A Comparison of Morphological and Molecular-Based Surveys to Estimate the Species Richness of Chaetoceros and Thalassiosira (Bacillariophyta), in the Bay of Fundy

Abstract

The goal of this study was to compare the ability of morphology and molecular-based surveys to estimate species richness for two species-rich diatom genera, Chaetoceros Ehrenb. and Thalassiosira Cleve, in the Bay of Fundy. Phytoplankton tows were collected from two sites at intervals over two years and subsampled for morphology-based surveys (2010, 2011), a culture-based DNA reference library (DRL; 2010), and a molecular-based survey (2011). The DRL and molecular-based survey utilized the 3′ end of the RUBISCO large subunit (rbcL-3P) to identify genetic species groups (based on 0.1% divergence in rbcL-3P), which were subsequently identified morphologically to allow comparisons to the morphology-based survey. Comparisons were compiled for the year (2011) by site (n = 2) and by season (n = 3). Of the 34 taxa included in the comparisons, 50% of taxa were common to both methods, 35% were unique to the molecular-based survey, and 12% were unique to the morphology-based survey, while the remaining 3% of taxa were unidentified genetic species groups. The morphology-based survey excelled at identifying rare taxa in individual tow subsamples, which were occasionally missed with the molecular approach used here, while the molecular methods (the DRL and molecular-based survey), uncovered nine cryptic species pairs and four previously overlooked species. The last mentioned were typically difficult to identify and were generically assigned to Thalassiosira spp. during the morphology-based survey. Therefore, for now we suggest a combined approach encompassing routine morphology-based surveys accompanied by periodic molecular-based surveys to monitor for cryptic and difficult to identify taxa. As sequencing technologies improve, molecular-based surveys should become routine, leading to a more accurate representation of species composition and richness in monitoring programs.

Definition of a High-Resolution Molecular Marker for Tracking the Genetic Diversity of the Harmful Algal Species Eucampia zodiacus Through Comparative Analysis of Mitochondrial Genomes

“…All eight strains shared the same percent identity (PID, which was used to quantify the similarity between the biomolecular sequence) (99.94%) when compared to the reference sequence of E. zodiacus on full-length 18S rDNA ( Sorhannus, 2007 ). Similar high PIDs were found for other molecular markers including 28S rDNA D1-D2 (100%) ( Hamsher et al, 2013 ), ITS (99.28%) ( Guo et al, 2015 ), CO1 (99.25%) ( Guo et al, 2015 ), and rbcL (100%) ( Guo et al, 2015 ), respectively. Phylogenetic analysis of molecular marker sequences obtained for all eight strains indicated that they all clustered well with corresponding E. zodiacus sequence records at GenBank ( Supplementary Figure S1 ), further confirming that these strains were all indeed E. zodiacus .…”

“…Many common molecular markers of E. zodiacus including 18S rDNA, 28S rDNA, ITS, rbcL , and CO1 have been sequenced and applied to characterize E. zodiacus ( Sorhannus, 2007 ; Rampen et al, 2009 ; Sorhannus and Fox, 2011 ; Ashworth et al, 2013 ; Hamsher et al, 2013 ; Guo et al, 2015 ). However, these molecular markers have not been evaluated for their ability to study intra-species genetic diversity of E. zodiacus .…”

Shionodiscus gaarderaesp. nov. (Thalassiosirales, Thalassiosiraceae), a bloom-producing diatom from the southwestern Atlantic Ocean, and emendation ofShionodiscus bioculatusvar.bioculatus

“…exiguus was reported in samples from Cape Wankarema and the Kara Sea (Grunow 1884). It was also registered in the Saint Laurent Gulf (northern Canada) and Arctic regions by Bérard-Therriault et al (1999), as well as in the Bay of Fundy by Hamsher et al (2013).…”

Metabarcoding Reveals Temporal Patterns of Community Composition and Realized Thermal Niches of Thalassiosira Spp. (Bacillariophyceae) from the Narragansett Bay Long-Term Plankton Time Series

“…Morphologically identical or "cryptic" species have been identified in the ecologically important diatom genus Thalassiosira [9,10]. Globally, Thalassiosira is one of the most abundant and diverse diatom genera [11] and includes species that are ecologically important components of phytoplankton communities in estuarine, coastal, and open ocean regions [12][13][14][15][16][17].…”

“…In many cases, community composition may be more accurately obtained through the use of molecular methods. For example, Hamsher et al [10] were able to classify more Thalassiosira species from individual cells and colonies using molecular methods than LM, including rarely occurring species. Metabarcoding, or the high-throughput sequencing of PCR amplicons from an entire community, has been used to identify diatoms, including Thalassiosira, from complex communities [21][22][23].…”