Select appropriate soil nematode primers and databases based on target classification level


Soil nematodes are a major component of soil communities in terrestrial ecosystems and play important roles in regulating nutrient cycling and soil health. High-throughput sequencing technology is increasingly used in studying nematode biodiversity. This study shows that the choice of different primers and databases affected the annotation of nematode taxa, but nematode community diversity showed a consistent pattern between different vegetation types. Our results emphasize the need to choose appropriate primers and databases according to the taxonomic level of the target. The researchers’ findings appeared in Soil Ecology Letters on July 26, 2022.

The advent of high-throughput sequencing has completely changed the field of molecular taxonomy, capable of capturing more details about biodiversity. Even though high-throughput sequencing technology has been in use for more than ten years, the choice of primers and databases will affect the sequencing results. Still, few studies have comprehensively assessed the combined effects of different primers and databases on identifying nematode communities.

Changbai Mountain offers the widest range of altitudes of well-preserved forest habitats in Northeast China. Along the elevation gradient, variable environmental conditions such as temperature, soil moisture and soil pH have resulted in an apparent trend in biodiversity. Therefore, the differences in diversity and composition of soil nematode communities in the Changbai Mountains provide an ideal platform to examine the influence of different primers and databases on nematode sequencing annotation.

In this study, they compared two pairs of primers (3NDf/C_1132rmod and NF1F/18Sr2bR) and three databases (databases NT_v20200604, Silva138/18s Eukaryota and PR2_v4.5) to study the nematode communities in different vegetation types along the altitude gradient of Changbai Mountain. For the 3NDF primer, the number of annotated taxa in the three databases differed at the genus and species levels; while for the NF1F primer significant family-level differences were found between the three databases. Differences in nematode taxa were also discovered among different databases. The finer the taxonomic level, the fewer taxa were shared between the three databases. The distribution patterns of nematode diversity obtained by different primers and databases were similar in different vegetation. Therefore, when choosing primers and databases, we should pay more attention to the classification level according to our actual needs. Regarding the annotation effect in this study, 3NDF primers with NT database could provide more information than other combinations at genus or species level.

This study suggests that when the main goal is to study species composition and taxonomy, the sequencing method still suffers from low consistency, so traditional microscopic identification is still indispensable. Therefore, further validations and studies are needed in the future to compare in depth the agreement between the morphological and molecular methods. In addition, despite the rapid development of molecular techniques, some databases still contain incomplete information. In the future, we should add more primers and database information to further improve the accuracy of molecular analysis in ecological nematode research.

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About Soil Ecology Letters

Soil Ecology Letters is an international journal dedicated to the rapid publication of original research articles of scientific importance that illustrate and explain ecological processes occurring in soil. It also publishes letters to the editor, perspectives, reviews, commentaries, etc. The scope of Soil Ecology Letters is extensive and encompasses all aspects of recent research in soil ecology. Some of the topics that are attracting growing attention are soil biodiversity, soil microbial interactions and food web, soil microbiome, soil-plant interactions, soil biogeochemical cycles, soil bioremediation and restoration, soil multifunctionality, response and adaptation of soil organisms of environmental changes, and breakthrough technologies, novel theories and modeling of soil ecological processes.

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