Wiebe Hendrik Cornelis Frederik Kooistra

Stazione Zoologica Anton Dohrn | Stazione Zoologica · Laboratory of Ecology and Evolution of Plankton

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...

Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing an...

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...

Marine planktonic diatom species can exhibit contrasting distribution patterns, from endemic to cosmopolitan. Endemicity is counter-intuitive for planktonic species given their potentially large population sizes and ample migration opportunities by means of ocean currents. Here, we analyse the biogeography of six species of the diatom genus Bacteri...

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...

Hyalosira gene sequences are divided into two clades within different families. We examined authentic material of Hyalosira (isotype material of H. obtusangula, synonymous with H. delicatula) and voucher specimens of published sequences, and pooled our observations of Hyalosira-like taxa from benthic and epizoic habitats in several parts of the glo...

Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling cove...

Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “noise” in electropherograms and these variants have been charac...

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...

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 b...

The diatom family Chaetocerotaceae (Bacillariophyta) is common in the marine plankton worldwide, especially in coastal areas and upwelling zones. Its defining character constitutes hollow processes, called setae, which emerge from the valves of the vegetative cells. The family comprises two extant genera: Bacteriastrum and Chaetoceros. Current syst...

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...

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...

Marine biotechnology is the key to harness the huge economic potential of the unique biodiversity of marine organisms. This potential remains largely underexploited due to three major issues: (1) lack of connectivity between research services, (2) practical and cultural difficulties in connecting science with industry and (3) uneven regional develo...

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...

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...

This document is intended for Stakeholders concerned with the management of Research Infrastructures, and in particular for their role in the use of marine biological resources for fundamental and applied research. It describes the organisation of the European Marine Biological Resource Centre (EMBRC-ERIC), its scope, user strategy, governance and...

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 speci...

Previous records of species in the C. lorenzianus complex. Evaluation of previously published records of species in the C. lorenzianus complex using EM. (DOCX)

Molecular phylogenetic tree based on analyses of the SSU rDNA sequences. Numbers indicated on the branches are posterior probability of Bayesian analyses (MrB) and bootstrap support of neighbor joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. (TIF)

List of cultures of the C. lorenzianus complex used in molecular analysis inferred from SSU, showing strain designation, sampling location and date, as well as SSU accession number. (DOCX)

Auxospores of Chaetoceros decipiens under LM; strain Ro2A4. Fig 1: Three auxospores (arrows) forming on the girdle of the mother cells. Scale bar 20 μm. (TIF)

Auxospore of Chaetoceros decipiens under LM; strain Ro2A4. Fig 2: A nearly developed daughter colony and an auxospore (arrow). Scale bar 20 μm. (TIF)

List of cultures of the C. lorenzianus complex used in molecular analysis inferred from LSU, showing strain designation, sampling location and date, as well as LSU accession number. NA means no molecular data. (DOCX)

We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER)-MC site in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using a metabarcoding approach. The ILLUMINA analysis of the V4 and V9 fragments of the 18S rDNA produced 869,522 and 1,410,071 sequences resulting in 6,517 and 6,519 OTUs, respectivel...

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbour greater diversity than planktonic environments. We t...

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We te...

Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the...

Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies of the Plagiogrammaceae were inferred but included only up to six genera: Plagiogramma, Dimeregramma, Neofragilaria, Talaroneis, Psammogramma and Psammo...

Diatoms are a highly diverse group of unicellular microalgae. Their multipart silica cell wall, called a frustule, is morphologically highly elaborate and shows many fine-details reminiscent of what designers and civil engineers would readily recognize as solutions to challenges in construction. This makes diatom frustules ideal objects for biomime...

Although protists are critical components of marine ecosystems they are still poorly characterized. Here we analyzed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental DNA and RNA from three size-fractions (pico-, nano-, and micro/meso-plankton) as well as from dissol...

Four colonial species of the multipolar centric diatom genus Bacteriastrum – B. furcatum, B. hyalinum, B. jadranum and B. mediterraneum – were investigated using field samples from the Adriatic Sea and cultured strains obtained from these samples. Morphology and frustule ultrastructure were examined using light and electron microscopy, and nuclear-...

A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) o...

Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencin...

Background: Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, where most constituent taxa are usually extremely rare. Yet, microbiologists normally do not differentiate between abundant and rare sub-communities, although they may present intrinsic c...

A new toxin-producing marine diatom, Nitzschia bizertensis sp. nov., isolated from the Bizerte Lagoon (Tunisia, Southwest Mediterranean Sea) is, based on studies on eight different strains, characterized morphologically by light microscopy, transmission and scanning electron microscopy, and phylogeneti- cally using the nuclear rDNA regions: SSU, IT...

The planktonic diatom Fragilariopsis kerguelensis plays an important role in the biogeochemical cycles of the Southern Ocean, where remains of its frustules form the largest deposit of biogenic silica anywhere in the world.We assessed the genetic identity of 26 strains, from cells collected at various sites in the Southern Ocean, using three molecu...

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequenc...

The planktonic diatom genus Pseudo-nitzschia contains several genetically closely related species. Some of these can produce domoic acid, a potent neurotoxin. Thus, monitoring programs are needed to screen for the presence of these toxic species. Unfortunately, many are impossible to distinguish using light microscopy. Therefore, we assessed the ap...

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 Leptocy...

Oxylipins are low-molecular weight secondary metabolites derived from the incorporation of oxygen into the carbon chains of polyunsaturated fatty acids (PUFAs). Oxylipins are produced in many prokaryotic and eukaryotic lineages where they are involved in a broad spectrum of actions spanning from stress and defense responses, regulation of growth an...

Pseudo-nitzschia strains analysed for oxylipin production. Species name and strain code, date in which the chemical characterization was carried out, LSU rDNA GenBank accession number, rbcL GenBank accession number. When LSU and rbcL sequences were identical to sequences already deposited in GenBank, the reference number of the deposited sequences...

In the scope of the development of a microarray PhyloChip for the detection of toxic phytoplankton species, we designed a large series of probes specific against targets in the nuclear large subunit (LSU) rRNA of a range of Pseudo-nitzschia species and spotted these onto the microarray. Hybridisation with rRNA extracted from monoclonal cultures and...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

We analysed the molecular and morphological features of strains of Chattonella subsalsa isolated from the western Adriatic coast (Mediterranean Sea), with the aim of confirming their classification and elucidating their phylogenetic positions within the Raphidophyceae. We sequenced parts of the ribosomal operon, including the small subunit (SSU), t...

The planktonic diatom Fragilariopsis kerguelensis plays an important role in the biogeochemical cycles of the Southern Ocean, where remains of its frustules form the largest deposit of biogenic silica anywhere in the world. We assessed the genetic identity of 26 strains, from cells collected at various sites in the Southern Ocean, using three molec...

Marine phytoplankton, the photosynthetic microorganisms drifting in the illuminated waters of our planet, are extremely diverse, being distributed across major eukaryotic lineages. About 5000 eukaryotic species have been described with traditional morphological methods, but recent environmental molecular surveys are unveiling an ever-increasing div...

The diatom Pseudo-nitzschia multistriata exhibits a diplontic life cycle composed of an extensive phase of vegetative cell division and a brief phase of sexual reproduction. To explore genotypic stability, we genotyped seven polymorphic microsatellite loci in 26 monoclonal strains over 3-16 months in a culture maintenance regime. Moreover, to asses...

Skeletonema comprises a planktonic genus of centric diatoms occurring in coastal and brackish waters worldwide. The most commonly reported species, Skeletonema costatum, was believed to be ubiquitous, morphologically plastic and euryhaline. Yet, recent studies showed that this perceived taxon consists of a series of species, including a more narrow...

Seven microsatellite loci were characterized for the toxic diatom Pseudo-nitzschia multistriata Takano (Takano) to investigate intraspecific variability and estimate population genetic structure over blooms, seasons, and sexual and vegetative reproduction. Selected microsatellites consisted of di- and trinucleotide repeats in the core region, and s...

The diatom family Chaetocerotaceae (Mediophyceae) includes two exclusively phytoplanktonic genera: Chaetoceros and Bacteriastrum. Its hallmark feature constitutes setae: hollow, spine-like appendages protruding from the valves. Chaetoceros is morphologically diverse, includes c. 400 described species and is common worldwide; whereas, Bacteriastrum...

We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has...

The planktonic diatom genus Skeletonema is common in Indian coastal waters. Recent taxonomic studies have uncovered high diversity in this genus, and it is expected that several species occur also in the highly diverse marine habitats along the Indian coastline. In the present study, material of a culture raised from a specimen isolated from a wate...

Twenty-six Pseudo-nitzschia multistriata cultures were tested for intracellular domoic acid production and fourteen were found to be toxic. Four suboptimal growth conditions were compared with conditions observed to be optimal to explore possible triggers for intracellular domoic acid production. Silica- and phosphate-limitation and low light treat...

One of the key tasks in the project MIDTAL (MIcroarrays for the Detection of Toxic ALgae) is to demonstrate the applicability of microarrays to monitor harmful algae across a broad range of ecological niches and toxic species responsible for harmful algal events. Water samples are collected from a series of sites used in national phytoplankton and...

Aim : Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus H...

The red alga, Asparagopsis taxiformis, has recently expanded its distribution range into the Western Mediterranean Sea, and populations have now even been found on the Portuguese South coast. All Western Mediterranean populations belong to a single mitochondrial cryptic lineage (referred to as lineage 2 in earlier studies) and probably result from...

The unarmoured dinoflagellate assemblage of the Gulf of Naples has been investigated in the frame of a 1-year sampling of natural surface samples collected weekly at a coastal station c. 2 miles offshore. Twenty-six strains of unarmoured dinoflagellates were brought into culture by means of serial dilution. Observations at both light and scanning e...

SUMMARYA marine araphid pennate diatom obtained from sand grains sampled at two sites at Vigo, Spain is described as Psammogramma vigoensis S. Sato et Medlin, a member of the family Plagiogrammaceae, based on observations of frustule fine structure. The species possesses elongated valves with apical pore fields and parallel rows of striae oriented...

The planktonic diatom Pseudo-nitzschia multistriata is a potentially toxic species recorded during late summer-autumn in the Gulf of Naples (Tyrrhenian Sea, Italy). We analysed the genetic structure by amplifying the internal transcribed spacer (ITS-1-5.8S-ITS-2) region of the ribosomal DNA of 44 strains isolated along 2 years. Polymorphism in the...

Pennate diatoms are monophyletic. Their principal cell wall elements, called valves, are shaped like a ship’s hull. Within the pennates, the araphids are paraphyletic; they possess rimoportulae and pore fields located at the valve apices. The pore fields exude mucilage pads with which cells attach to one another to form chains. Many taxa use the pa...

With the use of a new kit from Qiagen to amplify total genome quantity, DNA was bulked up from two diatoms that are difficult to grow (Ardissonea and Climacosphenia), and the nuclear SSU rRNA gene was successfully amplified. Results of Bayesian analyses showed that these diatoms are sister to Toxarium and belong to the bi- and multipolar centric di...

2008. A new araphid diatom genus Psammoneis gen. nov. (Plagiogrammaceae, Bacillariophyta) with three new species based on SSU and LSU rDNA sequence data and morphology. Phycologia 47: 510–528. Five strains of a hitherto undescribed diatom genus, Psammoneis, were established from Japanese and Senegalese marine benthic samples. The strains were analy...

Recent studies have shown that the cosmopolitan diatom Skeletonema costatum sensu lato is composed of several morphologically and genetically distinct species. To assess whether the separate species have a cosmopolitan distribution, we analysed 184 strains from marine and estuarine sites worldwide. We identified the strains using light and electron...

Resting cysts of the marine phytoplanktonic dinoflagellate Scrippsiella spp. are encountered in coastal habitats and shallow seas all over the world. Identification of Scrippsiella species needs additional information from cyst morphology because the plate pattern of the flagellated cell is more conserved. Cysts from sediments of the East China Sea...

Diatoms constitute the single-most diverse group of microalgae. Their hallmark is the compound silica cell wall, the frustule, which encases the cell completely but, nevertheless, permits growth and cell division. Silica cell wall elements are encountered also in their resting stages and during the brief sexual phase in the diatom life cycle, namel...