18S rRNA Identification of Hydrobionts of Nizhniy Kaban Lake & Diversity Study through Next Generation Sequencing Method

Author Name(s): Ludmila Frolova, Anthony Elias Sverdrup
Author Email: Lucie.Frolova@gmail.com

Abstract

The paper presents the results of a study of the species diversity of freshwater Nizhniy Kaban Lake (Kazan, Russia) by the gene 18S rRNA based on the next-generation sequencing method. Nizhniy Kaban, Verhniy Kaban, and Sredniy Kaban Lakes are included in the system of urban Kaban Lakes, which are polluted lakes according to ecological studies. Sequences of the 18S rRNA gene fragment of the freshwater Nizhniy Kaban Lake hydrobionts were submitted to the international SRA database on NCBI website in fastq format with numbers SRR7510988, SRR7516481, SRR7465568. A total of 39505 (2016) and 22619 (2017) high-quality reads were obtained; 89.4% (2016) and 83.8% (2017) of the hydrobionts was classified to the kingdom level, while 74.7% (2016) and 81% (2017) was classified to the phylum level, 48.2% (2016) and 79.5% (2017) was classified to the class level, 80% (2017) was classified to the family level, 79.6% (2017) was classified to the genus level, and 41.9% (2017) was classified to the species level. Analysis of the metagenomic data for Nizhniy Kaban Lake shows that indicator organisms identified by the 18S rRNA gene are grouped near the bmesosaprobity. Nizhniy Kaban Lake can be characterized as contaminated, in terms of water quality, transitional from b- to a-mesosaprobity.

Introduction

At present time, the rapid development of metagenomics is associated with the proliferation of next-generation sequencing methods. Metagenomics can provide valuable information on the functional ecology of environmental communities [1]. We previously used metagenomic DNA sequencing to analyze species diversity by marker genes СО1 of animal organisms and rbcL of plants to assess the ecological state of freshwater Nizhniy Kaban Lake by bioindication [2, 3]. In contrast to the marker genes СО1 and rbcL, the gene 18S rRNA is present in all eukaryotes. The ribosomal genes (rRNA) are one of the most conserved genes. Therefore, the systematic position of the organism and the time of discrepancy with similar species can be determined on the basis of the analysis of similarities and differences in rRNA sequences [4]. For eukaryotes, it is most convenient to analyze 18S rRNA of the three types of rRNA. The paper presents the results of a study of the species diversity of the freshwater Nizhniy Kaban Lake (Kazan, Russia) according to the gene 18S rRNA of freshwater organisms based on the next generation sequencing method. Nizhniy Kaban, Verhniy Kaban, and Sredniy Kaban Lakes are included in the system of urban Kaban Lakes, which are polluted lakes according to ecological studies.

Conclusion

Usage of the next-generation sequencing method allows the identification of a large number of hydrobionts. The method can be used for bioindication for assessing the ecological state of water reservoirs. This is great practical interest in the field of monitoring of water reservoirs

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