, whereas increasing aridity in xeric grasslands led to loss of nematode diversity. The non-linear responses of nematodes to aridity could result in non-linear shifts in ecosystem functioning as well, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.
Genetic disruption of synthesis pathways of Arabidopsis secondary metabolites dramatically affects root-associated nematode populations directly and via modulation of microbial communities
<p>Dataset of nematode, fungal and bacterial sequence reads of Arabidopsis roots. Dataset of fungal and bacterial sequence reads of Arabidopsis microbial suspension. DNA concentration of Arabidopsis root microbial suspension. Meloidogyne incognita J2 invasion into tomato roots. qPCR dataset of Meloidogyne hapla infection pressure into Arabidopsis roots. </p>
Fig. 6 in Spatial Distribution Of Tropical Estuarine Nematode Communities In Sarawak, Malaysia (Borneo)
Fig. 6. Percentage of contribution of each functional feeding group
Fig. 5. a in Spatial Distribution Of Tropical Estuarine Nematode Communities In Sarawak, Malaysia (Borneo)
Fig. 5. a, Two-dimensional MDS ordination constructed from the
Fig. 5 in Nematode morphometry and biomass patterns in relation to community characteristics and environmental variables in the Mekong Delta, Vietnam
Fig. 5. Frequency distribution of L/W ratios at the mouth stations (a) and Co Chien estuary (b).
Centaurea population effects on nematode communities
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Data from: Nonlinear responses of soil nematode community composition to increasing aridity
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Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
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Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community
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Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways
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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: High-throughput sequencing of nematode communities from total soil DNA extractions
Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDNA
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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