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

Markmann, M., & Tautz, D. (2005). Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360(1462), 1917-1924. doi:10.1098/rstb.2005.1723.

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Markmann, M.1, Author
Tautz, D.2, Author           
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1external, ou_persistent22              
2External, ou_persistent22              

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 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'.

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 Dates: 20052005
 Publication Status: Issued
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 Identifiers: ISI: 000232719300012
DOI: 10.1098/rstb.2005.1723
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Title: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Source Genre: Journal
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Publ. Info: London : Royal Society
Pages: - Volume / Issue: 360 (1462) Sequence Number: - Start / End Page: 1917 - 1924 Identifier: ISSN: 0962-8436
CoNE: https://pure.mpg.de/cone/journals/resource/963017382021_1