Diatom assemblages of the brackish Bolshaya Samoroda River (Russia) studied via light microscopy and DNA metabarcoding

Abstract

Diatoms are highly diverse and widely spread aquatic photosynthetic protists. Studies of regional patterns of diatom diversity are substantial for understanding taxonomy and biogeography of diatoms, as well as for ecological perspectives and applied purposes. DNA barcoding is a modern approach, which can resolve many problems of diatoms identification and can provide valuable information about their diversity in different ecosystems. However, only few studies focused on diatom assemblages of brackish rivers and none of them applied the genetic tools. Herein, we analyzed taxonomic composition and abundance of diatom assemblages in the brackish mixohaline Bolshaya Samoroda River flowing into the Elton Lake (Volgograd region, Russia) using light microscopy and high-throughput sequencing of the V4 region of the 18S rDNA gene amplicons. In total, light microscopy of the samples taken in 2011-2014 and 2018 allowed to distinguish 39 diatom genera, represented by 76 species and infraspecies taxa. Twenty three species of diatoms were recorded in the river for the first time. Next-generation sequencing revealed a larger number of diatom taxa (26 genera and 47 OTUs in two samples vs. 20 genera and 37 species estimated by light microscopy). As a result, sequences of Haslea, Fistulifera, Gedaniella were recorded in the river for the first time. Significant differences in the data obtained with molecular and light microscopy approaches are discussed. Some V4 18S rDNA sequences were characterized by a low similarity with homologues from the reference database. We revealed high spatial-temporal heterogeneity of the diatom assemblages, occurrence of freshwater species together with brackish and marine ones, and predominance of benthic and plankto-benthic species. Thus, investigations of diatoms in brackish rivers based on both morphological and molecular approaches provide a good chance of improving an understanding of diversity, ecology and biogeography of Bacillariophyta.

Algal and cyanobacterial diversity in saline rivers of the Elton Lake Basin (Russia) studied via light microscopy and next-generation sequencing

“…Compared to the previously reported data (Burkova, 2012(Burkova, , 2015Gorokhova & Zinchenko, 2014;Yatsenko-Stepanova et al, 2015;Selivanova et al, 2019) our study revealed new taxa for the algae flora of the saline Elton rivers. Thus, 18 taxa belonging to the phyla Chlorophyta (5), Ochrophyta (4), Euglenozoa (4), Cryptophyta (3), Haptophyta (1), Cyanobacteria (1) have been recorded in the Bolshaya Samoroda River for the first time.…”

“…On the other hand, the LM method is also not devoid of error. The diatomic analysis could take into account the forms represented by frustules of dead diatoms, which, due to their siliceous composition, can be retained for a long time in the reservoir (Rivera et al, 2018b;Selivanova et al, 2019). This can be confirmed by the fact that, for example, Navicula sp.…”

“…At the same time, it should be noted that the Euglenozoa registered in the assemblage of microalgae of the middle course of the Bolshaya Samoroda River by morphological analysis were not detected by high-throughput sequencing. This discrepancy may be due to the use of universal primers, which (compared to selective primer pairs) due to insufficient coverage reveal only half of the OTUs (Lentendu et al, 2014;Selivanova et al, 2019). In addition, the use of universal primers does not allow for a clear differentiation of species within the genus (Arora et al, 2013).…”

“…However, all the studies carried-out were based solely on the morphological approach using the methods of light microscopy. At the same time, the application of the molecular methods that use the techniques of next-generation sequencing in the study of diatom assemblages of the brackish Bolshaya Samoroda River demonstrated the need to use an integrated approach, including both morphological and molecular methods (Selivanova et al, 2019).…”

Novel Approach to Freshwater Diatom Profiling and Identification Using Raman Spectroscopy and Chemometric Analysis

“…For this reason, a great effort has recently been directed to developing faster and less cumbersome identification methods and metrics. These are mainly based either on DNA metabarcoding or a combination of diatom imaging acquisition and deep learning methods [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27]. While these alternatives show promising results and take advantage of state-of-the-art sequencing and imaging methods, they are still laborious and quite expensive, which limits their application to routine monitoring of water quality.…”