A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing.

Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most studies have utilized short read sequences to assess protist diversity. One limitation of using short read sequences is the low resolution of the markers.

De novo transcriptome assembly and gene annotation for the toxic dinoflagellate Dinophysis.

Species within the dinoflagellate genus Dinophysis can produce okadiac acid and dinophysistoxins leading to diarrhetic shellfish poisoning. Since the first report of D. ovum from the Gulf of Mexico in 2008, reports of other Dinophysis species across US have increased.

Horizontal and vertical distribution of Gambierdiscus spp. (Dinophyceae) including novel phylotypes in Japan identified by 18S rDNA metabarcoding.

The genus Gambierdiscus is a marine benthic/epiphytic dinoflagellate considered the causative agent of ciguatera poisoning (CP). Clarifying the geographical distribution of this genus to understand the potential risk of CP is important. Many studies have focused only on the species/phylotype composition of Gambierdiscus in shallow waters, but no study has investigated the species/phylotype composition of the genus in deep waters.

Application of a convolutional neural network to improve automated early warning of harmful algal blooms.

Continuous monitoring and early warning together represent an important mitigation strategy for harmful algal blooms (HAB). The coast of Texas experiences periodic blooms of three HAB dinoflagellates: Karenia brevis, Dinophysis ovum, and Prorocentrum texanum. A plankton image data set acquired by an Imaging FlowCytobot over a decade of operation was used to train and evaluate two new automated image classifiers.

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity.

High-throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4-metabarcode haplotypes gathered from 48 time-series samples using the marine planktonic diatoms Chaetoceros and Bacteriastrum as test case.

Global distribution and diversity of (Bacillariophyta, Mediophyceae): integration of classical and novel strategies.

Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data.

Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae.

The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes.

Two new species in the Chaetoceros socialis complex (Bacillariophyta): C. sporotruncatus and C. dichatoensis, and characterization of its relatives, C. radicans and C. cinctus.

The diatom genus Chaetoceros is one of the most abundant and diverse phytoplankton in marine and brackish waters worldwide. Within this genus, Chaetoceros socialis has been cited as one of the most common species. However, recent studies from different geographic areas have shown the presence of pseudo-cryptic diversity within the C.

Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters.

Chaetoceros is one of the most species rich, widespread and abundant diatom genera in marine and brackish habitats worldwide. It therefore forms an excellent model for in-depth biodiversity studies, assessing morphological and genetic differentiation among groups of strains. The global Chaetoceros lorenzianus complex presently comprises three species known to science.

Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment.

Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven by the intensity of rainfall. Vibrio spp.