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Introduction
Publications
Publications (258)
The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory among designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water co...
iatom resting stages can remain viable in sediments for decades and germinate when exposed to suitable environmental
conditions, inoculating the water column and the surface sediments with new populations of cells. Classical methods, based on
acid-cleaning of diatom frustules in sediment samples, do not discriminate between living and dead cells an...
The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecologi...
Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species’ adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediter...
To expand knowledge of Pseudo-nitzschia species in the Southeast Pacific, we isolated specimens from coastal waters of central Chile (36 • S-30 • S), the Gulf of Corcovado, and the oceanic Robinson Crusoe Island (700 km offshore) and grew them into monoclonal strains. A total of 123 Pseudo-nitzschia strains were identified to 11 species based on se...
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 met...
Phytoplankton dynamics are regulated by external cues, such as light and nutrients, as well as by biotic interactions and endogenous controls linked to life cycle characteristics. The planktonic pennate diatom Pseudo-nitzschia multistriata, with a heterothallic mating system with two opposite mating types (MTs), represents a model for the study of...
Background
Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cells) that can withstand long periods of adverse environmental conditions.
Results
We present the first gene expression study during...
Diatoms are photosynthetic microorganisms playing a key role in the functioning of aquatic ecosystems; they are at the base of the food web and are the main drivers of biogeochemical processes. These microalgae have a unique diplontic life cycle in which the vegetative phase entails a cell size reduction that would lead to the extinction of the cel...
The presence of phytoplankton parasites along the water column was explored at the Long‐Term Ecological Station MareChiara (LTER‐MC) in the Gulf of Naples (Mediterranean Sea) in October 2019. Microscopy analyses showed diatoms dominating the phytoplankton community in the upper layers (0–20 m). Metabarcoding data from the water column showed the pr...
Background
Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cells) that can withstand long periods of adverse environmental conditions.
Results
We present the first gene expression study during...
Plankton is the basis of pelagic food webs and is essential in supporting marine biodiversity and thus socio-economic activities, such as fisheries and aquaculture. It is therefore important to investigate the structure and functionality of plankton communities to understand ecosystem processes. In the frame of the FEAMP-IISPA program, we conducted...
Pseudo-nitzschia is a widespread genus of marine pennate diatoms comprising 58 species of which 28 can produce the neurotoxin domoic acid, causative of Amnesic Shellfish Poisoning (ASP). Species of the genus are found in both oceanic and coastal waters where they can form large blooms. The timing and magnitude of blooms is generally described based...
Chaetoceros is one of the most abundant and diverse diatom genera in the phytoplankton of the world’s oceans. The genus was erected by Ehrenberg in 1844 for two species from the Southern Ocean: C. dichaeta and C. tetrachaeta. According to his description, the former possesses two setae per valve and the latter possesses four. Chaetoceros tetrachaet...
Abstract Diatoms’ bloom dynamics, with seasonal cycling of waxes and wanes of cell abundance, imply frequent bottleneck and expansion events that can leave signatures in the genetic structure and diversity of populations. We explored changes in genetic diversity and structure within multiple species of the planktonic marine diatom genus Pseudo‐nitz...
Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We foun...
Diatom life cycles are unusual among microalgae by being diplontic with a long diploid vegetative phase and a short-lived haploid phase (gametes). Life cycle progression in diatoms is controlled by the cell size reduction-restitution cycle and is intimately linked to their peculiar mode of cell division and siliceous cell wall. Sexual reproduction...
Diatom life cycles are unusual among microalgae by being diplontic with a long diploid vegetative phase and a short-lived haploid phase (gametes). Life cycle progression in diatoms is controlled by the cell size reduction-restitution cycle and is intimately linked to their peculiar mode of cell division and siliceous cell wall. Sexual reproduction...
In the present study we describe and illustrate a new species in the genus Chaetoceros, C. turingii sp. nov., from the Gulf of Naples, Italy. Colonies have a brush-like appearance due to the apparent randomness in seta orientation. The defining feature of this species is the regular pattern of narrow ridges on the exterior of the terminal valve fac...
The former-industrial site of Bagnoli (Naples, Southern Italy), the second Italian largest steelwork, has been negatively affected by the discharges of heavy metals and hydrocarbons that have markedly altered the water and sediment quality as well as the biota living therein. On the basis of benthic foraminiferal traditional morphology-based approa...
The cosmopolitan, species-rich diatom genus Pseudo-nitzschia represents a good system for the study of speciation, evolution and diversity. Understanding elements linked to population dynamics and life cycle regulation for these species is of particular importance in view of their ability to produce the toxin domoic acid and cause harmful blooms. P...
Algal viruses are important contributors to carbon cycling, recycling nutrients and organic material through host lysis. Although viral infection has been described as a primary mechanism of phytoplankton mortality, little is known about host defense responses.
We show that viral infection of the bloom‐forming, planktonic diatom Chaetoceros sociali...
We review the spatial distribution of toxic marine microalgal species and the impacts of all types of harmful algal events (Harmful Algal Blooms, HABs) in the Mediterranean Sea (MS), including the Black Sea, the Sea of Marmara, coastal lagoons and transitional waters, based on two databases compiled in the Ocean Biogeographic Information System (OB...
Resting stages are reported for several unicellular eukaryotes including diatoms that can produce spores or resting cells. These stages represent a repository of diversity in sediments but the factors that induce their formation are elusive. We investigated spore formation in the marine diatom Chaetoceros socialis. Our results confirm that nitrogen...
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‐m...
A recently published study analyzed the phylogenetic relationship between the genera Centrodinium and Alexandrium, confirming an earlier publication showing the genus Alexandrium as paraphyletic. This most recent manuscript retained the genus Alexandrium, introduced a new genus Episemicolon, resurrected two genera, Gessnerium and Protogonyaulax, an...
Dinoflagellate species of Dinophysis, in particular D. acuminata and D. acuta, produce lipophilic toxins that pose a threat to human health when concentrated in shellfish and jeopardize shellfish exploitations in western Europe. In northwestern Iberia, D. acuminata has a long growing season, from spring to early autumn, and populations develop as s...
Planktonic diatoms thrive in the water column, and several species can transform into resting stages – spores or resting cells – that sink to the bottom of the sea. Resting stages are generally produced when environmental conditions are not optimal for growth and can remain viable in sediments for a long time. We tested different aspects related to...
Diatoms form an essential part of marine food webs, but may also cause harm by producing secondary metabolites like oxylipins, the neurotoxins β-N-methylamino-L-alanine (BMAA) and domoic acid (DA). Oxylipins comprise polyunsaturated aldehydes (PUAs), which may act as allelochemicals and alter the reproductive abilities of grazers, thereby affecting...
Following the publication of this article [1], the authors reported that the link to Additional file 11 linked to the wrong set of data. The correct supplementary data is provided in this Correction article (Additional file 11).
Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual pha...
Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental chang...
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 ta...
Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from...
A broad diversity of sex-determining systems has evolved in eukaryotes. However, information on the mechanisms of sex determination for unicellular microalgae is limited, including for diatoms, key-players of ocean food webs. Here we report the identification of a mating type (MT) determining gene for the diatom Pseudo-nitzschia multistriata. By co...
The Mediterranean Sea (MS) is a temperate-subtropical basin characterized by oligotrophic offshore waters and coastal waters ranging from almost pristine to heavily impacted. Main resources are tourism and fisheries, whereas aquaculture is more developed in the western MS and continental Greek coasts, which are also the most intensively monitored....
Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be...
This article addresses the recent nomenclature changes in the “Alexandrium tamarense (Dinophyceae) species complex” with the goal of helping researchers and resource managers understand how those changes may affect species designations in their regions. These nomenclatural changes are particularly important because they apply to several of the wide...
Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Sinc...
The genesis of phytoplankton blooms and the fate of their biomass in iron-limited, high-nutrient−low-chlorophyll regions can be studied under natural conditions with ocean iron fertilization (OIF) experiments. The Indo-German OIF experiment LOHAFEX was carried out over 40 d in late summer 2009 within the cold core of a mesoscale eddy in the product...
Aggregates of mucilaginous material have been at times observed in coastal and oceanic sea waters. In the Adriatic Sea (Mediterranean Sea), these events have been known since the 18th century as ‘mare sporco' (= dirty sea), and in recent years, they have been associated with the dinoflagellate Gonyaulax fragilis; whereas, in New Zealand mucilage ev...
Life cycle-based adaptations are integral to the ecology of most organisms. For the toxic microalgal species Pyrodinium bahamense, Alexandrium fundyense, Pseudo-nitzschia spp., and Nodularia spumigena, the properties and behaviours of their life cycle stages enable them to thrive in diverse marine environments. Planktonic blooms of these species ar...
Coastal systems partially surrounded by land such as coastal embayments, estuaries and fjords have characteristics that affect the development of harmful algal blooms. These include stronger links between the water column and bottom sediments, a limited exchange with offshore waters and greater cell retention. Sub-mesoscale and high-frequency proce...
GlobalHAB, “Global Harmful Algal Blooms,” is a new scientific programme on harmful algal blooms (HABs) cosponsored by the Intergovernmental Oceanographic Commission (IOC) of UNESCO and the Scientific Committee on Oceanic Research (SCOR) that will operate for 10 years from 2016 to 2025. GlobalHAB builds on the solid foundation established by the for...
Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high throughput sequencing (HTS) is increasingly applied to assess diversity and abu...
Genetic diversity is what selection acts on, thus shaping the adaptive potential of populations. We studied micro-evolutionary patterns of the key planktonic diatom Pseudo-nitzschia multistriata at a long-term sampling site over 2 consecutive years by genotyping isolates with 22 microsatellite markers. We show that both sex and vegetative growth in...
The LOHAFEX iron fertilization experiment was conducted for 39. days in the closed core of a cyclonic mesoscale eddy located along the Antarctic Polar Front in the Atlantic sector of the Southern Ocean. Mixed layer (ML) waters were characterized by high nitrate (~. 20. μM), low dissolved iron (DFe ~. 0.2. nM) and low silicate concentrations (below...
Table S15 Rate of evolution of homologous pairs of Pseudo‐nitzschia multistriata and Pseudo‐nitzschia multiseries
Fig. S1 General statistics of the Pseudo‐nitzschia multistriata genome assembly.
Fig. S2 Putative association of conserved noncoding elements in Pseudo‐nitzschia multistriata with regulation of transcription.
Fig. S3 Coverage of repeat elements and estimation of long terminal repeat (LTR) insertion period in the Pseudo‐nitzschia multistriata geno...
Table S2 Genomic coordinates of the Pseudo‐nitzschia multistriata conserved noncoding elements, together with coordinates in other diatom species, where each element remains conserved
Table S6 Details of eukaryotic and prokaryotic organisms considered for the generation of the protein clusters for the Pseudo‐nitzschia multistriata proteome
Table S7 Annotation for the Pseudo‐nitzschia/diatom/stramenopile/SAR (Stramenopile, Alveolates and Rhizaria)‐specific genes of bacterial origin
Table S11 LogFC (fold change) and false discovery rate (FDR) values for all Pseudo‐nitzschia multistriata transcripts for the same conditions as in Table S10
Table S14 Differentially expressed genes predicted to be orphan genes in Pseudo‐nitzschia multistriata
Table S1 Validation of a selected subset of genes differentially expressed during sexual reproduction in Pseudo‐nitzschia multistriata by quantitative PCR
Table S4 Insertion period estimation of complete long terminal repeats (LTRs) identified in diatom genomes
Table S8 Annotation for diatom genes of red algal origin
Table S9 Summary statistics...
Table S3 The core, plant and fungal transcription factor families which show enrichment of binding sites on the Pseudo‐nitzschia multistriata conserved noncoding elements
Table S5 Number of proteins from stramenopile genomes represented by different superfamilies from the SUPERFAMILY database
Table S10 Differential expression analyses of all sexualized samples vs all control samples, MT+ sexualized samples against MT+ controls, and MT− sexualized samples against MT− controls, at two different time points
Table S13 Differentially expressed genes predicted to be gene gain events in diatoms post‐divergence from Phaeodactylum tricornutum
Table S16 Genes predicted to be introduced via horizontal gene transfer (HGT) in diatoms, showing differential expression during sexual reproduction in Pseudo‐nitzschia multistriata
The diatom genus Chaetoceros is one of the most abundant and diverse phytoplankton in marine and brackish waters worldwide. Within this genus, Chaetoceros socialis Lauder 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. sociali...
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo‐nitzschia multistriata, we investigated the cell response to cues released during sexual reprod...
Harmful algal blooms (HABs) are natural phenomena that result from the interplay of biological, chemical, physical, and sedimentary processes occurring at different temporal and spatial scales. This paper provides an integrated description of HAB dynamics occurring at the mesoscale (10–100 km, sensu Haury et al., 1978) in confined and semi-confined...