Abstract
The small subunit ribosomal gene (SSU rDNA) is used in both environmental and phylogenetic studies of nematodes. However, currently described SSU rDNA primers near to the 5′ end of the gene show mismatches with a number of different nematode sequences. Here a new SSU rDNA 5′ forward primer, Nem_SSU_F74, is designed from existing database sequences and its performance compared with a previously described forward primer, SSU_F04, by sequencing from nematode assemblage DNA, in combination with a previously described reverse primer. DNA was extracted from three nematode assemblages isolated from arable soil and, in total, six clone libraries were created: three amplified with established forward primer SSU_F04 and three with the novel primer Nem_SSU_F74. Ninety six clones were sequenced from each library. Nem_SSU_F74 libraries yielded a higher number of nematode sequences than SSU_F04 libraries, and a greater number of nematode taxa were found using the novel forward primer. The most abundant sequences were common to libraries created with either forward primer. Data from a morphological survey of the same samples revealed that biomass was more closely related to molecular analysis than simple counts of nematodes. For all but one nematode order (Aphelenchida), percentage assemblage composition was not significantly different between biomass and sequences obtained with the novel forward primer Nem_SSU_F74.
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Acknowledgements
This work was supported by the Scottish Government through the Rural and Environmental Research and Analysis Directorate and a BBSRC Quota studentship (BBS/S/K/2004/11271). Advice on data analysis methodology was received from Bioinformatics and Statistics Scotland (BioSS).
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Donn, S., Neilson, R., Griffiths, B.S. et al. Greater coverage of the phylum Nematoda in SSU rDNA studies. Biol Fertil Soils 47, 333–339 (2011). https://doi.org/10.1007/s00374-010-0534-0
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DOI: https://doi.org/10.1007/s00374-010-0534-0