DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador

Abstract

The use of suitable DNA barcodes and the generation of databases with reference sequences have been considered a promissory approach for the identification of Chlorophyta and Cyanophyta microalgae. In this study, we carried out a molecular characterization and identification of strains isolated from freshwater systems in Ecuador using a dual barcode method. The target sequences for Chlorophyta were 18S rDNA and rbcL genes, and 16S rDNA and 16S-23S rDNA intergenic spacer (ITS) for Cyanophyta. We reported these DNA barcodes for 20 different Molecular Operational Taxonomic Units (MOTUs) for Chlorophyta and 10 for Cyanophyta. Our results show that the 18S V4 hypervariable region (300 bp) is sufficient for differentiating between isolates, but rbcL is a determinant for genus identification in Scenedesmaceae and Chlorellaceae strains. In Cyanophyta, both barcodes enabled the genuslevel assignment of 9 out of 10 MOTUs. These results highlight the necessity of a second barcode additional to small ribosomal subunit sequences to improve molecular identification. Furthermore, the present study significantly contributes to the body of Ecuadorian barcode sequences of microalgae that are currently documented, making them available for future comparative diversity studies.

Screening of cyanotoxin producing genes in Ecuadorian freshwater systems

“…The closest match to the cyrE2 sequence at the GenBank was 98% identity to cyrE related to Aphanizomenon sp., which has been described as a benthic cyanobacterium genus (Gaget et al, 2017). In South America, most isolated strains from R. raciborskii are reported to produce saxitoxins (Hoff-Risseti et al, 2013), although CN producers have also been found in Brazil and Venezuela (Antunes et al, 2015;Mowe et al, 2015), and Ecuador (Ballesteros et al, 2021;Van Colen et al, 2017;Venegas et al, 2018). Even though R. racibosrkii has been reported in Yahuarcocha and San Pablo in association with the presence of CN (Van Colen et al, 2017), cyrJ was not amplified from samples in these water bodies.…”

“…To check the success of the DNA extraction and the absence of inhibition in the PCR reaction, the amplification of the region 16S rDNA gene was carried out as a positive control using the primers CYA106F / CYA781R (Nübel et al, 1997) and PCR conditions, as outlined by Ballesteros et al (2021). eDNA samples with a positive amplification for the 16S were considered suitable for further analysis.…”

Molecular Identification of Brown Algae Sargassum sp. from the Lombok Coastal Waters

“…ITS2 DNA barcoding identifies short region genes with efficient DNA barcodes, 700 base pairs in one partial gene region. (Ballesteros et al, 2021).…”

Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples

“…Microalgae identification can also be made through the molecular level analysis of conserved regions of the DNA, such as Ribulose Bisphosphate Carboxylase Large subunit gene (rbcL), 16S and 18S ribosomal RNA (rRNA) genes used for the profiling of prokaryotic and eukaryotic microalgae [15][16][17]. The reference database to align the sequenced results is equally important to the DNA barcodes sequenced.…”

“…The influence of enrichment media on microalgae population growth and diversity in the literature remains elusive; however, still utilized [17,[22][23][24]. We previously investigated the efficiency of the commonly used BG-11 and BBM in microalgae enrichment for diversity identification and the effect of vitamin enrichment and reduced media nutrient on diversity enrichment.…”