Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.

Transcriptional Response of Osmolyte Synthetic Pathways and Membrane Transporters in a Euryhaline Diatom During Long-term Acclimation to a Salinity Gradient

How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.

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.

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

Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first-last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages. Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells. We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present-day diatom diversity.

Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta)

We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.

Morphological diversity and phylogeny of the diatom genus Entomoneis (Bacillariophyta) in marine plankton: six new species from the Adriatic Sea

The diatom genus Entomoneis is known from the benthos and plankton of marine, brackish, and freshwaters. Entomoneis includes diatoms with a bilobate keel elevated above the valve surface, a sigmoid canal raphe, and numerous girdle bands. Owing mostly to the scarcity of molecular data for a diverse set of species, the phylogeny of Entomoneis has not been investigated in depth. The few previous studies that included Entomoneis were focused on broader questions and the available data were from a small number of either unidentified Entomoneis or well-known species (e.g., E. paludosa). Since the first description of new species combining both molecular and morphological characters (E. tenera), we have continued to cultivate and investigate Entomoneis in the plankton of the Adriatic Sea. Combined multigene phylogeny (SSU rDNA sequences, rbcL, and psbC genes) and morphological observations (LM, SEM and TEM) revealed six new Entomoneis species supported by phylogenetic and morphological data: E. pusilla, E. gracilis, E. vilicicii, E. infula, E. adriatica, and E. umbratica. The most important morphological features for species delineation were cell shape, the degree and mode of torsion, valve apices, the appearance and structure of the transition between keel and valve body, the ultrastructure and the shape of the girdle bands, and the arrangement and density of perforations along the valve and valvocopulae. Our results highlight the underappreciated diversity of Entomoneis and call for a more in-depth morphological and molecular investigation of this genus especially in planktonic habitats.

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.

Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)

Although the plastid genomes of diatoms maintain a conserved architecture and core gene set, considerable variation about this core theme exists and can be traced to several different processes. Gene duplication, pseudogenization, and loss, as well as intracellular transfer of genes to the nuclear genome, have all contributed to variation in gene content among diatom species. In addition, some noncoding sequences have highly restricted phylogenetic distributions that suggest a recent foreign origin. We sequenced the plastid genome of the marine diatom, Toxarium undulatum, and found that the genome contains three genes (chlB, chlL, and chlN) involved in light-independent chlorophyll a biosynthesis that were not previously known from diatoms. Phylogenetic and syntenic data suggest that these genes were differentially retained in this one lineage as they were repeatedly lost from most other diatoms. Unique among diatoms and other heterokont algae sequenced so far, the genome also contains a large group II intron within an otherwise intact psaA gene. Although the intron is most similar to one in the plastid-encoded psaA gene of some green algae, high sequence divergence between the diatom and green algal introns rules out recent shared ancestry. We conclude that the psaA intron was likely introduced into the plastid genome of T. undulatum, or some earlier ancestor, by horizontal transfer from an unknown donor. This genome further highlights the myriad processes driving variation in gene and intron content in the plastid genomes of diatoms, one of the world's foremost primary producers.

Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms

Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.

Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae)

The ocellate and pseudocellate diatoms in the Eupodiscaceae and Biddulphiaceae (respectively) are common inhabitants of the marine littoral (and plankton zone) with a rich fossil history making them important components of marine stratigraphic studies and good candidates for molecular dating work. These diatoms are important for un-derstanding the phylogeny of the diatoms as a whole, as molecular phylogenies have blurred the traditional distinction between the pennate and multipolar non-pennate diatoms. However, the convoluted taxonomic history of these groups has the potential to disrupt both stratigraphic and molecular dating studies. Although efforts have been made to examine frustule morphology of several ocellate and pseudocellate diatoms and develop a morphological scheme to define genera, very little work has been done to determine how these groups are interrelated. In this study, we use nuclear and chloroplast molecular markers to construct a phylogeny of a diverse sampling of Eupodiscaceae and Biddulphiaceae taxa. The ocellus-bearing taxa (Eupodiscaceae) are monophyletic, and thus the ocellus may be a useful character in delimiting the Eupodiscaceae, the Biddulphiaceae are polyphyletic and scattered across a number of lineages of multipolar non-pennate diatoms. Hypothesis testing aimed at assessing the likeliness of several morphology based hypotheses against the molecular data highlights uncertainty in both types of data. We present evidence that there are monophyletic genera within both the Biddulphiaceae and Eupodiscaceae, and recommend the taxa within the Odontella mobilensis/sinensis/regia clade be transferred to a new genus: Trieres Ashworth & Theriot.