Tatiana A. Rynearson

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the worlds oceans.

Marine phytoplankton temperature versus growth responses from polar to tropical waters – outcome of a scientific community-wide study

“It takes a village to finish (marine) science these days” Paraphrased from Curtis Huttenhower (the Human Microbiome project) The rapidity and complexity of climate change and its potential effects on ocean biota are challenging how ocean scientists conduct research. One way in which we can begin to better tackle these challenges is to conduct community-wide scientific studies. This study provides physiological datasets fundamental to understanding functional responses of phytoplankton growth rates to temperature. While physiological experiments are not new, our experiments were conducted in many laboratories using agreed upon protocols and 25 strains of eukaryotic and prokaryotic phytoplankton isolated across a wide range of marine environments from polar to tropical, and from nearshore waters to the open ocean. This community-wide approach provides both comprehensive and internally consistent datasets produced over considerably shorter time scales than conventional individual and often uncoordinated lab efforts. Such datasets can be used to parameterise global ocean model projections of environmental change and to provide initial insights into the magnitude of regional biogeographic change in ocean biota in the coming decades. Here, we compare our datasets with a compilation of literature data on phytoplankton growth responses to temperature. A comparison with prior published data suggests that the optimal temperatures of individual species and, to a lesser degree, thermal niches were similar across studies. However, a comparison of the maximum growth rate across studies revealed significant departures between this and previously collected datasets, which may be due to differences in the cultured isolates, temporal changes in the clonal isolates in cultures, and/or differences in culture conditions. Such methodological differences mean that using particular trait measurements from the prior literature might introduce unknown errors and bias into modelling projections. Using our community-wide approach we can reduce such protocol-driven variability in culture studies, and can begin to address more complex issues such as the effect of multiple environmental drivers on ocean biota.

GENETIC DIFFERENTIATION AMONG POPULATIONS OF THE PLANKTONIC MARINE DIATOM DITYLUM BRIGHTWELLII (BACILLARIOPHYCEAE)1

Population genetic structure was determined for the planktonic diatom Ditylum brightwellii (West) Grunow in two connected estuaries—Puget Sound and the Strait of Juan de Fuca (WA, USA). Three genetically distinct populations were detected that were characterized by different microsatellite allele distributions and unique alleles. Isolates from the two most genetically diverged populations displayed identical full‐length 18S rDNA sequences suggesting that either a single or two recently diverged species were sampled. The extent of genetic differentiation between populations was not correlated with distance between water samples or time between sampling. Instead, distinct populations were associated with different estuaries. In Puget Sound waters, one population was detected three times over the course of 28 months. Cells from this population were likely maintained inside Puget Sound over long periods through water recirculation within the Sound. In Strait of Juan de Fuca waters, two additional populations were detected. Maximum growth rates of Puget Sound isolates were significantly different from Strait of Juan de Fuca isolates, indicating that populations were composed of cells with different physiological capabilities. The genetic and physiological differentiation observed between populations from intermixing estuaries suggested that genetic exchange between populations was restricted through differential selection. Despite the potential for widespread dispersal in planktonic organisms, it appears that populations with distinct genetic and physiological characteristics can be maintained over long time periods through a combination of hydrology and differential selection.

The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response

Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.

Maintenance of clonal diversity during a spring bloom of the centric diatom Ditylum brightwellii

Maintenance of genetic diversity in eukaryotic microbes reflects a synergism between reproductive mode (asexual vs. sexual) and environmental conditions. We determined clonal diversity in field samples of the planktonic marine diatom, Ditylum brightwellii, during a bloom, when cell number increased by seven‐fold because of rapid asexual division. The genotypes at three microsatellite loci were determined for 607 individual cell lines isolated during the 11 days of sampling. Genetic diversity remained high during the bloom and 87% of the cells sampled each day were genetically distinct. Sixty‐nine clonal lineages were sampled two or more times during the bloom, and two clones were sampled seven times. Based on the frequency of resampled clonal lineages, capture–recapture statistics were used to determine that at least 2400 genetically distinct clonal lineages comprised the bloom population. No significant differences in microsatellite allele frequencies were observed among daily samples indicating that the bloom was comprised of a single population. No sexual stages were observed, although linkage equilibrium at two loci, high levels of allelic and genotypic diversity, and heterozygote deficiencies were all indicative of past sexual reproduction events. At the height of the bloom, a windstorm diluted cell numbers by 51% and coincided with a change in the frequency distribution of some resampled lineages. The extensive clonal diversity generated through past sexual reproduction events coupled with frequent environmental changes appear to prevent individual clonal lineages from becoming numerically dominant, maintaining genetic diversity and the adaptive potential of the population.

Evolutionary potential of marine phytoplankton under ocean acidification

Marine phytoplankton have many obvious characters, such as rapid cell division rates and large population sizes, that give them the capacity to evolve in response to global change on timescales of weeks, months or decades. However, few studies directly investigate if this adaptive potential is likely to be realized. Because of this, evidence of to whether and how marine phytoplankton may evolve in response to global change is sparse. Here, we review studies that help predict evolutionary responses to global change in marine phytoplankton. We find limited support from experimental evolution that some taxa of marine phytoplankton may adapt to ocean acidification, and strong indications from studies of variation and structure in natural populations that selection on standing genetic variation is likely. Furthermore, we highlight the large body of literature on plastic responses to ocean acidification available, and evolutionary theory that may be used to link plastic and evolutionary responses. Because of the taxonomic breadth spanned by marine phytoplankton, and the diversity of roles they fill in ocean ecosystems and biogeochemical cycles, we stress the necessity of treating taxa or functional groups individually.

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Significance Nutrient availability plays a central role in driving the activities and large-scale distributions of phytoplankton, yet there are still fundamental gaps in understanding how phytoplankton metabolize nutrients, like nitrogen (N) and phosphorus (P), and how this metabolic potential is modulated in field populations. Here, we show that cooccurring diatoms in a dynamic coastal marine system have apparent differences in their metabolic capacity to use N and P. Further, bioinformatic approaches enabled the identification and species-specific comparison of resource-responsive (RR) genes. Variation of these RR gene sets highlights the disparate transcriptional responses these species have to the same environment, which likely reflects the role resource partitioning has in facilitating the vast diversity of the phytoplankton. Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this “paradox of the plankton,” but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates

BackgroundRecent technological advancements have made high throughput sequencing an increasingly popular approach for transcriptome analysis. Advantages of sequencing-based transcriptional profiling over microarrays have been reported, including lower technical variability. However, advances in technology do not remove biological variation between replicates and this variation is often neglected in many analyses.ResultsWe propose an empirical Bayes method, titled Analysis of Sequence Counts (ASC), to detect differential expression based on sequencing technology. ASC borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. Compared to current approaches that simply tests for equality of proportions in two samples, ASC is less biased towards highly expressed sequences and can identify more genes with a greater log fold change at lower overall abundance.ConclusionsASC unifies the biological and statistical significance of differential expression by estimating the posterior mean of log fold change and estimating false discovery rates based on the posterior mean. The implementation in R is available at http://www.stat.brown.edu/Zwu/research.aspx.

Metapopulation Structure in the Planktonic Diatom Ditylum brightwellii (Bacillariophyceae).

Approximately 200,000 diatom species are thought to exist and yet the underlying processes of speciation in diatoms are unknown. Because genetic subdivision within species can reveal potential speciation mechanisms, we examined genetic differentiation and patterns of gene flow among four populations of the diatom Ditylum brightwellii. Single-cell isolates were examined at two microsatellite markers and two rDNA loci (18S and internal transcribed spacer region I (ITSI)). Among isolates, rDNA sequences varied by 0.08+/-0.04% (18S) and 0.7+/-0.3% (ITSI) and there were no compensatory base pair changes in the predicted ITSI secondary structure, all suggesting that a single species was represented. Two numerically dominant ITSI sequence types were detected and their distribution among isolates from genetically distinct populations was significantly different. Two populations shared ITSI sequence type 1 and two shared ITSI sequence type 2, indicating differences in relatedness among populations. The signature of unequal gene flow among populations suggested that D. brightwellii exhibited a metapopulation structure: the species was subdivided into populations of populations. The identification of metapopulations suggests a possible mechanism of speciation through reduced levels of gene flow, providing newly evolved taxa with a large repository of genetic and physiological diversity and perhaps significant adaptive potential.

Experimental evolution gone wild.

Because of their large population sizes and rapid cell division rates, marine microbes have, or can generate, ample variation to fuel evolution over a few weeks or months, and subsequently have the potential to evolve in response to global change. Here we measure evolution in the marine diatom Skeletonema marinoi evolved in a natural plankton community in CO2-enriched mesocosms deployed in situ. Mesocosm enclosures are typically used to study how the species composition and biogeochemistry of marine communities respond to environmental shifts, but have not been used for experimental evolution to date. Using this approach, we detect a large evolutionary response to CO2 enrichment in a focal marine diatom, where population growth rate increased by 1.3-fold in high CO2-evolved lineages. This study opens an exciting new possibility of carrying out in situ evolution experiments to understand how marine microbial communities evolve in response to environmental change.