Advanced search
Add to list

A novel metabarcoding strategy for studying nematode communities

Author
Organization
Abstract
Nematodes are widely abundant soil metazoa and often referred to as indicators of soil health. While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the ecology of nematodes remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. Objectives of the present study were (i) to compare commonly used primer sets and to identify the most suitable primer set for metabarcoding of nematodes; (ii) to establish and validate a high-throughput sequencing strategy for nematodes using Illumina paired-end sequencing. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition); SSU_04F/SSU_22R (18S rRNA, V1-V2 region); Nemf/18Sr2b (18S rRNA, V6-V8 region) from earlier studies; and MMSF/MMSR (18S rRNA, V4-V5 region), a newly developed primer set from this study. In order to test the primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 spiked soil samples (mock communities in soil), and 4 root/rhizosphere soil samples. We successfully amplified the target regions (I3-M11 partition of the COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were efficient in detecting nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets are suggested for studies of nematode communities in agricultural environments.

Citation

Please use this url to cite or link to this publication:

MLA
Sikder, Md. Maniruzzaman, et al. “A Novel Metabarcoding Strategy for Studying Nematode Communities.” BIORXIV, 2020, doi:10.1101/2020.01.27.921304.
APA
Sikder, M. M., Vestergård, M., Sapkota, R., Kyndt, T., & Nicolaisen, M. (2020). A novel metabarcoding strategy for studying nematode communities. BIORXIV. https://doi.org/10.1101/2020.01.27.921304
Chicago author-date
Sikder, Md. Maniruzzaman, Mette Vestergård, Rumakanta Sapkota, Tina Kyndt, and Mogens Nicolaisen. 2020. “A Novel Metabarcoding Strategy for Studying Nematode Communities.” BIORXIV. https://doi.org/10.1101/2020.01.27.921304.
Chicago author-date (all authors)
Sikder, Md. Maniruzzaman, Mette Vestergård, Rumakanta Sapkota, Tina Kyndt, and Mogens Nicolaisen. 2020. “A Novel Metabarcoding Strategy for Studying Nematode Communities.” BIORXIV. doi:10.1101/2020.01.27.921304.
Vancouver
1.
Sikder MM, Vestergård M, Sapkota R, Kyndt T, Nicolaisen M. A novel metabarcoding strategy for studying nematode communities. BIORXIV. 2020.
IEEE
[1]
M. M. Sikder, M. Vestergård, R. Sapkota, T. Kyndt, and M. Nicolaisen, “A novel metabarcoding strategy for studying nematode communities,” BIORXIV. 2020.
@misc{8655751,
  abstract     = {Nematodes are widely abundant soil metazoa and often referred to as indicators of soil health. While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the ecology of nematodes remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. Objectives of the present study were (i) to compare commonly used primer sets and to identify the most suitable primer set for metabarcoding of nematodes; (ii) to establish and validate a high-throughput sequencing strategy for nematodes using Illumina paired-end sequencing. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition); SSU_04F/SSU_22R (18S rRNA, V1-V2 region); Nemf/18Sr2b (18S rRNA, V6-V8 region) from earlier studies; and MMSF/MMSR (18S rRNA, V4-V5 region), a newly developed primer set from this study. In order to test the primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 spiked soil samples (mock communities in soil), and 4 root/rhizosphere soil samples. We successfully amplified the target regions (I3-M11 partition of the COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were efficient in detecting nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets are suggested for studies of nematode communities in agricultural environments.},
  author       = {Sikder, Md. Maniruzzaman and Vestergård, Mette and Sapkota, Rumakanta and Kyndt, Tina and Nicolaisen, Mogens},
  language     = {eng},
  series       = {BIORXIV},
  title        = {A novel metabarcoding strategy for studying nematode communities},
  url          = {http://dx.doi.org/10.1101/2020.01.27.921304},
  year         = {2020},
}

Altmetric
View in Altmetric