A comparison of morphological and molecular-based surveys to estimate the species richness of Chaetoceros and Thalassiosira (bacillariophyta), in the Bay of Fundy.

Sarah E Hamsher,Murielle M Legresley,Gary W Saunders,Jennifer L Martin,Keith A Crandall

doi:10.1371/journal.pone.0073521

Sarah E Hamsher, Murielle M Legresley + Show 3 more

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https://doi.org/10.1371/journal.pone.0073521

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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.

Highlights

Planktonic marine diatoms are a key component to oceanic primary productivity, contributing,40% of the organic carbon generated in the sea each year [1], but their diversity is not well known [2,3,4]
For the molecular-based survey, each tow subsample was settled in a 50 mL FalconTM tube for 2–4 hours, the supernatant was removed by reverse osmosis filtration, and 95% ethanol was added for cell preservation
Of the 20 Chaetoceros spp., 20% were unique to a single tow subsample

Summary

Introduction

Planktonic marine diatoms are a key component to oceanic primary productivity, contributing ,40% of the organic carbon generated in the sea each year [1], but their diversity is not well known [2,3,4]. Perag.), establish a baseline of diversity, and determine seasonal trends and distribution of species [6,7,8,9,10,11,12]. These extensive monitoring efforts have allowed the DFO to track the introduction of new species into the flora and density changes in harmful algal bloom-forming species [10]. These genera are widespread, difficult to identify due to the morphological similarity of their constituent species, and each genus is known to contain .100 species [13,14,15] Their identification in the BoF has been based solely on morphology

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