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

Abstract

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'.

Infestation ofLernaea cyprinacea(Copepoda: Lernaeidae) in two invasive fish species in Romania,Lepomis gibbosusandPseudorasbora parva

“…Given this controversy, we used a fragment of the hypervariable region D1-D2 of the 28S rRNA to confirm that the copepod specimens collected on both host species in our study are indeed conspecific. The hypervariable regions of 28S rRNA have been used by other authors as species diagnostic markers in arthropods, annelids and mollusks (Markmann and Tautz, 2005;Raupach et al, 2010;Song et al, 2008). All eight examined sequences (from two host species) were identical.…”

Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding

“…Thus, they also have the potential to more accurately evaluate the extent to which biodiversity is being lost as a function of anthropogenic reef degradation. It is extremely challenging to apply quantitative sampling on coral reefs because of their heterogeneous, rigid and complex structure; this makes them unsuitable for quantified sieving, as is used for soft sediments (Markmann and Tautz 2005). Because of the extraordinary diversity of coral reefs, exhaustive inventories of reef-associated fauna also still remain impractical.…”

A likelihood ratio test for species membership based on DNA sequence data

“…This situation may arise in many cases, for example in screens of invasive species, pathogenic bacterial strains, toxic algae or products from protected species (e.g. Tautz et al 2002Tautz et al , 2003Armstrong & Ball 2005;Lorenz et al 2005;Markmann & Tautz 2005). We will assume that more than one sequence from the focal species is known.…”