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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.

 

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.

 

Abstract The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms. 

The large population sizes and high dispersal potential of microbes suggests that a given microbial species should be found in all suitable habitats worldwide. Consequently, microbes should not exhibit the kinds of biogeographic patterns seen in macroorganisms. This paradigm is challenged by a growing list of exotic microbes with biogeographic disjunctions that instead promotes microbial dispersal as inherently limited. We sampled water bodies in the United States and compiled records from the literature and public databases to characterize the distribution of the freshwater planktonic diatom, Discostella asterocostata (Xie, Lin, and Cai) Houk and Klee. Discostella asterocostata was thought to be restricted to the Far East, but we report its presence in ecologically similar water bodies across the eastern United States. Populations from the U.S. and China are indistinguishable morphometrically, suggesting they may be recently separated—a hypothesis supported by paleolimnological data, which support an introduction of D. asterocostata into the U.S. as recently as the mid-1980s. The overlapping distributions of D. asterocostata and invasive carp species, in both their native and nonnative ranges, highlighted Asian carp as a possible vector for introduction of the diatom in the U.S. The existence of exotic diatoms underscores natural constraints on microbial dispersal, resulting in biogeographic distributions that can be upended through human activity. 

Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom,NitzschiaNitz4, to determine how carbon metabolism was altered in the wake of this trophic shift.

NitzschiaNitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular‐wide and included losses of photosynthesis‐related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β‐ketoadipate pathway that may allowNitzschiaNitz4 to metabolize lignin‐derived compounds.

Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids.

The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.

 

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 acclimatedC. crypticaexhibited 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.

 

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 genusNitzschiahave 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 apochloriticNitzschiasuggests a single loss of photosynthesis in their common ancestor, previous phylogenetic analyses suggested that photosynthesis was lost multiple times.

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 nonphotosyntheticNitzschiaspecies.

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

A better understanding of the phylogeny and ecology of apochloriticNitzschia, 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.