A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinv...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023-11-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3941 |
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| author | L. S. Kravtsova T. E. Peretolchina T. I. Triboy I. A. Nebesnykh A. E. Tupikin M. R. Kabilov |
| author_facet | L. S. Kravtsova T. E. Peretolchina T. I. Triboy I. A. Nebesnykh A. E. Tupikin M. R. Kabilov |
| author_sort | L. S. Kravtsova |
| collection | DOAJ |
| description | The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p < 0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius grega rius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring. |
| format | Article |
| id | doaj-art-f01394fc94eb4572ab91e6a927388785 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-11-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-f01394fc94eb4572ab91e6a9273887852025-02-01T09:58:12ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592023-11-0127669470210.18699/VJGB-23-801396A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcodingL. S. Kravtsova0T. E. Peretolchina1T. I. Triboy2I. A. Nebesnykh3A. E. Tupikin4M. R. Kabilov5Limnological Institute of the Siberian Branch of the Russian Academy of SciencesLimnological Institute of the Siberian Branch of the Russian Academy of SciencesLimnological Institute of the Siberian Branch of the Russian Academy of SciencesLimnological Institute of the Siberian Branch of the Russian Academy of SciencesInstitute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of SciencesInstitute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of SciencesThe diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p < 0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius grega rius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring.https://vavilov.elpub.ru/jour/article/view/3941communities of macroinvertebratesdiversitydna metabarcodingcoihigh-throughput sequencing technologieslake baikal |
| spellingShingle | L. S. Kravtsova T. E. Peretolchina T. I. Triboy I. A. Nebesnykh A. E. Tupikin M. R. Kabilov A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding Вавиловский журнал генетики и селекции communities of macroinvertebrates diversity dna metabarcoding coi high-throughput sequencing technologies lake baikal |
| title | A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding |
| title_full | A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding |
| title_fullStr | A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding |
| title_full_unstemmed | A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding |
| title_short | A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding |
| title_sort | study of macroinvertebrate communities in bolshiye koty bay of lake baikal using dna metabarcoding |
| topic | communities of macroinvertebrates diversity dna metabarcoding coi high-throughput sequencing technologies lake baikal |
| url | https://vavilov.elpub.ru/jour/article/view/3941 |
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