Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

Abstract

Photosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.

Freshwater protists: unveiling the unexplored in a large floodplain system

“…The PCR conditions and the MiSeq Illumina sequencing were carried out following the protocol previously applied in the study by Metz et al . (2019a). Sequences have been deposited at the European Nucleotide Archive (ENA) under the BioProject number (PRJEB24677).…”

“…Followed by a PCR amplification using the TAReuk454FWD1 (Stoeck et al, 2010) and V4 18S Next.Rev primers (Piredda et al, 2017) for the second round. The PCR conditions and the MiSeq Illumina sequencing were carried out following the protocol previously applied in the study by Metz et al (2019a). Sequences have been deposited at the European Nucleotide Archive (ENA) under the BioProject number (PRJEB24677).…”

Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches

“…Indeed, most (40.5%) sequences from MA and (98.7%) from FW, data sets have been retrieved from ‘pico’ fraction (0.8–5 μm) suggesting that a large part of the Trebouxiophyceae diversity is composed of tiny‐sized organisms. This assumption is confirmed by several works based on flow cytometry that found Trebouxiophyceae to dominate picoeukaryotic diversity in certain freshwater assemblages (Pálffy et al ., ; Metz et al ., ).…”

Mapping of ecosystems of Mala planina Mt, Bulgaria

“…The factors influencing the phytoplankton development and diversity in different environments, as a background for phytoplankton interactions and drivers of phytoplankton diversity, were also discussed Becker et al 2017;Colina et al 2017;Descy et al 2017;Di Pasquale et al 2017). Different aspects of the phytoplankton diversity were also presented Metz et al 2017) with special emphasis on biodiversity conservation . Traditionally, methodological support for microscopic plankton counts and size measurements (Zohary 2017) and trait-based approaches (Borics et al 2017) were among the side-topics of the workshop.…”