Evaluation of combined morphological and molecular techniques for marine nematode (Terschellingia spp.) identification

Bhadury, Punyasloke; Austen, Melanie C.; Bilton, David T.; Lambshead, P. J. D.; Rogers, Alex D.; Smerdon, Gary R.

doi:10.1007/s00227-008-0945-8

Cited by 74 publications

(70 citation statements)

References 25 publications

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“…The dominant morpho-species mentioned above are not only tolerant to a variety of disturbances; but rather they have been also recognized as cosmopolitans. However, morphologically cryptic species complexes have been identified for Terschellingia longicaudata (Bhadury et al, 2008) and possibly exist also for the widely distributed…”

Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 99%

Effects of organic enrichment on nematode assemblages in a microcosm experiment

Armenteros

Pérez-García

Ruiz-Abierno

et al. 2010

Marine Environmental Research

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Marine nematodes from subtidal tropical sediments of Cienfuegos Bay were subjected to organic enrichment in a microcosm experiment for 32 days. Nematode abundance and diversity decreased, and the taxonomic and trophic structure was altered. The results suggested that the nematodes were not food limited in the microcosms or in their natural environment. Chemical stressors such as ammonia and hydrogen sulfide derived from reduced conditions in sediments may be important factors affecting the assemblages. Hypoxic conditions occurred in all experimental units, as well as in the field, suggesting a nematode assemblage adapted to naturally enriched sediments. However, tolerant species showed a grade of sensitivity to reduced conditions. In agreement with the model by Pearson and Rosenberg (1978), we predict that further organic enrichment in sediments from Cienfuegos Bay may cause a phase shift into a strongly depleted benthic fauna and reduced conditions in water and sediments.

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Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 99%

Effects of organic enrichment on nematode assemblages in a microcosm experiment

Armenteros

Pérez-García

Ruiz-Abierno

et al. 2010

Marine Environmental Research

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“…We also collected two large males (2375 and 2438 mm) with tail unusually short (c 0 :5.5 and 8.6) and large spicules (113 mm both specimens). A recent study (Bhadury et al, 2008), combining morphological and molecular tools points to the presence of cryptic species of T. longicaudata. In our study, the exploration of ultrastructure-based characters by SEM (as suggested by Bhadury et al, 2008) did not add any additional character of diagnostic value for discrimination among putatively cryptic species of T. longicaudata.…”

Section: T E R S C H E L L I N G I a L O N G I C A U D A T A D E M A mentioning

confidence: 99%

“…A recent study (Bhadury et al, 2008), combining morphological and molecular tools points to the presence of cryptic species of T. longicaudata. In our study, the exploration of ultrastructure-based characters by SEM (as suggested by Bhadury et al, 2008) did not add any additional character of diagnostic value for discrimination among putatively cryptic species of T. longicaudata. Therefore, future refining of molecular techniques on this species (in combination with morphological analysis) is the most promising way forward for dealing with this taxonomically problematic species.…”

Section: T E R S C H E L L I N G I a L O N G I C A U D A T A D E M A mentioning

confidence: 99%

A morphometric analysis of the genus Terschellingia (Nematoda: Linhomoeidae) with redefinition of the genus and key to the species

et al. 2009

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The cosmopolitan and often ecologically dominant genus Terschellingia (Nematoda: Linhomoeidae), with 38 nominal species, is taxonomically a problematic taxon. Its species show high morphological plasticity, possess few diagnostic characters and identification keys are lacking. A revision of the genus was carried out based on morphological and morphometric data from the literature and from observations of specimens collected in Cienfuegos Bay, Caribbean Sea, Cuba. The diagnosis of the genus Terschellingia is emended. Of the current 38 nominal species, 15 are considered as valid species based on morphological characters related to size and position of amphidial fovea, presence/position of cephalic and cervical setae, presence/size/shape of pharyngeal bulb, shape of spicular apparatus and shape of tail. Tabular and pictorial keys were provided based on these characters. Three sympatric species: T. communis, T. gourbaultae and T. longicaudata were redescribed based on recently collected Cuban specimens. Each of them showed relatively large differences in body size in comparison with the respective type specimens, suggesting possible variation due to local environmental differences. The highest intraspecific variation pertains for the most widely spread cosmopolitan species T. longicaudata, suggesting that morphological plasticity enhanced adaptation to different environmental conditions. The notable taxonomic inflation within the genus (14 species inquirendae, 9 junior synonyms), probably also present in other highly specious genera of marine nematodes, can lead to an overestimation of the alpha-diversity.

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“…Results clearly indicate a steady degradation of genomic DNA in nematodes stored in slide mounts for more than 2 weeks, whereas unmounted specimens extracted from preservative solution showed no decline in PCR success or quality. We suggest a maximum storage period of 2 weeks on slides if mounted nematodes are to be used for molecular analyses.Keywords -DESS, DNA, glycerin, integrated methods, molecular, morphology.The use of molecular data in nematode studies is now ubiquitous, yet it is still routine for researchers to corroborate DNA sequences with morphology in order to assess the biological relevance of molecular patterns (Griffiths et al, 2006;Stock & Nadler, 2006;Bhadury et al, 2008). DNA barcoding studies promote visual identification of specimens as well as the retention of 'morphological voucher images' to record taxonomic features before nematodes are destroyed for DNA extraction (De Ley et al, 2005;Bhadury et al, 2006a).…”

mentioning

confidence: 99%

“…The use of molecular data in nematode studies is now ubiquitous, yet it is still routine for researchers to corroborate DNA sequences with morphology in order to assess the biological relevance of molecular patterns (Griffiths et al, 2006;Stock & Nadler, 2006;Bhadury et al, 2008). DNA barcoding studies promote visual identification of specimens as well as the retention of 'morphological voucher images' to record taxonomic features before nematodes are destroyed for DNA extraction (De Ley et al, 2005;Bhadury et al, 2006a).…”

mentioning

confidence: 99%

Rapid decline of PCR amplification from genomic extracts of DESS-preserved, slide-mounted nematodes

Bik

Hawkins

Hughes

et al. 2009

Nematol

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Summary -Many studies use integrative methods to study both morphology and gene sequences of nematode species, yet there is little evidence to indicate the optimum criteria for merging taxonomic and molecular protocols. Preliminary evidence suggests that standard methods of desiccation and slide mounting nematode specimens in glycerin can sporadically result in degradation of genomic DNA. A time series experiment was constructed in order to assess whether this degradation of genomic DNA could be recorded and quantified. Two groups of nematode specimens were desiccated, mounted on slides, and stored at either 4 • C or at room temperature for specified time intervals. Genomic DNA was extracted and PCR was conducted to amplify a section of the 18S rRNA gene at each time point. The resulting gel photographs were used to record the outcome of PCR and quantify the strength of amplification if successful. Results from slide-mounted specimens were compared to PCR products derived from unmounted nematodes extracted directly from the preservative solution at specified time intervals. The desiccation and slide mounting process appears to reduce overall band intensity after 1 day in slide mounts. Unmounted specimens consistently exhibit high success rates of PCR and a high overall DNA content per band at all time points, whereas slide-mounted nematodes show a decrease in the number of successful PCRs and weakening band intensity as time progresses. Results clearly indicate a steady degradation of genomic DNA in nematodes stored in slide mounts for more than 2 weeks, whereas unmounted specimens extracted from preservative solution showed no decline in PCR success or quality. We suggest a maximum storage period of 2 weeks on slides if mounted nematodes are to be used for molecular analyses.Keywords -DESS, DNA, glycerin, integrated methods, molecular, morphology.The use of molecular data in nematode studies is now ubiquitous, yet it is still routine for researchers to corroborate DNA sequences with morphology in order to assess the biological relevance of molecular patterns (Griffiths et al., 2006;Stock & Nadler, 2006;Bhadury et al., 2008). DNA barcoding studies promote visual identification of specimens as well as the retention of 'morphological voucher images' to record taxonomic features before nematodes are destroyed for DNA extraction (De Ley et al., 2005;Bhadury et al., 2006a). These barcoding studies have also provided empirical evidence concerning the resolution of different genetic loci used in species identification, with the nuclear 18S ribosomal subunit gene currently recommended as the ideal barcoding locus for nematodes (Bhadury et al., 2006a).Despite the frequent integration of morphological and molecular protocols in nematode studies, there is little * Corresponding author, e-mail: h.bik@nhm.ac.uk published information to suggest how these two disparate approaches might best be optimised to obtain the most robust data. Taxonomic protocols are designed to maximise the clarity of specimens viewed under a microsco...

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Evaluation of combined morphological and molecular techniques for marine nematode (Terschellingia spp.) identification

Cited by 74 publications

References 25 publications

Effects of organic enrichment on nematode assemblages in a microcosm experiment

Effects of organic enrichment on nematode assemblages in a microcosm experiment

A morphometric analysis of the genus Terschellingia (Nematoda: Linhomoeidae) with redefinition of the genus and key to the species

Rapid decline of PCR amplification from genomic extracts of DESS-preserved, slide-mounted nematodes

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