Cookies Policy

This site uses cookies. By continuing to browse the site you are agreeing to our use of cookies.

I accept this policy

Find out more here

The D3-D5 region of large subunit ribosomal DNA provides good resolution of German limnic and terrestrial nematode communities

No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.

Brill’s MyBook program is exclusively available on BrillOnline Books and Journals. Students and scholars affiliated with an institution that has purchased a Brill E-Book on the BrillOnline platform automatically have access to the MyBook option for the title(s) acquired by the Library. Brill MyBook is a print-on-demand paperback copy which is sold at a favorably uniform low price.

Access this article

+ Tax (if applicable)
Add to Favorites
You must be logged in to use this functionality

image of Nematology
For more content, see Nematologica.

Reliable and well-developed DNA barcode databases are indispensable for the identification of microscopic life. However, effectiveness of molecular barcoding in identifying terrestrial specimens, and nematodes in particular, has received little attention. In this study, ca 600 ribosomal large subunit DNA fragments (D3-D5 region) were successfully amplified for 79 limnic and terrestrial nematode species sampled at 147 locations across Germany. Distinctive DNA motifs in the LSU region were identified in 80% of all species examined. For 13 supposedly single morphospecies, 2-7 LSU barcode groups were detected with a wide range of intraspecific variations (0.09-7.9%). This region seems to be more suitable for the assessment of limno-terrestrial nematode diversity than the frequently used mitochondrial gene COI, as amplification success of the latter fragment is low for several nematode species. Our reference database for nematodes may serve as a starting point for applied and fundamental studies for these ubiquitous, ecologically highly relevant, organisms.

Affiliations: 1: 1Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany ; 2: 2Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany ; 3: 3Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1 (RADIX building), 6708 PB Wageningen, The Netherlands

*Corresponding author, e-mail:

Full text loading...


Data & Media loading...

1. Alphei J. (1998). "Differences in soil nematode community structure of beech forests: comparison between a mull and a moder soil". Applied Soil Ecology Vol 9, 9-15. DOI: 10.1016/S0929-1393(98)00047-X [Crossref]
2. Andrássy I. (1984). "Klasse Nematoda: (Ordnungen Monhysterida, Desmoscolecida, Araeolaimida, Chromadorida, Rhabditida)". In: Franz H. (Ed.). Bestimmungsbücher zur Bodenfauna Europas. Stuttgart, Germany, Gustav Fischer.
3. Andrássy I. (2005). Free-living nematodes of Hungary (Nematoda errantia), I. Pedozoologica Hungarica No. 3, (Series Editors Csuzdi C., Mahunka S.). Budapest, Hungary, Hungarian Natural History Museum and Systematic Zoology Research Group of the Hungarian Academy of Sciences.
4. Andrássy I. (2007). Free-living nematodes of Hungary (Nematoda errantia), II. Pedozoologica Hungarica No. 4, (Series Editors Csuzdi C., Mahunka S.). Budapest, Hungary, Hungarian Natural History Museum and Systematic Zoology Research Group of the Hungarian Academy of Sciences.
5. Andrássy I. (2009). Free-living nematodes of Hungary (Nematoda errantia), III. Pedozoologica Hungarica No. 5, (Series Editors Csuzdi C., Mahunka S.). Budapest, Hungary, Hungarian Natural History Museum and Systematic Zoology Research Group of the Hungarian Academy of Sciences.
6. Artois T., Fontaneto D., Hummon W.D., McInnes S.J., Todaro M.A., Sørensen M.V., Martin V., Zullini A. (2011). "Ubiquity of microscopic animals? Evidence from the morphological approach in species identification". In: Fontaneto D. (Ed.). Biogeography of microscopic organisms: is everything small everywhere? Cambridge, UK, Cambridge University Press, pp.  244-249. [Crossref]
7. Bain O., Baldwin J.G., Beveridge I., Bezerra T.C., Braeckman U., Coomans A., Decraemer W., Derycke S., Durette-Desset M., Fonseca G. (2014). Nematoda. Berlin, Germany, De Gruyter.
8. Baird D.J., Hajibabaei M. (2012). "Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing". Molecular Ecology Vol 21, 2039-2044. DOI: 10.1111/j.1365-294X.2012.05519.x [Crossref]
9. Ball S.L., Hebert P.D., Burian S.K., Webb J.M. (2005). "Biological identifications of mayflies (Ephemeroptera) using DNA barcodes". Journal of the North American Benthological Society Vol 24, 508-524. DOI: 10.1899/04-142.1 [Crossref]
10. Beier S., Traunspurger W. (2003). "Seasonal distribution of free-living nematodes in the Krähenbach, a fine-grained submountain carbonate stream in southwest Germany". Nematology Vol 5, 113-136. DOI: 10.1163/156854102765216740 [Crossref]
11. Blaxter M.L. (2004). "The promise of a DNA taxonomy". Philosophical Transactions of the Royal Society B: Biological Sciences Vol 359, 669-679. DOI: 10.1098/rstb.2003.1447 [Crossref]
12. Blaxter M.L., De Ley P., Garey J.R., Liu L.X., Scheldeman P., Vierstraete A., Vanfleteren J.R., Mackey L.Y., Dorris M., Frisse L.M. , et al (1998). "A molecular evolutionary framework for the phylum Nematoda". Nature Vol 392, 71-75. DOI: 10.1038/32160 [Crossref]
13. Blaxter M.L., Mann J., Chapman T., Thomas F., Whitton C., Floyd R., Abebe E. (2005). "Defining operational taxonomic units using DNA barcode data". Philosophical Transactions of the Royal Society B: Biological Sciences Vol 360, 1935-1943. DOI: 10.1098/rstb.2005.1725 [Crossref]
14. Boag B., Yeates G.W. (1998). "Soil nematode biodiversity in terrestrial ecosystems". Biodiversity and Conservation Vol 7, 617-630. DOI: 10.1023/A:1008852301349 [Crossref]
15. Brzeski M.W. (1998). Nematodes of Tylenchina in Poland and temperate Europe. Warsaw, Poland, Muzeum i Instytutu Zoologii, Polska Akademia Nauk (MiIZ PAN).
16. Creer S., Fonseca V.G., Porazinska D.L., Giblin-Davis R.M., Sung W., Power D.M., Packer M., Carvalho G.R., Blaxter M.L., Lamshead P.J.D. , et al (2010). "Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises". Molecular Ecology Vol 19, 4-20. DOI: 10.1111/j.1365-294X.2009.04473.x [Crossref]
17. De Ley P., De Ley I.T., Morris K., Abebe E., Mundo-Ocampo M., Yoder M., Heras J., Waumann D., Rocha-Olivares A., Jay Burr A.H.J. , et al (2005). "An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding". Philosophical Transactions of the Royal Society B: Biological Sciences Vol 360, 1945-1958. DOI: 10.1098/rstb.2005.1726 [Crossref]
18. de Meester L., Gomez A., Okamura S., Schwenk K. (2002). "The monopolization hypothesis and the dispersal-gene flow paradox in aquatic organisms". Acta Oecologica Vol 23, 121-135. DOI: 10.1016/S1146-609X(02)01145-1 [Crossref]
19. Decker H. (1969). Phytonematologie. Berlin, Germany, Deutscher Landwirtschftsverlag.
20. Derycke S., Backeljau T., Moens T. (2013). "Dispersal and gene flow in free-living marine nematodes". Frontiers in Zoology Vol 10, 1-12. DOI: 10.1186/1742-9994-10-1 [Crossref]
21. Geiger M.F., Astrin J.J., Borsch T., Burkhardt U., Grobe P., Hand R., Hausmann A., Hohberg K., Krogmann L., Lutz M. , et al (2016). "How to tackle the molecular species inventory for an industrialized nation-lessons from the first phase of the German Barcode of Life initiative GBOL (2012-2015)". Genome Vol 59, 1-10. DOI: 10.1139/gen-2015-0185 [Crossref]
22. Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W., Hebert P.D. (2006). "DNA barcodes distinguish species of tropical Lepidoptera". Proceedings of the National Academy of Sciences of the United States of America Vol 103, 968-971. DOI: 10.1073/pnas.0510466103 [Crossref]
23. Hebert P.D., Cywinska A., Ball S.L., deWaard J.R. (2003). "Biological identifications through DNA barcodes". Proceedings of the Royal Society B: Biological Sciences Vol 270, 313-321. DOI: 0.1098/rspb.2002.2218 [Crossref]
24. Hebert P.D., Stoeckle M.Y., Zemlak T.S., Francis C.M. (2004). "Identification of birds through DNA barcodes". PLoS Biology Vol 2, 1657-1663. DOI: 10.1371/journal.pbio.0020312 [Crossref]
25. Hohberg K., Traunspurger W. (2005). "Predator-prey interaction in soil food web: functional response, size-dependent foraging efficiency, and the influence of soil texture". Biology and Fertility of Soils Vol 41, 419-427. DOI: 10.1007/s00374-005-0852-9 [Crossref]
26. Holterman M., Rybarczyk K., van den Elsen S., van Megen H., Mooyman P., Peña-Santiago R., Bongers T., Bakker J., Helder J. (2008). "A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats". Molecular Ecology Resources Vol 8, 23-34. DOI: 10.1111/j.1471-8286.2007.01963.x [Crossref]
27. Holterman M., Karssen G., van den Elsen S., van Megen H., Bakker J., Helder J. (2009). "Small subunit rDNA-based phylogeny of the Tylenchida sheds light on relationships among some high-impact plant-parasitic nematodes and the evolution of plant feeding". Phytopathology Vol 99, 227-235. DOI: 10.1094/PHYTO-99-3-0227 [Crossref]
28. Hugot J.-P., Baujard P., Morand S. (2001). "Biodiversity in helminths and nematodes as a field of study: an overview". Nematology Vol 3, 199-208. DOI: 10.1163/156854101750413270 [Crossref]
29. Ingham R.E., Trofymow J.A., Ingham E.R., Coleman D.C. (1985). "Interactions of bacteria, fungi, and their nematode grazers: effects on nutrient cycling and plant growth". Ecological Monographs Vol 55, 119-140. DOI: 10.2307/1942528 [Crossref]
30. Janzen D.H., Hajibabaei M., Burns J.M., Hallwachs W., Remigio E., Hebert P.D. (2005). "Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding". Philosophical Transactions of the Royal Society B: Biological Sciences Vol 360, 1835-1845. DOI: 10.1098/rstb.2005.1715 [Crossref]
31. Jörger K.M., Norenburg J.L., Wilson N.G., Schrödl M. (2012). "Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs". BMC Evolutionary Biology Vol 12, 1-18. DOI: 10.1186/1471-2148-12-245 [Crossref]
32. Lambshead P.I. (1993). "Recent developments in marine benthic biodiversity research". Oceanis Vol 19, 5-24.
33. Lejzerowicz F., Esling P., Pillet L., Wilding T.A., Black K.D., Pawlowski J. (2015). "High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems". Scientific Reports Vol 5, 1-10. DOI: 10.1038/srep13932 [Crossref]
34. Liao D. (1999). "Concerted evolution: molecular mechanism and biological implications". The American Journal of Human Genetics Vol 64, 24-30. DOI: 10.1086/302221 [Crossref]
35. Loof P.A.A. (1999). "Nematoda: Adenophorea (Dorylaimida)". In: Schwoerbel J., Zwick P. (Eds). Süßwasserfauna von Mitteleuropa, Vol 4/2-2. Heidelberg, Berlin, Spektrum.
36. Loof P.A.A. (2001). "Nematoda: Secernentea (Tylenchida, Aphelenchida)". In: Schwoerbel J., Zwick P. (Eds). Süßwasserfauna von Mitteleuropa, Vol 4/1-1. Heidelberg, Berlin, Spektrum.
37. Lydeard C., Cowie R.H., Ponder W.F., Bogan A.E., Bouchet P., Clark S.A., Cummings K.S., Frest T.J., Gargominy O., Herbert D.G. , et al (2004). "The global decline of nonmarine mollusks". BioScience Vol 54, 321-330. DOI: 10.1641/0006-3568(2004)054[0321:TGDONM]2.0.CO;2 [Crossref]
38. Maddison W.P., Knowles L.L. (2006). "Inferring phylogeny despite incomplete lineage sorting". Systematic Biology Vol 55, 21-30. DOI: 10.1080/10635150500354928 [Crossref]
39. Mahé F., Mayor J., Bunge J., Chi J., Siemensmeyer T., Stoeck T., Wahl B., Paprotka T., Filker S., Dunthorn M. (2015). "Comparing high-throughput platforms for sequencing the V4 Region of SSU-rDNA in environmental microbial eukaryotic diversity surveys". The Journal of Eukaryotic Microbiology Vol 62, 338-345. DOI: 10.1111/jeu.12187 [Crossref]
40. Majdi N., Traunspurger W. (2015). "Free-living nematodes in the freshwater food web: a review". Journal of Nematology Vol 47, 28-44.
41. Majdi N., Threis I., Traunspurger W. (2017). "It’s the little things that count: Meiofaunal density and production in the sediment of two headwater streams". Limnology and Oceanography Vol 62, 151-163. DOI: 10.1002/lno.10382 [Crossref]
42. 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 Vol 360, 1917-1924. DOI: 10.1098/rstb.2005.1723 [Crossref]
43. Meyer C.P., Paulay G. (2005). "DNA barcoding: error rates based on comprehensive sampling". PLoS Biology Vol 3, e422. DOI: 10.1371/journal.pbio.0030422
44. Mora C., Tittensor D.P., Adl S., Simpson A.G., Worm B. (2011). "How many species are there on Earth and in the ocean?" PLoS Biology Vol 9, e1001127. DOI: 10.1371/journal.pbio.1001127
45. Mutanen M., Kekkonen M., Prosser S.W., Hebert P.D., Kaila L. (2015). "One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire". Molecular Ecology Resources Vol 15, 967-984. DOI: 10.1111/1755-0998.12361 [Crossref]
46. Nadler S. (2002). "Species delimitation and nematode biodiversity: phylogenies rule". Nematology Vol 4, 615-625. DOI: 10.1163/15685410260438908 [Crossref]
47. Nkem J.N., Wall D.H., Virginia R.A., Barrett J.E., Broos E.J., Porazinska D.L., Adams B.J. (2006). "Wind dispersal of soil invertebrates in the McMurdo Dry Valleys, Antarctica". Polar Biology Vol 29, 346-352. DOI: 10.1007/s00300-005-0061-x [Crossref]
48. Norton D.C. (1978). Ecology of plant-parasitic nematodes. New York, NY, USA, Wiley.
49. Pfannkuche O., Thiel H. (1988). "Sample processing". In: Higgins R.P., Thiel H. (Eds). Introduction to the study of Meiofauna. Washington, DC, USA, Smithsonian Institution Press, pp.  134-145.
50. Prosser S.W., Velarde-Aguilar M.G., Leon-Regagnon V., Hebert P.D. (2013). "Advancing nematode barcoding: a primer cocktail for the cytochrome C oxidase subunit I gene from vertebrate parasitic nematodes". Molecular Ecology Resources Vol 13, 1108-1115. DOI: 10.1111/1755-0998.12082
51. Puillandre N., Lambert A., Brouillet S., Achaz G. (2012). "ABGD, Automatic Barcode Gap Discovery for primary species delimitation". Molecular Ecology Vol 21, 1864-1877. DOI: 10.1111/j.1365-294X.2011.05239.x [Crossref]
52. Ristau K., Steinfartz S., Traunspurger W. (2013). "First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis)". Molecular Ecology Vol 22, 4562-4575. DOI: 10.1111/mec.12414 [Crossref]
53. Sands C.J., Convey P., Linse K., McInnes S.J. (2008). "Assessing meiofaunal variation among individuals utilising morphological and molecular approaches: an example using the Tardigrada". BMC Ecology Vol 8, 1-11. DOI: 10.1186/1472-6785-8-7 [Crossref]
54. Sauer J., Hausdorf B. (2012). "A comparison of DNA-based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy". Cladistics Vol 28, 300-316. DOI: 10.1111/j.1096-0031.2011.00382.x [Crossref]
55. Schenk J., Traunspurger W., Ristau K. (2016). "Genetic diversity of widespread moss-dwelling nematode species in German beech forests". European Journal of Soil Biology Vol 74, 23-31. DOI: 10.1016/j.ejsobi.2016.03.002 [Crossref]
56. Schmid-Araya J.M., Schmid P.E. (2000). "Trophic relationships: integrating meiofauna into a realistic benthic food web". Freshwater Biology Vol 44, 149-163. DOI: 10.1046/j.1365-2427.2000.00594.x [Crossref]
57. Slatkin M. (1987). "Gene flow and the geographic structure of natural populations". Science Vol 236, 787-792. [Crossref]
58. Sonnenberg R., Nolte A.W., Tautz D. (2007). "An evaluation of LSU rDNA D1-D2 sequences for their use in species identification". Frontiers in Zoology Vol 4, 1-12. DOI: 10.1186/1742-9994-4-6 [Crossref]
59. Sturhan D., Hohberg K. (2016). "Nematodes of the order Tylenchida in Germany – the non-phytoparasitic species". Soil Organisms Vol 88, 19-41.
60. Suzuki Y., Nijhout H.F. (2006). "Evolution of a polyphenism by genetic accommodation". Science Vol 311, 650-652. DOI: 10.1126/science.1118888 [Crossref]
61. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. (2013). "MEGA6: molecular evolutionary genetics analysis version 6.0". Molecular Biology and Evolution Vol 30, 2725-2729. DOI: 10.1093/molbev/mst197 [Crossref]
62. Tavaré S. (1986). "Some probabilistic and statistical problems in the analysis of DNA sequences". Lectures on Mathematics in the Life Sciences Vol 17, 57-86.
63. Traunspurger W. (2002). "Nematoda". In: Rundle S.D., Robertson A.L., Schmid-Araya J.M. (Eds). Freshwater meiofauna: biology and ecology. Leiden, The Netherlands, Backhuys Publishers, pp.  63-104.
64. Traunspurger W. (2014). "Ecology of freshwater nematodes". In: Schmidt-Rhaesa A. (Ed.). Handbook of zoology; Gastrotricha, Cycioneuralia and Gnathifera, volume 2: Nematoda. Berlin, Germany, De Gruyter, pp.  153-169.
65. Traunspurger W., Michiels I.C., Eyualem-Abebe (2006). "Composition and distribution of free-living freshwater nematodes: global and local perspectives". In: Eyualem-Abebe, Andrássy I., Traunspurger W. (Eds). Freshwater nematodes: ecology and taxonomy. Wallingford, UK, CABI Publishing, pp.  46-76. [Crossref]
66. van Megen H., van den Elsen S., Holterman M., Karssen G., Mooyman P., Bongers T., Holovachov O., Bakker J., Helder J. (2009). "A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences". Nematology Vol 11, 927-950. DOI: 10.1163/156854109X456862 [Crossref]
67. Vanschoenwinkel B., Gielen S., Seaman M., Brendonck L. (2009). "Wind mediated dispersal of freshwater invertebrates in a rock pool metacommunity: differences in dispersal capacities and modes". Hydrobiologia Vol 635, 363-372. DOI: 10.1007/s10750-009-9929-z [Crossref]
68. Yang L., Tan Z., Wang D., Xue L., Guan M.-x., Huang T., Ronghua L. (2014). "Species identification through mitochondrial rRNA genetic analysis". Scientific Reports Vol 4, 1-11. DOI: 10.1038/srep04089
69. Yeates G.W., Bongers T., De Goede R.G.M., Freckman D.W., Georgieva S.S. (1993). "Feeding habits in soil nematode families and genera – an outline for soil ecologists". Journal of Nematology Vol 25, 315-331.

Article metrics loading...



Can't access your account?
  • Tools

  • Add to Favorites
  • Printable version
  • Email this page
  • Subscribe to ToC alert
  • Get permissions
  • Recommend to your library

    You must fill out fields marked with: *

    Librarian details
    Your details
    Why are you recommending this title?
    Select reason:
    Nematology — Recommend this title to your library
  • Export citations
  • Key

  • Full access
  • Open Access
  • Partial/No accessInformation