Technological advancements and their importance for nematode identification

Ahmed, Mona M.; Sapp, Melanie; Prior, Thomas; Karssen, Gerrit; Back, Matthew A.

doi:10.5194/soil-2-257-2016

Cited by 11 publications

(13 citation statements)

References 111 publications

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“…One factor hampering the study of management effects across multiple study sites is that traditional microscopy is the most common method to study nematodes, which is time‐consuming, requires specialists and is expensive (Ritz, Black, Campbell, Harris, & Wood, ). Molecular methods to assess nematode absolute abundances (qPCR) and diversity (high‐throughput amplicon sequencing, DGGE, T‐RFLP) are faster, cheaper, and allow higher throughput than visual methods (Ahmed, Sapp, Prior, Karssen, & Back, ; Geisen et al, ). Amplicon sequencing may allow identification of taxa that cannot be distinguished morphologically.…”

Section: Introductionmentioning

confidence: 99%

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments

et al. 2019

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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 10 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.

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Section: Introductionmentioning

confidence: 99%

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments

et al. 2019

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“…The mtDNA evolves, creating sufficient nucleotide variation for species‐level diagnosis (García & Sánchez‐Puerta, ). Mitochondrial DNA COI was proposed as a molecular marker for DNA barcoding and is capable of discriminating between RKN species more than the rRNA genes (Ahmed et al ., ). Moreover, the mtDNA COII /16S rRNA region has been used in diagnosis and large‐scale regional RKN surveys through PCR and RFLP (Tigano et al ., ; Humphreys‐Pereira et al ., ; Baidoo et al ., ; Karuri et al ., ).…”

Section: Discussionmentioning

confidence: 98%

Meloidogyne luci, a new root‐knot nematode parasitizing potato in Portugal

et al. 2017

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In 2013, during a field survey conducted in Portugal on potato, Solanum tuberosum, an unusual esterase (EST) phenotype was detected in a root‐knot nematode (RKN) from potato roots collected in Coimbra. This Portuguese isolate was purified and maintained on tomato, S. lycopersicum, and morphological, biochemical and molecular characteristics were studied. Perineal pattern morphology was highly variable, similar to Meloidogyne ethiopica and not useful for identification. The EST phenotype, from young egg‐laying females, displayed three bands similar to the Brazilian M. luci (L3) and distinct from M. ethiopica (E3). Phylogenetic analyses of mitochondrial cytochrome oxidase subunit I and the mitochondrial DNA region between COII and 16S rRNA genes revealed that the Portuguese isolate grouped with M. luci isolates close to M. ethiopica isolates. However, considering the ITS1‐5.8S‐ITS2 region, the Portuguese isolate grouped with isolates of M. luci, M. ethiopica and M. hispanica, which limits the confidence of this region for M. luci diagnosis, and its differentiation from other species with morphological similarities. The M. luci pathogenicity to potato was also assessed in 16 commercial cultivars and compared with M. chitwoodi, considered to be a quarantine RKN species by EPPO. All potato cultivars were susceptible to both Meloidogyne species with gall indices of 5 and higher reproduction factor values ranging from 12.5 to 122.3, which suggests that M. luci may constitute a potential threat to potato production. In the present study, M. luci is reported for the first time attacking potato in Portugal.

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“…The mitochondrial genes coxI and coxII have been widely used as DNA markers in various large organismal groups in the animal kingdom [ 60 ]. In terms of resolution, coxI is more capable of discriminating between species than either of the rRNA genes [ 61 ]. Sequence characterized amplified region (SCAR) markers have proven to be a very sensitive and reliable tool for the identification of RKNs and to provide an easy and rapid assessment of a large number of samples by a simple visual evaluation of gels [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

A new root-knot nematode, Meloidogyne vitis sp. nov. (Nematoda: Meloidogynidae), parasitizing grape in Yunnan

Yang

Liu

et al. 2021

PLoS ONE

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An unknown root-knot nematode was found at high density on grape roots collected from Yunnan Province. Morphometric traits and measurements, isozyme phenotypes, and molecular analysis clearly differentiated this nematode from previously described root-knot nematodes. This new species is described, illustrated and named Meloidogyne vitis sp. nov. The new species can be distinguished from other Meloidogyne spp. by a unique combination of characters. Females display a prominent neck, an excretory pore is located on the ventral region between 23rd and 25th annule behind lips, an EP/ST ratio of approximately 2.5 (1.98–2.96), a perineal pattern with two large and prominent phasmids, and a labial disc fused with the medial lips to form a dumbbell-shaped structure. Males display an obvious head region, a labial disc fused with the medial lips to form a dumbbell-shaped structure, no lateral lips, a prominent slit-like opening between the labial disc and medial lips, a distinct sunken appearance of the middle of the medial lips, and four incisures in the lateral field. Second-stage juveniles are characterized by a head region with slightly wrinkled mark, a labial disc fused with the medial lips to form a dumbbell-shaped structure, a slightly sunken appearance of the middle of the medial lips, a slit-like amphidial openings between the labial disc and lateral lips, and four incisures in the lateral field. The new species has rare Mdh (N3d) and Est phenotypes (VF1). Phylogenetic analysis based on ITS1-5.8S-ITS2, D2D3 fragments of rDNA, and coxI and coxII fragments of mtDNA sequences clearly separated the new species from other root-knot nematodes, and the closest relative was Meloidogyne mali. Meloidogyne mali was collected for amplifying these sequences as mentioned above, which were compared with the corresponding sequences of new species, the result showed that all of these sequences with highly base divergence (48–210 base divergence). Moreover, sequence characterized amplified region (SCAR) primers for rapid identification of this new species were designed.

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Technological advancements and their importance for nematode identification

Cited by 11 publications

References 111 publications

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments

Meloidogyne luci, a new root‐knot nematode parasitizing potato in Portugal

A new root-knot nematode, Meloidogyne vitis sp. nov. (Nematoda: Meloidogynidae), parasitizing grape in Yunnan

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