Diatom Life Cycle Research Articles

Differential cell size reduction of two sympatric Epithemia (Bacillariophyta) taxa in Nakaikemi Wetland, Japan

SUMMARYWe observed contrasting temporal changes in cell size between two Epithemia taxa. The life cycle of diatoms is closely linked to their cell size, with a gradual decrease during the vegetative stage and a recovery through sexual reproduction. Sexual reproduction is triggered when cells become smaller than a species‐specific size threshold and receive species‐specific environmental cues. Few studies have documented the life cycles and frequency of sexual reproduction in diatoms, combining field observations and laboratory culture. We collected two Epithemia taxa, Epithemia gibba var. ventricosa and Epithemia sp. from a pond in Nakaikemi Wetland, and measured their valve lengths monthly for almost 3 years. Additionally, we established cultures of both taxa to examine the rates of cell size reduction, which affect the duration of the vegetative stage. In the field, E. gibba var. ventricosa exhibited a wide range of cell sizes and signs of size recovery. Furthermore, the cultures of this taxon showed a clear decrease in cell size through division, suggesting that sexual reproduction is required for size recovery. On the other hand, Epithemia sp. showed no obvious change in cell size both in the field and in the laboratory. This suggests that either sexual reproduction is not necessary for this taxon to maintain its population or their life cycle extends over several years to several decades. Thus, our findings reveal congeneric taxa sharing a common habitat and substratum, yet exhibiting distinct sexual and asexual strategies. Furthermore, we question the validity of taxonomic classifications previously assigned to these diatoms based on the range of morphological characteristics observed in the present study.

The pennate diatom Pseudo-nitzschia multistriata as a model for diatom life cycles, from the laboratory to the sea.

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 diatom life cycles. P. multistriata is a toxic species, able to produce the neurotoxin domoic acid. First described in Japan in 1993, it was detected at the long-term monitoring station MareChiara (Gulf of Naples, Italy) in 1995. Since then, P. multistriata has been reported from several worldwide coastal sites. A large body of knowledge has been produced on its ecology, genetic diversity, and life cycle characteristics. The availability of these data, the ecological relevance of the Pseudo-nitzschia genus, and its controllable life cycle with a short generation time made it an ideal species to develop a genetic model system for diatoms. To enable functional studies, a 59 Mb genome sequence and several transcriptomic data were produced, and genetic transformation was optimized. These tools allowed the discovery of the first mating-type determining gene for diatoms. Gene expression studies and metabolomics analyses defined genes and molecules underpinning different phases of the process of sexual reproduction. This model system, developed to explore the genetics of diatom life cycles, offers the opportunity to parallel experimental observations in the laboratory using in situ meta-omics analyses along space and time, empowering knowledge on the biology and ecology of the genus.

Molecular and cellular mechanisms of diatom response to environmental changes

Abstract. The review is devoted adaptations of diatom under environmental changes and stress factors. Life cycle of diatoms is influenced by various environmental changes, including changes in light intensity, temperature, nutrient availability, and exposure to infochemicals, algicidal bacteria, and viruses. During evolution diatoms have evolved many molecular pathways to respond to stress factors: altering their metabolism to react on abiotic stressors, or producing secondary metabolites to protect themselves from competitors and predators. Prolonged exposure to a stress factor leads to a variety of disorders in cells oxidative stress, disruption of photosynthesis, mitochondrial function, protein folding, resulting in cell death. It is assumed that these mechanisms have allowed diatoms to adapt to a variety of conditions and successfully exist in ecosystems for many millions of years.

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

Diatom cultures can help answer taxonomic, biogeographic and ecological questions on a local and global scale. Unialgal cultures are derived from a single cell and provide abundant material for morphological and molecular analyses. The link between the historic morphological species concept and the molecular data is becoming increasingly important with the use of eDNA metabarcoding. Additionally, cultures provide insights into the life cycle of diatoms and thereby complement taxonomy and species ecology. In this study, we present an approach to extract benthic diatoms from an environmental sample to generate unialgal cultures. We explored diatom diversity in preserved assemblages and by culturing as many different taxa as possible from benthic freshwater samples taken on the same day from the Bow River in Calgary, Canada. With both methods we found a total of 221 different benthic diatom taxa, of which 182 were identified in the preserved diatom assemblages. Interestingly, an additional 39 taxa only appeared in the cultures. In total 129 strains were cultivated representing 71 different taxa. This study includes pictures of living cells demonstrating the additional merits of unialgal cultures, as they provide information on plastid details, auxospores and endosymbionts. Both, the identification of the diatom assemblages and the generation and identification of strains provide the foundation for additional water quality assessment tools, taxonomic insights and molecular references libraries.

Diffeomorphic transforms for data augmentation of highly variable shape and texture objects

Background and objective: Training a deep convolutional neural network (CNN) for automatic image classification requires a large database with images of labeled samples. However, in some applications such as biology and medicine only a few experts can correctly categorize each sample. Experts are able to identify small changes in shape and texture which go unnoticed by untrained people, as well as distinguish between objects in the same class that present drastically different shapes and textures. This means that currently available databases are too small and not suitable to train deep learning models from scratch. To deal with this problem, data augmentation techniques are commonly used to increase the dataset size. However, typical data augmentation methods introduce artifacts or apply distortions to the original image, which instead of creating new realistic samples, obtain basic spatial variations of the original ones.Methods: We propose a novel data augmentation procedure which generates new realistic samples, by combining two samples that belong to the same class. Although the idea behind the method described in this paper is to mimic the variations that diatoms experience in different stages of their life cycle, it has also been demonstrated in glomeruli and pollen identification problems. This new data augmentation procedure is based on morphing and image registration methods that perform diffeomorphic transformations.Results: The proposed technique achieves an increase in accuracy over existing techniques of 0.47%, 1.47%, and 0.23% for diatom, glomeruli and pollen problems respectively.Conclusions: For the Diatom dataset, the method is able to simulate the shape changes in different diatom life cycle stages, and thus, images generated resemble newly acquired samples with intermediate shapes. In fact, the other methods compared obtained worse results than those which were not using data augmentation. For the Glomeruli dataset, the method is able to add new samples with different shapes and degrees of sclerosis (through different textures). This is the case where our proposed DA method is more beneficial, when objects highly differ in both shape and texture. Finally, for the Pollen dataset, since there are only small variations between samples in a few classes and this dataset has other features such as noise which are likely to benefit other existing DA techniques, the method still shows an improvement of the results.

Is the diatom sex clock a clock?

The unique life cycle of diatoms with continuous decreasing and restoration of the cell size leads to periodic fluctuations in cell size distribution and has been regarded as a multi-annual clock. To understand the long-term behaviour of a population analytically, generic mathematical models are investigated algebraically and numerically for their capability to describe periodic oscillations. Whereas the generally accepted simple concepts for the proliferation dynamics do not sustain oscillating behaviour owing to broadening of the size distribution, simulations show that a proposed limited lifetime of a newly synthesized cell wall slows down the relaxation towards a time-invariant equilibrium state to the order of a hundred thousand generations. In combination with seasonal perturbation events, the proliferation scheme with limited lifetime is able to explain long-lasting rhythms that are characteristic for diatom population dynamics. The life cycle thus resembles a pendulum clock that has to be wound up from time to time by seasonal perturbations rather than an oscillator represented by a limit cycle.

Enlarge or die! An auxospore perspective on diatom diversification

Sexual reproductive cells and processes are highly conserved in a wide range of organisms. A specialized, expandable zygote called the auxospore is a cell known only in diatoms. Auxospores perform two critical functions in the life cycle of most diatoms: (1) as in other sexual organisms, they confer the benefits of genetic recombination to diatom progeny, and (2) restore larger cell size and allow a new cycle of vegetative cell size diminution to commence. Because of this dual importance in the diatom life cycle, the auxospore is strongly conserved, in contrast to the astounding diversity of forms among diatom vegetative cells. The auxospore is a complex cell which develops in a specific sequence of stages with a variety of characteristic structures recognizable across all diatoms. With only two major blueprints for auxospore growth and development (isodiametric and anisodiametric) and a number of highly conserved associated structures, studying this aspect of the diatom life cycle may reveal much about their deep evolutionary history. In the evolutionarily more recent arrivals (i.e., pennates), additional reproductive characters may be informative, e.g., mode of gamete motility, anisogamy vs. isogamy. We argue that combined with the widely varying but taxon-specific aspects of diatom gametogenetic processes, auxospores are excellent tools for cross group comparisons that provide insight into their evolutionary relationships. Expanding our dataset from 21 genera presented in 2004 to 65 polar centrics, nonpolar centrics, and araphid pennates, we repostulate that the evolutionarily informative capacity of auxospore development stands on its own.

Virus-induced spore formation as a defense mechanism in marine diatoms.

Summary 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 socialis induces the mass formation of resting spores, a heavily silicified life cycle stage associated with carbon export due to rapid sinking.Although viral RNA was detected within spores, mature virions were not observed. ‘Infected’ spores were capable of germinating, but did not propagate or transmit infectious viruses.These results demonstrate that diatom spore formation is an effective defense strategy against viral‐mediated mortality. They provide a possible mechanistic link between viral infection, bloom termination, and mass carbon export events and highlight an unappreciated role of viruses in regulating diatom life cycle transitions and ecological success.

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in natural circumstances and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatom Seminavis robusta. We observe marked gene expression changes associated with SIP treatment in both mating types, including an inhibition of S phase progression, chloroplast division, mitosis, and cell wall formation. Meanwhile, meiotic genes are upregulated in response to SIP, including a sexually induced diatom specific cyclin. Our data further suggest an important role for reactive oxygen species, energy metabolism, and cGMP signaling during the early stages of sexual reproduction. In addition, we identify several genes with a mating type specific response to SIP, and link their expression pattern with physiological specialization, such as the production of the attraction pheromone diproline in mating type − (MT−) and mate-searching behavior in mating type + (MT+). Combined, our results provide a model for early sexual reproduction in pennate diatoms and significantly expand the suite of target genes to detect sexual reproduction events in natural diatom populations.

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.

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 phase of the centric planktonic diatom Skeletonema marinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschia multistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets.

Diatom identification including life cycle stages through morphological and texture descriptors.

Diatoms are unicellular algae present almost wherever there is water. Diatom identification has many applications in different fields of study, such as ecology, forensic science, etc. In environmental studies, algae can be used as a natural water quality indicator. The diatom life cycle consists of the set of stages that pass through the successive generations of each species from the initial to the senescent cells. Life cycle modeling is a complex process since in general the distribution of the parameter vectors that represent the variations that occur in this process is non-linear and of high dimensionality. In this paper, we propose to characterize the diatom life cycle by the main features that change during the algae life cycle, mainly the contour shape and the texture. Elliptical Fourier Descriptors (EFD) are used to describe the diatom contour while phase congruency and Gabor filters describe the inner ornamentation of the algae. The proposed method has been tested with a small algae dataset (eight different classes and more than 50 samples per type) using supervised and non-supervised classification techniques obtaining accuracy results up to 99% and 98% respectively.

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

BackgroundFlagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce.ResultsIn the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world’s seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes.ConclusionOur analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment.

Diatom life cycles and ecology in the Cretaceous.

The earliest known diatom fossils with well-preserved siliceous frustules are from Lower Cretaceous neritic marine deposits in Antarctica. In this study, we analyzed the cell wall structure to establish whether their cell and life cycles were similar to modern forms. At least two filamentous species (Basilicostephanus ornatus and Archepyrgus melosiroides) had girdle band structures that functioned during cell division in a similar way to present day Aulacoseira species. Also, size analyses of cell diameter indicated that the cyclic process of size decline and size restoration used to time modern diatom life cycles was present in five species from the Lower Cretaceous (B.ornatus, A.melosiroides, Gladius antiquus, Ancylopyrgus reticulatus, Kreagra forfex) as well as two species from Upper Cretaceous deposits (Trinacria anissimowii and Eunotogramma fueloepi) from the Southwest Pacific. The results indicate that the "Diatom Sex Clock" was present from an early evolutionary stage. Other ecological adaptations included changes in mantle height and coiling. Overall, the results suggest that at least some of the species in these early assemblages are on a direct ancestral line to modern forms.

Morphometric Asymmetry of Frustule Outlines in the Pennate Diatom Luticola poulickovae (Bacillariophyceae)

Side orientation of cells is usually ambiguous in unicellular organisms, making it impossible to separate components of directional asymmetry (DA) and fluctuating asymmetry (FA). However, frustules of the diatom Luticola poulickovae have biradially symmetric outlines, and their central areas bear ornamentation that is asymmetric across the apical axis. The goal of this study was to explore differentiation of morphometric asymmetry across the apical axis into DA and FA components. Is there detectable DA of the valve outlines of two L. poulickovae strains that may be related to the asymmetric central areas? Given that the life cycle of diatoms involves cell-size diminution, and cell shape is strongly affected by allometry, we also explored the question of whether asymmetry is correlated with cell size. The extent of symmetric variation among individuals in each strain, as well as DA and FA across the apical axis, were quantified using two Procrustes ANOVA models. The results revealed no correlation of either total asymmetry or FA with valve size. DA was significant and considerably more pronounced than FA in both strains, indicating that there is previously unknown systematic asymmetry of valve outlines of L. poulickovae, which may be related to the asymmetry of its central area.

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta.

Although sexual reproduction is believed to play a major role in the high diversification rates and species richness of diatoms, a mechanistic understanding of diatom life cycle control is virtually lacking. Diatom sexual signalling is controlled by a complex, yet largely unknown, pheromone system. Here, a sex-inducing pheromone (SIP+) of the benthic pennate diatom Seminavis robusta was identified by comparative metabolomics, subsequently purified, and physicochemically characterized. Transcriptome analysis revealed that SIP+ triggers the switch from mitosis-to-meiosis in the opposing mating type, coupled with the transcriptional induction of proline biosynthesis genes, and the release of the proline-derived attraction pheromone. The induction of cell cycle arrest by a pheromone, chemically distinct from the one used to attract the opposite mating type, highlights the existence of a sophisticated mechanism to increase chances of mate finding, while keeping the metabolic losses associated with the release of an attraction pheromone to a minimum.

A theoretical investigation of the diatom cell size reduction–restitution cycle

An individual based model for the life cycle of diatoms (DiaLCM) has been developed to investigate the combined effects of the cell cycle and the cell size reduction–restitution cycle (SRRC) of this important marine phytoplankton group. Growth, grazing mortality and sinking are considered as size-dependent processes. The model is tested against laboratory results and reproduces the typical saw tooth pattern of mean population size as the result of the SRRC. The development of cell-size distribution patterns, their dependence on the environment and their influence on the ecosystem is investigated in a one-dimensional water column setting, where the diatoms face competition by a bulk phytoplankton species. Using a perpetual-year forcing, we find that the SRRC introduces interannual variability with periods of diatoms dominance interrupted by dominance of other phytoplankton. We find that inter- and intraspecific competition explains several of the observed characteristics in size frequency distributions, in particular the relatively narrow cell size spectra. In agreement with observations modeled auxosporulation events are rare with low numbers of auxospores.

The dynamics of sexual phase in the marine diatom Pseudo-nitzschia multistriata (Bacillariophyceae).

Sexual reproduction represents a fundamental phase in the life cycle of diatoms, linked to both the production of genotypic diversity and the formation of large-sized initial cells. Only cells below a certain size threshold can be sexualized, but various environmental factors can modulate the success of sexual reproduction. We investigated the role of cell density and physiological conditions of parental strains in affecting the success and timing of sexual reproduction in the marine heterothallic diatom Pseudo-nitzschia multistriata. We also studied the dynamics of the sexual phase in still conditions allowing cell sedimentation and in gently mixed conditions that keep cells in suspension. Our results showed that successful sexual reproduction can only be achieved when crossing parental strains in the exponential growth phase. Evidence was provided for the fact that sexual reproduction is a density-dependent event and requires a threshold cell concentration to start, although this might vary considerably amongst strains. Moreover, the onset of the sexual phase was coupled to a marked reduction in growth of the vegetative parental cells. The crosses carried out in physically mixed conditions produced a significantly reduced number of sexual stages as compared to crosses in still conditions, showing that mixing impairs sexualization. The results of our experiments suggest that the signaling that triggers the sexual phase is favored when cells can accumulate, reducing the distance between them and facilitating contacts and/or the perception of chemical cues. Information on the progression of the sexual phase in laboratory conditions help understanding the conditions at which sex occurs in the natural environment.

Transcriptomic Insights into the Life History of Bolidophytes, the Sister Lineage to Diatoms.

Diatoms are perhaps the most diverse lineage of eukaryotic algae, with their siliceous cell wall and diplontic life history often considered to have played important roles in their extraordinary diversification. The characteristic diminution of the diatom cell wall over the course of vegetative growth provides a reliable, intrinsic trigger for sexual reproduction, establishing a direct link between the evolution of their cell-wall and life-history features. It is unclear, however, whether the diplontic life cycle of diatoms represents an ancestral or derived trait. This uncertainty is based in part on our lack of understanding of the life cycle of the sister lineage to diatoms, which includes a mix of two free-living and separately classified forms: naked biflagellate unicells in the genus Bolidomonas and silicified forms in the order Parmales. These two forms might represent different life-history stages, although directly establishing such links can be difficult. We sequenced transcriptomes for Bolidomonas and two diatoms and found that ~0.1% of the coding regions in the two diploid diatoms are heterozygous, whereas Bolidomonas is virtually devoid of heterozygous alleles, consistent with expectations for a haploid genome. These results suggest that Bolidomonas is haploid and predict that parmaleans represent the diploid phase of a haplodiplontic life cycle. These data fill an important gap in our understanding of the origin of the diplontic life history of diatoms, which may represent an evolutionarily derived, adaptive feature.

Molecular regulation of the diatom cell cycle

Accounting for almost one-fifth of the primary production on Earth, the unicellular eukaryotic group of diatoms plays a key ecological and biogeochemical role in our contemporary oceans. Furthermore, as producers of various lipids and pigments, and characterized by their finely ornamented silica cell wall, diatoms hold great promise for different industrial fields, including biofuel production, nanotechnology, and pharmaceutics. However, in spite of their major ecological importance and their high commercial value, little is known about the mechanisms that control the diatom life and cell cycle. To date, both microscopic and genomic analyses have revealed that diatoms exhibit specific and unique mechanisms of cell division compared with those found in the classical model organisms. Here, we review the structural peculiarities of diatom cell proliferation, highlight the regulation of their major cell cycle checkpoints by environmental factors, and discuss recent progress in molecular cell division research.

Proposals for a terminology for diatom sexual reproduction, auxospores and resting stages

The past few decades have brought about a significant expansion in our understanding of the diatom life cycle, particularly its sexual part. Presented here is a set of proposals for the terminology of processes and structures associated with sexual reproduction and for the resting stages of diatoms, some of which have at times been confused with each other. The proposals fill the void present in widely used publications offering standardized terminology related to diatom frustule micro-architecture.