Molecular barcodes for soil nematode identification - PubMed (original) (raw)
Molecular barcodes for soil nematode identification
Robin Floyd et al. Mol Ecol. 2002 Apr.
Abstract
Using a molecular barcode, derived from single-specimen polymerase chain reaction (PCR) and sequencing of the 5' segment of the small subunit ribosomal RNA (SSU) gene, we have developed a molecular operational taxonomic unit (MOTU) scheme for soil nematodes. Individual specimens were considered to belong to the same MOTU when the sequenced segment of 450 bases was > 99.5% identical. A Scottish upland Agrostis-Festuca grassland soil was sampled, using both culture-based and random selection methods. One hundred and sixty-six cultured isolates were sequenced, and clustered into five MOTU. From 74 randomly sampled individuals across the study site, 19 MOTU were defined. A subsequent sample of 18 individuals from a single subplot contained eight MOTU, four of which were unique to the single subplot sample. Interestingly, seven of these MOTU were not present in the culture-independent sampling. Overall, a total of 23 MOTU were defined from only 240 sequences. Many MOTU could readily be assigned to classical, morphologically defined taxonomic units using a database of SSU sequences from named nematode species. The MOTU technique allows a rapid assessment of nematode taxon diversity in soils. Correlation with a database of sequences from known species offers a route to application of the technique in ecological surveys addressing biological as well as genetic diversity.
Similar articles
- Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene.
Kenmotsu H, Uchida K, Hirose Y, Eki T. Kenmotsu H, et al. PLoS One. 2020 Oct 7;15(10):e0240336. doi: 10.1371/journal.pone.0240336. eCollection 2020. PLoS One. 2020. PMID: 33027282 Free PMC article. - Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions.
Kenmotsu H, Ishikawa M, Nitta T, Hirose Y, Eki T. Kenmotsu H, et al. PLoS One. 2021 Apr 15;16(4):e0249571. doi: 10.1371/journal.pone.0249571. eCollection 2021. PLoS One. 2021. PMID: 33857177 Free PMC article. - Profiling nematode communities in unmanaged flowerbed and agricultural field soils in Japan by DNA barcode sequencing.
Morise H, Miyazaki E, Yoshimitsu S, Eki T. Morise H, et al. PLoS One. 2012;7(12):e51785. doi: 10.1371/journal.pone.0051785. Epub 2012 Dec 20. PLoS One. 2012. PMID: 23284767 Free PMC article. - Nematode molecular diagnostics: from bands to barcodes.
Powers T. Powers T. Annu Rev Phytopathol. 2004;42:367-83. doi: 10.1146/annurev.phyto.42.040803.140348. Annu Rev Phytopathol. 2004. PMID: 15497206 Review. - Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes.
Gasser RB, Chilton NB. Gasser RB, et al. Vet Parasitol. 2001 Nov 22;101(3-4):201-13. doi: 10.1016/s0304-4017(01)00567-2. Vet Parasitol. 2001. PMID: 11707297 Review.
Cited by
- Marine catfishes (Ariidae-Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?
Lutz Í, Martins T, Santana P, Ferreira C, Miranda J, Matos S, Muhala V, Sampaio I, Vallinoto M, Evangelista-Gomes G. Lutz Í, et al. PeerJ. 2024 Aug 28;12:e17581. doi: 10.7717/peerj.17581. eCollection 2024. PeerJ. 2024. PMID: 39221281 Free PMC article. - Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions.
Jung J, Loschko T, Reich S, Rassoul-Agha M, Werner MS. Jung J, et al. Proc Biol Sci. 2024 Mar 13;291(2018):20232653. doi: 10.1098/rspb.2023.2653. Epub 2024 Mar 13. Proc Biol Sci. 2024. PMID: 38471558 Free PMC article. - Entomopathogenic nematodes and their symbiotic bacteria: from genes to field uses.
Tarasco E, Fanelli E, Salvemini C, El-Khoury Y, Troccoli A, Vovlas A, De Luca F. Tarasco E, et al. Front Insect Sci. 2023 Aug 29;3:1195254. doi: 10.3389/finsc.2023.1195254. eCollection 2023. Front Insect Sci. 2023. PMID: 38469514 Free PMC article. Review. - First report of Paracapillaria philippinensis infection in flowerhorn cichlid in India.
Arumugam U, Pandian RG, Jayasimhan P, Sudarsanan GB, Sornappan G. Arumugam U, et al. Parasitol Res. 2024 Mar 5;123(3):150. doi: 10.1007/s00436-024-08175-4. Parasitol Res. 2024. PMID: 38438689 - Use of PCR-DGGE-Based Molecular Methods to Analyze Nematode Community Diversity.
Festa M, Abbruscato P, Manachini B. Festa M, et al. Methods Mol Biol. 2024;2756:247-255. doi: 10.1007/978-1-0716-3638-1_6. Methods Mol Biol. 2024. PMID: 38427297
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases