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According to the target classification level to select appropriate primers and databases for soil nematodes

Peer-Reviewed Publication

Higher Education Press

According to the target classification level to select appropriate primers and databases for soil nematodes

image: NMDS indicated that there were significant differences in the nematode communities obtained by different primers and different database annotations (A and B). Compared with the primer NF1F, higher values were found in indices annotated by the primer 3NDF, especially for evenness index. For the primer 3NDF, the Chao index obtained by the three databases were slightly different, with higher values observed in the NT database (C and D) view more 

Credit: Higher Education Press Limited Company

Soil nematodes represent a major component of soil communities in terrestrial ecosystems, and play an important role in regulating nutrient cycling and soil health. High-throughput sequencing technology is increasingly used in the study of nematode biodiversity. This study demonstrates 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 primers and databases according to the target taxonomic level. The researchers finding appeared July 26, 2022 in Soil Ecology Letters

The emergence of high-throughput sequencing has entirely transformed the field of molecular taxonomy, it can capture 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. Nonetheless, few studies have comprehensively evaluated the combined impacts of different primers and databases on the identification of nematode communities.

Changbai Mountain offers the largest altitudinal range of well-preserved forest habitats in northeast China. Along the altitude gradient, variable environmental conditions such as temperature, soil moisture and soil pH, have resulted in an obvious trend of biodiversity. Thus, the differences in diversity and composition of soil nematode communities in Changbai Mountain provide an ideal platform to verify the influence of different primers and databases on the annotation of nematode sequencing.

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

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


About Higher Education Press

Founded in May 1954, Higher Education Press Limited Company (HEP), affiliated with the Ministry of Education, is one of the earliest institutions committed to educational publishing after the establishment of P. R. China in 1949. After striving for six decades, HEP has developed into a major comprehensive publisher, with products in various forms and at different levels. Both for import and export, HEP has been striving to fill in the gap of domestic and foreign markets and meet the demand of global customers by collaborating with more than 200 partners throughout the world and selling products and services in 32 languages globally. Now, HEP ranks among China's top publishers in terms of copyright export volume and the world's top 50 largest publishing enterprises in terms of comprehensive strength.

The Frontiers Journals series published by HEP includes 28 English academic journals, covering the largest academic fields in China at present. Among the series, 13 have been indexed by SCI, 6 by EI, 2 by MEDLINE, 1 by A&HCI. HEP's academic monographs have won about 300 different kinds of publishing funds and awards both at home and abroad.


About Soil Ecology Letters

Soil Ecology Letters is an international journal for fast publishing original research articles of scientific significance that depict 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 includes all aspects of recent research in soil ecology. Some of the subjects that are attracting growing attention are soil biodiversity, soil microbial interactions and food web, soil microbiome, soil-plant interactions, soil biogeochemical cycling, soil bioremediation and restoration, soil multifunctionality, response and adaptation of soil biota to environmental changes, and breakthrough technologies, novel theories and modeling of soil ecological processes.

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