Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

Channels of Evolution: Unveiling Evolutionary Patterns in Diatom Ca2+ Signalling

Diatoms are important primary producers in marine and freshwater environments, but little is known about the signalling mechanisms they use to detect changes in their environment. All eukaryotic organisms use Ca2+ signalling to perceive and respond to environmental stimuli, employing a range of Ca2+-permeable ion channels to facilitate the movement of Ca2+ across cellular membranes. We investigated the distribution of different families of Ca2+ channels in diatom genomes, with comparison to other members of the stramenopile lineage. The four-domain voltage-gated Ca2+ channels (Cav) are present in some centric diatoms but almost completely absent in pennate diatoms, whereas single-domain voltage-gated EukCatA channels were found in all diatoms. Glutamate receptors (GLRs) and pentameric ligand-gated ion channels (pLGICs) also appear to have been lost in several pennate species. Transient receptor potential (TRP) channels are present in all diatoms, but have not undergone the significant expansion seen in brown algae. All diatom species analysed lacked the mitochondrial uniporter (MCU), a highly conserved channel type found in many eukaryotes, including several stramenopile lineages. These results highlight the unique Ca2+-signalling toolkit of diatoms and indicate that evolutionary gains or losses of different Ca2+ channels may contribute to differences in cellular-signalling mechanisms between species.

Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction

Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.

The Photoprotective Behavior of a Motile Benthic Diatom as Elucidated from the Interplay Between Cell Motility and Physiological Responses to a Light Microgradient Using a Novel Experimental Setup

It has long been hypothesized that benthic motile pennate diatoms use phototaxis to optimize photosynthesis and minimize photoinhibitory damage by adjusting their position within vertical light gradients in coastal benthic sediments. However, experimental evidence to test this hypothesis remains inconclusive, mainly due to methodological difficulties in studying cell behavior and photosynthesis over realistic spatial microscale gradients of irradiance and cell position. In this study, a novel experimental approach was developed and used to test the hypothesis of photosynthesis optimization through motility, based on the combination of single-cell in vivo chlorophyll fluorometry and microfluidic chips. The approach allows the concurrent study of behavior and photosynthetic activity of individual cells of the epipelic diatom species Craspedostauros britannicus exposed to a light microgradient of realistic dimensions, simulating the irradiance and distance scales of light microgradients in benthic sediments. Following exposure to light, (i) cells explored their light environment before initiating light-directed motility; (ii) cells used motility to lower their light dose, when exposed to the highest light intensities; and (iii) motility was combined with reversible non-photochemical quenching, to allow cells to avoid photoinhibition. The results of this proof-of-concept study not only strongly support the photoprotective nature of photobehavior in the studied species but also revealed considerable variability in how individual cells reacted to a light microgradient. The experimental setup can be readily applied to study motility and photosynthetic light responses of other diatom species or natural assemblages, as well as other photoautotrophic motile microorganisms, broadening the toolset for experimental microbial ecology research.

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes

The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis.

Climbing mechanisms and the diversification of neotropical climbing plants across time and space

Climbers germinate on the ground but need external support to sustain their stems, which are maintained attached to supports through modified organs, that is, climbing mechanisms. Specialized climbing mechanisms have been linked to higher diversification rates. Also, different mechanisms may have different support diameter restrictions, which might influence climbers' spatial distribution. We test these assumptions by linking climbing mechanisms to the spatiotemporal diversification of neotropical climbers. A dataset of climbing mechanisms is presented for 9071 species. WCVP was used to standardize species names, map geographical distributions, and estimate diversification rates of lineages with different mechanisms. Twiners appear concentrated in the Dry Diagonal of South America and climbers with adhesive roots in the Chocó region and Central America. However, climbing mechanisms do not significantly influence the distribution of neotropical climbers. Also, we found no strong support for correlations between specialized climbing mechanisms and higher diversification rates. Climbing mechanisms do not strongly impact the spatiotemporal diversification of neotropical climbers on a macroevolutionary scale. We argue that the climbing habit is a synnovation, meaning the spatiotemporal diversification it promotes is due to the sum effect of all the habit's traits rather than isolated traits, such as climbing mechanisms.

Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance

Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.

Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation

Biofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit intertidal substrata. The development of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. However, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown. Here, we have used proteomics, immunolocalization, comparative genomics, phylogenetics and structural homology analysis to investigate the evolutionary history and function of diatom adhesive proteins. Our study identified eight proteins from the adhesive trails of Craspedostauros australis, of which four form a new protein family called Trailins that contain an enigmatic Choice-of-Anchor A (CAA) domain, which was acquired through horizontal gene transfer from bacteria. Notably, the CAA-domain shares a striking structural similarity with one of the most widespread domains found in ice-binding proteins (IPR021884). Our work offers new insights into the molecular basis for diatom biofilm formation, shedding light on the function and evolution of diatom adhesive proteins. This discovery suggests that there is a transition in the composition of biomolecules required for initial surface colonization and those utilized for 3D biofilm matrix formation.

Cooperative motility, force generation and mechanosensing in a foraging non-photosynthetic diatom

Diatoms are ancestrally photosynthetic microalgae. However, some underwent a major evolutionary transition, losing photosynthesis to become obligate heterotrophs. The molecular and physiological basis for this transition is unclear. Here, we isolate and characterize new strains of non-photosynthetic diatoms from the coastal waters of Singapore. These diatoms occupy diverse ecological niches and display glucose-mediated catabolite repression, a classical feature of bacterial and fungal heterotrophs. Live-cell imaging reveals deposition of secreted extracellular polymeric substance (EPS). Diatoms moving on pre-existing EPS trails (runners) move faster than those laying new trails (blazers). This leads to cell-to-cell coupling where runners can push blazers to make them move faster. Calibrated micropipettes measure substantial single-cell pushing forces, which are consistent with high-order myosin motor cooperativity. Collisions that impede forward motion induce reversal, revealing navigation-related force sensing. Together, these data identify aspects of metabolism and motility that are likely to promote and underpin diatom heterotrophy.

Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS

Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.

Stronger effects of simultaneous warming and precipitation increase than the individual factor on soil bacterial community composition and assembly processes in an alpine grassland

Composition and traits of soil microbial communities that closely related to their ecological functions received extensive attention in the context of climate changes. We investigated the responses of soil bacterial community structure, traits, and functional genes to the individual warming, precipitation increases, and the combination of warming and precipitation increases in an alpine grassland in the Qinghai-Tibet Plateau that is experiencing warming and wetting climate change. Soil properties, plant diversity and biomass were measured, and the ecological processes and environmental factors driving bacterial community changes were further explored. Results indicated that the Shannon diversity of soil bacterial communities decreased significantly only under the combination treatment, which might due to the decreased plant diversity. Soil bacterial community composition was significantly correlated with soil pH, and was affected obviously by the combination treatment. At the taxonomic classification, the relative abundance of Xanthobacteraceae and Beijerinckiaceae increased 127.67 and 107.62%, while the relative abundance of Rubrobacteriaceae and Micromonosporaceae decreased 78.29 and 54.72% under the combination treatment. Functional genes related to nitrogen and phosphorus transformation were enhanced in the combination treatment. Furthermore, weighted mean ribosomal operon copy numbers that positively correlated with plant aboveground biomass increased remarkably in the combination treatment, indicating a trend of life-history strategies shift from oligotrophic to copiotrophic. Stochastic processes dominated soil bacterial community, and the proportion of stochasticity increased under the combination treatment. Our study highlights the significant effects of simultaneous warming and precipitation increase on soil bacterial community.

Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.

Spatial fragmentation in the distribution of diatom endosymbionts from the taxonomically clarified dinophyte Kryptoperidinium triquetrum (= Kryptoperidinium foliaceum, Peridiniales)

Among the photosynthetically active dinophytes, the Kryptoperidiniaceae are unique in having a diatom as endosymbiont instead of the widely present peridinin chloroplast. Phylogenetically, it is unresolved at present how the endosymbionts are inherited, and the taxonomic identities of two iconic dinophyte names, Kryptoperidinium foliaceum and Kryptoperidinium triquetrum, are also unclear. Multiple strains were newly established from the type locality in the German Baltic Sea off Wismar and inspected using microscopy as well as molecular sequence diagnostics of both host and endosymbiont. All strains were bi-nucleate, shared the same plate formula (i.e., po, X, 4', 2a, 7'', 5c, 7s, 5''', 2'''') and exhibited a narrow and characteristically L-shaped precingular plate 7''. Within the molecular phylogeny of Bacillariaceae, endosymbionts were scattered over the tree in a highly polyphyletic pattern, even if they were gained from different strains of a single species, namely K. triquetrum. Notably, endosymbionts from the Baltic Sea show molecular sequences distinct from the Atlantic and the Mediterranean Sea, which is the first report of such a spatial fragmentation in a planktonic species of dinophytes. The two names K. foliaceum and K. triquetrum are taxonomically clarified by epitypification, with K. triquetrum having priority over its synonym K. foliaceum. Our study underlines the need of stable taxonomy for central questions in evolutionary biology.

Uncertainties surrounding the oldest fossil record of diatoms

Molecular clocks estimate that diatom microalgae, one of Earth's foremost primary producers, originated near the Triassic-Jurassic boundary (200 Ma), which is close in age to the earliest, generally accepted diatom fossils of the genus Pyxidicula. During an extensive search for Jurassic diatoms from twenty-five sites worldwide, three sites yielded microfossils initially recognized as diatoms. After applying stringent safeguards and evaluation criteria, however, the fossils found at each of the three sites were rejected as new diatom records. This led us to systematically reexamine published evidence in support of Lower- and Middle-Jurassic Pyxidicula fossils. Although Pyxidicula resembles some extant radial centric diatoms and has character states that may have been similar to those of ancestral diatoms, we describe numerous sources of uncertainty regarding the reliability of these records. We conclude that the Lower Jurassic Pyxidicula fossils were most likely calcareous nannofossils, whereas the Middle Jurassic Pyxidicula species has been reassigned to the Lower Cretaceous and is likely a testate amoeba, not a diatom. Excluding the Pyxidicula fossils widens the gap between the estimated time of origin and the oldest abundant fossil diatom record to 75 million years. This study underscores the difficulties in discovering and validating ancient microfossils.

Diatom endemism and taxonomic turnover: Assessment in high-altitude alpine lakes covering a large geographical range

Diatoms are widely used as ecological indicators and show various degrees of endemism. Many studies that support the idea of endemic species integrate several climate zones, a variety of ecosystem types, and often focus on a global scale. Here, we investigated whether endemism could be detected when considering a homogeneous type of ecosystem in a single climate zone. We sampled stone biofilms at 40-50 cm depth in high-altitude lakes in the Alpine climate zone. A total of 149 samples were obtained from the French and Georgian mountains, two areas separated by ∼3000 km. Using Amplicon Sequence Variants derived from DNA metabarcoding, we assessed taxonomic turnover and Zeta-diversity (a measure of endemism). We ran haplotype networks and phylogenetic tests to measure geographical signal in the phylogenies of dominant taxa. The French and Georgian communities shared 51 % of species. Species that were not shared across both regions were mostly rare, and often not characteristic of lakes but of neighboring habitats instead. In contrast, at the sub-species level, 87 % of the genotypes showed restricted distributions. Whereas endemism was the rule at sub-species level, most species were shared across both French and Georgian lakes, suggesting that geographic barriers strongly limited dispersal at the sub-species level but not species level. Dominant species hosted higher levels of sub-specific diversity than rare species. In contrast to global-scale studies, we did not find any significant geographical structuring in the phylogeny of the investigated species. This could indicate ongoing dispersal at a frequency fast enough to prevent allopatric divergence, yet slow enough to prevent sharing most haplotypes between France and Georgia. These results have implications for biomonitoring: depending on the taxonomic level chosen, robust generic tools (species level) or tools dedicated to a region able to discriminate fine pressures differences (sub-species level) may be developed.

Trait-dependent diversification in angiosperms: Patterns, models and data

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.

Deciphering factors driving soil microbial life-history strategies in restored grasslands

In macroecology, the concept of r- and K-strategy has been widely applied, yet, there have been limited studies on microbial life-history strategies in temperate grasslands using multiple sequencing approaches. Total phospholipid fatty acid (PLFA) analysis, high-throughput meta-genomic sequencing, and GeoChip technologies were used to examine the changes in microbial life-history traits in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration). Grassland restoration increased the relative abundances of Actinobacteria, Proteobacteria, and Bacteroidetes but reduced the relative abundances of Acidobacteria, Planctomycetes, and Chloroflexi. PLFA analysis revealed that grassland restoration reduced the fungi:bacteria and Gram-positive:Gram-negative bacteria ratios. Combined with the meta-genomic data, we found that grassland restoration shifted microorganisms from oligotrophic (K-) to copiotrophic (r-) groups, consistent with the increased rRNA operon copy number of the microbial community. Structural equation modeling showed that soil properties positively (p < 0.05) while plant properties negatively (p < 0.05) affected microbial life-history traits. We built a framework to highlight the importance of plant and soil properties in driving microbial life-history traits during grassland restoration. Finally, by incorporating meta-genomic and other microbiological data, this study showed that microbial life-history traits support the idea that rRNA operon copy number is a trait that reflects resource availability to soil microorganisms.

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation

The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.

Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation

We show that obligate lignicoles in lichenized Micarea are predominately asexual whereas most facultative lignicoles reproduce sexually. Our phylogenetic analyses (ITS, mtSSU, Mcm7) together with ancestral state reconstruction show that the shift in reproduction mode has evolved independently several times within the group and that facultative and obligate lignicoles are sister species. The analyses support the assumption that the ancestor of these species was a facultative lignicole. We hypothezise that a shift in substrate requirement from bark to wood leads to differentiation in reproduction mode and becomes a driver of speciation. This is the first example of lichenized fungi where reproduction mode is connected to substrate requirement. This is also the first example where such an association is demonstrated to spark lichen speciation. Our main hypothesis is that obligate species on dead wood need to colonize new suitable substrata relatively fast and asexual reproduction is more effective a strategy for successful colonization.

What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age

The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).

Evolution of Phytoplankton in Relation to Their Physiological Traits

Defining the physiological traits that characterise phytoplankton involves comparison with related organisms in benthic habitats. Comparison of survival time in darkness under natural conditions requires more information. Gas vesicles and flagella as mechanisms of upward movement relative to surrounding water, allowing periodic vertical migration, are not confined to plankton, although buoyancy changes related to compositional changes of a large central vacuole may be restricted to plankton. Benthic microalgae have the same range of photosynthetic pigments as phytoplankton; it is not clear if there are differences in the rate of regulation and acclimation of photosynthetic machinery to variations in irradiance for phytoplankton and for microphytobenthos. There are inadequate data to determine if responses to variations in frequency or magnitude of changes in the supply of inorganic carbon, nitrogen or phosphorus differ between phytoplankton and benthic microalgae. Phagophotomixotrophy and osmophotomixotrophy occur in both phytoplankton and benthic microalgae. Further progress in identifying physiological traits specific to phytoplankton requires more experimentation on benthic microalgae that are closely related to planktonic microalgae, with attention to whether the benthic algae examined have, as far as can be determined, never been planktonic during their evolution or are derived from planktonic ancestors.

Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis

Skeletonema species are cosmopolitan coastal diatoms that exhibit important roles in ecological system. The chloroplast genomes (cpDNAs) have been proven to be important in the study of molecular evolution and genetic diversity. However, cpDNA of only a single Skeletonema species (S. pseudocostatum) has been constructed, hindering in-depth investigation on Skeletonema species. In this study, complete cpDNAs of five Skeletonema species were constructed with cpDNAs of four species S. marinoi, S. tropicum, S. costatum, and S. grevillea constructed for the first time. These cpDNAs had similar sizes and same numbers of genes. These cpDNAs were highly syntenic with no substantial expansions, contractions, or inversions. Interestingly, two copies of petF, which encodes ferredoxin with critical role in iron dependency, were found in all five Skeletonema species, with one copy in the cpDNA and another copy in the nuclear genome of each species. Selection analysis revealed that all PCGs of cpDNAs were undergoing purifying selection. Despite the high conservation of these cpDNAs, nine genomic regions with high sequence divergence were identified, which illustrated substantial variations that could be used as markers for phylogenetic inference and for tracking Skeletonema species in the field. Additionally, the numbers of simple sequence repeats varied among different cpDNAs, which were useful for detecting genetic polymorphisms. The divergence times estimated using PCGs of cpDNAs revealed that most of these species were established within ∼33 Mya, consistent with that estimated using mtDNAs. Overall, the current study deepened our understanding about the molecular evolution of Skeletonema cpDNAs.

Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation

Background

Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi.

Results

In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya.

Conclusions

The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07999-z.

Multigene phylogenetic data place monoraphid diatoms Schizostauron and Astartiella along with other fistula-bearing genera in the Stauroneidaceae1

Presented here are new insights into the marine monoraphid diatom genera Schizostauron and Astartiella, based on molecular and morphological data, including descriptions of new species. Although no unambiguous morphological synapomorphies between the two genera are currently recognized, they are closely related by DNA sequence data. Heterovalvate frustules of Schizostauron are characterized by a bifid stauros on the raphe-bearing valve and intricate areolate occlusions on the sternum valve. In Astartiella, the raphe-bearing valve is characterized by a process resembling a fistula by morphology, while the sternum valve presents a particular striation pattern. Observations by light and electron microscopy were made, along with a molecular phylogenetic analysis using a three-gene (SSU, rbcL, and psbC) concatenated dataset. Three new Schizostauron species are described (S. kajotkei, S. rawaii, S. papilliareae), and two new combinations proposed (S. citronella and S. trachyderma) for species that were previously included either in Achnanthes and Cocconeis, respectively. Likewise, six new species of Astartiella (A. almalikii, A. bornmanii, A. chunlianlii, A. marksii, A. persica, and A. wangii) are described. Molecular results exclude Schizostauron and Astartiella from three clades of exclusively monoraphid diatoms, the Achnanthaceae, Cocconeidaceae, and Achnanthidiaceae, instead placing them in the Stauroneidaceae. Morphological features of Schizostauron and Astartiella, such as the stauros, fistula, and coaxial internal proximal raphe endings, are found in other genera in this clade, whereas the only common feature with monoraphid diatoms as whole group is the heterovalvy of frustules.

Extinction of austral diatoms in response to large-scale climate dynamics in Antarctica

Despite evidence for microbial endemism, an understanding of the impact of geological and paleoclimate events on the evolution of regional protist communities remains elusive. Here, we provide insights into the biogeographical history of Antarctic freshwater diatoms, using lacustrine fossils from mid-Miocene and Quaternary Antarctica, and dovetail this dataset with a global inventory of modern freshwater diatom communities. We reveal the existence of a diverse mid-Miocene diatom flora bearing similarities with several former Gondwanan landmasses. Miocene cooling and Plio-Pleistocene glaciations triggered multiple extinction waves, resulting in the selective depauperation of this flora. Although extinction dominated, in situ speciation and new colonizations ultimately shaped the species-poor, yet highly adapted and largely endemic, modern Antarctic diatom flora. Our results provide a more holistic view on the scale of biodiversity turnover in Neogene and Pleistocene Antarctica than the fragmentary perspective offered by macrofossils and underscore the sensitivity of lacustrine microbiota to large-scale climate perturbations.

Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution

Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.

Diatom DNA barcodes for forensic discrimination of drowning incidents

The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens.

Re-examination of two diatom reference genomes using long-read sequencing

Background

The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds.

Results

We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes.

Conclusion

Despite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is ‘better’ than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07666-3.

Molecular Insights into the Genetic Variability of ORF Virus in a Mediterranean Region (Sardinia, Italy)

Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a study aimed to assess the genetic variation of ORFV in Sardinia that hosts a large affected small ruminant population. We also found a high worldwide mutational viral evolutionary rate, which resulted, in turn, higher than the rate we detected for the strains isolated in Sardinia. In addition, a well-supported genetic divergence was found between the viral strains isolated from sheep and those from goats, but no relevant connection was evidenced between the severity of lesions produced by ORFV and specific polymorphic patterns in the two species of hosts. Such a finding suggests that ORFV infection-related lesions are not necessarily linked to the expression of one of the three genes here analyzed and could rather be the effect of the expression of other genes or rather represents a multifactorial character.

Pheromone Mediated Sexual Reproduction of Pennate Diatom Cylindrotheca closterium

Benthic diatoms dominate primary production in marine subtidal and intertidal environments. Their extraordinary species diversity and ecological success is thought to be linked with their predominantly heterothallic sexual reproduction. Little is known about pheromone involvement during mating of pennate diatoms. Here we describe pheromone guided mating in the coastal raphid diatom Cylindrotheca closterium. We show that the two mating types (mt⁺ and mt⁻) have distinct functions. Similar to other benthic diatoms, mt⁺ cells are searching for the mt⁻ cells to pair. To enhance mating efficiency mt⁻ exudes an attraction pheromone which we proved by establishing a novel capillary assay. Further, two more pheromones produced by mt⁻ promote the sexual events. One arrests the cell cycle progression of mt⁺ while the other induces gametogenesis of mt⁺. We suggest that C. closterium shares a functionally similar pheromone system with other pennate diatoms like Seminavis robusta and Pseudostaurosira trainorii which synchronize sexual events and mate attraction. Remarkably, we found no evidence of mt⁺ producing pheromones, which differentiates C. closterium from other pennates and suggests a less complex pheromone system in C. closterium.

Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms

Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

An Insight into the Algal Evolution and Genomics

With the increase in biotechnological, environmental, and nutraceutical importance of algae, about 100 whole genomic sequences of algae have been published, and this figure is expected to double in the coming years. The phenotypic and ecological diversity among algae hints at the range of functional capabilities encoded by algal genomes. In order to explore the biodiversity of algae and fully exploit their commercial potential, understanding their evolutionary, structural, functional, and developmental aspects at genomic level is a pre-requisite. So forth, the algal genomic analysis revealed us that algae evolved through endosymbiotic gene transfer, giving rise to around eight phyla. Amongst the diverse algal species, the unicellular green algae Chlamydomonas reinhardtii has attained the status of model organism as it is an ideal organism to elucidate the biological processes critical to plants and animals, as well as commercialized to produce range of bio-products. For this review, an overview of evolutionary process of algae through endosymbiosis in the light of genomics, as well as the phylogenomic, studies supporting the evolutionary process of algae was reviewed. Algal genomics not only helped us to understand the evolutionary history of algae but also may have an impact on our future by helping to create algae-based products and future biotechnological approaches.

Symmetric and Asymmetric Components of Shape Variation in the Diatom Genus Frustulia (Bacillariophyta)

Irregularities in cell division can produce asymmetry in symmetric structures, such as outlines of diatom cells, which can reflect genetic, environmental, or random variability in developmental processes. This study examined 12 phylogenetic lineages of the diatom genus Frustulia using landmark-based geometric morphometrics to assess the variation between cell segments separated by apical and transapical axes. Although asymmetric variation within cells differed in some lineages, these irregularities most likely did not reflect the evolutionary history of the lineages. The intraclonal phenotypic plasticity of diatom frustules was induced rather by nongenetic factors, i.e., inherited valve abnormalities, constraints of siliceous cell walls, and random developmental instability during morphogenesis. The positive correlations between the symmetric and asymmetric components of shape variation indicated that the morphogenesis of diatom cell walls affected irregularities within cells and variability among the symmetrized cells to a similar extent.

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.

Global radiation in a rare biosphere soil diatom

Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms.

It is generally thought many microbes, owing to their ubiquity and dispersal capability, lack biogeographic structuring and clear speciation patterns compared to macroorganisms. However, Pinseel et al. demonstrate multiple cycles of colonization and diversification in Pinnularia borealis, a rare biosphere soil diatom.

Morphology, phylogeny, and molecular dating in Plagiogrammaceae family focused on Plagiogramma-Dimeregramma complex (Urneidophycidae, Bacillariophyceae)

Although previous phylogenetic analyses suggested that the araphid diatom family Plagiogrammaceae is monophyletic, there is still not a clear understanding of relationships among the genera, and the taxonomy of several genera--Dimeregramma and Plagiogramma--remains questionable in light of paraphyly for both genera using molecular and morphological data. We have expanded the available DNA for molecular work for dozens of plagiogrammacean clones and analyzed 29 morphological characters from plagiogrammarian taxa and closely related genera, to increase understanding of the evolutionary history and systematics of the family and re-evaluate the current taxonomical classification of plagiogrammacean genera. The addition of more taxa and more data confirm the results from previous molecular phylogenies: most plagiogrammacean genera are monophyletic, except for Dimeregramma and Plagiogramma. Interestingly, the morphological analysis resolves only Talaroneis and Glyphodesmis as monophyletic. Given these results, we feel there is limited support for retaining Dimeregramma and Plagiogramma as distinct genera, and formally propose amending Plagiogramma and transferring six Dimeregramma species. As the Plagiogrammaceae is also one of the first-diverging clades of pennate diatoms, we also used these molecular data to estimate the age of the family, based on multiple calibration points derived from fossil taxa within or close to the Plagiogrammaceae. The results indicated that the Plagiogrammaceae evolved more than 114 million year ago and its diversification appears to correspond to a time of climate cooling. Additionally, we described a new monotypic genus (Coccinelloidea) with one new species C. gracilis, and five new species within established genera, e.g. Plagiogramma marginalis, Plagiogramma harenae, Plagiogramma porcipellis, Neofragilaria montgomeryii and Psammogramma anacarae.

Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms

Despite important progress, uncertainty persists regarding the ecological forces driving microbial community assembly. Here, we present the first study to use phylogenetic information to interpret the structure and diversity of diatom communities. We examined local phylogenetic divergence and beta- phylogenetic diversity in a large dataset of 595 freshwater benthic diatom communities and we investigated how this diversity is influenced by gradients in nutrients, pH, organic matter and catchment size. Overall, we found that diatom communities were phylogenetically clustered, i.e. species within communities were more closely related than expected by chance. Phylogenetic clustering was stronger in nutrient-poor environments and in sites with a small catchment area. The variation of the phylogenetic beta-diversity index was much better explained by space and environment than the variation of the taxonomic index was. Both approaches detected a significant effect of environment and space on diatom community turnover. Our results support the view that diatom communities are primarily shaped by environmental filtering, in particular by nutrient availability. Moreover, they highlight the importance of considering dispersal-related processes and the depth of phylogenetic signal in functional traits when interpreting patterns of diversity.

Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.

A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta)

PREMISE OF THE STUDY

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of "apochloritic" diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic Nitzschia suggests a single loss of photosynthesis in their common ancestor, previous phylogenetic analyses suggested that photosynthesis was lost multiple times.

METHODS

We analyzed genes from the nuclear, plastid, and mitochondrial genomes for a broad set of taxa to test whether photosynthesis was lost one or multiple times in Bacillariales. We also sequenced and characterized the plastid genome of a nonphotosynthetic Nitzschia species.

KEY RESULTS

Phylogenetic analyses showed that genes from all three genetic compartments either supported or failed to reject monophyly of apochloritic Nitzschia species, consistent with a single loss of photosynthesis in this group. The plastid genomes of two apochloritic Nitzschia are highly similar in all respects, indicating streamlining of the plastid genome before the split of these two species.

CONCLUSIONS

A better understanding of the phylogeny and ecology of apochloritic Nitzschia, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group of diatoms. Finally, some habitats host diverse communities of co-occurring nonphotosynthetic diatoms, reflecting resource abundance or resource partitioning in ecologically favorable habitats.

Phylogenetic Analysis Reveals that the 'Radial Centric' Diatom Orthoseira Thwaites (Orthoseiraceae, Bacillariophyta) is a Member of a 'Multipolar' Diatom Lineage

The diatom genus Orthoseira Thwaites (Bacillariophyta) is a ubiquitous taxon in aerial diatom assemblages, with species found globally. Cylindrical cell shape and radial symmetry of this genus has led to its historical placement in the Coscinodiscophyceae ('radial centric' diatoms), but its systematic relationships have remained uncertain. We present a five-gene phylogeny, based on nuclear (nSSU rDNA) and chloroplast (rbcL, psbC, psbA, and psaB) genes to determine the phylogenetic placement of Orthoseira among the diatoms. The concatenated multi-gene phylogenies and nSSU-only gene tree demonstrate that Orthoseira is deeply embedded within a clade of the Mediophyceae ('multipolar centric' diatoms). Throughout all phylogenetic analyses, Orthoseira was shown to be sister to the genera Terpsinoë and Hydrosera. Through comparison of topologies reflecting competing hypotheses about the placement of Orthoseira, it was determined that the hypothesis that Orthoseira, represented here by O. dendroteres and O. roeseana, is a member of the Melosirales should be rejected. Therefore, lack of morphological similarity between Hydrosera, Orthoseira, and Terpsinoë is hypothesized to be the result of changes in habitat preferences that lead to an ancient divergence event between the Orthoseirales and the Hydrosera, Terpsinoë clade.

Extensive Cryptic Diversity in the Terrestrial Diatom Pinnularia borealis (Bacillariophyceae)

With the increasing application of molecular techniques for diatom species discovery and identification, it is important both from a taxonomic as well as an ecological and applied perspective, to understand in which groups morphological species delimitation is congruent with molecular approaches, or needs reconsideration. Moreover, such studies can improve our understanding of morphological trait evolution in this important group of microalgae. In this study, we used morphometric analysis on light microscopy (LM) micrographs in SHERPA, detailed scanning electron microscopy (SEM), and cytological observations in LM to examine 70 clones belonging to eight distinct molecular lineages of the cosmopolitan terrestrial diatom Pinnularia borealis. Due to high within-lineage variation, no conclusive morphological separation in LM nor SEM could be detected. Morphological stasis due to the "low-morphology" problem or stabilizing selection, as well as parallel/convergent evolution, phenotypic plasticity and structural inheritance are discussed as potential drivers for the observations. Altogether, P. borealis is truly cryptic, in contrast to the majority of other diatom species complexes which turned out to be pseudo-cryptic following detailed morphological analysis.

Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time

Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively lower Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a metabarcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some have had more time to diversify than others. However, species richness was largely independent of genus age, suggesting that disparities in species richness among genera were better explained by variation in rates of speciation and extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

PREMISE OF THE STUDY

Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well.

METHODS

We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species.

KEY RESULTS

Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.

CONCLUSIONS

Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.