Database and primer selections affect nematode community composition under different vegetations of Changbai Mountain

Highlights

● Different primers will affect nematode annotation at different taxonomic levels.

● Sequencing analysis with different primers cannot be compared directly.

● 3NDf primers with NT database could provide more taxa than other combinations.

Abstract

High-throughput sequencing technology is increasingly used in the study of nematode biodiversity. However, the annotation difference of commonly used primers and reference databases on nematode community is still unclear. We compared two pairs of primers (3NDf/C_1132rmod, NF1F/18Sr2bR) and three databases (NT_v20200604, SILVA138/18s Eukaryota and PR2_v4.5 databases) on the determination of nematode community from four different vegetation types in Changbai Mountain, including mixed broadleaf-conifer forest, dark coniferous forest, betula ermanii Cham and alpine tundra. Our results showed that the selection of different primers and databases influenced the annotation of nematode taxa, but the diversity of nematode community showed consistent pattern among different vegetation types. Our findings emphasize that it is necessary to select appropriate primer and database according to the target taxonomic level. The difference in primers will affect the result of nematode taxa at different classification levels, so sequencing analysis cannot be used for comparison with studies using different primers. In terms of annotation effect in this study, 3NDf/C_1132rmod primers with NT_v20200604 database could provide more information than other combinations at the genus or species levels.

Graphical abstract

Keywords

Soil nematodes / Primer / Database / High-throughput sequencing / Community composition

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. U20A2083), the K.C. Wong Education Foundation (Grant No. GJTD-2019-10) and China Postdoctoral Science Foundation (Grant No. 2021T140697).

Compliance and ethics

All authors report no conflicts of interest.

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-022-0153-3 and is accessible for authorized users.

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