Studying Bacterial Diversity of Verhniy Kaban Lake by 16S rRNA Analysis

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

Abstract

The article presents the results of a study of the bacterial diversity of Verhniy Kaban Lake (Kazan, Russia) for 2016-2017 using the marker gene 16S rRNA of hydrobionts based on the next-generation sequencing method. Verhniy Kaban Lake with Sredniy Kaban Lake and Nizhniy Kaban Lake are included in the system of Kaban Lakes. The lakes are located in the center of a big industrial city and experience anthropogenic load. According to ecological studies, Kaban Lakes are polluted lakes. The sequences of 16S rRNA Bacteria of freshwater Verhniy Kaban Lake in 2016-2017 were submitted to the international SRA database on the NCBI website in the fastq format with numbers SRR7510928, SRR7465228, SRR7516245. A comparative analysis of metagenomic data showed a significant change in bacterial diversity over the years. A total of 110467 (2016) and 87093 (2017) high-quality reads were obtained; 30% (2016) and 32% (2017) of the bacterial population was classified to the genus level, while 0.4% (2017) was classified to the species level. A total of 19 species of Bacteria were identified, among which the bacteria most commonly found in the gastrointestinal tract of humans and/or animals are most common. These types of bacteria can pose a threat to human health. Therefore, the species composition of the bacterial community must be taken into account when assessing the ecological state of water bodies.

Introduction

The objective of microbiomes research is to characterize the diversity of microorganisms found in the environment. It is known that biological communities respond to numerous factors of anthropogenic and natural environmental changes. Identification of the nonspecific response of living organisms to changing environmental conditions, for example, pollution or purification is used to assess the ecological state of ecosystems [1]. Free-floating freshwater bacteria are at the center of biogeochemical cycles and affect water quality. Currently, there is insufficient information on the composition of the community and the ecology of lake bacteria [2, 3]. Recently, the cost reducing of next-generation sequencing technology has allowed identifying large numbers of organisms. We used this technology to identify zooplankton by the СО1 gene and phytoplankton by the rbcL gene to assess the ecological state of freshwater Verhniy Kaban Lake [4, 5]. The dominant tool for studying microbial ecology is sequencing of the 16S rRNA gene [6]. The advantages of the 16S rRNA gene sequencing are its presence in all prokaryotes, the gene rarely undergoes horizontal transfer, and also has a higher degree of conservation than genes encoding enzymes [7]. Unfortunately, when a 16S rRNA gene is selected as a marker for sequencing, a large number of organisms are not determined to the exact species. The article presents the results of a study of the bacterial diversity of Verhniy Kaban Lake (Kazan, Russia) for 2016-2017 using the marker gene 16S rRNA of hydrobionts based on the next-generation sequencing method. Verhniy Kaban Lake with Sredniy Kaban Lake and Nizhniy Kaban Lake are included in the system of Kaban Lakes. The lakes are located in the center of a big industrial city and experience anthropogenic load. According to ecological studies, Kaban Lakes are polluted.

Conclusion

The obtained results are of great practical interest in monitoring of water reservoirs. The next-generation sequencing method can be successfully used to monitor water reservoirs in particular and to assess the ecological state of water reservoirs in general.

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