Comparative analysis of freshwater phytoplankton communities in two lakes of Burabay National Park using morphological and molecular approaches.

We analyzed phytoplankton assemblages' variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.

Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.

A case of oral foreign-body granuloma due to diatoms.

Diatoms are photosynthetic algae with a siliceous exoskeleton. Diatoms are utilized by a wide array of industries for applications such as filtration and pest control. Unsubstantiated claims have also propelled their societal reach to trendy oral and topical uses. This case highlights a rare case of an oral granuloma secondary to diatoms. An 80-year-old woman presented with a mobile, firm, asymptomatic submucosal mass on her lower left mandibular vestibular mucosa. Histopathology showed a non-caseating granulomatous reaction to diatoms. Her only verified contact with a diatomaceous earth product was a dental impression using alginate after upper front teeth trauma 5 months before. Although there have been several cases of allergic contact dermatitis attributed to diatoms, there are no reported cases of diatom-induced granuloma formation found in the literature. There are, however, ample data on granulomas initiated by silica. Given the silica-based composition of diatoms, and the broad use of diatoms in industry and alternative medicine, it is unclear why diatom-induced granulomas are not more widely described. This report may alert clinicians to the existence of diatom granulomas and incline them to tailor their history to cover questions about possible exposure when evaluating patients presenting with a localized oral lesion.

Exopolysaccharides directed embellishment of diatoms triggered on plastics and other marine litter.

In the present study, embellishment or beautification of diatoms on substrates like plastics, polydimethylsiloxane, graphite, glass plate, and titanium dioxide, triggered by exopolysaccharides was examined under laboratory conditions. Exopolysaccharides are secreted mainly by primary colonisers, bacteria, which is succeeded by secondary colonisers i.e. diatoms. Both diatom (Nitzschia sp.4) and bacteria (Bacillus subtilis) were exposed with substrates separately for 30 days. Diatoms adhere on substrates strongly, not only because of surface roughness of different substrates but also the nanoporous architecture of diatoms which enhanced their embellishment. This study attempted to identify the substrates that adhere to diatoms strongly and was mainly analyzed by scanning electron microscope and further the observations are well supported by math work software (MATLAB). The variation of diatom's binding on different substrates is due to the influence of marine litters on diatom population in ocean beds where they undergo slow degradation releasing macro, micro and nanoparticles besides radicals and ions causing cell death. Therefore a proof-of-concept model is developed to successfully deliver a message concerning benefit of using different diatom species.

Virus-host coexistence in phytoplankton through the genomic lens.

Virus-microbe interactions in the ocean are commonly described by "boom and bust" dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this "accordion" chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.

Hidden Secrets Behind Dots: Improved Phytoplankton Taxonomic Resolution Using High-Throughput Imaging Flow Cytometry.

Phytoplankton are aquatic, microscopically small primary producers, accounting for almost half of the worldwide carbon fixation. As early indicators of environmental change, they play a crucial role in water quality management. Human activities like climate change, eutrophication, or international shipping traffic strongly impact diversity of these organisms. Phytoplankton monitoring is a crucial step in the recognition of changes in community composition. The common standard for monitoring programs is manual microscopic counting, which strongly limits sample number and sampling frequency. In contrast, high-throughput technologies like standard flow cytometry (FCM) are restricted to a low taxonomic resolution, which makes them unsuitable for the identification of indicator species. Imaging flow cytometers (IFC) could overcome these limitations as they combine microscopy and high-throughput analysis. In comparison to single fluorescence values, image information not only allows for a wide variety of possibilities to characterize different species as well as immediate and fast measurements but also provides an archivable data output. Taxonomic resolution of IFC (ImageStream X Mk II) was proven comparable to standard FCM (FACSAria II) by the help of numerical evaluations. This is demonstrated on different levels of taxonomic differentiation of laboratory grown cultures in this study. Phytoplankton species discrimination by an imaging flow cytometer could be useful as supportive tool to make machine-learning classifications more robust, reliable, and flexible. Furthermore, this study provides examples, demonstrating the possibility of discrimination between species with similar fluorescence properties, strains, and even subpopulations. In contrast to standard FCM, each cell is not only represented as a dot in a cytogram but is also linked to microscopic brightfield and the author presents a new way to visualize this as image-based cytograms. The source code is supplied and could be useful for all kind of IFC data in general. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.

A new widespread subclass of carbonic anhydrase in marine phytoplankton.

Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn2+ to Zn2+ as a cofactor, which is potentially of ecological relevance since Mn2+ is more abundant than Zn2+ in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.

Morphology and molecular phylogeny of epizoic araphid diatoms on marine zooplankton, including Pseudofalcula hyalina gen. & comb. nov. (Fragilariophyceae, Bacillariophyta).

Some diatoms are able to colonize as epibionts on their potential zooplankton predators. Here, we report Pseudohimantidium pacificum living on the copepod Corycaeus giesbrechti and as a new finding on Oithona nana, Protoraphis atlantica living on the copepod Pontellopsis brevis, Protoraphis hustedtiana on the cypris larvae of barnacles, and Falcula hyalina on the copepod Acartia lilljeborgii. The epizoic diatoms were able to grow as free-living forms under culture conditions. Pseudohimantidium pacificum and P. atlantica appeared as the most derived species from their benthic diatom ancestors. The mucilage pad or stalk of the strains of these species showed important morphological distinction when compared with their epizoic forms. Barnacle larvae explore benthic habitats before settlement, and epibiosis on them is an example where P. hustedtiana profits from the host behavior for dispersal of its benthic populations. Molecular phylogenies based on the SSU rRNA and RuBisCO large subunit (rbcL) gene sequences revealed F. hyalina as an independent lineage within the Fragilariales (Tabularia, Catacombas, and others), consistent with its morphological distinction in the low number of rows (≤6) in the ocellulimbus, among other features. We propose the transfer of F. hyalina to the genus Pseudofalcula gen. nov. Molecular phylogeny suggests a single order for the members of the Cyclophorales and the Protoraphidales, and that the epibioses of araphid diatoms on marine zooplankton have been independently acquired several times. These clades are constituted of both epizoic and epiphytic/epilithic forms that evidence a recent acquisition of the epizoic modus vivendi.

Phylogenetic analysis and a review of the history of the accidental phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta).

The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.

Morphology and toxicity of Pseudo-nitzschia species in the northern Benguela Upwelling System.

The Benguela upwelling system, considered the world's most productive marine ecosystem, has a long record of potentially toxic diatoms belonging to the genus Pseudo-nitzschia. Species of Pseudo-nitzschia were reported as early as 1936 from the northern Benguela upwelling system (nBUS). For the current study, long-term phytoplankton monitoring data (2004-2011) for the Namibian coast were analysed to examine inshore and offshore temporal distribution of Pseudo-nitzschia species, their diversity and ultrastructure. The potentially toxigenic P. pungens and P. australis were the dominant inshore species, whereas offshore Pseudo-nitzschia showed a higher diversity that also included potentially toxic species. During a warming event, a community shift from P. pungens and P. australis dominance to P. fraudulenta and P. multiseries was documented in the central nBUS. A case study of a toxic event (August 2004) revealed that P. australis and P. pungens were present at multiple inshore and offshore stations, coincident with fish (pilchard) and bird mortalities reported from the central part of Namibia. Toxin analyses (LC-MS/MS) of samples collected from June to August 2004 revealed the presence of particulate domoic acid (DA) in seawater at multiple stations (maximum ∼180 ng DA/L) in the >0.45 µm size-fraction, as well as detectable DA (0.12 µg DA/g) in the gut of one of two pilchard samples tested. These findings indicate that DA may have been associated with the fish and bird mortalities reported from this event in the nBUS. However, the co-occurrence of very high biomass phytoplankton blooms suggests that other explanations may be possible.

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export.

Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO2 on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2-20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.

Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health.

Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. While this first synthesis shows that notable efforts exist, vast regions such as the ocean depths, the open ocean, the polar oceans, and most of the Southern Hemisphere lack consistent observation. To secure a coordinated future for a global microbial observing system, existing long-term efforts must be better networked to generate shared bioindicators of the Global Ocean's state and health.

A Laplacian characterization of phytoplankton shape.

Phytoplankton exhibit pronounced morphological diversity, impacting a range of processes. Because these impacts are challenging to quantify, however, phytoplankton are often approximated as spheres, and when effects of non-sphericity are studied it is usually experimentally or via geometrical approximations. New methods for quantifying phytoplankton size and shape generally, so all phytoplankton are analyzable by the same procedure, can complement advances in microscopic imagery and automated classification to study the influence of shape in phytoplankton. Here we apply to phytoplankton a technique for defining the size of arbitrary shapes based on the Laplacian-the operator that governs processes, such as nutrient uptake and fluid flow, where phytoplankton shape is expected to have the greatest effect. Deviations from values given by spherical approximation are a measure of phytoplankton shape and indicate the fitness increases for phytoplankton conferred by their non-spherical shapes. Comparison with surface-to-volume quotients suggests the Laplacian-based metric is insensitive to small-scale features which can increase surface area without affecting key processes, but is otherwise closely related to surface-area-to-volume, demonstrating this metric is a meaningful measure. While our analysis herein is limited to axisymmetric phytoplankton due to relative sparsity of 3D information about other phytoplankton shapes, the definition and method are directly generalizable to 3D shape data, which will in the near future be more readily available.

Diatom Frustule Morphogenesis and Function: a Multidisciplinary Survey.

Diatoms represent the major component of phytoplankton and are responsible for about 20-25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions. In the present article the main reported data related to frustule morphogenesis and functionalities with contributions from fundamental biology, genetics, mathematics, geometry and physics are reviewed.

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. socialis complex. Members of this complex are characterized by curved chains (primary colonies) aggregating into globular clusters, where one of the four setae of each cell curves toward the center of the cluster and the other three orient outwards. New light and electron microscopy observations as well as molecular data on marine planktonic diatoms from the coastal waters off Chile revealed the presence of two new species, Chaetoceros sporotruncatus sp. nov. and C. dichatoensis. sp. nov. belonging to the C. socialis complex. The two new species are similar to other members of the complex (i.e., C. socialis and C. gelidus) in the primary and secondary structure of the colony, the orientation pattern of the setae, and the valve ultrastructure. The only morphological characters that can be used to differentiate the species of this complex are aspects related to resting spore morphology. The two newly described species are closely related to each other and form a sister clade to C. gelidus in molecular phylogenies. We also provide a phylogenetic status along with the morphological characterization of C. radicans and C. cintus, which are genetically related to the C. socialis complex.

All-passive pixel super-resolution of time-stretch imaging.

Based on image encoding in a serial-temporal format, optical time-stretch imaging entails a stringent requirement of state-of-the-art fast data acquisition unit in order to preserve high image resolution at an ultrahigh frame rate - hampering the widespread utilities of such technology. Here, we propose a pixel super-resolution (pixel-SR) technique tailored for time-stretch imaging that preserves pixel resolution at a relaxed sampling rate. It harnesses the subpixel shifts between image frames inherently introduced by asynchronous digital sampling of the continuous time-stretch imaging process. Precise pixel registration is thus accomplished without any active opto-mechanical subpixel-shift control or other additional hardware. Here, we present the experimental pixel-SR image reconstruction pipeline that restores high-resolution time-stretch images of microparticles and biological cells (phytoplankton) at a relaxed sampling rate (≈2-5 GSa/s)-more than four times lower than the originally required readout rate (20 GSa/s) - is thus effective for high-throughput label-free, morphology-based cellular classification down to single-cell precision. Upon integration with the high-throughput image processing technology, this pixel-SR time-stretch imaging technique represents a cost-effective and practical solution for large scale cell-based phenotypic screening in biomedical diagnosis and machine vision for quality control in manufacturing.

Effects of the bacterial algicide IRI-160AA on cellular morphology of harmful dinoflagellates.

The algicide, IRI-160AA, induces mortality in dinoflagellates but not other species of algae, suggesting that a shared characteristic or feature renders this class of phytoplankton vulnerable to the algicide. In contrast to other eukaryotic species, the genome of dinoflagellates is stabilized by high concentrations of divalent cations and transition metals and contains large amounts of DNA with unusual base modifications. These distinctions set dinoflagellates apart from other phytoplankton and suggest that the nucleus may be a dinoflagellate-specific target for IRI-160AA. In this study, morphological and ultrastructural changes in three dinoflagellate species, Prorocentrum minimum, Karlodinium veneficum and Gyrodinium instriatum, were evaluated after short-term exposure to IRI-160AA using super resolution structured illumination microscopy (SR-SIM) and transmission electron microscopy (TEM). Exposure to the algicide resulted in cytoplasmic membrane blebbing, differing chloroplast morphologies, nuclear expansion, and chromosome expulsion and/or destabilization. TEM analysis showed that chromosomes of algicide-treated K. veneficum appeared electron dense with fibrous protrusions. In algicide-treated P. minimum and G. instriatum, chromosome decompaction occurred, while for P. minimum, nuclear expulsion was also observed for several cells. Results of this investigation demonstrate that exposure to the algicide destabilizes dinoflagellate chromosomes, although it was not clear if the nucleus was the primary target of the algicide or if the observed effects on chromosomal structure were due to downstream impacts. In all cases, changes in cellular morphology and ultrastructure were observed within two hours, suggesting that the algicide may be an effective and rapid approach to mitigate dinoflagellate blooms.

Imaging flow cytometry for phytoplankton analysis.

This review highlights the concepts and instrumentation of imaging flow cytometry technology and in particular its use for phytoplankton analysis. Imaging flow cytometry, a hybrid technology combining speed and statistical capabilities of flow cytometry with imaging features of microscopy, is rapidly advancing as a cell imaging platform that overcomes many of the limitations of current techniques and contributed significantly to the advancement of phytoplankton analysis in recent years. This review presents the various instrumentation relevant to the field and currently used for assessment of complex phytoplankton communities' composition and abundance, size structure determination, biovolume estimation, detection of harmful algal bloom species, evaluation of viability and metabolic activity and other applications. Also we present our data on viability and metabolic assessment of Aphanizomenon sp. cyanobacteria using Imagestream X Mark II imaging cytometer. Herein, we highlight the immense potential of imaging flow cytometry for microalgal research, but also discuss limitations and future developments.

Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex.

Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.

Algal toxin profiles in Nigerian coastal waters (Gulf of Guinea) using passive sampling and liquid chromatography coupled to mass spectrometry.

Algal toxins may accumulate in fish and shellfish and thus cause poisoning in consumers of seafood. Such toxins and the algae producing them are regularly surveyed in many countries, including Europe, North America, Japan and others. However, very little is known regards the occurrence of such algae and their toxins in most African countries. This paper reports on a survey of phytoplankton and algal toxins in Nigerian coastal waters. Seawater samples were obtained from four sites for phytoplankton identification, on three occasions between the middle of October 2014 and the end of February 2015 (Bar Beach and Lekki in Lagos State, Port Harcourt in Rivers State and Uyo in Akwa Ibom State). The phytoplankton community was generally dominated by diatoms and cyanobacteria; however several species of dinoflagellates were also identified: Dinophysis caudata, Lingulodinium polyedrum and two benthic species of Prorocentrum. Passive samplers (containing Diaion(®) HP-20 resin) were deployed for several 1-week periods on the same four sites to obtain profiles of algal toxins present in the seawater. Quantifiable amounts of okadaic acid (OA) and pectenotoxin 2 (PTX2), as well as traces of dinophysistoxin 1 (DTX1) were detected at several sites. Highest concentrations (60 ng OA g(-1) HP-20 resin) were found at Lekki and Bar Beach stations, which also had the highest salinities. Non-targeted analysis using full-scan high resolution mass spectrometry showed that algal metabolites differed from site to site and for different sampling occasions. Screening against a marine natural products database indicated the potential presence of cyanobacterial compounds in the water column, which was also consistent with phytoplankton analysis. During this study, the occurrence of the marine dinoflagellate toxins OA and PTX2 has been demonstrated in coastal waters of Nigeria, despite unfavourable environmental conditions, with regards to the low salinities measured. Hence shellfish samples should be monitored in future to assess the risk for public health through accumulation of such toxins in seafood.