Data from: High-throughput sequencing of nematode communities from total soil DNA extractions

Background: Nematodes are extremely diverse and numbers of species are
predicted to be more than a million. Studies on nematode diversity are
difficult and laborious using standard methods such as identification
based on morphology and therefore high-throughput sequencing is an
attractive alternative. Generally, primers that have been used for
generating amplicons for sequencing are not nematode specific and also
amplify other groups such as fungi and plantae. Thus a nematode enrichment
step must be included that may introduce biases. Results: An amplification
strategy, including a new primer, which selectively amplifies nematodes
and other metazoans was developed. When this strategy was tested on DNA
templates from a set of 22 agricultural soils, we obtained 64.4 %
sequences of nematode origin in total, whereas the remaining sequences
were almost entirely metazoan. The nematode sequences were derived from a
broad taxonomic range and most sequences were from nematode taxa that have
previously been found to be abundant in soil such as Tylenchida,
Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This
amplification and sequencing strategy for assessing nematode diversity was
demonstrated to be able to collect a broad taxonomy of nematodes without
prior enrichment and thus the method will be highly valuable in ecological
studies of nematodes. Keywords: nematode, community, next-generation
sequencing, SSU, diversity, 18S, rDNA