Search

Dinoflagellates constitute an abundant and diversified component of marine plankton, mostly associated with stratified conditions typical of late spring through autumn in temperate regions. Yet, difficulties with the identification of many species limit the knowledge of their composition and seasonal succession. Here we use a 3‐year V4‐18S rDNA metabarcoding dataset (4,366,007 reads, 4650 Amplicon Sequence Variants, ASVs) collected on 48 dates at the Long‐Term Ecological Research site MareChiara (LTER–MC) to explore the diversity and temporal distribution of dinoflagellates in the Gulf of Naples (Mediterranean Sea). A large fraction of dinoflagellate ASVs (55%, 68% of the reads) were assigned to 187 species in 85 genera, while 33% (23% of the reads) were attributed to undetermined Syndiniales, and the remainder to unidentified groups. A total of 147 ASVs were assigned at 100% similarity to 135 reference sequences, corresponding to 116 species, 46 of which were putative new records for the Gulf of Naples. Cluster analysis conducted on a normalized dataset of 1199 ASVs identified four sample clusters that corresponded largely to the spring, summer, autumn and winter seasons, respectively, each including samples from all 3 years. Syndiniales were particularly abundant (43.1%) in the winter cluster, whereas Gyrodinium reached higher percentages in the summer and autumn ones (38.6% and 57.8%), Gymnodiniales sensu stricto were more abundant in spring (11.5%) and Gonyaulacales in summer (13.5%). Almost half of the ASVs analysed (561) were significantly associated with one of the four seasonal clusters (p <.05). The winter group of ASVs was particularly rich (348 ASVs) and mainly consisted of naked and parasitic taxa, which are impossible to identify in routine phytoplankton observations in light microscopy. Despite biases mainly ascribed to both the incompleteness of the reference dataset and the limited resolution of the marker gene, the metabarcoding approach has provided new insights into the ecology and distribution of this important component of the plankton, highlighting its marked seasonality along with the existence of a diversified and previously overlooked dinoflagellate community in winter. [ABSTRACT FROM AUTHOR]

Several diatom species produce resting stages as part of their life cycle. These resting stages accumulate in the sediments where they can remain for a long time before being re-suspended in the water column and switching to active growth. Until now, the abundance and diversity of viable diatom resting stages have been assessed using the Serial Dilution Culture (SDC) method. In the present study, surface sediment samples from the Gulf of Naples were used to compare results obtained with the SDC method with those provided by HTS metabarcoding based on DNA extracted from the same sediment sample; the marker used was the V4 region of 18S rDNA. HTS metabarcoding showed a marked dominance of polar centric diatoms, among which Chaetoceros species were the most represented, in terms of both sequence and ribotype number. Almost all the most abundant ribotypes identified with metabarcoding matched records of species observed in SDCs. In some cases, however, this marker region could not distinguish between morphologically and phylogenetically distinct species, e.g., Skeletonema pseudocostatum and S. tropicum. As expected, molecular analysis provided a higher number of ribotypes as compared to the number of taxa recorded by SDC. Despite the well-known biases of both methodologies for quantitative assessments, our results show that DNA metabarcoding via HTS sequencing is a promising approach to explore the diversity of diatom resting stages. This study also confirms the importance of curated reference sequences to fully interpret the diversity stored in environmental sediment samples. [ABSTRACT FROM AUTHOR]

In diatoms, as in other organisms, many genetically distinct and reproductively isolated species may show identical or highly similar morphological features. Such groups of species are defined as cryptic and pseudo-cryptic species, respectively. The difficulty of discriminating them with optical means impairs the study of their temporal patterns and geographic ranges. This is also the case for Pseudo-nitzschia , a worldwide distributed planktonic diatom genus which includes several toxigenic species. Using a Pseudo-nitzschia -specific pair of large sub-units ribosomal DNA (LSU rDNA) primers, we generated clone libraries from 19 samples collected at the Long Term Ecological Station MareChiara (LTER-MC) in the Gulf of Naples (GoN) from 2009 to 2010 and compared sequence records with light microscopy (LM) counts from the same samples. Our aim was to elucidate the diversity and the seasonal patterns of taxa within Pseudo-nitzschia . Most of the Pseudo-nitzschia species already known from the GoN were identified within the 1643 obtained sequences. In addition, two species known from elsewhere and three un-described ribotypes were detected. Several cryptic species showed distinct temporal patterns of occurrence, with most species confined to restricted periods and only a few present year-round. Microscopic and molecular results generally concurred for species recognizable using LM, while clone libraries tended to overestimate the relative abundance of some of the species. Due to its high resolution and detection power, the DNA-barcoding approach used in our study is an optimal tool to trace the distribution of cryptic and toxigenic Pseudo-nitzschia species and the diversity of this key diatom genus in the natural environment. [ABSTRACT FROM AUTHOR]

A new photosynthetic planktonic marine dinoflagellate, Azadinium dexteroporum sp. nov., is described from the Gulf of Naples (South Tyrrhenian Sea, Mediterranean Sea). The plate formula of the species, Po, cp, X, 4′, 3a, 6″, 6C, 5?S, 6‴ and 2″″, is typical for this recently described genus. Azadinium dexteroporum is the smallest rep-resentative of the genus (8.5 μm average length, 6.2 μm average width) and shares the presence of a small antapical spine with the type species A. spinosum and with A. polongum. However, it differs from all other Azadinium species for the markedly asymmetrical Po plate and the position of the ventral pore, which is located at the right posterior end of the Po plate. Another peculiarity of A. dexteroporum is the pronounced concavity of the second intercalary plate (2a), which appears collapsed with respect to the other plates. Phylogenetic analyses based on the large subunit 28S rDNA (D1/D2) and the internal transcribed spacer ( ITS rDNA) support the attribution of A. dexteroporum to the genus Azadinium and its separation from the other known species. LC/ MS- TOF analysis shows that Azadinium dex-teroporum produces azaspiracids in low amounts. Some of them have the same molecular weight as known compounds such as azaspiracid-3 and -7 and Compound 3 from Amphidoma languida, as well as similar fragmentation patterns in some cases. This is the first finding of a species producing azapiracids in the Mediterranean Sea. [ABSTRACT FROM AUTHOR]

Centric diatoms of the genus Leptocylindrus are common in the marine plankton worldwide. Only two species, L. danicus Cleve and L. minimus Gran, so far clearly belong to this genus, whose diversity has not been fully investigated. We investigated frustule and spore morphology as well as three nuclear- and three plastid-encoded markers of 85 Leptocylindrus strains from the Gulf of Naples, and one from the Atlantic US. The strains grouped into five molecularly distinct species with different levels of morphological differentiation. Two species matched the description of L. danicus and produced similar spores but differed in morphometric characters and sub-central pore position, supporting the description of L. hargravesii Nanjappa and Zingone as a distinct species. Leptocylindrus danicus var. apora French III and Hargraves, lacking a sub-central pore and not forming spores, was raised to the species level as L. aporus ( French III and Hargraves) Nanjappa and Zingone. A fourth species with convex valves was described as L. convexus Nanjappa and Zingone. The fifth species matched the description of L. belgicus Meunier, considered as synonym of L. minimus. However, ultrastructural differences from all other Leptocylindrus supported the erection of the genus Tenuicylindrus Nanjappa and Zingone with T. belgicus ( Meunier) Nanjappa and Zingone as type species. None of the sequences matched the L. minimus sequence in GenBank. The species analyzed showed different or partially overlapping seasonal distributions. Despite the addition of the new taxa, the ancient diatom lineage of the Leptocylindraceae shows a relative species poorness and considerable morphological stasis. [ABSTRACT FROM AUTHOR]