An improved protocol for separating meiofauna from sediments using colloidal silica sols

Burgess, Robert M.

doi:10.3354/meps214161

Cited by 215 publications

(112 citation statements)

References 8 publications

(15 reference statements)

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“…For a further removal of anorganic material, we used centrifugation in polysilicate buffer (Burgess 2001). The polysilicate (LudoxTM 50, Dupot de Nemours, Antwerpen) was diluted to 1.14 g cm K3 with water (approximately 30 vol.% Ludox) and adjusted to pH 7.0 with HCl.…”

Section: Methodsmentioning

confidence: 99%

Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences

Markmann

Tautz

2005

Phil. Trans. R. Soc. B

156

144

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Organisms living in or on the sediment layer of water bodies constitute the benthos fauna, which is known to harbour a large number of species of diverse taxonomic groups. The benthos plays a significant role in the nutrient cycle and it is, therefore, of high ecological relevance. Here, we have explored a DNA-taxonomic approach to access the meiobenthic organismic diversity, by focusing on obtaining signature sequences from a part of the large ribosomal subunit rRNA (28S), the D3-D5 region. To obtain a broad representation of taxa, benthos samples were taken from 12 lakes in Germany, representing different ecological conditions. In a first approach, we have extracted whole DNA from these samples, amplified the respective fragment by PCR, cloned the fragments and sequenced individual clones. However, we found a relatively large number of recombinant clones that must be considered PCR artefacts. In a second approach we have, therefore, directly sequenced PCR fragments that were obtained from DNA extracts of randomly picked individual organisms. In total, we have obtained 264 new unique sequences, which can be readily placed into taxon groups, based on phylogenetic comparison with currently available database sequences. The group with the highest taxon abundance were nematodes and protozoa, followed by chironomids. However, we find also that we have by far not exhausted the diversity of organisms in the samples. Still, our data provide a framework within which a meiobenthos DNA signature sequence database can be constructed, that will allow to develop the necessary techniques for studying taxon diversity in the context of ecological analysis. Since many taxa in our analysis are initially only identified via their signature sequences, but not yet their morphology, we propose to call this approach 'reverse taxonomy'.

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Section: Methodsmentioning

confidence: 99%

Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences

Markmann

Tautz

2005

Phil. Trans. R. Soc. B

156

144

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“…Meiofauna were extracted from sediment using isopycnic centrifugation in Ludox-AM® silica sol, as described by Burgess (2001). Nematodes and harpacticoids were removed from total meiofauna using a dissecting microscope, and taxa were placed separately in glycerol droplets on 2-× 3-inch glass ring slides in preparation for digital photography.…”

Section: Materials and Proceduresmentioning

confidence: 99%

“…Instead, samples were processed immediately or stored in a refrigerator at 2°C for a maximum of 3 d prior to processing. Freshwater was used during the extraction process to avoid trapping specimens in an insoluble matrix of silica crystals formed by reaction between divalent cations in seawater during isopycnic extraction (Burgess 2001). Exposure of living or moribund nematodes to freshwater during the sieving process caused osmotic damage in some individuals.…”

Section: Baguley Et Al Measurement Of Meiofaunal Biomass 183mentioning

confidence: 99%

A semi‐automated digital microphotographic approach to measure meiofaunal biomass

Baguley

Hyde

Montagna

2004

Limnology & Ocean Methods

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Meiofauna studies often investigate community structure and function where biomass estimates and taxonomic analysis are required. Nondestructive methods of biomass estimation are necessary to preserve specimens for subsequent taxonomic analysis. A semi-automated protocol to estimate meiofaunal biomass was developed to meet this need. The method improves upon previous indirect biomass techniques by using digital microphotography and analytical graphics software to obtain better estimates of biovolume. The technique is not fully automated because the digital images require some manipulation. Dry mass and carbon mass were estimated for two dominant components of marine benthic meiofauna (Nematoda and Harpacticoida) as the product of conversion factors and body volumes. The technique was validated by comparing indirect dry and carbon mass estimates to direct measurements using an analytical balance and carbon-hydrogen-nitrogen (CHN) elemental analyzer. No significant difference was found between the semi-automated method and direct measurements for harpacticoid dry or carbon mass (P = 0.68 and P = 0.74, respectively), or nematode dry mass (P = 0.28) or carbon content (P = 0.17). The semi-automated indirect method was used to estimate the biomass of meiofauna (13,279 harpacticoids and 12,288 nematodes) collected from the deep-sea Gulf of Mexico. Estimated average wet mass was compared to direct analytical balance measurements from an earlier, independent study in the same area. Wet mass estimates generated by the indirect method (2.67 ± 0.86 µg/harpacticoid and 0.85 ± 4.78 µg/ nematode) were similar to direct measurements in the earlier study (2.80 µg/harpacticoid and 0.85 µg/nematode). The semi-automated indirect method is about three times faster than traditional microscope methods to measure body volume, estimates biomass comparably to direct methods, and conserves samples and images of samples for other analyses.

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“…Higgins, 1984;Sørensen and Pardos, 2008) and extracted in the field through a 63 µm mesh sieve. The concentrated sample was fixed in 4% formalin mixed with sea water, and the meiofauna was subsequently extracted by flotation in Ludox ® (DuPont) HS 40 (Burgess, 2001). The kinorhynch specimens were sorted out from the mixed meiobenthos under a highmagnification LEICA MZ 8 stereomicroscope.…”

Section: Introductionmentioning

confidence: 99%

<i>Echinoderes rex</i> n. sp. (Kinorhyncha: Cyclorhagida), the largest <i>Echinoderes</i> species found so far

2010

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SUMMARY: A new kinorhynch species, Echinoderes rex n. sp., is described from the Korea Strait. The new species is characterized by a pair of diminutive lateral terminal spines (19-23 µm) and a trunk length of 482-528 µm, making it the largest Echinoderes described so far. Unique for the new species is also the presence of a type of putative glandular cell outlets that have not been described previously. This paper presents light and scanning electron micrographs of the new structure. In addition, E. rex n. sp. is characterized by having a single middorsal spine on segment 4, lateroventral tubules on segment 5 and 8 and lateroventral acicular spines on segments 6 and 7. A pair of distinct and conspicuously large sieve plates, only described from two other species of the genus, is present on segment 9 in E. rex n. sp. A comparison is made with other species of Echinoderes and the similarities are discussed.Keywords: Echinoderidae, Korea Strait, meiofauna, morphology, new species. RESUMEN: EchinodErEs rEx n. sp. (Kinorhyncha: Cyclorhagida), la especie de EchinodErEs más grande encontrada hasta el momento. -Se describe una nueva especie de kinorrinco, Echinoderes rex n. sp., del estrecho de Corea. La nueva especie se caracteriza por un par de diminutas espinas lateroterminales (19-23 µm) y una longitud total del tronco de 482-528 µm, lo que la convierte en el mayor Echinoderes conocido. Además, la nueva especie presenta como carácter exclusivo un nuevo tipo de posible poro glandular que no ha sido descrito previamente, y que se describe en este trabajo con microscopía óptica y de barrido. E. rex presenta una única espina mediodorsal en el segmento 4, túbulos lateroventrales en los segmentos 5 y 8, y espinas aciculares lateroventrales en los segmentos 6 y 7. En el segmento 9 aparecen un par de grandes y conspicuas placas cribadas, semejantes a las descritas únicamente en otras dos especies del género. Se compara la nueva especie con otros Echinoderes y se discuten sus semejanzas.

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An improved protocol for separating meiofauna from sediments using colloidal silica sols

Cited by 215 publications

References 8 publications

Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences

Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences

A semi‐automated digital microphotographic approach to measure meiofaunal biomass

<i>Echinoderes rex</i> n. sp. (Kinorhyncha: Cyclorhagida), the largest <i>Echinoderes</i> species found so far

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