vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-22-12vavilov-3259Research ArticleМЕДИЦИНСКАЯ ГЕНЕТИКА, НЕЙРОГЕНЕТИКА, ИММУНОГЕНЕТИКА, БИОМЕДИЦИНАPOPULATION GENETICSДНК-метабаркодинг бентосных водорослей и ассоциированных с ними эукариот оз. Байкал в условиях быстрых экологических измененийDNA metabarcoding of benthic algae and associated eukaryotes from Lake Baikal in the face of rapid environmental changeshttps://orcid.org/0000-0002-4534-3846БукинЮ. С.BukinYu. S.

Иркутск

Irkutsk

https://orcid.org/0000-0003-0862-4726КравцоваЛ. С.KravtsovaL. S.

Иркутск

Irkutsk

https://orcid.org/0000-0002-2950-9762ПеретолчинаТ. Е.PeretolchinaT. E.

Иркутск

Irkutsk

https://orcid.org/0000-0003-3020-9895ФедотовА. П.FedotovA. P.

Иркутск

Irkutsk

https://orcid.org/0000-0002-8194-0322ТупикинА. Е.TupikinA. E.

 Новосибирск

 Novosibirsk

https://orcid.org/0000-0003-2777-0833КабиловМ. Р.KabilovM. R.

 Новосибирск

 Novosibirsk

https://orcid.org/0000-0002-1410-392XЩербаковД. Ю.SherbakovD. Yu.

Иркутск

Irkutsk

https://orcid.org/0000-0003-4447-6345МинчеваЕ. В.MinchevaE. V.

Иркутск

Irkutsk

Лимнологический институт Сибирского отделения Российской академии наук; Иркутский государственный университетРоссияLimnological Institute of the Siberian Branch of the Russian Academy of Sciences; Irkutsk State UniversityRussian FederationЛимнологический институт Сибирского отделения Российской академии наукРоссияLimnological Institute of the Siberian Branch of the Russian Academy of SciencesRussian FederationИнститут химической биологии и фундаментальной медицины Сибирского отделения Российской академии наукРоссияInstitute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of SciencesRussian FederationЛимнологический институт Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияLimnological Institute of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian Federation2022010320222618695Copyright © Букин Ю.С., Кравцова Л.С., Перетолчина Т.Е., Федотов А.П., Тупикин А.Е., Кабилов М.Р., Щербаков Д.Ю., Минчева Е.В., 20222022Букин Ю.С., Кравцова Л.С., Перетолчина Т.Е., Федотов А.П., Тупикин А.Е., Кабилов М.Р., Щербаков Д.Ю., Минчева Е.В.Bukin Y.S., Kravtsova L.S., Peretolchina T.E., Fedotov A.P., Tupikin A.E., Kabilov M.R., Sherbakov D.Y., Mincheva E.V.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3259

Впервые приводится оценка разнообразия фитобентосных сообществ на основе ДНК-метабаркодинга с использованием ампликонов фрагмента гена 18S рРНК и технологии Illumina MiSeq. Исследование проведено в связи с цветением нитчатых водорослей (преимущественно рода Spirogyra) и цианобактерий в прибрежной зоне озера Байкал в условиях изменения климата и антропогенного воздействия. С помощью ДНК-метабаркодинга определен видовой состав водорослей, а также таксономическое разнообразие ассоциированных с ними эукариот в разных районах Байкала (у острова Большой Ушканий, в заливе Лиственничный) и в р. Кая (в черте г. Иркутска), находящейся в одном водосборном бассейне с оз. Байкал. С помощью NGS (next generation sequencing) получено более 15 тыс. прочтений 18S рРНК маркера. Выявлены виды водорослей, доминирующие по количеству прочтений, а также трудно идентифицируемые таксоны Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa и др., играющие важную роль в функционировании и формировании структуры водорослевых сообществ. Охарактеризовано разнообразие грибов и грибоподобных организмов в изучаемых сообществах. Индекс Шеннона рассмотренных сообществ колеблется от 1.56 до 2.72. Показаны преимущества и слабые стороны использования ДНК-метабаркодинга на основе фрагмента гена 18S рРНК для изучения структуры сообществ водорослей. Метод позволяет более полно учесть разнообразие таксонов эукариот, трудно идентифицируемых по морфологии, без привлечения большого числа специалистов, что характеризует его преимущество. Недостатком метода являются искажения, возникающие при проведении ПЦР. Предложены пути решения для устранения этого недостатка. Результаты исследования показывают, что для анализа минорной компоненты сообщества эукариот в образцах (организмы с малой биомассой), состоящих из смеси многоклеточных и одноклеточных организмов, требуется глубина прочтения не менее чем 100000 последовательностей на пробу. В целом метод ДНК-метабаркодинга рекомендован для исследования структуры сообществ водорослей и ассоциированных с ними эукариот.

Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of filamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using DNAmetabarcoding. About 15 thousand reads of the 18S rRNA marker were obtained by applying NGS (next-generation sequencing). The species of algae dominating in the number of reads, as well as the difficult-to-identify taxa (Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa, etc.), which play an important role in the functioning and formation of the structure of algal communities, were revealed. The Shannon index of the communities studied ranges from 1.56 to 2.72. The advantages and weaknesses of using DNA-metabarcoding based on the 18S rRNA gene fragment for studying the structure of algal communities are shown. The advantage of this method is the possibility to more fully determine the diversity of eukaryotes taxa, which are difficult to identify by morphology, without involving a large number of specialists, while the disadvantage of the method is the distortion that may occur during the PCR. Here, ways of solving this problem are proposed. The results of the study show that the analysis of the minor component of the eukaryotic community in samples (organisms with low biomass) consisting of a mixture of multicellular and unicellular organisms requires a read-depths of at least 100,000 sequences per sample. In general, the DNA-metabarcoding method is recommended for studying the structure of algal communities and eukaryotes associated with them.

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The authors declare that there are no conflicts of interest present.