Abundance of small individuals influences the effectiveness of processing techniques for deep-sea nematodes

Nematodes are the most abundant metazoans of deep-sea benthic communities, but knowledge of their distribution is limited relative to larger organisms. Whilst some aspects of nematode processing techniques, such as extraction, have been extensively studied, other key elements have attracted little attention. We compared the effect of (1) mesh size (63, 45, and 32 μm) on estimates of nematode abundance, biomass, and body size, and (2) microscope magnification (50 and 100×) on estimates of nematode abundance at bathyal sites (250-3100 m water depth) on the Challenger Plateau and Chatham Rise, south-west Pacific Ocean. Variation in the effectiveness of these techniques was assessed in relation to nematode body size and environmental parameters (water depth, sediment organic matter content, %silt/clay, and chloroplastic pigments). The 63-μm mesh retained a relatively low proportion of total nematode abundance (mean ±SD = 55 ±9%), but most of nematode biomass (90 ± 4%). The proportion of nematode abundance retained on the 45-μm mesh in surface (0-1 cm) and subsurface (1-5 cm) sediment was significantly correlated (P < 0.01) with %silt/clay (R² = 0.39) and chloroplastic pigments (R² = 0.29), respectively. Variation in median nematode body weight showed similar trends, but relationships between mean nematode body weight and environmental parameters were either relatively weak (subsurface sediment) or not significant (surface sediment). Using a low magnification led to significantly lower (on average by 43%) nematode abundance estimates relative to high magnification (P < 0.001), and the magnitude of this difference was significantly correlated (P < 0.05) with total nematode abundance (R²p = 0.53) and the number of small (≤ 250 μm length) individuals (R²p = 0.05). Our results suggest that organic matter input and sediment characteristics influence the abundance of small nematodes in bathyal communities. The abundance of small individuals can, in turn, influence abundance estimates obtained using different mesh sizes and microscope magnifications

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio

Phylogenetic relationships of the Wolbachia of nematodes and arthropods

Wolbachia are well known as bacterial symbionts of arthropods, where they are reproductive parasites, but have also been described from nematode hosts, where the symbiotic interaction has features of mutualism. The majority of arthropod Wolbachia belong to clades A and B, while nematode Wolbachia mostly belong to clades C and D, but these relationships have been based on analysis of a small number of genes. To investigate the evolution and relationships of Wolbachia symbionts we have sequenced over 70 kb of the genome of wOvo, a Wolbachia from the human-parasitic nematode Onchocerca volvulus, and compared the genes identified to orthologues in other sequenced Wolbachia genomes. In comparisons of conserved local synteny, we find that wBm, from the nematode Brugia malayi, and wMel, from Drosophila melanogaster, are more similar to each other than either is to wOvo. Phylogenetic analysis of the protein-coding and ribosomal RNA genes on the sequenced fragments supports reciprocal monophyly of nematode and arthropod Wolbachia. The nematode Wolbachia did not arise from within the A clade of arthropod Wolbachia, and the root of the Wolbachia clade lies between the nematode and arthropod symbionts. Using the wOvo sequence, we identified a lateral transfer event whereby segments of the Wolbachia genome were inserted into the Onchocerca nuclear genome. This event predated the separation of the human parasite O. volvulus from its cattle-parasitic sister species, O. ochengi. The long association between filarial nematodes and Wolbachia symbionts may permit more frequent genetic exchange between their genomes

Factors influencing the nematode community during composting and nematode-based criteria for compost maturity

Pilot studies indicate that shifts in the nematode species composition, life strategies and feeding behavior during composting appear to be fairly consistent and, therefore, promising as a potential tool to assess compost maturity. However, this has been only based on a limited number of, mainly, non-replicated observations. In this study, we tested whether the nematode community succession patterns are recurrent for parallel processes and assessed the relationship between the changes in the nematode community and potential important variables (i.e., temperature, duration of composting and the microbial community). The nematode and microbial community of three simultaneously running Controlled Farm Composting and a reference Green Waste composting process were analyzed through time. Bacterial-feeding enrichment opportunists were most numerous during and directly after the heat peaks. Subsequently, the bacterial-feeding/predator community dominated and the fungal-feeding nematodes became more dominant during maturation, confirming general community patterns from previous experiments. Nematode abundances significantly fluctuated with temperature and the relative abundance of fungal-feeding nematodes increased as the duration of the curing process increased. The amount of fungal-feeding nematodes was associated significantly with both duration of composting and temperature, and the F/(F + B) ratio was only significantly associated with duration of composting. Based on these results, and additional data from an industrial reference compost process and on available literature, a Nematode-based Index of Compost Maturity (NICM) is proposed, combining four nematode-based criteria (i.e., nematode abundance, F/(F + B) ratio, the presence of more than one fungal-feeding taxon and the presence of diplogasterids). Nevertheless, the NICM should be considered as work in progress which should be tested for a wider range of composts from diverse feedstock mixtures, locations (sites) and composting techniques, to validate the use of the index and allow more reliable interpretation of particular values of this index

Prevalence of endoparasite in some commercially important freshwater fishes of Bida area, Niger State: a preliminary report

The result of this preliminary report highlighted prevalence of an endoparasite (nematode) in order of prevalence. Four non-scaly commercially important fishes, namely:- Clarias sp Hererobranchus bidorsalis. Bagrus sp and Synodontis sp.; and nine scaly fishes, namely; - Gymnarchus sp, Protopterus annectus. Tilapia sp, Lates niloticus. Heterotis niloticus, Mormyrops sp, Channa Obscurus, Labeo sp and Distochodus rostratus of freshwater fadama of the Bida Area, Niger State. The extent of the spread was evaluated. While the reactions of fishermen, middlemen (fishmongers) and fish-eaters in order to appreciate the impacts of the nematode infested fishes on the populace were recorded. The paper suggested areas for further studies towards evoking desirable management strategies for the study area as follows. Such suggested areas are:- Identification and confirmation of the nematode species; life cycle of the nematode species; influence of season on the prevalence, spread and pathology in the nematode infested fishes, et

The role of bacteria in pine wilt disease: insights from microbiome analysis.

Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient Gel Electrophoresis, 16S rRNA gene pyrosequencing, and a functional inference-based approach (PICRUSt). The bacterial community structure of the nematode was significantly different from the infected trees but closely related to the insect vector, supporting the hypothesis that the nematode microbiome might be in part inherited from the insect. Sampling location influenced mostly the tree microbiome (P < 0.05). Genes related both with plant growth promotion and phytopathogenicity were predicted for the tree microbiome. Xenobiotic degradation functions were predicted in the nematode and insect microbiomes. Phytotoxin biosynthesis was also predicted for the nematode microbiome, supporting the theory of a direct contribution of the microbiome to tree-wilting. This is the first study that simultaneously characterized the nematode, tree and insect-vector microbiomes from the same affected areas, and overall the results support the hypothesis that the PWD microbiome plays an important role in the disease's development

Soil nematode communities in grasslands

This thesis summarizes the results of five studies investigating the effect of plant species on soil nematode communities in grasslands. Nematodes (roundworms) are ubiquitous members of the soil fauna and have been much used as indicators of soil conditions. Plants have the ability to affect soil organisms through structural modification of the soil habitat and through the quantity and quality of organic matter that is returned to soil, in the form of plant litter and root exudates. The influence of grassland plant species on the soil nematode fauna was investigated in an experimental grassland, a glasshouse experiment and in a semi-natural grassland. Monocultures of 12 grassland plant species belonging to three plant functional groups, viz. grasses, legumes and non-leguminous forbs, were investigated in the field experiment and a subset of these in the other two systems. Plant species effects were common, for example, plant feeding and bacterial feeding nematodes responded positively to legumes and grasses, while forbs enhanced fungal feeding nematodes. Plant species identity appeared to be much more important than plant functional group for the nematode fauna. The effects of plants were quite consistent between field and glasshouse experiments. The influence of plant species diversity and functional diversity on the nematode fauna was investigated in the experimental grassland. Plant species composition proved to be more important for soil nematode communities than any of the plant diversity measures, but the hypothesis that species or functional diversity of plants affect nematode diversity or composition could not be rejected. My results also suggest that plant species identity may be an important determinant of spatial structure in natural grasslands. There was a succession of the nematode fauna during the eight years after establishment of the experimental grassland, especially indicated by the increase in maturity index of the nematode fauna. The results highlight the need for long-term experiments to reveal successional trends in soil nematode communities after cessation of agriculture. The increase of plant feeders with time, the slow colonization rate and the enhanced abundance of fungal feeders in soil under forbs have implications for nature restoration of former agricultural land

Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance

peer-reviewedThe objective of this study was to identify Scottish Blackface lambs that were at the extremes of the spectrum of resistance to gastrointestinal nematodes and characterise their response to an experimental nematode challenge. Lambs (n = 90) were monitored for faecal egg count (FEC) (2 samples from each of 2 independent natural infections). The most resistant (n = 10) and susceptible (n = 10) individuals were selected and challenged with 30,000 Teladorsagia circumcincta larvae (L3) at 9 months of age. Response to infection was monitored by measuring FEC, plasma pepsinogen, serum antibodies against nematode larval antigens and haematology profile, until necropsy at 71 days post infection. Worm burden, worm fecundity and the level of anti-nematode antibodies in abomasal mucosa were determined at necropsy. FEC was consistently higher in susceptible animals (P < 0.05), validating the selection method. Worm fecundity was significantly reduced in resistant animals (P = 0.03). There was also a significant correlation (r = 0.88; P < 0.001) between the number of adult worms and FEC at slaughter. There was no effect of phenotype (resistance/susceptibility) on plasma pepsinogen or on haematology profile. Phenotype had a significant effect on the level of anti-nematode IgA antibodies in serum (P < 0.01), reflecting a higher peak in resistant animals at day 7 post infection. It is concluded that significant variation in the response to gastrointestinal nematode challenge exists within the Scottish Blackface population with resistant animals displaying significantly lower FEC, lower worm fecundity and higher concentration of anti-nematode IgA antibodies in serum.Kathryn McRae was supported by a Teagasc Walsh fellowship and the Allan and Grace Kay Overseas Scholarship

Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8